Found the following hidden files and directories:
  vignettes/.Rhistory
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘abind’ ‘svUnit’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
simSummary: no visible global function definition for ‘abind’
simSummary_unitTests: no visible global function definition for
  ‘clearLog’
simSummary_unitTests: no visible global function definition for
  ‘runTest’
simSummary_unitTests: no visible global function definition for
  ‘svSuite’
simSummary_unitTests: no visible global function definition for ‘Log’
simSummary_unitTests: no visible global function definition for ‘stats’
simSummary_unitTests: no visible global function definition for
  ‘metadata’
simSummary_unitTests: no visible global function definition for
  ‘errorLog’
Undefined global functions or variables:
  Log abind clearLog errorLog metadata runTest stats svSuite
evalGrids: no visible global function definition for ‘sessionInfo’
meanAndNormCI: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd sessionInfo
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "sessionInfo")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  plot.CorrAn plot.SimAn summary.CorrAn summary.SimAn
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.CorrAn : SAPplot: no visible global function definition for ‘plot’
plot.CorrAn : SAPtitle: no visible global function definition for
  ‘title’
plot.CorrAn : SAPtitle: no visible global function definition for
  ‘mtext’
plot.CorrAn : SAPplotpuntos: no visible global function definition for
  ‘points’
plot.CorrAn : SAPplotpuntos: no visible global function definition for
  ‘text’
plot.CorrAn: no visible global function definition for ‘dev.new’
plot.SimAn : SAPplot: no visible global function definition for ‘plot’
plot.SimAn : SAPtitle: no visible global function definition for
  ‘title’
plot.SimAn : SAPtitle: no visible global function definition for
  ‘mtext’
plot.SimAn : SAPplotpuntos: no visible global function definition for
  ‘points’
plot.SimAn : SAPplotpuntos: no visible global function definition for
  ‘text’
plot.SimAn: no visible global function definition for ‘dev.new’
plot.SimAn: no visible global function definition for ‘points’
plot.SimAn: no visible global function definition for ‘text’
plot.SimAn: no visible global function definition for ‘par’
plot.SimAn: no visible global function definition for ‘plot’
plot.SimAn: no visible global function definition for ‘title’
plot.SimAn: no visible global function definition for ‘axis’
plot.SimAn: no visible global function definition for ‘arrows’
Undefined global functions or variables:
  arrows axis dev.new mtext par plot points text title
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "arrows", "axis", "mtext", "par", "plot",
             "points", "text", "title")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  plot.siRSM plot.siRSM.default plot.siRSM.default print.siRSM
  print.siRSM.default print.siRSM.default siRSM.default
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘sivipm/libs/sivipm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  logLik.PiecewiseLinear logLik.bent_cable
  plot.LocallyWeightedPolynomial plot.PiecewiseLinear plot.SiZer
  predict.PiecewiseLinear predict.bent_cable print.PiecewiseLinear
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
cvskda: no visible global function definition for ‘detectCores’
cvskda: no visible global function definition for ‘makeCluster’
cvskda: no visible global function definition for ‘clusterApplyLB’
cvskda: no visible global function definition for ‘mclapply’
cvskda: no visible global function definition for ‘stopCluster’
Undefined global functions or variables:
  clusterApplyLB detectCores makeCluster mclapply stopCluster
File ‘skda/libs/skda.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  print.summary.skewhypFit
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
dskt: no visible global function definition for ‘dt’
pskt: no visible global function definition for ‘pt’
qskt: no visible global function definition for ‘qt’
rskt: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dt pt qt runif
Consider adding
  importFrom("stats", "dt", "pt", "qt", "runif")
to your NAMESPACE file.
Package which this enhances but not available for checking: ‘kmndirs’
Unavailable namespace imported from by a ':::' call: ‘kmndirs’
  See the note in ?`:::` about the use of this operator.
File ‘skm/libs/skm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘slam/libs/slam.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  plot.sla print.sla print.summary.sla sla.default summary.sla
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.sla: no visible global function definition for ‘title’
plot.sla: no visible global function definition for ‘abline’
print.sla: no visible global function definition for ‘coef’
sla.default: no visible global function definition for ‘lm’
sla.default: no visible global function definition for ‘anova’
Undefined global functions or variables:
  abline anova coef lm title
Consider adding
  importFrom("graphics", "abline", "title")
  importFrom("stats", "anova", "coef", "lm")
to your NAMESPACE file.
slcestimates: no visible global function definition for ‘par’
slcestimates: no visible global function definition for ‘plot’
slcestimates: no visible global function definition for ‘abline’
slcestimates: no visible global function definition for ‘lines’
slcestimates: no visible global function definition for ‘axis’
slcestimates: no visible global function definition for ‘points’
slcestimates: no visible global function definition for ‘title’
Undefined global functions or variables:
  abline axis lines par plot points title
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "par", "plot",
             "points", "title")
to your NAMESPACE file.
File ‘sld/libs/sld.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘slfm/libs/slfm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SLHD/libs/SLHD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SLOPE/libs/SLOPE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘slp/libs/slp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘smaa/libs/smaa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
cvsmac: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
File ‘smac/libs/smac.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘smam/libs/smam.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  fitted.sma
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘smco/R/smco.R’:
  .onAttach calls:
    cat(paste("This is smco package", version, "\n"))

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

smco: no visible global function definition for ‘runif’
smco: no visible global function definition for ‘rnorm’
smco: no visible global function definition for ‘qnorm’
smco: no visible global function definition for ‘pnorm’
smco: no visible global function definition for ‘optim’
Undefined global functions or variables:
  optim pnorm qnorm rnorm runif
Consider adding
  importFrom("stats", "optim", "pnorm", "qnorm", "rnorm", "runif")
to your NAMESPACE file.
SMCP : fun: no visible global function definition for ‘cor’
manipulate : fun: no visible global function definition for ‘sd’
sp: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  cor sd
Consider adding
  importFrom("stats", "cor", "sd")
to your NAMESPACE file.
File ‘SMCP/libs/SMCP.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SMC/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage("##\n", "## Sequential Monte Carlo Package (SMC)\n",     "##\n", "## Functionality: sequential Monte Carlo (SMC) or sequential importance\n",     "## sampling (SIS) or hidden Markov models (HMM), particle filter (PF)\n",     "## and auxiliary particle filter (APF)\n", "##\n", "## Use: \"help(package = SMC)\" at the R prompt for more info\n",     "##\n", "## Copyright (C) 2006-", this.year, " Gopi Goswami\n",     "##\n", "##    Created by: Gopi Goswami <goswami@stat.harvard.edu>\n",     "## Maintained by: Gopi Goswami <grgoswami@gmail.com>\n",     "##\n")

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

.MHUpdateFuncGen.PF : MHUpdateFunc: no visible global function
  definition for ‘runif’
MarkovSwitchingFuncGenerator : generateNextStreamsFunc: no visible
  global function definition for ‘runif’
MarkovSwitchingFuncGenerator: no visible global function definition for
  ‘rnorm’
MarkovSwitchingFuncGenerator: no visible global function definition for
  ‘runif’
MarkovSwitchingFuncGenerator : logObsDensFunc: no visible global
  function definition for ‘dnorm’
MarkovSwitchingFuncGenerator : propagateFunc: no visible global
  function definition for ‘dnorm’
MarkovSwitchingFuncGenerator : propagateFunc: no visible global
  function definition for ‘runif’
Undefined global functions or variables:
  dnorm rnorm runif
Consider adding
  importFrom("stats", "dnorm", "rnorm", "runif")
to your NAMESPACE file.
File ‘SMC/libs/SMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
em: no visible global function definition for ‘coxph’
em: no visible global function definition for ‘optim’
plotpredictsmcure: no visible global function definition for ‘plot’
plotpredictsmcure: no visible global function definition for ‘matplot’
plotpredictsmcure: no visible global function definition for ‘lines’
smcure: no visible binding for global variable ‘na.omit’
smcure: no visible global function definition for ‘model.frame’
smcure: no visible global function definition for ‘model.extract’
smcure: no visible global function definition for ‘model.matrix’
smcure: no visible global function definition for ‘coxph’
smcure: no visible global function definition for ‘survreg’
smcure: no visible binding for global variable ‘var’
smcure: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  coxph lines matplot model.extract model.frame model.matrix na.omit
  optim plot pnorm survreg var
Consider adding
  importFrom("graphics", "lines", "matplot", "plot")
  importFrom("stats", "model.extract", "model.frame", "model.matrix",
             "na.omit", "optim", "pnorm", "var")
to your NAMESPACE file.
branching.resample: no visible global function definition for ‘rbinom’
cov.weights: no visible global function definition for ‘var’
inverse.cdf.weights: no visible global function definition for ‘runif’
multinomial.resample: no visible global function definition for ‘runif’
stratified.resample: no visible global function definition for ‘runif’
systematic.resample: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rbinom runif var
Consider adding
  importFrom("stats", "rbinom", "runif", "var")
to your NAMESPACE file.
Rd file 'resampling.Rd':
  \usage lines wider than 90 characters:
     residual.resample(   weights, num.samples = length(weights), engine="R", rrf = "stratified")

These lines will be truncated in the PDF manual.
File ‘smcUtils/libs/smcUtils.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘proxy’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘proxy’ ‘tm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
normalize: no visible binding for global variable ‘sd’
simDic: no visible global function definition for ‘simil’
simDoc: no visible global function definition for ‘simil’
Undefined global functions or variables:
  sd simil
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Rd file 'simDic.Rd':
  \usage lines wider than 90 characters:
     simDic(docMatrix1, docMatrix2, scoreDict, breaks = seq(-1, 1, length = 11), norm = FALSE, method = "cosine", scoreFunc = mean)

These lines will be truncated in the PDF manual.
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.
File ‘smds/libs/smds.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘lattice’ ‘splines’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘lattice’ ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  plot.sme sme.data.frame sme.default sme.list
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
getRoughnessMatrix: no visible global function definition for ‘ns’
plotSmeDiagnostic: no visible global function definition for ‘layout’
plotSmeDiagnostic: no visible global function definition for ‘plot’
plotSmeModel: no visible global function definition for ‘plot’
plotSmeModel: no visible global function definition for ‘lines’
plotSmeModel: no visible global function definition for ‘col2rgb’
plotSmeModel: no visible global function definition for ‘polygon’
plotSmeModel: no visible global function definition for ‘rgb’
plotSmeRaw: no visible global function definition for ‘xyplot’
plotSmeRaw : <anonymous>: no visible global function definition for
  ‘panel.xyplot’
plotSmeRaw : <anonymous>: no visible global function definition for
  ‘panel.lines’
sme.default: no visible global function definition for ‘ns’
sme.list: no visible binding for global variable ‘ns’
sme.list : <anonymous>: no visible global function definition for ‘ns’
vcov.sme: no visible global function definition for ‘ns’
Undefined global functions or variables:
  col2rgb layout lines ns panel.lines panel.xyplot plot polygon rgb
  xyplot
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
  importFrom("graphics", "layout", "lines", "plot", "polygon")
to your NAMESPACE file.
File ‘sme/libs/sme.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘ggplot2’ ‘reshape’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘corpcor’ ‘ggplot2’ ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘smfsb/libs/smfsb.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls in package code:
  ‘MASS’ ‘survival’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following apparent S3 methods exported but not registered:
  disparity.glm disparity.lm summary.treg
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
lines.SmithWilsonYieldCurve: no visible global function definition for
  ‘lines’
plot.SmithWilsonYieldCurve: no visible global function definition for
  ‘plot’
points.SmithWilsonYieldCurve: no visible global function definition for
  ‘points’
Undefined global functions or variables:
  lines plot points
Consider adding
  importFrom("graphics", "lines", "plot", "points")
to your NAMESPACE file.
Fourier2d: no visible global function definition for ‘fft’
kernel2dsmooth: no visible global function definition for ‘fft’
Undefined global functions or variables:
  fft
Consider adding
  importFrom("stats", "fft")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: items ‘package:smotefamily’ were removed from the search path
Found the following apparent S3 methods exported but not registered:
  pairs.mod plot.glm.diag
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'plot.glm.diag.Rd':
  \usage lines wider than 90 characters:
     plot(x, glmdiag = glm.diag(x), subset = NULL, iden = FALSE, labels = NULL, ret = FALSE, ...)

Rd file 'poi.beta.laplace.Rd':
  \usage lines wider than 90 characters:
     poi.beta.laplace(data, alpha = get.alpha(data), phi = 1, nu = 0.1, beta = seq(from = 0, to = 7, length = 1000))

These lines will be truncated in the PDF manual.
'library' or 'require' calls in package code:
  ‘akima’ ‘misc3d’ ‘rgl’ ‘rpanel’ ‘tkrplot’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
File ‘sm/libs/sm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
dNMR: no visible global function definition for ‘pnorm’
dNMR: no visible global function definition for ‘dnorm’
pNMR: no visible global function definition for ‘pnorm’
pNMR: no visible global function definition for ‘dnorm’
rMR: no visible global function definition for ‘rnorm’
rMR: no visible global function definition for ‘rchisq’
Undefined global functions or variables:
  dnorm pnorm rchisq rnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm", "rchisq", "rnorm")
to your NAMESPACE file.
SMVar.paired : <anonymous>: no visible global function definition for
  ‘var’
SMVar.paired: no visible global function definition for ‘var’
SMVar.paired: no visible global function definition for ‘pt’
SMVar.paired: no visible global function definition for ‘p.adjust’
SMVar.paired: no visible global function definition for ‘write.table’
SMVar.unpaired : <anonymous>: no visible global function definition for
  ‘var’
SMVar.unpaired: no visible global function definition for ‘var’
SMVar.unpaired: no visible global function definition for ‘pt’
SMVar.unpaired: no visible global function definition for ‘p.adjust’
SMVar.unpaired: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  p.adjust pt var write.table
Consider adding
  importFrom("stats", "p.adjust", "pt", "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Rd file 'SMVar.paired.Rd':
  \usage lines wider than 90 characters:
     SMVar.paired(geneNumbers, logratio, fileexport = NULL, minrep = 2, method = "BH", threshold = 0.05)

Rd file 'SMVar.unpaired.Rd':
  \usage lines wider than 90 characters:
     SMVar.unpaired(geneNumbers, listcond, fileexport = NULL, minrep = 2, method = "BH", threshold = 0.05)

These lines will be truncated in the PDF manual.
File ‘sna/libs/sna.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
sclust: no visible global function definition for ‘var’
snipEM: no visible global function definition for ‘cov’
stEM: no visible global function definition for ‘cov’
stEM: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  cov quantile var
Consider adding
  importFrom("stats", "cov", "quantile", "var")
to your NAMESPACE file.
File ‘snipEM/libs/snipEM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘snnR/libs/snnR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SnowballC/libs/SnowballC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘snowboot/libs/snowboot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package in Depends field not imported from: ‘snow’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  [.cluster
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
KS.test: no visible global function definition for ‘quantile’
KS.test : Fgaus: no visible global function definition for ‘pnorm’
KS.test: no visible global function definition for ‘setNames’
cs.test: no visible global function definition for ‘pbinom’
cs.test: no visible global function definition for ‘pnorm’
cs.test: no visible global function definition for ‘setNames’
kde: no visible global function definition for ‘quantile’
kde : Fgaus: no visible global function definition for ‘pnorm’
kde: no visible global function definition for ‘par’
kre: no visible global function definition for ‘quantile’
kre: no visible global function definition for ‘lines’
ns.test: no visible global function definition for ‘complete.cases’
ns.test: no visible global function definition for ‘qnorm’
ns.test: no visible global function definition for ‘pnorm’
ns.test: no visible global function definition for ‘pchisq’
ns.test: no visible global function definition for ‘setNames’
ns.test: no visible global function definition for ‘qt’
quant.test: no visible global function definition for ‘complete.cases’
quant.test: no visible global function definition for ‘pbinom’
quant.test: no visible global function definition for ‘pnorm’
quant.test: no visible global function definition for ‘setNames’
quant.test: no visible global function definition for ‘quantile’
quant.test: no visible global function definition for ‘phyper’
runs.test: no visible global function definition for ‘median’
runs.test: no visible global function definition for ‘setNames’
runs.test: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  complete.cases lines median par pbinom pchisq phyper pnorm qnorm qt
  quantile setNames
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "complete.cases", "median", "pbinom", "pchisq",
             "phyper", "pnorm", "qnorm", "qt", "quantile", "setNames")
to your NAMESPACE file.
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/genotypes.Rmd’
(Is a VignetteBuilder field missing?)
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘mvtnorm’ ‘combinat’
A package should be listed in only one of these fields.
chisq.test.a: no visible global function definition for ‘chisq.test’
maxsel: no visible global function definition for ‘complete.cases’
maxsel.asymp.test: no visible global function definition for
  ‘complete.cases’
Undefined global functions or variables:
  chisq.test complete.cases
Consider adding
  importFrom("stats", "chisq.test", "complete.cases")
to your NAMESPACE file.
prepare_Rd: maxsel.rd:27-29: Dropping empty section \details
prepare_Rd: transf.inter.rd:23-25: Dropping empty section \details
MDSplot: no visible global function definition for ‘par’
MDSplot: no visible global function definition for ‘rainbow’
MDSplot: no visible global function definition for ‘plot’
MDSplot: no visible global function definition for ‘pairs’
classCenter : <anonymous>: no visible binding for global variable
  ‘median’
grow.snpRF: no visible global function definition for ‘update’
na.roughfix.data.frame : roughfix: no visible global function
  definition for ‘median’
na.roughfix.default: no visible global function definition for ‘median’
outlier.default: no visible global function definition for ‘median’
outlier.default: no visible global function definition for ‘mad’
plot.margin: no visible global function definition for
  ‘installed.packages’
plot.margin: no visible global function definition for ‘rainbow’
plot.margin: no visible global function definition for ‘plot.default’
plot.snpRF: no visible global function definition for ‘matplot’
tuneSnpRF: no visible global function definition for ‘axis’
varImpPlot: no visible global function definition for ‘par’
varImpPlot: no visible global function definition for ‘dotchart’
varImpPlot: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  axis dotchart installed.packages mad matplot median mtext pairs par
  plot plot.default rainbow update
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "dotchart", "matplot", "mtext", "pairs",
             "par", "plot", "plot.default")
  importFrom("stats", "mad", "median", "update")
  importFrom("utils", "installed.packages")
to your NAMESPACE file.
File ‘snpRF/libs/snpRF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘colorspace’ ‘snpStats’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
check.args: no visible global function definition for ‘is’
write.sbams: no visible global function definition for ‘as’
write.sbams: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  as is write.table
Consider adding
  importFrom("methods", "as", "is")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘snpStatsWriter/libs/snpStatsWriter.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘Biostrings’ ‘GenomicRanges’ ‘IRanges’ ‘Rsamtools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following calls to attach():
File ‘SOAR/R/SOAR.R’:
  attach(NULL, pos, basename(directory))
See section ‘Good practice’ in ‘?attach’.
calculate.areas: no visible global function definition for ‘runif’
calculate.gradedareas: no visible global function definition for
  ‘rnorm’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
File ‘SocialNetworks/libs/SocialNetworks.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Warning: no function found corresponding to methods exports from ‘SoDA’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Missing or unexported object: ‘base::WHAT’
Call with DUP:
   .Fortran("GEODISTV", as.double(lat1), as.double(lon1), as.double(lat2), 
       as.double(lon2), dist = double(nok), as.integer(nok), DUP = DUP, 
       PACKAGE = "SoDA")
DUP is no longer supported and will be ignored.
File ‘SoDA/libs/SoDA.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘MASS’ ‘magic’ ‘ppls’ ‘psych’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
get.hnx.B.initialW: no visible global function definition for
  ‘normalize.vector’
get.hnx.B.initialW: no visible global function definition for ‘adiag’
hclust.wrap: no visible global function definition for ‘hclust’
hclust.wrap: no visible global function definition for ‘dist’
hclust.wrap: no visible global function definition for ‘cutree’
my.normdata.gen: no visible global function definition for ‘mvrnorm’
my.normdata.gen: no visible global function definition for ‘rnorm’
odc.clust: no visible binding for global variable ‘kmeans’
odc.cv: no visible global function definition for ‘ginv’
odc.optimallambda2: no visible global function definition for ‘tr’
odc.optimallambda2: no visible global function definition for ‘ginv’
odc.optimallambda2: no visible binding for global variable ‘sd’
sodc.clust: no visible binding for global variable ‘kmeans’
Undefined global functions or variables:
  adiag cutree dist ginv hclust kmeans mvrnorm normalize.vector rnorm
  sd tr
Consider adding
  importFrom("stats", "cutree", "dist", "hclust", "kmeans", "rnorm",
             "sd")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  plot.sod_sq3
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
hsvScale: no visible global function definition for ‘hsv’
plotConcentric: no visible global function definition for ‘plot’
plotConcentric: no visible global function definition for ‘points’
plotConcentric: no visible global function definition for ‘legend’
plotPoints: no visible global function definition for ‘plot’
plotStress: no visible global function definition for ‘plot’
plotStress: no visible global function definition for ‘polygon’
plotStress: no visible global function definition for ‘points’
Undefined global functions or variables:
  hsv legend plot points polygon
Consider adding
  importFrom("grDevices", "hsv")
  importFrom("graphics", "legend", "plot", "points", "polygon")
to your NAMESPACE file.
File ‘SOD/libs/SOD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
HardKMeansDemo: no visible global function definition for
  ‘graphics.off’
HardKMeansDemo: no visible global function definition for ‘plot’
HardKMeansDemo: no visible global function definition for ‘points’
initializeMeansMatrix: no visible global function definition for
  ‘runif’
initializeMeansMatrix: no visible global function definition for ‘dist’
normalizeMatrix: no visible global function definition for ‘sd’
plotRoughKMeans: no visible global function definition for
  ‘graphics.off’
plotRoughKMeans: no visible global function definition for ‘plot’
plotRoughKMeans: no visible global function definition for ‘points’
Undefined global functions or variables:
  dist graphics.off plot points runif sd
Consider adding
  importFrom("grDevices", "graphics.off")
  importFrom("graphics", "plot", "points")
  importFrom("stats", "dist", "runif", "sd")
to your NAMESPACE file.
Ssimpute.als: no visible global function definition for ‘rnorm’
Ssvd.als: no visible global function definition for ‘rnorm’
cs.default: no visible binding for global variable ‘weighted.mean’
simpute.als: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm weighted.mean
Consider adding
  importFrom("stats", "rnorm", "weighted.mean")
to your NAMESPACE file.
File ‘softImpute/libs/softImpute.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘aqp’ ‘lattice’ ‘methods’ ‘munsell’ ‘splancs’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  head.profile.data.frame plot.profile.data.frame
  print.profile.data.frame summary.profile.data.frame
  tail.profile.data.frame
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
'library' or 'require' calls in package code:
  ‘chemometrics’ ‘spatstat’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following apparent S3 methods exported but not registered:
  plot.Spectra plot.ken.sto plot.trans predict.SpectraPoints
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘solidearthtide/libs/solidearthtide.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
plot.soma: no visible global function definition for ‘plot’
soma: no visible global function definition for ‘runif’
Undefined global functions or variables:
  plot runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
to your NAMESPACE file.
bm: no visible global function definition for ‘rnorm’
bm: no visible global function definition for ‘ts’
fbm: no visible global function definition for ‘fft’
fbm: no visible global function definition for ‘rnorm’
fbm: no visible global function definition for ‘ts’
gbm: no visible global function definition for ‘rnorm’
gbm: no visible global function definition for ‘ts’
Undefined global functions or variables:
  fft rnorm ts
Consider adding
  importFrom("stats", "fft", "rnorm", "ts")
to your NAMESPACE file.
getAlpha: no visible global function definition for ‘pbinom’
kfweOrd: no visible global function definition for ‘qnbinom’
Undefined global functions or variables:
  pbinom qnbinom
Consider adding
  importFrom("stats", "pbinom", "qnbinom")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from ‘someMTP’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
'library' or 'require' call to ‘hexbin’ which was already attached by Depends.
  Please remove these calls from your code.
hexbinpie: no visible global function definition for ‘quantile’
hexbinpie: no visible global function definition for ‘polygon’
hexbinpie: no visible global function definition for ‘text’
makehexbinplot: no visible global function definition for ‘rainbow’
makehexbinplot: no visible global function definition for ‘col2rgb’
makehexbinplot: no visible global function definition for ‘edit’
makehexbinplot: no visible global function definition for ‘dev.new’
makehexbinplot: no visible global function definition for ‘plot.new’
makehexbinplot: no visible global function definition for ‘plot.window’
makehexbinplot: no visible global function definition for ‘box’
makehexbinplot: no visible global function definition for ‘axis’
makehexbinplot: no visible global function definition for ‘legend’
som.plot: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  axis box col2rgb dev.new edit legend plot.new plot.window polygon
  quantile rainbow read.table text
Consider adding
  importFrom("grDevices", "col2rgb", "dev.new", "rainbow")
  importFrom("graphics", "axis", "box", "legend", "plot.new",
             "plot.window", "polygon", "text")
  importFrom("stats", "quantile")
  importFrom("utils", "edit", "read.table")
to your NAMESPACE file.
File ‘som/libs/som.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
dfrag: no visible global function definition for ‘qgeom’
dfrag: no visible global function definition for ‘plogis’
dfrag: no visible global function definition for ‘dgeom’
estAbund: no visible global function definition for ‘xtabs’
mmN : <anonymous>: no visible global function definition for ‘uniroot’
pfrag: no visible global function definition for ‘qgeom’
phi.deriv.default: no visible global function definition for
  ‘model.matrix’
phi.deriv.default: no visible binding for global variable ‘sd’
phi.update.default: no visible global function definition for ‘glm’
phi.update.default: no visible binding for global variable
  ‘quasipoisson’
phi.update.default: no visible global function definition for ‘predict’
phi.update.lframe: no visible global function definition for ‘glm’
phi.update.lframe: no visible binding for global variable
  ‘quasipoisson’
phi.update.lframe: no visible global function definition for ‘predict’
pr.y.given.x : <anonymous>: no visible global function definition for
  ‘dpois’
pr.y.given.x : <anonymous> : <anonymous>: no visible global function
  definition for ‘dpois’
pr.y.given.x : <anonymous>: no visible global function definition for
  ‘convolve’
qfrag: no visible global function definition for ‘qgeom’
rfrag: no visible global function definition for ‘qgeom’
simSonic: no visible global function definition for ‘rpois’
Undefined global functions or variables:
  convolve dgeom dpois glm model.matrix plogis predict qgeom
  quasipoisson rpois sd uniroot xtabs
Consider adding
  importFrom("stats", "convolve", "dgeom", "dpois", "glm",
             "model.matrix", "plogis", "predict", "qgeom",
             "quasipoisson", "rpois", "sd", "uniroot", "xtabs")
to your NAMESPACE file.
plot.soo_function: no visible global function definition for
  ‘terrain.colors’
plot.soo_function: no visible binding for global variable ‘image’
plot.soo_function: no visible binding for global variable ‘contour’
plot3d: no visible global function definition for ‘persp3d’
plot3d: no visible global function definition for ‘terrain.colors’
random_parameters.soo_function: no visible global function definition
  for ‘runif’
random_rotation_matrix: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  contour image persp3d runif terrain.colors
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "contour", "image")
  importFrom("stats", "runif")
to your NAMESPACE file.
File ‘soobench/libs/soobench.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard files/directories found at top level:
  ‘README.markdown’ ‘build_package.sh’ ‘upload.sh’
simdata_contaminated : <anonymous>: no visible global function
  definition for ‘rbinom’
simdata_uniform : multivariate_uniform : <anonymous>: no visible global
  function definition for ‘runif’
which_min: no visible global function definition for ‘head’
which_min: no visible global function definition for ‘tail’
Undefined global functions or variables:
  head rbinom runif tail
Consider adding
  importFrom("stats", "rbinom", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
convert_municipality_names: no visible global function definition for
  ‘read.csv’
regression_plot: no visible binding for global variable ‘loess’
regression_plot: no visible global function definition for
  ‘colorRampPalette’
regression_plot: no visible global function definition for
  ‘loess.control’
regression_plot: no visible global function definition for ‘predict’
regression_plot : <anonymous>: no visible global function definition
  for ‘quantile’
regression_plot : <anonymous>: no visible global function definition
  for ‘pnorm’
regression_plot: no visible global function definition for
  ‘flush.console’
regression_plot: no visible global function definition for ‘density’
Undefined global functions or variables:
  colorRampPalette density flush.console loess loess.control pnorm
  predict quantile read.csv
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "density", "loess", "loess.control", "pnorm",
             "predict", "quantile")
  importFrom("utils", "flush.console", "read.csv")
to your NAMESPACE file.
Non-standard files/directories found at top level:
  ‘sandbox’ ‘sos4R-Ex.R’
'library' or 'require' call to ‘rgdal’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  as.data.frame.OmMeasurement as.data.frame.OmObservation
  as.list.OmObservationCollection length.OmObservationCollection
  names.OmMeasurement names.OmObservation names.OmObservationCollection
  plot.SOS plot.SensorML plot.SosObservationOffering
  print.summary.GmlTimePeriod print.summary.OmObservation
  print.summary.OmObservationCollection print.summary.OwsRange
  print.summary.SOS print.summary.SosObservationOffering
  summary.GmlTimePeriod summary.OmObservation
  summary.OmObservationCollection summary.OwsRange summary.SOS
  summary.SosObservationOffering
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘SoundexBR/libs/SoundexBR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
analyzeSP23Design: no visible global function definition for ‘plot’
exploreSP23Design: no visible global function definition for
  ‘txtProgressBar’
exploreSP23Design: no visible global function definition for
  ‘setTxtProgressBar’
generateClinicalTrialData : <anonymous>: no visible global function
  definition for ‘runif’
generateClinicalTrialData: no visible global function definition for
  ‘rbinom’
generateClinicalTrialData: no visible global function definition for
  ‘rexp’
mHP.b : crossingProbDiff: no visible global function definition for
  ‘pnorm’
mHP.b : crossingProbDiff: no visible global function definition for
  ‘Miwa’
mHP.b: no visible global function definition for ‘qnorm’
mHP.b: no visible global function definition for ‘uniroot’
mHP.c : crossingProbDiff: no visible global function definition for
  ‘Miwa’
mHP.c: no visible global function definition for ‘uniroot’
mHP.c: no visible global function definition for ‘qnorm’
performInterimLook: no visible global function definition for ‘optim’
performInterimLook: no visible global function definition for
  ‘constrOptim’
performInterimLook: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  Miwa constrOptim optim plot pnorm qnorm rbinom rexp runif
  setTxtProgressBar txtProgressBar uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "constrOptim", "optim", "pnorm", "qnorm", "rbinom",
             "rexp", "runif", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
SPA: no visible global function definition for ‘var’
Score.Test.Interact: no visible global function definition for ‘pchisq’
Score.Test.Overall: no visible global function definition for ‘var’
Score.Test.Overall: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq var
Consider adding
  importFrom("stats", "pchisq", "var")
to your NAMESPACE file.
File ‘SpaCCr/libs/SpaCCr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘glasso’ ‘limSolve’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
glasso.miss: no visible global function definition for ‘cov’
glasso.miss: no visible global function definition for ‘glasso’
glasso.miss: no visible global function definition for ‘Solve’
space.miss: no visible global function definition for ‘Solve’
Undefined global functions or variables:
  Solve cov glasso
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
Rd file 'glasso.miss.Rd':
  \examples lines wider than 100 characters:
     data(finStocksCn)  ##data of finance sector of Chinese Stock Market, from January 4th, 2011 to July 26th, 2011

Rd file 'space.miss.Rd':
  \examples lines wider than 100 characters:
     data(finStocksCn)  ##data of finance sector of Chinese Stock Market, from January 4th, 2011 to July 26th, 2011

These lines will be truncated in the PDF manual.
File ‘spaceExt/libs/spaceExt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘Matrix’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Matrix’ ‘igraph’ ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'SJ.Rd':
  \examples lines wider than 100 characters:
     #with standard deviations of 1, 0.5 and 0.5, (i.e. giving more weight to linear association than quadratic or cubic)
     #Fit conditional independence graph at one lambda , using the default basis functions (cubic polynomials).
     plot(g, layout=mylayout, edge.color = "gray50", vertex.color = "red", vertex.size = 3, vertex.label = NA, edge.arrow.size = 0.4, main=" ... [TRUNCATED]

Rd file 'generate.dag.data.Rd':
  \usage lines wider than 90 characters:
     generate.dag.data(g, n, basesd = 1, basemean = 0, bfuns = function(x){cbind(x, x^2, x^3)}, 
  \examples lines wider than 100 characters:
     #with standard deviations of 1, 0.5 and 0.5, (i.e. giving more weight to linear association than quadratic or cubic)

Rd file 'spacejam-package.Rd':
  \examples lines wider than 100 characters:
     #with standard deviations of 1, 0.5 and 0.5, (i.e. giving more weight to linear association than quadratic or cubic)
     plot(g, layout=mylayout, edge.color = "gray50", vertex.color = "red", vertex.size = 3, vertex.label = NA, edge.arrow.size = 0.4, main=" ... [TRUNCATED]

These lines will be truncated in the PDF manual.
File ‘spacejam/libs/spacejam.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
GenPar: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Rd file 'space.joint.Rd':
  \examples lines wider than 100 characters:
     #################### view the network corresponding to the parcial correlation matrix in the simulation example
     #plot(temp, vertex.size=3, vertex.frame.color="white",layout=layout.fruchterman.reingold, vertex.label=NA, edge.color=grey(0.5))

Rd file 'space.neighbor.Rd':
  \examples lines wider than 100 characters:
     #################### view the network corresponding to the parcial correlation matrix in the simulation example
     #################### view the network corresponding to the parcial correlation matrix in the simulation example
     #plot(temp, vertex.size=3, vertex.frame.color="white",layout=layout.fruchterman.reingold, vertex.label=NA, edge.color=grey(0.5))

These lines will be truncated in the PDF manual.
File ‘space/libs/space.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘colorspace’ ‘picante’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'phy.dotplot.Rd':
  \usage lines wider than 90 characters:
     phy.dotplot(sp.plot, phy, edge.width = 0.2, lab.adj = c(0, 0), tips.adj = c(0.5, 3), tips.cex = 1.0, pch = 21, print.labs = FALSE, outf ... [TRUNCATED]

Rd file 'spacodi.by.nodes.Rd':
  \usage lines wider than 90 characters:
     spacodi.by.nodes(sp.plot, phy, sp.parm = "Bst", obs.only = FALSE, return.all = TRUE, n.rep = 10, method = "1s", parm = NULL, dmat = NUL ... [TRUNCATED]

Rd file 'spacodi.calc.Rd':
  \usage lines wider than 90 characters:
     spacodi.calc(sp.plot, phy = NULL, sp.traits = NULL, all.together = TRUE, prune = TRUE, pairwise = FALSE, ...)

Rd file 'spacodi.permutplot.Rd':
  \usage lines wider than 90 characters:
       spacodi.permutplot(spacodi.permutations, cex=list(pch=1.5, rand=0.1, node=0.5, legend=0.75), transp=0.8, col = list("black", "lightgr ... [TRUNCATED]
       bg = list("white", "lightgray", "black"), all.points = TRUE, add.id = TRUE, sig.plot = TRUE, cut.off = 0.05, envelope = FALSE, outfil ... [TRUNCATED]

Rd file 'spacodi.treeplot.Rd':
  \usage lines wider than 90 characters:
     spacodi.treeplot(spacodi.permutations, phy, cex=list(pch = 1.5, tip = 0.5, legend = 0.75), transp=0.8, sig.plot = TRUE, cut.off = 0.05, ... [TRUNCATED]

These lines will be truncated in the PDF manual.
File ‘spacodiR/libs/spacodiR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘spaero/libs/spaero.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
hausman: no visible global function definition for ‘pchisq’
span.formula: no visible global function definition for ‘model.frame’
span.formula: no visible global function definition for ‘model.matrix’
span.formula: no visible global function definition for
  ‘model.response’
spbe: no visible global function definition for ‘cor’
spbe: no visible global function definition for ‘pt’
spfe: no visible global function definition for ‘cor’
spfe: no visible global function definition for ‘pt’
sprandom: no visible global function definition for ‘cor’
sprandom: no visible global function definition for ‘pt’
summary.span: no visible global function definition for ‘printCoefmat’
Undefined global functions or variables:
  cor model.frame model.matrix model.response pchisq printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.frame", "model.matrix",
             "model.response", "pchisq", "printCoefmat", "pt")
to your NAMESPACE file.
plot.spa: no visible global function definition for ‘plot’
plot.spa: no visible global function definition for ‘lines’
plot.spa: no visible global function definition for ‘points’
plot.spa: no visible global function definition for ‘gray’
plot.spa: no visible global function definition for ‘box’
predict.spa: no visible global function definition for ‘fitted’
predict.spa: no visible global function definition for ‘coef’
spa.gcv: no visible global function definition for ‘density’
spa.gcv: no visible global function definition for ‘quantile’
spa.sim: no visible global function definition for ‘runif’
spa.sim: no visible global function definition for ‘rnorm’
spa.sim: no visible global function definition for ‘rbinom’
update.spa: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  box coef density fitted gray lines plot points quantile rbinom rnorm
  runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "box", "lines", "plot", "points")
  importFrom("stats", "coef", "density", "fitted", "quantile", "rbinom",
             "rnorm", "runif")
to your NAMESPACE file.
Rd file 'predict.spa.Rd':
  \examples lines wider than 100 characters:
     title(switch(attr(dat,"type"),moon="Two Moon Simulated Data",supervised="Supervised Border Simulated set"))

These lines will be truncated in the PDF manual.
Found the following apparent S3 methods exported but not registered:
  plot.HierarchicalSparseCluster plot.HierarchicalSparseCluster.permute
  plot.KMeansSparseCluster plot.KMeansSparseCluster.permute
  print.HierarchicalSparseCluster
  print.HierarchicalSparseCluster.permute print.KMeansSparseCluster
  print.KMeansSparseCluster.permute
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'ColorDendrogram.Rd':
  \usage lines wider than 90 characters:
     ColorDendrogram(hc, y, main = "", branchlength = 0.7, labels = NULL, xlab = NULL, sub = NULL, ylab = "", cex.main = NULL)

Rd file 'HierarchicalSparseCluster.Rd':
  \usage lines wider than 90 characters:
     HierarchicalSparseCluster(x=NULL, dists=NULL,method=c("average","complete", "single","centroid"),
     wbound=NULL,niter=15,dissimilarity=c("squared.distance","absolute.value"), uorth=NULL,silent=FALSE,
  \examples lines wider than 100 characters:
       # faster than   sparsehc <- HierarchicalSparseCluster(x=x,wbound=perm.out$bestw, method="complete")
       sparsehc <- HierarchicalSparseCluster(dists=perm.out$dists, wbound=perm.out$bestw, method="complete", dissimilarity="absolute.value")

Rd file 'HierarchicalSparseCluster.permute.Rd':
  \examples lines wider than 100 characters:
       sparsehc <- HierarchicalSparseCluster(dists=perm.out$dists, wbound=perm.out$bestw, method="complete")

Rd file 'HierarchicalSparseCluster.wrapper.Rd':
  \usage lines wider than 90 characters:
     HierarchicalSparseCluster.wrapper(file,  method=c("average", "complete", "single", "centroid"),
     "single","centroid"),output.cluster.files=TRUE,outputfile.prefix=NULL,maxnumgenes=5000,standardize.arrays=TRUE)

These lines will be truncated in the PDF manual.
File ‘sparcl/libs/sparcl.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sparc/libs/sparc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘RCurl’ ‘XML’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SPARQL : <anonymous>: no visible global function definition for
  ‘URLencode’
SPARQL: no visible binding for global variable ‘getURL’
SPARQL: no visible global function definition for ‘URLencode’
SPARQL: no visible binding for global variable ‘xmlParse’
SPARQL: no visible global function definition for ‘getNodeSet’
SPARQL: no visible global function definition for ‘xpathApply’
SPARQL: no visible binding for global variable ‘postForm’
get_attr: no visible global function definition for ‘getNodeSet’
get_attr : <anonymous> : <anonymous>: no visible global function
  definition for ‘getNodeSet’
get_attr : <anonymous> : <anonymous>: no visible global function
  definition for ‘xmlDoc’
get_value: no visible global function definition for ‘xmlDoc’
get_value: no visible global function definition for ‘xpathSApply’
get_value: no visible binding for global variable ‘xmlValue’
get_value: no visible global function definition for ‘xpathApply’
get_value: no visible binding for global variable ‘xmlGetAttr’
readCSVstring: no visible global function definition for ‘read.csv’
readTSVstring: no visible global function definition for ‘read.delim’
Undefined global functions or variables:
  URLencode getNodeSet getURL postForm read.csv read.delim xmlDoc
  xmlGetAttr xmlParse xmlValue xpathApply xpathSApply
Consider adding
  importFrom("utils", "URLencode", "read.csv", "read.delim")
to your NAMESPACE file.
f.I2.cont: no visible global function definition for ‘combn’
f.I2.dich: no visible global function definition for ‘combn’
f.pstar.cont: no visible global function definition for ‘combn’
f.pstar.dich: no visible global function definition for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
image.matrixBC: no visible global function definition for ‘dev.new’
image.matrixBC: no visible global function definition for ‘image’
image.matrixBC: no visible global function definition for ‘heat.colors’
image.matrixBC: no visible global function definition for ‘axis’
image.matrixBC: no visible global function definition for ‘title’
image.sparseBC: no visible global function definition for ‘dev.new’
image.sparseBC: no visible global function definition for ‘image’
image.sparseBC: no visible global function definition for ‘heat.colors’
image.sparseBC: no visible global function definition for ‘axis’
image.sparseBC: no visible global function definition for ‘tail’
image.sparseBC: no visible global function definition for ‘title’
matrixBC: no visible global function definition for ‘kmeans’
sparseBC: no visible global function definition for ‘kmeans’
sparseBC.choosekr: no visible global function definition for ‘kmeans’
sparseBC.choosekr: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  axis dev.new heat.colors image kmeans sd tail title
Consider adding
  importFrom("grDevices", "dev.new", "heat.colors")
  importFrom("graphics", "axis", "image", "title")
  importFrom("stats", "kmeans", "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
Unexported object imported by a ':::' call: ‘igraph:::as_graphnel’
  See the note in ?`:::` about the use of this operator.
File ‘SparseFactorAnalysis/libs/SparseFactorAnalysis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sparseLTSEigen/libs/sparseLTSEigen.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  coef.cv.sparsenet
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘sparsenet/libs/sparsenet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sparsereg/libs/sparsereg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sparseSEM/libs/sparseSEM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sparsesvd/libs/sparsesvd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sparseSVM/libs/sparseSVM.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SparseTSCGM/libs/SparseTSCGM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Clarketest: no visible global function definition for ‘pbinom’
Clarketest: no visible global function definition for ‘qbinom’
DIC: no visible global function definition for ‘model.matrix’
LogLike: no visible global function definition for ‘model.matrix’
Vuongtest: no visible global function definition for ‘var’
Vuongtest: no visible global function definition for ‘qnorm’
Vuongtest: no visible global function definition for ‘pnorm’
est.sc: no visible global function definition for ‘model.matrix’
gpind: no visible global function definition for ‘rgamma’
nbind: no visible global function definition for ‘rgamma’
poiind: no visible global function definition for ‘rgamma’
zigpind: no visible global function definition for ‘rbinom’
zigpind: no visible global function definition for ‘rgamma’
zipind: no visible global function definition for ‘rbinom’
zipind: no visible global function definition for ‘rgamma’
Undefined global functions or variables:
  model.matrix pbinom pnorm qbinom qnorm rbinom rgamma var
Consider adding
  importFrom("stats", "model.matrix", "pbinom", "pnorm", "qbinom",
             "qnorm", "rbinom", "rgamma", "var")
to your NAMESPACE file.
Rd file 'est.sc.Rd':
  \examples lines wider than 100 characters:
     # gamma.true = vector of spatial effects according to the CAR model with mean 0, psi = 3 and sigma = 1
     nb <- est.sc(sim.Yin, ~1+sim.fm.X[,1]+sim.fm.X[,2], sim.region, model="NB", sim.gmat, sim.nmat, totalit=10)
     gp <- est.sc(sim.Yin, ~1+sim.fm.X[,1]+sim.fm.X[,2], sim.region, model="GP", sim.gmat, sim.nmat, totalit=10)
     zip <- est.sc(sim.Yin, ~1+sim.fm.X[,1]+sim.fm.X[,2], sim.region, model="ZIP", sim.gmat, sim.nmat, totalit=10)
     zigp <- est.sc(sim.Yin, ~1+sim.fm.X[,1]+sim.fm.X[,2], sim.region, model="ZIGP", sim.gmat, sim.nmat, totalit=10)
     Vuong.poi.nb <- Vuongtest(ll.poi, ll.nb, alpha = 0.05, p = DIC.poi$p.D, q = DIC.nb$p.D, correction = TRUE)
     Vuong.poi.gp <- Vuongtest(ll.poi, ll.gp, alpha = 0.05, p = DIC.poi$p.D, q = DIC.gp$p.D, correction = TRUE)
     Vuong.poi.zip <- Vuongtest(ll.poi, ll.zip, alpha = 0.05, p = DIC.poi$p.D, q = DIC.zip$p.D, correction = TRUE)
     Vuong.poi.zigp <- Vuongtest(ll.poi, ll.zigp, alpha = 0.05, p = DIC.poi$p.D, q = DIC.zigp$p.D, correction = TRUE)
     Clarke.poi.nb <- Clarketest(ll.poi, ll.nb, alpha = 0.05, p = DIC.poi$p.D, q = DIC.nb$p.D, correction = TRUE)
     Clarke.poi.gp <- Clarketest(ll.poi, ll.gp, alpha = 0.05, p = DIC.poi$p.D, q = DIC.gp$p.D, correction = TRUE)
     Clarke.poi.zip <- Clarketest(ll.poi, ll.zip, alpha = 0.05, p = DIC.poi$p.D, q = DIC.zip$p.D, correction = TRUE)
     Clarke.poi.zigp <- Clarketest(ll.poi, ll.zigp, alpha = 0.05, p = DIC.poi$p.D, q = DIC.zigp$p.D, correction = TRUE)

These lines will be truncated in the PDF manual.
File ‘spatcounts/libs/spatcounts.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘spate/libs/spate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SpatialEpi/libs/SpatialEpi.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Registered S3 method from a standard package overwritten by 'SpatialExtremes':
  method          from    
  predict.pspline survival
File ‘spatialfil/libs/spatialfil.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
gev.impute: no visible global function definition for ‘rnorm’
gev.init: no visible global function definition for ‘rbinom’
gev.init: no visible global function definition for ‘var’
gev.init: no visible global function definition for ‘optimize’
gev.logscore: no visible global function definition for ‘density’
gev.logscore: no visible global function definition for ‘splinefun’
gev.update.M: no visible global function definition for ‘runif’
gev.update.hyper: no visible global function definition for ‘rgamma’
gev.update.lambda: no visible global function definition for ‘rnorm’
gev.update.lambda: no visible global function definition for ‘dgamma’
gev.update.lambda: no visible global function definition for ‘dnorm’
gev.update.lambda: no visible global function definition for ‘runif’
gev.update.tau.kappa: no visible global function definition for ‘rnorm’
gev.update.tau.kappa: no visible global function definition for ‘dnorm’
gev.update.tau.kappa: no visible global function definition for ‘runif’
gev.update.tau.mu: no visible global function definition for ‘rnorm’
gev.update.tau.mu: no visible global function definition for ‘dnorm’
gev.update.tau.mu: no visible global function definition for ‘runif’
gev.update.tau.xi: no visible global function definition for ‘rnorm’
gev.update.tau.xi: no visible global function definition for ‘dnorm’
gev.update.tau.xi: no visible global function definition for ‘runif’
gev.update.theta: no visible global function definition for ‘rnorm’
gp.like.lambda: no visible global function definition for ‘dgamma’
Undefined global functions or variables:
  density dgamma dnorm optimize rbinom rgamma rnorm runif splinefun var
Consider adding
  importFrom("stats", "density", "dgamma", "dnorm", "optimize", "rbinom",
             "rgamma", "rnorm", "runif", "splinefun", "var")
to your NAMESPACE file.
codisp: no visible global function definition for ‘complete.cases’
cor.spatial: no visible global function definition for ‘complete.cases’
modified.ttest: no visible global function definition for
  ‘complete.cases’
modified.ttest: no visible global function definition for ‘cor’
plot.codisp: no visible global function definition for ‘plot’
plot.codisp: no visible global function definition for ‘title’
Undefined global functions or variables:
  complete.cases cor plot title
Consider adding
  importFrom("graphics", "plot", "title")
  importFrom("stats", "complete.cases", "cor")
to your NAMESPACE file.
I2BR: no visible global function definition for ‘pnorm’
I2SmD2: no visible global function definition for ‘pnorm’
IBR: no visible global function definition for ‘pnorm’
ISmD2: no visible global function definition for ‘pnorm’
MestimatorBR: no visible global function definition for ‘optim’
MestimatorSmith: no visible global function definition for ‘optim’
psidotBR: no visible global function definition for ‘dnorm’
psidotBR: no visible global function definition for ‘pnorm’
psidotSmD2: no visible global function definition for ‘dnorm’
psidotSmD2: no visible global function definition for ‘pnorm’
tailBRInt: no visible global function definition for ‘pnorm’
tailSmithInt: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dnorm optim pnorm
Consider adding
  importFrom("stats", "dnorm", "optim", "pnorm")
to your NAMESPACE file.
File ‘spatialTailDep/libs/spatialTailDep.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
bbox_to_SpatialPolygons: no visible global function definition for
  ‘CRS’
bbox_to_SpatialPolygons: no visible global function definition for
  ‘Polygon’
bbox_to_SpatialPolygons: no visible global function definition for
  ‘Polygons’
bbox_to_SpatialPolygons: no visible global function definition for
  ‘SpatialPolygons’
list.raster.files: no visible global function definition for ‘CRS’
list.raster.files: no visible global function definition for
  ‘spTransform’
list.raster.files: no visible global function definition for
  ‘SpatialPolygonsDataFrame’
list.raster.files: no visible global function definition for ‘spChFIDs’
predict_rasterEngine : predict.rasterEngine_function: no visible global
  function definition for ‘complete.cases’
projectRaster_rigorous : chunk_function: no visible global function
  definition for ‘spTransform’
projectRaster_rigorous : chunk_function: no visible global function
  definition for ‘CRS’
spatial_sync_raster: no visible global function definition for ‘bbox’
spatial_sync_vector: no visible global function definition for
  ‘spTransform’
spatial_sync_vector: no visible global function definition for ‘CRS’
Undefined global functions or variables:
  CRS Polygon Polygons SpatialPolygons SpatialPolygonsDataFrame bbox
  complete.cases spChFIDs spTransform
Consider adding
  importFrom("stats", "complete.cases")
to your NAMESPACE file.
File ‘SpatialTools/libs/SpatialTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SpaTimeClus/libs/SpaTimeClus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard file/directory found at top level:
  ‘Rd_examples’
File ‘SpatioTemporal/libs/SpatioTemporal.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
GenerateCliquesCovariance: no visible global function definition for
  ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
File ‘spcr/libs/spcr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘spDataLarge’
bartlett: no visible global function definition for ‘pchisq’
local.rbfdot: no visible binding for global variable ‘sd’
local.rbfdot: no visible global function definition for ‘dist’
local.rbfdot : <anonymous>: no visible global function definition for
  ‘median’
speccalt: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  dist kmeans median pchisq sd
Consider adding
  importFrom("stats", "dist", "kmeans", "median", "pchisq", "sd")
to your NAMESPACE file.
File ‘SpeciesMix/libs/SpeciesMix.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
ChaoBunge: no visible global function definition for ‘qnorm’
ChaoLee1992: no visible global function definition for ‘qnorm’
Pmix: no visible global function definition for ‘dpois’
PmixSCon: no visible global function definition for ‘dbeta’
bootPCG: no visible global function definition for ‘flush.console’
bootPCG: no visible global function definition for ‘quantile’
bootPnpmle: no visible global function definition for ‘flush.console’
bootPnpmle: no visible global function definition for ‘quantile’
bootUnpmle: no visible global function definition for ‘flush.console’
bootUnpmle: no visible global function definition for ‘quantile’
chao1984: no visible global function definition for ‘qnorm’
jackknife: no visible global function definition for ‘dbinom’
jackknife: no visible global function definition for ‘qnorm’
pcg: no visible global function definition for ‘flush.console’
unpmle: no visible global function definition for ‘flush.console’
untrunPmix: no visible global function definition for ‘dpois’
Undefined global functions or variables:
  dbeta dbinom dpois flush.console qnorm quantile
Consider adding
  importFrom("stats", "dbeta", "dbinom", "dpois", "qnorm", "quantile")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
File ‘SPECIES/libs/SPECIES.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  print.summary.specificity summary.specificity
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
randomCorrelations: no visible global function definition for ‘cor’
specGlm : <anonymous>: no visible global function definition for ‘coef’
specLm : <anonymous>: no visible global function definition for ‘coef’
Undefined global functions or variables:
  coef cor
Consider adding
  importFrom("stats", "coef", "cor")
to your NAMESPACE file.
Missing or unexported objects:
  ‘ChemoSpec::readJDX’ ‘hyperSpec::spc.NA.linapprox’
Running examples in ‘specmine-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: impute_nas_linapprox
> ### Title: Impute missing values with linear approximation
> ### Aliases: impute_nas_linapprox
> ### Keywords: missing values
> 
> ### ** Examples
> 
>   ## Example of NA imputation with linear approximation
>   data(propolis)
>   dataset = impute_nas_linapprox(propolis)
Error: 'spc.NA.linapprox' is not an exported object from 'namespace:hyperSpec'
Execution halted
File ‘spectral/libs/spectral.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘leaps’ which was already attached by Depends.
  Please remove these calls from your code.
modSearch: no visible global function definition for ‘glm’
modSearch: no visible binding for global variable ‘binomial’
modSearch: no visible global function definition for ‘na.omit’
modSearch: no visible global function definition for ‘as.formula’
speff: no visible binding for global variable ‘na.pass’
speff: no visible global function definition for ‘model.matrix’
speff: no visible global function definition for ‘terms’
speff: no visible global function definition for ‘model.response’
speff: no visible global function definition for ‘as.formula’
speff: no visible global function definition for ‘predict’
speff: no visible global function definition for ‘na.omit’
speff: no visible global function definition for ‘glm’
speff: no visible binding for global variable ‘na.omit’
speffSurv: no visible global function definition for ‘model.matrix’
speffSurv: no visible global function definition for ‘terms’
speffSurv: no visible global function definition for ‘model.response’
speffSurv: no visible global function definition for ‘as.formula’
speffSurv: no visible global function definition for ‘uniroot’
summary.speff: no visible global function definition for ‘qnorm’
summary.speff: no visible global function definition for ‘pnorm’
summary.speffSurv: no visible global function definition for ‘qnorm’
summary.speffSurv: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  as.formula binomial glm model.matrix model.response na.omit na.pass
  pnorm predict qnorm terms uniroot
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "model.matrix",
             "model.response", "na.omit", "na.pass", "pnorm", "predict",
             "qnorm", "terms", "uniroot")
to your NAMESPACE file.
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of ‘nr’ to ‘nrow’
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of ‘nc’ to ‘ncol’
spe: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
File ‘spe/libs/spe.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package in Depends field not imported from: ‘rgl’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
pointsphere: no visible global function definition for ‘runif’
rgl.sphMW: no visible global function definition for ‘plot3d’
rgl.sphcirc: no visible global function definition for ‘rotate3d’
rgl.sphcirc: no visible global function definition for ‘lines3d’
rgl.sphgrid: no visible global function definition for ‘open3d’
rgl.sphgrid: no visible global function definition for ‘plot3d’
rgl.sphgrid: no visible global function definition for ‘lines3d’
rgl.sphgrid: no visible global function definition for ‘text3d’
rgl.sphpoints: no visible global function definition for ‘points3d’
rgl.sphsun: no visible global function definition for ‘plot3d’
rgl.sphtext: no visible global function definition for ‘text3d’
Undefined global functions or variables:
  lines3d open3d plot3d points3d rotate3d runif text3d
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  summary.sphet
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘spikeSlabGAM/libs/spikeSlabGAM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘lars’ ‘parallel’ ‘randomForest’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘spikeslab/libs/spikeslab.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘quadprog’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘quadprog’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SPIn: no visible global function definition for ‘density’
SPIn: no visible global function definition for ‘quantile’
SPIn: no visible global function definition for ‘solve.QP’
bootSPIn: no visible global function definition for ‘runif’
plot.SPIn: no visible global function definition for ‘hist’
plot.SPIn: no visible global function definition for ‘lines’
plot.SPIn: no visible global function definition for ‘text’
plot.SPIn: no visible global function definition for ‘quantile’
plot.SPIn: no visible global function definition for ‘legend’
Undefined global functions or variables:
  density hist legend lines quantile runif solve.QP text
Consider adding
  importFrom("graphics", "hist", "legend", "lines", "text")
  importFrom("stats", "density", "quantile", "runif")
to your NAMESPACE file.
spi: no visible global function definition for ‘read.table’
spi: no visible global function definition for ‘ecdf’
spi: no visible global function definition for ‘qnorm’
spi: no visible global function definition for ‘colorRampPalette’
spi: no visible global function definition for ‘filled.contour’
spi: no visible global function definition for ‘axis’
Undefined global functions or variables:
  axis colorRampPalette ecdf filled.contour qnorm read.table
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "filled.contour")
  importFrom("stats", "ecdf", "qnorm")
  importFrom("utils", "read.table")
to your NAMESPACE file.
prepare_Rd: spi.Rd:117-119: Dropping empty section \note
prepare_Rd: spi.Rd:123-125: Dropping empty section \seealso
Rd file 'spi.Rd':
  \examples lines wider than 100 characters:
     spi(7,"spi.txt",1963,2010,"Standardized Precipitation Index - Rio Grande do Norte State",1,"years","months")

These lines will be truncated in the PDF manual.
NoSep: no visible global function definition for ‘setNames’
Reshape: no visible global function definition for ‘setNames’
Reshape: no visible global function definition for ‘reshape’
read.concat: no visible global function definition for ‘count.fields’
read.concat: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  count.fields read.table reshape setNames
Consider adding
  importFrom("stats", "reshape", "setNames")
  importFrom("utils", "count.fields", "read.table")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  coef.sgpls coef.spls coef.splsda plot.spls predict.sgpls predict.spls
  predict.splsda print.sgpls print.spls print.splsda
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘splus2R/libs/splus2R.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  all.equal.list all.equal.list
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘spMC/libs/spMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
R2.global: no visible global function definition for ‘var’
calculer.var.exp: no visible global function definition for ‘var’
creer.noeud: no visible global function definition for ‘var’
ponderer.classe: no visible global function definition for ‘var’
ponderer.classe: no visible global function definition for ‘cov’
spodt: no visible global function definition for ‘model.frame’
spodt.tree: no visible global function definition for ‘plot.new’
spodt.tree: no visible global function definition for ‘par’
spodt.tree: no visible global function definition for ‘plot.window’
spodt.tree: no visible global function definition for ‘text’
spodt.tree: no visible global function definition for ‘segments’
test.spodt: no visible global function definition for ‘model.frame’
test.spodt: no visible global function definition for ‘hist’
test.spodt: no visible global function definition for ‘abline’
tracer.noeud: no visible global function definition for ‘text’
tracer.noeud: no visible global function definition for ‘segments’
Undefined global functions or variables:
  abline cov hist model.frame par plot.new plot.window segments text
  var
Consider adding
  importFrom("graphics", "abline", "hist", "par", "plot.new",
             "plot.window", "segments", "text")
  importFrom("stats", "cov", "model.frame", "var")
to your NAMESPACE file.
File ‘SPODT/libs/SPODT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
prepare_Rd: H.Binv.Rd:48-50: Dropping empty section \note
prepare_Rd: V.theta.Rd:28-30: Dropping empty section \details
prepare_Rd: V.theta.Rd:43-45: Dropping empty section \note
prepare_Rd: V.theta.Rd:49-51: Dropping empty section \seealso
prepare_Rd: V.theta.Rd:52-53: Dropping empty section \examples
prepare_Rd: confid.int.theta.Rd:62-64: Dropping empty section \note
prepare_Rd: dd.est.Rd:39-41: Dropping empty section \note
prepare_Rd: dd.est.Rd:45-47: Dropping empty section \seealso
prepare_Rd: ell.theta.Rd:60-62: Dropping empty section \note
prepare_Rd: ell.theta.Rd:69-70: Dropping empty section \examples
prepare_Rd: grad.hessinv.Rd:47-49: Dropping empty section \note
prepare_Rd: ks.sporm.Rd:43-45: Dropping empty section \note
prepare_Rd: ks.stat.Rd:39-41: Dropping empty section \note
prepare_Rd: mrle.sporm.Rd:66-68: Dropping empty section \note
prepare_Rd: mrle.sporm.Rd:72-74: Dropping empty section \seealso
prepare_Rd: newton.theta.Rd:47-49: Dropping empty section \note
prepare_Rd: phi.Rd:32-38: Dropping empty section \value
prepare_Rd: phi.Rd:48-50: Dropping empty section \note
prepare_Rd: plotor.Rd:26-32: Dropping empty section \value
prepare_Rd: plotor.Rd:42-44: Dropping empty section \note
prepare_Rd: plotor.Rd:48-50: Dropping empty section \seealso
prepare_Rd: sporm-package.Rd:53-54: Dropping empty section \seealso
prepare_Rd: sporm-package.Rd:55-56: Dropping empty section \examples
prepare_Rd: test.theta.Rd:54-56: Dropping empty section \note
prepare_Rd: elltheta.rd:53-55: Dropping empty section \note
prepare_Rd: elltheta.rd:62-63: Dropping empty section \examples
fetch_NBAPlayerStatistics: no visible global function definition for
  ‘read.table’
Undefined global functions or variables:
  read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  coef.Lifedata.MLE coef.deglmx.MLE logLik.Lifedata.MLE plot.MICsplines
  print.Lifedata.MLE print.deglmx print.summary.Lifedata.MLE sqrt.mat
  summary.Lifedata.MLE
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Registered S3 methods from standard package(s) overwritten by 'sprint':
  method            from   
  print.pam         cluster
  print.summary.pam cluster
  summary.pam       cluster
'library' or 'require' call to ‘RankProd’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
pRP: no visible global function definition for ‘plotRP’
pRPadvance: no visible global function definition for ‘plotRP’
pboot: no visible global function definition for ‘runif’
prandomForest.formula: no visible binding for global variable ‘na.fail’
prandomForest.formula: no visible global function definition for
  ‘model.response’
prandomForest.formula: no visible global function definition for
  ‘model.frame’
prandomForest.formula: no visible global function definition for
  ‘terms’
prandomForest.formula: no visible global function definition for
  ‘reformulate’
Undefined global functions or variables:
  model.frame model.response na.fail plotRP reformulate runif terms
Consider adding
  importFrom("stats", "model.frame", "model.response", "na.fail",
             "reformulate", "runif", "terms")
to your NAMESPACE file.
Note: information on .o files is not available
File ‘sprint/libs/sprint.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

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

These lines will be truncated in the PDF manual.
plot.SPRT: no visible global function definition for ‘par’
plot.SPRT: no visible global function definition for ‘plot’
plot.SPRT: no visible global function definition for ‘abline’
print.SPRT: no visible global function definition for ‘head’
Undefined global functions or variables:
  abline head par plot
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("utils", "head")
to your NAMESPACE file.
fssa20: no visible global function definition for ‘runif’
fssa2d: no visible global function definition for ‘runif’
fssa30: no visible global function definition for ‘runif’
fssa3d: no visible global function definition for ‘runif’
ssa20: no visible global function definition for ‘runif’
ssa2d: no visible global function definition for ‘runif’
ssa30: no visible global function definition for ‘runif’
ssa3d: no visible global function definition for ‘runif’
ssi20: no visible global function definition for ‘runif’
ssi2d: no visible global function definition for ‘runif’
ssi30: no visible global function definition for ‘runif’
ssi3d: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Rd file 'fssa30.Rd':
  \examples lines wider than 100 characters:
     main="Relative frequency distribution in the z=17 slice\n of anisotropic 3D clusters with (1,0)-neighborhood")

Rd file 'fssa3d.Rd':
  \examples lines wider than 100 characters:
     main="Relative frequency distribution in the z=17 slice\n of anisotropic 3D clusters with (1,1)-neighborhood")

Rd file 'fssi30.Rd':
  \examples lines wider than 100 characters:
     main="Relative frequency distribution in the z=17 slice\n of isotropic 3D clusters with (1,0)-neighborhood")

Rd file 'fssi3d.Rd':
  \examples lines wider than 100 characters:
     main="Relative frequency distribution in the z=17 slice\n of isotropic 3D clusters with (1,1)-neighborhood")

These lines will be truncated in the PDF manual.
File ‘SPSL/libs/SPSL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
plotThin: no visible global function definition for ‘par’
plotThin: no visible global function definition for ‘dev.interactive’
plotThin: no visible global function definition for ‘plot’
plotThin: no visible global function definition for ‘hist’
thin: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  dev.interactive hist par plot write.csv
Consider adding
  importFrom("grDevices", "dev.interactive")
  importFrom("graphics", "hist", "par", "plot")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  chaos.default chaos.spt chaos.st plot.spt plot.st print.spt print.st
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
.GameSPT: no visible global function definition for ‘runif’
.GameSPT: no visible global function definition for ‘points’
.GameST: no visible global function definition for ‘runif’
.GameST: no visible global function definition for ‘points’
.arc: no visible global function definition for ‘lines’
.ptpedal: no visible global function definition for ‘polygon’
.sptpedal2: no visible global function definition for ‘segments’
.sptpedal3: no visible global function definition for ‘polygon’
.sptpedal4: no visible global function definition for ‘polygon’
chaos.spt: no visible global function definition for ‘plot’
chaos.spt: no visible global function definition for ‘polygon’
chaos.spt: no visible global function definition for ‘runif’
chaos.spt: no visible global function definition for ‘points’
chaos.st: no visible global function definition for ‘plot’
chaos.st: no visible global function definition for ‘polygon’
chaos.st: no visible global function definition for ‘runif’
chaos.st: no visible global function definition for ‘points’
plot.spt: no visible global function definition for ‘plot’
plot.spt: no visible global function definition for ‘polygon’
plot.st: no visible global function definition for ‘plot’
plot.st: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  lines plot points polygon runif segments
Consider adding
  importFrom("graphics", "lines", "plot", "points", "polygon",
             "segments")
  importFrom("stats", "runif")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  mean.transectHolder mean.trapTransect print.transectHolder
  print.trapTransect simulate.transectHolder
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
CMCSimulation: no visible global function definition for ‘rexp’
CMCSimulation: no visible global function definition for ‘plot’
CMCSimulation: no visible global function definition for ‘axis’
booking_clerkMC: no visible global function definition for ‘runif’
booking_clerkMC: no visible global function definition for ‘rexp’
fixedpoint_show: no visible global function definition for ‘plot’
fixedpoint_show: no visible global function definition for ‘lines’
mean.trapTransect: no visible global function definition for
  ‘weighted.mean’
newtonraphson_show: no visible global function definition for ‘plot’
newtonraphson_show: no visible global function definition for ‘lines’
print.transectHolder: no visible global function definition for ‘str’
print.trapTransect: no visible global function definition for ‘str’
sd.transectHolder: no visible global function definition for ‘sd’
simulate.transectHolder: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  axis lines plot rexp runif sd str weighted.mean
Consider adding
  importFrom("graphics", "axis", "lines", "plot")
  importFrom("stats", "rexp", "runif", "sd", "weighted.mean")
  importFrom("utils", "str")
to your NAMESPACE file.
sGda : <anonymous>: no visible global function definition for ‘cov’
sortgene: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  cov model.matrix
Consider adding
  importFrom("stats", "cov", "model.matrix")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘RJDBC’ ‘RMySQL’ ‘RODBC’ ‘RPostgreSQL’ ‘RSQLite’ ‘tcltk’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
cacheQuery: no visible global function definition for ‘read.csv’
cacheQuery: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  read.csv write.csv
Consider adding
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
SQN: no visible binding for global variable ‘median’
SQN: no visible global function definition for ‘quantile’
SQN.demo.data: no visible global function definition for ‘rnorm’
mix.qn: no visible global function definition for ‘ecdf’
mix.qn: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  ecdf median quantile rnorm
Consider adding
  importFrom("stats", "ecdf", "median", "quantile", "rnorm")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: items ‘package:SQRL’, ‘SQRL:Face’ were removed from the search path
  Warning: items ‘package:SQRL’, ‘SQRL:Face’ were removed from the search path
plot.srafit: no visible global function definition for ‘layout’
plot.srafit: no visible global function definition for ‘par’
sraData : vartruncGauss : ff: no visible global function definition for
  ‘dnorm’
sraData : vartruncGauss : ff: no visible global function definition for
  ‘pnorm’
sraData : vartruncGauss: no visible global function definition for
  ‘uniroot’
sraPlotMean: no visible global function definition for ‘axis’
sraPlotMean: no visible global function definition for ‘points’
sraPlotMean: no visible global function definition for ‘lines’
sraPlotMeanResid: no visible global function definition for ‘axis’
sraPlotMeanResid: no visible global function definition for ‘abline’
sraPlotMeanResid: no visible global function definition for ‘points’
sraPlotVar: no visible global function definition for ‘axis’
sraPlotVar: no visible global function definition for ‘points’
sraPlotVar: no visible global function definition for ‘lines’
sraPlotVarResid: no visible global function definition for ‘axis’
sraPlotVarResid: no visible global function definition for ‘abline’
sraPlotVarResid: no visible global function definition for ‘points’
sraPlotlegend: no visible global function definition for ‘legend’
sraStartingvalues : sraStartingvalues.mu0: no visible global function
  definition for ‘rnorm’
sraStartingvalues : sraStartingvalues.logvarA0: no visible global
  function definition for ‘rnorm’
sraStartingvalues : sraStartingvalues.logvarE0: no visible global
  function definition for ‘rnorm’
sraStartingvalues: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline axis dnorm layout legend lines par pnorm points rnorm uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "layout", "legend", "lines",
             "par", "points")
  importFrom("stats", "dnorm", "pnorm", "rnorm", "uniroot")
to your NAMESPACE file.
Found the following hidden files and directories:
  .Rapp.history
  inst/script/.Rapp.history
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
File ‘sROC/R/onload.R’:
  .onLoad calls:
    packageStartupMessage("sROC 0.1-2 loaded")

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

AUC : TrapezInt: no visible global function definition for ‘approx’
AUC : SimpsonInt: no visible global function definition for ‘approx’
CI.CDF: no visible global function definition for ‘qnorm’
bw.CDF: no visible global function definition for ‘sd’
bw.CDF: no visible global function definition for ‘IQR’
bw.CDF.pi: no visible global function definition for ‘sd’
bw.CDF.pi: no visible global function definition for ‘bw.nrd0’
bw.CDF.pi: no visible global function definition for ‘bw.nrd’
bw.CDF.pi: no visible global function definition for ‘bw.ucv’
bw.CDF.pi: no visible global function definition for ‘bw.bcv’
bw.CDF.pi: no visible global function definition for ‘bw.SJ’
bw.CDF.pi: no visible global function definition for ‘IQR’
plot.CDF: no visible global function definition for ‘plot.default’
plot.CDF: no visible global function definition for ‘lines’
plot.CDF: no visible global function definition for ‘polygon’
plot.ROC: no visible global function definition for ‘plot.default’
plot.ROC: no visible global function definition for ‘abline’
Undefined global functions or variables:
  IQR abline approx bw.SJ bw.bcv bw.nrd bw.nrd0 bw.ucv lines
  plot.default polygon qnorm sd
Consider adding
  importFrom("graphics", "abline", "lines", "plot.default", "polygon")
  importFrom("stats", "IQR", "approx", "bw.SJ", "bw.bcv", "bw.nrd",
             "bw.nrd0", "bw.ucv", "qnorm", "sd")
to your NAMESPACE file.
Rd file 'CI.CDF.Rd':
  \examples lines wider than 100 characters:
     curve(pnorm(x, mean=-2, sd=1)/2 + pnorm(x, mean=3, sd=0.8)/2, from =-6, to=6, add=TRUE, lty=2, col="blue")

Rd file 'kCDF.Rd':
  \examples lines wider than 100 characters:
     curve(pnorm(x, mean=-2, sd=1)/2 + pnorm(x, mean=3, sd=0.8)/2, from =-6, to=6, add=TRUE, lty=2, col="blue")

Rd file 'kROC.Rd':
  \usage lines wider than 90 characters:
     kROC(x, y, bw.x="pi_ucv", bw.y="pi_ucv", adjust=1, kernel=c("normal", "epanechnikov"), xgrid, 

These lines will be truncated in the PDF manual.
File ‘sROC/libs/sROC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ssa/libs/ssa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
ssd : correction_method_D: no visible global function definition for
  ‘rnorm’
ssd : generate_bootstrap: no visible global function definition for
  ‘rmultinom’
ssd : bootstrap_method: no visible global function definition for
  ‘median’
ssd : bootstrap_method: no visible global function definition for
  ‘quantile’
ssd : unbalanced_generate_bootstrap: no visible global function
  definition for ‘rmultinom’
ssd : unbalanced_bootstrap_method: no visible global function
  definition for ‘median’
ssd : unbalanced_bootstrap_method: no visible global function
  definition for ‘quantile’
ssd: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  median qchisq quantile rmultinom rnorm
Consider adding
  importFrom("stats", "median", "qchisq", "quantile", "rmultinom",
             "rnorm")
to your NAMESPACE file.
L_hNV: no visible global function definition for ‘pnorm’
L_hNV_rho: no visible global function definition for ‘pnorm’
eff.ssfa: no visible global function definition for ‘pnorm’
plot_fitted: no visible global function definition for ‘lines’
plot_moran: no visible global function definition for ‘residuals’
print.summary.ssfa: no visible global function definition for
  ‘printCoefmat’
ssfa: no visible global function definition for ‘model.frame’
ssfa: no visible global function definition for ‘model.response’
ssfa.fit: no visible global function definition for ‘lm’
ssfa.fit: no visible global function definition for ‘var’
ssfa.fit: no visible global function definition for ‘logLik’
summary.ssfa: no visible global function definition for ‘pnorm’
summary.ssfa: no visible global function definition for ‘logLik’
summary.ssfa: no visible global function definition for ‘pchisq’
summary.ssfa: no visible binding for global variable ‘df’
u.ssfa: no visible global function definition for ‘dnorm’
u.ssfa: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  df dnorm lines lm logLik model.frame model.response pchisq pnorm
  printCoefmat residuals var
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "df", "dnorm", "lm", "logLik", "model.frame",
             "model.response", "pchisq", "pnorm", "printCoefmat",
             "residuals", "var")
to your NAMESPACE file.
Package in Depends field not imported from: ‘survey’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fit.model: no visible global function definition for ‘hadamard’
Undefined global functions or variables:
  hadamard
mem.usage: no visible global function definition for ‘read.delim’
Undefined global functions or variables:
  read.delim
Consider adding
  importFrom("utils", "read.delim")
to your NAMESPACE file.
sslCoTrain: no visible global function definition for ‘predict’
sslSelfTrain: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
File ‘SSL/libs/SSL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  coef.heckit5rob coef.heckitrob fitted.heckit5rob fitted.heckitrob
  print.heckit5rob print.heckitrob print.summary.heckit5rob
  print.summary.heckitrob residuals.heckit5rob residuals.heckitrob
  summary.heckit5rob summary.heckitrob vcov.heckit5rob vcov.heckitrob
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/Rtmp82Ph9a’, resetting
Examples with CPU or elapsed time > 5s
                  user system elapsed
createSSN        9.968  0.044  10.026
subsetSSN        5.352  0.016   5.371
splitPredictions 5.104  0.024   5.152
map.world: no visible global function definition for ‘par’
map.world: no visible global function definition for ‘plot.new’
map.world: no visible global function definition for ‘plot.window’
map.world: no visible global function definition for ‘lines’
map.world: no visible global function definition for ‘title’
map.world: no visible global function definition for ‘axis’
map.world: no visible global function definition for ‘box’
plot.smooth.sspline: no visible global function definition for
  ‘predict’
plot.smooth.sspline: no visible global function definition for
  ‘filled.contour’
plot.smooth.sspline: no visible binding for global variable
  ‘terrain.colors’
plot.smooth.sspline: no visible global function definition for ‘title’
plot.smooth.sspline: no visible global function definition for ‘axis’
station: no visible binding for global variable ‘WTdiff’
station: no visible global function definition for ‘points’
Undefined global functions or variables:
  WTdiff axis box filled.contour lines par plot.new plot.window points
  predict terrain.colors title
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "axis", "box", "filled.contour", "lines", "par",
             "plot.new", "plot.window", "points", "title")
  importFrom("stats", "predict")
to your NAMESPACE file.
File ‘sspline/libs/sspline.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
calcgroup : probtotrating: no visible global function definition for
  ‘convolve’
enterratdata: no visible global function definition for ‘edit’
gplot.SSrat: no visible global function definition for ‘par’
gplot.SSrat: no visible global function definition for ‘plot’
gplot.SSrat: no visible global function definition for ‘legend’
Undefined global functions or variables:
  convolve edit legend par plot
Consider adding
  importFrom("graphics", "legend", "par", "plot")
  importFrom("stats", "convolve")
  importFrom("utils", "edit")
to your NAMESPACE file.
SS.ID: no visible global function definition for ‘var’
SS.sim.chol: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm var
Consider adding
  importFrom("stats", "rnorm", "var")
to your NAMESPACE file.
error.est : <anonymous>: no visible global function definition for
  ‘median’
holm.robust: no visible global function definition for ‘pnorm’
holm.robust: no visible global function definition for ‘median’
holm.robust: no visible global function definition for ‘mad’
huberize: no visible global function definition for ‘quantile’
ssvd.initial: no visible global function definition for ‘mad’
ssvd.iter.thresh: no visible global function definition for ‘mad’
Undefined global functions or variables:
  mad median pnorm quantile
Consider adding
  importFrom("stats", "mad", "median", "pnorm", "quantile")
to your NAMESPACE file.
File ‘stable/libs/stable.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.ls.objects: no visible binding for global variable ‘object.size’
Undefined global functions or variables:
  object.size
Consider adding
  importFrom("utils", "object.size")
to your NAMESPACE file.
.expandLevels: no visible global function definition for ‘na.omit’
.ffStack: no visible global function definition for ‘na.omit’
.ffffStack: no visible global function definition for ‘na.omit’
Stack : <anonymous>: no visible global function definition for
  ‘na.omit’
ffStack,ffdf-data.frame: no visible global function definition for
  ‘na.omit’
ffStack,ffdf-ffdf: no visible global function definition for ‘na.omit’
ffStack,ffdf-list: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
genericPlot: no visible global function definition for ‘dev.new’
genericPlot: no visible global function definition for ‘par’
genericPlot: no visible global function definition for ‘rainbow’
genericPlot: no visible global function definition for ‘plot’
genericPlot: no visible global function definition for ‘lines’
genericPlot: no visible global function definition for ‘legend’
genericPlot: no visible global function definition for ‘dev.copy2pdf’
genericPlot: no visible global function definition for ‘dev.copy2eps’
genericPlot: no visible global function definition for ‘dev.print’
genericPlot: no visible binding for global variable ‘png’
genericPlot: no visible binding for global variable ‘tiff’
plotStrains: no visible global function definition for ‘rainbow’
plotStrains: no visible global function definition for ‘dev.new’
plotStrains: no visible global function definition for ‘par’
plotStrains: no visible global function definition for ‘plot’
plotStrains: no visible global function definition for ‘lines’
plotStrains: no visible global function definition for ‘legend’
plotStrains: no visible global function definition for ‘dev.copy2pdf’
plotStrains: no visible global function definition for ‘dev.copy2eps’
plotStrains: no visible global function definition for ‘dev.print’
plotStrains: no visible binding for global variable ‘png’
plotStrains: no visible binding for global variable ‘tiff’
Undefined global functions or variables:
  dev.copy2eps dev.copy2pdf dev.new dev.print legend lines par plot png
  rainbow tiff
Consider adding
  importFrom("grDevices", "dev.copy2eps", "dev.copy2pdf", "dev.new",
             "dev.print", "png", "rainbow", "tiff")
  importFrom("graphics", "legend", "lines", "par", "plot")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘Licence’
'library' or 'require' calls to packages already attached by Depends:
  ‘np’ ‘sp’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘np’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
stkde: no visible global function definition for ‘npudensbw’
stkde: no visible global function definition for ‘npudens’
stkde: no visible global function definition for ‘quantile’
stkde: no visible global function definition for ‘heat.colors’
stkde: no visible global function definition for ‘par’
stkde: no visible global function definition for ‘image’
stkde: no visible global function definition for ‘contour’
stkde.base: no visible global function definition for ‘npudensbw’
stkde.base: no visible global function definition for ‘npudens’
stkde.sig: no visible global function definition for ‘SpatialPoints’
stkde.sig: no visible global function definition for ‘spsample’
stkde.sig: no visible global function definition for ‘bbox’
stkde.sig: no visible global function definition for ‘quantile’
stkde.sig: no visible global function definition for ‘heat.colors’
stkde.sig: no visible global function definition for ‘par’
stkde.sig: no visible global function definition for ‘image’
stkde.sig: no visible global function definition for ‘contour’
Undefined global functions or variables:
  SpatialPoints bbox contour heat.colors image npudens npudensbw par
  quantile spsample
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "contour", "image", "par")
  importFrom("stats", "quantile")
to your NAMESPACE file.

Found the following calls to attach():
File ‘stam/R/stkde.sig.r’:
  attach(samdata)
See section ‘Good practice’ in ‘?attach’.
Rd file 'stkde.sig.rd':
  \examples lines wider than 100 characters:
     system.time(stkde.sig(d[,1],d[,2],d[,3],xgrids=20,ygrids=20,breaks=0.05,sim=3,alpha=0.05,nrowspar=1))
     #determines how much real and CPU time (in seconds) the currently running R process has already taken
     system.time(stkde.sig(d[,1],d[,2],d[,3],xgrids=20,ygrids=20,breaks=0.05,sim=3,alpha=0.05,nrowspar=2))
     #determines how much real and CPU time (in seconds) the currently running R process has already taken

These lines will be truncated in the PDF manual.
find.names: no visible global function definition for ‘na.omit’
generate.names: no visible global function definition for ‘na.omit’
standardize.countrynames: no visible global function definition for
  ‘data’
standardize.names: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
Rd file 'standardize.countrynames.Rd':
  \usage lines wider than 90 characters:
     standardize.countrynames(input, input.column = NULL, standard = "default", standard.column = NULL, only.names = FALSE, na.rm = FALSE, s ... [TRUNCATED]

Rd file 'standardize.text.Rd':
  \usage lines wider than 90 characters:
     standardize.text(input, input.column = NULL, standard, standard.column = NULL, regex = NULL, codes = NULL, match = FALSE, only.names =  ... [TRUNCATED]

These lines will be truncated in the PDF manual.
File ‘starma/libs/starma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘codetools’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘codetools’ ‘gss’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘STAR/libs/STAR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following hidden files and directories:
  inst/.Renviron.d
  inst/.Rprofile.d
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running ‘texi2dvi’ on ‘StatCharrms.tex’ failed.
LaTeX errors:
! Too many }'s.
l.351 ...tion}{Other Endpoints Specification Tab}}
                                                  
You've closed more groups than you opened.
Such booboos are generally harmless, so keep going.
! Too many }'s.
l.455 ...oc}{subsection}{Other Endpoints Results}}
                                                  
You've closed more groups than you opened.
Such booboos are generally harmless, so keep going.
! You can't use `macro parameter character #' in horizontal mode.
<argument> Lower.##
                   ##..CI
l.485 			\item \textbf{Lower.##..CI}
                                    : The lower 1-alpha percent (defaults to...
! You can't use `macro parameter character #' in horizontal mode.
<argument> Lower.####
                     ..CI
l.485 			\item \textbf{Lower.##..CI}
                                    : The lower 1-alpha percent (defaults to...
! You can't use `macro parameter c
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
File ‘statcomp/libs/statcomp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  print.corsign
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(statisticalModeling)
  Loading required package: ggplot2
  > 
  > test_check("statisticalModeling")
  ── 1. Error: (unknown) (@test_models.R#5)  ─────────────────────────────────────
  gwm() has been removed from `mosaic'.  
      It will be replaced by better tools in `mosaicModel'.
  1: mosaic::gwm(sex ~ domhand + biggerfoot, data = mosaicData::KidsFeet) at testthat/test_models.R:5
  2: .Defunct(msg = "gwm() has been removed from `mosaic'.  \n    It will be replaced by better tools in `mosaicModel'.")
  3: stop(paste(msg, collapse = ""), call. = FALSE, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 21 SKIPPED: 1 FAILED: 1
  1. Error: (unknown) (@test_models.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 303-306 (modeling.Rmd) 
Error: processing vignette ‘modeling.Rmd’ failed with diagnostics:
Invalid formula type for gf_point.
Execution halted
actvspred: no visible global function definition for ‘quantile’
actvspred: no visible global function definition for ‘aggregate’
actvspred: no visible global function definition for ‘par’
actvspred: no visible global function definition for ‘plot’
actvspred: no visible global function definition for ‘lines’
auc: no visible global function definition for ‘par’
auc: no visible global function definition for ‘plot’
decile: no visible global function definition for ‘quantile’
dqcontinuous : numoutliers: no visible global function definition for
  ‘quantile’
dqcontinuous : <anonymous>: no visible global function definition for
  ‘sd’
dqcontinuous : <anonymous>: no visible global function definition for
  ‘quantile’
gini: no visible global function definition for ‘par’
gini: no visible global function definition for ‘plot’
gini: no visible global function definition for ‘abline’
iv: no visible global function definition for ‘quantile’
iv: no visible global function definition for ‘aggregate’
ks: no visible global function definition for ‘aggregate’
ks: no visible global function definition for ‘par’
ks: no visible global function definition for ‘plot’
ks: no visible global function definition for ‘lines’
outliers: no visible global function definition for ‘quantile’
outliers: no visible global function definition for ‘na.omit’
pentile: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  abline aggregate lines na.omit par plot quantile sd
Consider adding
  importFrom("graphics", "abline", "lines", "par", "plot")
  importFrom("stats", "aggregate", "na.omit", "quantile", "sd")
to your NAMESPACE file.
inspect: no visible global function definition for ‘par’
inspect: no visible global function definition for ‘abline’
inspect: no visible global function definition for ‘lines’
inspect: no visible global function definition for ‘points’
plotfit: no visible global function definition for ‘dev.off’
plotfit: no visible global function definition for ‘par’
plotfit: no visible global function definition for ‘lines’
plotfit: no visible global function definition for ‘points’
plotfit: no visible global function definition for ‘legend’
plothill: no visible global function definition for ‘par’
plothill: no visible global function definition for ‘abline’
plothill: no visible global function definition for ‘points’
plotmultifit: no visible global function definition for ‘par’
plotmultifit: no visible global function definition for ‘lines’
plotmultifit: no visible global function definition for ‘points’
plotmultifit: no visible global function definition for ‘pexp’
plotmultifit: no visible global function definition for ‘plnorm’
plotmultifit: no visible global function definition for ‘ppois’
plotmultifit: no visible global function definition for ‘legend’
plotols: no visible global function definition for ‘dev.off’
plotols: no visible global function definition for ‘lm’
plotols: no visible global function definition for ‘par’
plotols: no visible global function definition for ‘abline’
plotols: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline dev.off legend lines lm par pexp plnorm points ppois
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("graphics", "abline", "legend", "lines", "par", "points")
  importFrom("stats", "lm", "pexp", "plnorm", "ppois")
to your NAMESPACE file.
File ‘staTools/libs/staTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘STB/libs/STB.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘steadyICA/libs/steadyICA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘steepness/libs/steepness.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Stem.Bootstrap: no visible global function definition for ‘runif’
filtering: no visible global function definition for ‘is.ts’
filtering: no visible global function definition for ‘ts’
filtering: no visible global function definition for ‘start’
filtering: no visible global function definition for ‘end’
filtering: no visible global function definition for ‘frequency’
kalman: no visible global function definition for ‘ts’
smoothing: no visible global function definition for ‘is.ts’
smoothing: no visible global function definition for ‘ts’
smoothing: no visible global function definition for ‘start’
smoothing: no visible global function definition for ‘end’
smoothing: no visible global function definition for ‘frequency’
Undefined global functions or variables:
  end frequency is.ts runif start ts
Consider adding
  importFrom("stats", "end", "frequency", "is.ts", "runif", "start",
             "ts")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  anova.stepplr predict.plr predict.stepplr print.plr print.stepplr
  summary.plr summary.stepplr
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
cv.step.plr: no visible global function definition for ‘binomial’
cv.step.plr: no visible global function definition for ‘predict’
cv.step.plr: no visible binding for global variable ‘var’
plr: no visible global function definition for ‘binomial’
predict.stepplr: no visible global function definition for ‘predict’
summary.plr: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  binomial pnorm predict var
Consider adding
  importFrom("stats", "binomial", "pnorm", "predict", "var")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'plr-internal':
  ‘anova.stepplr’ ‘print.plr’ ‘print.stepplr’ ‘summary.plr’
  ‘summary.stepplr’

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

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘stepPlr/libs/stepPlr.so’:
  Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Object: ‘cg_descent.o’
  Found ‘_gfortran_stop_string’, possibly from ‘stop’ (Fortran)
    Object: ‘cg_descent.o’
File ‘stepPlr/libs/stepPlr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘stepp/libs/stepp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘stepwise/libs/stepwise.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘StepwiseTest/libs/StepwiseTest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
d1spectrum: no visible global function definition for ‘fft’
d2spectrum: no visible global function definition for ‘fft’
plot.d1nat: no visible global function definition for ‘plot’
plot.d1nat: no visible global function definition for ‘lines’
plot.d1nat: no visible global function definition for ‘legend’
plot.d1nat: no visible global function definition for ‘title’
plot.d1spec: no visible global function definition for ‘plot’
plot.d1spec: no visible global function definition for ‘lines’
plot.d1spec: no visible global function definition for ‘legend’
plot.d1spec: no visible global function definition for ‘title’
plot.d2spec: no visible global function definition for ‘plot’
plot.d2spec: no visible global function definition for ‘lines’
plot.d2spec: no visible global function definition for ‘legend’
plot.d2spec: no visible global function definition for ‘title’
plot.pvalign: no visible global function definition for ‘plot’
plot.pvalign: no visible global function definition for ‘lines’
plot.pvalign: no visible global function definition for ‘legend’
plot.pvalign: no visible global function definition for ‘title’
print.d1nat: no visible global function definition for ‘plot’
print.d1spec: no visible global function definition for ‘plot’
print.d2spec: no visible global function definition for ‘plot’
print.pvalign: no visible global function definition for ‘plot’
utild1bin: no visible global function definition for ‘median’
utild1bin: no visible global function definition for ‘sd’
utild1clean: no visible global function definition for ‘sd’
utild1filt: no visible global function definition for ‘convolve’
Undefined global functions or variables:
  convolve fft legend lines median plot sd title
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "title")
  importFrom("stats", "convolve", "fft", "median", "sd")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  na.stinterp.default
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
na.stinterp.default: no visible global function definition for ‘time’
na.stinterp.default: no visible global function definition for
  ‘na.omit’
Undefined global functions or variables:
  na.omit time
Consider adding
  importFrom("stats", "na.omit", "time")
to your NAMESPACE file.
File ‘stlplus/libs/stlplus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/Rtmp3vRkm3’, resetting
myQQNorm: no visible global function definition for ‘mad’
myQQNorm: no visible global function definition for ‘qnorm’
myQQNorm: no visible global function definition for ‘plot’
myQQNorm: no visible global function definition for ‘matlines’
myQQNorm: no visible global function definition for ‘points’
myQQNorm: no visible global function definition for ‘qqline’
myQQNorm: no visible global function definition for ‘box’
qqnormSim,lm: no visible global function definition for ‘resid’
Undefined global functions or variables:
  box mad matlines plot points qnorm qqline resid
Consider adding
  importFrom("graphics", "box", "matlines", "plot", "points")
  importFrom("stats", "mad", "qnorm", "qqline", "resid")
to your NAMESPACE file.
File ‘StMoSim/libs/StMoSim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
sharpe: no visible global function definition for ‘sd’
sortino: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
File ‘stocks/libs/stocks.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Rd file 'calc.stoich.coef.Rd':
  \usage lines wider than 90 characters:
     calc.stoich.coef(alpha, name, subst, subst.norm, nu.norm = 1, constraints = list(), eps = 1e-5, verbose = TRUE)

These lines will be truncated in the PDF manual.
Namespace with empty importFrom: ‘tcltk2’
DetailOpLines: no visible global function definition for
  ‘tkProgressBar’
DetailOpLines: no visible global function definition for
  ‘setTkProgressBar’
MultiTrainWithInventory: no visible global function definition for
  ‘tkProgressBar’
MultiTrainWithInventory: no visible global function definition for
  ‘setTkProgressBar’
SimHistory: no visible global function definition for ‘tkProgressBar’
SimHistory: no visible global function definition for
  ‘setTkProgressBar’
Undefined global functions or variables:
  setTkProgressBar tkProgressBar
File ‘stosim/libs/stosim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘cubature’ ‘deldir’ ‘splancs’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  plot.devresid plot.gridresid plot.stpp plot.superthin plot.supresid
  plot.tessdev plot.tessresid plot.thinresid print.devresid
  print.gridresid print.stgrid print.stpp print.stwin print.superthin
  print.supresid print.tessdev print.tessresid print.thinresid
  summary.superthin summary.supresid summary.thinresid
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'gridresid.Rd':
  \usage lines wider than 90 characters:
     gridresid(X, cifunction, theta = NULL, lambda = NULL, grid = c(10, 10), gf = NULL, resid = c("raw", "pearson", "inverse"), algthm = c(" ... [TRUNCATED]

These lines will be truncated in the PDF manual.
StratPhyloCongruence: no visible global function definition for ‘runif’
StratPhyloCongruence: no visible global function definition for
  ‘txtProgressBar’
StratPhyloCongruence: no visible global function definition for
  ‘setTxtProgressBar’
StratPhyloCongruence: no visible global function definition for ‘pnorm’
StratPhyloCongruence: no visible global function definition for ‘sd’
geoscalePhylo: no visible global function definition for ‘data’
geoscalePhylo: no visible global function definition for ‘par’
geoscalePhylo: no visible global function definition for ‘text’
geoscalePhylo: no visible global function definition for ‘segments’
geoscalePhylo: no visible global function definition for ‘rect’
geoscalePhylo: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  data par pnorm rect rgb runif sd segments setTxtProgressBar text
  txtProgressBar
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "par", "rect", "segments", "text")
  importFrom("stats", "pnorm", "runif", "sd")
  importFrom("utils", "data", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
File ‘strat/libs/strat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  plot.icweib print.icweib
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
HRatio: no visible global function definition for ‘qnorm’
icweib: no visible global function definition for ‘model.frame’
icweib: no visible binding for global variable ‘na.pass’
icweib: no visible global function definition for ‘complete.cases’
icweib: no visible global function definition for ‘model.matrix’
icweib: no visible global function definition for ‘optim’
icweib: no visible global function definition for ‘pchisq’
icweib: no visible global function definition for ‘pnorm’
plot.icweib : getstat: no visible global function definition for
  ‘qnorm’
plot.icweib: no visible global function definition for ‘plot’
plot.icweib: no visible global function definition for ‘lines’
plot.icweib: no visible global function definition for ‘legend’
print.icweib: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  complete.cases legend lines model.frame model.matrix na.pass optim
  pchisq plot pnorm qnorm
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "complete.cases", "model.frame", "model.matrix",
             "na.pass", "optim", "pchisq", "pnorm", "qnorm")
to your NAMESPACE file.
'library' or 'require' call to ‘ROAuth’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
File ‘stremr/libs/stremr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File which contains pragma(s) suppressing important diagnostics:
  ‘src/icu55/i18n/decNumber.c’
breakpoints.formula: no visible global function definition for
  ‘%dopar%’
breakpoints.formula: no visible binding for global variable ‘i’
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
sctest.default: no visible global function definition for ‘tail’
Undefined global functions or variables:
  %dopar% i tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
PlotHypTree: no visible global function definition for ‘browseURL’
treePValues: no visible global function definition for ‘lm’
treePValues: no visible global function definition for ‘pf’
plot,GBH-ANY: no visible binding for global variable ‘sorted.hyp’
plot,GBH-ANY: no visible binding for global variable ‘pval’
plot,GBH-ANY: no visible binding for global variable ‘group’
plot,GBH-ANY: no visible binding for global variable ‘type’
Undefined global functions or variables:
  browseURL group lm pf pval sorted.hyp type
Consider adding
  importFrom("stats", "lm", "pf")
  importFrom("utils", "browseURL")
to your NAMESPACE file.
File ‘strum/libs/strum.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Warning: no function found corresponding to methods exports from ‘stsm.class’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
stsm.model: no visible global function definition for ‘is.ts’
stsm.model: no visible global function definition for ‘var’
stsm.model: no visible global function definition for ‘frequency’
stsm.model: no visible global function definition for ‘na.omit’
stsm.model: no visible global function definition for ‘fft’
stsm.model: no visible global function definition for ‘new’
stsm.sgf: no visible global function definition for ‘frequency’
char2numeric,stsm: no visible global function definition for
  ‘frequency’
set.cpar,stsm: no visible global function definition for ‘validObject’
set.nopars,stsm: no visible global function definition for
  ‘validObject’
set.pars,stsm: no visible global function definition for ‘validObject’
transPars,stsm: no visible global function definition for ‘var’
Undefined global functions or variables:
  fft frequency is.ts na.omit new validObject var
Consider adding
  importFrom("methods", "new", "validObject")
  importFrom("stats", "fft", "frequency", "is.ts", "na.omit", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘stsm/libs/stsm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  predict.sublasso
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
SubLasso: no visible global function definition for ‘predict’
SubLasso: no visible global function definition for ‘coef’
SubLasso: no visible global function definition for ‘dev.new’
SubLasso: no visible global function definition for ‘cor’
SubLasso: no visible global function definition for ‘boxplot’
predict.sublasso: no visible global function definition for ‘predict’
Undefined global functions or variables:
  boxplot coef cor dev.new predict
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "boxplot")
  importFrom("stats", "coef", "cor", "predict")
to your NAMESPACE file.
identifyGraph: no visible global function definition for ‘phyper’
mytriangle: no visible global function definition for ‘symbols’
plotGraph: no visible global function definition for ‘par’
plotGraph: no visible global function definition for ‘plot’
updateOrgEnvir: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  par phyper plot read.table symbols
Consider adding
  importFrom("graphics", "par", "plot", "symbols")
  importFrom("stats", "phyper")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  predict.subsemble
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
predict.subsemble: no visible global function definition for ‘predict’
predict.subsemble: no visible binding for global variable ‘family’
subsemble: no visible global function definition for ‘gaussian’
subsemble: no visible global function definition for ‘detectCores’
subsemble : .make_Z_l: no visible global function definition for
  ‘parSapply’
subsemble : .make_Z_l: no visible global function definition for
  ‘makeCluster’
subsemble : .make_Z_l: no visible global function definition for
  ‘stopCluster’
subsemble: no visible global function definition for ‘parSapply’
subsemble: no visible global function definition for ‘makeCluster’
subsemble: no visible global function definition for ‘stopCluster’
subsemble: no visible global function definition for ‘predict’
Undefined global functions or variables:
  detectCores family gaussian makeCluster parSapply predict stopCluster
Consider adding
  importFrom("stats", "family", "gaussian", "predict")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘ROCR’ ‘penalized’
  Please remove these calls from your code.
ELF: no visible global function definition for ‘pt’
ELF: no visible global function definition for ‘qnorm’
ELF: no visible global function definition for ‘lm’
ELF: no visible global function definition for ‘lowess’
ELF: no visible global function definition for ‘dnorm’
ELF: no visible global function definition for ‘approx’
subtype: no visible global function definition for ‘runif’
subtype: no visible global function definition for ‘hclust’
subtype: no visible global function definition for ‘dist’
subtype: no visible global function definition for ‘cutree’
subtype: no visible global function definition for ‘pt’
subtype: no visible global function definition for ‘heatmap’
test_subtype_only: no visible global function definition for ‘pt’
test_subtype_only: no visible global function definition for ‘survdiff’
test_subtype_only: no visible global function definition for ‘survfit’
test_subtype_only: no visible global function definition for ‘title’
ufun: no visible global function definition for ‘dnorm’
ufun: no visible global function definition for ‘lowess’
Undefined global functions or variables:
  approx cutree dist dnorm hclust heatmap lm lowess pt qnorm runif
  survdiff survfit title
Consider adding
  importFrom("graphics", "title")
  importFrom("stats", "approx", "cutree", "dist", "dnorm", "hclust",
             "heatmap", "lm", "lowess", "pt", "qnorm", "runif")
to your NAMESPACE file.
Rd file 'subtype.Rd':
  \usage lines wider than 90 characters:
     subtype(GEset, outcomeLabels, treatment=NULL, Npermutes=10, Nchunks = 25, minClusterSizeB = 20, NclustersASet = 100, FDRpermutation = T ... [TRUNCATED]
  \examples lines wider than 100 characters:
     summary(A,f.out=0)  ### f.out can be used for filtering out uninteresting subtypes. e.g. if f.out=2, we ignore subtypes having N01_0<=2 ... [TRUNCATED]

Rd file 'summary.Rd':
  \examples lines wider than 100 characters:
     summary(A,f.out=0)  ### f.out can be used for filtering out uninteresting subtypes. e.g. if f.out=2, we ignore subtypes having N01_0<=2 ... [TRUNCATED]

These lines will be truncated in the PDF manual.
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.
Rd file 'SUE.lm.Rd':
  \examples lines wider than 100 characters:
     ##We analysis the well known stackloss data by using ordinary linear method and the subsampling method. 
     ##proportion of outliers in the data. The subsample size is chosen to be the default size of ns = 11.
     plot(SUE.fitted.values(a2),SUE.residuals(a2),xlab="(b) fitted values",ylab="residuals",ylim=c(-12,12))
     plot(SUE.fitted.values(a3),SUE.residuals(a3),xlab="(c) fitted values",ylab="residuals",ylim=c(-12,12))

These lines will be truncated in the PDF manual.
MCMCCV: no visible global function definition for ‘rnorm’
MLCVGauss: no visible global function definition for ‘runif’
MLCVGauss: no visible global function definition for ‘optim’
SimSunderData: no visible global function definition for ‘runif’
SimSunderData: no visible global function definition for ‘dist’
SimSunderData: no visible global function definition for ‘rnorm’
SimSunderData: no visible global function definition for ‘qgamma’
SimSunderData: no visible global function definition for ‘pnorm’
SimSunderData: no visible global function definition for ‘rmultinom’
Undefined global functions or variables:
  dist optim pnorm qgamma rmultinom rnorm runif
Consider adding
  importFrom("stats", "dist", "optim", "pnorm", "qgamma", "rmultinom",
             "rnorm", "runif")
to your NAMESPACE file.
File ‘Sunder/libs/Sunder.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
sunter: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
supcluster : itgamma: no visible global function definition for
  ‘rgamma’
supcluster : itgamma: no visible global function definition for
  ‘dgamma’
supcluster : itgamma: no visible global function definition for ‘runif’
supcluster : itbeta: no visible global function definition for ‘rnorm’
supcluster : itbeta: no visible global function definition for ‘runif’
supcluster : itj: no visible global function definition for ‘dmultinom’
supcluster: no visible global function definition for ‘kmeans’
tab1: no visible global function definition for ‘image’
tab1: no visible global function definition for ‘gray’
tab1: no visible global function definition for ‘var’
Undefined global functions or variables:
  dgamma dmultinom gray image kmeans rgamma rnorm runif var
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "image")
  importFrom("stats", "dgamma", "dmultinom", "kmeans", "rgamma", "rnorm",
             "runif", "var")
to your NAMESPACE file.
Call with DUP:
   .C(R_clusterer, E = as.double(E), X = as.double(X), W = as.double(W), 
       P = as.double(P), y = as.double(y), prob = as.double(prob), 
       theta = as.double(theta), lambda = as.double(lambda * n), 
       n = as.integer(n), g = as.integer(g), m = as.integer(m), 
       p = as.integer(p), critflag = as.integer(critflag), penflag = as.integer(penflag), 
       blockflag = as.integer(blockflag), valiflag = as.integer(valiflag), 
       traceflag = as.integer(trace), genliste = integer(lSize), 
       kriterium = double(lSize), DUP = FALSE)
DUP is no longer supported and will be ignored.
File ‘supclust/libs/supclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
HCLtree: no visible global function definition for ‘hclust’
HCLtree: no visible global function definition for ‘as.dist’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘matplot’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘matlines’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘axis’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘box’
plotProfilesWithinBicluster: no visible global function definition for
  ‘matplot’
plotProfilesWithinBicluster: no visible global function definition for
  ‘title’
plotProfilesWithinBicluster: no visible global function definition for
  ‘axis’
plotProfilesWithinBicluster: no visible global function definition for
  ‘par’
plotProfilesWithinBicluster: no visible global function definition for
  ‘box’
plotProfilesWithinBicluster: no visible global function definition for
  ‘matlines’
plotProfilesWithinBicluster: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  as.dist axis box hclust legend matlines matplot par title
Consider adding
  importFrom("graphics", "axis", "box", "legend", "matlines", "matplot",
             "par", "title")
  importFrom("stats", "as.dist", "hclust")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘boa’ ‘coda’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
superdiag: no visible global function definition for ‘as.mcmc.list’
superdiag: no visible global function definition for ‘as.mcmc’
superdiag: no visible global function definition for ‘runif’
superdiag: no visible global function definition for ‘geweke.diag’
superdiag: no visible global function definition for ‘heidel.diag’
superdiag: no visible global function definition for ‘raftery.diag’
superdiag: no visible global function definition for ‘gelman.diag’
Undefined global functions or variables:
  as.mcmc as.mcmc.list gelman.diag geweke.diag heidel.diag raftery.diag
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
TrainSuperMDS: no visible global function definition for ‘rnorm’
TrainSuperMDSOnce: no visible global function definition for ‘cmdscale’
TrainSuperMDSOnce: no visible global function definition for ‘quantile’
distmat: no visible global function definition for ‘dist’
Undefined global functions or variables:
  cmdscale dist quantile rnorm
Consider adding
  importFrom("stats", "cmdscale", "dist", "quantile", "rnorm")
to your NAMESPACE file.
File ‘SuperRanker/libs/SuperRanker.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SuppDists/libs/SuppDists.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/copulas-concordance.tex’
   ‘vignettes/surrosurv.tex’
(Is a VignetteBuilder field missing?)
Found the following apparent S3 methods exported but not registered:
  print.SurvAM
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Est.Var.CCH.trueweights: no visible binding for global variable ‘var’
getEstimatesSP: no visible global function definition for ‘quantile’
getEstimatesSP: no visible global function definition for ‘resid’
prepareDataNP: no visible global function definition for
  ‘complete.cases’
prepareDataSP: no visible global function definition for
  ‘complete.cases’
processRawOutput: no visible global function definition for ‘qnorm’
survAM.estimate: no visible global function definition for ‘median’
survAM.estimate: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  complete.cases median qnorm quantile resid sd var
Consider adding
  importFrom("stats", "complete.cases", "median", "qnorm", "quantile",
             "resid", "sd", "var")
to your NAMESPACE file.
File ‘survAccuracyMeasures/libs/survAccuracyMeasures.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘survAUC/libs/survAUC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Est.PH: no visible global function definition for ‘coxph’
Inf.Cval: no visible global function definition for ‘rexp’
Inf.Cval: no visible global function definition for ‘var’
Inf.Cval.Delta: no visible global function definition for ‘rexp’
Inf.Cval.Delta: no visible global function definition for ‘var’
cvC: no visible global function definition for ‘coxph’
cvC: no visible global function definition for ‘weighted.mean’
Undefined global functions or variables:
  coxph rexp var weighted.mean
Consider adding
  importFrom("stats", "rexp", "var", "weighted.mean")
to your NAMESPACE file.
File ‘survC1/libs/survC1.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/survClip.Rnw’
(Is a VignetteBuilder field missing?)
pearson: no visible global function definition for ‘cor’
plot.survcorr: no visible global function definition for ‘pnorm’
plot.survcorr: no visible global function definition for ‘par’
plot.survcorr: no visible global function definition for ‘plot’
plot.survcorr: no visible global function definition for ‘points’
survcorr: no visible global function definition for ‘model.frame’
survcorr: no visible global function definition for ‘qnorm’
survcorr: no visible global function definition for ‘runif’
survcorr: no visible global function definition for ‘pnorm’
survcorr: no visible global function definition for ‘var’
survcorr: no visible global function definition for ‘qt’
Undefined global functions or variables:
  cor model.frame par plot pnorm points qnorm qt runif var
Consider adding
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "cor", "model.frame", "pnorm", "qnorm", "qt",
             "runif", "var")
to your NAMESPACE file.
File ‘surveybootstrap/libs/surveybootstrap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘survival’ which was already attached by Depends.
  Please remove these calls from your code.
Survgini: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘survC1’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Est.HR.FUN: no visible global function definition for ‘coxph’
Est.HR.FUN: no visible global function definition for ‘basehaz’
Est.HR.FUN: no visible global function definition for ‘approx’
Ghat.FUN: no visible global function definition for ‘survfit’
IDI.INF: no visible global function definition for ‘kmcens’
IDI.INF: no visible global function definition for ‘quantile’
IDI.INF.GRAPH: no visible global function definition for ‘plot’
IDI.INF.GRAPH: no visible global function definition for ‘lines’
IDI.INF.GRAPH: no visible global function definition for ‘abline’
IDI.INF.GRAPH: no visible global function definition for ‘points’
IDI.INF.GRAPH: no visible global function definition for ‘title’
PTB.IDI.FUN: no visible global function definition for ‘rexp’
shade: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  abline approx basehaz coxph kmcens lines plot points polygon quantile
  rexp survfit title
Consider adding
  importFrom("graphics", "abline", "lines", "plot", "points", "polygon",
             "title")
  importFrom("stats", "approx", "quantile", "rexp")
to your NAMESPACE file.
Rd file 'IDI.INF.GRAPH.Rd':
  \usage lines wider than 90 characters:
     IDI.INF.GRAPH(x, main = NULL, xlab = NULL, ylab = NULL, cex.main = NULL, cex.lab = NULL, ...)

Rd file 'IDI.INF.Rd':
  \usage lines wider than 90 characters:
     IDI.INF(indata, covs0, covs1, t0, npert = 300, npert.rand = NULL, seed1 = NULL, alpha = 0.05)

These lines will be truncated in the PDF manual.
File ‘survIDINRI/libs/survIDINRI.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘survivalROC/libs/survivalROC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
betaEst: no visible global function definition for ‘is’
fullKernel: no visible global function definition for ‘is’
halfKernel: no visible global function definition for ‘is’
kernelAuto: no visible global function definition for ‘quantile’
kernelAuto: no visible global function definition for ‘lm’
kernelAuto: no visible global function definition for ‘pnorm’
kernelFixed: no visible global function definition for ‘pnorm’
lastValue: no visible global function definition for ‘pnorm’
nearValue: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  is lm pnorm quantile
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "lm", "pnorm", "quantile")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘survSNP/libs/survSNP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
fitModel: no visible global function definition for ‘var’
fitModel: no visible global function definition for ‘cov’
svpls: no visible global function definition for ‘pt’
Undefined global functions or variables:
  cov pt var
Consider adding
  importFrom("stats", "cov", "pt", "var")
to your NAMESPACE file.
Registered S3 method from a standard package overwritten by 'svars':
  method    from
  plot.boot boot
Calls with DUP:
   .C("myInversion", Senv$diag, Senv$env, Senv$xenv, Senv$N, Senv$Nenv, 
       Senv$Nplus1, DUP = FALSE, PACKAGE = "svcm")
   .C("myTrace", Senv$diag, Senv$env, Senv$xenv, Senv$N, Senv$Nenv, 
       Senv$Nplus1, BBenv$diag, BBenv$env, BBenv$xenv, BBenv$N, 
       BBenv$Nenv, BBenv$Nplus1, ED = ED, DUP = FALSE, PACKAGE = "svcm")
   .C("dsC2env", N, A@x, as.integer(A@i), as.integer(A@p), diagvec = diagvec, 
       env = env, xenv = as.integer(xenv), DUP = FALSE)
DUP is no longer supported and will be ignored.
File ‘svcm/libs/svcm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.jgrRun: no visible global function definition for ‘capture.output’
.macDlgList: no visible global function definition for ‘select.list’
.unixDlgForm: no visible global function definition for ‘as’
.unixDlgMessage: no visible global function definition for ‘alarm’
.winDlgList: no visible global function definition for ‘select.list’
dlgForm.textCLI: no visible global function definition for ‘as’
dlgList.textCLI: no visible global function definition for
  ‘select.list’
dlgMessage.textCLI: no visible global function definition for
  ‘select.list’
dlgSave.textCLI: no visible global function definition for
  ‘select.list’
Undefined global functions or variables:
  alarm as capture.output select.list
Consider adding
  importFrom("methods", "as")
  importFrom("utils", "alarm", "capture.output", "select.list")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
dlgMessage.tcltkGUI: no visible global function definition for ‘alarm’
Undefined global functions or variables:
  alarm
Consider adding
  importFrom("utils", "alarm")
to your NAMESPACE file.
svd3dplot: no visible global function definition for ‘wireframe’
svd3dplot: no visible global function definition for ‘levelplot’
Undefined global functions or variables:
  levelplot wireframe
startHttpServer : <anonymous> : Rjsonp: no visible global function
  definition for ‘localeToCharset’
Undefined global functions or variables:
  localeToCharset
Consider adding
  importFrom("utils", "localeToCharset")
to your NAMESPACE file.
.onAttach : svBrowser: no visible global function definition for
  ‘browseURL’
.onAttach: no visible global function definition for ‘loadhistory’
Undefined global functions or variables:
  browseURL loadhistory
Consider adding
  importFrom("utils", "browseURL", "loadhistory")
to your NAMESPACE file.
File ‘svmadmm/libs/svmadmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
completion : finalize : <anonymous>: no visible global function
  definition for ‘existsFunction’
listMethods: no visible global function definition for ‘findFunction’
tempvar: no visible global function definition for ‘runif’
Undefined global functions or variables:
  existsFunction findFunction runif
Consider adding
  importFrom("methods", "existsFunction", "findFunction")
  importFrom("stats", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in ‘svMisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: toRjson
> ### Title: Convert R object to and from RJSON specification
> ### Aliases: toRjson evalRjson listToJson
> ### Keywords: utilities
> 
> ### ** Examples
> 
> ## A complex R object
> Robj <- structure(list(
+ 	a = as.double(c(1:5, 6)),
+ 	LETTERS,
+ 	c = c(c1 = 4.5, c2 = 7.8, c3 = Inf, c4 = -Inf, NA, c6 = NaN),
+ 	c(TRUE, FALSE, NA),
+ 	e = factor(c("a", "b", "a")),
+ 	f = "this is a \"string\"\nwith\tspecial chars",
+ 	g = matrix(rnorm(4), ncol = 2),
+ 	`h&'$@` = data.frame(x = 1:3, y = rnorm(3),
+ 		fact = factor(c("b", "a", "b"))),
+ 	i = Sys.Date(),
+     j = list(1:5, y = "another item")),
+     comment = "My comment\n\"",
+     anAttrib = 1:10,
+     anotherAttrib = list(TRUE, y = 1:4))
> 
> ## Convert to simplest RJSON, without attributes
> Rjson1 <- toRjson(Robj)
> Rjson1
[1] list(c(1., 2., 3., 4., 5., 6.), c("A", "B", "C", "D", "E", "F",                              
[2] "G", "H", "I", "J", "K", "L", "M", "N", "O", "P", "Q", "R", "S",                             
[3] "T", "U", "V", "W", "X", "Y", "Z"), c(4.5, 7.8, Inf, -Inf, NA,                               
[4] NaN), c(TRUE, FALSE, NA), c("a", "b", "a"), "this is a \\"string\\"\\nwith\\tspecial chars", 
[5]     c(-0.626453810742332, 0.183643324222082, -0.835628612410047,                             
[6]     1.59528080213779), list(seq(1, 3), c(0.329507771815361, -0.820468384118015,              
[7]     0.487429052428485), c("b", "a", "b")), "2017-12-17", list(                               
[8]         seq(1, 5), "another item"))                                                          
> evalRjson(Rjson1)
Error in .getClassesFromCache(Class) : 
  class should be either a character-string name or a class definition
Calls: evalRjson ... new -> getClass -> getClassDef -> .getClassesFromCache
Execution halted
Package in Depends field not imported from: ‘kernlab’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'svmmajcrossval.Rd':
  \usage lines wider than 90 characters:
     svmmajcrossval(X,y,search.grid=list(lambda=2^seq(5,-5,length.out=19)),...,convergence=1e-4, 
                       weights.obs=1, check.positive = TRUE, print.progress=FALSE, ngroup = 5, groups = NULL)

These lines will be truncated in the PDF manual.
File ‘SVMMatch/libs/SVMMatch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘svmpath/libs/svmpath.so’:
  Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’
File ‘svmpath/libs/svmpath.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
processSocket: no visible global function definition for ‘URLdecode’
Undefined global functions or variables:
  URLdecode
Consider adding
  importFrom("utils", "URLdecode")
to your NAMESPACE file.
completeCol: no visible global function definition for ‘colors’
completeCol: no visible global function definition for ‘col2rgb’
completeCol: no visible global function definition for ‘palette’
Undefined global functions or variables:
  col2rgb colors palette
Consider adding
  importFrom("grDevices", "col2rgb", "colors", "palette")
to your NAMESPACE file.
.formatResult : capture.str: no visible global function definition for
  ‘str’
createLog: no visible global function definition for ‘sessionInfo’
protocol_junit.svSuiteData: no visible global function definition for
  ‘xmlNode’
protocol_junit.svSuiteData: no visible global function definition for
  ‘addChildren’
protocol_junit.svSuiteData: no visible global function definition for
  ‘saveXML’
protocol_junit.svTestData: no visible global function definition for
  ‘xmlNode’
protocol_junit.svTestData: no visible global function definition for
  ‘addChildren’
Undefined global functions or variables:
  addChildren saveXML sessionInfo str xmlNode
Consider adding
  importFrom("utils", "sessionInfo", "str")
to your NAMESPACE file.
svycox.calibrate: no visible global function definition for ‘quantile’
svycox.calibrate: no visible binding for global variable ‘median’
svycox.calibrate: no visible global function definition for
  ‘as.formula’
svycox.calibrate: no visible global function definition for ‘plot’
svycox.calibrate: no visible global function definition for ‘arrows’
svycox.calibrate: no visible global function definition for ‘abline’
svycox.nomogram: no visible global function definition for ‘predict’
svycox.nomogram: no visible global function definition for ‘as.formula’
svycox.validate : internal.validate.func: no visible global function
  definition for ‘as.formula’
svycox.validate : internal.validate.func: no visible global function
  definition for ‘formula’
Undefined global functions or variables:
  abline arrows as.formula formula median plot predict quantile
Consider adding
  importFrom("graphics", "abline", "arrows", "plot")
  importFrom("stats", "as.formula", "formula", "median", "predict",
             "quantile")
to your NAMESPACE file.
additional_comp: no visible global function definition for ‘aggregate’
additional_compPV : <anonymous>: no visible global function definition
  for ‘aggregate’
cor.aux.func : <anonymous>: no visible global function definition for
  ‘cov.wt’
eta.func : <anonymous>: no visible global function definition for ‘lm’
eta.func : <anonymous>: no visible global function definition for
  ‘anova’
glm.dummy.no.std: no visible global function definition for
  ‘as.formula’
pv_by: no visible binding for global variable ‘var’
pv_perc: no visible binding for global variable ‘var’
pv_quantile: no visible binding for global variable ‘var’
svyPVcor: no visible global function definition for ‘update’
svyPVcor: no visible global function definition for ‘var’
svyPVeta: no visible global function definition for ‘update’
svyPVeta: no visible global function definition for ‘var’
svyPVglm: no visible global function definition for ‘gaussian’
svyPVglm: no visible binding for global variable ‘as.formula’
svyPVglm: no visible binding for global variable ‘var’
svyPVglm: no visible global function definition for ‘pt’
svyPVttest: no visible binding for global variable ‘as.formula’
svyPVttest: no visible global function definition for ‘var’
svyPVttest: no visible global function definition for ‘pt’
svyPVttest: no visible binding for global variable ‘var’
t.test.aux: no visible global function definition for ‘as.formula’
t.test.aux: no visible global function definition for ‘complete.cases’
Undefined global functions or variables:
  aggregate anova as.formula complete.cases cov.wt gaussian lm pt
  update var
Consider adding
  importFrom("stats", "aggregate", "anova", "as.formula",
             "complete.cases", "cov.wt", "gaussian", "lm", "pt",
             "update", "var")
to your NAMESPACE file.
File ‘SwarmSVM/libs/SwarmSVM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
readSWAT: no visible global function definition for ‘read.fortran’
runSWAT2005: no visible global function definition for ‘read.fortran’
runSWAT2009: no visible global function definition for ‘read.fortran’
runSWAT2012: no visible global function definition for ‘read.fortran’
Undefined global functions or variables:
  read.fortran
Consider adding
  importFrom("utils", "read.fortran")
to your NAMESPACE file.
Rd file 'build_swat_basic.Rd':
  \examples lines wider than 100 characters:
     build_swat_basic(dirname="test", iyr="1979", nbyr=13, wsarea=40, elev=200, declat=45, declon=-72, hist_wx=hist_wx) 

Rd file 'readSWAT.Rd':
  \examples lines wider than 100 characters:
       } else { print ("You need to add your file type to this function if it is not output.sub or output.rch")}

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(swirlify)
  > library(swirl)
  
  | Hi! Type swirl() when you are ready to begin.
  
  
  Attaching package: 'swirl'
  
  The following object is masked from 'package:testthat':
  
      skip
  
  > 
  > test_check("swirlify")
  ── 1. Failure: test_lesson() passes with well-formed lesson (@test_test_lesson.R
  all(correct_output %in% readLines(file.path(path, "test.log"))) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 7 SKIPPED: 0 FAILED: 1
  1. Failure: test_lesson() passes with well-formed lesson (@test_test_lesson.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
Packages in Depends field not imported from:
  ‘MASS’ ‘fda’ ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fj_pl: no visible global function definition for ‘getbasismatrix’
fj_pl: no visible global function definition for ‘create.bspline.basis’
fj_pl: no visible global function definition for ‘getbasispenalty’
forward_backward.quantities : <anonymous>: no visible global function
  definition for ‘dnorm’
function_cases1AND2: no visible global function definition for ‘dnorm’
function_cases3AND4: no visible global function definition for ‘dnorm’
pij_iid: no visible global function definition for ‘dnorm’
pilj: no visible global function definition for ‘dnorm’
updateLambda: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  create.bspline.basis dnorm getbasismatrix getbasispenalty optimize
Consider adding
  importFrom("stats", "dnorm", "optimize")
to your NAMESPACE file.
calc_MW: no visible global function definition for ‘read.table’
cfba_moment: no visible global function definition for ‘median’
cfba_moment: no visible global function definition for ‘write.csv’
cfba_moment_mr: no visible global function definition for ‘median’
cfba_moment_mr: no visible global function definition for ‘write.csv’
cfba_moment_pw: no visible global function definition for ‘median’
cfba_moment_pw: no visible global function definition for ‘write.csv’
readmodel: no visible global function definition for ‘as’
Undefined global functions or variables:
  as median read.table write.csv
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "median")
  importFrom("utils", "read.table", "write.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
FECorr: no visible global function definition for ‘is’
FECorr: no visible global function definition for ‘write.csv’
FECorr: no visible global function definition for ‘aggregate’
FECorr: no visible global function definition for ‘lm’
FECorr: no visible global function definition for ‘nlm’
eFBA_gene: no visible global function definition for ‘is’
eFBA_gene: no visible global function definition for ‘as’
eFBA_rxn : adjustTol: no visible global function definition for ‘is’
eFBA_rxn: no visible global function definition for ‘is’
eFBA_rxn: no visible global function definition for ‘as’
findFluxGeneExpr: no visible global function definition for ‘as’
findMDCFlux: no visible global function definition for ‘is’
findMDCFlux: no visible global function definition for ‘as’
gene2Rule: no visible global function definition for ‘is’
Undefined global functions or variables:
  aggregate as is lm nlm write.csv
Consider adding
  importFrom("methods", "as", "is")
  importFrom("stats", "aggregate", "lm", "nlm")
  importFrom("utils", "write.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages suggested but not available for checking:
  ‘sylly.de’ ‘sylly.en’ ‘sylly.es’
symbol: no visible global function definition for ‘plot.new’
symbol: no visible global function definition for ‘plot.window’
symbol: no visible global function definition for ‘axis’
symbol: no visible global function definition for ‘box’
symbol: no visible global function definition for ‘title’
symbol: no visible global function definition for ‘rainbow’
symbol: no visible global function definition for ‘hsv’
symbol: no visible global function definition for ‘rect’
symbol: no visible global function definition for ‘polygon’
symbol: no visible global function definition for ‘lines’
symbol: no visible global function definition for ‘text’
Undefined global functions or variables:
  axis box hsv lines plot.new plot.window polygon rainbow rect text
  title
Consider adding
  importFrom("grDevices", "hsv", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "polygon", "rect", "text", "title")
to your NAMESPACE file.
Rd file 'symbol.Rd':
  \usage lines wider than 90 characters:
     symbol(df, type="star", colin=NULL, colout=NULL, colin2=NA, colout2=1, ssize=NULL, labels=0, labelsize=0.6,
            scheme=1, sortby=0, descending=FALSE, coorx=NULL, coory=NULL, lty=1, main=NULL, sub=NULL, xlab=NULL, ylab=NULL,
            add=FALSE, xlim=NULL, ylim=NULL, facew=0.5, faceh=0.5, eyes=0.5, eyed=0.5, mouthw=0.5, mouthc=0.5, brows=0.5,
            browp=0.5, nosel=0.5, nosew=0.5, ears=0.5, pupils=0.5, body=0.5, limb1=0.5, limb2=0.5, limb3=0.5, limb4=0.5, defcol=NA)

These lines will be truncated in the PDF manual.
integrate.polynomial : f: no visible global function definition for
  ‘dmvnorm’
Undefined global functions or variables:
  dmvnorm
Found the following apparent S3 methods exported but not registered:
  [.GenMap [.relationshipMatrix
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘synchronicity/libs/synchronicity.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package in Depends field not imported from: ‘fields’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cwt_fw: no visible global function definition for ‘fft’
cwt_iw: no visible global function definition for ‘fft’
est_riskshrink_thresh: no visible global function definition for
  ‘median’
Undefined global functions or variables:
  fft median
Consider adding
  importFrom("stats", "fft", "median")
to your NAMESPACE file.
File ‘SynchWave/libs/SynchWave.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SyncRNG/libs/SyncRNG.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
ProgressBAR: no visible global function definition for ‘txtProgressBar’
ProgressBAR: no visible global function definition for
  ‘setTxtProgressBar’
cor.matrix: no visible global function definition for ‘cor’
cor.matrix.partial: no visible global function definition for ‘cor’
optimal: no visible global function definition for ‘combn’
optimal: no visible global function definition for ‘cor’
Undefined global functions or variables:
  combn cor setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "cor")
  importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘RCurl’ ‘RJSONIO’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'available_ranges.Rd':
  \usage lines wider than 90 characters:
       available_ranges(authority = "ensembl", species = "Homo sapiens", domain = "hgnc_symbol")

Rd file 'synergizer.Rd':
  \usage lines wider than 90 characters:
       synergizer(authority = "ensembl", species = "Homo sapiens", domain = "hgnc_symbol", range = "entrezgene", ids = NULL, file = NULL)
  \examples lines wider than 100 characters:
     symbols.ids <- synergizer( authority = "ensembl", species = "Homo sapiens", domain="affy_hg_u95av2", range="hgnc_symbol",ids=c("1939_at ... [TRUNCATED]
     entrez.ids <- synergizer( authority = "ensembl", species = "Homo sapiens", domain="hgnc_symbol", range="entrezgene",ids=c("snph", "pja1 ... [TRUNCATED]

These lines will be truncated in the PDF manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘tcltk’ ‘tkrplot’
  Please remove these calls from your code.
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.
Namespaces with empty importFrom:
  ‘Rcpp’ ‘methods’
File ‘synlik/libs/synlik.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘synthACS/libs/synthACS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls in package code:
  ‘LowRankQP’ ‘rgenoud’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
fn.V: no visible global function definition for ‘LowRankQP’
gaps.plot: no visible global function definition for ‘abline’
path.plot: no visible global function definition for ‘lines’
path.plot: no visible global function definition for ‘abline’
path.plot: no visible global function definition for ‘legend’
synth: no visible binding for global variable ‘sd’
synth: no visible binding for global variable ‘var’
synth: no visible global function definition for ‘LowRankQP’
Undefined global functions or variables:
  LowRankQP abline legend lines sd var
Consider adding
  importFrom("graphics", "abline", "legend", "lines")
  importFrom("stats", "sd", "var")
to your NAMESPACE file.
.checkDimAndTest: no visible global function definition for
  ‘chisq.test’
.checkDimAndTest: no visible global function definition for
  ‘fisher.test’
plotTable1Heatmap: no visible global function definition for ‘par’
plotTable1Heatmap: no visible global function definition for ‘image’
plotTable1Heatmap: no visible global function definition for ‘abline’
plotTable1Heatmap: no visible global function definition for ‘axis’
plotTable1Heatmap: no visible global function definition for ‘text’
plotTable1Heatmap: no visible global function definition for ‘legend’
plotTable1Heatmap: no visible global function definition for ‘box’
Undefined global functions or variables:
  abline axis box chisq.test fisher.test image legend par text
Consider adding
  importFrom("graphics", "abline", "axis", "box", "image", "legend",
             "par", "text")
  importFrom("stats", "chisq.test", "fisher.test")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  rbind.tableList rbind.tableMatrix
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'rbind.tableList':
  ‘rbind.tableList’

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'library' or 'require' call to ‘grid’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to ‘perturb’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘grid’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cellgram: no visible global function definition for ‘grid.rect’
cellgram: no visible global function definition for ‘gpar’
cellgram: no visible global function definition for ‘grid.segments’
cellgram: no visible global function definition for ‘grid.circle’
cellgram: no visible global function definition for ‘grid.polygon’
cellgram: no visible global function definition for ‘grid.text’
cellgram: no visible global function definition for ‘unit’
compare: no visible global function definition for ‘sd’
tableplot.colldiag: no visible global function definition for
  ‘colldiag’
tableplot.colldiag: no visible global function definition for ‘xtabs’
tableplot.default: no visible global function definition for
  ‘grid.newpage’
tableplot.default: no visible global function definition for
  ‘grid.layout’
tableplot.default: no visible global function definition for ‘unit’
tableplot.default: no visible global function definition for
  ‘pushViewport’
tableplot.default: no visible global function definition for ‘viewport’
tableplot.default: no visible global function definition for
  ‘grid.text’
tableplot.default: no visible global function definition for
  ‘upViewport’
tableplot.default: no visible global function definition for ‘gpar’
tableplot.default: no visible global function definition for
  ‘grid.rect’
tableplot.default: no visible global function definition for
  ‘popViewport’
Undefined global functions or variables:
  colldiag gpar grid.circle grid.layout grid.newpage grid.polygon
  grid.rect grid.segments grid.text popViewport pushViewport sd unit
  upViewport viewport xtabs
Consider adding
  importFrom("stats", "sd", "xtabs")
to your NAMESPACE file.
Rd file 'Linehan.Rd':
  \examples lines wider than 100 characters:
             cell.specs=list(list(0,"grey50",1,1,"red",1,"white","grey90",2,.7,"black",FALSE,"black",99)),
             cell.specs=list(list(0,c("black","blue"),1,1,c("black","blue"),1,"white","grey80",2,.7,"black",FALSE,"black",99))

Rd file 'cellgram.Rd':
  \usage lines wider than 90 characters:
     cellgram(cell, shape = 0, shape.col = "black", shape.lty = 1, shape.neg = 0, shape.col.neg = "red", shape.lty.neg = 1, cell.fill = "whi ... [TRUNCATED]

Rd file 'congruence.array.Rd':
  \usage lines wider than 90 characters:
     congruence.array(X, FUN = congruence.coef, stat.name = "phi", round = FALSE, scale = 1, ref = "last")

Rd file 'make.specs0.Rd':
  \usage lines wider than 90 characters:
     make.specs0(n = NULL, as.data.frame = FALSE, shape = 0, shape.col = "black", shape.lty = 1, shape.neg = 0, shape.col.neg = "red", shape ... [TRUNCATED]
     cell.fill = "white", back.fill = "white", label = 0, label.size = 0.7, label.col = "black", ref.lines = FALSE, ref.col = "gray80",  sca ... [TRUNCATED]

Rd file 'tableplot.Rd':
  \usage lines wider than 90 characters:
             v.parts = 0, h.parts = 0, gap = 2, text.m = 0, empty.text.size = 0.8, empty.text.col = "grey30", 
             title = NULL, table.label = TRUE, label.size = 0.8, side.rot = 0, left.space = 10, top.space = 10+10*(!is.null(title)), ...)
  \examples lines wider than 100 characters:
             cell.specs = list(list(0,"grey50",1,0,"red",1,"white","grey80",1,0.7,"black",FALSE,"black",93)),

These lines will be truncated in the PDF manual.
Found the following apparent S3 methods exported but not registered:
  print.plist
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
TCRsink: no visible global function definition for ‘head’
Undefined global functions or variables:
  head
Consider adding
  importFrom("utils", "head")
to your NAMESPACE file.
itabplot : <anonymous>: no visible global function definition for
  ‘capture.output’
itabplot: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL capture.output
Consider adding
  importFrom("utils", "browseURL", "capture.output")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  plot.tabu summary.tabu
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.tabu: no visible global function definition for ‘image’
plot.tabu: no visible global function definition for ‘gray’
plot.tabu: no visible global function definition for ‘par’
plot.tabu: no visible global function definition for ‘layout’
plot.tabu: no visible global function definition for ‘plot’
Undefined global functions or variables:
  gray image layout par plot
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "image", "layout", "par", "plot")
to your NAMESPACE file.
File ‘tagcloud/libs/tagcloud.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tailDepFun/libs/tailDepFun.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  proj.data proj.dir proj.dir2
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
NANOVA.test: no visible global function definition for ‘ecdf’
NANOVA.test2: no visible global function definition for ‘ecdf’
NANOVA.test3: no visible global function definition for ‘ecdf’
fdr.table: no visible global function definition for ‘median’
fdr.table: no visible global function definition for ‘quantile’
gene.classifier1: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  ecdf median quantile write.table
Consider adding
  importFrom("stats", "ecdf", "median", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Rd file 'NANOVA.test.Rd':
  \usage lines wider than 90 characters:
     NANOVA.test2(data,f1,f2,type,time.course,equal.size=FALSE,B=100,robustify=FALSE,eb=FALSE,df=0)

Rd file 'tanova.Rd':
  \usage lines wider than 90 characters:
     tanova(data, f1, f2, tp, B=100, FDR=0.05,robustify=FALSE, equal.size=FALSE, qt=-1, longitudinal=TRUE, test.type=0,eb=FALSE,df=0)
     gene.classifier1(data, f1, f2, B=100,FDR=0.05, robustify=FALSE, equal.size=FALSE, eb=FALSE,qt=-1)
     gene.classifier2(data, f1, f2, B=100,FDR=0.05, robustify=FALSE, equal.size=FALSE, time.course, qt=-1,eb=FALSE,df=1)

These lines will be truncated in the PDF manual.
File ‘TAQMNGR/libs/TAQMNGR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls in package code:
  ‘gdata’ ‘ggplot2’ ‘grid’ ‘lattice’ ‘xtable’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following apparent S3 methods exported but not registered:
  as.matrix.by stack.list
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
AnalyzeLVZ: no visible global function definition for ‘approx’
ConvP2Vdepthinv: no visible global function definition for ‘approx’
DistSummary: no visible global function definition for ‘heat.colors’
Earthplot: no visible global function definition for ‘heat.colors’
Earthplot: no visible global function definition for ‘par’
Earthplot: no visible global function definition for ‘plot’
Earthplot: no visible global function definition for ‘approx’
Earthplot: no visible global function definition for ‘image’
Earthplot: no visible binding for global variable ‘lines’
FindRoots: no visible global function definition for ‘uniroot’
InterpModel: no visible global function definition for ‘approx’
LinInterp: no visible global function definition for ‘approx’
PolarPlot: no visible binding for global variable ‘plot’
Rayfan: no visible binding for global variable ‘lines’
polaraxis: no visible global function definition for ‘text’
Undefined global functions or variables:
  approx heat.colors image lines par plot text uniroot
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "image", "lines", "par", "plot", "text")
  importFrom("stats", "approx", "uniroot")
to your NAMESPACE file.
Rd file 'DistSummary.Rd':
  \usage lines wider than 90 characters:
     DistSummary(delta, h, model, phaselist = 'default', prop = "vp", image.col = heat.colors(500), n = 200, ...)

Rd file 'Rayfan.Rd':
  \usage lines wider than 90 characters:
     Rayfan(phaselist, h, model, deltalist = 1:17 * 20, minp = 0.5, plot = TRUE, add = TRUE, col = rep("black", length(phaselist)), verbose  ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following apparent S3 methods exported but not registered:
  end.TawnyPortfolio start.TawnyPortfolio
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
end.TawnyPortfolio: no visible global function definition for ‘end’
start.TawnyPortfolio: no visible global function definition for ‘start’
Undefined global functions or variables:
  end start
Consider adding
  importFrom("stats", "end", "start")
to your NAMESPACE file.
Running examples in ‘taxa-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: filter_obs
> ### Title: Filter observations with a list of conditions
> ### Aliases: filter_obs
> 
> ### ** Examples
> 
> # Filter by row index
> filter_obs(ex_taxmap, "info", 1:2)
<Taxmap>
  17 taxa: b. Mammalia, c. Plantae ... q. lycopersicum, r. tuberosum
  17 edges: NA->b, NA->c, b->d, b->e ... j->o, k->p, l->q, l->r
  4 data sets:
    info:
      # A tibble: 2 x 4
          name n_legs dangerous taxon_id
        <fctr>  <dbl>     <lgl>    <chr>
      1  tiger      4      TRUE        m
      2    cat      4     FALSE        n
    phylopic_ids:  e148eabb-f138-43c6-b1e4-5cda2180485a ... 63604565-0406-460b-8cb8-1abe954b3f3a
    foods: a list with 6 items
    And 1 more data sets: abund
  1 functions:
 reaction
> 
> # Filter by TRUE/FALSE
> filter_obs(ex_taxmap, "info", dangerous == FALSE)
<Taxmap>
  17 taxa: b. Mammalia, c. Plantae ... q. lycopersicum, r. tuberosum
  17 edges: NA->b, NA->c, b->d, b->e ... j->o, k->p, l->q, l->r
  4 data sets:
    info:
      # A tibble: 4 x 4
          name n_legs dangerous taxon_id
        <fctr>  <dbl>     <lgl>    <chr>
      1    cat      4     FALSE        n
      2   mole      4     FALSE        o
      3 tomato      0     FALSE        q
      # ... with 1 more rows
    phylopic_ids:  e148eabb-f138-43c6-b1e4-5cda2180485a ... 63604565-0406-460b-8cb8-1abe954b3f3a
    foods: a list with 6 items
    And 1 more data sets: abund
  1 functions:
 reaction
> 
> # Remove taxa whose obserservation were filtered out
> filter_obs(ex_taxmap, "info", dangerous == FALSE, drop_taxa = TRUE)
Error in names(selection) <- self$taxon_ids() : 
  'names' attribute [17] must be the same length as the vector [2]
Calls: filter_obs ... filter_obs.Taxmap -> <Anonymous> -> <Anonymous> -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 258-259 (taxa-vignette.Rmd) 
Error: processing vignette ‘taxa-vignette.Rmd’ failed with diagnostics:
‘names’ attribute [14] must be the same length as the vector [2]
Execution halted
Found the following significant warnings:
  Warning: working directory was changed to ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/taxlist/cyperus’, resetting
Error in re-building vignettes:
  ...
This is taxlist 0.1.2

Attaching package: 'taxlist'

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

    levels

Calling http://taxosaurus.org/retrieve/c660a336a52431940e615c276ffebb33
Quitting from lines 105-108 (taxlist-intro.Rmd) 
Error: processing vignette ‘taxlist-intro.Rmd’ failed with diagnostics:
HTTP status 503 - Service Unavailable
Execution halted
File ‘tbart/libs/tbart.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Found the following apparent S3 methods exported but not registered:
  slice.fun
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'top.fun':
  ‘slice.fun’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘tcR/libs/tcR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
cluster_cutoff_at_first_empty_bin: no visible global function
  definition for ‘hist’
mapper1D: no visible global function definition for ‘dist’
mapper1D: no visible global function definition for ‘as.dist’
mapper1D: no visible global function definition for ‘hclust’
mapper1D: no visible global function definition for ‘cutree’
mapper2D: no visible global function definition for ‘dist’
mapper2D: no visible global function definition for ‘as.dist’
mapper2D: no visible global function definition for ‘hclust’
mapper2D: no visible global function definition for ‘cutree’
Undefined global functions or variables:
  as.dist cutree dist hclust hist
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "as.dist", "cutree", "dist", "hclust")
to your NAMESPACE file.
File ‘TDboost/libs/TDboost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘RSEIS’ ‘pracma’ ‘signal’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
makeCircles: no visible global function definition for ‘quantile’
targetDiagram: no visible global function definition for ‘as.formula’
targetDiagram: no visible global function definition for ‘modifyList’
targetDiagram: no visible global function definition for ‘extendrange’
tdStats : sdo: no visible global function definition for ‘sd’
tdStats : sdm: no visible global function definition for ‘sd’
tdStats : r2: no visible global function definition for ‘cor’
Undefined global functions or variables:
  as.formula cor extendrange modifyList quantile sd
Consider adding
  importFrom("grDevices", "extendrange")
  importFrom("stats", "as.formula", "cor", "quantile", "sd")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
tdt.quad: no visible global function definition for ‘runif’
tdt.rr: no visible global function definition for ‘pf’
tdt.rr: no visible global function definition for ‘qbeta’
Undefined global functions or variables:
  pf qbeta runif
Consider adding
  importFrom("stats", "pf", "qbeta", "runif")
to your NAMESPACE file.
File ‘tdthap/libs/tdthap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
E.2SI: no visible binding for global variable ‘var’
E.2SI: no visible global function definition for ‘var’
E.BE: no visible global function definition for ‘var’
E.Beta: no visible global function definition for ‘var’
E.PO: no visible global function definition for ‘var’
E.PPS: no visible global function definition for ‘var’
E.SI: no visible global function definition for ‘var’
E.STPPS: no visible global function definition for ‘var’
E.STSI: no visible global function definition for ‘var’
E.STpiPS: no visible global function definition for ‘var’
E.SY: no visible global function definition for ‘var’
E.WR: no visible global function definition for ‘var’
E.piPS: no visible global function definition for ‘var’
GREG.SI: no visible global function definition for ‘var’
S.BE: no visible global function definition for ‘runif’
S.PO: no visible global function definition for ‘runif’
S.PPS: no visible global function definition for ‘runif’
S.SI: no visible global function definition for ‘runif’
S.STPPS: no visible global function definition for ‘runif’
S.WR: no visible global function definition for ‘rbinom’
S.piPS: no visible global function definition for ‘runif’
p.WR: no visible global function definition for ‘dmultinom’
Undefined global functions or variables:
  dmultinom rbinom runif var
Consider adding
  importFrom("stats", "dmultinom", "rbinom", "runif", "var")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  predict.Weights predict.Weights2
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
TeachNet: no visible global function definition for ‘predict’
createWeights1: no visible global function definition for ‘rnorm’
createWeights2: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  predict rnorm
Consider adding
  importFrom("stats", "predict", "rnorm")
to your NAMESPACE file.
aniplotevents: no visible global function definition for ‘plot’
aniplotevents: no visible global function definition for ‘lines’
cbfs: no visible global function definition for ‘rnorm’
cbfs: no visible global function definition for ‘runif’
cbfs_red: no visible global function definition for ‘arima.sim’
cbfs_red: no visible global function definition for ‘runif’
eventCluster: no visible global function definition for ‘princomp’
eventCluster: no visible global function definition for ‘kmeans’
measures: no visible global function definition for ‘sd’
measures: no visible global function definition for ‘var’
measures: no visible global function definition for ‘PP.test’
noiseTests: no visible global function definition for ‘Box.test’
noiseTests: no visible global function definition for ‘PP.test’
noiseTests: no visible global function definition for ‘ar’
plotevents: no visible global function definition for ‘plot’
plotevents: no visible global function definition for ‘lines’
ur.za.fast : roll: no visible global function definition for ‘coef’
ur.za.fast : roll: no visible global function definition for ‘lm’
Undefined global functions or variables:
  Box.test PP.test ar arima.sim coef kmeans lines lm plot princomp
  rnorm runif sd var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "Box.test", "PP.test", "ar", "arima.sim", "coef",
             "kmeans", "lm", "princomp", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
File ‘teigen/libs/teigen.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  $.tensor ^.tensor as.contravariate.character as.covariate.character
  as.tensor.default as.tensor.tensor is.contravariate.character
  is.contravariate.numeric is.contravariate.tensor
  is.covariate.character is.covariate.numeric is.covariate.tensor
  mean.tensor |.tensor
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Calls with DUP:
   .C(tensoraCmulhelper, dimx = as.integer(c(outerx, inner, para)), 
       as.integer(c(inner, outery, para)), as.integer(c(outerx, 
           outery, para)), as.complex(X[xtidx]), as.complex(Y[ytidx]), 
       erg = complex(outerx * outery * para), NAOK = TRUE, DUP = FALSE)
   .C(tensoramulhelper, dimx = as.integer(c(outerx, inner, para)), 
       as.integer(c(inner, outery, para)), as.integer(c(outerx, 
           outery, para)), as.numeric(X[xtidx]), as.numeric(Y[ytidx]), 
       erg = numeric(outerx * outery * para), NAOK = TRUE, DUP = FALSE)
DUP is no longer supported and will be ignored.
S3 methods shown with full name in documentation object 'mean.tensor':
  ‘mean.tensor’

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘tensorA/libs/tensorA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
TER.deesc.1.B : A1.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.1.B : A1.f: no visible binding for global variable ‘ID’
TER.deesc.1.B : A2.n.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.1.B : A2.n.f: no visible binding for global variable ‘ID’
TER.deesc.1.B: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.1.B: no visible binding for global variable ‘ID’
TER.deesc.A.B : A1.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : A1.f: no visible binding for global variable ‘ID’
TER.deesc.A.B : A3.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : A3.f: no visible binding for global variable ‘ID’
TER.deesc.A.B : A2.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : A2.f: no visible binding for global variable ‘ID’
TER.deesc.A.B : B1.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : B1.f: no visible binding for global variable ‘ID’
TER.deesc.A.B: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B: no visible binding for global variable ‘ID’
Undefined global functions or variables:
  ID
Found the following apparent S3 methods exported but not registered:
  plot.df_curves plot.dyntermstrc_nss plot.dyntermstrc_param
  plot.dyntermstrc_yields plot.error plot.fwr_curves plot.ir_curve
  plot.s_curves plot.spot_curves plot.spsearch plot.termstrc_cs
  plot.termstrc_nss plot.zeroyields print.couponbonds
  print.dyncouponbonds print.dyntermstrc_nss print.dyntermstrc_yields
  print.summary.dyntermstrc_nss print.summary.dyntermstrc_param
  print.summary.dyntermstrc_yields print.summary.termstrc_cs
  print.summary.termstrc_nss print.termstrc_cs print.termstrc_nss
  print.zeroyields summary.dyntermstrc_nss summary.dyntermstrc_param
  summary.dyntermstrc_yields summary.termstrc_cs summary.termstrc_nss
  summary.zeroyields
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘termstrc/libs/termstrc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Depends: includes the non-default packages:
  ‘grid’ ‘quadprog’ ‘maps’ ‘maptools’ ‘mapdata’ ‘dichromat’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  ‘dichromat’ ‘grid’ ‘mapdata’ ‘maps’ ‘maptools’ ‘quadprog’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  plot.tverify tverify.default
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘TESS/libs/TESS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘testforDEP/libs/testforDEP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File which contains pragma(s) suppressing diagnostics:
  ‘inst/include/testthat/vendor/catch.h’
File ‘texmexseq/libs/texmexseq.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: quad.table
> ### Title: Create and plot "quads" of samples
> ### Aliases: quad.table quad.plot
> ### Keywords: hplot manip design
> 
> ### ** Examples
> 
> # make up some data
> sim.data <- function() rpoilog(1000, 1.0, 1.0, condS=TRUE)
> otu <- data.frame(sample0=sim.data())
> for (i in 1:10) otu[[paste('sample', i, sep='')]] <- sim.data()
> otu.ids <- paste('otu', seq(1:1000), sep='')
> rownames(otu) <- otu.ids
> z.table <- z.transform.table(otu)
Warning in value[[3L]](cond) : fit 1 failed
Warning in value[[3L]](cond) : fit 1 failed
Warning in value[[3L]](cond) : fit 2 failed
> 
> # pull out a quad, imagining that samples 1 and 2 were the control samples
> # and 3 and 4 were the treatment
> q <- quad.table(z.table, 'sample1', 'sample2', 'sample3', 'sample4')
> 
> # plot it
> p <- quad.plot(q)
Error in get("d.control") : object 'd.control' not found
Calls: quad.plot ... lapply -> FUN -> overscope_eval_next -> .Call -> get
Execution halted
Found the following apparent S3 methods exported but not registered:
  print.tepAssign print.tepBADA print.tepDICA print.tepGPLS
  print.tepGraphs print.tepPLS print.tepPLSCA print.texpoOutput
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
phyper_right: no visible global function definition for ‘dhyper’
progression: no visible global function definition for ‘density’
progression: no visible global function definition for ‘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.
File ‘textreg/libs/textreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘textreuse/libs/textreuse.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.dea_create_model: no visible global function definition for
  ‘getSrcFilename’
.wMean: no visible global function definition for ‘weighted.mean’
Undefined global functions or variables:
  getSrcFilename weighted.mean
Consider adding
  importFrom("stats", "weighted.mean")
  importFrom("utils", "getSrcFilename")
to your NAMESPACE file.
transfer: no visible global function definition for ‘rgamma’
transfer: no visible global function definition for ‘rnorm’
transfer: no visible global function definition for ‘rnbinom’
transfer: no visible global function definition for ‘rpois’
transfer: no visible global function definition for ‘rbinom’
transfer: no visible global function definition for ‘runif’
plot,transfer: no visible global function definition for ‘barplot’
plot,transfer: no visible global function definition for ‘axis’
plot,transfer: no visible global function definition for ‘par’
plot,transfer: no visible global function definition for ‘hist’
Undefined global functions or variables:
  axis barplot hist par rbinom rgamma rnbinom rnorm rpois runif
Consider adding
  importFrom("graphics", "axis", "barplot", "hist", "par")
  importFrom("stats", "rbinom", "rgamma", "rnbinom", "rnorm", "rpois",
             "runif")
to your NAMESPACE file.
File ‘TFMPvalue/libs/TFMPvalue.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
ParseTrueFX: no visible global function definition for ‘read.csv’
TrueFXRef: no visible global function definition for ‘download.file’
TrueFXRef: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL download.file read.csv
Consider adding
  importFrom("utils", "browseURL", "download.file", "read.csv")
to your NAMESPACE file.
File ‘tgcd/libs/tgcd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tgp/libs/tgp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Calls with DUP:
   .C("zstat_pathway_perm", as.double(g), as.integer(m), as.integer(length(m)), 
       as.double(aff), as.integer(length(aff)), as.double(thresh), 
       as.integer(gsubsetmatrix), as.integer(nrow(gsubsetmatrix)), 
       as.integer(use_sign), as.integer(use_weight), as.integer(strategy), 
       as.integer(nperm), ret_pvalue, DUP = FALSE)
   .C("zstat_perm", as.double(g), as.integer(m), as.integer(length(m)), 
       as.double(aff), as.integer(length(aff)), as.double(thresh), 
       as.integer(gsubsetmatrix), as.integer(nrow(gsubsetmatrix)), 
       as.integer(use_sign), as.integer(use_weight), as.integer(strategy), 
       as.integer(nperm), ret_pvalue, DUP = FALSE)
DUP is no longer supported and will be ignored.
File ‘thgenetics/libs/thgenetics.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Thinknum: no visible global function definition for ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
File ‘ThreeArmedTrials/libs/ThreeArmedTrials.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
coef_traceplot: no visible global function definition for ‘rainbow’
coef_traceplot: no visible global function definition for ‘plot’
coef_traceplot: no visible global function definition for ‘abline’
coef_traceplot : <anonymous>: no visible global function definition for
  ‘lines’
coef_traceplot: no visible global function definition for ‘text’
ee.GEE.aux : <anonymous>: no visible global function definition for
  ‘combn’
Undefined global functions or variables:
  abline combn lines plot rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "plot", "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
summary.tsls: no visible global function definition for ‘printCoefmat’
threesls: no visible global function definition for ‘cor’
threesls: no visible global function definition for ‘pt’
tsls.formula: no visible global function definition for ‘model.matrix’
tsls.formula: no visible global function definition for
  ‘model.response’
Undefined global functions or variables:
  cor model.matrix model.response printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.matrix", "model.response",
             "printCoefmat", "pt")
to your NAMESPACE file.
.LoadTickDataHK: no visible global function definition for ‘read.csv’
.LoadTickDataSHSZ: no visible global function definition for ‘read.csv’
DrawDown: no visible global function definition for ‘na.omit’
PerformanceReport: no visible global function definition for
  ‘aggregate’
PerformanceReport: no visible global function definition for ‘sd’
Undefined global functions or variables:
  aggregate na.omit read.csv sd
Consider adding
  importFrom("stats", "aggregate", "na.omit", "sd")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
newTiddler: no visible global function definition for ‘new’
twImage: no visible global function definition for ‘new’
twLink: no visible global function definition for ‘new’
twList: no visible global function definition for ‘new’
twTable: no visible global function definition for ‘new’
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
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 the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tiff/libs/tiff.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  plot.tight.clust
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.tight.clust: no visible global function definition for ‘hclust’
plot.tight.clust: no visible global function definition for ‘dist’
plot.tight.clust: no visible global function definition for ‘image’
plot.tight.clust: no visible global function definition for
  ‘colorRampPalette’
plot.tight.clust: no visible global function definition for ‘axis’
plot.tight.clust: no visible global function definition for ‘lines’
tight.clust : find.candidates : kmeans.classify: no visible global
  function definition for ‘kmeans’
write.tight.clust: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  axis colorRampPalette dist hclust image kmeans lines write.table
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "image", "lines")
  importFrom("stats", "dist", "hclust", "kmeans")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Rd file 'tight.clust.Rd':
  \usage lines wider than 90 characters:
     tight.clust(x, target, k.min, alpha = 0.1, beta = 0.6, top.can = 7, seq.num = 2, resamp.num = 10, samp.p = 0.7, nstart = 1, remain.p =  ... [TRUNCATED]

These lines will be truncated in the PDF manual.
File ‘tikzDevice/libs/tikzDevice.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.viterbiTrainingEmission,contHMM-list-list: no visible global function
  definition for ‘var’
sampleObs,tDist-numeric: no visible global function definition for ‘rt’
Undefined global functions or variables:
  rt var
Consider adding
  importFrom("stats", "rt", "var")
to your NAMESPACE file.
File ‘tileHMM/libs/tileHMM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpIoV78k’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpIoV78k’, resetting
'library' or 'require' call to ‘shiny’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘ggplot2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
timeline: no visible global function definition for ‘ggplot’
timeline: no visible global function definition for ‘geom_segment’
timeline: no visible global function definition for ‘aes_string’
timeline: no visible global function definition for ‘geom_rect’
timeline: no visible global function definition for ‘geom_text’
timeline: no visible global function definition for ‘theme’
timeline: no visible global function definition for ‘element_blank’
timeline: no visible global function definition for ‘xlab’
timeline: no visible global function definition for ‘ylab’
timeline: no visible global function definition for ‘xlim’
timeline: no visible global function definition for
  ‘scale_y_continuous’
timeline: no visible global function definition for ‘geom_point’
timeline: no visible global function definition for ‘scale_color_grey’
timeline: no visible global function definition for ‘geom_hline’
Undefined global functions or variables:
  aes_string element_blank geom_hline geom_point geom_rect geom_segment
  geom_text ggplot scale_color_grey scale_y_continuous theme xlab xlim
  ylab
Found the following apparent S3 methods exported but not registered:
  density.tm mean.tm print.tm quantile.tm summary.tm
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
density.tm: no visible global function definition for ‘density’
mu.mle: no visible global function definition for ‘optimize’
pophistory.tm: no visible binding for global variable ‘quantile’
quantile.tm: no visible global function definition for ‘quantile’
sample.pop: no visible global function definition for ‘runif’
summary.tm: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  density optimize quantile runif
Consider adding
  importFrom("stats", "density", "optimize", "quantile", "runif")
to your NAMESPACE file.
File ‘TimeMachine/libs/TimeMachine.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
generatelatencies: no visible binding for global variable ‘allNames’
generatetimedeltas: no visible global function definition for ‘head’
generatetimedeltas: no visible global function definition for ‘tail’
generatevertexedgelist : <anonymous>: no visible global function
  definition for ‘head’
generatevertexedgelist : <anonymous>: no visible global function
  definition for ‘tail’
plotnetworkslices: no visible global function definition for ‘par’
plotnetworkslices: no visible global function definition for ‘text’
plottanet: no visible global function definition for ‘plot’
plottonet: no visible global function definition for ‘plot’
shortesttimepath : <anonymous>: no visible global function definition
  for ‘tail’
Undefined global functions or variables:
  allNames head par plot tail text
Consider adding
  importFrom("graphics", "par", "plot", "text")
  importFrom("methods", "allNames")
  importFrom("utils", "head", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' calls in package code:
  ‘ggplot2’ ‘plyr’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Matrix’ ‘lubridate’ ‘timeDate’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
is.Bizday: no visible global function definition for ‘isWeekday’
plotCalendarHeatmap: no visible global function definition for ‘ddply’
plotCalendarHeatmap: no visible global function definition for ‘.’
plotCalendarHeatmap: no visible binding for global variable ‘year’
plotCalendarHeatmap: no visible binding for global variable ‘month’
plotCalendarHeatmap: no visible binding for global variable ‘week’
plotCalendarHeatmap: no visible global function definition for ‘ggplot’
plotCalendarHeatmap: no visible global function definition for ‘aes’
plotCalendarHeatmap: no visible binding for global variable ‘monthweek’
plotCalendarHeatmap: no visible binding for global variable ‘weekday’
plotCalendarHeatmap: no visible global function definition for
  ‘geom_tile’
plotCalendarHeatmap: no visible global function definition for
  ‘facet_grid’
plotCalendarHeatmap: no visible global function definition for
  ‘scale_fill_gradientn’
projectDate: no visible global function definition for ‘holidayNYSE’
projectDate: no visible global function definition for
  ‘sparse.model.matrix’
Undefined global functions or variables:
  . aes ddply facet_grid geom_tile ggplot holidayNYSE isWeekday month
  monthweek scale_fill_gradientn sparse.model.matrix week weekday year
Found the following apparent S3 methods exported but not registered:
  [.Event
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
boot_autocov: no visible global function definition for ‘is.ts’
boot_autocov: no visible global function definition for ‘tsboot’
boot_autocov: no visible global function definition for ‘quantile’
boot_autocov: no visible global function definition for ‘par’
boot_autocov: no visible global function definition for ‘frequency’
boot_autocov: no visible global function definition for ‘polygon’
boot_autocov: no visible global function definition for ‘lines’
boot_autocov: no visible global function definition for ‘abline’
boot_autocov: no visible global function definition for ‘acf’
boot_spec: no visible global function definition for ‘is.ts’
boot_spec: no visible global function definition for ‘tsboot’
boot_spec: no visible global function definition for ‘spec.pgram’
boot_spec: no visible global function definition for ‘quantile’
boot_spec: no visible global function definition for ‘polygon’
boot_spec: no visible global function definition for ‘lines’
redraw: no visible global function definition for ‘spec.pgram’
statistic: no visible global function definition for ‘acf’
Undefined global functions or variables:
  abline acf frequency is.ts lines par polygon quantile spec.pgram
  tsboot
Consider adding
  importFrom("graphics", "abline", "lines", "par", "polygon")
  importFrom("stats", "acf", "frequency", "is.ts", "quantile",
             "spec.pgram")
to your NAMESPACE file.
createHstore.ts: no visible global function definition for ‘time’
exploreDb : <anonymous>: no visible global function definition for
  ‘plot’
exportTsList : <anonymous>: no visible global function definition for
  ‘time’
exportTsList: no visible global function definition for ‘write.csv2’
importTsList: no visible global function definition for ‘read.csv2’
importTsList : <anonymous>: no visible global function definition for
  ‘as.ts’
plot.tslist: no visible global function definition for ‘plot’
plot.tslist : <anonymous>: no visible global function definition for
  ‘time’
plot.tslist: no visible global function definition for ‘par’
plot.tslist: no visible global function definition for ‘legend’
readTimeSeries : <anonymous>: no visible global function definition for
  ‘ts’
resolveOverlap: no visible global function definition for ‘is.ts’
resolveOverlap: no visible global function definition for ‘frequency’
resolveOverlap: no visible global function definition for ‘time’
resolveOverlap: no visible global function definition for ‘ts’
storeTimeSeries: no visible binding for global variable ‘frequency’
zooLikeDateConvert: no visible global function definition for ‘time’
zooLikeDateConvert: no visible global function definition for
  ‘frequency’
zooLikeDateConvert: no visible global function definition for ‘cycle’
Undefined global functions or variables:
  as.ts cycle frequency is.ts legend par plot read.csv2 time ts
  write.csv2
Consider adding
  importFrom("graphics", "legend", "par", "plot")
  importFrom("stats", "as.ts", "cycle", "frequency", "is.ts", "time",
             "ts")
  importFrom("utils", "read.csv2", "write.csv2")
to your NAMESPACE file.
author.search: no visible binding for global variable ‘na.omit’
reference.list: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
drawGraph: no visible global function definition for ‘pdf’
drawGraph: no visible global function definition for ‘par’
drawGraph: no visible global function definition for ‘plot’
drawGraph: no visible global function definition for ‘segments’
drawGraph: no visible global function definition for ‘lines’
drawGraph: no visible global function definition for ‘text’
drawGraph: no visible global function definition for ‘dev.off’
drugRank: no visible global function definition for ‘aggregate’
floating2: no visible global function definition for ‘cor’
timma: no visible global function definition for ‘median’
timma: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  aggregate cor dev.off lines median par pdf plot segments text
  write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "plot", "segments", "text")
  importFrom("stats", "aggregate", "cor", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
File ‘timma/libs/timma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘TIMP/libs/TIMP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘timsac/libs/timsac.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘ExPosition’ ‘InPosition’ ‘TExPosition’ ‘prettyGraphs’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  print.tepBADA.inference.battery print.tepDICA.inference.battery
  print.tinpoAllBoots print.tinpoBoot print.tinpoBootTests
  print.tinpoComponents print.tinpoLOO print.tinpoOmni
  print.tinpoOutput print.tinpoR2
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Non-standard files/directories found at top level:
  ‘DESCRIPTION.orig’ ‘README.rst’
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.
Registered S3 methods from standard package(s) overwritten by 'tis':
  method         from
  format.default base
  format.POSIXct base
  format.POSIXlt base
File ‘tis/libs/tis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘boot’ ‘lattice’ ‘splines’ ‘tcltk’
  Please remove these calls from your code.
ls.tree: no visible global function definition for ‘lm’
ls.tree: no visible global function definition for ‘coef’
Undefined global functions or variables:
  coef lm
Consider adding
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
File ‘TKF/libs/TKF.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘rgl’ ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'par3dsave.Rd':
  \usage lines wider than 90 characters:
     par3dsave(params = c("userMatrix", "scale", "zoom", "FOV"), times = FALSE, dev = rgl.cur())

These lines will be truncated in the PDF manual.
Found an obsolete/platform-specific call in the following function:
  ‘.my.tkdev’
Found the platform-specific device:
  ‘X11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
.my.tkdev: no visible global function definition for ‘X11’
tkpersp : draw: no visible global function definition for ‘par’
tkpersp : draw: no visible global function definition for ‘persp’
Undefined global functions or variables:
  X11 par persp
Consider adding
  importFrom("grDevices", "X11")
  importFrom("graphics", "par", "persp")
to your NAMESPACE file.
File ‘tkrplot/libs/tkrplot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
FLXmclust.Density: no visible global function definition for ‘dmvnorm’
FLXmclust.Estimate: no visible global function definition for ‘flexmix’
FLXmclust.Estimate: no visible global function definition for
  ‘FLXmclust’
coefmclust: no visible global function definition for ‘parameters’
flexmix.Density: no visible global function definition for
  ‘model.matrix’
flexmix.Density: no visible global function definition for
  ‘model.response’
flexmix.Density: no visible global function definition for
  ‘model.frame’
flexmix.Density: no visible global function definition for ‘dnorm’
flexmix.Density: no visible global function definition for ‘dpois’
flexmix.Density: no visible global function definition for ‘dbinom’
flexmix.Estimate: no visible global function definition for ‘flexmix’
flexmix.Estimate: no visible global function definition for ‘FLXglm’
tleplot,TLE-data.frame: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  FLXglm FLXmclust dbinom dmvnorm dnorm dpois flexmix legend
  model.frame model.matrix model.response parameters
Consider adding
  importFrom("graphics", "legend")
  importFrom("stats", "dbinom", "dnorm", "dpois", "model.frame",
             "model.matrix", "model.response")
to your NAMESPACE file.
'library' or 'require' call to ‘mvtnorm’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
EMN: no visible global function definition for ‘dmvnorm’
EMN: no visible global function definition for ‘pmvnorm’
EMT: no visible global function definition for ‘GenzBretz’
EMT: no visible global function definition for ‘dmvt’
EMT: no visible global function definition for ‘pmvt’
MomemNT: no visible global function definition for ‘pnorm’
MomemNT: no visible global function definition for ‘dnorm’
MomemNT: no visible global function definition for ‘pmvnorm’
MomemNT: no visible global function definition for ‘dmvnorm’
TT.moment: no visible global function definition for ‘GenzBretz’
TT.moment: no visible global function definition for ‘pmvt’
TT.moment: no visible global function definition for ‘dt’
TT.moment: no visible global function definition for ‘pt’
TT.moment: no visible global function definition for ‘dmvt’
cdfNI: no visible global function definition for ‘pnorm’
cdfNI: no visible global function definition for ‘pt’
inits: no visible global function definition for ‘lm’
Undefined global functions or variables:
  GenzBretz dmvnorm dmvt dnorm dt lm pmvnorm pmvt pnorm pt
Consider adding
  importFrom("stats", "dnorm", "dt", "lm", "pnorm", "pt")
to your NAMESPACE file.
Rd file 'UTIdata.Rd':
  \examples lines wider than 100 characters:
     x = cbind((UTIdata$Fup==0)+0, (UTIdata$Fup==1)+0, (UTIdata$Fup==3)+0, (UTIdata$Fup==6)+0, (UTIdata$Fup==9)+0, (UTIdata$Fup==12)+0, (UTI ... [TRUNCATED]

These lines will be truncated in the PDF manual.
search_collection: no visible global function definition for
  ‘URLencode’
search_company: no visible global function definition for ‘URLencode’
search_keyword: no visible global function definition for ‘URLencode’
search_list: no visible global function definition for ‘URLencode’
search_movie: no visible global function definition for ‘URLencode’
search_multi: no visible global function definition for ‘URLencode’
search_person: no visible global function definition for ‘URLencode’
search_tv: no visible global function definition for ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
File ‘tmg/libs/tmg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tmlenet/libs/tmlenet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
extractContentDOM: no visible global function definition for
  ‘capture.output’
extractHTMLStrip: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  capture.output
Consider adding
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Packages suggested but not available for checking:
  ‘Rcampdf’ ‘tm.lexicon.GeneralInquirer’
File ‘tmvnsim/libs/tmvnsim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tmvtnorm/libs/tmvtnorm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tokenizers/libs/tokenizers.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘corpus.JSS.papers’
File ‘TopKLists/libs/TopKLists.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
flowlength: no visible global function definition for ‘is’
river: no visible global function definition for ‘is’
sinkfill: no visible global function definition for ‘is’
subcatch: no visible global function definition for ‘is’
topidx: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘topmodel/libs/topmodel.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Tosls.formula: no visible global function definition for ‘model.matrix’
Tosls.formula: no visible global function definition for
  ‘model.response’
summary: no visible global function definition for ‘coef’
summary: no visible global function definition for ‘pt’
Undefined global functions or variables:
  coef model.matrix model.response pt
Consider adding
  importFrom("stats", "coef", "model.matrix", "model.response", "pt")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘Cairo’ ‘RGtk2’ ‘colorspace’ ‘gWidgets’ ‘tourr’
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘TeachingDemos’ ‘ash’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Cairo’ ‘RGtk2’ ‘colorspace’ ‘gWidgets’ ‘tourr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: ‘rmongodb’
ConfA: no visible global function definition for ‘qf’
EstM2Sn: no visible global function definition for ‘nlm’
EstM2Sn: no visible global function definition for ‘qnorm’
TV.model: no visible global function definition for ‘dev.new’
TV.model: no visible global function definition for ‘points’
betaBino: no visible global function definition for ‘pbinom’
doseD: no visible global function definition for ‘lm’
doseD: no visible global function definition for ‘dev.new’
doseD: no visible global function definition for ‘par’
doseD: no visible global function definition for ‘plot’
doseD: no visible global function definition for ‘axTicks’
doseD: no visible global function definition for ‘axis’
doseD: no visible global function definition for ‘lines’
doseD: no visible global function definition for ‘abline’
doseD: no visible global function definition for ‘legend’
setD: no visible global function definition for ‘dev.new’
setD: no visible global function definition for ‘par’
setD: no visible global function definition for ‘pbinom’
setD: no visible global function definition for ‘abline’
setD: no visible global function definition for ‘axis’
setD: no visible global function definition for ‘rect’
setD: no visible global function definition for ‘lines’
setD: no visible global function definition for ‘text’
setD: no visible global function definition for ‘axTicks’
setD: no visible global function definition for ‘legend’
spoD : spoD_A: no visible global function definition for ‘chisq.test’
Undefined global functions or variables:
  abline axTicks axis chisq.test dev.new legend lines lm nlm par pbinom
  plot points qf qnorm rect text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axTicks", "axis", "legend", "lines",
             "par", "plot", "points", "rect", "text")
  importFrom("stats", "chisq.test", "lm", "nlm", "pbinom", "qf", "qnorm")
to your NAMESPACE file.
align1d : obj: no visible global function definition for ‘dist’
align2d : obj: no visible global function definition for ‘dist’
align2d : pen: no visible global function definition for ‘dist’
align2d: no visible global function definition for ‘dist’
sumt: no visible global function definition for ‘optim’
tpe1d: no visible global function definition for ‘hclust’
tpe2d: no visible global function definition for ‘hclust’
tpe2d: no visible global function definition for ‘cmdscale’
Undefined global functions or variables:
  cmdscale dist hclust optim
Consider adding
  importFrom("stats", "cmdscale", "dist", "hclust", "optim")
to your NAMESPACE file.
File ‘TP.idm/libs/TP.idm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as.data.frame.survTP
> ### Title: as.data.frame method for a survTP object
> ### Aliases: as.data.frame.survTP
> ### Keywords: manip methods survival
> 
> ### ** Examples
> 
> # Example for the "TPmsm" format
> weiTP <- dgpTP(n=100, corr=1, dist="weibull", dist.par=c(2, 7, 2, 7),
+ model.cens="exponential", cens.par = 6, state2.prob=0.6)
*** invalid %N$ use detected ***
Aborted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/tpr.Rcheck/00install.out’ for details.
Found the following calls to attach():
File ‘track/R/track.attach.R’:
  attach(what = NULL, pos = pos, name = name)
See section ‘Good practice’ in ‘?attach’.
DeadReckoning: no visible global function definition for ‘filter’
DeadReckoning: no visible global function definition for ‘approx’
DeadReckoning: no visible global function definition for ‘lm’
Mapper: no visible global function definition for ‘colorRampPalette’
Mapper: no visible global function definition for ‘terrain.colors’
Mapper: no visible global function definition for ‘points’
Mapper: no visible global function definition for ‘axis’
Standardize: no visible global function definition for ‘lm’
Undefined global functions or variables:
  approx axis colorRampPalette filter lm points terrain.colors
Consider adding
  importFrom("grDevices", "colorRampPalette", "terrain.colors")
  importFrom("graphics", "axis", "points")
  importFrom("stats", "approx", "filter", "lm")
to your NAMESPACE file.
File ‘TransferEntropy/libs/TransferEntropy.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
microsoftTranslate: no visible global function definition for
  ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
File ‘tranSurv/libs/tranSurv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
rtrapezoid: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
File ‘trapezoid/libs/trapezoid.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘treeclim/libs/treeclim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Build_JTree: no visible global function definition for ‘flush.console’
Run_JTree: no visible global function definition for ‘cov2cor’
Undefined global functions or variables:
  cov2cor flush.console
Consider adding
  importFrom("stats", "cov2cor")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
LikAge: no visible global function definition for ‘read.table’
bd.ME.optim: no visible global function definition for ‘optim’
bd.ME.optim.rho: no visible global function definition for ‘optim’
bd.ME.optim.rho.all: no visible global function definition for ‘optim’
bd.MEyule.optim: no visible global function definition for ‘optimize’
bd.MEyule.optim: no visible global function definition for ‘optim’
bd.age.optim.matlab: no visible global function definition for
  ‘read.table’
bd.groups.conf: no visible global function definition for ‘uniroot’
bd.shifts.plot: no visible global function definition for ‘plot’
bd.shifts.plot: no visible global function definition for ‘lines’
bdsky.stt.optim: no visible global function definition for ‘optim’
create.mat: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  lines optim optimize plot read.table uniroot write.table
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "optim", "optimize", "uniroot")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
plot.treeperm: no visible global function definition for ‘hist’
plot.treeperm: no visible global function definition for ‘points’
plot.treeperm: no visible global function definition for ‘text’
treeperm.formula: no visible global function definition for
  ‘model.frame’
treeperm.formula: no visible global function definition for
  ‘model.response’
Undefined global functions or variables:
  hist model.frame model.response points text
Consider adding
  importFrom("graphics", "hist", "points", "text")
  importFrom("stats", "model.frame", "model.response")
to your NAMESPACE file.
File ‘treeperm/libs/treeperm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘TrialSize/libs/TrialSize.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: working directory was changed to ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/trib/exdata/tribometer’, resetting
  Warning: working directory was changed to ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/trib/exdata/tribometer’, resetting
  Warning: working directory was changed to ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/trib/exdata/profile’, resetting
  Warning: working directory was changed to ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/trib/exdata/profile’, resetting
File ‘triebeard/libs/triebeard.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  plot.trifield
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.trifield: no visible global function definition for ‘topo.colors’
plot.trifield: no visible global function definition for ‘plot’
plot.trifield: no visible global function definition for ‘image’
plot.trifield: no visible global function definition for ‘contour’
plot.trifield: no visible global function definition for ‘text’
ternary.legend: no visible global function definition for ‘arrows’
ternary.legend: no visible global function definition for ‘text’
triaxes: no visible global function definition for ‘lines’
tribox: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  arrows contour image lines plot polygon text topo.colors
Consider adding
  importFrom("grDevices", "topo.colors")
  importFrom("graphics", "arrows", "contour", "image", "lines", "plot",
             "polygon", "text")
to your NAMESPACE file.
Rd file 'plot.trifield.Rd':
  \usage lines wider than 90 characters:
     plot(x, contours = TRUE, col = topo.colors(256), lab1 = "A = 0", lab2 = "B = 0", lab3 = "C = 0", tribox = TRUE, axis.lines = TRUE, ...)

Rd file 'ternary.legend.Rd':
  \usage lines wider than 90 characters:
     ternary.legend(x0 = 0.2, y0 = 0.8, radius = 0.1, lab1 = "A", lab2 = "B", lab3 = "C", infl = 1.5, cex = 0.75, length = 0.05, ...)

These lines will be truncated in the PDF manual.
'library' or 'require' call to ‘fpc’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following apparent S3 methods exported but not registered:
  plot.tkm print.tkm
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.tkm: no visible global function definition for ‘plotcluster’
plot.tkm: no visible global function definition for ‘plot’
plot.tkm: no visible global function definition for ‘points’
plot.tkm: no visible global function definition for ‘lines’
plot.tkm: no visible global function definition for ‘discrcoord’
Undefined global functions or variables:
  discrcoord lines plot plotcluster points
Consider adding
  importFrom("graphics", "lines", "plot", "points")
to your NAMESPACE file.
cinbag: no visible global function definition for ‘var’
trimTrees: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict var
Consider adding
  importFrom("stats", "predict", "var")
to your NAMESPACE file.
File ‘trimTrees/libs/trimTrees.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘gtools’ ‘mgcv’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘gtools’ ‘mgcv’ ‘msm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
HtoGp: no visible global function definition for ‘odd’
HtoGp: no visible global function definition for ‘even’
plot.pirls.gam: no visible global function definition for ‘par’
plot.pirls.gam: no visible global function definition for ‘plot’
plot.pirls.gam: no visible global function definition for ‘title’
plot.pirls.gam: no visible global function definition for ‘lines’
plot.pirls.gam: no visible global function definition for ‘rug’
plot.pirls.gam: no visible global function definition for ‘mtext’
test.trioGxE: no visible global function definition for ‘write.table’
trioGxE: no visible global function definition for ‘quantile’
trioGxE: no visible global function definition for ‘qtnorm’
trioplot: no visible global function definition for ‘quantile’
trioplot: no visible global function definition for ‘formula’
trioplot: no visible global function definition for ‘gam’
trioplot: no visible global function definition for ‘binomial’
Undefined global functions or variables:
  binomial even formula gam lines mtext odd par plot qtnorm quantile
  rug title write.table
Consider adding
  importFrom("graphics", "lines", "mtext", "par", "plot", "rug", "title")
  importFrom("stats", "binomial", "formula", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
File ‘tripack/libs/tripack.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  Ops.VectorAddr print.VectorAddr update.VectorAddr
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘TRSbook/libs/TRSbook.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
DrawMargin: no visible global function definition for ‘qnorm’
DrawProbability: no visible global function definition for ‘pnorm’
Factor: no visible global function definition for ‘new’
Gaussian: no visible global function definition for ‘new’
LikelihoodFactor: no visible global function definition for ‘new’
Parameters: no visible global function definition for ‘new’
Player: no visible global function definition for ‘new’
PriorFactor: no visible global function definition for ‘new’
SumFactor: no visible global function definition for ‘new’
TruncateFactor: no visible global function definition for ‘new’
Variable: no visible global function definition for ‘new’
Vdraw: no visible global function definition for ‘dnorm’
Vdraw: no visible global function definition for ‘pnorm’
Vwin: no visible global function definition for ‘dnorm’
Vwin: no visible global function definition for ‘pnorm’
Wdraw: no visible global function definition for ‘dnorm’
Wdraw: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dnorm new pnorm qnorm
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "dnorm", "pnorm", "qnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
cdens: no visible global function definition for ‘head’
dplot: no visible global function definition for ‘knots’
dplot: no visible global function definition for ‘median’
dplot: no visible global function definition for ‘par’
dplot: no visible global function definition for ‘plot.stepfun’
dplot: no visible global function definition for ‘abline’
edf: no visible global function definition for ‘approxfun’
mctest : rdist: no visible global function definition for ‘runif’
mctest : S: no visible global function definition for ‘optim’
qplot: no visible global function definition for ‘plot’
qplot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline approxfun head knots median optim par plot plot.stepfun runif
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("stats", "approxfun", "knots", "median", "optim",
             "plot.stepfun", "runif")
  importFrom("utils", "head")
to your NAMESPACE file.
File ‘truncgof/libs/truncgof.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘truncnorm/libs/truncnorm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard file/directory found at top level:
  ‘changes’
'library' or 'require' calls to packages already attached by Depends:
  ‘leaps’ ‘locfit’ ‘mgcv’
  Please remove these calls from your code.
':::' calls which should be '::':
  ‘stats:::ARMAacf’ ‘stats:::acf’ ‘stats:::arima’
  See the note in ?`:::` about the use of this operator.
Found the following apparent S3 methods exported but not registered:
  fitted.Arima plot.Arima plot.armasubsets predict.TAR rstandard.Arima
  summary.armasubsets tsdiag.Arima tsdiag.TAR
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
dmvnb: no visible global function definition for ‘dbinom’
drvts: no visible global function definition for ‘dnorm’
drvts: no visible global function definition for ‘dbinom’
dsvts: no visible global function definition for ‘dnorm’
rescale: no visible global function definition for ‘qlogis’
rescale: no visible global function definition for ‘plogis’
tslogl: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dbinom dnorm plogis qlogis
Consider adding
  importFrom("stats", "dbinom", "dnorm", "plogis", "qlogis")
to your NAMESPACE file.
Found the following significant warnings:
  ./tsBSS.h:10:22: warning: 'varExx_k' has C-linkage specified, but returns user-defined type 'arma::mat' (aka 'Mat<double>') which is incompatible with C [-Wreturn-type-c-linkage]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/tsBSS.Rcheck/00install.out’ for details.
Found the following apparent S3 methods exported but not registered:
  print.tsbugs
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'ar.bugs.Rd':
  \examples lines wider than 100 characters:
     ar2 <- ar.bugs(y = diff(LH), ar.order = 2, ar.prior = "dunif(-1,1)", var.prior = "dgamma(0.001,0.001)")

Rd file 'rv.bugs.Rd':
  \usage lines wider than 90 characters:
                     rv.tol0.prior = "dgamma(0.000001,0.000001)", rv.eps.prior = "dbeta(1, 100)", 
  \examples lines wider than 100 characters:
       plot(NULL, type = "n", xlim = tsp(sigma.pn)[1:2], ylim = range(sigma.pn[, 1:95]), main = "sigma_t")

Rd file 'sv.bugs.Rd':
  \examples lines wider than 100 characters:
       plot(NULL, type = "n", xlim = tsp(sigma.pn)[1:2], ylim = range(sigma.pn[, 1:95]), main = "sigma_t")

These lines will be truncated in the PDF manual.
tfDetails: no visible global function definition for ‘start’
tfDetails: no visible global function definition for ‘end’
Undefined global functions or variables:
  end start
Consider adding
  importFrom("stats", "end", "start")
to your NAMESPACE file.
Qhat: no visible global function definition for ‘pnorm’
plrt: no visible global function definition for ‘uniroot’
plrt: no visible global function definition for ‘optimize’
simulatedata: no visible global function definition for ‘rnorm’
tsc.test: no visible global function definition for ‘shapiro.test’
tsc.test: no visible global function definition for ‘p.adjust’
tsc.test: no visible global function definition for ‘glm’
tsc.test : f: no visible global function definition for ‘pnorm’
tsc.test: no visible global function definition for ‘uniroot’
tsc.test: no visible global function definition for ‘optimize’
variance: no visible global function definition for ‘density’
variance: no visible global function definition for ‘ecdf’
Undefined global functions or variables:
  density ecdf glm optimize p.adjust pnorm rnorm shapiro.test uniroot
Consider adding
  importFrom("stats", "density", "ecdf", "glm", "optimize", "p.adjust",
             "pnorm", "rnorm", "shapiro.test", "uniroot")
to your NAMESPACE file.
File ‘tsc/libs/tsc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘FinTS’
File ‘tsDyn/libs/tsDyn.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package in Depends field not imported from: ‘deSolve’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  plot.ami plot.d2 plot.false.nearest print.d2 print.false.nearest
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'sim.cont.Rd':
  \examples lines wider than 100 characters:
     rossler.ts <- sim.cont(rossler.syst, start=0, end=650, dt=0.1, start.x=c(0,0,0), parms=c(0.15, 0.2, 10))

These lines will be truncated in the PDF manual.
File ‘tseriesChaos/libs/tseriesChaos.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
vintageMap: no visible global function definition for ‘read.table’
TSget,character-TSfameLocalConnection: no visible global function
  definition for ‘as.ts’
TSget,character-TSfameLocalConnection: no visible global function
  definition for ‘zoo’
TSget,character-TSfameLocalConnection: no visible global function
  definition for ‘frequency’
TSget,character-TSfameServerConnection: no visible global function
  definition for ‘as.ts’
TSget,character-TSfameServerConnection: no visible global function
  definition for ‘zoo’
TSget,character-TSfameServerConnection: no visible global function
  definition for ‘frequency’
Undefined global functions or variables:
  as.ts frequency read.table zoo
Consider adding
  importFrom("stats", "as.ts", "frequency")
  importFrom("utils", "read.table")
to your NAMESPACE file.
DstandardizedLoadings.TSFmodel: no visible global function definition
  for ‘cov’
FAfitStats.TSFmodel: no visible global function definition for ‘cov’
FAfitStats.default: no visible global function definition for ‘cor’
FAfitStats.default: no visible global function definition for
  ‘factanal’
FAfitStats.default: no visible global function definition for ‘pchisq’
FAmodelFitStats: no visible global function definition for ‘pchisq’
checkResiduals.TSFmodel: no visible global function definition for
  ‘cov’
distribution.factorsEstEval: no visible global function definition for
  ‘par’
distribution.factorsEstEval: no visible binding for global variable
  ‘par’
distribution.factorsEstEval: no visible global function definition for
  ‘density’
distribution.factorsEstEval: no visible global function definition for
  ‘matplot’
distribution.factorsEstEval: no visible global function definition for
  ‘title’
summary.TSFmodel: no visible global function definition for ‘start’
summary.TSFmodel: no visible global function definition for ‘end’
Undefined global functions or variables:
  cor cov density end factanal matplot par pchisq start title
Consider adding
  importFrom("graphics", "matplot", "par", "title")
  importFrom("stats", "cor", "cov", "density", "end", "factanal",
             "pchisq", "start")
to your NAMESPACE file.
Func.SAX: no visible global function definition for ‘sd’
Func.SAX: no visible global function definition for ‘qnorm’
Func.matrix: no visible global function definition for ‘qnorm’
Func.motif: no visible global function definition for ‘sd’
Func.motif: no visible global function definition for ‘na.omit’
Func.motif: no visible global function definition for ‘combn’
Func.motif.multivariate: no visible global function definition for
  ‘txtProgressBar’
Func.motif.multivariate: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  combn na.omit qnorm sd setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit", "qnorm", "sd")
  importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
dLag : dlag.f: no visible global function definition for
  ‘complete.cases’
distmat: no visible global function definition for ‘dist’
fitCity: no visible global function definition for ‘glm.control’
fitCity: no visible global function definition for ‘terms’
ldmvnorm: no visible global function definition for ‘mahalanobis’
lspline: no visible global function definition for ‘quantile’
plot.tsdecomp: no visible global function definition for ‘par’
plot.tsdecomp: no visible global function definition for ‘plot’
setupFormula: no visible global function definition for ‘as.formula’
spatialgibbs: no visible global function definition for ‘rnorm’
spatialgibbs: no visible global function definition for ‘rgamma’
spatialgibbs: no visible global function definition for ‘runif’
tsdecomp: no visible global function definition for ‘fft’
Undefined global functions or variables:
  as.formula complete.cases dist fft glm.control mahalanobis par plot
  quantile rgamma rnorm runif terms
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "as.formula", "complete.cases", "dist", "fft",
             "glm.control", "mahalanobis", "quantile", "rgamma", "rnorm",
             "runif", "terms")
to your NAMESPACE file.
covTranspose11: warning in glasso(sc, 2 * rhoc/n, wi.init = gc$wi,
  w.init = gc$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of ‘penalize.diag’ to
  ‘penalize.diagonal’
covTranspose11: warning in glasso(sr, 2 * rhor/p, wi.init = gr$wi,
  w.init = gr$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of ‘penalize.diag’ to
  ‘penalize.diagonal’
.help.ESS: no visible global function definition for ‘index.search’
TransSphere : ttin: no visible global function definition for ‘t.test’
TransSphere: no visible global function definition for ‘sd’
TransSphere: no visible global function definition for ‘quantile’
TransSphere: no visible global function definition for ‘pt’
Undefined global functions or variables:
  index.search pt quantile sd t.test
Consider adding
  importFrom("stats", "pt", "quantile", "sd", "t.test")
to your NAMESPACE file.
File ‘tspmeta/libs/tspmeta.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
TT.GS : TT.GS.sp: no visible global function definition for ‘qt’
TT.GS : TT.GS.sp: no visible global function definition for ‘runif’
TT.GS : TT.GS.sp: no visible global function definition for ‘pt’
TT.moment: no visible global function definition for ‘dt’
TT.moment: no visible global function definition for ‘pt’
Undefined global functions or variables:
  dt pt qt runif
Consider adding
  importFrom("stats", "dt", "pt", "qt", "runif")
to your NAMESPACE file.
ttScreening: no visible global function definition for ‘gaussian’
ttScreening: no visible global function definition for ‘glm.control’
ttScreening: no visible global function definition for ‘model.response’
ttScreening: no visible global function definition for ‘is.empty.model’
ttScreening: no visible global function definition for ‘model.matrix’
ttScreening: no visible global function definition for ‘na.omit’
ttScreening: no visible global function definition for ‘terms’
ttScreening: no visible global function definition for ‘capture.output’
ttScreening: no visible global function definition for ‘glm’
ttScreening: no visible binding for global variable ‘gaussian’
ttScreening: no visible global function definition for ‘pt’
ttScreening: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  capture.output gaussian glm glm.control is.empty.model model.matrix
  model.response na.omit p.adjust pt terms
Consider adding
  importFrom("stats", "gaussian", "glm", "glm.control", "is.empty.model",
             "model.matrix", "model.response", "na.omit", "p.adjust",
             "pt", "terms")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
.saveDevice: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off
Consider adding
  importFrom("grDevices", "dev.off")
to your NAMESPACE file.
ttwa: no visible global function definition for ‘aggregate’
ttwa: no visible global function definition for ‘txtProgressBar’
ttwa: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  aggregate setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "aggregate")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  TukeyC.aov TukeyC.aovlist TukeyC.default TukeyC.nest TukeyC.nest.aov
  TukeyC.nest.aov TukeyC.nest.aovlist TukeyC.nest.aovlist
  TukeyC.nest.default TukeyC.nest.default plot.TukeyC summary.TukeyC
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
http.connection: no visible global function definition for ‘setNames’
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘gsl’ ‘igraph’ ‘snowfall’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following apparent S3 methods exported but not registered:
  predict.TuneParetoModel print.TuneParetoClassifier
  print.TuneParetoModel print.TuneParetoResult
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘TunePareto/libs/TunePareto.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
accelerate: no visible global function definition for ‘modifyList’
boxplot.turbosim: no visible global function definition for ‘par’
boxplot.turbosim: no visible global function definition for ‘axis’
boxplot.turbosim: no visible global function definition for ‘mtext’
dataprof.turbosim: no visible global function definition for ‘quantile’
dataprof.turbosim: no visible global function definition for ‘par’
dataprof.turbosim: no visible global function definition for ‘plot’
dataprof.turbosim: no visible global function definition for ‘lines’
dataprof.turbosim: no visible global function definition for ‘segments’
dataprof.turbosim: no visible global function definition for ‘legend’
line.search: no visible global function definition for ‘optimize’
pairs.turbosim: no visible global function definition for ‘par’
pairs.turbosim: no visible global function definition for ‘plot’
pairs.turbosim: no visible global function definition for ‘legend’
pairs.turbosim: no visible global function definition for ‘axis’
pairs.turbosim: no visible global function definition for ‘title’
pairs.turbosim: no visible global function definition for ‘coef’
pairs.turbosim: no visible global function definition for ‘abline’
pairs.turbosim: no visible global function definition for ‘text’
plot.turbo: no visible global function definition for ‘plot’
plot.turbo: no visible global function definition for ‘lines’
plot.turbo: no visible global function definition for ‘legend’
turboSim: no visible binding for global variable ‘par’
turboem: no visible global function definition for ‘modifyList’
Undefined global functions or variables:
  abline axis coef legend lines modifyList mtext optimize par plot
  quantile segments text title
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "mtext",
             "par", "plot", "segments", "text", "title")
  importFrom("stats", "coef", "optimize", "quantile")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
turf: no visible global function definition for ‘read.table’
turf: no visible global function definition for ‘flush.console’
turf.combos: no visible global function definition for ‘combn’
Undefined global functions or variables:
  combn flush.console read.table
Consider adding
  importFrom("utils", "combn", "flush.console", "read.table")
to your NAMESPACE file.
File ‘TUWmodel/libs/TUWmodel.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tvd/libs/tvd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tweenr/libs/tweenr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
TwoCop: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
File ‘TwoCop/libs/TwoCop.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘TwoPhaseInd/libs/TwoPhaseInd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  print.twoStageGwasPower print.twoStageNull
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
condnorm: no visible global function definition for ‘pnorm’
condnorm: no visible global function definition for ‘dnorm’
find.p.joint: no visible global function definition for ‘integrate’
find.p.joint.alt: no visible global function definition for ‘integrate’
termsInt: no visible global function definition for ‘pnorm’
termsInt.alt: no visible global function definition for ‘pnorm’
twoStageNull: no visible global function definition for ‘qnorm’
twoStageNull: no visible global function definition for ‘optimize’
twoStagePower: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dnorm integrate optimize pnorm qnorm
Consider adding
  importFrom("stats", "dnorm", "integrate", "optimize", "pnorm", "qnorm")
to your NAMESPACE file.
Rd file 'twoStageGwasPower.Rd':
  \usage lines wider than 90 characters:
     twoStageGwasPower(pD, pG, grr, inheritance = "multiplicative", pi.samples, pi.markers, alpha.marker, n.cases, n.controls)

These lines will be truncated in the PDF manual.
txtacf: no visible binding for global variable ‘na.fail’
txtacf: no visible global function definition for ‘acf’
txtboxplot : <anonymous>: no visible global function definition for
  ‘boxplot.stats’
txtboxplot: no visible global function definition for ‘boxplot.stats’
txtdensity: no visible global function definition for ‘density’
Undefined global functions or variables:
  acf boxplot.stats density na.fail
Consider adding
  importFrom("grDevices", "boxplot.stats")
  importFrom("stats", "acf", "density", "na.fail")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpY4jywB/treePos/2017_12_17/run’, resetting
Crm: no visible global function definition for ‘integrate’
Crm : <anonymous>: no visible global function definition for
  ‘integrate’
Crm: no visible global function definition for ‘optimize’
ail1: no visible global function definition for ‘uniroot’
ail2 : fu : <anonymous>: no visible global function definition for
  ‘integrate’
ail2: no visible global function definition for ‘uniroot’
aip : fu : <anonymous>: no visible global function definition for
  ‘integrate’
aip: no visible global function definition for ‘uniroot’
ait1: no visible global function definition for ‘uniroot’
ait2 : fu : <anonymous>: no visible global function definition for
  ‘integrate’
ait2: no visible global function definition for ‘uniroot’
sim3p3: no visible global function definition for ‘rbinom’
simCrm: no visible global function definition for ‘rbinom’
simCrm: no visible global function definition for ‘palette’
simCrm: no visible global function definition for ‘gray’
simCrm: no visible global function definition for ‘plot’
simCrm: no visible global function definition for ‘abline’
simCrm: no visible global function definition for ‘lines’
ssim3p3: no visible global function definition for ‘txtProgressBar’
ssim3p3: no visible global function definition for ‘setTxtProgressBar’
ssimCrm: no visible global function definition for ‘txtProgressBar’
ssimCrm: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  abline gray integrate lines optimize palette plot rbinom
  setTxtProgressBar txtProgressBar uniroot
Consider adding
  importFrom("grDevices", "gray", "palette")
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "integrate", "optimize", "rbinom", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
rmd2pdf: no visible global function definition for ‘tail’
rnw2pdf: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
File ‘ucminf/libs/ucminf.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘udunits2/libs/udunits2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Rd file 'dataItemExplorer.Rd':
  \usage lines wider than 90 characters:
       apiurl = "http://marketinformation.natgrid.co.uk/MIPIws-public/public/publicwebservice.asmx")

These lines will be truncated in the PDF manual.
ubRacing : predCandidate: no visible global function definition for
  ‘predict’
ubRacing : aux2.friedman.edit: no visible global function definition
  for ‘pchisq’
ubRacing : aux2.friedman.edit: no visible global function definition
  for ‘qt’
ubRacing : aux.friedman.edit: no visible global function definition for
  ‘wilcox.test’
ubRacing : aux.ttest.edit: no visible global function definition for
  ‘t.test’
ubRacing : aux.ttest.edit: no visible global function definition for
  ‘p.adjust’
ubRacing : idFolds: no visible global function definition for
  ‘quantile’
ubRacing: no visible binding for global variable ‘sd’
ubSmoteExs: no visible global function definition for ‘runif’
Undefined global functions or variables:
  p.adjust pchisq predict qt quantile runif sd t.test wilcox.test
Consider adding
  importFrom("stats", "p.adjust", "pchisq", "predict", "qt", "quantile",
             "runif", "sd", "t.test", "wilcox.test")
to your NAMESPACE file.
med: no visible global function definition for ‘quantile’
uh: no visible global function definition for ‘mad’
uh.bu: no visible global function definition for ‘mad’
Undefined global functions or variables:
  mad quantile
Consider adding
  importFrom("stats", "mad", "quantile")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  predict.uniCox print.uniCoxCVFit print.uniCoxFit
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
permute.rows: no visible global function definition for ‘runif’
uniCox: no visible global function definition for ‘quantile’
uniCoxCV: no visible global function definition for ‘quantile’
uniCoxCV: no visible global function definition for ‘coxph’
uniCoxCV: no visible binding for global variable ‘var’
Undefined global functions or variables:
  coxph quantile runif var
Consider adding
  importFrom("stats", "quantile", "runif", "var")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'predict.uniCox':
  ‘predict.uniCox’

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘uniCox/libs/uniCox.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
dudewicz.unif.test: no visible global function definition for ‘runif’
frosini.unif.test: no visible global function definition for ‘runif’
hegazy.unif.test: no visible global function definition for ‘runif’
kolmogorov.unif.test: no visible global function definition for ‘runif’
kuiper.unif.test: no visible global function definition for ‘runif’
neyman.unif.test: no visible global function definition for ‘runif’
quesenberry.unif.test: no visible global function definition for
  ‘runif’
sarkadi.unif.test: no visible global function definition for ‘runif’
sherman.unif.test: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
cumcount: no visible global function definition for ‘setNames’
uniqtag: no visible global function definition for ‘setNames’
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
Registered S3 methods from standard package(s) overwritten by 'uniqueAtomMat':
  method               from
  unique.matrix        base
  duplicated.matrix    base
  anyDuplicated.matrix base
File ‘unsystation/libs/unsystation.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  +.census +.count plot.census plot.count plot.preston print.preston
  print.summary.count summary.census summary.count
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Found the following apparent S3 methods exported but not registered:
  plot.upclassfit print.upclassfit summary.upclassfit
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.upclassfit: no visible global function definition for ‘frame’
plot.upclassfit: no visible global function definition for ‘par’
plot.upclassfit: no visible global function definition for ‘axis’
plot.upclassfit: no visible global function definition for ‘matplot’
plot.upclassfit: no visible global function definition for ‘legend’
plot.upclassfit: no visible global function definition for ‘title’
Undefined global functions or variables:
  axis frame legend matplot par title
Consider adding
  importFrom("graphics", "axis", "frame", "legend", "matplot", "par",
             "title")
to your NAMESPACE file.
File ‘urca/libs/urca.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘urltools/libs/urltools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘uroot/libs/uroot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘USAboundariesData’
readSEER: no visible global function definition for ‘read.fwf’
Undefined global functions or variables:
  read.fwf
Consider adding
  importFrom("utils", "read.fwf")
to your NAMESPACE file.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘UScensus2000cdp/R/zzz.R’:
  .First.lib calls:
    cat(paste("'", ehelp[4], "'\n", "Version ", ehelp[2], " created on ",     ehelp[3], ".\n", sep = ""))
    cat(paste(substring(ehelp[3], first = 16), "\n", "Version ",     substring(ehelp[4], first = 16), " created on ", substring(ehelp[5],         first = 16), ".\n", sep = ""))
    cat(paste("copyright (c) 2009, Zack W. Almquist, University of California-Irvine\n",     sep = ""))
    cat("For citation information, type citation(\"UScensus2000cdp\").\n")
    cat("Type help(package=\"UScensus2000cdp\") to get started.\n")

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

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.
'library' or 'require' call to ‘rgdal’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘foreign’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'MSA.Rd':
  \usage lines wider than 90 characters:
     MSA(msafips = NULL, msaname = NULL, state=NULL , statefips=FALSE, level = c("tract", "blk", "blkgrp"), proj = NULL)

Rd file 'areaPoly.Rd':
  \examples lines wider than 100 characters:
     choropleth(oregon.county10,"den00",color = list(fun = "rainbow", attr = list(4)),main="2010 US Counties \n Oregon",type="plot",border=" ... [TRUNCATED]

Rd file 'choropleth.Rd':
  \usage lines wider than 90 characters:
     choropleth(sp, dem = "P0010001", cuts = list("quantile", seq(0, 1, 0.25)), color = list(fun = "hsv", attr = list(h = c(0.4, 0.5, 0.6, 0 ... [TRUNCATED]
  \examples lines wider than 100 characters:
     choropleth(oregon.county10,"P0010001",color = list(fun = "rainbow", attr = list(4)),main="2010 Counties \n Oregon",type="plot",border=" ... [TRUNCATED]
     choropleth(oregon.county10,"P0010001",main="2010 Counties \n Oregon",border="transparent",type="spplot")

Rd file 'choropleth.plot.Rd':
  \usage lines wider than 90 characters:
     choropleth.plot(sp, dem = "P0010001", cuts = list("quantile", seq(0, 1, 0.25)), color = list(fun = "hsv", attr = list(h = c(0.4, 0.5, 0 ... [TRUNCATED]

Rd file 'choropleth.spplot.Rd':
  \usage lines wider than 90 characters:
     choropleth.spplot(sp, dem = "P0010001", cuts = list("quantile", seq(0, 1, 0.25)), color = list(fun = "hsv", attr = list(h = c(0.4, 0.5, ... [TRUNCATED]

Rd file 'county.Rd':
  \usage lines wider than 90 characters:
     county(fips = NULL, name = NULL, state, level = c("tract", "blk", "blkgrp"), statefips = FALSE, sp.object=NULL, proj=NULL)

These lines will be truncated in the PDF manual.
File ‘utf8latex/libs/utf8latex.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘uuid/libs/uuid.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘gen_uuid.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘gen_uuid.o’
File ‘uuid/libs/uuid.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
histw: no visible global function definition for ‘plot.new’
histw: no visible global function definition for ‘plot.window’
histw: no visible global function definition for ‘axis’
histw: no visible global function definition for ‘rect’
histw: no visible global function definition for ‘lines’
uwham.boot: no visible binding for global variable ‘var’
Undefined global functions or variables:
  axis lines plot.new plot.window rect var
Consider adding
  importFrom("graphics", "axis", "lines", "plot.new", "plot.window",
             "rect")
  importFrom("stats", "var")
to your NAMESPACE file.
Packages suggested but not available for checking: ‘vaers’ ‘vaersND’
File ‘validatejsonr/libs/validatejsonr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘valorate/libs/valorate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘valuer/libs/valuer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/News.Rmd’
(Is a VignetteBuilder field missing?)
File ‘varband/libs/varband.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘VariABEL/libs/VariABEL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard file/directory found at top level:
  ‘Todo’
Packages in Depends field not imported from:
  ‘MASS’ ‘strucchange’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
black_scholes: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
burdenPlot: no visible global function definition for ‘density’
burdenPlot: no visible global function definition for ‘axis’
burdenPlot: no visible global function definition for ‘points’
burdenPlot: no visible global function definition for ‘lines’
burdenPlot: no visible global function definition for ‘abline’
burdenPlot: no visible global function definition for ‘text’
burdenPlot: no visible global function definition for ‘sd’
burdenPlot: no visible global function definition for ‘segments’
vbdm: no visible global function definition for ‘var’
vbdm: no visible global function definition for ‘pchisq’
vbdmR : run_discrete_mixture_vanilla: no visible global function
  definition for ‘var’
vbdmR: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  abline axis density lines pchisq points sd segments text var
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "points", "segments",
             "text")
  importFrom("stats", "density", "pchisq", "sd", "var")
to your NAMESPACE file.
File ‘vbdm/libs/vbdm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘VBLPCM/libs/VBLPCM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
compute_KL : rtnorm: no visible global function definition for ‘runif’
compute_KL : rtnorm: no visible global function definition for ‘dnorm’
compute_KL: no visible global function definition for ‘qnorm’
compute_KL: no visible global function definition for ‘dnorm’
compute_KL: no visible global function definition for ‘pnorm’
compute_KL: no visible global function definition for ‘var’
compute_KL: no visible global function definition for ‘rbinom’
compute_KL: no visible global function definition for ‘rnorm’
compute_KL: no visible global function definition for ‘sd’
vbsr: no visible global function definition for ‘qchisq’
vbsr: no visible global function definition for ‘var’
vbsr: no visible global function definition for ‘pchisq’
vbsr: no visible global function definition for ‘sd’
vbsr: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  dnorm pchisq pnorm qchisq qnorm rbinom rnorm runif sd var
Consider adding
  importFrom("stats", "dnorm", "pchisq", "pnorm", "qchisq", "qnorm",
             "rbinom", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
File ‘vbsr/libs/vbsr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
cv.vda.le.default: no visible global function definition for ‘predict’
cv.vda.r.default: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
File ‘VDA/libs/VDA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘Vdgraph/libs/Vdgraph.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘vdg/libs/vdg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
calculateParameters,AffineTransformation: no visible global function
  definition for ‘lm’
calculateParameters,AffineTransformation: no visible global function
  definition for ‘coef’
calculateParameters,SimilarityTransformation: no visible global
  function definition for ‘lm’
calculateParameters,SimilarityTransformation: no visible global
  function definition for ‘coef’
plotGridTransformation,Cartesian2DCoordinateTransformation: no visible
  global function definition for ‘points’
plotGridTransformation,Cartesian2DCoordinateTransformation: no visible
  global function definition for ‘legend’
Undefined global functions or variables:
  coef legend lm points
Consider adding
  importFrom("graphics", "legend", "points")
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
vsetdiff : <anonymous>: no visible global function definition for
  ‘head’
Undefined global functions or variables:
  head
Consider adding
  importFrom("utils", "head")
to your NAMESPACE file.
DrawDensity3D: no visible global function definition for ‘colorRamp’
DrawDensity3D: no visible global function definition for ‘rgb’
ReadFromFile3D: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  colorRamp read.table rgb
Consider adding
  importFrom("grDevices", "colorRamp", "rgb")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'library' or 'require' call to ‘stats’ which was already attached by Depends.
  Please remove these calls from your code.
H: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = H, func.arg = list(func.arg), boot.arg)):
  partial argument match of ‘arg’ to ‘args’
M.homog: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = M.homog, func.arg = list(func.arg),
  boot.arg)): partial argument match of ‘arg’ to ‘args’
Rel.homog: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = Rel.homog, func.arg = list(func.arg),
  boot.arg)): partial argument match of ‘arg’ to ‘args’
bootstrap: warning in do.call(what = func, arg = list(boots[, , i])):
  partial argument match of ‘arg’ to ‘args’
bootstrap: warning in do.call(what = func, arg = c(abundances =
  list(boots[, , i]), func.arg)): partial argument match of ‘arg’ to
  ‘args’
d: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = d, func.arg = list(func.arg), boot.arg)):
  partial argument match of ‘arg’ to ‘args’
sim.groups: warning in do.call(what = bootstrap, arg = c(abundances =
  list(rbind(scores[i, ], scores[j, ])), func = similarity, func.arg =
  list(func.arg), boot.arg)): partial argument match of ‘arg’ to ‘args’
sim.table: warning in do.call(what = bootstrap, arg = c(abundances =
  list(rbind(scores[i, ], scores[j, ])), func = similarity, func.arg =
  list(func.arg), boot.arg)): partial argument match of ‘arg’ to ‘args’
similarity: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = similarity, func.arg = list(func.arg),
  boot.arg)): partial argument match of ‘arg’ to ‘args’
turnover: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = turnover, func.arg = list(func.arg),
  boot.arg)): partial argument match of ‘arg’ to ‘args’
prepare_Rd: H.Rd:41-42: Dropping empty section \note
prepare_Rd: M.homog.Rd:19-21: Dropping empty section \details
prepare_Rd: M.homog.Rd:35-36: Dropping empty section \note
prepare_Rd: Rel.homog.Rd:24-25: Dropping empty section \note
prepare_Rd: bootstrap.Rd:34: Dropping empty section \note
prepare_Rd: d.Rd:35-36: Dropping empty section \note
prepare_Rd: normalize.rows.Rd:26-27: Dropping empty section \note
prepare_Rd: p.q.sum.Rd:23-24: Dropping empty section \note
prepare_Rd: p.q.sum.Rd:26: Dropping empty section \examples
prepare_Rd: sim.groups.Rd:27-28: Dropping empty section \note
prepare_Rd: sim.table.Rd:25-26: Dropping empty section \note
prepare_Rd: similarity.Rd:25-26: Dropping empty section \note
prepare_Rd: turnover.Rd:17-18: Dropping empty section \details
prepare_Rd: turnover.Rd:29-30: Dropping empty section \note
plot.VennDiagram : <anonymous>: no visible global function definition
  for ‘hcl’
plot.VennDiagram: no visible global function definition for ‘plot.new’
plot.VennDiagram: no visible global function definition for
  ‘plot.window’
plot.VennDiagram: no visible global function definition for ‘col2rgb’
plot.VennDiagram: no visible global function definition for ‘rgb’
plot.VennDiagram: no visible global function definition for ‘polygon’
plot.VennDiagram: no visible global function definition for ‘text’
plot.VennDiagram: no visible global function definition for ‘title’
Undefined global functions or variables:
  col2rgb hcl plot.new plot.window polygon rgb text title
Consider adding
  importFrom("grDevices", "col2rgb", "hcl", "rgb")
  importFrom("graphics", "plot.new", "plot.window", "polygon", "text",
             "title")
to your NAMESPACE file.
File ‘vertexenum/libs/vertexenum.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘VideoComparison/libs/VideoComparison.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘VIFCP/libs/VIFCP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
vif: no visible global function definition for ‘sd’
vif: no visible global function definition for ‘lm’
vif: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  lm pnorm sd
Consider adding
  importFrom("stats", "lm", "pnorm", "sd")
to your NAMESPACE file.
Rd file 'vif.Rd':
  \usage lines wider than 90 characters:
             vif(y, x, w0 = 0.05, dw = 0.05, subsize = 200, trace = TRUE, mode = c("dense", "sparse"))
  \examples lines wider than 100 characters:
             vif.sel <- vif(housingexp$y, housingexp$x, w0 = 0.0005, dw = 0.005, subsize = 300, trace = FALSE);

These lines will be truncated in the PDF manual.
hyperpara: no visible binding for global variable ‘var’
hyperpara: no visible global function definition for ‘hist’
Undefined global functions or variables:
  hist var
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "var")
to your NAMESPACE file.
File ‘VIGoR/libs/VIGoR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘vines/libs/vines.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
panel.meansdplot : meansdplot.stats: no visible global function
  definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
prepare_Rd: panel.meansdplot.Rd:42-45: Dropping empty section \value
prepare_Rd: panel.meansdplot.Rd:49-51: Dropping empty section \note
prepare_Rd: panel.violinm.Rd:40-42: Dropping empty section \details
prepare_Rd: panel.violinm.Rd:43-49: Dropping empty section \value
prepare_Rd: panel.violinm.Rd:53-55: Dropping empty section \note
prepare_Rd: panel.violinm.Rd:50-52: Dropping empty section \author
prepare_Rd: violinmplot.Rd:34-36: Dropping empty section \details
prepare_Rd: violinmplot.Rd:48-50: Dropping empty section \note
Package in Depends field not imported from: ‘sm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
vioplot: no visible global function definition for ‘quantile’
vioplot: no visible global function definition for ‘median’
vioplot: no visible global function definition for ‘plot.new’
vioplot: no visible global function definition for ‘plot.window’
vioplot: no visible global function definition for ‘axis’
vioplot: no visible global function definition for ‘box’
vioplot: no visible global function definition for ‘polygon’
vioplot: no visible global function definition for ‘lines’
vioplot: no visible global function definition for ‘rect’
vioplot: no visible global function definition for ‘points’
Undefined global functions or variables:
  axis box lines median plot.new plot.window points polygon quantile
  rect
Consider adding
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "points", "polygon", "rect")
  importFrom("stats", "median", "quantile")
to your NAMESPACE file.
viopoints.default: no visible global function definition for ‘par’
viopoints.default: no visible global function definition for ‘plot.new’
viopoints.default: no visible global function definition for
  ‘plot.window’
viopoints.default: no visible global function definition for ‘axis’
viopoints.default: no visible global function definition for ‘arrows’
viopoints.default: no visible global function definition for
  ‘getFromNamespace’
viopoints.default: no visible global function definition for ‘title’
viopoints.default: no visible global function definition for ‘box’
Undefined global functions or variables:
  arrows axis box getFromNamespace par plot.new plot.window title
Consider adding
  importFrom("graphics", "arrows", "axis", "box", "par", "plot.new",
             "plot.window", "title")
  importFrom("utils", "getFromNamespace")
to your NAMESPACE file.
File ‘vita/libs/vita.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Decile.Plot: no visible global function definition for ‘barplot’
Decile.Plot: no visible global function definition for ‘axis’
Sliding.Window: no visible global function definition for ‘plot’
Sliding.Window: no visible global function definition for ‘lines’
Sliding.Window: no visible global function definition for ‘legend’
Undefined global functions or variables:
  axis barplot legend lines plot
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines", "plot")
to your NAMESPACE file.
RCplot: no visible global function definition for ‘residuals’
RCplot: no visible global function definition for ‘predict’
RCplot: no visible global function definition for ‘par’
RCplot: no visible global function definition for ‘plot.new’
RCplot: no visible global function definition for ‘plot.window’
RCplot: no visible global function definition for ‘strwidth’
RCplot: no visible global function definition for ‘plot’
RCplot: no visible global function definition for ‘abline’
RCplot: no visible global function definition for ‘text’
RCplot: no visible global function definition for ‘mtext’
fitted.vlmc: no visible global function definition for ‘predict’
print.vlmc: no visible global function definition for ‘AIC’
residuals.vlmc: no visible global function definition for ‘predict’
simulate.vlmc: no visible global function definition for ‘runif’
summary.vlmc: no visible global function definition for ‘predict’
vlmc: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  AIC abline mtext par plot plot.new plot.window predict qchisq
  residuals runif strwidth text
Consider adding
  importFrom("graphics", "abline", "mtext", "par", "plot", "plot.new",
             "plot.window", "strwidth", "text")
  importFrom("stats", "AIC", "predict", "qchisq", "residuals", "runif")
to your NAMESPACE file.
File ‘VLMC/libs/VLMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
voss1d: no visible global function definition for ‘approx’
voss1d: no visible global function definition for ‘rnorm’
voss1g: no visible global function definition for ‘dchisq’
voss1g: no visible global function definition for ‘approx’
voss1g: no visible global function definition for ‘rnorm’
voss2d: no visible global function definition for ‘rnorm’
voss2g: no visible global function definition for ‘dchisq’
voss2g: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  approx dchisq rnorm
Consider adding
  importFrom("stats", "approx", "dchisq", "rnorm")
to your NAMESPACE file.
add.spread.vowelplot: no visible global function definition for
  ‘points’
add.spread.vowelplot: no visible binding for global variable ‘mtext’
add.spread.vowelplot: no visible global function definition for ‘lines’
add.spread.vowelplot: no visible global function definition for
  ‘prcomp’
add.spread.vowelplot: no visible global function definition for
  ‘arrows’
add.spread.vowelplot: no visible global function definition for
  ‘legend’
add.spread.vowelplot: no visible global function definition for ‘text’
add.vowelplot: no visible global function definition for ‘points’
add.vowelplot: no visible binding for global variable ‘mtext’
add.vowelplot: no visible global function definition for ‘arrows’
add.vowelplot: no visible global function definition for ‘text’
compute.medians: no visible global function definition for ‘median’
compute.sds: no visible global function definition for ‘sd’
load.vowels: no visible global function definition for ‘read.table’
norm.lobanov: no visible global function definition for ‘sd’
vowelplot: no visible global function definition for ‘plot’
vowelplot: no visible global function definition for ‘legend’
vowelplot: no visible global function definition for ‘arrows’
vowelplot: no visible global function definition for ‘text’
Undefined global functions or variables:
  arrows legend lines median mtext plot points prcomp read.table sd
  text
Consider adding
  importFrom("graphics", "arrows", "legend", "lines", "mtext", "plot",
             "points", "text")
  importFrom("stats", "median", "prcomp", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'library' or 'require' call to ‘raster’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
level: no visible global function definition for ‘quantile’
obj.rec: no visible global function definition for ‘txtProgressBar’
obj.rec: no visible global function definition for ‘setTxtProgressBar’
project: no visible global function definition for ‘aggregate’
raster.proj: no visible global function definition for ‘quantile’
raster.proj: no visible global function definition for ‘rasterFromXYZ’
raster.proj: no visible global function definition for ‘plot.new’
raster.proj: no visible global function definition for ‘plot’
raster.proj: no visible global function definition for ‘legend’
sub.obj: no visible global function definition for ‘aggregate’
sub.obj: no visible global function definition for ‘txtProgressBar’
sub.obj: no visible global function definition for ‘setTxtProgressBar’
surface: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  aggregate legend plot plot.new quantile rasterFromXYZ
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "legend", "plot", "plot.new")
  importFrom("stats", "aggregate", "quantile")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
'library' or 'require' call to ‘misc3d’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.vscc: no visible global function definition for ‘rainbow’
plot.vscc: no visible global function definition for ‘pairs’
Undefined global functions or variables:
  pairs rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "pairs")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘vwr-Ex.R’
Packages in Depends field not imported from:
  ‘lattice’ ‘latticeExtra’ ‘stringdist’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ald: no visible global function definition for ‘detectCores’
ald: no visible global function definition for ‘mclapply’
coltheart.N: no visible global function definition for ‘detectCores’
coltheart.N: no visible global function definition for ‘mclapply’
hamming.distance: no visible global function definition for
  ‘stringdist’
ldknn: no visible global function definition for ‘detectCores’
ldknn: no visible global function definition for ‘mclapply’
ldknn.odds: no visible global function definition for ‘glm’
ldknn.odds: no visible binding for global variable ‘binomial’
ldknn.odds: no visible global function definition for ‘coefficients’
levenshtein.damerau.distance: no visible global function definition for
  ‘stringdist’
levenshtein.distance: no visible global function definition for
  ‘stringdist’
plot.ldknn.run: no visible global function definition for ‘histogram’
plot.ldknn.run: no visible global function definition for
  ‘theEconomist.theme’
plot.ldknn.run: no visible global function definition for ‘xyplot’
plot.ldknn.run: no visible global function definition for ‘as.layer’
Undefined global functions or variables:
  as.layer binomial coefficients detectCores glm histogram mclapply
  stringdist theEconomist.theme xyplot
Consider adding
  importFrom("stats", "binomial", "coefficients", "glm")
to your NAMESPACE file.
Package in Depends field not imported from: ‘Rcpp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'waffect-package.Rd':
  \examples lines wider than 100 characters:
     ## Not run: Typical usage to simulate case/control phenotypes under H1 (in this example: 5 individuals, 2 cases, 3 controls, the probab ... [TRUNCATED]
     ## Not run: Simulation of phenotypes in the multiclass case (in this example: 4 individuals and  3 classes, 1 individual in class 1, 2  ... [TRUNCATED]

Rd file 'waffect.Rd':
  \examples lines wider than 100 characters:
     ## Not run: Typical usage to simulate case/control phenotypes under H1 (in this example: 12 individuals, 7 cases, 5 controls, the proba ... [TRUNCATED]
     waffect(prob =  c(0.2, 0.4, 0.9, 0.6, 0.9, 0.1, 0.4, 0.6, 0.6, 0.3, 0.8, 0.1), count=c(7,5), label=c(1,0))
     waffect(prob =  c(0.2, 0.4, 0.9, 0.6, 0.9, 0.1, 0.4, 0.6, 0.6, 0.3, 0.8, 0.1), count=c(7,5), label=c(1,0))
     waffect(prob =  c(0.2, 0.4, 0.9, 0.6, 0.9, 0.1, 0.4, 0.6, 0.6, 0.3, 0.8, 0.1), count=7, label=c(1,0))
     ## Not run: If prob is not specified then a constant vector of probabilities is assumed by default. This is equivalent to simulate phen ... [TRUNCATED]

These lines will be truncated in the PDF manual.
File ‘waffect/libs/waffect.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘waffect.o’
File ‘waffect/libs/waffect.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
summary.whc: no visible global function definition for ‘printCoefmat’
wahc.fit: no visible global function definition for ‘pt’
wahc.fit: no visible global function definition for ‘cor’
whc: no visible global function definition for ‘model.frame’
whc: no visible global function definition for ‘model.matrix’
whc: no visible global function definition for ‘model.response’
Undefined global functions or variables:
  cor model.frame model.matrix model.response printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.frame", "model.matrix",
             "model.response", "printCoefmat", "pt")
to your NAMESPACE file.
File ‘wand/libs/wand.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpbmfUQP’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpbmfUQP’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpbmfUQP’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpbmfUQP’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpbmfUQP’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpbmfUQP’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpbmfUQP’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpbmfUQP’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpbmfUQP’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpbmfUQP’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpbmfUQP’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpbmfUQP’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpbmfUQP’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpbmfUQP’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpbmfUQP’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpbmfUQP’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpbmfUQP’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpbmfUQP’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpbmfUQP’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpbmfUQP’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpbmfUQP’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpbmfUQP’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpbmfUQP’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpbmfUQP’, resetting
Examples with CPU or elapsed time > 5s
           user system elapsed
coor.test 7.168  0.036   7.206
Rd file 'p.storage.Rd':
  \examples lines wider than 100 characters:
     d.wasim.out <- read.results("", "weisseritz",ts.length=21937,subcatchments=2, ending="ww100.txt")    # Datensatz heisst jetzt d.wasim.o ... [TRUNCATED]
     d.meas.all<-read.table("weisseritz/ww100-rh.txt",header=TRUE, na.strings ="999", skip=4)  # gemessene Daten einlesen

Rd file 'read.results.Rd':
  \examples lines wider than 100 characters:
     d.wasim.out <- read.results("", "weisseritz",ts.length=21937,subcatchments=2, ending="ww100.txt")    # Datensatz heisst jetzt d.wasim.o ... [TRUNCATED]

Rd file 'wasim-package.Rd':
  \examples lines wider than 100 characters:
     d.wasim.out <- read.results("", "weisseritz",ts.length=21937,subcatchments=2, ending="ww100.txt")    # Datensatz heisst jetzt d.wasim.o ... [TRUNCATED]
     d.meas.all<-read.table("weisseritz/ww100-rh.txt",header=TRUE, na.strings ="999", skip=4)  # gemessene Daten einlesen

These lines will be truncated in the PDF manual.
Found the following apparent S3 methods exported but not registered:
  plot.wb
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.wb: no visible global function definition for ‘plot’
plot.wb: no visible global function definition for ‘lines’
power.sum: no visible global function definition for ‘plot’
power.sum: no visible global function definition for ‘lines’
test.data: no visible global function definition for ‘var’
test.data: no visible global function definition for ‘rnorm’
test.data: no visible global function definition for ‘plot’
test.data: no visible global function definition for ‘lines’
wave.band: no visible binding for global variable ‘var’
wave.band: no visible global function definition for ‘pnorm’
wave.band: no visible global function definition for ‘qnorm’
wave.band: no visible global function definition for ‘plot’
wave.band: no visible global function definition for ‘lines’
wb.johnson.lims: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  lines plot pnorm qnorm rnorm var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "pnorm", "qnorm", "rnorm", "var")
to your NAMESPACE file.
File ‘waveband/libs/waveband.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  plot.wvd summary.wvd
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'FWaveD.Rd':
  \usage lines wider than 90 characters:
     FWaveD(y, g = 1, L = 3, deg = 3, F = (log2(length(y)) - 1), thr = rep(0, log2(length(y))), SOFT = FALSE)

Rd file 'WaveD.Rd':
  \usage lines wider than 90 characters:
     WaveD(yobs, g = c(1, rep(0, (length(yobs) - 1))), MC = FALSE, SOFT = FALSE, F = find.j1(g, scale(yobs))[2], L = 3, deg = 3, eta = sqrt( ... [TRUNCATED]

Rd file 'multires.Rd':
  \usage lines wider than 90 characters:
     multires(wcUntrimmed, lowest = 3, coarse = 3, highestplot = NULL, descending = FALSE, sc = 1)

These lines will be truncated in the PDF manual.
Found the following apparent S3 methods exported but not registered:
  plot.dwt plot.dwt.multiple plot.modwt print.dwt print.modwt
  print.wt.filter summary.dwt summary.modwt summary.wt.filter
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘wavelets/libs/wavelets.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  plot.dwt.2d
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘waveslim/libs/waveslim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘wavethresh/libs/wavethresh.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
changepoints.sbs: no visible global function definition for ‘mad’
changepoints.wbs: no visible global function definition for ‘var’
changepoints.wbs: no visible global function definition for ‘quantile’
plot.sbs: no visible global function definition for ‘ts.plot’
plot.sbs: no visible global function definition for ‘lines’
plot.sbs: no visible global function definition for ‘title’
random.intervals: no visible global function definition for ‘runif’
sbs.default: no visible global function definition for ‘var’
wbs.default: no visible global function definition for ‘var’
Undefined global functions or variables:
  lines mad quantile runif title ts.plot var
Consider adding
  importFrom("graphics", "lines", "title")
  importFrom("stats", "mad", "quantile", "runif", "ts.plot", "var")
to your NAMESPACE file.
File ‘wbs/libs/wbs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Quitting from lines 240-250 (Using_the_wbstats_package.Rmd) 
Error: processing vignette ‘Using_the_wbstats_package.Rmd’ failed with diagnostics:
argument is of length zero
Execution halted
File ‘wbsts/libs/wbsts.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  knots.WCE
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
onesamplemeantest: no visible global function definition for ‘pnorm’
twosamplemeantest: no visible global function definition for ‘pnorm’
wcq: no visible global function definition for ‘var’
wcq: no visible global function definition for ‘pnorm’
wcq.fdrc: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  p.adjust pnorm var
Consider adding
  importFrom("stats", "p.adjust", "pnorm", "var")
to your NAMESPACE file.
Package in Depends field not imported from: ‘RJSONIO’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
WDI: no visible binding for global variable ‘WDI_data’
WDIcache: no visible global function definition for ‘fromJSON’
WDIsearch: no visible binding for global variable ‘WDI_data’
Undefined global functions or variables:
  WDI_data fromJSON
File ‘webreadr/libs/webreadr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Title field: should not end in a period.
Deprecated license: BSD
Non-standard file/directory found at top level:
  ‘webvis_0.0.1.tar.gz’
Found the following apparent S3 methods exported but not registered:
  +.webvis
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘webvis/R/zzz.R’:
  .onLoad calls:
    print("Welcome to the webvis pacakge.")

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

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

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘weco/libs/weco.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Weighted.Box.test: no visible global function definition for ‘acf’
Weighted.Box.test: no visible binding for global variable ‘na.pass’
Weighted.Box.test: no visible global function definition for ‘pgamma’
Weighted.Box.test: no visible global function definition for ‘pchisq’
Weighted.LM.test: no visible global function definition for ‘acf’
Weighted.LM.test: no visible binding for global variable ‘na.pass’
Weighted.LM.test: no visible global function definition for ‘pgamma’
Undefined global functions or variables:
  acf na.pass pchisq pgamma
Consider adding
  importFrom("stats", "acf", "na.pass", "pchisq", "pgamma")
to your NAMESPACE file.
File ‘weightedScores/libs/weightedScores.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘sbw’
File ‘weights/libs/weights.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
print.palette: no visible global function definition for ‘par’
print.palette: no visible global function definition for ‘image’
print.palette: no visible global function definition for ‘rect’
print.palette: no visible global function definition for ‘rgb’
print.palette: no visible global function definition for ‘text’
wes_palette: no visible global function definition for
  ‘colorRampPalette’
Undefined global functions or variables:
  colorRampPalette image par rect rgb text
Consider adding
  importFrom("grDevices", "colorRampPalette", "rgb")
  importFrom("graphics", "image", "par", "rect", "text")
to your NAMESPACE file.
Package in Depends field not imported from: ‘snpStats’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Z.value: no visible global function definition for ‘sd’
Z.value: no visible global function definition for ‘pnorm’
pairtest: no visible global function definition for ‘is’
pairtest: no visible global function definition for ‘new’
pairtest: no visible global function definition for ‘rbind2’
pairtest: no visible global function definition for ‘p.value’
pairtest: no visible global function definition for ‘single.snp.tests’
scoretest: no visible global function definition for ‘pchisq’
varplot : <anonymous>: no visible global function definition for ‘var’
varplot: no visible global function definition for ‘plot’
varplot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline is new p.value pchisq plot pnorm rbind2 sd single.snp.tests
  var
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("methods", "is", "new", "rbind2")
  importFrom("stats", "pchisq", "pnorm", "sd", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' call to ‘markdown’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
dlog.norm: no visible global function definition for ‘rnorm’
fun.load.hals.a: no visible global function definition for ‘sfExport’
fun.load.hals.a: no visible global function definition for ‘sfLibrary’
fun.load.hals.fill: no visible global function definition for
  ‘sfExport’
fun.load.hals.fill: no visible global function definition for
  ‘sfLibrary’
fun.load.widals.a: no visible global function definition for ‘sfExport’
fun.load.widals.a: no visible global function definition for
  ‘sfLibrary’
fun.load.widals.fill: no visible global function definition for
  ‘sfExport’
fun.load.widals.fill: no visible global function definition for
  ‘sfLibrary’
unif.mh: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rnorm runif sfExport sfLibrary
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
File ‘widals/libs/widals.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls in package code:
  ‘genefilter’ ‘parallel’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.onAttach: no visible global function definition for
  ‘packageDescription’
.relax.cvcompute: no visible binding for global variable
  ‘weighted.mean’
.relax.widenet.cv.elnet: no visible global function definition for
  ‘predict’
.relax.widenet.cv.elnet: no visible binding for global variable
  ‘weighted.mean’
.relax.widenet.cv.lognet: no visible global function definition for
  ‘predict’
.relax.widenet.cv.lognet: no visible binding for global variable
  ‘weighted.mean’
.widenet.cv.elnet: no visible global function definition for ‘predict’
.widenet.cv.elnet: no visible binding for global variable
  ‘weighted.mean’
.widenet.cv.lognet: no visible global function definition for ‘predict’
.widenet.cv.lognet: no visible binding for global variable
  ‘weighted.mean’
predict.widenet: no visible global function definition for ‘predict’
screen.cor : <anonymous>: no visible global function definition for
  ‘var’
screen.cor : <anonymous>: no visible global function definition for
  ‘cor.test’
screen.ttest: no visible global function definition for ‘colttests’
widenet: no visible global function definition for ‘mc.reset.stream’
widenet: no visible global function definition for ‘mclapply’
widenet: no visible global function definition for ‘predict’
Undefined global functions or variables:
  colttests cor.test mc.reset.stream mclapply packageDescription
  predict var weighted.mean
Consider adding
  importFrom("stats", "cor.test", "predict", "var", "weighted.mean")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
File ‘widenet/libs/widenet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Bundesliga.Mannschaft: no visible global function definition for ‘data’
Bundesliga.Mannschaft: no visible binding for global variable
  ‘Bundesliga’
Bundesliga.Tabelle: no visible global function definition for ‘data’
Bundesliga.Tabelle: no visible binding for global variable ‘Bundesliga’
Bundesliga.XML: no visible global function definition for ‘data’
Bundesliga.XML: no visible binding for global variable ‘Bundesliga’
sens.spec: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘wikibooks/R/Bundesliga.Mannschaft.R’:
  data(Bundesliga)
File ‘wikibooks/R/Bundesliga.Tabelle.R’:
  data(Bundesliga)
File ‘wikibooks/R/Bundesliga.XML.R’:
  data(Bundesliga)
See section ‘Good practice’ in ‘?data’.
wilcox.selection.split: no visible global function definition for
  ‘pnorm’
wilcox.test2: no visible global function definition for ‘wilcox.test’
Undefined global functions or variables:
  pnorm wilcox.test
Consider adding
  importFrom("stats", "pnorm", "wilcox.test")
to your NAMESPACE file.
Cs: no visible global function definition for ‘wilcox.test’
Don: no visible global function definition for ‘points’
Don: no visible global function definition for ‘chisq.test’
Lixn: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  chisq.test pchisq points wilcox.test
Consider adding
  importFrom("graphics", "points")
  importFrom("stats", "chisq.test", "pchisq", "wilcox.test")
to your NAMESPACE file.
plotTrait: no visible global function definition for ‘plot’
plotTrait: no visible global function definition for ‘points’
plotTrait: no visible global function definition for ‘legend’
test.windex: no visible global function definition for ‘hist’
test.windex: no visible global function definition for ‘abline’
test.windex: no visible global function definition for ‘legend’
windex: no visible global function definition for ‘sd’
windex: no visible global function definition for ‘var’
windex: no visible global function definition for ‘dist’
windex: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  abline dist hist legend plot points quantile sd var
Consider adding
  importFrom("graphics", "abline", "hist", "legend", "plot", "points")
  importFrom("stats", "dist", "quantile", "sd", "var")
to your NAMESPACE file.
File ‘wingui/libs/wingui.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [8s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(withr)
  > 
  > test_check("withr")
  ── 1. Failure: (unknown) (@test-sink.R#50)  ────────────────────────────────────
  readLines(tmp) not identical to "message".
  Lengths differ: 0 is not 1
  
  ── 2. Failure: (unknown) (@test-sink.R#50)  ────────────────────────────────────
  readLines(tmp) not identical to c("message", "message 2").
  Lengths differ: 0 is not 2
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 244 SKIPPED: 0 FAILED: 2
  1. Failure: (unknown) (@test-sink.R#50) 
  2. Failure: (unknown) (@test-sink.R#50) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘wle/libs/wle.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘WMCapacity/libs/WMCapacity.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
dbayes: no visible global function definition for ‘mahalanobis’
dbayes: no visible global function definition for ‘var’
wmd: no visible global function definition for ‘cor’
wmd: no visible global function definition for ‘var’
Undefined global functions or variables:
  cor mahalanobis var
Consider adding
  importFrom("stats", "cor", "mahalanobis", "var")
to your NAMESPACE file.
fit,Leader: no visible global function definition for ‘lm’
plotfit,Leader: no visible global function definition for ‘par’
plotfit,Leader: no visible global function definition for ‘plot’
Undefined global functions or variables:
  lm par plot
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "lm")
to your NAMESPACE file.
File ‘wnominate/libs/wnominate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
prepareData: no visible global function definition for ‘tokenize’
Undefined global functions or variables:
  tokenize
Error in re-building vignettes:
  ...
Auto-disconnecting MySQLConnection
Quitting from lines 27-31 (wordbankr.Rmd) 
Error: processing vignette ‘wordbankr.Rmd’ failed with diagnostics:
nrow(instruments) not greater than 0
Execution halted
'library' or 'require' call to ‘tm’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
File ‘wordcloud/libs/wordcloud.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘plyr’ ‘reshape2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
wordmatch: no visible global function definition for ‘llply’
wordmatch : <anonymous>: no visible global function definition for
  ‘llply’
wordmatch: no visible global function definition for ‘melt’
wordmatch: no visible global function definition for ‘count’
Undefined global functions or variables:
  count llply melt
pickList : <anonymous>: no visible global function definition for
  ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
File ‘wordspace/libs/wordspace.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘wrassp/libs/wrassp.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘wrswoR/libs/wrswoR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘wskm/libs/wskm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Rd file 'simul.wsvm.Rd':
  \usage lines wider than 90 characters:
         simul.wsvm(set.seeds = 123, obs.num = 1000, mu = c(0,0), cov.mat = 0.2*diag(2), X = NULL, Y = NULL)

Rd file 'wsvm.boost.Rd':
  \usage lines wider than 90 characters:
         wsvm.boost(X, Y, new.X, new.Y, c.n, B = 50, kernel.type = list(type = "rbf", par= 0.5), C = 4, eps = 1e-10, plotting = FALSE)

These lines will be truncated in the PDF manual.
File
  inst/LICENCE
will install at top-level and is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
  ‘CONTENTS’
Rd file 'classroom.Rd':
  \examples lines wider than 100 characters:
     {boxplot(classroom.first8$mathgain[classroom.first8$schoolid==i] ~ classroom.first8$classid[classroom.first8$schoolid==i],ylab="Mathgai ... [TRUNCATED]

These lines will be truncated in the PDF manual.
File ‘xgboost/libs/xgboost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
quadplot: no visible global function definition for ‘median’
xgobi: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  median write.table
Consider adding
  importFrom("stats", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
XHWE: no visible global function definition for ‘read.table’
result: no visible global function definition for ‘pchisq’
result: no visible global function definition for ‘rbinom’
result: no visible global function definition for ‘rmultinom’
Undefined global functions or variables:
  pchisq rbinom read.table rmultinom
Consider adding
  importFrom("stats", "pchisq", "rbinom", "rmultinom")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  +.CellStyle CellBlock.default CellStyle.default
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
.xssfcolor: no visible global function definition for ‘col2rgb’
Undefined global functions or variables:
  col2rgb
Consider adding
  importFrom("grDevices", "col2rgb")
to your NAMESPACE file.
R5.value.default: no visible binding for global variable ‘data.table’
R5.value.default: no visible global function definition for
  ‘as.data.table’
R5.value.parse: no visible binding for global variable ‘data.table’
R5.value.parse: no visible global function definition for
  ‘is.data.table’
R5.value.parse: no visible global function definition for
  ‘as.data.table’
stampme: no visible global function definition for ‘flush.console’
stampmsg: no visible global function definition for ‘flush.console’
write.data.table: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  as.data.table data.table flush.console is.data.table write.table
Consider adding
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE file.
File ‘xml2/libs/xml2.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_WriteConnection’
File ‘xml2/libs/xml2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: read_xml
> ### Title: Read HTML or XML.
> ### Aliases: read_xml read_html read_xml.character read_xml.raw
> ###   read_xml.connection
> 
> ### ** Examples
> 
> # Literal xml/html is useful for small examples
> read_xml("<foo><bar /></foo>")
{xml_document}
<foo>
[1] <bar/>
> read_html("<html><title>Hi<title></html>")
{xml_document}
<html>
[1] <head>\n<meta http-equiv="Content-Type" content="text/html; charset=UTF-8 ...
> read_html("<html><title>Hi")
{xml_document}
<html>
[1] <head>\n<meta http-equiv="Content-Type" content="text/html; charset=UTF-8 ...
> 
> # From a local path
> read_html(system.file("extdata", "r-project.html", package = "xml2"))
{xml_document}
<html lang="en">
[1] <head>\n<meta http-equiv="Content-Type" content="text/html; charset=UTF-8 ...
[2] <body>\n    <div class="container page">\n      <div class="row">\n       ...
> 
> # From a url
> cd <- read_xml("http://www.xmlfiles.com/examples/cd_catalog.xml")
Error in doc_parse_raw(x, encoding = encoding, base_url = base_url, as_html = as_html,  : 
  Specification mandate value for attribute async [41]
Calls: read_xml ... read_xml.connection -> read_xml.raw -> doc_parse_raw -> .Call
Execution halted
Non-standard files/directories found at top level:
  ‘Bug.R’ ‘Bugs.html’ ‘Check’ ‘CodeDetails’ ‘DESCRIPTION.in’ ‘Docs’
  ‘FAQ.html’ ‘FIXME_NOW’ ‘GNUmakefile’ ‘GNUmakefile.admin’
  ‘Makevars.in’ ‘MemoryBug.R’ ‘NAMESPACE.in’ ‘NodeFuns’ ‘Notes’
  ‘QuestionSolutions’ ‘README.windows’ ‘Rsamples’ ‘TAGS’
  ‘Todo-orig.html’ ‘Todo.xml’ ‘VersionInfo’ ‘addFinalizer’ ‘checkLinks’
  ‘dotCalls’ ‘expat’ ‘index.html’ ‘index.html.in’ ‘libxml’
  ‘libxml2.9.R’ ‘scrapingData.xml’ ‘testRemoveFinalizers.R’
  ‘testRemoveFinalizers.c’ ‘xpathPointer.xml’
newXMLDoc: no visible binding for global variable ‘doc’
source: no visible binding for global variable ‘use_file’
xmlFlatListTree : f: no visible binding for global variable ‘nodeNames’
xmlFlatListTree : f: no visible binding for global variable ‘idx’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘nodeSet’
xmlFlatListTree : addNode: no visible binding for global variable
  ‘nodeSet’
xmlFlatListTree : addNode: no visible binding for global variable ‘idx’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘nodeNames’
xmlFlatListTree : addNode: no visible binding for global variable
  ‘nodeNames’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘idx’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘parentCount’
xmlFlatListTree : addNode: no visible binding for global variable
  ‘parentCount’
xmlFlatListTree : <anonymous>: no visible binding for global variable
  ‘e’
xmlFlatTree : <anonymous>: no visible binding for global variable ‘e’
[[,XMLCodeFile: possible error in updateIds(doc, save = x): unused
  argument (save = x)
Undefined global functions or variables:
  doc e idx nodeNames nodeSet parentCount use_file
Rd file 'makeClassTemplate.Rd':
  \examples lines wider than 100 characters:
     "<doc><part><name>ABC</name><type>XYZ</type><cost>3.54</cost><status>available</status></part></doc>"

Rd file 'xmlClone.Rd':
  \examples lines wider than 100 characters:
     xmlParse('<doc><author id="dtl"><firstname>Duncan</firstname><surname>Temple Lang</surname></author></doc>')

Rd file 'xmlToS4.Rd':
  \examples lines wider than 100 characters:
      "<doc><part><name>ABC</name><type>XYZ</type><cost>3.54</cost><status>available</status></part></doc>"

These lines will be truncated in the PDF manual.
File ‘XML/libs/XML.so’:
  Found ‘stderr’, possibly from ‘stderr’ (C)
    Object: ‘DocParse.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
LPGM: no visible global function definition for ‘flush.console’
PGM: no visible global function definition for ‘flush.console’
PGM.path.neighborhood: no visible global function definition for
  ‘runif’
PGMSim: no visible global function definition for ‘rpois’
PGMSim: no visible global function definition for ‘par’
WPGMSim: no visible global function definition for ‘rpois’
XMRF.Sim: no visible global function definition for ‘cov2cor’
XMRF.Sim: no visible global function definition for ‘rbinom’
XMRF.Sim: no visible global function definition for ‘rnorm’
glm.generic: no visible global function definition for ‘flush.console’
mymult: no visible global function definition for ‘rmultinom’
plot.GMS: no visible global function definition for ‘pdf’
plot.GMS: no visible global function definition for ‘dev.off’
plotNet: no visible global function definition for ‘pdf’
plotNet: no visible global function definition for ‘dev.off’
print.GMS: no visible global function definition for ‘str’
processSeq: no visible binding for global variable ‘quantile’
processSeq: no visible binding for global variable ‘var’
processSeq: no visible global function definition for ‘ks.test’
rmpois : <anonymous>: no visible global function definition for ‘rpois’
Undefined global functions or variables:
  cov2cor dev.off flush.console ks.test par pdf quantile rbinom
  rmultinom rnorm rpois runif str var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par")
  importFrom("stats", "cov2cor", "ks.test", "quantile", "rbinom",
             "rmultinom", "rnorm", "rpois", "runif", "var")
  importFrom("utils", "flush.console", "str")
to your NAMESPACE file.
File ‘XMRF/libs/XMRF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘XNomial/libs/XNomial.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘xoi/libs/xoi.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘xseq/libs/xseq.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Registered S3 method from a standard package overwritten by 'xts':
  method          from
  as.Date.numeric base
Non-standard file/directory found at top level:
  ‘CONTRIBUTORS’
Found the following apparent S3 methods exported but not registered:
  plot.cca print.F.test.cca print.cca print.summary.cca summary.cca
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘yakmoR/libs/yakmoR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
big.read.table: no visible global function definition for ‘read.table’
big.read.table: no visible global function definition for ‘object.size’
sparkline: no visible global function definition for ‘is.ts’
sparkline: no visible global function definition for ‘time’
sparkline: no visible global function definition for ‘boxplot’
Undefined global functions or variables:
  boxplot is.ts object.size read.table time
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "is.ts", "time")
  importFrom("utils", "object.size", "read.table")
to your NAMESPACE file.
bootstrapswapcurve: no visible global function definition for ‘ts’
fitted: no visible global function definition for ‘ts’
forwardrates: no visible global function definition for ‘ts’
residuals: no visible global function definition for ‘ts’
tZC_NS: no visible global function definition for ‘cmpfun’
tZC_NS_extra: no visible global function definition for ‘cmpfun’
tZC_SV: no visible global function definition for ‘cmpfun’
tZC_SV_extra: no visible global function definition for ‘cmpfun’
ycextra: no visible global function definition for ‘new’
ycinter: no visible global function definition for ‘new’
ycplot: no visible global function definition for ‘par’
ycplot: no visible global function definition for ‘points’
ycplot: no visible global function definition for ‘abline’
ycplot: no visible global function definition for ‘hist’
ycplot: no visible global function definition for ‘lines’
ycplot: no visible global function definition for ‘density’
ycplot: no visible global function definition for ‘qqnorm’
ycplot: no visible global function definition for ‘qqline’
ycsummary: no visible global function definition for ‘shapiro.test’
ycsummary: no visible global function definition for ‘pf’
Undefined global functions or variables:
  abline cmpfun density hist lines new par pf points qqline qqnorm
  shapiro.test ts
Consider adding
  importFrom("graphics", "abline", "hist", "lines", "par", "points")
  importFrom("methods", "new")
  importFrom("stats", "density", "pf", "qqline", "qqnorm",
             "shapiro.test", "ts")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘yCrypticRNAs/libs/yCrypticRNAs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.NS.estimator: no visible global function definition for ‘lm’
.NS.estimator: no visible global function definition for ‘coef’
.NS.estimator: no visible global function definition for ‘na.omit’
.NS.estimator: no visible global function definition for ‘resid’
.NSS.estimator: no visible global function definition for ‘lm’
.NSS.estimator: no visible global function definition for ‘coef’
.NSS.estimator: no visible global function definition for ‘na.omit’
.NSS.estimator: no visible global function definition for ‘resid’
NSrates: no visible global function definition for ‘time’
Nelson.Siegel: no visible global function definition for ‘optimize’
Srates: no visible global function definition for ‘time’
Svensson: no visible global function definition for ‘median’
Svensson: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  coef lm median na.omit optimize resid time
Consider adding
  importFrom("stats", "coef", "lm", "median", "na.omit", "optimize",
             "resid", "time")
to your NAMESPACE file.
Rd file 'ECBYieldCurve.Rd':
  \examples lines wider than 100 characters:
     plot(mat.ECB, ECBYieldCurve[i,], type="o", xlab="Maturities structure in years", ylab="Interest rates values")

Rd file 'FedYieldCurve.Rd':
  \examples lines wider than 100 characters:
     plot(mat, FedYieldCurve[i,], type="o", xlab="Maturities structure in years", ylab="Interest rates values")

These lines will be truncated in the PDF manual.
kmeansN: no visible global function definition for ‘kmeans’
kmeansN: no visible global function definition for ‘aggregate’
kmeansN2: no visible global function definition for ‘aggregate’
kmeansN2: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  aggregate kmeans sd
Consider adding
  importFrom("stats", "aggregate", "kmeans", "sd")
to your NAMESPACE file.
File ‘YplantQMC/libs/YplantQMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘deSolve’ ‘triangle’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Deprecated license: CC BY-SA 2.0 + file LICENSE
Package suggested but not available for checking: ‘zdat’
Found the following apparent S3 methods exported but not registered:
  cbind.zoocat
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'merge':
  ‘cbind.zoocat’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
.getPath: no visible global function definition for ‘predict’
ZIClass: no visible binding for global variable ‘na.omit’
ZIClass: no visible global function definition for ‘predict’
analyzeClass: no visible global function definition for ‘plot’
calibrate : findmax: no visible global function definition for ‘lowess’
calibrate: no visible global function definition for ‘lm’
calibrate: no visible global function definition for ‘anova’
calibrate: no visible global function definition for ‘coef’
focusGraph: no visible global function definition for ‘dev.list’
getTrain: no visible global function definition for ‘na.omit’
makeClass : selectVars: no visible global function definition for
  ‘as.formula’
predict.ZIClass: no visible global function definition for ‘predict’
processSampleAll: no visible global function definition for ‘predict’
viewResults: no visible global function definition for ‘par’
viewResults: no visible global function definition for ‘plot’
viewResults: no visible global function definition for ‘points’
viewResults: no visible global function definition for ‘text’
zidbDrawVignette: no visible global function definition for ‘dev.size’
zidbDrawVignette: no visible global function definition for ‘par’
zidbDrawVignette: no visible global function definition for ‘dev.cur’
zidbDrawVignette: no visible global function definition for
  ‘rasterImage’
zidbPlotNew: no visible global function definition for ‘par’
zidbPlotNew: no visible global function definition for ‘plot’
Undefined global functions or variables:
  anova as.formula coef dev.cur dev.list dev.size lm lowess na.omit par
  plot points predict rasterImage text
Consider adding
  importFrom("grDevices", "dev.cur", "dev.list", "dev.size")
  importFrom("graphics", "par", "plot", "points", "rasterImage", "text")
  importFrom("stats", "anova", "as.formula", "coef", "lm", "lowess",
             "na.omit", "predict")
to your NAMESPACE file.
File which contains pragma(s) suppressing diagnostics:
  ‘src/third_party/zstd-1.2.0/lib/dictBuilder/divsufsort.c’
ztable.glm: no visible global function definition for ‘confint’
ztable.glm: no visible global function definition for ‘coef’
ztable.nls: no visible global function definition for ‘formula’
Undefined global functions or variables:
  coef confint formula
Consider adding
  importFrom("stats", "coef", "confint", "formula")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  confint.zyp
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
confint.zyp: no visible global function definition for ‘qnorm’
confint.zyp: no visible global function definition for ‘var’
zyp.sen: no visible global function definition for ‘terms’
zyp.sen: no visible global function definition for ‘median’
zyp.trend.csv: no visible global function definition for ‘read.csv’
zyp.trend.csv: no visible global function definition for ‘write.csv’
zyp.yuepilon: no visible global function definition for ‘acf’
zyp.yuepilon: no visible binding for global variable ‘na.pass’
zyp.yuepilon: no visible global function definition for ‘confint’
zyp.yuepilon: no visible global function definition for ‘lm’
zyp.zhang: no visible global function definition for ‘acf’
zyp.zhang: no visible binding for global variable ‘na.pass’
zyp.zhang: no visible global function definition for ‘confint’
zyp.zhang: no visible global function definition for ‘lm’
Undefined global functions or variables:
  acf confint lm median na.pass qnorm read.csv terms var write.csv
Consider adding
  importFrom("stats", "acf", "confint", "lm", "median", "na.pass",
             "qnorm", "terms", "var")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/Rtmp3A5Mj2/filematrices’, resetting
Examples with CPU or elapsed time > 5s
                 user system elapsed
multithreadACME 0.662  0.053  22.712
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
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
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 ‘animation-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ani.record
> ### Title: Record and replay animations
> ### Aliases: ani.record ani.replay
> 
> ### ** Examples
> 
> library(animation)
> 
> n = 20
> x = sort(rnorm(n))
> y = rnorm(n)
> ## set up an empty frame, then add points one by one
> par(bg = "white")  # ensure the background color is white
> plot(x, y, type = "n")
> 
> ani.record(reset = TRUE)  # clear history before recording
> 
> for (i in 1:n) {
+     points(x[i], y[i], pch = 19, cex = 2)
+     ani.record()  # record the current frame
+ }
> 
> ## now we can replay it, with an appropriate pause between frames
> oopts = ani.options(interval = 0.5)
> ani.replay()
> 
> ## or export the animation to an HTML page
> saveHTML(ani.replay(), img.name = "record_plot")
Warning in file(con, "w") :
  cannot open file './js/record_plot.js': Permission denied
Error in file(con, "w") : cannot open the connection
Calls: saveHTML -> writeLines -> file
Execution halted
Running examples in ‘anipaths-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: animate_paths
> ### Title: animate paths
> ### Aliases: animate_paths
> 
> ### ** Examples
> 
> ##
> vultures$POSIX <- as.POSIXct(vultures$timestamp, tz = "UTC")
> vultures_paths <- vultures[format(vultures$POSIX, "%Y") == 2009, ]
> animate_paths(paths = vultures_paths,
+               delta.t = "month",
+               coord = c("location.long", "location.lat"),
+               Time.name = "POSIX",
+               ID.name = "individual.local.identifier")

 frame 1 out of 10 (10%) [0.17 seconds]

 frame 2 out of 10 (20%) [0.12 seconds]

 frame 3 out of 10 (30%) [0.09 seconds]

 frame 4 out of 10 (40%) [0.07 seconds]

 frame 5 out of 10 (50%) [0.09 seconds]

 frame 6 out of 10 (60%) [0.09 seconds]

 frame 7 out of 10 (70%) [0.07 seconds]

 frame 8 out of 10 (80%) [0.09 seconds]

 frame 9 out of 10 (90%) [0.07 seconds]

 frame 10 out of 10 (100%) [0.09 seconds]
Warning in file(con, "w") :
  cannot open file './js/Rplot.js': Permission denied
Error in file(con, "w") : cannot open the connection
Calls: animate_paths -> <Anonymous> -> writeLines -> file
Execution halted
Running examples in ‘ApacheLogProcessor-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: read.multiple.apache.access.log
> ### Title: Reads multiple files of apache web server.
> ### Aliases: read.multiple.apache.access.log
> 
> ### ** Examples
> 
> path <- system.file("examples", package="ApacheLogProcessor")
> path <- paste(path, "/", sep="")
> 
> #read multiple gziped logs with the prefix m_access_log_combined_
> dfLog <- read.multiple.apache.access.log(path, "m_access_log_combined_")
[1] "Starting the log processing. This may take a long time..."
[1] "Processing file  m_access_log_combined_1.log.gz"
[1] "Unziping  m_access_log_combined_1.log.gz"
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/ApacheLogProcessor/examples/m_access_log_combined_1.log': Permission denied
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: read.multiple.apache.access.log -> write -> cat -> file
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 358-360 (jss2342.Rnw) 
Error: processing vignette ‘jss2342.Rnw’ failed with diagnostics:
cannot open the connection
Execution halted
Running examples in ‘ASIP-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: arvi
> ### Title: Atmospherically Resistant Vegetation Index
> ### Aliases: arvi
> 
> ### ** Examples
> 
> library (raster)
Loading required package: sp
> library (rgdal)
rgdal: version: 1.2-16, (SVN revision 701)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.2.2, released 2017/09/15
 Path to GDAL shared files: /usr/share/gdal/2.2
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.2-5 
> # Finding the path of the sample satellite image directory.
> # User may define paths directly like "/home/ur_folder" or "C:/ur_folder"
> path <- system.file ("TM_sample", package = "ASIP")
> shapefil <- paste0 (path, "/test.shp")
> arvi (directory = path, crop = "y", ext2crop = shapefil)
OGR data source with driver: ESRI Shapefile 
Source: "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/ASIP/TM_sample/test.shp", layer: "test"
with 1 features
It has 1 fields
Integer64 fields read as strings:  id 
Error in .local(.Object, ...) : Dataset copy failed
Calls: arvi ... <Anonymous> -> new -> initialize -> initialize -> .local -> .Call
Execution halted
Running examples in ‘atsd-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: save_connection
> ### Title: Write connection parameters to configuration file.
> ### Aliases: save_connection
> 
> ### ** Examples
> 
> # Write the current values of the connection parameters to the configuration file
> save_connection()
Warning in writeLines(l, fileConn) :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/atsd/connection.config': Permission denied
Error in writeLines(l, fileConn) : cannot open the connection
Calls: save_connection -> writeLines
Execution halted
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/audio.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: working directory was changed to ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bayesMCClust.Rcheck/bayesMCClust-wd’, resetting
Examples with CPU or elapsed time > 5s
               user system elapsed
mcClustering 12.553  0.058  17.529
Found the following significant warnings:
  Gspline.cpp:1064:29: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ writing 41 bytes into a region of size 20 overflows the destination [-Wstringop-overflow=]
  Gspline.cpp:1065:29: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ writing 49 bytes into a region of size 20 overflows the destination [-Wstringop-overflow=]
  Gspline.cpp:1066:29: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ writing 39 bytes into a region of size 20 overflows the destination [-Wstringop-overflow=]
  classCovMatrix.cpp:231:27: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ writing 16 bytes into a region of size 15 overflows the destination [-Wstringop-overflow=]
  classRandomEff.cpp:248:24: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ writing 14 bytes into a region of size 10 overflows the destination [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bayesSurv.Rcheck/00install.out’ for details.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/Makefile.win
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Error in re-building vignettes:
  ...
Warning in gzfile(file, "wb") :
  cannot open compressed file ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Bchron/data/intcal09.rda’, probable reason ‘Permission denied’
Quitting from lines 279-283 (Bchron.Rmd) 
Error: processing vignette ‘Bchron.Rmd’ failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘bcmaps.rdata’
Found the following significant warnings:
  bcrypt/bcrypt.c:144:24: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=]
  bcrypt/bcrypt.c:254:29: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bcrypt.Rcheck/00install.out’ for details.
Running examples in ‘bibliospec-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Bibliospec-class
> ### Title: R access to Bibliospec File
> ### Aliases: Bibliospec Bibliospec-class bibliospec blib
> 
> ### ** Examples
> 
> 
> library(bibliospec)
> 
> # use the sqlite file provided in the package
> dbfile <- file.path(path.package("bibliospec"),
+  "extdata/peptideStd.sqlite")
> 
> # call constructor
> BS <- Bibliospec(dbfile=dbfile)
database connected
> 
> # test; should return TRUE
> BS$getNrPSM() == 137
     count(*)
[1,]     TRUE
> 
> S <- BS$getPsmSet()
SELECT RefSpectra.id as RefSpectraId, numPeaks,  peptideSeq,
precursorCharge, precursorMZ, retentionTime,
peptideModSeq, score, SpectrumSourceFiles.fileName
FROM SpectrumSourceFiles, RefSpectra
WHERE SpectrumSourceFiles.id = RefSpectra.fileID;
getspectra
preparing Peaks as a list, will take a while if you blib file is large.
 extracted MZ
 extracted Intensity
assigning 28 modifications ...
> 
> ## Not run: 
> ##D  library(specL)
> ##D  print(S)
> ##D  lapply(S[1:10], plot)
> ## End(Not run)
> 
> peaks <- BS$getPeaks()
getspectra
preparing Peaks, will take a while if you blib file is large.
 extracted MZ
 extracted Intensity
to data frame
Error in rsqlite_send_query(conn@ptr, statement) : 
  attempt to write a readonly database
Calls: <Anonymous> ... initialize -> initialize -> rsqlite_send_query -> .Call
Execution halted
finalize
[1] "disconnected"
Running examples in ‘biclique-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bi.format
> ### Title: Add number of vertices and edges to the input file
> ### Aliases: bi.format
> 
> ### ** Examples
> 
> bi.format(system.file("extdata", "example2.el", package = "biclique"))
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/biclique/extdata/example2.el': Permission denied
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: bi.format -> cat -> file
Execution halted
Running examples in ‘BigQuic-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BigQuic
> ### Title: Big Quadratic Inverse Covariance Estimation
> ### Aliases: BigQuic
> ### Keywords: BigQUIC package covariance regularization graphical model
> ###   lasso Newton coordinate descent
> 
> ### ** Examples
> 
> lambda <- 0.91
> exampleResult <- BigQuic(inputFileName = paste(path.package("BigQuic"), 
+                          "/extdata/testInput", sep = ""), lambda = lambda, 
+                          numthreads = 1, memory_size = 512, seed = 1, 
+                          use_ram = TRUE)

 *** caught segfault ***
address 0xc0, cause 'memory not mapped'

Traceback:
 1: .Call("BigQuic_BigQuicHelper", PACKAGE = "BigQuic", argvPasser)
 2: BigQuicHelper(argvPasser = c("-l", lambda[i], "-n", numthreads,     "-t", maxit, "-e", epsilon, "-k", k, "-m", memory_size, "-q",     verbose, "-r", isnormalized, inputFileName, outputFileName))
 3: BigQuic(inputFileName = paste(path.package("BigQuic"), "/extdata/testInput",     sep = ""), lambda = lambda, numthreads = 1, memory_size = 512,     seed = 1, use_ram = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Running examples in ‘bigstatsr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: asPlotlyText
> ### Title: Plotly text
> ### Aliases: asPlotlyText
> 
> ### ** Examples
> 
> set.seed(1)
> 
> X <- big_attachExtdata()
> svd <- big_SVD(X, big_scale(), k = 10)
Error in getXPtrFBM(.self$backingfile, .self$nrow, .self$ncol, .self$type) : 
  File '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigstatsr/extdata/example.bk' not found.
Calls: big_SVD ... extractVec -> $ -> $ -> get -> <Anonymous> -> getXPtrFBM
Execution halted
Running examples in ‘binst-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create_breaks
> ### Title: A convenience functon for creating breaks with various methods.
> ### Aliases: create_breaks
> 
> ### ** Examples
> 
> kmeans_breaks <- create_breaks(1:10)
> create_bins(1:10, kmeans_breaks)
 [1] 1 1 1 2 2 2 3 3 3 3
> 
> # passing the k means parameter "centers" = 4
> kmeans_breaks <- create_breaks(1:10, list(centers=4))
> create_bins(1:10, kmeans_breaks)
 [1] 1 1 1 1 2 2 2 3 3 3
> 
> entropy_breaks <- create_breaks(1:10, rep(c(1,2), each = 5), method="entropy")
> create_bins(1:10, entropy_breaks)
 [1] 1 1 1 1 1 2 2 2 2 2
> 
> dt_breaks <- create_breaks(iris$Sepal.Length, iris$Species, method="dt")
Error in extree_data(formula = y ~ x, data = list(x = c(5.1, 4.9, 4.7,  : 
  could not find function "extree_data"
Calls: create_breaks ... create_dtbreaks -> do.call -> <Anonymous> -> eval -> eval
Execution halted
Error in re-building vignettes:
  ...
trying URL ‘https://github.com/Miachol/ftp/blob/master/files/GRCh37_MT_ensGene.txt’
downloaded 41 KB

successful!
Quitting from lines 46-70 (BioInstaller.Rmd) 
Error: processing vignette ‘BioInstaller.Rmd’ failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/biorxivr.Rcheck/vign_test/biorxivr") :
  Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/index.Rmd’
(Is a VignetteBuilder field missing?)
Quitting from lines 17-20 (vignette.Rmd) 
Error: processing vignette ‘vignette.Rmd’ failed with diagnostics:
failed to load external entity "http://www.biorxiv.org/search/Ecology?page=0"
Execution halted
Running ‘testthat.R’ [6s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(callr)
  > 
  > Sys.unsetenv("R_TESTS")
  > 
  > test_check("callr")
  ── 1. Error: debugger is called (@test-error.R#45)  ────────────────────────────
  Can't mock functions in base packages (utils)
  1: with_mock(`utils::debugger` = function(...) called <<- TRUE, r(function() {
         1 + "A"
     }, error = "debugger")) at testthat/test-error.R:45
  2: extract_mocks(new_values = new_values[!code_pos], .env = .env, eval_env = parent.frame())
  3: lapply(stats::setNames(nm = mock_qual_names), function(qual_name) {
         pkg_name <- gsub(pkg_and_name_rx, "\\1", qual_name)
         if (is_base_pkg(pkg_name)) {
             stop("Can't mock functions in base packages (", pkg_name, ")", call. = FALSE)
         }
         name <- gsub(pkg_and_name_rx, "\\2", qual_name)
         if (pkg_name == "") 
             pkg_name <- .env
         env <- asNamespace(pkg_name)
         if (!exists(name, envir = env, mode = "function")) 
             stop("Function ", name, " not found in environment ", environmentName(env), 
                 ".", call. = FALSE)
         mock(name = name, env = env, new = eval(new_values[[qual_name]], eval_env, eval_env))
     })
  4: FUN(X[[i]], ...)
  5: stop("Can't mock functions in base packages (", pkg_name, ")", call. = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 28 SKIPPED: 0 FAILED: 1
  1. Error: debugger is called (@test-error.R#45) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/cda.Rcheck/00install.out’ for details.
Found the following significant warnings:
  BlockCEM.h:52:44: warning: ‘BlockCEM<double>::Y’ will be initialized after [-Wreorder]
  BlockCEM.h:51:44: warning:   ‘FortranLinalg::DenseMatrix<double> BlockCEM<double>::X’ [-Wreorder]
  BlockCEM.h:152:5: warning:   when initialized here [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/cems.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: working directory was changed to ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS’, resetting
Running examples in ‘climtrends-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CreateReferenceSeriesFromFilesMean
> ### Title: Create a reference series (averaging)
> ### Aliases: CreateReferenceSeriesFromFilesMean
> ### Keywords: programming
> 
> ### ** Examples
> 
> # c_As00_o.txt, c_Hori2.txt and c_Kada2.txt are from AnClim freeware distribution
> setwd(system.file('extdata/', package='climtrends'))
> vFiles=c('c_As00_o.txt','c_Hori2.txt','c_Kada2.txt')
> refSeries=CreateReferenceSeriesFromFilesMean(vFiles)
> 
> 
> 
> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
> base::cat("CreateReferenceSeriesFromFiles.mean", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file 'climtrends-Ex.timings': Permission denied
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: <Anonymous> -> file
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(clust.bin.pair)
  > 
  > test_check("clust.bin.pair")
  ── 1. Error: McNemar scores datasets correctly (@test_clust_bin_pair.R#11)  ────
  'check.attributes' must be logical
  1: expect_equal(.mcnemar.impl(psychiatry$bh, psychiatry$ch), 11.85, tolerance = 0.1, 
         scale = NULL, "psychiatry") at testthat/test_clust_bin_pair.R:11
  2: compare(act$val, exp$val, ...)
  3: compare.numeric(act$val, exp$val, ...)
  4: all.equal(x, y, tolerance = tolerance, check.attributes = check.attributes, ...)
  5: all.equal.numeric(x, y, tolerance = tolerance, check.attributes = check.attributes, 
         ...)
  6: stop(gettextf("'%s' must be logical", "check.attributes"), domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 44 SKIPPED: 0 FAILED: 1
  1. Error: McNemar scores datasets correctly (@test_clust_bin_pair.R#11) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘CREAM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CREAM
> ### Title: CREAM is the main function for CORE identification
> ### Aliases: CREAM
> 
> ### ** Examples
> 
> CREAM(system.file("extdata", "A549_Chr21.bed", package = "CREAM"),
+ system.file("extdata", "A549_Chr21_COREs.bed", package = "CREAM"),
+ MinLength = 1000, peakNumMin = 2)
[1] 10
[1] 10
[1] 50
[1] 50
[1] 170
[1] 170
[1] 270
[1] 270
[1] 270
[1] 270
[1] 390
[1] 390
[1] 390
[1] 390
[1] 390
[1] 390
[1] 390
[1] 390
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/CREAM/extdata/A549_Chr21_COREs.bed': Permission denied
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: CREAM -> write.table -> file
Execution halted
Package suggested but not available for checking: ‘gputools’
Found the following significant warnings:
  convert_util.cpp:299:20: warning: null destination pointer [-Wformat-overflow=]
  convert_util.cpp:307:20: warning: null destination pointer [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DatABEL.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [11s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("data.tree")
  Loading required package: data.tree
  ── 1. Error: partykid (@test-treeConversionParty.R#37)  ────────────────────────
  could not find function "extree_data"
  1: partykit::ctree(Ozone ~ ., data = airq) at testthat/test-treeConversionParty.R:37
  2: eval(mf, parent.frame())
  3: eval(mf, parent.frame())
  
                            levelName    cost
  1  Acme Inc.                             NA
  2   ¦--Accounting                        NA
  3   ¦   ¦--New Software             1000000
  4   ¦   °--New Accounting Standards  500000
  5   ¦--Research                          NA
  6   ¦   ¦--New Product Line         2000000
  7   ¦   °--New Labs                  750000
  8   °--IT                                NA
  9       ¦--Outsource                 400000
  10      ¦--Go agile                  250000
  11      °--Switch to R                50000
    levelName  b             1
  1 Root      NA              
  2  °--a      2              
  3      °--c NA 1, 2, 3, 4, 5
    levelName a
  1     Root   
  2      °--a 2
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 352 SKIPPED: 2 FAILED: 1
  1. Error: partykid (@test-treeConversionParty.R#37) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘ddeploy-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: duke_predict
> ### Title: Predict using deployed model using REST API.
> ### Aliases: duke_predict
> 
> ### ** Examples
> 
> duke_auth <- list(
+ user_name = "try_it",
+ api_key   = "db1542b66f16aba5768d8a19c27dec4facf9168a",
+ endpoint = "/api/v1.0"
+ )
> example_data <- as.data.frame(cbind(gl(3,50),rnorm(150)));names(example_data) <- c("x","y")
> duke_predict(auth_details=duke_auth,model_name="example_fit",example_data)
Error: lexical error: invalid char in json text.
                                       <html>   <head>     <title>Inte
                     (right here) ------^
Execution halted
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/Rtmpy1p2HE’, resetting
Running ‘has-devel.R’ [1s/3s]
  Running ‘test-that.R’ [50s/103s]
Running the tests in ‘tests/test-that.R’ failed.
Complete output:
  > library(testthat)
  > test_check("devtools")
  Loading required package: devtools
  
  Attaching package: 'devtools'
  
  The following object is masked from 'package:testthat':
  
      setup
  
  ── 1. Failure: Github repos with submodules are identified correctly (@test-gith
  github_has_remotes(github_remote("armstrtw/rzmq")) not equal to TRUE.
  1 element mismatch
  
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 395 SKIPPED: 9 FAILED: 1
  1. Failure: Github repos with submodules are identified correctly (@test-github.r#82) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  DPPmcmc.h:91:16: warning: ‘DPPmcmc::model’ will be initialized after [-Wreorder]
  DPPmcmc.h:82:12: warning:   ‘Rcpp::Function DPPmcmc::effectiveSizeFunction’ [-Wreorder]
  DPPmcmc.cpp:11:1: warning:   when initialized here [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DPP.Rcheck/00install.out’ for details.
Running examples in ‘EasyStrata-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: EasyStrata
> ### Title: Function to run EasyStrata (v8.6).
> ### Aliases: EasyStrata
> 
> ### ** Examples
> 
> extDataDir=system.file("extdata", package="EasyStrata")
> ## Example Pipeline:
> ecfPipe=paste(extDataDir,"example_pipeline.ecf",sep="/")
> EasyStrata(ecfPipe)
Warning message:
In file(fileLog, open = "a") :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/EasyStrata/extdata/example_pipeline.ecf.out': Permission denied
Execution halted
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpjuQHlU’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpjuQHlU’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpjuQHlU’, resetting
Examples with CPU or elapsed time > 5s
              user system elapsed
partitioning 4.675  0.012   6.541
expansion    4.138  0.008   5.492
Found the following significant warnings:
  Matrix.h:42:7: warning: ‘myMatrix::numrow’ will be initialized after [-Wreorder]
  Matrix.h:41:7: warning:   ‘int myMatrix::numcol’ [-Wreorder]
  Matrix.h:8:12: warning:   when initialized here [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Emcdf.Rcheck/00install.out’ for details.
Running examples in ‘EmiStatR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: EmiStatR-methods
> ### Title: S4 Methods for Function 'EmiStatR'
> ### Aliases: EmiStatR-methods EmiStatR
> ### Keywords: methods input EmiStatR
> 
> ### ** Examples
> 
> ## running GUI 
> library("EmiStatR")
> 
> appDir <- system.file("shiny", package = "EmiStatR")
> setwd(appDir)
> 
> ## (uncomment for running)
> # runApp("EmiStatR_input")
> # runApp("EmiStatR_inputCSO")
> 
> ## executing EmiStatR
> input.default <- input() 
> sim   <- EmiStatR(input.default)
Error in setwd(dir.output) : cannot change working directory
Calls: EmiStatR -> EmiStatR -> setwd
Execution halted
Running examples in ‘ETLUtils-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: write.dbi.ffdf
> ### Title: Write ffdf data to a database table by using a DBI connection.
> ### Aliases: write.dbi.ffdf
> 
> ### ** Examples
> 
> require(ff)
> 
> ##
> ## Example query using data in sqlite
> ##
> require(RSQLite)
Loading required package: RSQLite
> dbfile <- system.file("smalldb.sqlite3", package="ETLUtils")
> drv <- dbDriver("SQLite")
> query <- "select * from testdata limit 10000"
> x <- read.dbi.ffdf(query = query, dbConnect.args = list(drv = drv, dbname = dbfile),
+ first.rows = 100, next.rows = 1000, VERBOSE=TRUE)
read.dbi.ffdf 1..100 (100)  dbi-read=0.001sec ffdf-write=0.013sec
read.dbi.ffdf 101..1100 (1000)  dbi-read=0.002sec ffdf-write=0.004sec
read.dbi.ffdf 1101..2100 (1000)  dbi-read=0.002sec ffdf-write=0.004sec
read.dbi.ffdf 2101..2860 (760)  dbi-read=0.001sec ffdf-write=0.021sec
 dbi-read=0.006sec  ffdf-write=0.042sec  TOTAL=0.048sec
> 
> write.dbi.ffdf(x = x, name = "helloworld", row.names = FALSE, overwrite = TRUE,
+   dbConnect.args = list(drv = drv, dbname = dbfile),
+   by = 1000, VERBOSE=TRUE)
2017-12-22 16:10:17 dbWriteTable chunk 1/3
Error in rsqlite_send_query(conn@ptr, statement) : 
  attempt to write a readonly database
Calls: write.dbi.ffdf ... initialize -> initialize -> rsqlite_send_query -> .Call
Execution halted
Found the following significant warnings:
  Warning: iteration 7 invokes undefined behavior [-Waggressive-loop-optimizations]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/expoRkit.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FastRWeb.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [7s/38s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(FedData)
  Loading required package: sp
  > 
  > test_check("FedData")
  ── 1. Error: The NHD Subregion boundaries dataset is availableat the correct URL
  Timeout was reached: Connection timed out after 10000 milliseconds
  1: expect_false(suppressWarnings(httr::http_error(url))) at testthat/test.NHD.R:7
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: suppressWarnings(httr::http_error(url))
  5: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  6: httr::http_error(url)
  7: http_error.character(url)
  8: http_error(HEAD(x, ...))
  9: HEAD(x, ...)
  10: request_perform(req, hu$handle$handle)
  11: request_fetch(req$output, req$url, handle)
  12: request_fetch.write_memory(req$output, req$url, handle)
  13: curl::curl_fetch_memory(url, handle = handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 25 SKIPPED: 0 FAILED: 1
  1. Error: The NHD Subregion boundaries dataset is availableat the correct URL (@test.NHD.R#7) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  In if (!is.character(x)) x <- as.character(x) :
    closing unused connection 4 (ftp://ftp.ncdc.noaa.gov/pub/data/paleo/treering/chronologies/)
  Execution halted
Running ‘test-all.R’ [14s/21s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library('testthat')
  > library('finch')
  > 
  > test_check('finch')
  ── 1. Error: dwca_get - works with a zip file - read=FALSE (@test-dwca_get.R#21)
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/finch/examples/0000154-150116162929234/multimedia.txt': Permission denied
  1: dwca_read(zip, read = FALSE) at testthat/test-dwca_get.R:21
  2: process(x)
  3: utils::unzip(x, exdir = dirpath)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 29 SKIPPED: 2 FAILED: 1
  1. Error: dwca_get - works with a zip file - read=FALSE (@test-dwca_get.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘FishResp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: QC.activity
> ### Title: Quality Control of Animal Activity
> ### Aliases: QC.activity
> 
> ### ** Examples
> 
> # if the data have been already loaded to R,
> # skip the first two lines of the code:
> setwd(path.package("FishResp", quiet = FALSE))
> load("data/SMR.clean.RData")
> 
> QC.activity(SMR.clean, compare = TRUE)
> 
> 
> 
> 
> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
> base::cat("QC.activity", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file 'FishResp-Ex.timings': Permission denied
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: <Anonymous> -> file
Execution halted
Running ‘boot.R’ [3s/4s]
  Running ‘disttests.R’ [1s/2s]
Running the tests in ‘tests/disttests.R’ failed.
Complete output:
  > library(flexclust)
  Loading required package: grid
  Loading required package: lattice
  Loading required package: modeltools
  Loading required package: stats4
  > 
  > ## create a random matrix
  > x <- matrix(rnorm(1000), ncol=4)
  > rownames(x) <- 1:nrow(x)
  > 
  > ## test canberra at margin
  > x[1:10,1] <- 0
  > x[1:20,2] <- 0
  > x[1:30,3] <- 0
  > 
  > stopifnot(all.equal(dist2(x,x,"eucl"), as.matrix(dist(x, "eucl"))))
  > stopifnot(all.equal(dist2(x,x,"man"), as.matrix(dist(x, "man"))))
  > stopifnot(all.equal(dist2(x,x,"max"), as.matrix(dist(x, "max"))))
  > stopifnot(all.equal(dist2(x,x,"bin"), as.matrix(dist(x, "bin"))))
  > stopifnot(all.equal(dist2(x,x,"can"), as.matrix(dist(x, "can"))))
  Error: dist2(x, x, "can") and as.matrix(dist(x, "can")) are not equal:
    Mean relative difference: 0.9403406
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 159-164 (format.Rmd) 
Error: processing vignette ‘format.Rmd’ failed with diagnostics:
Error closing file
Execution halted
Running ‘testthat.R’ [33s/48s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fuzzyjoin)
  > 
  > test_check("fuzzyjoin")
  ── 1. Failure: Can do inner joins on intervals with findOverlaps arguments (@tes
  j_maxgap$id1 not equal to c(1, 1, 2, 2, 3).
  Lengths differ: 6 is not 5
  
  ── 2. Failure: Can do inner joins on intervals with findOverlaps arguments (@tes
  j_maxgap$id2 not equal to c(1, 2, 1, 2, 3).
  Lengths differ: 6 is not 5
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 224 SKIPPED: 0 FAILED: 2
  1. Failure: Can do inner joins on intervals with findOverlaps arguments (@test_interval_join.R#50) 
  2. Failure: Can do inner joins on intervals with findOverlaps arguments (@test_interval_join.R#51) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘gap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: makeped
> ### Title: A function to prepare pedigrees in post-MAKEPED format
> ### Aliases: makeped
> ### Keywords: datagen
> 
> ### ** Examples
> 
> cwd <- getwd()
> cs.dir <- file.path(path.package("gap"),"tests","kinship")
> setwd(cs.dir)
> dir()
 [1] "bdsmatrix.R" "gaw14.c"     "gaw14.h"     "gaw14frq.c"  "gcta.R"     
 [6] "gcta.sh"     "gdef.h"      "h2.R"        "kin.c"       "kindrv.c"   
[11] "l51.R"       "l51.sas"     "nghds.h"     "nshd.R"      "nshd.dat"   
[16] "ped.1.3.pre" "ped7.lop"    "ped7.pre"    "pedtodot.sh" "readme"     
[21] "setup.R"     "solar.R"     "solar.sh"    "werner.kin"  "werner.pre" 
> makeped("ped7.pre","ped7.ped",0,1,"ped7.lop")

           MAKEPED Version 2.21

 Constants in effect 
Maximum number of pedigrees                2400
Maximum number of individuals              8000
Maximum characters used in phenotypic data 200
Maximum number of characters in an id      11

Error in makeped("ped7.pre", "ped7.ped", 0, 1, "ped7.lop") : 
ERROR: Cannot open ped7.ped
Calls: makeped -> .C
Execution halted
Found the following significant warnings:
  m4_prod2_ms.cpp:19:12: warning: ‘paraPro2::v’ will be initialized after [-Wreorder]
  m4_prod2_ms.cpp:18:16: warning:   ‘const size_t paraPro2::r’ [-Wreorder]
  m4_prod2_ms.cpp:24:3: warning:   when initialized here [-Wreorder]
  m4_prod2_ms.cpp:30:3: warning:   when initialized here [-Wreorder]
  m4_prod2_p.cpp:18:12: warning: ‘paraPro2_p::v’ will be initialized after [-Wreorder]
  m4_prod2_p.cpp:17:16: warning:   ‘const size_t paraPro2_p::r’ [-Wreorder]
  m4_prod2_p.cpp:23:3: warning:   when initialized here [-Wreorder]
  m4_prod2_p.cpp:30:3: warning:   when initialized here [-Wreorder]
  m4_prod_ms.cpp:19:18: warning: ‘paraPro_ms::v’ will be initialized after [-Wreorder]
  m4_prod_ms.cpp:18:16: warning:   ‘const size_t paraPro_ms::r’ [-Wreorder]
  m4_prod_ms.cpp:25:3: warning:   when initialized here [-Wreorder]
  m4_prod_p.cpp:18:18: warning: ‘paraPro_p::v’ will be initialized after [-Wreorder]
  m4_prod_p.cpp:17:16: warning:   ‘const size_t paraPro_p::r’ [-Wreorder]
  m4_prod_p.cpp:24:3: warning:   when initialized here [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gaston.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Gdmlib.cpp:1665:9: warning: specified bound 256 equals the size of the destination [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gdm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  convert_util.cpp:299:20: warning: null destination pointer [-Wformat-overflow=]
  convert_util.cpp:307:20: warning: null destination pointer [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GenABEL.Rcheck/00install.out’ for details.
Running examples in ‘GENEAread-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AccData
> ### Title: Methods for processing and summarising AccData.
> ### Aliases: AccData [.AccData $.AccData print.AccData plot.AccData
> ###   summary.AccData
> ### Keywords: methods
> 
> ### ** Examples
> 
> 
> binfile  = system.file("binfile/TESTfile.bin", package = "GENEAread")[1]
> 
> #Read in the entire file, calibrated
> procfile<-read.bin(binfile)
Loading required package: mmap
Error in mmap(binfile, char()) : 
  unable to open file: possible permission issue.
Calls: read.bin -> header.info -> mmap -> .Call
Execution halted
Running examples in ‘genepop-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Contingency-test
> ### Title: Exact test on a single contingency table
> ### Aliases: Contingency-test struc
> 
> ### ** Examples
> 
> infile <- system.file('extdata', 'structest.txt',package='genepop')
> locinfile <- 'structest.txt'
> check <- file.copy(infile,locinfile,overwrite=TRUE)
> struc(locinfile)
Error in RAnalyzingSingleContingencyTable(inputFile, dememorization, batches,  : 
  could not open file 
Calls: struc -> RAnalyzingSingleContingencyTable -> .Call
Execution halted
Running ‘runTests.R’ [8s/12s]
Running the tests in ‘tests/runTests.R’ failed.
Complete output:
  > BiocGenerics:::testPackage("geno2proteo")
  Timing stopped at: 1.485 0.027 2.582
  Error in file(file, ifelse(append, "a", "w")) : 
    cannot open the connection
  In addition: Warning message:
  In file(file, ifelse(append, "a", "w")) :
    cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/geno2proteo/extdata/Homo_sapiens.GRCh37.74_chromosome16_35Mlong.gtf.gz_CDS_transcript.txt': Permission denied
  Timing stopped at: 0.431 0.003 0.472
  Error in getWritablePathname.Arguments(static, ...) : 
    No write permission for directory: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/geno2proteo/extdata
  
  
  RUNIT TEST PROTOCOL -- Fri Dec 22 18:41:40 2017 
  *********************************************** 
  Number of test functions: 6 
  Number of errors: 2 
  Number of failures: 0 
  
   
  1 Test Suite : 
  geno2proteo RUnit Tests - 6 test functions, 2 errors, 0 failures
  ERROR in test_generatingCDSaaFile: Error in file(file, ifelse(append, "a", "w")) : 
    cannot open the connection
  ERROR in test_genomicLocToWholeDNASequence: Error in getWritablePathname.Arguments(static, ...) : 
    No write permission for directory: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/geno2proteo/extdata
  
  Test files with failing tests
  
     test_functionsInGeno2proteo.R 
       test_generatingCDSaaFile 
       test_genomicLocToWholeDNASequence 
  
  
  Error in BiocGenerics:::testPackage("geno2proteo") : 
    unit tests failed for package geno2proteo
  Execution halted
Error in re-building vignettes:
  ...

Error: processing vignette ‘geno2proteoIntroduction.Rnw’ failed with diagnostics:
 chunk 3 (label = example_generatingCDSaaFile) 
Error in getWritablePathname.Arguments(static, ...) : 
  No write permission for directory: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/geno2proteo/extdata
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 39-49 (genotypeR.Rmd) 
Error: processing vignette ‘genotypeR.Rmd’ failed with diagnostics:
cannot change working directory
Execution halted
Package suggested but not available for checking: ‘RFOC’
Package suggested but not available for checking: ‘statisticalModeling’
Error in re-building vignettes:
  ...
Quitting from lines 187-193 (ggformula.Rmd) 
Error: processing vignette ‘ggformula.Rmd’ failed with diagnostics:
there is no package called 'statisticalModeling'
Execution halted
Running ‘test-all.R’ [64s/96s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check('ggfortify')
  Loading required package: ggfortify
  Loading required package: ggplot2
  initial  value 7.505733 
  final  value 7.505688 
  converged
  Initial stress        : 0.01705
  stress after  10 iters: 0.00951, magic = 0.500
  stress after  20 iters: 0.00941, magic = 0.500
  initial  value 7.505733 
  final  value 7.505688 
  converged
  Initial stress        : 0.01705
  stress after  10 iters: 0.00951, magic = 0.500
  stress after  20 iters: 0.00941, magic = 0.500
  ── 1. Error: gglagplot (@test-tslib.R#103)  ────────────────────────────────────
  `x` must be a vector, not a ts object, do you want `stats::lag()`?
  1: gglagplot(AirPassengers) at testthat/test-tslib.R:103
  2: dplyr::bind_rows(lapply(seq(1:lags), .lag))
  3: flatten_bindable(dots_values(...))
  4: dots_values(...)
  5: map(dots, function(dot) eval_bare(dot$expr, dot$env))
  6: lapply(.x, .f, ...)
  7: FUN(X[[i]], ...)
  8: eval_bare(dot$expr, dot$env)
  9: lapply(seq(1:lags), .lag)
  10: FUN(X[[i]], ...)
  11: as.vector(lag(ts, k))
  12: lag(ts, k)
  13: bad_args("x", "must be a vector, not a ts object, do you want `stats::lag()`?")
  14: glubort(fmt_args(args), ..., .envir = .envir)
  15: .abort(text)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1442 SKIPPED: 9 FAILED: 1
  1. Error: gglagplot (@test-tslib.R#103) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘ggplot2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scale_date
> ### Title: Position scales for date/time data
> ### Aliases: scale_x_date scale_y_date scale_x_datetime scale_y_datetime
> ###   scale_x_time scale_y_time
> 
> ### ** Examples
> 
> last_month <- Sys.Date() - 0:29
> df <- data.frame(
+   date = last_month,
+   price = runif(30)
+ )
> base <- ggplot(df, aes(date, price)) +
+   geom_line()
> 
> # The date scale will attempt to pick sensible defaults for
> # major and minor tick marks. Override with date_breaks, date_labels
> # date_minor_breaks arguments.
> base + scale_x_date(date_labels = "%b %d")
Error in round.POSIXt(c(1511136000, 1511740800, 1512345600, 1512950400,  : 
  unused argument (units = "days")
Calls: <Anonymous> ... pretty -> pretty.Date -> makeOutput -> structure -> as.Date
Execution halted
Found the following significant warnings:
  hmg.h:20:38: warning: ‘HMG::p’ will be initialized after [-Wreorder]
  hmg.h:20:9: warning:   ‘arma::vec HMG::tau_par’ [-Wreorder]
  hmg.cpp:10:1: warning:   when initialized here [-Wreorder]
  hmg.h:20:27: warning: ‘HMG::gamma_par’ will be initialized after [-Wreorder]
  hmg.h:17:12: warning:   ‘double HMG::alpha’ [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/grove.Rcheck/00install.out’ for details.
Found the following significant warnings:
  readstat/sas/readstat_xport_write.c:339:13: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=]
  readstat/sas/readstat_xport_write.c:306:13: warning: ‘%-40s’ directive output may be truncated writing between 40 and 99 bytes into a region of size 49 [-Wformat-truncation=]
  readstat/sas/readstat_sas.c:304:14: warning: ‘%1ld’ directive output may be truncated writing between 1 and 16 bytes into a region of size 8 [-Wformat-truncation=]
  readstat/sas/readstat_sas7bdat_read.c:517:101: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size between 435 and 954 [-Wformat-truncation=]
  readstat/spss/readstat_sav_write.c:610:52: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 6 [-Wformat-truncation=]
  readstat/spss/readstat_sav_write.c:638:56: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 6 [-Wformat-truncation=]
  readstat/spss/readstat_sav_write.c:697:51: warning: ‘%05d’ directive output may be truncated writing between 5 and 11 bytes into a region of size between 1 and 10 [-Wformat-truncation=]
  readstat/spss/readstat_sav_write.c:716:51: warning: ‘%05d’ directive output may be truncated writing between 5 and 11 bytes into a region of size between 1 and 10 [-Wformat-truncation=]
  readstat/spss/readstat_spss.c:139:58: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/haven.Rcheck/00install.out’ for details.
Found the following significant warnings:
  lassoModels/IPenalizedSolver.h:221:28: warning: ‘HD::IPenalizedSolver::p_y_’ will be initialized after [-Wreorder]
  lassoModels/IPenalizedSolver.h:217:18: warning:   ‘STK::Real HD::IPenalizedSolver::threshold_’ [-Wreorder]
  lassoModels/IPenalizedSolver.h:112:7: warning:   when initialized here [-Wreorder]
  lassoModels/IPenalizedSolver.h:126:7: warning:   when initialized here [-Wreorder]
  lassoModels/LogisticFusedLassoSolver.h:154:21: warning: ‘HD::LogisticFusedLassoSolver::cginit_’ will be initialized after [-Wreorder]
  lassoModels/LogisticFusedLassoSolver.h:147:26: warning:   ‘HD::FusedLassoPenalty* HD::LogisticFusedLassoSolver::p_penalty_’ [-Wreorder]
  lassoModels/LogisticFusedLassoSolver.cpp:51:3: warning:   when initialized here [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/HDPenReg.Rcheck/00install.out’ for details.
Running ‘test-all.R’ [2s/3s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("hrbrthemes")
  Loading required package: hrbrthemes
  ── 1. Error: we can do something (@test-hrbrthemes.R#60)  ──────────────────────
  cannot open the connection
  1: import_roboto_condensed() at testthat/test-hrbrthemes.R:60
  2: suppressWarnings(suppressMessages(extrafont::font_import(rc_font_dir, prompt = FALSE)))
  3: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  4: suppressMessages(extrafont::font_import(rc_font_dir, prompt = FALSE))
  5: withCallingHandlers(expr, message = function(c) invokeRestart("muffleMessage"))
  6: extrafont::font_import(rc_font_dir, prompt = FALSE)
  7: ttf_import(paths, recursive, pattern)
  8: ttf_extract(ttfiles)
  9: gzcopy_exclude(paste(tmpfiles[i], ".afm", sep = ""), paste(outfiles[i], ".afm.gz", 
         sep = ""), delete = TRUE, exclusions = c("^Characters"))
  10: gzfile(dest, "w")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 3 SKIPPED: 0 FAILED: 1
  1. Error: we can do something (@test-hrbrthemes.R#60) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmppCnGHa’, resetting
  Warning: working directory was changed to ‘/tmp/RtmppCnGHa’, resetting
  Warning: working directory was changed to ‘/tmp/RtmppCnGHa’, resetting
  Warning: working directory was changed to ‘/tmp/RtmppCnGHa’, resetting
  Warning: working directory was changed to ‘/tmp/RtmppCnGHa’, resetting
  Warning: working directory was changed to ‘/tmp/RtmppCnGHa’, resetting
Examples with CPU or elapsed time > 5s
               user system elapsed
chip.support 46.834  0.141  68.888
nearest.snp  14.413  0.035  20.745
Error in re-building vignettes:
  ...
Quitting from lines 81-91 (IGM.MEAgeneralUsage.Rmd) 
Error: processing vignette ‘IGM.MEAgeneralUsage.Rmd’ failed with diagnostics:
cannot open the connection
Execution halted
Running examples in ‘inlinedocs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: do.not.generate
> ### Title: do not generate
> ### Aliases: do.not.generate
> 
> ### ** Examples
> 
> silly.pkg <- system.file("silly",package="inlinedocs")
> owd <- setwd(tempdir())
> file.copy(silly.pkg,".",recursive=TRUE)
[1] TRUE
> 
> ## define a custom Parser Function that will not generate some Rd
> ## files
> custom <- do.not.generate("silly-package","Silly-class")
> parsers <- c(default.parsers,list(exclude=custom))
> 
> ## At first, no Rd files in the man subdirectory.
> man.dir <- file.path("silly","man")
> dir(man.dir)
character(0)
> 
> ## Running package.skeleton.dx will generate bare-bones files for
> ## those specified in do.not.generate, if they do not exist.
> package.skeleton.dx("silly",parsers)
Creating directories ...
Warning in dir.create(path) :
  cannot create dir './silly', reason 'Permission denied'
Error in safe.dir.create(dir) : cannot create directory './silly'
Calls: package.skeleton.dx -> package.skeleton -> safe.dir.create
Execution halted
rm: cannot remove '/tmp/RtmpSFlgtG/silly/R/silly.R': Permission denied
rm: cannot remove '/tmp/RtmpSFlgtG/silly/DESCRIPTION': Permission denied
rm: cannot remove '/tmp/RtmpSFlgtG/silly/NAMESPACE': Permission denied
Found the following significant warnings:
  s_hull_pro.h:75:9: warning: ‘Shx::ro’ will be initialized after [-Wreorder]
  s_hull_pro.h:74:14: warning:   ‘float Shx::tr’ [-Wreorder]
  s_hull_pro.h:77:3: warning:   when initialized here [-Wreorder]
  s_hull_pro.h:74:17: warning: ‘Shx::tc’ will be initialized after [-Wreorder]
  s_hull_pro.h:73:7: warning:   ‘int Shx::id’ [-Wreorder]
  s_hull_pro.h:78:3: warning:   when initialized here [-Wreorder]
  s_hull_pro.h:112:11: warning: ‘Dupex::c’ will be initialized after [-Wreorder]
  s_hull_pro.h:111:7: warning:   ‘int Dupex::id’ [-Wreorder]
  s_hull_pro.h:115:3: warning:   when initialized here [-Wreorder]
  s_hull_pro.h:116:3: warning:   when initialized here [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/interp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  as_output.c:323:24: warning: ‘snprintf’ output truncated before the last format character [-Wformat-truncation=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/iotools.Rcheck/00install.out’ for details.
Running ‘test.R’ [2s/3s]
Running the tests in ‘tests/test.R’ failed.
Complete output:
  > # Use the default data to avoid token requirement for testing purposes
  > # Generate markdown text string
  > library(issueReporter)
  > setwd(tempdir())
  > 
  > testMD <- issuesData2md()
  > 
  > # Use default data to generate PDF
  > issuesGenPDF(style = "tint",
  +              RmdLocation =  system.file("rmarkdown/templates/", "tint.Rmd",
  +                                         package = "issueReporter"),
  +              outputFile = tempfile(pattern="ir", fileext=".pdf"),
  +              outputDir = tempdir(),
  +              md = testMD,
  +              setTitle = "Example Notes",
  +              setAuthor = "Author Name")
  
  
  processing file: tint.Rmd
     inline R code fragments
  
  label: setup (with options) 
  List of 1
   $ include: logi FALSE
  
    ordinary text without R code
  
  label: unnamed-chunk-1 (with options) 
  List of 2
   $ results: chr "asis"
   $ echo   : logi FALSE
  
    ordinary text without R code
  
  Error in file(con, "w") : cannot open the connection
  Calls: issuesGenPDF -> <Anonymous> -> <Anonymous> -> writeLines -> file
  In addition: Warning messages:
  1: In block_exec(params) : failed to tidy R code in chunk <setup>
  reason: Error in loadNamespace(name) : there is no package called 'formatR'
  
  2: In file(con, "w") : cannot open file 'tint.knit.md': Permission denied
  Execution halted
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Found the following significant warnings:
  Warning: working directory was changed to ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/KATforDCEMRI.Rcheck/KATforDCEMRI_benchmark_test’, resetting
Running examples in ‘knitr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: spin
> ### Title: Spin goat's hair into wool
> ### Aliases: spin
> 
> ### ** Examples
> 
> #' write normal text like this and chunk options like below
> 
> #+ label, opt=value
> 
> # /*
> #' these lines are treated as comments in spin()
> 1 + 1
[1] 2
> # */
> 
> (s = system.file("examples", "knitr-spin.R", package = "knitr"))
[1] "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/knitr/examples/knitr-spin.R"
> spin(s)  # default markdown
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/knitr/examples/knitr-spin.Rmd': Permission denied
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: spin -> cat -> file
Execution halted
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/Rtmpw4ViCT’, resetting
Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                  old_size new_size compress
  kzs.3d_data.rda    3.3Mb    3.0Mb       xz
Running ‘testthat.R’ [3s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # See https://github.com/r-lib/testthat/issues/86
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(later)
  > 
  > test_check("later")
  ── 1. Error: run_now wakes up when a background thread calls later() (@test-run_
  file io error: '/tmp/RtmpqyCyzv/sourceCpp-x86_64-pc-linux-gnu-0.12.14/sourcecpp_714c184d71b/bgtest.cpp'
  1: Rcpp::sourceCpp(system.file("bgtest.cpp", package = "later"), env = env) at testthat/test-run_now.R:44
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 10 SKIPPED: 0 FAILED: 1
  1. Error: run_now wakes up when a background thread calls later() (@test-run_now.R#44) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘varComp’
Running examples in ‘lmeVarComp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pseudo.rlr.test
> ### Title: Pseudo Restricted Likelihood Ratio Test for Zero Variance
> ###   Components
> ### Aliases: pseudo.rlr.test
> 
> ### ** Examples
> 
> # two-way random effects ANOVA
> n1 <- 5L
> n2 <- 6L
> n0 <- 4L
> n <- n1 * n2 * n0
> X <- cbind(rep(1, n))
> A <- gl(n1, n2 * n0)
> Z1 <- model.matrix(~ -1 + A, contrasts.arg = contr.treatment)
> B <- rep(gl(n2, n0), n1)
> Z2 <- model.matrix(~ -1 + B, contrasts.arg = contr.treatment)
> Z3 <- model.matrix(~ -1 + B : A, contrasts.arg = contr.treatment)
> set.seed(1L)
> Y <- (X %*% 1
+   + Z1 %*% rnorm(ncol(Z1), 0, 0.7)
+   + Z2 %*% rnorm(ncol(Z2), 0, 0.3)
+   + Z3 %*% rnorm(ncol(Z3), 0, 0.5)
+   + rnorm(n, 0, 1))
> Z <- list(Z1, Z2, Z3)
> Sigma <- lapply(Z, function(z) diag(ncol(z)))
> # tests interaction effects
> pseudo.rlr.test(Y, X, Z, Sigma, 2L, 2000L, 2L)
Loading required package: varComp
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘varComp’
Loading required package: RLRsim
Error in loadNamespace(name) : there is no package called ‘varComp’
Calls: pseudo.rlr.test ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Found the following significant warnings:
  Warning: ‘nsimp’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/localdepth.Rcheck/00install.out’ for details.
Found the following significant warnings:
  cvrout.c:286:32: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LogicOpt.Rcheck/00install.out’ for details.
Running examples in ‘LSDinterface-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: read.list.lsd
> ### Title: Read one or all instances of LSD variables (time series) from a
> ###   LSD results file into a list
> ### Aliases: read.list.lsd
> ### Keywords: interface file datasets database
> 
> ### ** Examples
> 
> # Save current work directory and change to the examples directory
> currWD <- getwd()
> setwd(system.file("extdata", package = "LSDinterface"))
> 
> # reads all instances of all variables from three files (one matrix each)
> tableList <- read.list.lsd(c("Sim1_1.res", "Sim1_2.res", "Sim1_3.res"))
> 
> # See parts of the 3D array in the data viewer (require package 'utils')
> #View(tableList[[ 1 ]])
> #View(tableList[[ 2 ]])
> #View(tableList[[ 3 ]])
> 
> # read all instances of a set of variables named '_A1p' and '_growth1'
> # and pool data
> abTable <- read.list.lsd(c("Sim1_1.res.gz", "Sim1_2.res.gz"), c("_A1p", "_growth1"), pool = TRUE)
> #View(abTable)
> 
> # reads instance 4 of all variables, skipping the initial 20 time steps
> # and keeping up to 50 time steps (from t = 21 up to t = 70)
> inst4List21_70 <- read.list.lsd(c("Sim1_1.res", "Sim1_2.res"), skip = 20, nrows = 50, instance = 4)
> #View(inst4List21_70[[ 1 ]])
> #View(inst4List21_70[[ 2 ]])
> 
> 
> 
> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
> base::cat("read.list.lsd", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file 'LSDinterface-Ex.timings': Permission denied
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: <Anonymous> -> file
Execution halted
Running examples in ‘LTRCtrees-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ICtree
> ### Title: Fit a survival tree for interval-censored survival data
> ### Aliases: ICtree
> 
> ### ** Examples
> 
> library(interval)
Loading required package: survival
Loading required package: perm
Loading required package: Icens
Loading required package: MLEcens
> library(LTRCtrees)
> data(bcos)
> 
> ## Fit ICtree survival tree
> Ctree <- ICtree(Surv(left,right,type="interval2")~treatment, data = bcos)
Error in extree_data(formula = Formula, data = DATA, yx = "none", nmax = c(yx = Inf,  : 
  could not find function "extree_data"
Calls: ICtree -> <Anonymous> -> eval -> eval
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 48-62 (LTRCtrees.Rmd) 
Error: processing vignette ‘LTRCtrees.Rmd’ failed with diagnostics:
could not find function "extree_data"
Execution halted
Running ‘testthat.R’ [21s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > if (packageVersion("testthat") >= "0.7.1.99") {
  +   library(testthat)  
  +   test_check("lubridate")
  + }
  Loading required package: lubridate
  
  Attaching package: 'lubridate'
  
  The following object is masked from 'package:base':
  
      date
  
  ── 1. Failure: interval handles POSIXlt inputs (@test-intervals.R#88)  ─────────
  unclass(interval(t1, t2)) not equal to unclass(...).
  Attributes: < Component "tzone": 1 string mismatch >
  
  ── 2. Failure: interval handles POSIXlt inputs (@test-intervals.R#95)  ─────────
  unclass(interval(t1, t2)) not equal to unclass(...).
  Attributes: < Component "tzone": 1 string mismatch >
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2456 SKIPPED: 36 FAILED: 2
  1. Failure: interval handles POSIXlt inputs (@test-intervals.R#88) 
  2. Failure: interval handles POSIXlt inputs (@test-intervals.R#95) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘MAGNAMWAR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: FormatMCLFastas
> ### Title: Format all raw GenBank fastas to single OrthoMCL compatible
> ###   fasta file
> ### Aliases: FormatMCLFastas
> 
> ### ** Examples
> 
> 
> dir <- system.file('extdata', 'fasta_dir', package='MAGNAMWAR')
> dir <- paste(dir,'/',sep='')
> formatted_file <- FormatMCLFastas(dir)
Warning in file.remove(outfile) :
  cannot remove file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/MAGNAMWAR/extdata/fasta_dir/MCLformatted_all.fasta', reason 'Permission denied'
Writing out to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/MAGNAMWAR/extdata/fasta_dir/MCLformatted_all.fasta 
Warning in file(description = file.out, open = open) :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/MAGNAMWAR/extdata/fasta_dir/MCLformatted_all.fasta': Permission denied
Error in file(description = file.out, open = open) : 
  cannot open the connection
Calls: FormatMCLFastas -> <Anonymous> -> file
Execution halted
Error in re-building vignettes:
  ...
Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Error in .local(.Object, ...) : 

Quitting from lines 110-131 (north.Rmd) 
Error: processing vignette ‘north.Rmd’ failed with diagnostics:
missing value where TRUE/FALSE needed
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/markmyassignment.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Quitting from lines 89-99 (meaRtoolsGeneralUsage.Rmd) 
Error: processing vignette ‘meaRtoolsGeneralUsage.Rmd’ failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmptAMZa8’, resetting
  Warning: working directory was changed to ‘/tmp/RtmptAMZa8’, resetting
  Warning: working directory was changed to ‘/tmp/RtmptAMZa8’, resetting
  Warning: working directory was changed to ‘/tmp/RtmptAMZa8’, resetting
Examples with CPU or elapsed time > 5s
                 user system elapsed
ind.analysis   18.334  0.071  23.177
MetaDE.rawdata  4.475  0.027   5.709
Running examples in ‘MetaSubtract-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: meta.subtract
> ### Title: Subtracts GWAS results from one or more cohorts from the
> ###   meta-GWAS results
> ### Aliases: meta.subtract
> ### Keywords: Correct meta-GWAS results Leave-one-out
> 
> ### ** Examples
> 
> metafile="meta_results.txt"
> cohortfiles=c("cohort1_results.txt","cohort2_results.txt")
> # Subtract summary statistics of the two cohorts from the meta summary statistics in metafile.
> # Genomic control correction of the imported meta summary statistics will be undone using 
> # lambda.meta. Genomic control will be applied to the corrected meta summary statistics 
> # (gc_meta=TRUE by default) based on a lambda derived from the new meta summary statistics 
> # (calculate_lambda.meta=TRUE by default). The cohorts summary statistics will always be first 
> # corrected for genomic control before subtracting them from the meta summary statistics. By 
> # default, the lambda will be calculated from the data (calculate_lambdas.cohort=TRUE by default).
> m1<-meta.subtract(metafile=metafile, cohortfiles=cohortfiles, lambda.meta=1.046, 
+       dir=system.file("extdata", package="MetaSubtract"))
[1] "Fri Dec 22 16:39:31 2017"
Reading meta_results.txt 
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file 'MetaSubtract.log': Permission denied
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: meta.subtract -> write.table -> file
Execution halted
Warning in utils::download.file(extDB, destfile = localDB, quiet = T) :
  URL https://github.com/cflagg/metScanR/raw/master/data/metScanR_DB.rda: cannot open destfile '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/metScanR/data/metScanR_DB.rda', reason 'Permission denied'
Warning in utils::download.file(extDB, destfile = localDB, quiet = T) :
  download had nonzero exit status
Warning in utils::download.file(extTermsDB, destfile = localTermsDB, quiet = T) :
  URL https://github.com/cflagg/metScanR/raw/master/data/metScanR_terms.rda: cannot open destfile '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/metScanR/data/metScanR_terms.rda', reason 'Permission denied'
Warning in utils::download.file(extTermsDB, destfile = localTermsDB, quiet = T) :
  download had nonzero exit status

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.
Running examples in ‘micropan-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bDist
> ### Title: Computes distances between sequences based on BLAST results
> ### Aliases: bDist
> 
> ### ** Examples
> 
> # Using BLAST result files in this package...
> # We need to uncompress them first:
> extdata.path <- file.path(path.package("micropan"),"extdata")
> filenames <- c("GID1_vs_GID1.txt",
+ "GID1_vs_GID2.txt",
+ "GID1_vs_GID3.txt",
+ "GID2_vs_GID1.txt",
+ "GID2_vs_GID2.txt",
+ "GID2_vs_GID3.txt",
+ "GID3_vs_GID1.txt",
+ "GID3_vs_GID2.txt",
+ "GID3_vs_GID3.txt")
> pth <- lapply( file.path( extdata.path, paste( filenames, ".xz", sep="" ) ), xzuncompress )
Warning in file(destname, open = "wb") :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/micropan/extdata/GID1_vs_GID1.txt': Permission denied
Error in file(destname, open = "wb") : cannot open the connection
Calls: lapply -> FUN -> file
Execution halted
Package suggested but not available for checking: ‘DiceView’
Running examples in ‘mistat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: LATHYPPISTON
> ### Title: Latin Hypercube Design for the Piston Simulator
> ### Aliases: LATHYPPISTON
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(LATHYPPISTON)
> 
> library(DiceEval)
Loading required package: DiceKriging
> 
> library(DiceView)
Error in library(DiceView) : there is no package called ‘DiceView’
Execution halted
Found the following significant warnings:
  ../inst/projects/MixAll/ILauncher.h:103:27: warning: ‘STK::ILauncher::v_models_’ will be initialized after [-Wreorder]
  ../inst/projects/MixAll/ILauncher.h:99:18: warning:   ‘STK::RDataHandler STK::ILauncher::handler_’ [-Wreorder]
  ILauncher.cpp:47:1: warning:   when initialized here [-Wreorder]
  ../inst/projects/MixAll/ILauncher.h:99:18: warning: ‘STK::ILauncher::handler_’ will be initialized after [-Wreorder]
  ../inst/projects/MixAll/ILauncher.h:88:46: warning:   ‘STK::DiagGaussianMixtureManager<STK::RDataHandler> STK::ILauncher::diagGaussianManager_’ [-Wreorder]
  ILauncher.cpp:63:1: warning:   when initialized here [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MixAll.Rcheck/00install.out’ for details.
Found the following significant warnings:
  nelder_mead_min.c:180:21: warning: ‘%5d’ directive writing between 5 and 10 bytes into a region of size 6 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mlegp.Rcheck/00install.out’ for details.
Running examples in ‘mlmm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mlmc
> ### Title: mlmc for missing and censored response in multilevel model.
> ### Aliases: mlmc
> 
> ### ** Examples
> 
> ## Don't show: 
> testfun=function()
+ {set.seed(100)
+  var2=abs(rnorm(50,0,1))
+  var1=(1/0.85)*var2;
+  geneid=rep(c(1:10),5);sid=c(rep(c(1:25),2),rep(c(26:50),2));
+  censor=rep(0,50)
+  pidname="geneid";sidname="sid";
+  miss_logit=var2*(-0.9);
+  miss=rbinom(50,1,exp(miss_logit)/(exp(miss_logit)+1));
+  censor=rep(0,50)
+  for (i in 1:50) {if (var1[i]<0.05) censor[i]=1}
+  for ( i in 1:50) {if ((miss[i]==1) & (censor[i]==1)) miss[i]=0};
+  for ( i in 1:50) {if (miss[i]==1) var1[i]=NA;
+  if (censor[i]==1) var1[i]=0.05}
+  pdata=data.frame(var1,var2,miss,censor,geneid,sid)
+  pathdir=getwd()
+  if (R.Version()$arch=="i386") fp=system.file("chunks","mlmc_i32.rds",package="mlmm")
+  if (R.Version()$arch=="x86_64") fp=system.file("chunks","mlmc_i64.rds",package="mlmm")
+  mcfit=readRDS(fp)
+  model1=mlmc(formula_completed=var1~var2,formula_missing=miss~var2,
+              formula_censor=censor~1,formula_subject=~var2,pdata=pdata,response_censorlim=0.05,
+              respond_dep_missing=TRUE,pidname="geneid",sidname="sid",pathname=pathdir,
+              iterno=10,chains=2,savefile=FALSE,usefit=TRUE,stanfit=mcfit)
+  }
> system.time(testfun())
Error in prep_call_sampler(object) : 
  the compiled object from C++ code for this model is invalid, possible reasons:
  - compiled with save_dso=FALSE;
  - compiled on a different platform;
  - does not exist (created from reading csv files).
Calls: system.time ... sampling -> .local -> <Anonymous> -> prep_call_sampler
Timing stopped at: 0.141 0.008 0.193
Execution halted
Running ‘testthat.R’ [14s/23s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(modmarg)
  > 
  > test_check("modmarg")
  ── 1. Error: Collinear cols treated right (@test_glm.R#288)  ───────────────────
  non-conformable arguments
  1: marg(mod = ols1, var_interest = "am", type = "effects", at = list(mpg = seq(15, 30, 
         5))) at testthat/test_glm.R:288
  2: marg.glm(mod = ols1, var_interest = "am", type = "effects", at = list(mpg = seq(15, 
         30, 5)))
  3: .marg(mod = mod, var_interest = var_interest, data = data, weights = weights, ...)
  4: lapply(data, function(x) {
         df_levels <- at_transforms(model_df = x, at_list = gen_at_list(df = x, var_interest = var_interest, 
             at_var_interest = at_var_interest))
         pred_se(df_levels = df_levels, model = mod, type = type, base_rn = base_rn, vcov_mat = vcov_mat, 
             weights = weights, link_func = NULL, deriv_func = NULL)
     })
  5: FUN(X[[i]], ...)
  6: pred_se(df_levels = df_levels, model = mod, type = type, base_rn = base_rn, vcov_mat = vcov_mat, 
         weights = weights, link_func = NULL, deriv_func = NULL)
  7: pred_se.glm(df_levels = df_levels, model = mod, type = type, base_rn = base_rn, vcov_mat = vcov_mat, 
         weights = weights, link_func = NULL, deriv_func = NULL)
  8: .pred_se(model = model, deriv_func = model$family$mu.eta, link_func = model$family$linkinv, 
         ...)
  9: calc_pred_se(vcov_mat, jacobs)
  10: diag(jac %*% vcov_model %*% t(jac))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 303 SKIPPED: 0 FAILED: 1
  1. Error: Collinear cols treated right (@test_glm.R#288) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  IPCATree.h:692:23: warning: ‘IPCATree<double>::stop’ will be initialized after [-Wreorder]
  IPCATree.h:689:16: warning:   ‘double IPCATree<double>::epsilon’ [-Wreorder]
  IPCATree.h:781:5: warning:   when initialized here [-Wreorder]
  IPCATree.h:696:19: warning: ‘IPCATree<double>::splitStrategy’ will be initialized after [-Wreorder]
  IPCATree.h:690:18: warning:   ‘unsigned int IPCATree<double>::minPoints’ [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mph.Rcheck/00install.out’ for details.
Found the following significant warnings:
  recursion.h:22:7: warning: ‘class_tree::K’ will be initialized after [-Wreorder]
  recursion.h:21:13: warning:   ‘arma::vec class_tree::nu_vec’ [-Wreorder]
  recursion.cpp:9:1: warning:   when initialized here [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MRS.Rcheck/00install.out’ for details.
Running examples in ‘mschart-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as_bar_stack
> ### Title: set a barchart as a stacked barchart
> ### Aliases: as_bar_stack
> 
> ### ** Examples
> 
> library(officer)
> 
> my_bar_stack_01 <- ms_barchart(data = browser_data, x = "browser",
+   y = "value", group = "serie")
> my_bar_stack_01 <- as_bar_stack( my_bar_stack_01 )
> 
> my_bar_stack_02 <- ms_barchart(data = browser_data, x = "browser",
+   y = "value", group = "serie")
> my_bar_stack_02 <- as_bar_stack( my_bar_stack_02, percent = TRUE,
+   dir = "horizontal" )
> 
> doc <- read_pptx()
> doc <- add_slide(doc,
+   layout = "Title and Content", master = "Office Theme")
Warning in doc_write_file(x$doc, file, options = options, encoding = encoding) :
  Permission denie [1501]
Warning in doc_write_file(x$doc, file, options = options, encoding = encoding) :
  Permission denie [1501]
Error in doc_write_file(x$doc, file, options = options, encoding = encoding) : 
  Error closing file
Calls: add_slide ... write_xml -> write_xml.xml_document -> doc_write_file -> .Call
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 63-68 (details.Rmd) 
Error: processing vignette ‘details.Rmd’ failed with diagnostics:
Error closing file
Execution halted
Found the following significant warnings:
  DE.c:128:36: warning: ‘snprintf’ output truncated before the last format character [-Wformat-truncation=]
  DE.c:301:40: warning: ‘snprintf’ output truncated before the last format character [-Wformat-truncation=]
  DE.c:322:34: warning: ‘snprintf’ output truncated before the last format character [-Wformat-truncation=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MSCMT.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [4s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(msde)
  > 
  > Sys.unsetenv("R_TESTS")
  > test_check("msde")
  ── 1. Error: (unknown) (@test-hest_diag.R#11)  ─────────────────────────────────
  file io error: '/tmp/RtmpTHwa6z/sourceCpp-x86_64-pc-linux-gnu-0.12.14/sourcecpp_651432be6f9e/msde-65142f2abaef_Exports.cpp'
  1: sde.make.model(ModelFile = ModelFile, param.names = param.names, data.names = data.names) at testthat/test-hest_diag.R:11
  2: sourceCpp(cppFile, env = .msdeglobalenv, ...)
  
  ── 2. Error: (unknown) (@test-hest_var.R#10)  ──────────────────────────────────
  PriorFile "/tmp/RtmpnX7V77/RLIBS_218314ac80ed/msde/include/mvnPrior.h" not found.
  1: sde.make.model(ModelFile = ModelFile, param.names = param.names, data.names = data.names) at testthat/test-hest_var.R:10
  2: .copy.cpp.files(ModelFile, PriorFile, OpenMP)
  3: stop("PriorFile \"", PriorFile, "\" not found.")
  
  ── 3. Error: (unknown) (@test-lv_prior.R#34)  ──────────────────────────────────
  PriorFile "lotvolPrior.h" not found.
  1: sde.make.model(ModelFile = "lotvolModel.h", PriorFile = "lotvolPrior.h", hyper.check = lvcheck, 
         data.names = data.names, param.names = param.names) at testthat/test-lv_prior.R:34
  2: .copy.cpp.files(ModelFile, PriorFile, OpenMP)
  3: stop("PriorFile \"", PriorFile, "\" not found.")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 210 SKIPPED: 0 FAILED: 3
  1. Error: (unknown) (@test-hest_diag.R#11) 
  2. Error: (unknown) (@test-hest_var.R#10) 
  3. Error: (unknown) (@test-lv_prior.R#34) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 223-231 (msde-quicktut.Rmd) 
Error: processing vignette ‘msde-quicktut.Rmd’ failed with diagnostics:
file io error: '/tmp/Rtmp88KXSA/sourceCpp-x86_64-pc-linux-gnu-0.12.14/sourcecpp_717f194d7f62/msde-717f4b65e864_Exports.cpp'
Execution halted
Running ‘testthat.R’ [56s/85s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mvtboost)
  > 
  > test_check("mvtboost")
  ── 1. Failure: covex-E (@test_covex.R#54)  ─────────────────────────────────────
  covex[covex > 0.01] not equal to rep(a, 3).
  1/3 mismatches
  [2] 1.06 - 1.09 == -0.0271
  1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 174 SKIPPED: 2 FAILED: 1
  1. Failure: covex-E (@test_covex.R#54) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpMsIjka’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpMsIjka’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpMsIjka’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpMsIjka’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpMsIjka’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpMsIjka’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpMsIjka’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpMsIjka’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpMsIjka’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpMsIjka’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpMsIjka’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpMsIjka’, resetting
Examples with CPU or elapsed time > 5s
               user system elapsed
ArrArrHexPlot 4.107  0.199   6.874
Running examples in ‘neurovault-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: download_nv_atlas
> ### Title: Download Neurovault Atlas and Label file
> ### Aliases: download_nv_atlas
> 
> ### ** Examples
> 
> res = download_nv_atlas(id = 1408)
GET command is:
Response [https://neurovault.org/api/atlases/1408/]
  Date: 2017-12-22 18:32
  Status: 200
  Content-Type: application/json; charset=utf-8
  Size: 751 B


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Unrecognized content encoding type. libcurl understands deflate, gzip content encodings.
Calls: download_nv_atlas ... request_fetch -> request_fetch.write_disk -> <Anonymous> -> .Call
Execution halted
Running ‘test-all.R’ [3s/5s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > if(require("testthat", quietly = TRUE)) {
  +     test_check("nloptr")
  + } else {
  +     print( "package 'testthat' not available, cannot run unit tests" )
  + }
  Loading required package: nloptr
  ── 1. Failure: Test derivative checker. (@test-derivative-checker.R#62)  ───────
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 3 - 2 == 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 42 SKIPPED: 0 FAILED: 1
  1. Failure: Test derivative checker. (@test-derivative-checker.R#62) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘NMF-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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 [2/32]
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: 0.009 0.008 0.033
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 633-644 (NMF-vignette.Rnw) 
Error: processing vignette ‘NMF-vignette.Rnw’ failed with diagnostics:
Error: memory could not be allocated for instance of type big.matrix
Execution halted
Found the following significant warnings:
  cc1: warning: ‘__builtin_memset’: writing between 256 and 17179869176 bytes into a region of size 248 overflows the destination [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/npsf.Rcheck/00install.out’ for details.
Running examples in ‘ODMconverter-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CDA2ODM
> ### Title: CDA2ODM
> ### Aliases: CDA2ODM
> ### Keywords: ODM
> 
> ### ** Examples
> 
> CDA2ODM(CDAfile=file.path(path.package("ODMconverter"),"extdata","CDA_letter_basic.xml"))
[1] "Generating /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/ODMconverter/extdata/CDA_letter_basic.xml.odm.xml"
Warning in file(file, if (append) "a" else "w") :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/ODMconverter/extdata/CDA_letter_basic.xml.odm.xml': Permission denied
Error in file(file, if (append) "a" else "w") : 
  cannot open the connection
Calls: CDA2ODM -> sink -> file
Execution halted
Running examples in ‘officer-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_slide
> ### Title: add a slide
> ### Aliases: add_slide
> 
> ### ** Examples
> 
> my_pres <- read_pptx()
> my_pres <- add_slide(my_pres,
+   layout = "Two Content", master = "Office Theme")
Warning in doc_write_file(x$doc, file, options = options, encoding = encoding) :
  Permission denie [1501]
Warning in doc_write_file(x$doc, file, options = options, encoding = encoding) :
  Permission denie [1501]
Error in doc_write_file(x$doc, file, options = options, encoding = encoding) : 
  Error closing file
Calls: add_slide ... write_xml -> write_xml.xml_document -> doc_write_file -> .Call
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 62-64 (powerpoint.Rmd) 
Error: processing vignette ‘powerpoint.Rmd’ failed with diagnostics:
Error closing file
Execution halted
Running examples in ‘opefimor-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: opefimor-package
> ### Title: Option Pricing and Estimation of Financial Models in R
> ### Aliases: opefimor-package opefimor
> ### Keywords: package
> 
> ### ** Examples
> 
> setwd(file.path(.libPaths()[1],"opefimor","book"))
> dir()
 [1] "appA.R" "appB.R" "cap2.R" "cap3.R" "cap4.R" "cap5.R" "cap6.R" "cap7.R"
 [9] "cap8.R" "cap9.R"
> 
> 
> 
> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
> base::cat("opefimor-package", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file 'opefimor-Ex.timings': Permission denied
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: <Anonymous> -> file
Execution halted
Running ‘testthat.R’ [1s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(optimus)
  This is optimus 0.1.0, roll out!
  > 
  > test_check("optimus")
  ── 1. Error: find_optimal() stops with wrong data or arguments (@test-find_optim
  argument "quo" is missing, with no default
  1: expect_error(expr = optimus::find_optimal(data = mixed, clustering = counts_cutree, 
         family = "poisson"), message = "some.*") at testthat/test-find_optimal.R:38
  2: quasi_capture(enquo(object), capture_error, label = label)
  3: label %||% quo_label(quo)
  4: quo_label(quo)
  5: expr_label(quo_expr(quo))
  6: quo_expr(quo)
  7: quo_splice(duplicate(quo), warn = warn)
  8: switch_expr(x, language = {
         if (is_quosure(x)) {
             if (!is_false(warn)) {
                 if (is_string(warn)) {
                     msg <- warn
                 }
                 else {
                     msg <- "Collapsing inner quosure"
                 }
                 warn(msg)
                 warn <- FALSE
             }
             while (is_quosure(x)) {
                 x <- f_rhs(x)
             }
             if (!is_null(parent)) {
                 mut_node_car(parent, x)
             }
             quo_splice(x, parent, warn = warn)
         }
         else {
             quo_splice(node_cdr(x), warn = warn)
         }
     }, pairlist = {
         while (!is_null(x)) {
             quo_splice(node_car(x), x, warn = warn)
             x <- node_cdr(x)
         }
     })
  9: expr_type_of(.x)
  10: typeof(x)
  11: duplicate(quo)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 5 SKIPPED: 0 FAILED: 1
  1. Error: find_optimal() stops with wrong data or arguments (@test-find_optimal.R#38) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in .local(x, ...) :
  The following sequence IDs are not in the dataset: 311, 222
Warning in .local(x, ...) :
  The following sequence IDs are not in the dataset: 311, 222
Warning in (if (out_format(c("latex", "sweave", "listings"))) sanitize_fn else paste0)(path,  :
  replaced special characters in figure filename "figs/OutbreakTools-out.width==".8\\textwidth"" -> "figs/OutbreakTools-out.width___.8\\textwidth_"
Warning in (if (out_format(c("latex", "sweave", "listings"))) sanitize_fn else paste0)(path,  :
  dots in figure paths replaced with _ ("figs/OutbreakTools-out_width____8//textwidth_")
Warning: The shape palette can deal with a maximum of 6 discrete values because
more than 6 becomes difficult to discriminate; you have 11. Consider
specifying shapes manually if you must have them.
Warning: Removed 58 rows containing missing values (geom_point).
Warning: `show_guide` has been deprecated. Please use `show.legend` instead.
Warning: `show_guide` has been deprecated. Please use `show.legend` instead.
Warning in download.file(url, destfile = tmp, quiet = !messaging, mode = "wb") :
  cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=51.516439,-0.171146&zoom=14&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false': HTTP status was '403 Forbidden'
Quitting from lines 1022-1023 (OutbreakTools.Rnw) 
Error: processing vignette ‘OutbreakTools.Rnw’ failed with diagnostics:
cannot open URL ‘http://maps.googleapis.com/maps/api/staticmap?center=51.516439,-0.171146&zoom=14&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false’
Execution halted
Found the following significant warnings:
  R_zmq_utility.c:34:24: warning: ‘sprintf’ writing a terminating nul past the end of the destination [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pbdZMQ.Rcheck/00install.out’ for details.
Running examples in ‘PBSmodelling-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: presentTalk
> ### Title: Run a Presentation in R
> ### Aliases: presentTalk
> 
> ### ** Examples
> 
> local(envir=.PBSmodEnv,expr={
+   cwd = getwd()
+   talk_dir <- system.file("examples", package = "PBSmodelling" )
+   setwd(talk_dir)
+   presentTalk( "swisstalk.xml" ) # closing the GUI should restore cwd
+ })
This short talk examines the "summary" method
and applies it to the "swiss" dataset. 
-----------------------------------< Press Go to continue >---------
> 
> 
> 
> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
> base::cat("presentTalk", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file 'PBSmodelling-Ex.timings': Permission denied
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: <Anonymous> -> file
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 45-47 (pcadapt.Rmd) 
Error: processing vignette ‘pcadapt.Rmd’ failed with diagnostics:
File conversion aborted.
Execution halted
Found the following significant warnings:
  sparse.c:926:16: warning: self-comparison always evaluates to false [-Wtautological-compare]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PET.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: working directory was changed to ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PGICA.Rcheck/Sim’, resetting
Running examples in ‘PlasmaMutationDetector-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BuildCtrlErrorRate
> ### Title: function BuildCtrlErrorRate
> ### Aliases: BuildCtrlErrorRate
> 
> ### ** Examples
> 
>    ctrl.dir = system.file("extdata", "4test_only/ctrl/", package = "PlasmaMutationDetector")
>    if (substr(ctrl.dir,nchar(ctrl.dir),nchar(ctrl.dir))!='/')
+      ctrl.dir = paste0(ctrl.dir,'/') # TO RUN UNDER WINDOWS
>    BuildCtrlErrorRate(ctrl.dir)
[1] "Looking for bam and bai in /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/PlasmaMutationDetector/extdata/4test_only/ctrl/rBAM/ ..."
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/PlasmaMutationDetector/extdata/4test_only/ctrl/BER/ctrl1-downsample-05_MAF.txt': Permission denied
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: BuildCtrlErrorRate -> MAF_from_BAM -> write.table -> file
Execution halted
Running examples in ‘ProFit-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: profitBenchmarkResultBest
> ### Title: Return best integration/convolution method from a
> ###   profitBenchmark result.
> ### Aliases: profitBenchmarkResultBest
> ### Keywords: data
> 
> ### ** Examples
> 
> 
> img = profitMakeGaussianPSF()
> bench=profitBenchmark(img, psf=img, nbench=1L, methods=profitAvailableConvolvers())
Device side queue is unimplemented (/build/pocl-H0HxNT/pocl-0.13/lib/CL/clCreateCommandQueueWithProperties.c:93)
Found the following significant warnings:
  gaussianProcesses/GaussianProcess.h:66:7: warning: ‘GaussianProcess::Observations’ will be initialized after [-Wreorder]
  gaussianProcesses/GaussianProcess.h:64:22: warning:   ‘CovarianceFunction& GaussianProcess::covFunc’ [-Wreorder]
  gaussianProcesses/GaussianProcess.cpp:3:1: warning:   when initialized here [-Wreorder]
  gaussianProcesses/GaussianProcess.h:64:22: warning: ‘GaussianProcess::covFunc’ will be initialized after [-Wreorder]
  gaussianProcesses/GaussianProcess.cpp:6:12: warning:   base ‘ForwardModel’ [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/psgp.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
trying URL ‘ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/11/PXD003133/txt_20min.zip’
Content type 'unknown' length 83554226 bytes (79.7 MB)
==================================================
Quitting from lines 62-63 (PTXQC_report_template.Rmd) 
Error: processing vignette ‘PTXQC-Basic_Guide_for_R_users.Rmd’ failed with diagnostics:
cannot open the connection
Execution halted
Running ‘testthat.R’ [5s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pxweb)
  pxweb: R tools for PX-WEB API.
  Copyright (C) 2014 Mans Magnusson, Leo Lahti, Love Hansson
  https://github.com/ropengov/pxweb
  
  New PXWEB API(s):
   - prognos.konj.se
   - data.ssb.no
   - pxweb.asub.ax
   - makstat.stat.gov.mk
   - data.csb.gov.lv
  
  Use update_pxweb_apis() to update the api catalogue.
  > test_check("pxweb")
  ── 1. Failure: pxweb_api_class (@test-pxweb_api_class.R#20)  ───────────────────
  NOT(success)
  
  ── 2. Failure: pxweb_api_class (@test-pxweb_api_class.R#22)  ───────────────────
  "foo.bar" %in% unlist(lapply(api_catalogue(), function(X) X$api)) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 98 SKIPPED: 16 FAILED: 2
  1. Failure: pxweb_api_class (@test-pxweb_api_class.R#20) 
  2. Failure: pxweb_api_class (@test-pxweb_api_class.R#22) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘panel.R’ [2s/4s]
  Running ‘rq.R’ [2s/4s]
  Running ‘rq.fit.panel.R’ [0s/1s]
  Running ‘run-demos.R’ [2s/2s]
Running the tests in ‘tests/run-demos.R’ failed.
Complete output:
  > library(quantreg)
  Loading required package: SparseM
  
  Attaching package: 'SparseM'
  
  The following object is masked from 'package:base':
  
      backsolve
  
  > 
  > (dDIR <- system.file("demo", package = "quantreg"))
  [1] "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/quantreg/demo"
  > setwd(dDIR)
  > set.seed(1) # since some demos randomly generate
  > 
  > cat("Running demos from package 'quantreg' : \n\n")
  Running demos from package 'quantreg' : 
  
  > for(ff in list.files(dDIR, pattern="\\.R$", full.names = TRUE)) {
  +    f <- basename(ff)
  +    cat("\n", f," :\n", paste(rep.int("-", nchar(f)), collapse=''),
  +        "\n", sep='')
  + 
  +    source(ff, echo = TRUE)
  + }
  
  Frank.R :
  -------
  
  > vFrank <- function(x, df, delta, u) -log(1 - (1 - 
  +     exp(-delta))/(1 + exp(-delta * pt(x, df)) * ((1/u) - 1)))/delta
  
  > FrankModel <- function(x, delta, mu, sigma, df, tau) {
  +     z <- qt(vFrank(x, df, delta, u = tau), df)
  +     mu + sigma * z
  + }
  
  > n <- 200
  
  > df <- 8
  
  > delta <- 8
  
  > set.seed(1989)
  
  > x <- sort(rt(n, df))
  
  > v <- vFrank(x, df, delta, u = runif(n))
  
  > y <- qt(v, df)
  
  > plot(x, y, pch = "o", col = "blue", cex = 0.25)
  Error in (function (file = if (onefile) "Rplots.pdf" else "Rplot%03d.pdf",  : 
    cannot open file 'Rplots.pdf'
  Calls: source ... eval -> plot -> plot.default -> dev.hold -> <Anonymous>
  Execution halted
Running examples in ‘R2GUESS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as.ESS.object
> ### Title: Compiles the main input and output files from a previous run of
> ###   'R2GUESS' and creates an ESS object.
> ### Aliases: as.ESS.object
> 
> ### ** Examples
> 
> dataX <- "data-X-C-CODE.txt"
> dataY <- "data-Y-ALL-C-CODE.txt"
> 
> path.input <- system.file("Input", package="R2GUESS")
> path.output <- system.file("Output", package="R2GUESS")
> path.par <- system.file("extdata", package="R2GUESS")
> file.par <- "Par_file_example_Hopx.xml"
> root.file.output <- "Example-GUESS-Y-Hopx"
> label.Y <- c("ADR","Fat","Heart","Kidney")
> my.env <- new.env()
> data(MAP.file,envir=my.env)
> MAP.file <- my.env$MAP.file
> modelY_Hopx <-as.ESS.object(dataY=dataY,dataX=dataX,path.input=path.input,
+     path.output=path.output,root.file.output=root.file.output,label.X=NULL,
+     label.Y=label.Y,path.par=path.par,file.par=file.par,MAP.file=MAP.file)
Warning in gzfile(file, "wb") :
  cannot open compressed file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/R2GUESS/Output/Example-GUESS-Y-Hopx_output_best_visited_models.RData', probable reason 'Permission denied'
Error in gzfile(file, "wb") : cannot open the connection
Calls: as.ESS.object -> get.best.models -> save -> gzfile
Execution halted
Found the following significant warnings:
  Warning: working directory was changed to ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS’, resetting
  Warning: working directory was changed to ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/r2lh.Rcheck/tmp’, resetting
Running examples in ‘rbacon-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Bacon.Age.d
> ### Title: Output all ages for a single depth.
> ### Aliases: Bacon.Age.d
> 
> ### ** Examples
> 
> Bacon(run=FALSE)
The run's files will be put in the folder Bacon_runs.
Warning in file(paste(coredir, core, "/", core, "_settings.txt", sep = ""),  :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rbacon.Rcheck/Bacon_runs/MSB2K/MSB2K_settings.txt': Permission denied
Error in file(paste(coredir, core, "/", core, "_settings.txt", sep = ""),  : 
  cannot open the connection
Calls: Bacon -> .Bacon.settings -> file
Execution halted
Error in re-building vignettes:
  ...
Loading required package: RCurl
Loading required package: bitops
Loading required package: RJSONIO

Error: processing vignette ‘rbiouml.Rnw’ failed with diagnostics:
 chunk 1 
Error in file(con, "r") : cannot open the connection
Execution halted
Found the following significant warnings:
  intersection.cc:384:1: warning: ‘%g’ directive writing 12 bytes into a region of size between 0 and 41 [-Wformat-overflow=]
  intersection.cc:384:1: warning: ‘%g’ directive writing 12 bytes into a region of size between 0 and 42 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RCALI.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Latexmk: This is Latexmk, John Collins, 1 January 2015, version: 4.41.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/bin/latexmk line 7482.
Loading required package: RcppGSL
Running ‘testthat.R’ [1s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(RcppThread)
  > 
  > test_check("RcppThread")
  ── 1. Failure: Thread class works (@tests.R#8)  ────────────────────────────────
  `RcppThread:::testThreadClass()` does not match "1234".
  Actual value: "123"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2 SKIPPED: 0 FAILED: 1
  1. Failure: Thread class works (@tests.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘Rd2roxygen-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Rd2roxygen
> ### Title: Convert all the Rd files of a package to roxygen comments
> ### Aliases: Rd2roxygen
> 
> ### ** Examples
> 
> ## a demo package
> pkg = system.file("examples", "pkgDemo", package = "Rd2roxygen")
> file.copy(pkg, tempdir(), recursive = TRUE)  # copy to temp dir first
[1] TRUE
> od = setwd(tempdir())
> 
> ## take a look at original R scripts
> file.show("pkgDemo/R/foo.R")
foo = function(a, b) {
    NULL
}

## you can use either <- or = to assign values to functions


> 
> options(roxygen.comment = "##' ")
> 
> ## convert Rd's under man to roxygen comments
> Rd2roxygen(file.path(tempdir(), "pkgDemo"))
Loading required package: pkgDemo
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘pkgDemo’
Warning in exported_names(pkg) :
  the package /tmp/Rtmpvp5i9G/pkgDemo does not have a NAMESPACE
##------ Fri Dec 22 17:07:20 2017 ------##
parsed: bar.Rd
looking for the object 'bar' in:
  bar.R: line 1
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/tmp/Rtmpvp5i9G/pkgDemo/R/bar.R': Permission denied
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: Rd2roxygen -> cat -> file
Execution halted
rm: cannot remove '/tmp/Rtmpvp5i9G/pkgDemo/R/foo.R': Permission denied
rm: cannot remove '/tmp/Rtmpvp5i9G/pkgDemo/R/bar.R': Permission denied
rm: cannot remove '/tmp/Rtmpvp5i9G/pkgDemo/man/data.Rd': Permission denied
rm: cannot remove '/tmp/Rtmpvp5i9G/pkgDemo/man/bar.Rd': Permission denied
rm: cannot remove '/tmp/Rtmpvp5i9G/pkgDemo/man/foo.Rd': Permission denied
rm: cannot remove '/tmp/Rtmpvp5i9G/pkgDemo/DESCRIPTION': Permission denied
Running ‘testthat.R’ [66s/96s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rdomains)
  > 
  > test_check("rdomains")
  ── 1. Error: dmoz cat (@test-dmoz-cat.R#5)  ────────────────────────────────────
  HTTP error 404.
  1: get_dmoz_data() at testthat/test-dmoz-cat.R:5
  2: curl_download("https://github.com/soodoku/domain_classifier/blob/master/rdomains/data-raw/dmoz/dmoz_domain_category.zip?raw=true", 
         tmp)
  
  Shallalist Data saved to the following destination: ./ 
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2 SKIPPED: 0 FAILED: 1
  1. Error: dmoz cat (@test-dmoz-cat.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [5s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(readODS)
  > test_check("readODS")
  ── 1. Error: Single column ODS (@test_write_ods.R#3)  ──────────────────────────
  Error closing file
  1: expect_true(write_ods(mtcars, "test.ods") %in% dir()) at testthat/test_write_ods.R:3
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: write_ods(mtcars, "test.ods") %in% dir()
  5: write_ods(mtcars, "test.ods")
  6: write_xml(content, contentfile)
  7: write_xml.xml_document(content, contentfile)
  8: doc_write_file(x$doc, file, options = options, encoding = encoding)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 22 SKIPPED: 0 FAILED: 1
  1. Error: Single column ODS (@test_write_ods.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
  rm: cannot remove '/tmp/Rtmps5MbLR/file4f00723c411a/META-INF/manifest.xml': Permission denied
Files which contain pragma(s) suppressing diagnostics:
  ‘src/RhpcMPI.c’ ‘src/worker/RhpcWorker.c’
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  jri/src/Makefile.win
  jri/src/win32/Makefile
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’,
    ‘R_GlobalContext’
File ‘rJava/libs/rJava.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  readPEDfile.c:321:74: warning: ‘%s’ directive output may be truncated writing up to 63 bytes into a region of size between 46 and 109 [-Wformat-truncation=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rJPSGCS.Rcheck/00install.out’ for details.
Found the following significant warnings:
  LASlib/laswriter_las.cpp:126:6: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  LASzip/laszip.cpp:275:6: warning: ‘ bytes’ directive writing 6 bytes into a region of size between 5 and 18 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rlas.Rcheck/00install.out’ for details.
Found the following significant warnings:
  newmat5.cpp:525:69: warning: throw will always call terminate() [-Wterminate]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rmixmod.Rcheck/00install.out’ for details.
Running examples in ‘RObsDat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RObsDat-package
> ### Title: R-Package to the observations Data Model from CUAHSI
> ### Aliases: RObsDat-package RObsDat
> ### Keywords: package
> 
> ### ** Examples
> 
> 	example(addDataValues)

addDtV> #connect to database
addDtV> getDefaultDB()
Loading required namespace: RSQLite

addDtV> ## Not run: 
addDtV> ##D #connect to postgreSQL database
addDtV> ##D require("RObsDat")
addDtV> ##D require("RPostgreSQL")
addDtV> ##D m <- dbDriver("PostgreSQL")
addDtV> ##D con <- dbConnect(m, user="a_user", password="secret", dbname="obsdat")
addDtV> ##D sqhandler <-  new("odm1_1Ver", con=con)
addDtV> ##D options(odm.handler=sqhandler)
addDtV> ##D 
addDtV> ##D #connect to MySQL database
addDtV> ##D require("RObsDat")
addDtV> ##D require("RMySQL")
addDtV> ##D m <- dbDriver("MySQL")
addDtV> ##D con <- dbConnect(m, user="a_user", password="secret", dbname="obsdat")
addDtV> ##D sqhandler <-  new("odm1_1Ver", con=con)
addDtV> ##D options(odm.handler=sqhandler)
addDtV> ##D 
addDtV> ##D #connect to SQLite database
addDtV> ##D require("RObsDat")
addDtV> ##D require("RSQLite")
addDtV> ##D m <- dbDriver("SQLite")
addDtV> ##D dbname = "database.db"
addDtV> ##D con <- dbConnect(m, dbname = dbname)
addDtV> ##D sqhandler <-  new("odm1_1Ver", con=con)
addDtV> ##D options(odm.handler=sqhandler)
addDtV> ##D 
addDtV> ## End(Not run)
addDtV> 
addDtV> #Store metadata in database
addDtV> addSite(Code="test", Name="Virtual test site", x=-5, y=46,
addDtV+ 	LatLongDatum="WGS84", Elevation=1500, State="Germany")
Error in rsqlite_send_query(conn@ptr, statement) : 
  attempt to write a readonly database
Calls: example ... initialize -> initialize -> rsqlite_send_query -> .Call
Execution halted
Error in re-building vignettes:
  ...
Loading required package: RObsDat
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

Loading required namespace: RSQLite

Error: processing vignette ‘RObsDat_Einstiegstutorial.Rnw’ failed with diagnostics:
 chunk 5 (label = part2) 
Error in rsqlite_send_query(conn@ptr, statement) : 
  attempt to write a readonly database
Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: viridisLite
Quitting from lines 34-54 (graphics_of_pm_25_concentrations_in_several_countries.Rmd) 
Error: processing vignette ‘graphics_of_pm_25_concentrations_in_several_countries.Rmd’ failed with diagnostics:
uh oh, the OpenAQ API seems to be having some issues, try again later
Execution halted
Found the following significant warnings:
  rph_tfbs.c:811:26: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 9 [-Wformat-truncation=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rphast.Rcheck/00install.out’ for details.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/libpq/Makefile.win
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Running ‘testthat.R’ [4s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rprojroot)
  > 
  > test_check("rprojroot")
  Error in readRDS(pfile) : 
    cannot read unreleased workspace version 3 written by experimental R 3.5.0
  Calls: cat ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
  Execution halted
  ── 1. Failure: thisfile works with Rscript (@test-thisfile.R#12)  ──────────────
  "scripts/thisfile-cat.R" not equal to res[[length(res)]].
  1/1 mismatches
  x[1]: "scripts/thisfile-cat.R"
  y[1]: "WARNING: ignoring environment value of R_HOME"
  
  Error in readRDS(pfile) : 
    cannot read unreleased workspace version 3 written by experimental R 3.5.0
  Calls: cat ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
  Execution halted
  ── 2. Failure: thisfile works with R (@test-thisfile.R#19)  ────────────────────
  "scripts/thisfile-cat.R" not equal to res[[length(res)]].
  1/1 mismatches
  x[1]: "scripts/thisfile-cat.R"
  y[1]: "WARNING: ignoring environment value of R_HOME"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 76 SKIPPED: 4 FAILED: 2
  1. Failure: thisfile works with Rscript (@test-thisfile.R#12) 
  2. Failure: thisfile works with R (@test-thisfile.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/Rtmp5F2sFo’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp5F2sFo’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp5F2sFo’, resetting
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pushSmetIntoIni
> ### Title: Pushes SMET object file into a 'meteoioini-class' object
> ### Aliases: pushSmetIntoIni
> 
> ### ** Examples
> 
> 
> ini <- as.meteoioini("test")
> 
> AA <- as.smet("test")
> BB <- as.smet("test")
> 
> 
> newini <- pushSmetIntoIni(AA,BB,ini=ini)
Warning in file(con, "w") :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RSMET/temp/test_station.smet': Permission denied
Error in file(con, "w") : cannot open the connection
Calls: pushSmetIntoIni -> lapply -> FUN -> print.smet -> <Anonymous> -> file
Execution halted
Running examples in ‘rSQM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rSQMSampleProject
> ### Title: function to create simple environment for package tutorial
> ### Aliases: rSQMSampleProject
> 
> ### ** Examples
> 
> library(rSQM)
> rSQMSampleProject()

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Warning in file.copy(spl_env, "./", overwrite = TRUE) :
  problem copying /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rSQM/extdata/rSQM.yaml to ./rSQM.yaml: Permission denied
Error in rSQMSampleProject() : 
  	An error occurs when sample data loaded, reinstall package and try again.
	If does not work again, contact <pablito@apcc21.org>, the maintainer.
Execution halted
Found the following significant warnings:
  rph_tfbs.c:811:26: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 9 [-Wformat-truncation=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rtfbs.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [5s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rvg)
  > 
  > test_check("rvg")
  ── 1. Error: ph_with_vg (@test-officer.R#7)  ───────────────────────────────────
  Error closing file
  1: add_slide(doc, "Title and Content", "Office Theme") at testthat/test-officer.R:7
  2: x$slide$update()
  3: lapply(filenames, function(x, container) {
         container$clone()$feed(x)$fortify_id()
     }, container = slide$new("ppt/slides"))
  4: FUN(X[[i]], ...)
  5: container$clone()$feed(x)$fortify_id()
  6: self$save()
  7: write_xml(private$doc, file = private$filename)
  8: write_xml.xml_document(private$doc, file = private$filename)
  9: doc_write_file(x$doc, file, options = options, encoding = encoding)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 236 SKIPPED: 4 FAILED: 1
  1. Error: ph_with_vg (@test-officer.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘RVowpalWabbit-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: vw
> ### Title: Run the Vowpal Wabbit fast out-of-core learner
> ### Aliases: vw
> ### Keywords: misc
> 
> ### ** Examples
> 
>   ## also see demo(vw) from which this is a subset
> 
>   library(RVowpalWabbit)
> 
>   # Test 3: without -d, training only
>   # {VW} train-sets/0002.dat    -f models/0002.model
>   test3 <- c("-t", system.file("test", "train-sets", "0002.dat", package="RVowpalWabbit"),
+              "-f", system.file("test", "models", "0002.model", package="RVowpalWabbit"))
> 
>   res <- vw(test3)
Error in Rvw(args) : 
  can't open: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RVowpalWabbit/test/models/0002.model.writing for writing, exiting
Calls: vw -> Rvw -> .Call
Execution halted
Running examples in ‘satscanMapper-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: satscanMapper
> ### Title: Function to map Results data produced by a SaTScan (TM) cluster
> ###   analysis
> ### Aliases: satscanMapper
> 
> ### ** Examples
> 
> ######
> #
> #  These examples focus on mapping the SaTScan (TM) data after the analysis
> #  has been completed.
> #  See the section on the CreateGeo4SS function for an example of how 
> #  to build a coordinates file (.geo) that matches the satscanMapper 
> #  boundary data.
> #
> ######
> 
> ######
> #
> #  Example # 1 - Mapping existing SaTScan (TM) results - "USStateLung" result files
> #     Make sure SaTScan (TM) results files are still located in the directories
> #     documented in the session saved (.prm) file.
> #
> #     This example maps data for the US States containing circular clusters.
> #
> #   Get location of .prm file and location to write mapping output files
> #
> 
> SSMInstDir <- system.file(package="satscanMapper", "extdata")
> 
> TT =c("Contiguous US States All Lung Cancer Mortality, 2004")
> 
> satscanMapper(resDir=SSMInstDir,                # path to .prm file location for output files. 
+                      prmFile  = "stateLung.prm", 
+                      title    = TT          )
Error in pdf(file = OutputFNpdf, width = vW, height = vH) : 
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/satscanMapper/extdata/stateLung-R01.pdf'
Calls: satscanMapper -> pdf
Execution halted
Found the following significant warnings:
  BGPscan.h:63:10: warning: ‘BGPscan::m_beta_alt’ will be initialized after [-Wreorder]
  BGPscan.h:49:15: warning:   ‘arma::uword BGPscan::m_inc_idx’ [-Wreorder]
  BGPscan.h:96:8: warning:   when initialized here [-Wreorder]
  USTscan.h:28:15: warning: ‘USTscanbase<arma::Mat<unsigned int>, unsigned int>::m_counts’ will be initialized after [-Wreorder]
  USTscan.h:23:15: warning:   ‘arma::uword USTscanbase<arma::Mat<unsigned int>, unsigned int>::m_num_locs’ [-Wreorder]
  USTscan.h:62:8: warning:   when initialized here [-Wreorder]
  USTscan.h:30:15: warning: ‘USTscanbase<arma::Mat<unsigned int>, unsigned int>::m_zone_lengths’ will be initialized after [-Wreorder]
  USTscan.h:26:15: warning:   ‘bool USTscanbase<arma::Mat<unsigned int>, unsigned int>::m_store_everything’ [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/scanstatistics.Rcheck/00install.out’ for details.
Found the following significant warnings:
  data/data_set.h:79:25: warning: ‘data_set::xpMat_’ will be initialized after [-Wreorder]
  data/data_set.h:64:7: warning:   ‘arma::mat data_set::Y’ [-Wreorder]
  data/data_set.h:23:3: warning:   when initialized here [-Wreorder]
  ./learn-rate/onedim_learn_rate.h:30:10: warning: ‘onedim_learn_rate::scale_’ will be initialized after [-Wreorder]
  ./learn-rate/onedim_learn_rate.h:27:10: warning:   ‘double onedim_learn_rate::gamma_’ [-Wreorder]
  ./learn-rate/onedim_learn_rate.h:18:3: warning:   when initialized here [-Wreorder]
  ./learn-rate/ddim_learn_rate.h:51:10: warning: ‘ddim_learn_rate::eta_’ will be initialized after [-Wreorder]
  ./learn-rate/ddim_learn_rate.h:48:10: warning:   ‘double ddim_learn_rate::a_’ [-Wreorder]
  ./learn-rate/ddim_learn_rate.h:24:3: warning:   when initialized here [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sgd.Rcheck/00install.out’ for details.
Found the following significant warnings:
  expression.h:80:10: warning: ‘ev3::Operand::exponent’ will be initialized after [-Wreorder]
  expression.h:58:7: warning:   ‘int ev3::Operand::dependency’ [-Wreorder]
  expression.cpp:271:1: warning:   when initialized here [-Wreorder]
  expression.cpp:276:1: warning:   when initialized here [-Wreorder]
  expression.cpp:281:1: warning:   when initialized here [-Wreorder]
  expression.cpp:286:1: warning:   when initialized here [-Wreorder]
  expression.h:83:11: warning: ‘ev3::Operand::depexponent’ will be initialized after [-Wreorder]
  expression.cpp:317:1: warning:   when initialized here [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/simplr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  NelderMead.c:140:24: warning: ‘%5d’ directive writing between 5 and 10 bytes into a region of size 6 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sme.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: items ‘package:smotefamily’ were removed from the search path
Examples with CPU or elapsed time > 5s
         user system elapsed
DBSMOTE 3.735  0.032   5.673
Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                old_size new_size compress
  spaceSimu.rda    1.2Mb    1.1Mb       xz
Error in re-building vignettes:
  ...
Quitting from lines 49-57 (fmri_processing_spm12r.Rmd) 
Error: processing vignette ‘fmri_processing_spm12r.Rmd’ failed with diagnostics:
non-character argument
Execution halted
Running examples in ‘ss3sim-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: case_tv
> ### Title: Write time varying casefiles to the disk
> ### Aliases: case_tv
> 
> ### ** Examples
> 
> temp_path <- file.path(tempdir(), "cod")
> dir.create(temp_path, showWarnings = FALSE)
> 
> d <- system.file("extdata", package = "ss3sim")
> 
> om <- file.path(d, "models", "cod-om")
> ig <- file.copy(om, temp_path, recursive = TRUE)
> ig <- file.rename(file.path(temp_path, "cod-om"), file.path(temp_path, "om"))
> verify_input(file.path(temp_path, "om"), type = "om")
Warning in file.rename(from = paste0(model_dir, "/", files[file.loc$f.ctl]),  :
  cannot rename file '/tmp/RtmpLpE3GM/cod/om/codOM.ctl' to '/tmp/RtmpLpE3GM/cod/om/om.ctl', reason 'Permission denied'
Warning in file.rename(from = paste0(model_dir, "/", files[file.loc$f.dat]),  :
  cannot rename file '/tmp/RtmpLpE3GM/cod/om/codOM.dat' to '/tmp/RtmpLpE3GM/cod/om/ss3.dat', reason 'Permission denied'
Warning in writeLines(starter.ss, file.ext) :
  cannot open file '/tmp/RtmpLpE3GM/cod/om/starter.ss': Permission denied
Error in writeLines(starter.ss, file.ext) : cannot open the connection
Calls: verify_input -> writeLines
Execution halted
rm: cannot remove '/tmp/RtmpLpE3GM/cod/om/ss3.par': Permission denied
rm: cannot remove '/tmp/RtmpLpE3GM/cod/om/forecast.ss': Permission denied
rm: cannot remove '/tmp/RtmpLpE3GM/cod/om/starter.ss': Permission denied
rm: cannot remove '/tmp/RtmpLpE3GM/cod/om/codOM.dat': Permission denied
rm: cannot remove '/tmp/RtmpLpE3GM/cod/om/codOM.ctl': Permission denied
Running examples in ‘Stickbreaker-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sim.data.from.priors.for.mod.selection
> ### Title: Simulate data from priors for doing model selection
> ### Aliases: sim.data.from.priors.for.mod.selection
> 
> ### ** Examples
> 
>  n.muts <- 4
>  n.muts <- length(Khan.data[1,])-1
>  geno.matrix <- Khan.data[,seq(1, n.muts)]
>  fit.matrix <- as.matrix(Khan.data[,(n.muts+1)])
>  outdir <- system.file("extdata",package="Stickbreaker")
>  file.name <- paste("Training_simulated_priors_fit_data_", n.muts, "muts.txt", sep="")
>  outpath <- paste(outdir, file.name, sep="/")
>  sim.data.from.priors.for.mod.selection(n.muts,
+    c(0.05, 0.5),
+    c(0, 0.25),
+    c(4),
+    1,
+    c(0.1, 10),
+    1.1,
+    1,
+    c(2,1),
+    outpath,
+    50,
+    coe.sim.model="identical",
+    coe.dist.par=NA,
+    print.interval=NA)
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Stickbreaker/extdata/Training_simulated_priors_fit_data_5muts.txt': Permission denied
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: sim.data.from.priors.for.mod.selection -> write.table -> file
Execution halted
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpRHVGff’, resetting
Found the following significant warnings:
  RMcrt.h:80:13: warning: ‘extendedleaps::rmdata::gdt’ will be initialized after [-Wreorder]
  RMcrt.h:76:10: warning:   ‘bool extendedleaps::rmdata::unreliable’ [-Wreorder]
  RMcrt.cpp:19:1: warning:   when initialized here [-Wreorder]
  RVcrt.h:101:18: warning: ‘extendedleaps::rvdata::e’ will be initialized after [-Wreorder]
  RVcrt.h:99:10: warning:   ‘bool extendedleaps::rvdata::unreliable’ [-Wreorder]
  RVcrt.cpp:36:1: warning:   when initialized here [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/subselect.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘gputools’
Running examples in ‘svMisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: toRjson
> ### Title: Convert R object to and from RJSON specification
> ### Aliases: toRjson evalRjson listToJson
> ### Keywords: utilities
> 
> ### ** Examples
> 
> ## A complex R object
> Robj <- structure(list(
+ 	a = as.double(c(1:5, 6)),
+ 	LETTERS,
+ 	c = c(c1 = 4.5, c2 = 7.8, c3 = Inf, c4 = -Inf, NA, c6 = NaN),
+ 	c(TRUE, FALSE, NA),
+ 	e = factor(c("a", "b", "a")),
+ 	f = "this is a \"string\"\nwith\tspecial chars",
+ 	g = matrix(rnorm(4), ncol = 2),
+ 	`h&'$@` = data.frame(x = 1:3, y = rnorm(3),
+ 		fact = factor(c("b", "a", "b"))),
+ 	i = Sys.Date(),
+     j = list(1:5, y = "another item")),
+     comment = "My comment\n\"",
+     anAttrib = 1:10,
+     anotherAttrib = list(TRUE, y = 1:4))
> 
> ## Convert to simplest RJSON, without attributes
> Rjson1 <- toRjson(Robj)
> Rjson1
[1] list(c(1., 2., 3., 4., 5., 6.), c("A", "B", "C", "D", "E", "F",                              
[2] "G", "H", "I", "J", "K", "L", "M", "N", "O", "P", "Q", "R", "S",                             
[3] "T", "U", "V", "W", "X", "Y", "Z"), c(4.5, 7.8, Inf, -Inf, NA,                               
[4] NaN), c(TRUE, FALSE, NA), c("a", "b", "a"), "this is a \\"string\\"\\nwith\\tspecial chars", 
[5]     c(-0.626453810742332, 0.183643324222082, -0.835628612410047,                             
[6]     1.59528080213779), list(seq(1, 3), c(0.329507771815361, -0.820468384118015,              
[7]     0.487429052428485), c("b", "a", "b")), "2017-12-22", list(                               
[8]         seq(1, 5), "another item"))                                                          
> evalRjson(Rjson1)
Error in .getClassesFromCache(Class) : 
  class should be either a character-string name or a class definition
Calls: evalRjson ... new -> getClass -> getClassDef -> .getClassesFromCache
Execution halted
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/Makefile.win
  src/SWAT2005/Makefile
  src/SWAT2005/Makefile.win
  src/SWAT2009/Makefile
  src/SWAT2009/Makefile.win
  src/SWAT2012/Makefile
  src/SWAT2012/Makefile.dan
  src/SWAT2012/Makefile.orig
  src/SWAT2012/Makefile.win
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Running ‘testthat.R’ [3s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(swirlify)
  > library(swirl)
  
  | Hi! Type swirl() when you are ready to begin.
  
  
  Attaching package: 'swirl'
  
  The following object is masked from 'package:testthat':
  
      skip
  
  > 
  > test_check("swirlify")
  ── 1. Failure: test_lesson() passes with well-formed lesson (@test_test_lesson.R
  all(correct_output %in% readLines(file.path(path, "test.log"))) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 7 SKIPPED: 0 FAILED: 1
  1. Failure: test_lesson() passes with well-formed lesson (@test_test_lesson.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  sybilSBML.c:2236:32: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=]
  sybilSBML.c:2247:34: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sybilSBML.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘radiomics’
Error in re-building vignettes:
  ...
Loading required package: data.table
No methods found in package ‘RSQLite’ for request: ‘dbGetQuery’ when loading ‘tcpl’
tcpl (v1.2.2) loaded with the following settings:
  TCPL_DB:    /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/tcpl/sql/tcpldb.sqlite
  TCPL_USER:  NA
  TCPL_HOST:  NA
  TCPL_DRVR:  SQLite
Default settings stored in TCPL.conf. See ?tcplConf for more information.

Error: processing vignette ‘tcpl_Overview.Rnw’ failed with diagnostics:
 chunk 4 
Error in rsqlite_send_query(conn@ptr, statement) : 
  attempt to write a readonly database
Execution halted
Package unavailable to check Rd xrefs: ‘dada2’
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpLfqLz9’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpLfqLz9’, resetting
Package in Depends field not imported from: ‘lgtdl’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ci.plot: no visible global function definition for ‘gaussian’
ci.plot: no visible global function definition for ‘qnorm’
ci.plot: no visible global function definition for ‘plot’
ci.plot: no visible global function definition for ‘lines’
cst.fit.ff: no visible global function definition for ‘pnorm’
cstfit.1: no visible global function definition for ‘var’
gof.test.boots.pf: no visible binding for global variable ‘sd’
gof.test.int.1.ff: no visible global function definition for ‘quantile’
gof.test.int.1.ff: no visible global function definition for ‘var’
gof.test.int.ff: no visible global function definition for ‘pnorm’
gofTest: no visible binding for global variable ‘sd’
plotGof: no visible global function definition for ‘plot’
plotGof : <anonymous>: no visible global function definition for
  ‘lines’
plotGof: no visible global function definition for ‘lines’
sig.test.int.1.ff: no visible global function definition for ‘quantile’
sig.test.int.1.ff: no visible global function definition for ‘var’
sig.test.int.ff: no visible global function definition for ‘pnorm’
test.boots.1: no visible binding for global variable ‘sd’
tpr: no visible global function definition for ‘poisson’
tpr: no visible global function definition for ‘glm.fit’
tpr: no visible global function definition for ‘coef’
tpr: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx coef gaussian glm.fit lines plot pnorm poisson qnorm quantile
  sd var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "approx", "coef", "gaussian", "glm.fit", "pnorm",
             "poisson", "qnorm", "quantile", "sd", "var")
to your NAMESPACE file.
Rd file 'ci.plot.Rd':
  \usage lines wider than 90 characters:
     ci.plot(x, y, se, level = 0.95, ylim = NULL, newplot = TRUE, fun = gaussian()$linkinv, dfun = gaussian()$mu.eta, ...)

These lines will be truncated in the PDF manual.
File ‘tpr/libs/tpr.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’
File ‘tpr/libs/tpr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
It is good practice to register native routines and to disable symbol
search.

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: trib.CoF
> ### Title: 'trib.CoF' gets file name length and returns coeficient of
> ###   friction in bar plot generates global var CF
> ### Aliases: trib.CoF
> 
> ### ** Examples
> 
> setwd(paste(path.package("trib"),"/exdata/tribometer",sep=""))
> trib.CoF(2)
> tribDATA<-trib.CoF(2,DATAOUT = TRUE)
> 
> 
> 
> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
> base::cat("trib.CoF", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file 'trib-Ex.timings': Permission denied
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: <Anonymous> -> file
Execution halted
Found the following significant warnings:
  cc1: warning: ‘__builtin_memset’: writing between 256 and 17179869176 bytes into a region of size 248 overflows the destination [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TukeyRegion.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpW0md9g/treePos/2017_12_22/run’, resetting
Found the following significant warnings:
  libunrtf/convert.c:1397:21: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/unrtf.Rcheck/00install.out’ for details.
Found the following significant warnings:
  convert_util.cpp:299:20: warning: null destination pointer [-Wformat-overflow=]
  convert_util.cpp:307:20: warning: null destination pointer [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/VariABEL.Rcheck/00install.out’ for details.
Found the following significant warnings:
  EM.c:386:25: warning: ‘sprintf’ writing a terminating nul past the end of the destination [-Wformat-overflow=]
  EM.c:391:25: warning: ‘sprintf’ writing a terminating nul past the end of the destination [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/VBmix.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpP73Psv’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpP73Psv’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpP73Psv’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpP73Psv’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpP73Psv’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpP73Psv’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpP73Psv’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpP73Psv’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpP73Psv’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpP73Psv’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpP73Psv’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpP73Psv’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpP73Psv’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpP73Psv’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpP73Psv’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpP73Psv’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpP73Psv’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpP73Psv’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpP73Psv’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpP73Psv’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpP73Psv’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpP73Psv’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpP73Psv’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpP73Psv’, resetting
Examples with CPU or elapsed time > 5s
           user system elapsed
coor.test 5.262  0.015   6.452
Error in re-building vignettes:
  ...
Quitting from lines 34-37 (Running_WhiteStripe.Rmd) 
Error: processing vignette ‘Running_WhiteStripe.Rmd’ failed with diagnostics:
File(s) not found!
Execution halted
Running examples in ‘WordR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: addFlexTables
> ### Title: Read Word document with bookmarks and create other Word document
> ###   with rendered tables in place.
> ### Aliases: addFlexTables
> 
> ### ** Examples
> 
> library(ReporteRs)
Loading required package: ReporteRsjars
> ft_mtcars <- vanilla.table(mtcars)
> ft_iris <- vanilla.table(iris)
> FT <- list(ft_mtcars=ft_mtcars,ft_iris=ft_iris)
> addFlexTables(
+   paste(examplePath(),'templates/templateFT.docx',sep = ''),
+   paste(examplePath(),'results/resultFT.docx',sep = ''),
+   FT)
Error in writeDoc.docx(doc, docxOut) : 
  writeDoc: Cannot write to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/WordR/examples/results/resultFT.docx
Calls: addFlexTables -> <Anonymous> -> writeDoc.docx
Execution halted
Found the following significant warnings:
  assp/asspfio.c:528:31: warning: ‘%s’ directive writing up to 3 bytes into a region of size between 0 and 11 [-Wformat-overflow=]
  assp/fmt.c:989:24: warning: ‘+.2e ’ directive writing 5 bytes into a region of size between 0 and 13 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/wrassp.Rcheck/00install.out’ for details.
Running examples in ‘XLConnect-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getCellStyleForType-methods
> ### Title: Querying the cell style per data type for the DATATYPE style
> ###   action
> ### Aliases: getCellStyleForType getCellStyleForType-methods
> ###   getCellStyleForType,workbook-method
> ### Keywords: methods utilities
> 
> ### ** Examples
> 
> file.copy(system.file("demoFiles/template2.xlsx", 
+                       package = "XLConnect"),
+           "datatype.xlsx", overwrite = TRUE)
[1] TRUE
> 
> # Load workbook
> wb <- loadWorkbook("datatype.xlsx")
> 
> # Get current (existing) cell style for numerics
> cs <- getCellStyleForType(wb, XLC$"DATA_TYPE.NUMERIC")
> # Could also say cs <- getCellStyleForType(wb, "numeric")
> 
> # Change style
> setBorder(cs, side = c("bottom", "right"), type = XLC$"BORDER.THICK", 
+           color = c(XLC$"COLOR.BLACK", XLC$"COLOR.RED"))
>           
> # Set style action to 'datatype'
> setStyleAction(wb, XLC$"STYLE_ACTION.DATATYPE")
> 
> # Write built-in data set 'mtcars' to the named region 
> # 'mtcars' as defined by the Excel template.
> writeNamedRegion(wb, mtcars, name = "mtcars")
> 
> # Save workbook
> saveWorkbook(wb)
Error: FileNotFoundException (Java): datatype.xlsx (Permission denied)
Execution halted
Running examples in ‘yCrypticRNAs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bam_to_reads
> ### Title: Convert BAM files into BED files containing the reads overlaping
> ###   the specified annotations.
> ### Aliases: bam_to_reads
> 
> ### ** Examples
> 
> bamfile <- system.file("extdata", "wt_rep1.bam", package = "yCrypticRNAs")
> data(annotations)
> bam_to_reads(bamfile, annotations)
Error in FUN(X[[i]], ...) : failed to build index
  file: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/yCrypticRNAs/extdata/wt_rep1.bam
Calls: bam_to_reads -> .index_bam
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 48-60 (yCrypticRNAs.Rmd) 
Error: processing vignette ‘yCrypticRNAs.Rmd’ failed with diagnostics:
failed to build index
  file: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/yCrypticRNAs/extdata/wt_rep1.bam
Execution halted
Dependence on R version ‘3.3.1’ not with patchlevel 0
Namespaces in Imports field not imported from:
  ‘devtools’ ‘httr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rARPACK’ ‘sparseLDA’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpfvtObB/filematrices’, resetting
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    R  14.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
Namespaces in Imports field not imported from:
  ‘plotly’ ‘shinydashboard’
  All declared Imports should be used.
asp: no visible global function definition for ‘as.formula’
asp: no visible global function definition for ‘var’
aspm: no visible binding for global variable ‘X.Declan’
aspm: no visible binding for global variable ‘Z.Jaida’
aspm: no visible binding for global variable ‘group.vec.Handan’
aspm: no visible global function definition for ‘as.formula’
aspm: no visible global function definition for ‘glm’
aspm: no visible global function definition for ‘binomial’
aspm: no visible global function definition for ‘poisson’
Undefined global functions or variables:
  X.Declan Z.Jaida as.formula binomial glm group.vec.Handan poisson var
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "poisson", "var")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘AdaptFit/R/aspm.R’:
  assign("group.vec.Handan", group.vec, pos = 1)
  assign("X.Declan", X, pos = 1)
  assign("Z.Jaida", Z, pos = 1)
Namespace in Imports field not imported from: ‘Benchmarking’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data       2.8Mb
    pictures   2.1Mb
Namespace in Imports field not imported from: ‘filehash’
  All declared Imports should be used.
Dependence on R version ‘3.4.1’ not with patchlevel 0
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Found the following significant warnings:
  ADM3.c:34:19: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:34:31: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:34:15: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:39:61: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:39:73: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:39:57: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:52:6: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:54:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:54:56: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:55:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:55:42: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:56:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:56:38: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/ADM3.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Namespaces in Imports field not imported from:
  ‘fields’ ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DBI’ ‘assertthat’ ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rjson’ ‘xml2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    data  15.6Mb
Found the following significant warnings:
  matrix.c:629:8: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  matrix.c:631:49: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  matrix.c:632:39: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/amei.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘unmarked’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rgdal’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘caret’
  All declared Imports should be used.
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
Dependence on R version ‘3.3.2’ not with patchlevel 0
Namespace in Imports field not imported from: ‘pls’
  All declared Imports should be used.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
runAPSIM: warning in scan(reports_file[i], "", sep = "", skip =
  length(temp), nline = 1): partial argument match of 'nline' to
  'nlines'
runAPSIM: no visible global function definition for ‘write.table’
runAPSIM: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Error in re-building vignettes:
  ...




More than one TSN found for taxon 'Canis lupus'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Canis latrans'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Acer saccharum'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Castor canadensis'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Alces alces'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Acer rubrum'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Vulpes vulpes'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Salix babylonica'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Odocoileus virginianus'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Betula alleghaniensis'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Rangifer tarandus'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Juniperus occidentalis'!

            Enter rownumber of taxon (other inputs will return 'NA'):





More than one TSN found for taxon 'Pinus strobus'!

            Enter rownumber of taxon (other inputs will return 'NA'):
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 ‘/data/gannet/ripley/R/packages/tests-clang/aqr.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.2Mb
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Dependence on R version ‘3.4.2’ not with patchlevel 0
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   9.6Mb
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
File ‘audio/libs/audio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java  10.6Mb
installed size is 67.2Mb
  sub-directories of 1Mb or more:
    java  67.2Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   8.9Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    libs   2.7Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/BAMBI.Rcheck/00install.out’ for details.
installed size is 100.7Mb
  sub-directories of 1Mb or more:
    libs  100.2Mb
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   3.3Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
Dependence on R version ‘3.3.3’ not with patchlevel 0
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Found the following significant warnings:
  Blasso.cpp:451:51: warning: assigning field to itself [-Wself-assign-field]
See ‘/data/gannet/ripley/R/packages/tests-clang/bayesCL.Rcheck/00install.out’ for details.
Running examples in ‘bayesCL-Ex.R’ failed
The error most likely occurred in:

> ### Name: lasso
> ### Title: Bayesian Lasso
> ### Aliases: lasso
> ### Keywords: regression
> 
> ### ** Examples
> 
> 
> set.seed(0)
> n_samples  <- 500
> n_features <- 40
> X <- matrix(rnorm(n_features * n_samples), nrow = n_samples)
> y <- 2 * X[,1] - 3 * X[,2] + rnorm(n_samples) # only features 1 & 2 are relevant
> 
> X_train <- X[1:400,]
> y_train <- y[1:400]
> X_test  <- X[401:500,]
> y_test  <- y[401:500]
> 
> 
> # START ------------------------------------------------------------------------
> 
> # first, standardize data !!!
> X_train <- scale(X_train)
> 
> tmp00 <- bayesCL::lasso(X = X_train, 
+                           y = y_train, 
+                           T = 500,  # number of Gibbs sampling iterations
+                           icept = T,
+                           device=0  ) # use constant term (intercept), we do
------------------------------
Platform and device selection

 *** caught segfault ***
address 0xac66150, cause 'memory not mapped'

Traceback:
 1: .Call("prepareCL", as.integer(platf), as.integer(device_id),     as.character(paste(.libPaths()[1], "/bayesCL", .Platform$file.sep,         "polyaGammaf.cl", sep = "")), as.character(paste(.libPaths()[1],         "/bayesCL", .Platform$file.sep, "polyaGammaf-", platf,         "-", device_id, ".bin", sep = "")), as.integer(params))
 2: prepare(precision = 0, device = device, parameters = parameters)
 3: bayesCL::lasso(X = X_train, y = y_train, T = 500, icept = T,     device = 0)
An irrecoverable exception occurred. R is aborting now ...
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  15.1Mb
installed size is 57.6Mb
  sub-directories of 1Mb or more:
    libs  56.9Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘inline’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/bayesMCClust.Rcheck/bayesMCClust-wd’, resetting
installed size is 28.2Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs  23.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     1.6Mb
    doc   3.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    ex-data   4.7Mb
installed size is 69.2Mb
  sub-directories of 1Mb or more:
    libs  69.1Mb
Namespace in Imports field not imported from: ‘inline’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘readxl’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
installed size is 52.6Mb
  sub-directories of 1Mb or more:
    libs  51.2Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘chron’ ‘colorspace’ ‘gtable’ ‘htmltools’ ‘htmlwidgets’
  ‘httpuv’ ‘magrittr’ ‘munsell’ ‘plyr’ ‘scales’ ‘stringi’ ‘xtable’
  ‘yaml’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘crochet’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
installed size is 141.6Mb
  sub-directories of 1Mb or more:
    include  141.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.8Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   5.2Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
installed size is 28.7Mb
  sub-directories of 1Mb or more:
    libs  28.6Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      7.0Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘lattice’ ‘zoo’
  All declared Imports should be used.
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  14.8Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   7.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Running examples in ‘binst-Ex.R’ failed
The error most likely occurred in:

> ### Name: create_breaks
> ### Title: A convenience functon for creating breaks with various methods.
> ### Aliases: create_breaks
> 
> ### ** Examples
> 
> kmeans_breaks <- create_breaks(1:10)
> create_bins(1:10, kmeans_breaks)
 [1] 1 1 1 2 2 2 3 3 3 3
> 
> # passing the k means parameter "centers" = 4
> kmeans_breaks <- create_breaks(1:10, list(centers=4))
> create_bins(1:10, kmeans_breaks)
 [1] 1 1 1 1 2 2 2 3 3 3
> 
> entropy_breaks <- create_breaks(1:10, rep(c(1,2), each = 5), method="entropy")
> create_bins(1:10, entropy_breaks)
 [1] 1 1 1 1 1 2 2 2 2 2
> 
> dt_breaks <- create_breaks(iris$Sepal.Length, iris$Species, method="dt")
Error in extree_data(formula = y ~ x, data = list(x = c(5.1, 4.9, 4.7,  : 
  could not find function "extree_data"
Calls: create_breaks ... create_dtbreaks -> do.call -> <Anonymous> -> eval -> eval
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   2.3Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Warning in buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-clang/biorxivr.Rcheck/vign_test/biorxivr") :
  Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/index.Rmd’
(Is a VignetteBuilder field missing?)
Quitting from lines 17-20 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
failed to load external entity "http://www.biorxiv.org/search/Ecology?page=0"
Execution halted
Package suggested but not available for checking: ‘IHW’
Package suggested but not available for checking: ‘RQuantLib’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RGtk2’ ‘cairoDevice’ ‘ergm’ ‘foreign’ ‘gWidgets’ ‘gWidgetsRGtk2’
  ‘haven’ ‘plot3D’ ‘plot3Drgl’ ‘rgl’ ‘sna’ ‘statnet.common’
  All declared Imports should be used.
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’
installed size is 39.2Mb
  sub-directories of 1Mb or more:
    libs  38.1Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
installed size is 31.9Mb
  sub-directories of 1Mb or more:
    libs  31.6Mb
File ‘BMN/libs/BMN.so’:
  Found ‘_ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
    Objects: ‘JunctionTree.o’, ‘pseudoLikelihood.o’
File ‘BMN/libs/BMN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  least.squares.c:250:24: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/bnlearn.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ./sampling.h:84:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/BNSP.Rcheck/00install.out’ for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.7Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘yaml’
  All declared Imports should be used.
installed size is 264.8Mb
  sub-directories of 1Mb or more:
    include    2.9Mb
    lib      261.7Mb
installed size is 47.0Mb
  sub-directories of 1Mb or more:
    libs  46.6Mb
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘tidyr’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Found the following significant warnings:
  rBGWM.cc:240:17: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  rBGWM.cc:599:18: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  rBGWM.cc:799:18: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/Branching.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
installed size is 29.6Mb
  sub-directories of 1Mb or more:
    libs  29.5Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘profileModel’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R     2.2Mb
    doc   2.4Mb
Namespaces in Imports field not imported from:
  ‘rworldxtra’ ‘sp’
  All declared Imports should be used.
Found the following significant warnings:
  helpers.c:365:19: warning: absolute value function 'fabsf' given an argument of type 'double' but has parameter of type 'float' which may cause truncation of value [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/BSquare.Rcheck/00install.out’ for details.
installed size is 28.9Mb
  sub-directories of 1Mb or more:
    libs  27.7Mb
installed size is 54.9Mb
  sub-directories of 1Mb or more:
    libs  54.6Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
Running ‘testthat.R’ [9s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(callr)
  > 
  > Sys.unsetenv("R_TESTS")
  > 
  > test_check("callr")
  ── 1. Error: debugger is called (@test-error.R#45)  ────────────────────────────
  Can't mock functions in base packages (utils)
  1: with_mock(`utils::debugger` = function(...) called <<- TRUE, r(function() {
         1 + "A"
     }, error = "debugger")) at testthat/test-error.R:45
  2: extract_mocks(new_values = new_values[!code_pos], .env = .env, eval_env = parent.frame())
  3: lapply(stats::setNames(nm = mock_qual_names), function(qual_name) {
         pkg_name <- gsub(pkg_and_name_rx, "\\1", qual_name)
         if (is_base_pkg(pkg_name)) {
             stop("Can't mock functions in base packages (", pkg_name, ")", call. = FALSE)
         }
         name <- gsub(pkg_and_name_rx, "\\2", qual_name)
         if (pkg_name == "") 
             pkg_name <- .env
         env <- asNamespace(pkg_name)
         if (!exists(name, envir = env, mode = "function")) 
             stop("Function ", name, " not found in environment ", environmentName(env), 
                 ".", call. = FALSE)
         mock(name = name, env = env, new = eval(new_values[[qual_name]], eval_env, eval_env))
     })
  4: FUN(X[[i]], ...)
  5: stop("Can't mock functions in base packages (", pkg_name, ")", call. = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 28 SKIPPED: 0 FAILED: 1
  1. Error: debugger is called (@test-error.R#45) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data     1.5Mb
    models   2.4Mb
Found the following significant warnings:
  slpcovis.cpp:381:12: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/catlearn.Rcheck/00install.out’ for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
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 17.0Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
Found the following significant warnings:
  ./MCMC_prob.h:2091:41: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/CCMnet.Rcheck/00install.out’ for details.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/cda.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘units’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘rgdal’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   5.8Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   9.3Mb
Found the following significant warnings:
  ./BlockCEM.h:154:71: warning: field 'Y' will be initialized after field 'X' [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-clang/cems.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
get.switch.time: warning in uniroot(f = switch.func, int =
  c(last_boundary, boundary), lower = last_boundary, upper = boundary,
  maxiter = 1000, tol = tol, e): partial argument match of 'int' to
  'interval'
plot.cggd: warning in axis(4, at = b[nrow(b), ], label = paste(cnums),
  cex = 0.8, adj = 0): partial argument match of 'label' to 'labels'
plot.cggd: no visible global function definition for ‘gen.beta’
plotCVcggd: no visible binding for global variable ‘cv’
plotCVcggd: no visible binding for global variable ‘cv.error’
predict.cggd: no visible binding for global variable ‘max.tk’
predict.cggd: no visible global function definition for ‘gen.beta’
Undefined global functions or variables:
  cv cv.error gen.beta max.tk
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang’, resetting
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 ‘/data/gannet/ripley/R/packages/tests-clang/changepoint.np.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘datasets’ ‘foreach’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gamlss.dist’
  All declared Imports should be used.
Running examples in ‘chillR-Ex.R’ failed
The error most likely occurred in:

> ### Name: handle_cimis
> ### Title: List, download or convert to chillR format data from the CIMIS
> ###   database
> ### Aliases: handle_cimis
> ### Keywords: utilities
> 
> ### ** Examples
> 
> 
> #handle_cimis(action="list_stations",location=c(x=-122,y=38.5),time_interval=c(2012,2012))
> 
> stat_list<-data.frame("Station Number"=c("119","139","6"),
+    Latitude=c(38.49500,38.50126,38.53569),Longitude=c(-122.0040,-121.9785,-121.7764),
+    Start_date=c("1993-08-21 UTC","1998-06-15 UTC","1982-07-17 UTC"),End_date=c("1995-01-25",
+      "2016-03-06","2016-03-06"))
> 
> gw<-handle_cimis(action="download_weather",location="6",time_interval=c(1982,1982),
+   station_list=stat_list)
trying URL 'ftp://ftpcimis.water.ca.gov/pub2/annualMetric/dailyStns1982.zip'
Warning in handle_cimis(action = "download_weather", location = "6", time_interval = c(1982,  :
  No weather data found for the time interval of interest.
> weather<-handle_cimis(gw)$weather
Error in `colnames<-`(`*tmp*`, value = `*vtmp*`) : 
  attempt to set 'colnames' on an object with less than two dimensions
Calls: handle_cimis -> colnames<-
Execution halted
Found the following significant warnings:
  chnpgt_boot.cc:70:19: warning: 'crossprod1' has C-linkage specified, but returns user-defined type 'Matrix<>' which is incompatible with C [-Wreturn-type-c-linkage]
See ‘/data/gannet/ripley/R/packages/tests-clang/chngpt.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tools’
  All declared Imports should be used.
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘stringr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘base64enc’ ‘rgl’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 21.9Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    extdata  12.4Mb
Running examples in ‘climtrends-Ex.R’ failed
The error most likely occurred in:

> ### Name: ReadEtmgegFile
> ### Title: Read USHCN files
> ### Aliases: ReadEtmgegFile
> ### Keywords: programming
> 
> ### ** Examples
> 
> # data from the ECA station series of Eelde (The Netherlands) from 1900 to 2000
> EtmgegData<-ReadEtmgegFile('etmgeg_280.txt',c(2,12,13,15))
Warning in file(file, "rt") :
  cannot open file 'etmgeg_280.txt': No such file or directory
Error in file(file, "rt") : cannot open the connection
Calls: ReadEtmgegFile -> read.csv -> read.table -> file
Execution halted
Running examples in ‘CLME-Ex.R’ failed
The error most likely occurred in:

> ### Name: VarCorr
> ### Title: Variance components
> ### Aliases: VarCorr VarCorr.summary.clme VarCorr.clme
> 
> ### ** Examples
> 
> 
> data( rat.blood )
> cons <- list(order = "simple", decreasing = FALSE, node = 1 )
> clme.out <- clme(mcv ~ time + temp + sex + (1|id), data = rat.blood , 
+                  constraints = cons, seed = 42, nsim = 0)
>                  
> VarCorr( clme.out )
Error in dimnames(x) <- dn : 
  length of 'dimnames' [1] not equal to array extent
Calls: VarCorr -> VarCorr.clme -> rownames<-
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(clust.bin.pair)
  > 
  > test_check("clust.bin.pair")
  ── 1. Error: McNemar scores datasets correctly (@test_clust_bin_pair.R#11)  ────
  'check.attributes' must be logical
  1: expect_equal(.mcnemar.impl(psychiatry$bh, psychiatry$ch), 11.85, tolerance = 0.1, 
         scale = NULL, "psychiatry") at testthat/test_clust_bin_pair.R:11
  2: compare(act$val, exp$val, ...)
  3: compare.numeric(act$val, exp$val, ...)
  4: all.equal(x, y, tolerance = tolerance, check.attributes = check.attributes, ...)
  5: all.equal.numeric(x, y, tolerance = tolerance, check.attributes = check.attributes, 
         ...)
  6: stop(gettextf("'%s' must be logical", "check.attributes"), domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 44 SKIPPED: 0 FAILED: 1
  1. Error: McNemar scores datasets correctly (@test_clust_bin_pair.R#11) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘R6’ ‘infuser’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
    pdf   2.2Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data     3.5Mb
    exdata   5.5Mb
Package suggested but not available for checking: ‘CNVtools’
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘grid’ ‘gridExtra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rscala’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    app   2.6Mb
    doc   2.2Mb
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘PearsonDS’ ‘VGAM’ ‘actuar’ ‘fExtremes’ ‘rmutil’
  All declared Imports should be used.
Found the following significant warnings:
  Utility.c:162:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:187:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:211:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:392:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:417:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:442:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/CompRandFld.Rcheck/00install.out’ for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data      6.5Mb
    extdata   2.6Mb
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘MASS’ ‘geepack’
  All declared Imports should be used.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   6.5Mb
Namespaces in Imports field not imported from:
  ‘Rtsne’ ‘scatterplot3d’
  All declared Imports should be used.
installed size is 28.7Mb
  sub-directories of 1Mb or more:
    libs  28.4Mb
Namespace in Imports field not imported from: ‘xtable’
  All declared Imports should be used.
Package in Depends field not imported from: ‘calibrate’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   4.8Mb
Namespace in Imports field not imported from: ‘maps’
  All declared Imports should be used.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Namespace in Imports field not imported from: ‘gstat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘misc3d’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is 38.5Mb
  sub-directories of 1Mb or more:
    libs  38.3Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
QR.cd: no visible global function definition for ‘quantile’
QR.lasso.cd: no visible global function definition for ‘quantile’
cqr.cd: no visible global function definition for ‘quantile’
cqr.lasso.cd: no visible global function definition for ‘quantile’
cqr.lasso.mm: no visible global function definition for ‘quantile’
cqr.mm: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
File ‘cqrReg/libs/cqrReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 11 marked Latin-1 strings
  Note: found 57 marked UTF-8 strings
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    libs  21.3Mb
Namespace in Imports field not imported from: ‘httpcode’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘qte’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    shp   7.8Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data  10.9Mb
Note: found 59670 marked Latin-1 strings
  Note: found 16 marked UTF-8 strings
Found the following significant warnings:
  ./ctl.h:38:23: warning: token pasting of ',' and __VA_ARGS__ is a GNU extension [-Wgnu-zero-variadic-macro-arguments]
  ./ctl.h:36:25: warning: token pasting of ',' and __VA_ARGS__ is a GNU extension [-Wgnu-zero-variadic-macro-arguments]
See ‘/data/gannet/ripley/R/packages/tests-clang/ctl.Rcheck/00install.out’ for details.
installed size is 32.0Mb
  sub-directories of 1Mb or more:
    extdata  31.9Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   5.0Mb
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    libs  20.7Mb
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DBI’ ‘Demerelate’ ‘misc3d’ ‘plotly’ ‘quadprog’ ‘rgl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
.onLoad : <anonymous>: no visible global function definition for
  ‘read.table’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbConnect’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbListTables’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbExistsTable’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbReadTable’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbWriteTable’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbDisconnect’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbRemoveTable’
Undefined global functions or variables:
  dbConnect dbDisconnect dbExistsTable dbListTables dbReadTable
  dbRemoveTable dbWriteTable read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
installed size is 72.7Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  70.5Mb
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
Running ‘testthat.R’ [16s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("data.tree")
  Loading required package: data.tree
  ── 1. Error: partykid (@test-treeConversionParty.R#37)  ────────────────────────
  could not find function "extree_data"
  1: partykit::ctree(Ozone ~ ., data = airq) at testthat/test-treeConversionParty.R:37
  2: eval(mf, parent.frame())
  3: eval(mf, parent.frame())
  
                            levelName    cost
  1  Acme Inc.                             NA
  2   ¦--Accounting                        NA
  3   ¦   ¦--New Software             1000000
  4   ¦   °--New Accounting Standards  500000
  5   ¦--Research                          NA
  6   ¦   ¦--New Product Line         2000000
  7   ¦   °--New Labs                  750000
  8   °--IT                                NA
  9       ¦--Outsource                 400000
  10      ¦--Go agile                  250000
  11      °--Switch to R                50000
    levelName  b             1
  1 Root      NA              
  2  °--a      2              
  3      °--c NA 1, 2, 3, 4, 5
    levelName a
  1     Root   
  2      °--a 2
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 352 SKIPPED: 2 FAILED: 1
  1. Error: partykid (@test-treeConversionParty.R#37) 
  
  Error: testthat unit tests failed
  Execution halted
browse: no visible global function definition for ‘slot’
browse: no visible global function definition for ‘page’
default.options: no visible binding for global variable ‘object.size’
heat.view: no visible global function definition for ‘head’
heat.view: no visible global function definition for ‘tail’
whos: no visible global function definition for ‘slotNames’
whos : <anonymous> : <anonymous>: no visible global function definition
  for ‘slot’
Undefined global functions or variables:
  head object.size page slot slotNames tail
Consider adding
  importFrom("methods", "slot", "slotNames")
  importFrom("utils", "head", "object.size", "page", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Compilation used the following non-portable flag(s):
  ‘-Werror’
Namespace in Imports field not imported from: ‘desc’
  All declared Imports should be used.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   6.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
Namespace in Imports field not imported from: ‘CDM’
  All declared Imports should be used.
Running examples in ‘ddeploy-Ex.R’ failed
The error most likely occurred in:

> ### Name: duke_predict
> ### Title: Predict using deployed model using REST API.
> ### Aliases: duke_predict
> 
> ### ** Examples
> 
> duke_auth <- list(
+ user_name = "try_it",
+ api_key   = "db1542b66f16aba5768d8a19c27dec4facf9168a",
+ endpoint = "/api/v1.0"
+ )
> example_data <- as.data.frame(cbind(gl(3,50),rnorm(150)));names(example_data) <- c("x","y")
> duke_predict(auth_details=duke_auth,model_name="example_fit",example_data)
Error: lexical error: invalid char in json text.
                                       <html>   <head>     <title>Inte
                     (right here) ------^
Execution halted
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    libs  23.8Mb
'library' or 'require' call to ‘UScensus2010’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘UScensus2010’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘JavaGD’ ‘OpenStreetMap’ ‘maptools’ ‘rgdal’ ‘scales’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Note: found 83 marked Latin-1 strings
  Note: found 71 marked UTF-8 strings
Bootstrapping.CI: no visible global function definition for ‘quantile’
D.Jost: no visible global function definition for ‘read.table’
D.Jost: no visible global function definition for ‘write.table’
Dv.locis.corrected.calc: no visible global function definition for
  ‘p.adjust’
Gst.Nei: no visible global function definition for ‘read.table’
Gst.Nei: no visible global function definition for ‘write.table’
H.out: no visible global function definition for ‘write.table’
Hardy.calc: no visible global function definition for ‘chisq.test’
critical.ci.values: no visible global function definition for
  ‘quantile’
inputformat: no visible global function definition for ‘read.table’
inputformat: no visible global function definition for ‘write.table’
over.all.pops: no visible global function definition for ‘write.table’
p.value.correcture: no visible global function definition for
  ‘p.adjust’
pair.pops: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  chisq.test p.adjust quantile read.table write.table
Consider adding
  importFrom("stats", "chisq.test", "p.adjust", "quantile")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
Found the following significant warnings:
  DEploid/updateHap.cpp:670:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
  DEploid/updateHap.cpp:678:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
  DEploid/updateHap.cpp:681:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
  DEploid/updateHap.cpp:682:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/DEploid.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    help   1.3Mb
    libs   1.3Mb
Packages suggested but not available for checking: ‘gurobi’ ‘Rcplex’
Compilation used the following non-portable flag(s):
  ‘-Wstrict-prototypes’
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   2.4Mb
    libs      2.7Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpANLTiW’, resetting
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs  18.3Mb
installed size is 45.7Mb
  sub-directories of 1Mb or more:
    libs  45.3Mb
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  16.9Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
Namespace in Imports field not imported from: ‘mgcv’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gplots’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    include  19.7Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Namespaces in Imports field not imported from:
  ‘GOstats’ ‘caTools’ ‘fdrtool’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Loading required package: doBy
Loading required package: Matrix
Warning in if (class(object) %in% c("matrix", "Matrix")) { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(object) %in% c("matrix", "Matrix")) { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(object) %in% c("matrix", "Matrix")) { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(object) %in% c("matrix", "Matrix")) { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(object) %in% c("matrix", "Matrix")) { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(object) %in% c("matrix", "Matrix")) { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(object) %in% c("matrix", "Matrix")) { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(object) %in% c("matrix", "Matrix")) { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(object) %in% c("matrix", "Matrix")) { :
  the condition has length > 1 and only the first element will be used

Error: processing vignette 'LSmeans.Rnw' failed with diagnostics:
 chunk 47 
Error in VV %*% kk : non-conformable arguments
Execution halted
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   5.6Mb
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘tidyverse’
  All declared Imports should be used.
installed size is 28.0Mb
  sub-directories of 1Mb or more:
    libs  26.1Mb
Found the following significant warnings:
  DPPmcmc.cpp:21:10: warning: field 'model' will be initialized after field 'effectiveSizeFunction' [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-clang/DPP.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘drc’ ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘readr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shapefiles’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   4.9Mb
perturbFBM: warning in circFBM(n, H, plot = FALSE): partial argument
  match of 'plot' to 'plotfBm'
circFBM: no visible global function definition for ‘fft’
circFBM: no visible global function definition for ‘rnorm’
circFBM: no visible global function definition for ‘par’
circFBM: no visible global function definition for ‘plot’
dvFBM: no visible global function definition for ‘filter’
dvFBM: no visible global function definition for ‘quantile’
dvFBM: no visible global function definition for ‘lm’
dvFBM: no visible global function definition for ‘plot’
dvFBM: no visible global function definition for ‘abline’
filt: no visible global function definition for ‘wavDaubechies’
perturbFBM: no visible global function definition for ‘rnorm’
perturbFBM: no visible global function definition for ‘rbinom’
perturbFBM: no visible global function definition for ‘par’
perturbFBM: no visible global function definition for ‘segments’
perturbFBM: no visible global function definition for ‘points’
Undefined global functions or variables:
  abline fft filter lm par plot points quantile rbinom rnorm segments
  wavDaubechies
Consider adding
  importFrom("graphics", "abline", "par", "plot", "points", "segments")
  importFrom("stats", "fft", "filter", "lm", "quantile", "rbinom",
             "rnorm")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘xml2’
  All declared Imports should be used.
installed size is 21.5Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.2Mb
    libs  15.8Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    models   4.3Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘reshape2’ ‘scales’ ‘xtable’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘base64enc’ ‘knitr’ ‘markdown’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Namespaces in Imports field not imported from:
  ‘corrplot’ ‘scorer’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    hac    4.0Mb
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmprCfaG5’, resetting
  Warning: working directory was changed to ‘/tmp/RtmprCfaG5’, resetting
  Warning: working directory was changed to ‘/tmp/RtmprCfaG5’, resetting
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
    doc    1.2Mb
installed size is 44.7Mb
  sub-directories of 1Mb or more:
    libs  44.4Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data  11.5Mb
Namespaces in Imports field not imported from:
  ‘prettyunits’ ‘ratelimitr’ ‘rgdal’
  All declared Imports should be used.
Found the following significant warnings:
  ./Matrix.h:8:36: warning: field 'numrow' will be initialized after field 'numcol' [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-clang/Emcdf.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘FNN’ ‘ggmap’ ‘simFrame’
  All declared Imports should be used.
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  16.1Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/EmiStatR.Rcheck/EmiStatR/shiny/EmiStatR_output’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/EmiStatR.Rcheck/EmiStatR/shiny/EmiStatR_output’, resetting
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    xsd   5.4Mb
'library' or 'require' calls to packages already attached by Depends:
  ‘clusterSim’ ‘earth’
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘clusterSim’ ‘earth’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.5Mb
Error in re-building vignettes:
  ...
'showtext.begin()' is now renamed to 'showtext_begin()'
The old version still works, but consider using the new function in future code
Quitting from lines 46-54 (phylomoji.Rmd) 
Error: processing vignette 'phylomoji.Rmd' failed with diagnostics:
there is no package called 'ggtree'
Execution halted
Note: found 23639 marked Latin-1 strings
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    Sweave   6.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    doc    2.1Mb
Package suggested but not available for checking: ‘faahKO’
Namespace in Imports field not imported from: ‘BiocParallel’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   3.4Mb
Found the following significant warnings:
  input2.c:767:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/epanet2toolkit.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘ROCR’ ‘c060’ ‘methods’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘colorspace’
  All declared Imports should be used.
Running examples in ‘Epi-Ex.R’ failed
The error most likely occurred in:

> ### Name: LCa.fit
> ### Title: Fit Lee-Carter-type models for rates to arbitrarily shaped
> ###   observations of rates in a Lexis diagram.
> ### Aliases: LCa.fit print.LCa summary.LCa plot.LCa predict.LCa
> ### Keywords: models regression
> 
> ### ** Examples
> 
> library( Epi )
> # Load the testis cancer data by Lexis triangles
> data( testisDK )
> tc <- subset( testisDK, A>14 & A<60 )
> head( tc )
    A    P D        Y
16 15 1943 0 31188.00
17 16 1943 0 31654.33
18 17 1943 0 32084.33
19 18 1943 0 32681.67
20 19 1943 0 33005.67
21 20 1943 0 33302.67
> 
> # We want to see rates per 100,000 PY
> tc$Y <- tc$Y / 10^5
> 
> # Fit the Lee-Carter model with age-period interaction (default)
> LCa.tc <- LCa.fit( tc, model="ACa", a.ref=30, p.ref=1980, quiet=FALSE, eps=10e-4, maxit=50 )
Error in vM[!is.na(cf), !is.na(cf)] <- vcv : 
  number of items to replace is not a multiple of replacement length
Calls: LCa.fit -> cbind -> ci.lin
Execution halted
Namespaces in Imports field not imported from:
  ‘llogistic’ ‘logitnorm’
  All declared Imports should be used.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘readr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘signal’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘EnvStats’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
Namespaces in Imports field not imported from:
  ‘curl’ ‘openxlsx’ ‘stringr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘polynom’
  All declared Imports should be used.
print.cdf : numform: warning in formatC(x, dig = digits): partial
  argument match of 'dig' to 'digits'
print.cdf: warning in get("x", env = environment(x)): partial argument
  match of 'env' to 'envir'
print.cdf: warning in get("y", env = environment(x)): partial argument
  match of 'env' to 'envir'
print.ogive : numform: warning in formatC(x, dig = digits): partial
  argument match of 'dig' to 'digits'
print.ogive: warning in get("x", env = environment(x)): partial
  argument match of 'env' to 'envir'
print.ogive: warning in get("y", env = environment(x)): partial
  argument match of 'env' to 'envir'
quantile.expert: warning in formatC(paste(100 * probs, "%", sep = ""),
  format = "fg", wid = 1, digits = dig): partial argument match of
  'wid' to 'width'
MS: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: iteration 7 invokes undefined behavior [-Waggressive-loop-optimizations]
See ‘/data/gannet/ripley/R/packages/tests-clang/expoRkit.Rcheck/00install.out’ for details.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
Running examples in ‘eyetrackingR-Ex.R’ failed
The error most likely occurred in:

> ### Name: analyze_time_clusters
> ### Title: Bootstrap analysis of time-clusters.
> ### Aliases: analyze_time_clusters analyze_time_clusters.time_cluster_data
> 
> ### ** Examples
> 
> data(word_recognition)
> data <- make_eyetrackingr_data(word_recognition, 
+                                participant_column = "ParticipantName",
+                                trial_column = "Trial",
+                                time_column = "TimeFromTrialOnset",
+                                trackloss_column = "TrackLoss",
+                                aoi_columns = c('Animate','Inanimate'),
+                                treat_non_aoi_looks_as_missing = TRUE )
`mutate_each()` is deprecated.
Use `mutate_all()`, `mutate_at()` or `mutate_if()` instead.
To map `funs` over a selection of variables, use `mutate_at()`
> response_window <- subset_by_window(data, window_start_time = 15500, window_end_time = 21000, 
+                                     rezero = FALSE)
Avg. window length in new data will be 5500
> response_time <- make_time_sequence_data(response_window, time_bin_size = 500, aois = "Animate", 
+                                          predictor_columns = "Sex")
> 
> time_cluster_data <- make_time_cluster_data(data = response_time, predictor_column = "SexM", 
+                          aoi = "Animate", test = "lmer", 
+                          threshold = 1.5, 
+                          formula = LogitAdjusted ~ Sex + (1|Trial) + (1|ParticipantName))
Error in UseMethod("analyze_time_bins") : 
  no applicable method for 'analyze_time_bins' applied to an object of class "data.frame"
Calls: make_time_cluster_data ... make_time_cluster_data.time_sequence_data -> do.call -> <Anonymous>
Execution halted
Running ‘testthat.R’ [124s/149s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(eyetrackingR)
  > 
  > test_check("eyetrackingR")
  Test Type:	 lmer 
  Predictor:	 (Intercept) 
  Formula:	 Prop ~ AOI + (1 | Trial) 
  Runs of Significant Time Bins: 
  Positive Run 1  ===== 
  	Time:		 15500 - 21000 Test Type:	 boot_splines 
  Predictor:	 Target 
  Formula:	 Prop ~ Target 
  Runs of Significant Time Bins: 
  Positive Run 1  ===== 
  	Time:		 15800 - 21000 ── 1. Error: (unknown) (@test_cluster_analysis.R#143)  ─────────────────────────
  no applicable method for 'make_time_cluster_data' applied to an object of class "data.frame"
  1: make_time_cluster_data(response_time_by_ppt, predictor_column = "Sex", test = "boot_splines", 
         within_subj = FALSE, smoother = "smooth.spline", alpha = 0.05) at testthat/test_cluster_analysis.R:143
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 42 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_cluster_analysis.R#143) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
pandoc: Could not fetch http://ropensci.org/public_images/github_footer.png
HttpExceptionRequest Request {
  host                 = "ropensci.org"
  port                 = 80
  secure               = False
  requestHeaders       = []
  path                 = "/public_images/github_footer.png"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (InternalException (HandshakeFailed Error_EOF))
Error: processing vignette 'ezknitr.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  15.6Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.9Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    libs  17.2Mb
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/data/gannet/ripley/R/packages/tests-clang/FastRWeb.Rcheck/00install.out’ for details.
Found the following significant warnings:
  fasttext.cc:121:27: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
  fasttext.cc:137:27: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/fastTextR.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘whisker’
  All declared Imports should be used.
Found the following significant warnings:
  cgFbat.cpp:222:13: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  cgFbat.cpp:265:13: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  cgFbat.cpp:358:40: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  cgFbat.cpp:2210:14: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  rmatrix.cpp:23:8: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  rmatrix.cpp:23:23: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  rmatrix.cpp:33:8: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  rmatrix.cpp:33:23: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  rvector.cpp:23:8: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  rvector.cpp:34:8: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/fbati.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.6Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is 51.0Mb
  sub-directories of 1Mb or more:
    libs  50.2Mb
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    libs  22.0Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   7.0Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Found the following significant warnings:
  ff.cpp:256:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ff.cpp:256:54: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/data/gannet/ripley/R/packages/tests-clang/ff.Rcheck/00install.out’ for details.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/FishResp.Rcheck/FishResp’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/FishResp.Rcheck/FishResp’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/FishResp.Rcheck/FishResp’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/FishResp.Rcheck/FishResp’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/FishResp.Rcheck/FishResp’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/FishResp.Rcheck/FishResp’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/FishResp.Rcheck/FishResp’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/FishResp.Rcheck/FishResp’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/FishResp.Rcheck/FishResp’, resetting
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Running ‘boot.R’
  Running ‘disttests.R’
  Running ‘grouping.R’
  Running ‘plots.R’
  Running ‘weights.R’
Running the tests in ‘tests/disttests.R’ failed.
Complete output:
  > library(flexclust)
  Loading required package: grid
  Loading required package: lattice
  Loading required package: modeltools
  Loading required package: stats4
  > 
  > ## create a random matrix
  > x <- matrix(rnorm(1000), ncol=4)
  > rownames(x) <- 1:nrow(x)
  > 
  > ## test canberra at margin
  > x[1:10,1] <- 0
  > x[1:20,2] <- 0
  > x[1:30,3] <- 0
  > 
  > stopifnot(all.equal(dist2(x,x,"eucl"), as.matrix(dist(x, "eucl"))))
  > stopifnot(all.equal(dist2(x,x,"man"), as.matrix(dist(x, "man"))))
  > stopifnot(all.equal(dist2(x,x,"max"), as.matrix(dist(x, "max"))))
  > stopifnot(all.equal(dist2(x,x,"bin"), as.matrix(dist(x, "bin"))))
  > stopifnot(all.equal(dist2(x,x,"can"), as.matrix(dist(x, "can"))))
  Error: dist2(x, x, "can") and as.matrix(dist(x, "can")) are not equal:
    Mean relative difference: 0.9706689
  Execution halted
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R   6.3Mb
Package required but not available: ‘flowWorkspace’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘stats’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
Running examples in ‘forega-Ex.R’ failed
The error most likely occurred in:

> ### Name: ForecastArima
> ### Title: Floating-Point Genetic Algorithms with Statistical Forecast
> ###   Based Inheritance Operator
> ### Aliases: ForecastArima
> ### Keywords: methods
> 
> ### ** Examples
> 
> 
> # Required package forega
> require("forega")
> 
> set.seed(12345)
> 
> # This function has the global minimum at x_1 = pi and x_2 = exp(1)
> f <- function (x){
+ 	return( (x[1]-pi)^2 + (x[2]-2.71828)^2 )
+ }
> 
> # Performing a floating-point genetic algorithm search with forecast probability of 0.10
> res <- forecasting_ga(evalFunc=f, chsize=2, minv=rep(-10.0,2),
+                       maxv=rep(10.0,2), crossprob=0.80, mutationprob=0.01, 
+                       popsize=100, maxiter=1000, MinimumForecastLength=20, 
+                       ForecastFunction=ForecastArima, elitism=2, forecastprob=0.01)
Error in forecasting_ga(evalFunc = f, chsize = 2, minv = rep(-10, 2),  : 
  Evaluation error: only replacement of elements is allowed.
Calls: forecasting_ga -> .Call
Execution halted
Namespaces in Imports field not imported from:
  ‘base’ ‘pbapply’ ‘stringr’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Found the following significant warnings:
  hcubature.c:923:12: warning: comparison of unsigned enum expression < 0 is always false [-Wtautological-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/frailtySurv.Rcheck/00install.out’ for details.
Found the following significant warnings:
  psplines.c:975:16: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  psplines.c:1087:15: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/freeknotsplines.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   5.7Mb
Package which this enhances but not available for checking: ‘dggrids’
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    1.6Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   8.8Mb
Namespaces in Imports field not imported from:
  ‘R.utils’ ‘grDevices’ ‘graphics’ ‘matrixStats’ ‘stats’
  All declared Imports should be used.
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
fuzzyBHexact: warning in round(pvals, d = dp): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(pprev, d = dp): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(p.minus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(p.plus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(a.minus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(a.plus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(new.p.minus, d = 4): partial argument
  match of 'd' to 'digits'
fuzzyBHexact: warning in round(new.p.plus, d = 4): partial argument
  match of 'd' to 'digits'
fuzzyBHexact: warning in round(pvals, d = 4): partial argument match of
  'd' to 'digits'
fuzzyBHexact: warning in round(pprev, d = 4): partial argument match of
  'd' to 'digits'
fuzzyBHexact: warning in round(tau, d = 4): partial argument match of
  'd' to 'digits'
probRejTies: no visible binding for global variable ‘nn’
Undefined global functions or variables:
  nn
Running ‘testthat.R’ [54s/52s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fuzzyjoin)
  > 
  > test_check("fuzzyjoin")
  ── 1. Failure: Can do inner joins on intervals with findOverlaps arguments (@tes
  j_maxgap$id1 not equal to c(1, 1, 2, 2, 3).
  Lengths differ: 6 is not 5
  
  ── 2. Failure: Can do inner joins on intervals with findOverlaps arguments (@tes
  j_maxgap$id2 not equal to c(1, 2, 1, 2, 3).
  Lengths differ: 6 is not 5
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 224 SKIPPED: 0 FAILED: 2
  1. Failure: Can do inner joins on intervals with findOverlaps arguments (@test_interval_join.R#50) 
  2. Failure: Can do inner joins on intervals with findOverlaps arguments (@test_interval_join.R#51) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘maptools’ ‘rgeos’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘gamlss’
  All declared Imports should be used.
finterp.data.frame: no visible global function definition for
  ‘as.formula’
finterp.data.frame: no visible global function definition for ‘terms’
finterp.data.frame: no visible global function definition for
  ‘model.matrix’
finterp.data.frame: no visible global function definition for
  ‘model.frame’
finterp.default: no visible global function definition for ‘terms’
finterp.default: no visible global function definition for
  ‘model.matrix’
finterp.default: no visible global function definition for
  ‘model.frame’
gamlss.nl: no visible global function definition for ‘nlm’
nl: no visible global function definition for ‘is’
nlgamlss: no visible global function definition for ‘NO’
nlgamlss: no visible global function definition for ‘as.gamlss.family’
nlgamlss: no visible global function definition for ‘nlm’
nlgamlss: no visible global function definition for ‘cov2cor’
summary.nlgamlss: no visible global function definition for ‘coef’
summary.nlgamlss: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  NO as.formula as.gamlss.family coef cov2cor is model.frame
  model.matrix nlm pnorm terms
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "as.formula", "coef", "cov2cor", "model.frame",
             "model.matrix", "nlm", "pnorm", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   8.2Mb
installed size is 62.5Mb
  sub-directories of 1Mb or more:
    libs  62.1Mb
Found the following significant warnings:
  m4_prod2_ms.cpp:25:73: warning: field 'v' will be initialized after field 'r' [-Wreorder]
  m4_prod2_ms.cpp:31:36: warning: field 'v' will be initialized after field 'r' [-Wreorder]
  m4_prod2_p.cpp:24:65: warning: field 'v' will be initialized after field 'r' [-Wreorder]
  m4_prod2_p.cpp:31:36: warning: field 'v' will be initialized after field 'r' [-Wreorder]
  m4_prod_ms.cpp:26:75: warning: field 'v' will be initialized after field 'r' [-Wreorder]
  m4_prod_p.cpp:25:64: warning: field 'v' will be initialized after field 'r' [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-clang/gaston.Rcheck/00install.out’ for details.
installed size is 70.7Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     67.7Mb
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  15.5Mb
Found the following significant warnings:
  cGetHCS.c:9:33: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  cIdentical.c:9:34: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/gdmp.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘rootSolve’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    java   5.4Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   4.7Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Found the following significant warnings:
  mpi.c:3951:10: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/GENLIB.Rcheck/00install.out’ for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    exdata   5.1Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.4Mb
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    data  26.0Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   8.7Mb
Error in re-building vignettes:
  ...
pandoc: Could not fetch http://www.ropensci.org/public_images/github_footer.png
HttpExceptionRequest Request {
  host                 = "www.ropensci.org"
  port                 = 80
  secure               = False
  requestHeaders       = []
  path                 = "/public_images/github_footer.png"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (InternalException (HandshakeFailed Error_EOF))
Error: processing vignette 'geoparser.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
Execution halted
Namespace in Imports field not imported from: ‘velociraptr’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘shinydashboard’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘alluvial’ ‘grid’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘plotly’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   6.1Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggmap’ ‘gridExtra’ ‘scales’ ‘tnet’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Namespaces in Imports field not imported from:
  ‘GGEBiplotGUI’ ‘gge’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colorspace’ ‘grid’ ‘rstan’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Quitting from lines 187-193 (ggformula.Rmd) 
Error: processing vignette 'ggformula.Rmd' failed with diagnostics:
there is no package called 'statisticalModeling'
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Running examples in ‘ggfortify-Ex.R’ failed
The error most likely occurred in:

> ### Name: gglagplot
> ### Title: Plot time series against lagged versions of themselves
> ### Aliases: gglagplot
> 
> ### ** Examples
> 
> gglagplot(AirPassengers)
Error: `x` must be a vector, not a ts object, do you want `stats::lag()`?
Execution halted
Running ‘test-all.R’ [95s/116s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check('ggfortify')
  Loading required package: ggfortify
  Loading required package: ggplot2
  initial  value 7.505733 
  final  value 7.505688 
  converged
  Initial stress        : 0.01705
  stress after  10 iters: 0.00951, magic = 0.500
  stress after  20 iters: 0.00941, magic = 0.500
  initial  value 7.505733 
  final  value 7.505688 
  converged
  Initial stress        : 0.01705
  stress after  10 iters: 0.00951, magic = 0.500
  stress after  20 iters: 0.00941, magic = 0.500
  ── 1. Error: gglagplot (@test-tslib.R#103)  ────────────────────────────────────
  `x` must be a vector, not a ts object, do you want `stats::lag()`?
  1: gglagplot(AirPassengers) at testthat/test-tslib.R:103
  2: dplyr::bind_rows(lapply(seq(1:lags), .lag))
  3: flatten_bindable(dots_values(...))
  4: dots_values(...)
  5: map(dots, function(dot) eval_bare(dot$expr, dot$env))
  6: lapply(.x, .f, ...)
  7: FUN(X[[i]], ...)
  8: eval_bare(dot$expr, dot$env)
  9: lapply(seq(1:lags), .lag)
  10: FUN(X[[i]], ...)
  11: as.vector(lag(ts, k))
  12: lag(ts, k)
  13: bad_args("x", "must be a vector, not a ts object, do you want `stats::lag()`?")
  14: glubort(fmt_args(args), ..., .envir = .envir)
  15: .abort(text)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1442 SKIPPED: 9 FAILED: 1
  1. Error: gglagplot (@test-tslib.R#103) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘lazyeval’ ‘readr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘XML’ ‘mapproj’ ‘moonBook’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘NHANES’ ‘gridExtra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gcookbook’ ‘ggthemes’ ‘moonBook’ ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘plyr’ ‘reshape2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘randomForest’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   2.0Mb
Namespaces in Imports field not imported from:
  ‘DBI’ ‘GGally’ ‘RColorBrewer’ ‘Rcpp’ ‘assertthat’ ‘backports’
  ‘colorspace’ ‘colourpicker’ ‘evaluate’ ‘futile.options’ ‘gdtools’
  ‘gtable’ ‘htmltools’ ‘htmlwidgets’ ‘httpuv’ ‘labeling’ ‘lambda.r’
  ‘lazyeval’ ‘magrittr’ ‘miniUI’ ‘munsell’ ‘plyr’ ‘reshape’ ‘rprojroot’
  ‘scales’ ‘stringi’ ‘stringr’ ‘svglite’ ‘tibble’ ‘xtable’ ‘yaml’
  All declared Imports should be used.
Found the following significant warnings:
  mainSVMtrain.cpp:296:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
  mainSVMtrain.cpp:297:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
See ‘/data/gannet/ripley/R/packages/tests-clang/gkmSVM.Rcheck/00install.out’ for details.
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    libs  28.4Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is 50.8Mb
  sub-directories of 1Mb or more:
    libs  50.1Mb
Error in re-building vignettes:
  ...
Quitting from lines 346-355 (glmmsr-vignette.Rmd) 
Error: processing vignette 'glmmsr-vignette.Rmd' failed with diagnostics:
incorrect number of dimensions
Execution halted
installed size is 45.1Mb
  sub-directories of 1Mb or more:
    libs  44.0Mb
Package suggested but not available for checking: ‘cplexAPI’
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  16.9Mb
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 ‘/data/gannet/ripley/R/packages/tests-clang/gnmf.Rcheck/00install.out’ for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R   5.7Mb
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Found the following significant warnings:
  findEd.c:1061:26: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/gRapHD.Rcheck/00install.out’ for details.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Namespaces in Imports field not imported from:
  ‘methods’ ‘raster’ ‘rgeos’ ‘sp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘deldir’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘BiasedUrn’
  All declared Imports should be used.
Found the following significant warnings:
  hmg.cpp:22:9: warning: field 'p' will be initialized after field 'tau_par' [-Wreorder]
  hmg.cpp:22:51: warning: field 'gamma_par' will be initialized after field 'alpha' [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-clang/grove.Rcheck/00install.out’ for details.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Namespace in Imports field not imported from: ‘rrcov’
  All declared Imports should be used.
installed size is 126.0Mb
  sub-directories of 1Mb or more:
    java  124.6Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
Found the following significant warnings:
  SNPHWEX.cpp:50:31: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  SNPHWEX.cpp:51:65: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/data/gannet/ripley/R/packages/tests-clang/HardyWeinberg.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ./City.h:82:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  City.cpp:93:26: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  City.cpp:94:26: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  City.cpp:95:26: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  City.cpp:96:26: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  MurmurHash3.cpp:87:8: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  MurmurHash3.cpp:89:8: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  MurmurHash3.cpp:267:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  MurmurHash3.cpp:268:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ./Spooky.h:285:36: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/data/gannet/ripley/R/packages/tests-clang/hashFunction.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ../inst/include/hashmap/sparsepp/spp.h:2342:21: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ../inst/include/hashmap/sparsepp/spp.h:2365:22: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/data/gannet/ripley/R/packages/tests-clang/hashmap.Rcheck/00install.out’ for details.
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
Namespace in Imports field not imported from: ‘hms’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
Found the following significant warnings:
  lassoModels/IPenalizedSolver.h:117:27: warning: field 'p_y_' will be initialized after field 'threshold_' [-Wreorder]
  lassoModels/IPenalizedSolver.h:136:25: warning: field 'p_y_' will be initialized after field 'threshold_' [-Wreorder]
  lassoModels/LogisticFusedLassoSolver.cpp:59:77: warning: field 'cginit_' will be initialized after field 'p_penalty_' [-Wreorder]
  ./lassoModels/IPenalizedSolver.h:117:27: warning: field 'p_y_' will be initialized after field 'threshold_' [-Wreorder]
  ./lassoModels/IPenalizedSolver.h:136:25: warning: field 'p_y_' will be initialized after field 'threshold_' [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-clang/HDPenReg.Rcheck/00install.out’ for details.
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  18.7Mb
Namespace in Imports field not imported from: ‘ratelimitr’
  All declared Imports should be used.
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    doc          13.7Mb
    htmlwidgets   1.9Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    highlight   1.1Mb
    libs        6.9Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   4.0Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
print.summary.hotspots: warning in sort(x$data, dec = TRUE): partial
  argument match of 'dec' to 'decreasing'
print.summary.hotspots: warning in sort(x$disprop$positive, dec =
  TRUE): partial argument match of 'dec' to 'decreasing'
print.summary.hotspots: warning in sort(x$disprop$negative, dec =
  TRUE): partial argument match of 'dec' to 'decreasing'
Lchs: no visible global function definition for ‘plot’
Lchs: no visible global function definition for ‘points’
disprop: no visible global function definition for ‘median’
hotspots: no visible global function definition for ‘median’
hotspots: no visible global function definition for ‘qnorm’
hotspots: no visible global function definition for ‘qt’
plot.hotspots: no visible global function definition for ‘par’
summary.hotspots: no visible global function definition for ‘median’
Undefined global functions or variables:
  median par plot points qnorm qt
Consider adding
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "median", "qnorm", "qt")
to your NAMESPACE file.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   2.5Mb
Found the following significant warnings:
  language.c:41:5: warning: flexible array initialization is a GNU extension [-Wgnu-flexible-array-initializer]
See ‘/data/gannet/ripley/R/packages/tests-clang/htmltidy.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘igraph’
  All declared Imports should be used.
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    data  12.3Mb
    doc    1.0Mb
Compilation used the following non-portable flag(s):
  ‘-Wno-unused-parameter’
including flag(s) suppressing warnings
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/Rtmp2XUiV6’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp2XUiV6’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp2XUiV6’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp2XUiV6’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp2XUiV6’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp2XUiV6’, resetting
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    dict   1.3Mb
    libs   4.4Mb
hyper.plot2d: warning in magmap(sigmas, lo = sigscale[1], hi =
  sigscale[2], flip = TRUE, type = "num"): partial argument match of
  'lo' to 'locut'
hyper.plot2d: warning in magmap(sigmas, lo = sigscale[1], hi =
  sigscale[2], flip = TRUE, type = "num"): partial argument match of
  'hi' to 'hicut'
hyper.plot2d: warning in magmap(seq(sigscale[1], sigscale[2], len =
  100), lo = sigscale[1], hi = sigscale[2], flip = TRUE, type = "num"):
  partial argument match of 'lo' to 'locut'
hyper.plot2d: warning in magmap(seq(sigscale[1], sigscale[2], len =
  100), lo = sigscale[1], hi = sigscale[2], flip = TRUE, type = "num"):
  partial argument match of 'hi' to 'hicut'
hyper.plot3d: warning in magmap(sigmas, lo = sigscale[1], hi =
  sigscale[2], flip = TRUE, type = "num"): partial argument match of
  'lo' to 'locut'
hyper.plot3d: warning in magmap(sigmas, lo = sigscale[1], hi =
  sigscale[2], flip = TRUE, type = "num"): partial argument match of
  'hi' to 'hicut'
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘ggplot2’ ‘pander’
  All declared Imports should be used.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   5.1Mb
Found the following significant warnings:
  IBDsim.c:27:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:39:20: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:54:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:61:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/IBDsim.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.2Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   3.3Mb
Note: found 14 marked Latin-1 strings
  Note: found 39 marked UTF-8 strings
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   1.3Mb
    doc    2.2Mb
    libs   1.3Mb
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      2.0Mb
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  23.7Mb
Found the following significant warnings:
  src/foreign-pajek-parser.y:449:41: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  src/foreign-pajek-parser.y:453:44: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  src/foreign-pajek-parser.y:464:41: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  src/foreign-pajek-parser.y:468:44: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  ./vector.pmt:1971:19: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  ./vector.pmt:1971:19: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/igraph.Rcheck/00install.out’ for details.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs  15.2Mb
installed size is 37.6Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       4.9Mb
    extdata   1.0Mb
    include   2.8Mb
    libs     27.0Mb
Namespace in Imports field not imported from: ‘jpeg’
  All declared Imports should be used.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R  10.7Mb
Namespace in Imports field not imported from: ‘mediation’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘count_compare’
Namespaces in Imports field not imported from:
  ‘lme4’ ‘reshape2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘rgeos’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘prodlim’
  All declared Imports should be used.
Found the following significant warnings:
  ./s_hull_pro.h:77:39: warning: field 'ro' will be initialized after field 'tr' [-Wreorder]
  ./s_hull_pro.h:77:57: warning: field 'tc' will be initialized after field 'id' [-Wreorder]
  ./s_hull_pro.h:78:48: warning: field 'ro' will be initialized after field 'id' [-Wreorder]
  ./s_hull_pro.h:115:35: warning: field 'c' will be initialized after field 'id' [-Wreorder]
  ./s_hull_pro.h:116:42: warning: field 'c' will be initialized after field 'id' [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-clang/interp.Rcheck/00install.out’ for details.
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    libs  25.9Mb
Namespace in Imports field not imported from: ‘png’
  All declared Imports should be used.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.4Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   6.8Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘gridExtra’ ‘rBayesianOptimization’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colorRamps’ ‘virtualspecies’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘fAssets’ ‘timeDate’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   6.4Mb
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘GGally’ ‘GPArotation’ ‘PMCMR’ ‘R6’ ‘afex’ ‘car’
  ‘ggridges’ ‘lavaan’ ‘lsmeans’ ‘multcomp’ ‘mvnormtest’ ‘psych’ ‘vcd’
  ‘vcdExtra’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.6Mb
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    include   1.5Mb
    libs      3.8Mb
    zmq       2.4Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/KATforDCEMRI.Rcheck/KATforDCEMRI_benchmark_test’, resetting
Namespaces in Imports field not imported from:
  ‘lme4’ ‘metafor’ ‘nlme’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespace in Imports field not imported from: ‘kirby21.t1’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Package in Depends field not imported from: ‘cluster’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   3.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    java   6.0Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R   7.3Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘tibble’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpdH8N4H’, resetting
kztp: warning in rowMeans(kztp, dim = 2): partial argument match of
  'dim' to 'dims'
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   8.3Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
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 ‘/data/gannet/ripley/R/packages/tests-clang/LambertW.Rcheck/00install.out’ for details.
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs          13.7Mb
    testdata       1.8Mb
    vignettedata   2.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Namespace in Imports field not imported from: ‘lavaan’
  All declared Imports should be used.
Found the following significant warnings:
  partial_order.cpp:45:51: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/ldat.Rcheck/00install.out’ for details.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    geojson  11.9Mb
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘htmlwidgets’ ‘shiny’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    htmlwidgets   4.5Mb
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘scales’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘memoise’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   7.8Mb
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    doc        1.5Mb
    libs      21.9Mb
    testdata   1.5Mb
lmec: warning in qr.Q(qrZ, compl = TRUE): partial argument match of
  'compl' to 'complete'
lmec: warning in qr.Q(qra, compl = TRUE): partial argument match of
  'compl' to 'complete'
lmec: no visible global function definition for ‘lm’
lmec: no visible global function definition for ‘pnorm’
lmec: no visible global function definition for ‘dnorm’
lmec : vtrnorm2: no visible global function definition for ‘runif’
lmec : vtrnorm2: no visible global function definition for ‘qnorm’
lmec : vtrnorm2: no visible global function definition for ‘pnorm’
lmec: no visible global function definition for ‘rnorm’
lmec: no visible global function definition for ‘ar’
Undefined global functions or variables:
  ar dnorm lm pnorm qnorm rnorm runif
Consider adding
  importFrom("stats", "ar", "dnorm", "lm", "pnorm", "qnorm", "rnorm",
             "runif")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘boot’
  All declared Imports should be used.
Running examples in ‘lmeVarComp-Ex.R’ failed
The error most likely occurred in:

> ### Name: pseudo.rlr.test
> ### Title: Pseudo Restricted Likelihood Ratio Test for Zero Variance
> ###   Components
> ### Aliases: pseudo.rlr.test
> 
> ### ** Examples
> 
> # two-way random effects ANOVA
> n1 <- 5L
> n2 <- 6L
> n0 <- 4L
> n <- n1 * n2 * n0
> X <- cbind(rep(1, n))
> A <- gl(n1, n2 * n0)
> Z1 <- model.matrix(~ -1 + A, contrasts.arg = contr.treatment)
> B <- rep(gl(n2, n0), n1)
> Z2 <- model.matrix(~ -1 + B, contrasts.arg = contr.treatment)
> Z3 <- model.matrix(~ -1 + B : A, contrasts.arg = contr.treatment)
> set.seed(1L)
> Y <- (X %*% 1
+   + Z1 %*% rnorm(ncol(Z1), 0, 0.7)
+   + Z2 %*% rnorm(ncol(Z2), 0, 0.3)
+   + Z3 %*% rnorm(ncol(Z3), 0, 0.5)
+   + rnorm(n, 0, 1))
> Z <- list(Z1, Z2, Z3)
> Sigma <- lapply(Z, function(z) diag(ncol(z)))
> # tests interaction effects
> pseudo.rlr.test(Y, X, Z, Sigma, 2L, 2000L, 2L)
Loading required package: varComp
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘varComp’
Loading required package: RLRsim
Error in loadNamespace(name) : there is no package called ‘varComp’
Calls: pseudo.rlr.test ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Namespace in Imports field not imported from: ‘mnormt’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: ‘nsimp’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-clang/localdepth.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘distr’
  All declared Imports should be used.
Package in Depends field not imported from: ‘logcondens’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  lsdall.c:2078:21: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2200:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2209:12: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2219:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2225:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/logspline.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
Note: found 143 marked Latin-1 strings
  Note: found 833 marked UTF-8 strings
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/LSDinterface.Rcheck/LSDinterface/extdata’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/LSDinterface.Rcheck/LSDinterface/extdata’, resetting
installed size is 46.6Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  44.9Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘lavaan’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tcltk2’
  All declared Imports should be used.
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)
Loading required package: survival
Loading required package: perm
Loading required package: Icens
Loading required package: MLEcens
> library(LTRCtrees)
> data(bcos)
> 
> ## Fit ICtree survival tree
> Ctree <- ICtree(Surv(left,right,type="interval2")~treatment, data = bcos)
Error in extree_data(formula = Formula, data = DATA, yx = "none", nmax = c(yx = Inf,  : 
  could not find function "extree_data"
Calls: ICtree -> <Anonymous> -> eval -> eval
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 48-62 (LTRCtrees.Rmd) 
Error: processing vignette 'LTRCtrees.Rmd' failed with diagnostics:
could not find function "extree_data"
Execution halted
Running ‘testthat.R’ [31s/42s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > if (packageVersion("testthat") >= "0.7.1.99") {
  +   library(testthat)  
  +   test_check("lubridate")
  + }
  Loading required package: lubridate
  
  Attaching package: 'lubridate'
  
  The following object is masked from 'package:base':
  
      date
  
  ── 1. Failure: interval handles POSIXlt inputs (@test-intervals.R#88)  ─────────
  unclass(interval(t1, t2)) not equal to unclass(...).
  Attributes: < Component "tzone": 1 string mismatch >
  
  ── 2. Failure: interval handles POSIXlt inputs (@test-intervals.R#95)  ─────────
  unclass(interval(t1, t2)) not equal to unclass(...).
  Attributes: < Component "tzone": 1 string mismatch >
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2456 SKIPPED: 36 FAILED: 2
  1. Failure: interval handles POSIXlt inputs (@test-intervals.R#88) 
  2. Failure: interval handles POSIXlt inputs (@test-intervals.R#95) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘e1071’ ‘utils’
  All declared Imports should be used.
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    data  16.0Mb
Running examples in ‘m4fe-Ex.R’ failed
The error most likely occurred in:

> ### Name: currentStocks
> ### Title: Current Stock Info (Yahoo Finance API)
> ### Aliases: currentStocks
> 
> ### ** Examples
> 
> currentStocks()
Warning in file(file, "rt") :
  cannot open URL 'http://download.finance.yahoo.com/d/quotes.csv?s=GOOGL&f=abb2b3poydr1qc1cc6k2p2d1d2t1c8c3m5m6m7m8m3m4ghk1ll1t8w1w4p1mm2g1g3g4g5g6t7t6i5l2l3v1v7s6kjj5k4j6k5wvj1j3f6nn4ss1xs2ee7e8e9b4j4p5p6rr2r5r6r7s7': HTTP status was '403 Forbidden'
Error in file(file, "rt") : 
  cannot open the connection to 'http://finance.yahoo.com/d/quotes.csv?s=GOOGL&f=abb2b3poydr1qc1cc6k2p2d1d2t1c8c3m5m6m7m8m3m4ghk1ll1t8w1w4p1mm2g1g3g4g5g6t7t6i5l2l3v1v7s6kjj5k4j6k5wvj1j3f6nn4ss1xs2ee7e8e9b4j4p5p6rr2r5r6r7s7'
Calls: currentStocks -> read.csv -> read.table -> file
Execution halted
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    TS_files     5.9Mb
    base_files   6.3Mb
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
installed size is 24.4Mb
  sub-directories of 1Mb or more:
    libs  24.1Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘cmprsk’ ‘colorspace’ ‘etm’ ‘fracdiff’ ‘gtable’ ‘munsell’
  ‘numDeriv’ ‘plyr’ ‘quadprog’ ‘scales’ ‘timeDate’ ‘tseries’ ‘zoo’
  All declared Imports should be used.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs   4.5Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/ManifoldOptim.Rcheck/00install.out’ for details.
installed size is 32.7Mb
  sub-directories of 1Mb or more:
    mapdata  32.6Mb
Found the following significant warnings:
  perspective.c:12:23: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/mapproj.Rcheck/00install.out’ for details.
Found the following significant warnings:
  mapclip.c:321:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/maps.Rcheck/00install.out’ for details.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/markmyassignment.Rcheck/00install.out’ for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   6.4Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   5.5Mb
Namespace in Imports field not imported from: ‘rgenoud’
  All declared Imports should be used.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
File ‘maxent/libs/maxent.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  10.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   2.7Mb
installed size is 35.6Mb
  sub-directories of 1Mb or more:
    libs  34.8Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
Namespaces in Imports field not imported from:
  ‘parallelMap’ ‘reshape2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.3Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   3.9Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/measuRing.Rcheck/measuRing’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/measuRing.Rcheck/measuRing’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/measuRing.Rcheck/measuRing’, resetting
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   7.7Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘ggplot2’ ‘lavaan’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘RGtk2’ ‘RNifti’ ‘cairoDevice’ ‘gtools’ ‘jsonlite’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘RColorBrewer’ ‘RODBC’ ‘formattable’ ‘ggplot2’ ‘ggthemes’ ‘mem’
  ‘openxlsx’ ‘plotly’ ‘readxl’ ‘shinyBS’ ‘shinydashboard’ ‘shinyjs’
  ‘shinythemes’ ‘stringr’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    libs  19.4Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   3.3Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpIaUWEN’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpIaUWEN’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpIaUWEN’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpIaUWEN’, resetting
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘shiny’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.1Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘lazyeval’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/MetaSubtract.Rcheck/MetaSubtract/extdata’, resetting
Found the following significant warnings:
  binomial-twostage.cpp:78:4: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  binomial-twostage.cpp:280:4: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/mets.Rcheck/00install.out’ for details.
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  13.8Mb
    misc   1.1Mb
File ‘mFilter/R/zzz.R’:
  .onLoad calls:
    writeLines(strwrap(txt, indent = 4, exdent = 4))

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

.onLoad: warning in packageDescription("mFilter", lib = mylib): partial
  argument match of 'lib' to 'lib.loc'
bkfilter: warning in ts(x.cycle, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
bkfilter: warning in ts(x.trend, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
bkfilter: warning in ts(x, star = tsp.x[1], frequency = tsp.x[3]):
  partial argument match of 'star' to 'start'
bwfilter: warning in ts(x.cycle, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
bwfilter: warning in ts(x.trend, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
bwfilter: warning in ts(x, star = tsp.x[1], frequency = tsp.x[3]):
  partial argument match of 'star' to 'start'
cffilter: warning in ts(x.cycle, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
cffilter: warning in ts(x.trend, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
cffilter: warning in ts(x, star = tsp.x[1], frequency = tsp.x[3]):
  partial argument match of 'star' to 'start'
hpfilter: warning in ts(x.cycle, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
hpfilter: warning in ts(x.trend, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
hpfilter: warning in ts(x, star = tsp.x[1], frequency = tsp.x[3]):
  partial argument match of 'star' to 'start'
Package suggested but not available for checking: ‘grasp2db’
Namespaces in Imports field not imported from:
  ‘DiceDesign’ ‘MaxPro’ ‘doSNOW’ ‘jpeg’
  All declared Imports should be used.
cdf.pval: no visible global function definition for ‘median’
cdf.pval: no visible binding for global variable ‘ecdf’
find_hits: no visible global function definition for ‘na.omit’
mad.scores: no visible global function definition for ‘as.formula’
mad.scores: no visible binding for global variable ‘median’
mad.scores: no visible binding for global variable ‘mad’
rm.outliers: no visible global function definition for ‘as.formula’
rm.outliers: no visible binding for global variable ‘median’
rm.outliers: no visible binding for global variable ‘mad’
Undefined global functions or variables:
  as.formula ecdf mad median na.omit
Consider adding
  importFrom("stats", "as.formula", "ecdf", "mad", "median", "na.omit")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘cluster’ ‘dendextend’ ‘npmv’ ‘utils’
  All declared Imports should be used.
Found the following significant warnings:
  ggum_derivs.cpp:299:47: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  ggum_derivs.cpp:299:51: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  ggum_derivs.cpp:301:49: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  ggum_derivs.cpp:301:53: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  ggum_derivs.cpp:306:50: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  ggum_derivs.cpp:306:54: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  ggum_derivs.cpp:1800:58: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  ggum_derivs.cpp:1800:62: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  ggum_derivs.cpp:1841:58: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  ggum_derivs.cpp:1841:62: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/mirt.Rcheck/00install.out’ for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   5.3Mb
Error in re-building vignettes:
  ...
pandoc: Could not fetch https://fonts.googleapis.com/css?family=Open+Sans:400,700,900
HttpExceptionRequest Request {
  host                 = "fonts.googleapis.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/css"
  queryString          = "?family=Open+Sans:400,700,900"
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (InternalException (HandshakeFailed Error_EOF))
Error: processing vignette 'misreport-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
Execution halted
Found the following significant warnings:
  simcensor.cpp:91:16: warning: comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:91:41: warning: comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:95:17: warning: comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/missDeaths.Rcheck/00install.out’ for details.
Running examples in ‘mistat-Ex.R’ failed
The error most likely occurred in:

> ### Name: LATHYPPISTON
> ### Title: Latin Hypercube Design for the Piston Simulator
> ### Aliases: LATHYPPISTON
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(LATHYPPISTON)
> 
> library(DiceEval)
Loading required package: DiceKriging
> 
> library(DiceView)
Error in library(DiceView) : there is no package called ‘DiceView’
Execution halted
Found the following significant warnings:
  ILauncher.cpp:50:31: warning: field 'v_models_' will be initialized after field 'handler_' [-Wreorder]
  ILauncher.cpp:51:31: warning: field 'handler_' will be initialized after field 'diagGaussianManager_' [-Wreorder]
  ILauncher.cpp:66:31: warning: field 'v_models_' will be initialized after field 'handler_' [-Wreorder]
  ILauncher.cpp:67:31: warning: field 'handler_' will be initialized after field 'diagGaussianManager_' [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-clang/MixAll.Rcheck/00install.out’ for details.
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    libs  15.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Namespace in Imports field not imported from: ‘rjags’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘foreach’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘iterators’ ‘parallel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
installed size is 42.3Mb
  sub-directories of 1Mb or more:
    chunks   3.4Mb
    libs    38.7Mb
Running examples in ‘mlmm-Ex.R’ failed
The error most likely occurred in:

> ### Name: mlmc
> ### Title: mlmc for missing and censored response in multilevel model.
> ### Aliases: mlmc
> 
> ### ** Examples
> 
> ## Don't show: 
> testfun=function()
+ {set.seed(100)
+  var2=abs(rnorm(50,0,1))
+  var1=(1/0.85)*var2;
+  geneid=rep(c(1:10),5);sid=c(rep(c(1:25),2),rep(c(26:50),2));
+  censor=rep(0,50)
+  pidname="geneid";sidname="sid";
+  miss_logit=var2*(-0.9);
+  miss=rbinom(50,1,exp(miss_logit)/(exp(miss_logit)+1));
+  censor=rep(0,50)
+  for (i in 1:50) {if (var1[i]<0.05) censor[i]=1}
+  for ( i in 1:50) {if ((miss[i]==1) & (censor[i]==1)) miss[i]=0};
+  for ( i in 1:50) {if (miss[i]==1) var1[i]=NA;
+  if (censor[i]==1) var1[i]=0.05}
+  pdata=data.frame(var1,var2,miss,censor,geneid,sid)
+  pathdir=getwd()
+  if (R.Version()$arch=="i386") fp=system.file("chunks","mlmc_i32.rds",package="mlmm")
+  if (R.Version()$arch=="x86_64") fp=system.file("chunks","mlmc_i64.rds",package="mlmm")
+  mcfit=readRDS(fp)
+  model1=mlmc(formula_completed=var1~var2,formula_missing=miss~var2,
+              formula_censor=censor~1,formula_subject=~var2,pdata=pdata,response_censorlim=0.05,
+              respond_dep_missing=TRUE,pidname="geneid",sidname="sid",pathname=pathdir,
+              iterno=10,chains=2,savefile=FALSE,usefit=TRUE,stanfit=mcfit)
+  }
> system.time(testfun())
Error in prep_call_sampler(object) : 
  the compiled object from C++ code for this model is invalid, possible reasons:
  - compiled with save_dso=FALSE;
  - compiled on a different platform;
  - does not exist (created from reading csv files).
Calls: system.time ... sampling -> .local -> <Anonymous> -> prep_call_sampler
Timing stopped at: 0.217 0.005 0.376
Execution halted
Namespace in Imports field not imported from: ‘sads’
  All declared Imports should be used.
Running ‘testthat.R’ [22s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(modmarg)
  > 
  > test_check("modmarg")
  ── 1. Error: Collinear cols treated right (@test_glm.R#288)  ───────────────────
  non-conformable arguments
  1: marg(mod = ols1, var_interest = "am", type = "effects", at = list(mpg = seq(15, 30, 
         5))) at testthat/test_glm.R:288
  2: marg.glm(mod = ols1, var_interest = "am", type = "effects", at = list(mpg = seq(15, 
         30, 5)))
  3: .marg(mod = mod, var_interest = var_interest, data = data, weights = weights, ...)
  4: lapply(data, function(x) {
         df_levels <- at_transforms(model_df = x, at_list = gen_at_list(df = x, var_interest = var_interest, 
             at_var_interest = at_var_interest))
         pred_se(df_levels = df_levels, model = mod, type = type, base_rn = base_rn, vcov_mat = vcov_mat, 
             weights = weights, link_func = NULL, deriv_func = NULL)
     })
  5: FUN(X[[i]], ...)
  6: pred_se(df_levels = df_levels, model = mod, type = type, base_rn = base_rn, vcov_mat = vcov_mat, 
         weights = weights, link_func = NULL, deriv_func = NULL)
  7: pred_se.glm(df_levels = df_levels, model = mod, type = type, base_rn = base_rn, vcov_mat = vcov_mat, 
         weights = weights, link_func = NULL, deriv_func = NULL)
  8: .pred_se(model = model, deriv_func = model$family$mu.eta, link_func = model$family$linkinv, 
         ...)
  9: calc_pred_se(vcov_mat, jacobs)
  10: diag(jac %*% vcov_model %*% t(jac))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 303 SKIPPED: 0 FAILED: 1
  1. Error: Collinear cols treated right (@test_glm.R#288) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘fields’ ‘iterpc’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    1.6Mb
    libs   2.7Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    2.3Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
Compilation used the following non-portable flag(s):
  ‘-Wno-format’
including flag(s) suppressing warnings
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   7.5Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘caret’ ‘ggformula’ ‘knitr’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.7Mb
Found the following significant warnings:
  ./Linalg.h:429:5: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
  ./Linalg.h:440:5: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
  ./IPCATree.h:782:57: warning: field 'stop' will be initialized after field 'epsilon' [-Wreorder]
  ./IPCATree.h:783:23: warning: field 'splitStrategy' will be initialized after field 'minPoints' [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-clang/mph.Rcheck/00install.out’ for details.
export.summary.mpm: warning in complex(real = x$Rows[, FdimsR[1]], imag
  = x$Rows[, FdimsR[2]]): partial argument match of 'imag' to
  'imaginary'
export.summary.mpm: warning in complex(real = x$Columns[, FdimsC[1]],
  imag = x$Columns[, FdimsC[2]]): partial argument match of 'imag' to
  'imaginary'
.onAttach: no visible global function definition for
  ‘packageDescription’
export.summary.mpm: no visible global function definition for
  ‘write.table’
mpm: no visible binding for global variable ‘median’
plot.mpm: no visible global function definition for ‘rainbow’
plot.mpm: no visible global function definition for ‘quantile’
plot.mpm: no visible global function definition for ‘par’
plot.mpm: no visible global function definition for ‘points’
plot.mpm: no visible global function definition for ‘smoothScatter’
plot.mpm: no visible global function definition for ‘colorRampPalette’
plot.mpm: no visible global function definition for ‘symbols’
plot.mpm: no visible global function definition for ‘text’
plot.mpm: no visible global function definition for ‘lines’
plot.mpm: no visible global function definition for ‘box’
Undefined global functions or variables:
  box colorRampPalette lines median packageDescription par points
  quantile rainbow smoothScatter symbols text write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "rainbow")
  importFrom("graphics", "box", "lines", "par", "points",
             "smoothScatter", "symbols", "text")
  importFrom("stats", "median", "quantile")
  importFrom("utils", "packageDescription", "write.table")
to your NAMESPACE file.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Found the following significant warnings:
  recursion.cpp:31:25: warning: field 'K' will be initialized after field 'nu_vec' [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-clang/MRS.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘moments’ ‘mvtnorm’
  All declared Imports should be used.
installed size is 43.8Mb
  sub-directories of 1Mb or more:
    libs  43.5Mb
Namespaces in Imports field not imported from:
  ‘hms’ ‘methods’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is 70.9Mb
  sub-directories of 1Mb or more:
    libs  70.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Found the following significant warnings:
  dmixtCpp.cpp:61:15: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  dmvtCpp.cpp:50:15: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  mahaCpp.cpp:69:13: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  msCpp.cpp:45:17: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  rmixnCpp.cpp:54:15: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  rmixtCpp.cpp:57:15: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  rmvnCpp.cpp:49:17: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  rmvtCpp.cpp:51:15: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/mvnfast.Rcheck/00install.out’ for details.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    java  13.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.7Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpKFYKMM’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpKFYKMM’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpKFYKMM’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpKFYKMM’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpKFYKMM’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpKFYKMM’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpKFYKMM’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpKFYKMM’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpKFYKMM’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpKFYKMM’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpKFYKMM’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpKFYKMM’, resetting
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   6.5Mb
Namespace in Imports field not imported from: ‘ggcorrplot’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   5.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Namespaces in Imports field not imported from:
  ‘mgcv’ ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘devtools’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
Namespaces in Imports field not imported from:
  ‘htmlTable’ ‘lme4’ ‘stringi’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    CppCode        1.0Mb
    R              3.4Mb
    classic-bugs   1.6Mb
    include        5.8Mb
    tests          1.2Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Namespaces in Imports field not imported from:
  ‘dparser’ ‘inline’ ‘n1qn1’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.3Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘XML’ ‘choroplethr’ ‘choroplethrMaps’ ‘data.table’
  ‘forcats’ ‘hurricaneexposure’ ‘plyr’
  All declared Imports should be used.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc   8.6Mb
Found the following significant warnings:
  utilities.c:175:32: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/npcp.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘mclust’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Namespace in Imports field not imported from: ‘rts’
  All declared Imports should be used.
Found the following significant warnings:
  libglpk/glpapi06.c:530:26: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  libglpk/glpapi06.c:539:20: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  libglpk/glpios01.c:224:17: warning: explicitly assigning value of variable of type 'IOSNPD *' (aka 'struct IOSNPD *') to itself [-Wself-assign]
  libglpk/glpmpl06.c:666:17: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  libglpk/glpmpl06.c:825:20: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  libglpk/glpmps.c:1280:19: warning: explicitly assigning value of variable of type 'GLPAIJ *' (aka 'struct GLPAIJ *') to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/npsf.Rcheck/00install.out’ for details.
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs  14.0Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   8.1Mb
Note: found 13172 marked Latin-1 strings
installed size is 39.0Mb
  sub-directories of 1Mb or more:
    extdata  38.9Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   8.7Mb
File ‘nws/R/zzz.R’:
  .onLoad calls:
    require(methods)

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

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

Found the following assignments to the global environment:
File ‘nws/R/workerLoop.R’:
  assign("SleighName", displayName, globalenv())
  assign("SleighNws", nws, globalenv())
  assign("SleighUserNws", userNws, globalenv())
  assign("SleighRank", rank, globalenv())
  assign("SleighWorkerCount", workerCount, globalenv())
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R            1.4Mb
    test_files   4.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    help   2.2Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/ODMconverter.Rcheck/ODMconverter/extdata’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/ODMconverter.Rcheck/ODMconverter/extdata’, resetting
installed size is 92.8Mb
  sub-directories of 1Mb or more:
    libs  92.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Namespaces in Imports field not imported from:
  ‘randomForest’ ‘ranger’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/opefimor.Rcheck/opefimor/book’, resetting
installed size is 146.2Mb
  sub-directories of 1Mb or more:
    R         2.3Mb
    libs    136.4Mb
    models    4.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    java     1.2Mb
    models   6.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(optimus)
  This is optimus 0.1.0, roll out!
  > 
  > test_check("optimus")
  ── 1. Error: find_optimal() stops with wrong data or arguments (@test-find_optim
  argument "quo" is missing, with no default
  1: expect_error(expr = optimus::find_optimal(data = mixed, clustering = counts_cutree, 
         family = "poisson"), message = "some.*") at testthat/test-find_optimal.R:38
  2: quasi_capture(enquo(object), capture_error, label = label)
  3: label %||% quo_label(quo)
  4: quo_label(quo)
  5: expr_label(quo_expr(quo))
  6: quo_expr(quo)
  7: quo_splice(duplicate(quo), warn = warn)
  8: switch_expr(x, language = {
         if (is_quosure(x)) {
             if (!is_false(warn)) {
                 if (is_string(warn)) {
                     msg <- warn
                 }
                 else {
                     msg <- "Collapsing inner quosure"
                 }
                 warn(msg)
                 warn <- FALSE
             }
             while (is_quosure(x)) {
                 x <- f_rhs(x)
             }
             if (!is_null(parent)) {
                 mut_node_car(parent, x)
             }
             quo_splice(x, parent, warn = warn)
         }
         else {
             quo_splice(node_cdr(x), warn = warn)
         }
     }, pairlist = {
         while (!is_null(x)) {
             quo_splice(node_car(x), x, warn = warn)
             x <- node_cdr(x)
         }
     })
  9: expr_type_of(.x)
  10: typeof(x)
  11: duplicate(quo)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 5 SKIPPED: 0 FAILED: 1
  1. Error: find_optimal() stops with wrong data or arguments (@test-find_optimal.R#38) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      3.1Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(optrdd)
  > 
  > test_check("optrdd")
  ── 1. Error: (unknown) (@test_all.R#52)  ───────────────────────────────────────
  invalid argument to unary operator
  1: optrdd(X = X, Y = Y, W = W, max.second.derivative = max.second.derivative, optimizer = "mosek", 
         verbose = FALSE) at testthat/test_all.R:52
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 8 SKIPPED: 1 FAILED: 1
  1. Error: (unknown) (@test_all.R#52) 
  
  Error: testthat unit tests failed
  Execution halted
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of 'nr' to 'nrow'
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of 'nc' to 'ncol'
bgmm: no visible global function definition for ‘ecdf’
bgmm : SplineGMM: no visible global function definition for
  ‘constrOptim’
blr: no visible global function definition for ‘ecdf’
blr: no visible global function definition for ‘constrOptim’
blr: no visible global function definition for ‘lm’
parentcdf : combinations: no visible global function definition for
  ‘combn’
parentcdf : solver: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  combn constrOptim ecdf lm uniroot
Consider adding
  importFrom("stats", "constrOptim", "ecdf", "lm", "uniroot")
  importFrom("utils", "combn")
to your NAMESPACE file.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    nifti   3.8Mb
est.lme : <anonymous>: warning in rank(iru, ties = "min"): partial
  argument match of 'ties' to 'ties.method'
est.lme : <anonymous>: no visible global function definition for ‘lme’
est.lme : <anonymous>: no visible global function definition for
  ‘VarCorr’
guo: no visible global function definition for ‘p.adjust’
guo: no visible global function definition for ‘na.omit’
pttest : ptest: no visible global function definition for ‘na.omit’
srt : <anonymous>: no visible global function definition for
  ‘rowttests’
Undefined global functions or variables:
  VarCorr lme na.omit p.adjust rowttests
Consider adding
  importFrom("stats", "na.omit", "p.adjust")
to your NAMESPACE file.
Found the following significant warnings:
  ccaRevolution.c:31:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:44:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:97:23: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:98:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:110:23: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:111:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/osc.Rcheck/00install.out’ for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   4.8Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
Package suggested but not available for checking: ‘Rcplex’
Namespace in Imports field not imported from: ‘quantreg’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   2.0Mb
[,ClassW: warning in switch(EXP = i, u1 = {: partial argument match of
  'EXP' to 'EXPR'
[,ClassW: warning in return(x@u1): partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in }, u2 = {: partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in return(x@u2): partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in }, w1 = {: partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in return(x@w1): partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in }): partial argument match of 'EXP' to 'EXPR'
[<-,ClassW: warning in switch(EXP = i, u1 = {: partial argument match
  of 'EXP' to 'EXPR'
[<-,ClassW: warning in x@u1 <- value: partial argument match of 'EXP'
  to 'EXPR'
[<-,ClassW: warning in }, u2 = {: partial argument match of 'EXP' to
  'EXPR'
[<-,ClassW: warning in x@u2 <- value: partial argument match of 'EXP'
  to 'EXPR'
[<-,ClassW: warning in }, w1 = {: partial argument match of 'EXP' to
  'EXPR'
[<-,ClassW: warning in x@w1 <- value: partial argument match of 'EXP'
  to 'EXPR'
[<-,ClassW: warning in }): partial argument match of 'EXP' to 'EXPR'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data        1.6Mb
    localdata   3.1Mb
Namespaces in Imports field not imported from:
  ‘curl’ ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
Namespace in Imports field not imported from: ‘ade4’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: CHARACTER expression at (1) is being truncated (6/1) [-Wcharacter-truncation]
  Warning: CHARACTER expression will be truncated in assignment (1/9) at (1) [-Wcharacter-truncation]
  Warning: CHARACTER expression will be truncated in assignment (1/19) at (1) [-Wcharacter-truncation]
  Warning: CHARACTER expression will be truncated in assignment (1/16) at (1) [-Wcharacter-truncation]
  Warning: CHARACTER expression will be truncated in assignment (1/12) at (1) [-Wcharacter-truncation]
See ‘/data/gannet/ripley/R/packages/tests-clang/pbdSLAP.Rcheck/00install.out’ for details.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    lib   9.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc        1.5Mb
    examples   1.7Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/PBSmodelling.Rcheck/PBSmodelling/examples’, resetting
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pander’
  All declared Imports should be used.
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   2.1Mb
    libs   6.4Mb
Found the following significant warnings:
  hess.cpp:57:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
  hess.cpp:65:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
  hess.cpp:66:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
See ‘/data/gannet/ripley/R/packages/tests-clang/pcaPP.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘fda’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘car’ ‘sandwich’
  All declared Imports should be used.
Found the following significant warnings:
  spectrum.c:707:14: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:715:20: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1606:41: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1654:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1654:63: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/Peaks.Rcheck/00install.out’ for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘devtools’ ‘ggplot2’ ‘haven’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘goft’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      4.4Mb
    data   3.1Mb
Found the following significant warnings:
  calc.c:741:18: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/PET.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘Rgraphviz’ ‘cluster’ ‘graph’
  All declared Imports should be used.
File ‘pgam/R/zzz.r’:
  .onLoad calls:
    require("stats", character.only = TRUE, quietly = TRUE, warn.conflicts = FALSE)
    require("utils", character.only = TRUE, quietly = TRUE, warn.conflicts = FALSE)
    cat("This is pgam library version", ver, "\n", sep = " ")

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

This is pgam library version 0.4.12 
pgam: warning in assign("loglik", NULL, env = pgam.env): partial
  argument match of 'env' to 'envir'
pgam: warning in get("loglik", env = pgam.env): partial argument match
  of 'env' to 'envir'
pgam.likelihood: warning in assign("loglik", loglik, env = env):
  partial argument match of 'env' to 'envir'
envelope.pgam: no visible global function definition for ‘par’
periodogram: no visible global function definition for ‘axis’
periodogram: no visible global function definition for ‘title’
periodogram: no visible global function definition for ‘lines’
plot.pgam: no visible global function definition for ‘plot’
Undefined global functions or variables:
  axis lines par plot title
Consider adding
  importFrom("graphics", "axis", "lines", "par", "plot", "title")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/PGICA.Rcheck/Sim’, resetting
Found the following significant warnings:
  LJMA_arms.c:297:11: warning: comparison of array 'env->p' equal to a null pointer is always false [-Wtautological-pointer-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/PhaseType.Rcheck/00install.out’ for details.
Found the following significant warnings:
  phreeqcpp/cvode.cpp:3783:8: warning: explicitly assigning value of variable of type 'realtype' (aka 'double') to itself [-Wself-assign]
  phreeqcpp/model.cpp:3047:7: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  phreeqcpp/model.cpp:3048:7: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:142:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:155:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:167:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:179:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:193:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:205:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/transport.cpp:630:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/phreeqc.Rcheck/00install.out’ for details.
installed size is 41.4Mb
  sub-directories of 1Mb or more:
    libs  40.6Mb
Namespaces in Imports field not imported from:
  ‘gplots’ ‘phytools’
  All declared Imports should be used.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
Package suggested but not available for checking: ‘ReportingTools’
installed size is 30.4Mb
  sub-directories of 1Mb or more:
    libs  30.3Mb
Found the following significant warnings:
  hcubature.c:917:15: warning: comparison of unsigned enum expression < 0 is always false [-Wtautological-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/planar.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘RColorBrewer’ ‘arm’ ‘epiDisplay’ ‘foreign’ ‘gbm’
  ‘grid’ ‘lattice’ ‘latticeExtra’ ‘lme4’ ‘nnet’ ‘parallel’ ‘splines’
  ‘survey’ ‘twang’ ‘xtable’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘hexbin’ ‘quantreg’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘stats’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   2.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘digest’ ‘htmltools’ ‘knitr’ ‘lazyWeave’ ‘lubridate’ ‘rJava’
  All declared Imports should be used.
Found the following significant warnings:
  heftall.c:1389:2: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  lsdall.c:2077:21: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  lspecall.c:505:12: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  lspecall.c:999:21: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  lspecall.c:1078:18: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2199:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2208:12: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2218:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2224:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/polspline.Rcheck/00install.out’ for details.
Found the following significant warnings:
  whopgenome/rdnapp_MAF.h:243:12: warning: explicitly assigning value of variable of type 'unsigned int' to itself [-Wself-assign]
  whopgenome/rdnapp_MAF.h:409:45: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
  whopgenome/whopgen_vcf.cpp:263:28: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
  whopgenome/whoptbi_info.cpp:115:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  whopgenome/whoptbi_info.cpp:120:7: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  whopgenome/whoptbi_info.cpp:152:44: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  whopgenome/whoptbi_region.cpp:78:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/PopGenome.Rcheck/00install.out’ for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
Found the following significant warnings:
  powell.c:398:17: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
  powell.c:499:17: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
  powell.c:700:14: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  powell.c:724:12: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/powell.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ppcctest_pearson3.c:19:66: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/ppcc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ./shared.h:56:9: warning: comparison of constant 2147483648 with expression of type 'int' is always false [-Wtautological-constant-out-of-range-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/praznik.Rcheck/00install.out’ for details.
Found the following significant warnings:
  computeA.c:62:19: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/prc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  sum.c:221:11: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  sum.c:221:22: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  sum.c:227:52: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  sum.c:227:60: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/PreciseSums.Rcheck/00install.out’ for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.5Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘graphics’ ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘methods’ ‘utils’
  All declared Imports should be used.
Packages suggested but not available for checking: ‘gurobi’ ‘lpsymphony’
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   6.4Mb
    libs      5.5Mb
Package suggested but not available for checking: ‘qtbase’
Namespaces in Imports field not imported from:
  ‘distcrete’ ‘incidence’
  All declared Imports should be used.
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.9Mb
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘forecast’ ‘knitr’
  All declared Imports should be used.
Found the following significant warnings:
  gaussianProcesses/GaussianProcess.cpp:5:21: warning: field 'Observations' will be initialized after field 'covFunc' [-Wreorder]
  gaussianProcesses/GaussianProcess.cpp:5:42: warning: field 'covFunc' will be initialized after base 'ForwardModel' [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-clang/psgp.Rcheck/00install.out’ for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Namespaces in Imports field not imported from:
  ‘rtf’ ‘tidyverse’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     1.6Mb
    doc   2.4Mb
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 ‘/data/gannet/ripley/R/packages/tests-clang/ptinpoly.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    dict   5.1Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc        3.8Mb
    examples   2.3Mb
installed size is 25.0Mb
  sub-directories of 1Mb or more:
    libs  24.6Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
Compilation used the following non-portable flag(s):
  ‘-Werror=format-security’ ‘-Wp,-D_FORTIFY_SOURCE=2’
Found the following significant warnings:
  upwindorderedv4.c:542:54: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  upwindorderedv4.c:542:72: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/QPot.Rcheck/00install.out’ for details.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  11.8Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    contrib   3.8Mb
    doc       2.9Mb
    libs      1.3Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   4.7Mb
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘gridExtra’ ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lmerTest’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    Output   2.2Mb
    bin      2.8Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/r2lh.Rcheck/tmp’, resetting
Namespaces in Imports field not imported from:
  ‘AlgDesign’ ‘psych’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    extdata   1.4Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    htmlwidgets   6.4Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   3.8Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘dtplyr’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs   2.0Mb
installed size is 28.5Mb
  sub-directories of 1Mb or more:
    libs  27.2Mb
Namespace in Imports field not imported from: ‘lme4’
  All declared Imports should be used.
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    blp    7.1Mb
    libs   6.7Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    java   7.8Mb
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    cont  23.3Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/RchivalTag.Rcheck/RchivalTag/example_files’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/RchivalTag.Rcheck/RchivalTag/example_files’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/RchivalTag.Rcheck/RchivalTag/example_files’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/RchivalTag.Rcheck/RchivalTag/example_files’, resetting
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
Package suggested but not available for checking: ‘ROpenOffice’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.0Mb
    po    2.2Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    include   5.1Mb
    libs      1.3Mb
Found the following warnings:
  ../inst/include/blaze/math/smp/openmp/Functions.h:98:1: warning: control may reach end of non-void function [-Wreturn-type]
See ‘/data/gannet/ripley/R/packages/tests-clang/RcppBlaze.Rcheck/00install.out’ for details.
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    include  25.5Mb
    libs      1.8Mb
installed size is 31.9Mb
  sub-directories of 1Mb or more:
    include   7.8Mb
    libs     23.4Mb
Error in re-building vignettes:
  ...
Latexmk: This is Latexmk, John Collins, 12 Dec. 2017, version: 4.54c.
Loading required package: RcppGSL
installed size is 51.4Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib      38.2Mb
    libs     11.1Mb
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    include   7.0Mb
    libs      6.5Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Compilation used the following non-portable flag(s):
  ‘-Wno-dangling-else’ ‘-Wno-non-virtual-dtor’ ‘-Wno-parentheses’
including flag(s) suppressing warnings
installed size is 23.0Mb
  sub-directories of 1Mb or more:
    include   8.9Mb
    libs     14.0Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    include   6.4Mb
    libs      3.9Mb
installed size is 150.3Mb
  sub-directories of 1Mb or more:
    include    4.6Mb
    lib      110.2Mb
    libs      35.3Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Found the following significant warnings:
  cwb/cqp/corpmanag.c:1832:12: warning: comparison of function 'split_subcorpus_name' equal to a null pointer is always false [-Wtautological-pointer-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/rcqp.Rcheck/00install.out’ for details.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘smcure’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rcompression’
Found the following significant warnings:
  json.c:44:17: warning: comparison of constant 65536 with expression of type 'unsigned short' is always true [-Wtautological-constant-out-of-range-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/RCurl.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘DT’ ‘shiny’
  All declared Imports should be used.
dieharder.default: no visible binding for global variable
  ‘.dieharder.generators’
dieharder.default: no visible binding for global variable
  ‘.dieharder.tests’
plot.dieharder: no visible global function definition for ‘par’
plot.dieharder: no visible global function definition for ‘hist’
plot.dieharder: no visible global function definition for ‘lines’
plot.dieharder: no visible global function definition for ‘density’
plot.dieharder: no visible global function definition for ‘plot’
plot.dieharder: no visible global function definition for ‘ecdf’
plot.dieharder: no visible global function definition for ‘segments’
plot.dieharder: no visible global function definition for ‘mtext’
plot.dieharder: no visible global function definition for ‘ks.test’
plot.dieharder: no visible global function definition for ‘wilcox.test’
summary.dieharder: no visible global function definition for ‘stem’
summary.dieharder: no visible global function definition for ‘ks.test’
summary.dieharder: no visible global function definition for
  ‘wilcox.test’
Undefined global functions or variables:
  .dieharder.generators .dieharder.tests density ecdf hist ks.test
  lines mtext par plot segments stem wilcox.test
Consider adding
  importFrom("graphics", "hist", "lines", "mtext", "par", "plot",
             "segments", "stem")
  importFrom("stats", "density", "ecdf", "ks.test", "wilcox.test")
to your NAMESPACE file.
Found the following significant warnings:
  methods_nonlinear.cpp:503:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/Rdimtools.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [93s/187s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rdomains)
  > 
  > test_check("rdomains")
  ── 1. Error: dmoz cat (@test-dmoz-cat.R#5)  ────────────────────────────────────
  HTTP error 404.
  1: get_dmoz_data() at testthat/test-dmoz-cat.R:5
  2: curl_download("https://github.com/soodoku/domain_classifier/blob/master/rdomains/data-raw/dmoz/dmoz_domain_category.zip?raw=true", 
         tmp)
  
  Shallalist Data saved to the following destination: ./ 
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2 SKIPPED: 0 FAILED: 1
  1. Error: dmoz cat (@test-dmoz-cat.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Subdirectory ‘src’ contains:
  CLRApi.hpp CLRFactory.hpp CLRObjectRef.hpp Common.hpp OS.hpp
  RValue.hpp TcpClient.hpp
These are unlikely file names for src files.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
Namespace in Imports field not imported from: ‘digest’
  All declared Imports should be used.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   8.5Mb
Found the following apparent object files/libraries:
  inst/obj/cube.obj inst/obj/cube_badmtl.obj
Object files/libraries should not be included in a source package.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Note: found 1 marked Latin-1 string
  Note: found 1 marked UTF-8 string
  Note: found 7 strings marked as "bytes"
xy: warning in assign(xname, X, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
xy: warning in assign(yname, y, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
bestmods: no visible global function definition for ‘abline’
bestmods: no visible global function definition for ‘axis’
bestmods: no visible global function definition for ‘lines’
cic: no visible global function definition for ‘lsfit’
cic: no visible global function definition for ‘var’
cvic: no visible global function definition for ‘lsfit’
cvic: no visible global function definition for ‘lm’
eic: no visible global function definition for ‘lsfit’
eic: no visible global function definition for ‘lm’
ic.min: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘var’
xy: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline axis lines lm lsfit rnorm var
Consider adding
  importFrom("graphics", "abline", "axis", "lines")
  importFrom("stats", "lm", "lsfit", "rnorm", "var")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘reams/R/xy.R’:
  assign(xname, X, env = .GlobalEnv)
  assign(yname, y, env = .GlobalEnv)
Error in re-building vignettes:
  ...
Loading required package: REBayes
Loading required package: Matrix
Loading required package: splines
Quitting from lines 212-310 (Bdecon.Rnw) 
Timing stopped at: 0.105 0.018 0.126
Error: processing vignette 'Bdecon.Rnw' failed with diagnostics:
Mosek error:  MSK_RES_ERR_SIZE_LICENSE_CON: The problem has too many constraints.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.8Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   4.3Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  15.2Mb
Package which this enhances but not available for checking: ‘Rcplex’
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    libs  20.2Mb
Namespaces in Imports field not imported from:
  ‘compiler’ ‘data.table’
  All declared Imports should be used.
Found the following significant warnings:
  gar.c:356:29: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  gar.c:356:80: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/repeated.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘dbplyr’
  All declared Imports should be used.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    java   5.8Mb
installed size is 54.4Mb
  sub-directories of 1Mb or more:
    libs  53.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    java   5.3Mb
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.6Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc     3.1Mb
    fonts   1.5Mb
    libs    2.5Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    extra   9.4Mb
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    help  10.5Mb
    libs   8.0Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc   9.5Mb
Found the following significant warnings:
  filterhr.c:21:11: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  filterhr.c:21:53: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  filterhr.c:21:95: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/RHRV.Rcheck/00install.out’ for details.
Found the following significant warnings:
  computePvals.c:488:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/ridge.Rcheck/00install.out’ for details.
Found the following significant warnings:
  lread.c:374:4: warning: explicitly assigning value of variable of type 'FILE *' (aka 'struct _IO_FILE *') to itself [-Wself-assign]
  mat.cpp:422:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
  mat.cpp:467:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
  mat.cpp:957:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
  mat.cpp:1009:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
  mat.cpp:1967:7: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
  mat.cpp:1974:7: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
  mat.cpp:1987:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
  mat.cpp:2051:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
  mat.cpp:2052:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
  mlrc.cpp:15:32: warning: unknown warning group '-Wunused-but-set-variable', ignored [-Wunknown-warning-option]
  wa.cpp:12:32: warning: unknown warning group '-Wunused-but-set-variable', ignored [-Wunknown-warning-option]
See ‘/data/gannet/ripley/R/packages/tests-clang/rioja.Rcheck/00install.out’ for details.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-clang/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’,
    ‘R_GlobalContext’
File ‘rJava/libs/rJava.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘crul’
  All declared Imports should be used.
Found the following significant warnings:
  libjson/Source/JSONGlobals.h:43:50: warning: empty macro arguments are a C99 feature [-Wc99-extensions]
  libjson/Source/JSONGlobals.h:44:49: warning: empty macro arguments are a C99 feature [-Wc99-extensions]
  libjson/Source/JSONSharedString.h:180:47: warning: field 'len' will be initialized after field '_str' [-Wreorder]
  libjson/Source/JSONSharedString.h:182:66: warning: field 'len' will be initialized after field '_str' [-Wreorder]
  JSONStream.cpp:8:130: warning: field 'state' will be initialized after field 'call' [-Wreorder]
  JSONStream.cpp:8:157: warning: field 'err_call' will be initialized after field 'buffer' [-Wreorder]
  JSONStream.cpp:12:64: warning: field 'state' will be initialized after field 'call' [-Wreorder]
  JSONStream.cpp:12:100: warning: field 'err_call' will be initialized after field 'buffer' [-Wreorder]
  JSONValidator.cpp:394:105: warning: empty macro arguments are a C99 feature [-Wc99-extensions]
  JSONValidator.cpp:397:104: warning: empty macro arguments are a C99 feature [-Wc99-extensions]
  internalJSONNode.cpp:78:117: warning: field '_name_encoded' will be initialized after field '_name' [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-clang/RJSONIO.Rcheck/00install.out’ for details.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    datasets   8.6Mb
installed size is 45.1Mb
  sub-directories of 1Mb or more:
    exe  45.0Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘arules’ ‘pmml’ ‘rJava’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    rmd   6.1Mb
.onLoad: warning in dir(dll.path, pattern = this.ext, full = FALSE):
  partial argument match of 'full' to 'full.names'
diagnos.envel: warning in apply(jumpDistRes, MARG = 2, FUN = quantile,
  probs = perc[1], na.rm = TRUE): partial argument match of 'MARG' to
  'MARGIN'
diagnos.envel: warning in apply(jumpDistRes, MARG = 2, FUN = quantile,
  probs = perc[2], na.rm = TRUE): partial argument match of 'MARG' to
  'MARGIN'
diagnos.envel: no visible global function definition for ‘quantile’
diagnos.envel: no visible global function definition for ‘qnorm’
diagnos.envel: no visible binding for global variable ‘quantile’
hrplot: no visible global function definition for ‘plot’
hrplot: no visible global function definition for ‘lines’
hrplot: no visible global function definition for ‘abline’
hrplot: no visible global function definition for ‘text’
sim.chain: no visible global function definition for ‘rnorm’
simRandWalk: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline lines plot qnorm quantile rnorm text
Consider adding
  importFrom("graphics", "abline", "lines", "plot", "text")
  importFrom("stats", "qnorm", "quantile", "rnorm")
to your NAMESPACE file.
File ‘RMC/libs/RMC.so’:
  Found ‘_ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
    Objects: ‘RMC.o’, ‘predict.o’
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘ap.o’
File ‘RMC/libs/RMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Found the following significant warnings:
  Clustering/ClusteringInput.cpp:132:12: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
  Kernel/IO/Input.cpp:212:12: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/Rmixmod.Rcheck/00install.out’ for details.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
mosek: no visible global function definition for ‘help’
mosek_lptoprob: no visible global function definition for ‘is’
mosek_lptoprob: no visible global function definition for ‘as’
mosek_qptoprob: no visible global function definition for ‘is’
mosek_qptoprob: no visible global function definition for ‘as’
mosek_read: no visible global function definition for ‘help’
mosek_write: no visible global function definition for ‘help’
obtain_sparsematrix: no visible global function definition for ‘is’
obtain_sparsematrix: no visible global function definition for ‘as’
Undefined global functions or variables:
  as help is
Consider adding
  importFrom("methods", "as", "is")
  importFrom("utils", "help")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘Rmosek/libs/Rmosek.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  ./Rmpfr_utils.h:89:13: warning: comparison of constant 9223372036854775807 with expression of type 'int' is always false [-Wtautological-constant-out-of-range-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/Rmpfr.Rcheck/00install.out’ for details.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/progress/include/RProgress.h:172:13: warning: variable length arrays are a C99 feature [-Wvla-extension]
  /data/gannet/ripley/R/test-clang/progress/include/RProgress.h:220:16: warning: variable length arrays are a C99 feature [-Wvla-extension]
See ‘/data/gannet/ripley/R/packages/tests-clang/rncl.Rcheck/00install.out’ for details.
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    libs  24.1Mb
installed size is 96.7Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     94.5Mb
Namespaces in Imports field not imported from:
  ‘cowplot’ ‘ggplot2’ ‘microbenchmark’ ‘reshape2’
  All declared Imports should be used.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R   9.7Mb
Found the following significant warnings:
  ./hammock.h:369:15: warning: assigning field to itself [-Wself-assign-field]
See ‘/data/gannet/ripley/R/packages/tests-clang/robfilter.Rcheck/00install.out’ for details.
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    libs  19.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
o.rocc: warning in factor(pr, level = c(0, 1)): partial argument match
  of 'level' to 'levels'
p.rocc: warning in factor(pr, level = c(0, 1)): partial argument match
  of 'level' to 'levels'
o.rocc: no visible global function definition for ‘prediction’
o.rocc: no visible global function definition for ‘performance’
o.rocc: no visible global function definition for ‘binom.test’
tr.rocc: no visible global function definition for ‘prediction’
tr.rocc: no visible global function definition for ‘performance’
Undefined global functions or variables:
  binom.test performance prediction
Consider adding
  importFrom("stats", "binom.test")
to your NAMESPACE file.
Package which this enhances but not available for checking: ‘ROI.plugin.cplex’
Namespace in Imports field not imported from: ‘matrixcalc’
  All declared Imports should be used.
installed size is 24.9Mb
  sub-directories of 1Mb or more:
    libs  24.8Mb
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: viridisLite
Quitting from lines 34-54 (graphics_of_pm_25_concentrations_in_several_countries.Rmd) 
Error: processing vignette 'graphics_of_pm_25_concentrations_in_several_countries.Rmd' failed with diagnostics:
uh oh, the OpenAQ API seems to be having some issues, try again later
Execution halted
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   5.0Mb
Namespaces in Imports field not imported from:
  ‘httpuv’ ‘utils’
  All declared Imports should be used.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.1Mb
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/RPPanalyzer.Rcheck/RPPanalyzer/extdata’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/RPPanalyzer.Rcheck/RPPanalyzer/extdata’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/RPPanalyzer.Rcheck/RPPanalyzer/extdata’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/RPPanalyzer.Rcheck/RPPanalyzer/extdata’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/RPPanalyzer.Rcheck/RPPanalyzer/extdata’, resetting
Running ‘testthat.R’ [6s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rprojroot)
  > 
  > test_check("rprojroot")
  Error in readRDS(pfile) : 
    cannot read unreleased workspace version 3 written by experimental R 3.5.0
  Calls: cat ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
  Execution halted
  ── 1. Failure: thisfile works with Rscript (@test-thisfile.R#12)  ──────────────
  "scripts/thisfile-cat.R" not equal to res[[length(res)]].
  1/1 mismatches
  x[1]: "scripts/thisfile-cat.R"
  y[1]: "WARNING: ignoring environment value of R_HOME"
  
  Error in readRDS(pfile) : 
    cannot read unreleased workspace version 3 written by experimental R 3.5.0
  Calls: cat ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
  Execution halted
  ── 2. Failure: thisfile works with R (@test-thisfile.R#19)  ────────────────────
  "scripts/thisfile-cat.R" not equal to res[[length(res)]].
  1/1 mismatches
  x[1]: "scripts/thisfile-cat.R"
  y[1]: "WARNING: ignoring environment value of R_HOME"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 76 SKIPPED: 4 FAILED: 2
  1. Failure: thisfile works with Rscript (@test-thisfile.R#12) 
  2. Failure: thisfile works with R (@test-thisfile.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   7.0Mb
Namespace in Imports field not imported from: ‘vegan’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpQr8dWg’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpQr8dWg’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpQr8dWg’, resetting
Namespaces in Imports field not imported from:
  ‘binman’ ‘httr’
  All declared Imports should be used.
Found the following significant warnings:
  Rserv.c:2976:16: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/Rserve.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-clang/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’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
Found the following significant warnings:
  SPACE.cpp:284:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
  SPACE.cpp:285:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
  SPACE.cpp:405:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
See ‘/data/gannet/ripley/R/packages/tests-clang/rSPACE.Rcheck/00install.out’ for details.
installed size is 50.8Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  49.4Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
Namespace in Imports field not imported from: ‘pkgconfig’
  All declared Imports should be used.
installed size is 154.5Mb
  sub-directories of 1Mb or more:
    doc     2.4Mb
    libs  150.6Mb
installed size is 292.6Mb
  sub-directories of 1Mb or more:
    libs  290.2Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Namespace in Imports field not imported from: ‘mc2d’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    Lib  11.9Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘stats’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       1.5Mb
    projects   2.3Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘rmarkdown’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   1.9Mb
Running examples in ‘RunuranGUI-Ex.R’ failed
The error most likely occurred in:

> ### Name: unuran.gui
> ### Title: A GUI for the UNU.RAN random variate generators.
> ### Aliases: unuran.gui
> ### Keywords: distribution datagen
> 
> ### ** Examples
> 
> ## start GUI to Runuran random number generator
> unuran.gui()
Error in unclass(x) : cannot unclass an external pointer
Calls: unuran.gui ... .delete -> .delete -> .delete -> ==.RGtkObject -> identical
Execution halted
installed size is 40.9Mb
  sub-directories of 1Mb or more:
    libs  40.2Mb
rvideopoker: warning in rp.radiogroup(mypanel, var =
  state$penny.nickel.quarter.dollar, initval = 1, values = c(1, 5, 25,
  100), title = "Bet (in Cents)", action = setbet): partial argument
  match of 'var' to 'variable'
rvideopoker: warning in rp.slider(mypanel, var = state$no.of.credits,
  from = 1, to = 5, initval = 1, title = "How many Credits?",
  resolution = 1, action = creditset, showvalue = TRUE): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC1, action = card1check, title = "Keep Card 1?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC2, action = card2check, title = "Keep Card 2?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC3, action = card3check, title = "Keep Card 3?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC4, action = card4check, title = "Keep Card 4?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC5, action = card5check, title = "Keep Card 5?"): partial
  argument match of 'var' to 'variable'
rvideopoker : plotFrame: no visible global function definition for
  ‘par’
rvideopoker : showBack: no visible global function definition for
  ‘title’
rvideopoker : showCardsInitially: no visible global function definition
  for ‘title’
Undefined global functions or variables:
  par title
Consider adding
  importFrom("graphics", "par", "title")
to your NAMESPACE file.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    include   5.4Mb
installed size is 50.7Mb
  sub-directories of 1Mb or more:
    libs  49.9Mb
installed size is 24.2Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
    test  19.6Mb
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 ‘/data/gannet/ripley/R/packages/tests-clang/RWiener.Rcheck/00install.out’ for details.
Found the following significant warnings:
  nchg.c:555:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/RxCEcolInf.Rcheck/00install.out’ for details.
Found the following significant warnings:
  call_dvode.c:746:18: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  lincmt.c:110:11: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
  sum.c:221:11: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  sum.c:221:22: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  sum.c:227:45: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  sum.c:227:53: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/RxODE.Rcheck/00install.out’ for details.
Found the following significant warnings:
  yacas/src/obmalloc.cpp:584:23: warning: comparison of constant 384307168202282325 with expression of type 'unsigned int' is always false [-Wtautological-constant-out-of-range-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/Ryacas.Rcheck/00install.out’ for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs    7.4Mb
    yacas   1.5Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    sample_data   3.1Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Namespace in Imports field not imported from: ‘spanel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘subplex’
  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 ‘/data/gannet/ripley/R/packages/tests-clang/SafeBayes.Rcheck/00install.out’ for details.
Running examples in ‘SAGA-Ex.R’ failed
The error most likely occurred in:

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

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

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


AICc weights were used to select the minimum number of models whose weights sum 
to greater than 95% this model set includes 12 model(s)
> plot(results)
Error in if (maxval < 0) maxval <- 0 : 
  missing value where TRUE/FALSE needed
Calls: plot -> plot.genarch
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 267-270 (model-averaged-analysis.Rmd) 
Error: processing vignette 'model-averaged-analysis.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
Execution halted
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Namespace in Imports field not imported from: ‘pvclust’
  All declared Imports should be used.
Found the following significant warnings:
  ./BGPscan.h:114:5: warning: field 'm_beta_alt' will be initialized after field 'm_inc_idx' [-Wreorder]
  ./USTscan.h:66:5: warning: field 'm_counts' will be initialized after field 'm_num_locs' [-Wreorder]
  ./USTscan.h:71:5: warning: field 'm_zone_lengths' will be initialized after field 'm_store_everything' [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-clang/scanstatistics.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘R6’ ‘cowplot’ ‘ggplot2’ ‘ggridges’ ‘ggstance’ ‘jmvcore’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.7Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘testthat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gbm’
  All declared Imports should be used.
Found the following significant warnings:
  pointinpolygon.c:60:7: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  slope.aspect.c:128:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  slope.aspect.c:128:33: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  vincenty.geodesics.c:50:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  vincenty.geodesics.c:126:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/SDMTools.Rcheck/00install.out’ for details.
Found the following significant warnings:
  BinNegative.cpp:108:5: warning: assigning field to itself [-Wself-assign-field]
See ‘/data/gannet/ripley/R/packages/tests-clang/Segmentor3IsBack.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘cluster’ ‘factoextra’ ‘tidyr’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘XML’ ‘mgcv’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘compiler’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘datasets’
  All declared Imports should be used.
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    doc    6.0Mb
    libs  12.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
Found the following significant warnings:
  vcf.c:253:15: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/seqminer.Rcheck/00install.out’ for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
capture: no visible binding for global variable ‘resultText’
restore.session: no visible binding for global variable
  ‘.save.session.packages’
restore.session: no visible binding for global variable
  ‘.save.session.search’
save.session: no visible global function definition for ‘dev.list’
save.session: no visible binding for '<<-' assignment to
  ‘.save.session.search’
save.session: no visible binding for '<<-' assignment to
  ‘.save.session.packages’
Undefined global functions or variables:
  .save.session.packages .save.session.search dev.list resultText
Consider adding
  importFrom("grDevices", "dev.list")
to your NAMESPACE file.
Package suggested but not available for checking: ‘MAST’
Found the following significant warnings:
  Warning: namespace ‘Biobase’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-clang/Seurat.Rcheck/00install.out’ for details.
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    doc     10.7Mb
    libs     4.0Mb
    sqlite   1.5Mb
Found the following significant warnings:
  ./data/data_set.h:24:31: warning: field 'xpMat_' will be initialized after field 'Y' [-Wreorder]
  ./learn-rate/onedim_learn_rate.h:19:5: warning: field 'scale_' will be initialized after field 'gamma_' [-Wreorder]
  ./learn-rate/ddim_learn_rate.h:26:34: warning: field 'eta_' will be initialized after field 'a_' [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-clang/sgd.Rcheck/00install.out’ for details.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    www   9.7Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘htmlwidgets’ ‘jsonlite’ ‘viridis’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘data.table’ ‘gridExtra’ ‘knitr’ ‘latticeExtra’ ‘msm’ ‘plotly’
  ‘xtable’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
pandoc: Could not fetch http://deanattali.com/img/blog/shinyjs-improvements/extendshinyjs-demo.gif
HttpExceptionRequest Request {
  host                 = "deanattali.com"
  port                 = 80
  secure               = False
  requestHeaders       = []
  path                 = "/img/blog/shinyjs-improvements/extendshinyjs-demo.gif"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (InternalException (HandshakeFailed Error_EOF))
Error: processing vignette 'shinyjs-extend.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
Execution halted
Namespaces in Imports field not imported from:
  ‘KGode’ ‘XML’ ‘ggplot2’ ‘gridExtra’ ‘mvtnorm’ ‘reshape2’ ‘shinyjs’
  ‘tools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘shinyBS’ ‘shinythemes’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    www   6.5Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    semantic   5.7Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘viridis’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘KernSmooth’ ‘MASS’ ‘class’ ‘cluster’ ‘lattice’ ‘nnet’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pwr’
  All declared Imports should be used.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  10.7Mb
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’
File ‘simpleboot/R/zzz.R’:
  .onLoad calls:
    require(boot)

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

lo.boot.resample: warning in sample(1:nrow(orig.data), rep = TRUE, prob
  = weights): partial argument match of 'rep' to 'replace'
lo.boot.resample: warning in sample(res, rep = TRUE, prob = weights):
  partial argument match of 'rep' to 'replace'
Found the following significant warnings:
  expression.cpp:273:19: warning: field 'exponent' will be initialized after field 'dependency' [-Wreorder]
  expression.cpp:278:19: warning: field 'exponent' will be initialized after field 'dependency' [-Wreorder]
  expression.cpp:283:19: warning: field 'exponent' will be initialized after field 'dependency' [-Wreorder]
  expression.cpp:287:19: warning: field 'exponent' will be initialized after field 'dependency' [-Wreorder]
  expression.cpp:322:3: warning: field 'depexponent' will be initialized after field 'dependency' [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-clang/simplr.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘metafor’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pracma’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Namespace in Imports field not imported from: ‘mcmc’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘prediction’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Note: found 15 marked Latin-1 strings
  Note: found 2 marked UTF-8 strings
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   8.1Mb
Found the following significant warnings:
  MCP_efficient.c:114:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  MCP_efficient.c:134:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  MCP_efficient.c:154:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/SMCP.Rcheck/00install.out’ for details.
Found the following significant warnings:
  SME.c:70:21: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  SME.c:71:20: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  SME.c:477:17: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  SME.c:478:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/sme.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘compiler’ ‘lmtest’
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   5.3Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘nlme’ ‘survival’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gtools’ ‘hashmap’ ‘reshape2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘rstudioapi’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘CircStats’ ‘RandomFields’ ‘grDevices’ ‘sp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘SpaDES.addins’ ‘SpaDES.core’ ‘SpaDES.tools’ ‘quickPlot’
  ‘reproducible’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘fastdigest’
  All declared Imports should be used.
installed size is 34.7Mb
  sub-directories of 1Mb or more:
    libs  33.6Mb
Namespace in Imports field not imported from: ‘foreach’
  All declared Imports should be used.
Package suggested but not available for checking: ‘RCy3’
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘SpatialEpi’ ‘dplyr’ ‘dygraphs’ ‘ggplot2’
  ‘htmlwidgets’ ‘knitr’ ‘leaflet’ ‘mapproj’ ‘maptools’ ‘rgdal’ ‘rgeos’
  ‘rmarkdown’ ‘shinyjs’ ‘spdep’ ‘xts’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘moments’ ‘poweRlaw’
  All declared Imports should be used.
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    R      4.9Mb
    doc    4.7Mb
    help   4.9Mb
    libs   1.7Mb
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  20.8Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data     2.6Mb
    shapes   3.2Mb
Running examples in ‘specmine-Ex.R’ failed
The error most likely occurred in:

> ### Name: impute_nas_linapprox
> ### Title: Impute missing values with linear approximation
> ### Aliases: impute_nas_linapprox
> ### Keywords: missing values
> 
> ### ** Examples
> 
>   ## Example of NA imputation with linear approximation
>   data(propolis)
>   dataset = impute_nas_linapprox(propolis)
Error: 'spc.NA.linapprox' is not an exported object from 'namespace:hyperSpec'
Execution halted
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nr' to 'nrow'
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nc' to 'ncol'
spe: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘maptools’
  All declared Imports should be used.
Note: found 8 marked Latin-1 strings
  Note: found 83 marked UTF-8 strings
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   7.3Mb
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs  11.9Mb
Namespaces in Imports field not imported from:
  ‘BayesX’ ‘BayesXsrc’ ‘automap’ ‘plyr’ ‘rgdal’ ‘splines’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘geoR’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shinyFiles’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/Rtmp5lnGJf’, resetting
stkde: no visible global function definition for ‘npudensbw’
stkde: no visible global function definition for ‘npudens’
stkde: no visible global function definition for ‘quantile’
stkde: no visible global function definition for ‘heat.colors’
stkde: no visible global function definition for ‘par’
stkde: no visible global function definition for ‘image’
stkde: no visible global function definition for ‘contour’
stkde.base: no visible global function definition for ‘npudensbw’
stkde.base: no visible global function definition for ‘npudens’
stkde.sig: no visible global function definition for ‘SpatialPoints’
stkde.sig: no visible global function definition for ‘spsample’
stkde.sig: no visible global function definition for ‘bbox’
stkde.sig: no visible global function definition for ‘quantile’
stkde.sig: no visible global function definition for ‘heat.colors’
stkde.sig: no visible global function definition for ‘par’
stkde.sig: no visible global function definition for ‘image’
stkde.sig: no visible global function definition for ‘contour’
Undefined global functions or variables:
  SpatialPoints bbox contour heat.colors image npudens npudensbw par
  quantile spsample
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "contour", "image", "par")
  importFrom("stats", "quantile")
to your NAMESPACE file.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    include   9.1Mb
    lib       1.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   4.9Mb
Namespace in Imports field not imported from: ‘MCMCpack’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'StatCharrms.tex' failed.
LaTeX errors:
! Too many }'s.
l.351 ...tion}{Other Endpoints Specification Tab}}
                                                  
You've closed more groups than you opened.
Such booboos are generally harmless, so keep going.
! Too many }'s.
l.455 ...oc}{subsection}{Other Endpoints Results}}
                                                  
You've closed more groups than you opened.
Such booboos are generally harmless, so keep going.
! You can't use `macro parameter character #' in horizontal mode.
<argument> Lower.##
                   ##..CI
l.485 			\item \textbf{Lower.##..CI}
                                    : The lower 1-alpha percent (defaults to...
! You can't use `macro parameter character #' in horizontal mode.
<argument> Lower.####
                     ..CI
l.485 			\item \textbf{Lower.##..CI}
                                    : The lower 1-alpha percent (defaults to...
! You can't use `macro parameter character
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘stringr’
  All declared Imports should be used.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
Namespaces in Imports field not imported from:
  ‘lattice’ ‘xtable’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpPQ82jo’, resetting
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘tm’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Namespaces in Imports field not imported from:
  ‘broom’ ‘car’ ‘lmerTest’ ‘pbkrtest’
  All declared Imports should be used.
Running ‘testthat.R’ [10s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(subprocess)
  > 
  > # See for more details:
  > # https://github.com/hadley/testthat/issues/144
  > # https://github.com/hadley/testthat/issues/86
  > # https://github.com/luckyrandom/cmaker/commit/b85813ac2b7aef69932eca8fbb4fa0ec225e0af0
  > #
  > # When R CMD check runs tests, it sets R_TESTS. When the tests
  > # themeselves run R CMD xxxx, as is the case with the tests in
  > # devtools, having R_TESTS set causes errors because it confuses
  > # the R subprocesses. Unsetting it here avoids those problems.
  > #
  > # We need this because we spawn child R processes and they get very
  > # confused if this variable (R_TESTS) is present in their environment.
  > Sys.setenv("R_TESTS" = "")
  > 
  > test_check("subprocess")
  ── 1. Error: child process is terminated in Linux (@test-termination.R#85)  ────
  is_process_handle(handle) is not TRUE
  1: expect_true(wait_until_appears(child_id)) at testthat/test-termination.R:85
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: wait_until_appears(child_id)
  5: process_wait(handle, TIMEOUT_IMMEDIATE) at /data/gannet/ripley/R/packages/tests-clang/subprocess.Rcheck/tests/testthat/helper-processes.R:58
  6: stopifnot(is_process_handle(handle))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 71 SKIPPED: 2 FAILED: 1
  1. Error: child process is terminated in Linux (@test-termination.R#85) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  RMcrt.cpp:20:83: warning: field 'gdt' will be initialized after field 'unreliable' [-Wreorder]
  RVcrt.cpp:37:97: warning: field 'e' will be initialized after field 'unreliable' [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-clang/subselect.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘fields’
  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 ‘/data/gannet/ripley/R/packages/tests-clang/SuppDists.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘matrixStats’ ‘nloptr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘curatedOvarianData’
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   1.5Mb
installed size is 68.9Mb
  sub-directories of 1Mb or more:
    libs  68.1Mb
Namespaces in Imports field not imported from:
  ‘Biobase’ ‘broom’ ‘data.table’ ‘magrittr’ ‘pander’ ‘png’ ‘readr’
  ‘survsim’ ‘testthat’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.6Mb
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Found the following significant warnings:
  trlan/trlcore.c:983:15: warning: comparison of array 'info->oldcpf' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlcore.c:1642:9: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  trlan/trlcore.c:1642:20: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  trlan/trlaux.c:28:13: warning: comparison of array 'info->log_file' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlaux.c:41:13: warning: comparison of array 'info->log_file' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlaux.c:62:13: warning: comparison of array 'info->cpfile' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlan.c:171:20: warning: comparison of array 'info->oldcpf' equal to a null pointer is always false [-Wtautological-pointer-compare]
  trlan/ztrlcore.c:1418:12: warning: comparison of array 'info->oldcpf' not equal to a null pointer is always true [-Wtautological-pointer-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/svd.Rcheck/00install.out’ for details.
Running examples in ‘svMisc-Ex.R’ failed
The error most likely occurred in:

> ### Name: toRjson
> ### Title: Convert R object to and from RJSON specification
> ### Aliases: toRjson evalRjson listToJson
> ### Keywords: utilities
> 
> ### ** Examples
> 
> ## A complex R object
> Robj <- structure(list(
+ 	a = as.double(c(1:5, 6)),
+ 	LETTERS,
+ 	c = c(c1 = 4.5, c2 = 7.8, c3 = Inf, c4 = -Inf, NA, c6 = NaN),
+ 	c(TRUE, FALSE, NA),
+ 	e = factor(c("a", "b", "a")),
+ 	f = "this is a \"string\"\nwith\tspecial chars",
+ 	g = matrix(rnorm(4), ncol = 2),
+ 	`h&'$@` = data.frame(x = 1:3, y = rnorm(3),
+ 		fact = factor(c("b", "a", "b"))),
+ 	i = Sys.Date(),
+     j = list(1:5, y = "another item")),
+     comment = "My comment\n\"",
+     anAttrib = 1:10,
+     anotherAttrib = list(TRUE, y = 1:4))
> 
> ## Convert to simplest RJSON, without attributes
> Rjson1 <- toRjson(Robj)
> Rjson1
[1] list(c(1., 2., 3., 4., 5., 6.), c("A", "B", "C", "D", "E", "F",                              
[2] "G", "H", "I", "J", "K", "L", "M", "N", "O", "P", "Q", "R", "S",                             
[3] "T", "U", "V", "W", "X", "Y", "Z"), c(4.5, 7.8, Inf, -Inf, NA,                               
[4] NaN), c(TRUE, FALSE, NA), c("a", "b", "a"), "this is a \\"string\\"\\nwith\\tspecial chars", 
[5]     c(-0.626453810742332, 0.183643324222082, -0.835628612410047,                             
[6]     1.59528080213779), list(seq(1, 3), c(0.329507771815361, -0.820468384118015,              
[7]     0.487429052428485), c("b", "a", "b")), "2017-12-22", list(                               
[8]         seq(1, 5), "another item"))                                                          
> evalRjson(Rjson1)
Error in .getClassesFromCache(Class) : 
  class should be either a character-string name or a class definition
Calls: evalRjson ... new -> getClass -> getClassDef -> .getClassesFromCache
Execution halted
Namespaces in Imports field not imported from:
  ‘MASS’ ‘graphics’ ‘methods’ ‘stats’
  All declared Imports should be used.
Package in Depends field not imported from: ‘kernlab’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: GNU Extension: Different type kinds at (1)
  Warning: GNU Extension: initialization of common block variable ‘iset’ in DATA statement at (1)
  Warning: GNU Extension: Variable ‘iset’ at (1) is in COMMON but only in BLOCK DATA initialization is allowed
  Warning: GNU Extension: Missing comma at (1)
  Warning: CHARACTER expression will be truncated in assignment (10/13) at (1) [-Wcharacter-truncation]
  Warning: ‘pst_kg’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘burn_frlb’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘harveff’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘hi_ovr’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘frac_harvk’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘cnop’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘lai_init’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘orig_tnylda’ is used uninitialized in this function [-Wuninitialized]
  Warning: CHARACTER expression will be truncated in assignment (1/3) at (1) [-Wcharacter-truncation]
  Warning: ‘fr_curb’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-clang/SWATmodel.Rcheck/00install.out’ for details.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘lazyeval’ ‘lubridate’ ‘tidyr’
  All declared Imports should be used.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(swirlify)
  > library(swirl)
  
  | Hi! Type swirl() when you are ready to begin.
  
  
  Attaching package: 'swirl'
  
  The following object is masked from 'package:testthat':
  
      skip
  
  > 
  > test_check("swirlify")
  ── 1. Failure: test_lesson() passes with well-formed lesson (@test_test_lesson.R
  all(correct_output %in% readLines(file.path(path, "test.log"))) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 7 SKIPPED: 0 FAILED: 1
  1. Failure: test_lesson() passes with well-formed lesson (@test_test_lesson.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R         1.2Mb
    extdata   3.1Mb
Namespaces in Imports field not imported from:
  ‘crayon’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘lazyeval’ ‘rlang’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/taxlist.Rcheck/taxlist/cyperus’, resetting
Namespace in Imports field not imported from: ‘PerformanceAnalytics’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    tklibs   4.9Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    sql   8.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.9Mb
installed size is 36.2Mb
  sub-directories of 1Mb or more:
    libs  35.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    apps   2.6Mb
    libs   1.5Mb
Namespaces in Imports field not imported from:
  ‘data.table’ ‘datasets’ ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘nlme’ ‘tidyr’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Namespace in Imports field not imported from: ‘rprojroot’
  All declared Imports should be used.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.5Mb
    libs   5.2Mb
Namespace in Imports field not imported from: ‘irlba’
  All declared Imports should be used.
Note: found 10051 marked UTF-8 strings
  Note: found 10523 strings marked as "bytes"
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   8.5Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    rda    3.8Mb
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘splancs’ ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘tibble’ ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘broom’ ‘curl’ ‘devtools’ ‘rvest’ ‘timeSeries’ ‘tseries’ ‘zoo’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dbplyr’ ‘reprex’ ‘rlang’
  All declared Imports should be used.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Found the following significant warnings:
  common.c:121:16: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/tiff.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpsT99zJ’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpsT99zJ’, resetting
Found the following significant warnings:
  tm.c:184:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  tm.c:185:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/TimeMachine.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘forecast’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘broom’ ‘tibble’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.3Mb
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    examples  13.9Mb
    include    3.0Mb
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    libs  23.7Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘jmvcore’
  All declared Imports should be used.
File ‘tpr/libs/tpr.so’:
  Found ‘_ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’
File ‘tpr/libs/tpr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.7Mb
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    libs  27.2Mb
installed size is 37.2Mb
  sub-directories of 1Mb or more:
    libs  36.7Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/trib.Rcheck/trib/exdata/tribometer’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/trib.Rcheck/trib/exdata/tribometer’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/trib.Rcheck/trib/exdata/profile’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/trib.Rcheck/trib/exdata/profile’, resetting
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Found the following significant warnings:
  ./tsBSS.h:10:22: warning: 'varExx_k' has C-linkage specified, but returns user-defined type 'arma::mat' (aka 'Mat<double>') which is incompatible with C [-Wreturn-type-c-linkage]
See ‘/data/gannet/ripley/R/packages/tests-clang/tsBSS.Rcheck/00install.out’ for details.
covTranspose11: warning in glasso(sc, 2 * rhoc/n, wi.init = gc$wi,
  w.init = gc$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
covTranspose11: warning in glasso(sr, 2 * rhor/p, wi.init = gr$wi,
  w.init = gr$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
.help.ESS: no visible global function definition for ‘index.search’
TransSphere : ttin: no visible global function definition for ‘t.test’
TransSphere: no visible global function definition for ‘sd’
TransSphere: no visible global function definition for ‘quantile’
TransSphere: no visible global function definition for ‘pt’
Undefined global functions or variables:
  index.search pt quantile sd t.test
Consider adding
  importFrom("stats", "pt", "quantile", "sd", "t.test")
to your NAMESPACE file.
Found the following significant warnings:
  libglpk/glpapi06.c:530:26: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  libglpk/glpapi06.c:539:20: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  libglpk/glpios01.c:224:17: warning: explicitly assigning value of variable of type 'IOSNPD *' (aka 'struct IOSNPD *') to itself [-Wself-assign]
  libglpk/glpmpl06.c:666:17: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  libglpk/glpmpl06.c:825:20: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  libglpk/glpmps.c:1280:19: warning: explicitly assigning value of variable of type 'GLPAIJ *' (aka 'struct GLPAIJ *') to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/TukeyRegion.Rcheck/00install.out’ for details.
Found the following significant warnings:
  frame.c:147:21: warning: comparison of constant 4 with expression of type 'enum mad_layer' is always false [-Wtautological-constant-out-of-range-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/tuneR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmphPNGdh/treePos/2017_12_22/run’, resetting
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    doc         2.2Mb
    dummydata   1.4Mb
    libs       21.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.6Mb
Namespace in Imports field not imported from: ‘mcmcplots’
  All declared Imports should be used.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    data  26.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    extdata   6.2Mb
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘maptools’ ‘rgeos’
  All declared Imports should be used.
H: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = H, func.arg = list(func.arg), boot.arg)):
  partial argument match of 'arg' to 'args'
M.homog: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = M.homog, func.arg = list(func.arg),
  boot.arg)): partial argument match of 'arg' to 'args'
Rel.homog: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = Rel.homog, func.arg = list(func.arg),
  boot.arg)): partial argument match of 'arg' to 'args'
bootstrap: warning in do.call(what = func, arg = list(boots[, , i])):
  partial argument match of 'arg' to 'args'
bootstrap: warning in do.call(what = func, arg = c(abundances =
  list(boots[, , i]), func.arg)): partial argument match of 'arg' to
  'args'
d: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = d, func.arg = list(func.arg), boot.arg)):
  partial argument match of 'arg' to 'args'
sim.groups: warning in do.call(what = bootstrap, arg = c(abundances =
  list(rbind(scores[i, ], scores[j, ])), func = similarity, func.arg =
  list(func.arg), boot.arg)): partial argument match of 'arg' to 'args'
sim.table: warning in do.call(what = bootstrap, arg = c(abundances =
  list(rbind(scores[i, ], scores[j, ])), func = similarity, func.arg =
  list(func.arg), boot.arg)): partial argument match of 'arg' to 'args'
similarity: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = similarity, func.arg = list(func.arg),
  boot.arg)): partial argument match of 'arg' to 'args'
turnover: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = turnover, func.arg = list(func.arg),
  boot.arg)): partial argument match of 'arg' to 'args'
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    libs  19.4Mb
installed size is 26.7Mb
  sub-directories of 1Mb or more:
    libs  26.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   2.6Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc           4.8Mb
    htmlwidgets   3.7Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    extdata  10.8Mb
Namespaces in Imports field not imported from:
  ‘iterators’ ‘knitr’ ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lubridate’ ‘tibble’
  All declared Imports should be used.
installed size is 50.1Mb
  sub-directories of 1Mb or more:
    libs  49.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘ENMeval’ ‘RColorBrewer’ ‘dismo’ ‘dplyr’ ‘leaflet.extras’
  ‘maptools’ ‘raster’ ‘rgdal’ ‘rgeos’ ‘shinyjs’ ‘shinythemes’ ‘spThin’
  ‘spocc’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘WRS2’ ‘ggplot2’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.1Mb
Namespaces in Imports field not imported from:
  ‘monitoR’ ‘proxy’ ‘signal’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/Rtmphp9htE’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmphp9htE’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmphp9htE’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmphp9htE’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmphp9htE’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmphp9htE’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmphp9htE’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmphp9htE’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmphp9htE’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmphp9htE’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmphp9htE’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmphp9htE’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmphp9htE’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmphp9htE’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmphp9htE’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmphp9htE’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmphp9htE’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmphp9htE’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmphp9htE’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmphp9htE’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmphp9htE’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmphp9htE’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmphp9htE’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmphp9htE’, resetting
Error in re-building vignettes:
  ...
Loading required package: maps
Loading required package: tuneR
Loading required package: seewave
Quitting from lines 102-109 (warbleR_workflow_phase1.Rmd) 
Error: processing vignette 'warbleR_workflow_phase1.Rmd' failed with diagnostics:
cannot open the connection to 'http://www.xeno-canto.org/api/2/recordings?query=Phaethornis&page=2'
Execution halted
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    doc  12.1Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    client   9.6Mb
    doc      1.0Mb
Found the following significant warnings:
  t_region.cpp:78:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:115:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:120:7: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/WhopGenome.Rcheck/00install.out’ for details.
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  15.2Mb
Namespace in Imports field not imported from: ‘RandomFields’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.7Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.2Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    data  11.4Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    data  14.1Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
Namespaces in Imports field not imported from:
  ‘mgcv’ ‘seplyr’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    bin   5.4Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    java  19.0Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    java   9.7Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
Running examples in ‘xml2-Ex.R’ failed
The error most likely occurred in:

> ### Name: read_xml
> ### Title: Read HTML or XML.
> ### Aliases: read_xml read_html read_xml.character read_xml.raw
> ###   read_xml.connection
> 
> ### ** Examples
> 
> # Literal xml/html is useful for small examples
> read_xml("<foo><bar /></foo>")
{xml_document}
<foo>
[1] <bar/>
> read_html("<html><title>Hi<title></html>")
{xml_document}
<html>
[1] <head>\n<meta http-equiv="Content-Type" content="text/html; charset=UTF-8 ...
> read_html("<html><title>Hi")
{xml_document}
<html>
[1] <head>\n<meta http-equiv="Content-Type" content="text/html; charset=UTF-8 ...
> 
> # From a local path
> read_html(system.file("extdata", "r-project.html", package = "xml2"))
{xml_document}
<html lang="en">
[1] <head>\n<meta http-equiv="Content-Type" content="text/html; charset=UTF-8 ...
[2] <body>\n    <div class="container page">\n      <div class="row">\n       ...
> 
> # From a url
> cd <- read_xml("http://www.xmlfiles.com/examples/cd_catalog.xml")
Error in doc_parse_raw(x, encoding = encoding, base_url = base_url, as_html = as_html,  : 
  Specification mandate value for attribute async [41]
Calls: read_xml ... read_xml.connection -> read_xml.raw -> doc_parse_raw -> .Call
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    exampleData   1.6Mb
    examples      4.6Mb
Namespaces in Imports field not imported from:
  ‘Amelia’ ‘MatchIt’ ‘WhatIf’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘lubridate’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.6Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/Rtmpie8xgl/filematrices’, resetting
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
asp: no visible global function definition for ‘as.formula’
asp: no visible global function definition for ‘var’
aspm: no visible binding for global variable ‘X.Declan’
aspm: no visible binding for global variable ‘Z.Jaida’
aspm: no visible binding for global variable ‘group.vec.Handan’
aspm: no visible global function definition for ‘as.formula’
aspm: no visible global function definition for ‘glm’
aspm: no visible global function definition for ‘binomial’
aspm: no visible global function definition for ‘poisson’
Undefined global functions or variables:
  X.Declan Z.Jaida as.formula binomial glm group.vec.Handan poisson var
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "poisson", "var")
to your NAMESPACE file.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data       2.8Mb
    pictures   2.1Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See ‘/data/gannet/ripley/R/packages/tests-devel/audio.Rcheck/00install.out’ for details.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    libs   3.7Mb
installed size is 153.6Mb
  sub-directories of 1Mb or more:
    libs  153.2Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   5.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.3Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  15.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Running examples in ‘bayesCL-Ex.R’ failed
The error most likely occurred in:

> ### Name: lasso
> ### Title: Bayesian Lasso
> ### Aliases: lasso
> ### Keywords: regression
> 
> ### ** Examples
> 
> 
> set.seed(0)
> n_samples  <- 500
> n_features <- 40
> X <- matrix(rnorm(n_features * n_samples), nrow = n_samples)
> y <- 2 * X[,1] - 3 * X[,2] + rnorm(n_samples) # only features 1 & 2 are relevant
> 
> X_train <- X[1:400,]
> y_train <- y[1:400]
> X_test  <- X[401:500,]
> y_test  <- y[401:500]
> 
> 
> # START ------------------------------------------------------------------------
> 
> # first, standardize data !!!
> X_train <- scale(X_train)
> 
> tmp00 <- bayesCL::lasso(X = X_train, 
+                           y = y_train, 
+                           T = 500,  # number of Gibbs sampling iterations
+                           icept = T,
+                           device=0  ) # use constant term (intercept), we do
------------------------------
Platform and device selection

 *** caught segfault ***
address 0x12da4e60, cause 'memory not mapped'

Traceback:
 1: .Call("prepareCL", as.integer(platf), as.integer(device_id),     as.character(paste(.libPaths()[1], "/bayesCL", .Platform$file.sep,         "polyaGammaf.cl", sep = "")), as.character(paste(.libPaths()[1],         "/bayesCL", .Platform$file.sep, "polyaGammaf-", platf,         "-", device_id, ".bin", sep = "")), as.integer(params))
 2: prepare(precision = 0, device = device, parameters = parameters)
 3: bayesCL::lasso(X = X_train, y = y_train, T = 500, icept = T,     device = 0)
An irrecoverable exception occurred. R is aborting now ...
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  17.3Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
installed size is 52.4Mb
  sub-directories of 1Mb or more:
    libs  51.6Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/bayesMCClust.Rcheck/bayesMCClust-wd’, resetting
installed size is 34.3Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs  29.6Mb
Found the following significant warnings:
  Gspline.cpp:1064:29: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ writing 41 bytes into a region of size 20 overflows the destination [-Wstringop-overflow=]
  Gspline.cpp:1065:29: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ writing 49 bytes into a region of size 20 overflows the destination [-Wstringop-overflow=]
  Gspline.cpp:1066:29: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ writing 39 bytes into a region of size 20 overflows the destination [-Wstringop-overflow=]
  classCovMatrix.cpp:231:27: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ writing 16 bytes into a region of size 15 overflows the destination [-Wstringop-overflow=]
  classRandomEff.cpp:248:24: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ writing 14 bytes into a region of size 10 overflows the destination [-Wstringop-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/bayesSurv.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is 77.0Mb
  sub-directories of 1Mb or more:
    libs  76.9Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Found the following significant warnings:
  bcrypt/bcrypt.c:144:24: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=]
  bcrypt/bcrypt.c:254:29: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=]
See ‘/data/gannet/ripley/R/packages/tests-devel/bcrypt.Rcheck/00install.out’ for details.
installed size is 48.2Mb
  sub-directories of 1Mb or more:
    libs  46.8Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.3Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   6.0Mb
installed size is 30.2Mb
  sub-directories of 1Mb or more:
    libs  30.0Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
bigglm.RODBC: no visible global function definition for ‘odbcQuery’
bigglm.RODBC : chunk: no visible global function definition for
  ‘odbcQuery’
bigglm.RODBC : chunk: no visible global function definition for
  ‘sqlGetResults’
bigglm,ANY-DBIConnection: no visible global function definition for
  ‘dbSendQuery’
bigglm,ANY-DBIConnection: no visible global function definition for
  ‘dbClearResult’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘dbClearResult’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘dbSendQuery’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘fetch’
Undefined global functions or variables:
  dbClearResult dbSendQuery fetch odbcQuery sqlGetResults
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      9.2Mb
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   5.8Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   3.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Error in re-building vignettes:
  ...
Warning in buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-devel/biorxivr.Rcheck/vign_test/biorxivr") :
  Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/index.Rmd’
(Is a VignetteBuilder field missing?)
Quitting from lines 17-20 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
failed to load external entity "http://www.biorxiv.org/search/Ecology?page=0"
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
blighty: no visible global function definition for ‘par’
blighty: no visible global function definition for ‘polygon’
blighty: no visible global function definition for ‘points’
blighty: no visible global function definition for ‘box’
blighty: no visible global function definition for ‘axis’
blighty: no visible global function definition for ‘abline’
map.scale: no visible global function definition for ‘locator’
map.scale: no visible global function definition for ‘segments’
map.scale: no visible global function definition for ‘text’
north.pointer: no visible global function definition for ‘locator’
north.pointer: no visible global function definition for ‘text’
north.pointer: no visible global function definition for ‘arrows’
north.pointer: no visible global function definition for ‘segments’
sqlimits: no visible global function definition for ‘frame’
sqlimits: no visible global function definition for ‘par’
Undefined global functions or variables:
  abline arrows axis box frame locator par points polygon segments text
Consider adding
  importFrom("graphics", "abline", "arrows", "axis", "box", "frame",
             "locator", "par", "points", "polygon", "segments", "text")
to your NAMESPACE file.
installed size is 49.2Mb
  sub-directories of 1Mb or more:
    libs  48.1Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
installed size is 33.1Mb
  sub-directories of 1Mb or more:
    libs  32.8Mb
installed size is 417.2Mb
  sub-directories of 1Mb or more:
    include    2.9Mb
    lib      414.1Mb
installed size is 80.0Mb
  sub-directories of 1Mb or more:
    libs  79.7Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    bin    2.2Mb
    doc    1.2Mb
    libs   2.2Mb
installed size is 36.8Mb
  sub-directories of 1Mb or more:
    libs  35.6Mb
installed size is 88.3Mb
  sub-directories of 1Mb or more:
    libs  87.9Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    libs  17.7Mb
Running ‘testthat.R’ [7s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(callr)
  > 
  > Sys.unsetenv("R_TESTS")
  > 
  > test_check("callr")
  ── 1. Error: debugger is called (@test-error.R#45)  ────────────────────────────
  Can't mock functions in base packages (utils)
  1: with_mock(`utils::debugger` = function(...) called <<- TRUE, r(function() {
         1 + "A"
     }, error = "debugger")) at testthat/test-error.R:45
  2: extract_mocks(new_values = new_values[!code_pos], .env = .env, eval_env = parent.frame())
  3: lapply(stats::setNames(nm = mock_qual_names), function(qual_name) {
         pkg_name <- gsub(pkg_and_name_rx, "\\1", qual_name)
         if (is_base_pkg(pkg_name)) {
             stop("Can't mock functions in base packages (", pkg_name, ")", call. = FALSE)
         }
         name <- gsub(pkg_and_name_rx, "\\2", qual_name)
         if (pkg_name == "") 
             pkg_name <- .env
         env <- asNamespace(pkg_name)
         if (!exists(name, envir = env, mode = "function")) 
             stop("Function ", name, " not found in environment ", environmentName(env), 
                 ".", call. = FALSE)
         mock(name = name, env = env, new = eval(new_values[[qual_name]], eval_env, eval_env))
     })
  4: FUN(X[[i]], ...)
  5: stop("Can't mock functions in base packages (", pkg_name, ")", call. = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 28 SKIPPED: 0 FAILED: 1
  1. Error: debugger is called (@test-error.R#45) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    libs  17.2Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/cda.Rcheck/00install.out’ for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.3Mb
Found the following significant warnings:
  BlockCEM.h:52:44: warning: ‘BlockCEM<double>::Y’ will be initialized after [-Wreorder]
  BlockCEM.h:51:44: warning:   ‘FortranLinalg::DenseMatrix<double> BlockCEM<double>::X’ [-Wreorder]
  BlockCEM.h:152:5: warning:   when initialized here [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-devel/cems.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel’, resetting
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    libs  21.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 30.1Mb
  sub-directories of 1Mb or more:
    libs  29.8Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   6.4Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 37.2Mb
  sub-directories of 1Mb or more:
    libs  37.0Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is 23.0Mb
  sub-directories of 1Mb or more:
    libs  21.6Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   6.1Mb
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    libs  23.1Mb
Found the following significant warnings:
  convert_util.cpp:299:20: warning: null destination pointer [-Wformat-overflow=]
  convert_util.cpp:307:20: warning: null destination pointer [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/DatABEL.Rcheck/00install.out’ for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is 53.0Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  50.8Mb
Running ‘testthat.R’ [16s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("data.tree")
  Loading required package: data.tree
  ── 1. Error: partykid (@test-treeConversionParty.R#37)  ────────────────────────
  could not find function "extree_data"
  1: partykit::ctree(Ozone ~ ., data = airq) at testthat/test-treeConversionParty.R:37
  2: eval(mf, parent.frame())
  3: eval(mf, parent.frame())
  
                            levelName    cost
  1  Acme Inc.                             NA
  2   ¦--Accounting                        NA
  3   ¦   ¦--New Software             1000000
  4   ¦   °--New Accounting Standards  500000
  5   ¦--Research                          NA
  6   ¦   ¦--New Product Line         2000000
  7   ¦   °--New Labs                  750000
  8   °--IT                                NA
  9       ¦--Outsource                 400000
  10      ¦--Go agile                  250000
  11      °--Switch to R                50000
    levelName  b             1
  1 Root      NA              
  2  °--a      2              
  3      °--c NA 1, 2, 3, 4, 5
    levelName a
  1     Root   
  2      °--a 2
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 352 SKIPPED: 2 FAILED: 1
  1. Error: partykid (@test-treeConversionParty.R#37) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   7.9Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is 24.1Mb
  sub-directories of 1Mb or more:
    libs  24.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    help   1.3Mb
    libs   1.7Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    extdata   2.4Mb
    libs      4.1Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/Rtmpo7yz8p’, resetting
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    libs  18.5Mb
installed size is 43.0Mb
  sub-directories of 1Mb or more:
    libs  42.6Mb
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  25.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Found the following significant warnings:
  dcm2niix/nii_dicom.cpp:577:5: warning: ‘%s’ directive output may be truncated writing up to 63 bytes into a region of size 24 [-Wformat-truncation=]
See ‘/data/gannet/ripley/R/packages/tests-devel/divest.Rcheck/00install.out’ for details.
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    include  19.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   6.3Mb
installed size is 32.7Mb
  sub-directories of 1Mb or more:
    libs  30.8Mb
Found the following significant warnings:
  DPPmcmc.h:91:16: warning: ‘DPPmcmc::model’ will be initialized after [-Wreorder]
  DPPmcmc.h:82:12: warning:   ‘Rcpp::Function DPPmcmc::effectiveSizeFunction’ [-Wreorder]
  DPPmcmc.cpp:11:1: warning:   when initialized here [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-devel/DPP.Rcheck/00install.out’ for details.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   9.1Mb
installed size is 25.0Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.2Mb
    libs  19.3Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    models   4.3Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpRxm4RP’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpRxm4RP’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpRxm4RP’, resetting
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 42.2Mb
  sub-directories of 1Mb or more:
    libs  41.9Mb
Found the following significant warnings:
  Matrix.h:42:7: warning: ‘myMatrix::numrow’ will be initialized after [-Wreorder]
  Matrix.h:41:7: warning:   ‘int myMatrix::numcol’ [-Wreorder]
  Matrix.h:8:12: warning:   when initialized here [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-devel/Emcdf.Rcheck/00install.out’ for details.
installed size is 29.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  27.4Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/EmiStatR.Rcheck/EmiStatR/shiny/EmiStatR_output’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/EmiStatR.Rcheck/EmiStatR/shiny/EmiStatR_output’, resetting
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Found the following significant warnings:
  Warning: iteration 7 invokes undefined behavior [-Waggressive-loop-optimizations]
See ‘/data/gannet/ripley/R/packages/tests-devel/expoRkit.Rcheck/00install.out’ for details.
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
Running ‘testthat.R’ [126s/151s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(eyetrackingR)
  > 
  > test_check("eyetrackingR")
  Test Type:	 lmer 
  Predictor:	 (Intercept) 
  Formula:	 Prop ~ AOI + (1 | Trial) 
  Runs of Significant Time Bins: 
  Positive Run 1  ===== 
  	Time:		 15500 - 21000 Test Type:	 boot_splines 
  Predictor:	 Target 
  Formula:	 Prop ~ Target 
  Runs of Significant Time Bins: 
  Positive Run 1  ===== 
  	Time:		 15900 - 21000 ── 1. Error: (unknown) (@test_cluster_analysis.R#143)  ─────────────────────────
  no applicable method for 'make_time_cluster_data' applied to an object of class "data.frame"
  1: make_time_cluster_data(response_time_by_ppt, predictor_column = "Sex", test = "boot_splines", 
         within_subj = FALSE, smoother = "smooth.spline", alpha = 0.05) at testthat/test_cluster_analysis.R:143
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 42 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_cluster_analysis.R#143) 
  
  Error: testthat unit tests failed
  Execution halted
Compilation used the following non-portable flag(s):
  ‘-Wmisleading-indentation’
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  15.7Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.4Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/data/gannet/ripley/R/packages/tests-devel/FastRWeb.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.8Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is 47.9Mb
  sub-directories of 1Mb or more:
    libs  47.2Mb
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    libs  23.1Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs  11.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/FishResp.Rcheck/FishResp’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/FishResp.Rcheck/FishResp’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/FishResp.Rcheck/FishResp’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/FishResp.Rcheck/FishResp’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/FishResp.Rcheck/FishResp’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/FishResp.Rcheck/FishResp’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/FishResp.Rcheck/FishResp’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/FishResp.Rcheck/FishResp’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/FishResp.Rcheck/FishResp’, resetting
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Running ‘boot.R’
  Running ‘disttests.R’
  Running ‘grouping.R’
  Running ‘plots.R’
  Running ‘weights.R’
Running the tests in ‘tests/disttests.R’ failed.
Complete output:
  > library(flexclust)
  Loading required package: grid
  Loading required package: lattice
  Loading required package: modeltools
  Loading required package: stats4
  > 
  > ## create a random matrix
  > x <- matrix(rnorm(1000), ncol=4)
  > rownames(x) <- 1:nrow(x)
  > 
  > ## test canberra at margin
  > x[1:10,1] <- 0
  > x[1:20,2] <- 0
  > x[1:30,3] <- 0
  > 
  > stopifnot(all.equal(dist2(x,x,"eucl"), as.matrix(dist(x, "eucl"))))
  > stopifnot(all.equal(dist2(x,x,"man"), as.matrix(dist(x, "man"))))
  > stopifnot(all.equal(dist2(x,x,"max"), as.matrix(dist(x, "max"))))
  > stopifnot(all.equal(dist2(x,x,"bin"), as.matrix(dist(x, "bin"))))
  > stopifnot(all.equal(dist2(x,x,"can"), as.matrix(dist(x, "can"))))
  Error: dist2(x, x, "can") and as.matrix(dist(x, "can")) are not equal:
    Mean relative difference: 0.9290849
  Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    1.6Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   9.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
Running ‘testthat.R’ [52s/61s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fuzzyjoin)
  > 
  > test_check("fuzzyjoin")
  ── 1. Failure: Can do inner joins on intervals with findOverlaps arguments (@tes
  j_maxgap$id1 not equal to c(1, 1, 2, 2, 3).
  Lengths differ: 6 is not 5
  
  ── 2. Failure: Can do inner joins on intervals with findOverlaps arguments (@tes
  j_maxgap$id2 not equal to c(1, 2, 1, 2, 3).
  Lengths differ: 6 is not 5
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 224 SKIPPED: 0 FAILED: 2
  1. Failure: Can do inner joins on intervals with findOverlaps arguments (@test_interval_join.R#50) 
  2. Failure: Can do inner joins on intervals with findOverlaps arguments (@test_interval_join.R#51) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  12.8Mb
installed size is 58.6Mb
  sub-directories of 1Mb or more:
    libs  58.2Mb
Found the following significant warnings:
  m4_prod2_ms.cpp:19:12: warning: ‘paraPro2::v’ will be initialized after [-Wreorder]
  m4_prod2_ms.cpp:18:16: warning:   ‘const size_t paraPro2::r’ [-Wreorder]
  m4_prod2_ms.cpp:24:3: warning:   when initialized here [-Wreorder]
  m4_prod2_ms.cpp:30:3: warning:   when initialized here [-Wreorder]
  m4_prod2_p.cpp:18:12: warning: ‘paraPro2_p::v’ will be initialized after [-Wreorder]
  m4_prod2_p.cpp:17:16: warning:   ‘const size_t paraPro2_p::r’ [-Wreorder]
  m4_prod2_p.cpp:23:3: warning:   when initialized here [-Wreorder]
  m4_prod2_p.cpp:30:3: warning:   when initialized here [-Wreorder]
  m4_prod_ms.cpp:19:18: warning: ‘paraPro_ms::v’ will be initialized after [-Wreorder]
  m4_prod_ms.cpp:18:16: warning:   ‘const size_t paraPro_ms::r’ [-Wreorder]
  m4_prod_ms.cpp:25:3: warning:   when initialized here [-Wreorder]
  m4_prod_p.cpp:18:18: warning: ‘paraPro_p::v’ will be initialized after [-Wreorder]
  m4_prod_p.cpp:17:16: warning:   ‘const size_t paraPro_p::r’ [-Wreorder]
  m4_prod_p.cpp:24:3: warning:   when initialized here [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-devel/gaston.Rcheck/00install.out’ for details.
installed size is 75.0Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     72.0Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  17.7Mb
Found the following significant warnings:
  Gdmlib.cpp:1665:9: warning: specified bound 256 equals the size of the destination [-Wstringop-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/gdm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  convert_util.cpp:299:20: warning: null destination pointer [-Wformat-overflow=]
  convert_util.cpp:307:20: warning: null destination pointer [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/GenABEL.Rcheck/00install.out’ for details.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   5.4Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   5.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   4.2Mb
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  13.2Mb
.ldots.set: no visible global function definition for ‘getS3method’
grf: no visible global function definition for ‘chull’
image.grf: no visible global function definition for ‘heat.colors’
image.krige.bayes: no visible global function definition for
  ‘heat.colors’
legend.krige: no visible global function definition for ‘heat.colors’
points.geodata: no visible global function definition for
  ‘terrain.colors’
points.geodata: no visible global function definition for ‘gray’
read.geodata: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  chull getS3method gray heat.colors read.table terrain.colors
Consider adding
  importFrom("grDevices", "chull", "gray", "heat.colors",
             "terrain.colors")
  importFrom("utils", "getS3method", "read.table")
to your NAMESPACE file.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Running ‘test-all.R’ [96s/113s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check('ggfortify')
  Loading required package: ggfortify
  Loading required package: ggplot2
  initial  value 7.505733 
  final  value 7.505688 
  converged
  Initial stress        : 0.01705
  stress after  10 iters: 0.00951, magic = 0.500
  stress after  20 iters: 0.00941, magic = 0.500
  initial  value 7.505733 
  final  value 7.505688 
  converged
  Initial stress        : 0.01705
  stress after  10 iters: 0.00951, magic = 0.500
  stress after  20 iters: 0.00941, magic = 0.500
  ── 1. Error: gglagplot (@test-tslib.R#103)  ────────────────────────────────────
  `x` must be a vector, not a ts object, do you want `stats::lag()`?
  1: gglagplot(AirPassengers) at testthat/test-tslib.R:103
  2: dplyr::bind_rows(lapply(seq(1:lags), .lag))
  3: flatten_bindable(dots_values(...))
  4: dots_values(...)
  5: map(dots, function(dot) eval_bare(dot$expr, dot$env))
  6: lapply(.x, .f, ...)
  7: FUN(X[[i]], ...)
  8: eval_bare(dot$expr, dot$env)
  9: lapply(seq(1:lags), .lag)
  10: FUN(X[[i]], ...)
  11: as.vector(lag(ts, k))
  12: lag(ts, k)
  13: bad_args("x", "must be a vector, not a ts object, do you want `stats::lag()`?")
  14: glubort(fmt_args(args), ..., .envir = .envir)
  15: .abort(text)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1442 SKIPPED: 9 FAILED: 1
  1. Error: gglagplot (@test-tslib.R#103) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   2.7Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 28.9Mb
  sub-directories of 1Mb or more:
    libs  28.7Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
installed size is 51.7Mb
  sub-directories of 1Mb or more:
    libs  51.0Mb
installed size is 45.3Mb
  sub-directories of 1Mb or more:
    libs  44.2Mb
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  14.8Mb
Found the following significant warnings:
  hmg.h:20:38: warning: ‘HMG::p’ will be initialized after [-Wreorder]
  hmg.h:20:9: warning:   ‘arma::vec HMG::tau_par’ [-Wreorder]
  hmg.cpp:10:1: warning:   when initialized here [-Wreorder]
  hmg.h:20:27: warning: ‘HMG::gamma_par’ will be initialized after [-Wreorder]
  hmg.h:17:12: warning:   ‘double HMG::alpha’ [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-devel/grove.Rcheck/00install.out’ for details.
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs  18.2Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
normalweight: no visible binding for global variable ‘NW_above’
normalweight: no visible binding for global variable ‘NW_below’
obese: no visible global function definition for ‘data’
obese: no visible binding for global variable ‘OB_above’
obese: no visible binding for global variable ‘OB_below’
overweight: no visible global function definition for ‘data’
overweight: no visible binding for global variable ‘OW_above’
overweight: no visible binding for global variable ‘OW_below’
Undefined global functions or variables:
  NW_above NW_below OB_above OB_below OW_above OW_below data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs  18.0Mb
Found the following significant warnings:
  readstat/sas/readstat_xport_write.c:339:13: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=]
  readstat/sas/readstat_xport_write.c:306:13: warning: ‘%-40s’ directive output may be truncated writing between 40 and 99 bytes into a region of size 49 [-Wformat-truncation=]
  readstat/sas/readstat_sas.c:304:14: warning: ‘%1ld’ directive output may be truncated writing between 1 and 16 bytes into a region of size 8 [-Wformat-truncation=]
  readstat/sas/readstat_sas7bdat_read.c:517:101: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size between 435 and 954 [-Wformat-truncation=]
  readstat/spss/readstat_sav_write.c:610:52: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 6 [-Wformat-truncation=]
  readstat/spss/readstat_sav_write.c:638:56: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 6 [-Wformat-truncation=]
  readstat/spss/readstat_sav_write.c:697:51: warning: ‘%05d’ directive output may be truncated writing between 5 and 11 bytes into a region of size between 1 and 10 [-Wformat-truncation=]
  readstat/spss/readstat_sav_write.c:716:51: warning: ‘%05d’ directive output may be truncated writing between 5 and 11 bytes into a region of size between 1 and 10 [-Wformat-truncation=]
  readstat/spss/readstat_spss.c:139:58: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=]
See ‘/data/gannet/ripley/R/packages/tests-devel/haven.Rcheck/00install.out’ for details.
Found the following significant warnings:
  lassoModels/IPenalizedSolver.h:221:28: warning: ‘HD::IPenalizedSolver::p_y_’ will be initialized after [-Wreorder]
  lassoModels/IPenalizedSolver.h:217:18: warning:   ‘STK::Real HD::IPenalizedSolver::threshold_’ [-Wreorder]
  lassoModels/IPenalizedSolver.h:112:7: warning:   when initialized here [-Wreorder]
  lassoModels/IPenalizedSolver.h:126:7: warning:   when initialized here [-Wreorder]
  lassoModels/LogisticFusedLassoSolver.h:154:21: warning: ‘HD::LogisticFusedLassoSolver::cginit_’ will be initialized after [-Wreorder]
  lassoModels/LogisticFusedLassoSolver.h:147:26: warning:   ‘HD::FusedLassoPenalty* HD::LogisticFusedLassoSolver::p_penalty_’ [-Wreorder]
  lassoModels/LogisticFusedLassoSolver.cpp:51:3: warning:   when initialized here [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-devel/HDPenReg.Rcheck/00install.out’ for details.
installed size is 28.4Mb
  sub-directories of 1Mb or more:
    libs  28.0Mb
print.tsum: warning in print.default(x$resid, digits = digits, na = "",
  print.gap = 2): partial argument match of 'na' to 'na.print'
print.tsum: no visible global function definition for ‘quantile’
print.tsum: no visible global function definition for ‘printCoefmat’
print.tsum: no visible global function definition for ‘symnum’
tlm: no visible global function definition for ‘formula’
tlm: no visible binding for global variable ‘na.fail’
tlm: no visible global function definition for ‘model.matrix’
tlm: no visible global function definition for ‘model.extract’
tlm: no visible binding for global variable ‘response’
tlm: no visible global function definition for ‘lm.fit’
tlm: no visible global function definition for ‘coef’
tlm: no visible global function definition for ‘resid’
tlm: no visible global function definition for ‘Gamma’
tlm: no visible binding for global variable ‘dofse’
tlm: no visible binding for global variable ‘logLik’
tscore: no visible global function definition for ‘model.extract’
tscore: no visible binding for global variable ‘response’
tscore : <anonymous>: no visible global function definition for
  ‘model.matrix’
tscore: no visible global function definition for ‘resid’
tscore: no visible global function definition for ‘pchisq’
tscore: no visible global function definition for ‘printCoefmat’
tsum: no visible global function definition for ‘pnorm’
tsum: no visible global function definition for ‘pt’
tsum: no visible global function definition for ‘residuals’
Undefined global functions or variables:
  Gamma coef dofse formula lm.fit logLik model.extract model.matrix
  na.fail pchisq pnorm printCoefmat pt quantile resid residuals
  response symnum
Consider adding
  importFrom("stats", "Gamma", "coef", "formula", "lm.fit", "logLik",
             "model.extract", "model.matrix", "na.fail", "pchisq",
             "pnorm", "printCoefmat", "pt", "quantile", "resid",
             "residuals", "symnum")
to your NAMESPACE file.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    highlight   1.1Mb
    libs        6.8Mb
PlotOptPower: no visible global function definition for ‘bmp’
PlotOptPower: no visible global function definition for
  ‘filled.contour’
PlotOptPower: no visible global function definition for ‘title’
PlotOptPower: no visible global function definition for ‘grey.colors’
PlotOptPower: no visible global function definition for ‘axis’
PlotOptPower: no visible global function definition for ‘polygon’
PlotOptPower: no visible global function definition for ‘legend’
PlotOptPower: no visible global function definition for ‘mtext’
PlotOptPower: no visible global function definition for ‘dev.off’
PlotOptPower: no visible global function definition for
  ‘terrain.colors’
ShowOptDesign: no visible global function definition for ‘head’
diffVariantError: no visible global function definition for ‘pbinom’
predictPoolNCP: no visible global function definition for ‘data’
probDetEqual3: no visible global function definition for ‘dbinom’
probDetEqual3: no visible global function definition for ‘pbinom’
Undefined global functions or variables:
  axis bmp data dbinom dev.off filled.contour grey.colors head legend
  mtext pbinom polygon terrain.colors title
Consider adding
  importFrom("grDevices", "bmp", "dev.off", "grey.colors",
             "terrain.colors")
  importFrom("graphics", "axis", "filled.contour", "legend", "mtext",
             "polygon", "title")
  importFrom("stats", "dbinom", "pbinom")
  importFrom("utils", "data", "head")
to your NAMESPACE file.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   4.3Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpSa7gvA’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpSa7gvA’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpSa7gvA’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpSa7gvA’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpSa7gvA’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpSa7gvA’, resetting
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    dict   1.3Mb
    libs   5.4Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   8.4Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   1.3Mb
    doc    2.2Mb
    libs   1.1Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      2.4Mb
installed size is 27.2Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  25.4Mb
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs  17.4Mb
installed size is 43.1Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       4.9Mb
    extdata   1.0Mb
    include   2.8Mb
    libs     32.4Mb
Interpol: no visible global function definition for ‘splinefun’
Undefined global functions or variables:
  splinefun
Consider adding
  importFrom("stats", "splinefun")
to your NAMESPACE file.
Found the following significant warnings:
  s_hull_pro.h:75:9: warning: ‘Shx::ro’ will be initialized after [-Wreorder]
  s_hull_pro.h:74:14: warning:   ‘float Shx::tr’ [-Wreorder]
  s_hull_pro.h:77:3: warning:   when initialized here [-Wreorder]
  s_hull_pro.h:74:17: warning: ‘Shx::tc’ will be initialized after [-Wreorder]
  s_hull_pro.h:73:7: warning:   ‘int Shx::id’ [-Wreorder]
  s_hull_pro.h:78:3: warning:   when initialized here [-Wreorder]
  s_hull_pro.h:112:11: warning: ‘Dupex::c’ will be initialized after [-Wreorder]
  s_hull_pro.h:111:7: warning:   ‘int Dupex::id’ [-Wreorder]
  s_hull_pro.h:115:3: warning:   when initialized here [-Wreorder]
  s_hull_pro.h:116:3: warning:   when initialized here [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-devel/interp.Rcheck/00install.out’ for details.
installed size is 27.1Mb
  sub-directories of 1Mb or more:
    libs  26.9Mb
Found the following significant warnings:
  as_output.c:323:24: warning: ‘snprintf’ output truncated before the last format character [-Wformat-truncation=]
See ‘/data/gannet/ripley/R/packages/tests-devel/iotools.Rcheck/00install.out’ for details.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.9Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   8.5Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   4.9Mb
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  21.4Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    include   1.5Mb
    libs      4.2Mb
    zmq       2.4Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/KATforDCEMRI.Rcheck/KATforDCEMRI_benchmark_test’, resetting
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
comp.npci: no visible global function definition for ‘qnorm’
epband.fun: no visible global function definition for ‘data’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.90’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.95’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.99’
hall.wellner.fun: no visible global function definition for ‘data’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.90’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.95’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.99’
lrt.confints: no visible global function definition for ‘qchisq’
rothman.fun: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  critical.value.hall.90 critical.value.hall.95 critical.value.hall.99
  critical.value.nair.90 critical.value.nair.95 critical.value.nair.99
  data qchisq qnorm
Consider adding
  importFrom("stats", "qchisq", "qnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   3.8Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpunbF0A’, resetting
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    libs          15.0Mb
    testdata       1.8Mb
    vignettedata   2.0Mb
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs     24.0Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   7.9Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 27.1Mb
  sub-directories of 1Mb or more:
    doc        1.5Mb
    libs      22.0Mb
    testdata   1.5Mb
Found the following significant warnings:
  Warning: ‘nsimp’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-devel/localdepth.Rcheck/00install.out’ for details.
Found the following significant warnings:
  cvrout.c:286:32: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/LogicOpt.Rcheck/00install.out’ for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      1.3Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/LSDinterface.Rcheck/LSDinterface/extdata’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/LSDinterface.Rcheck/LSDinterface/extdata’, resetting
installed size is 44.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  42.8Mb
Running ‘testthat.R’ [30s/37s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > if (packageVersion("testthat") >= "0.7.1.99") {
  +   library(testthat)  
  +   test_check("lubridate")
  + }
  Loading required package: lubridate
  
  Attaching package: 'lubridate'
  
  The following object is masked from 'package:base':
  
      date
  
  ── 1. Failure: interval handles POSIXlt inputs (@test-intervals.R#88)  ─────────
  unclass(interval(t1, t2)) not equal to unclass(...).
  Attributes: < Component "tzone": 1 string mismatch >
  
  ── 2. Failure: interval handles POSIXlt inputs (@test-intervals.R#95)  ─────────
  unclass(interval(t1, t2)) not equal to unclass(...).
  Attributes: < Component "tzone": 1 string mismatch >
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2456 SKIPPED: 36 FAILED: 2
  1. Failure: interval handles POSIXlt inputs (@test-intervals.R#88) 
  2. Failure: interval handles POSIXlt inputs (@test-intervals.R#95) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    libs  25.7Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs   6.0Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/markmyassignment.Rcheck/00install.out’ for details.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   8.6Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   6.4Mb
plot.mathgraph: no visible global function definition for ‘plot’
plot.mathgraph: no visible global function definition for ‘box’
plot.mathgraph: no visible global function definition for ‘segments’
plot.mathgraph: no visible global function definition for ‘arrows’
plot.mathgraph: no visible global function definition for ‘text’
Undefined global functions or variables:
  arrows box plot segments text
Consider adding
  importFrom("graphics", "arrows", "box", "plot", "segments", "text")
to your NAMESPACE file.
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  17.0Mb
installed size is 26.6Mb
  sub-directories of 1Mb or more:
    libs  25.8Mb
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   3.9Mb
    libs      1.3Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/measuRing.Rcheck/measuRing’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/measuRing.Rcheck/measuRing’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/measuRing.Rcheck/measuRing’, resetting
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   9.2Mb
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.5Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpHrUpXr’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpHrUpXr’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpHrUpXr’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpHrUpXr’, resetting
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/MetaSubtract.Rcheck/MetaSubtract/extdata’, resetting
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  16.6Mb
    misc   1.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   6.8Mb
Found the following significant warnings:
  ../inst/projects/MixAll/ILauncher.h:103:27: warning: ‘STK::ILauncher::v_models_’ will be initialized after [-Wreorder]
  ../inst/projects/MixAll/ILauncher.h:99:18: warning:   ‘STK::RDataHandler STK::ILauncher::handler_’ [-Wreorder]
  ILauncher.cpp:47:1: warning:   when initialized here [-Wreorder]
  ../inst/projects/MixAll/ILauncher.h:99:18: warning: ‘STK::ILauncher::handler_’ will be initialized after [-Wreorder]
  ../inst/projects/MixAll/ILauncher.h:88:46: warning:   ‘STK::DiagGaussianMixtureManager<STK::RDataHandler> STK::ILauncher::diagGaussianManager_’ [-Wreorder]
  ILauncher.cpp:63:1: warning:   when initialized here [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-devel/MixAll.Rcheck/00install.out’ for details.
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    libs  20.9Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Found the following significant warnings:
  nelder_mead_min.c:180:21: warning: ‘%5d’ directive writing between 5 and 10 bytes into a region of size 6 [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/mlegp.Rcheck/00install.out’ for details.
installed size is 42.3Mb
  sub-directories of 1Mb or more:
    chunks   3.4Mb
    libs    38.8Mb
Running examples in ‘mlmm-Ex.R’ failed
The error most likely occurred in:

> ### Name: mlmc
> ### Title: mlmc for missing and censored response in multilevel model.
> ### Aliases: mlmc
> 
> ### ** Examples
> 
> ## Don't show: 
> testfun=function()
+ {set.seed(100)
+  var2=abs(rnorm(50,0,1))
+  var1=(1/0.85)*var2;
+  geneid=rep(c(1:10),5);sid=c(rep(c(1:25),2),rep(c(26:50),2));
+  censor=rep(0,50)
+  pidname="geneid";sidname="sid";
+  miss_logit=var2*(-0.9);
+  miss=rbinom(50,1,exp(miss_logit)/(exp(miss_logit)+1));
+  censor=rep(0,50)
+  for (i in 1:50) {if (var1[i]<0.05) censor[i]=1}
+  for ( i in 1:50) {if ((miss[i]==1) & (censor[i]==1)) miss[i]=0};
+  for ( i in 1:50) {if (miss[i]==1) var1[i]=NA;
+  if (censor[i]==1) var1[i]=0.05}
+  pdata=data.frame(var1,var2,miss,censor,geneid,sid)
+  pathdir=getwd()
+  if (R.Version()$arch=="i386") fp=system.file("chunks","mlmc_i32.rds",package="mlmm")
+  if (R.Version()$arch=="x86_64") fp=system.file("chunks","mlmc_i64.rds",package="mlmm")
+  mcfit=readRDS(fp)
+  model1=mlmc(formula_completed=var1~var2,formula_missing=miss~var2,
+              formula_censor=censor~1,formula_subject=~var2,pdata=pdata,response_censorlim=0.05,
+              respond_dep_missing=TRUE,pidname="geneid",sidname="sid",pathname=pathdir,
+              iterno=10,chains=2,savefile=FALSE,usefit=TRUE,stanfit=mcfit)
+  }
> system.time(testfun())
Error in prep_call_sampler(object) : 
  the compiled object from C++ code for this model is invalid, possible reasons:
  - compiled with save_dso=FALSE;
  - compiled on a different platform;
  - does not exist (created from reading csv files).
Calls: system.time ... sampling -> .local -> <Anonymous> -> prep_call_sampler
Timing stopped at: 0.239 0.055 0.454
Execution halted
listGenoToTable: no visible binding for global variable ‘dummy’
Undefined global functions or variables:
  dummy
Running ‘testthat.R’ [22s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(modmarg)
  > 
  > test_check("modmarg")
  ── 1. Error: Collinear cols treated right (@test_glm.R#288)  ───────────────────
  non-conformable arguments
  1: marg(mod = ols1, var_interest = "am", type = "effects", at = list(mpg = seq(15, 30, 
         5))) at testthat/test_glm.R:288
  2: marg.glm(mod = ols1, var_interest = "am", type = "effects", at = list(mpg = seq(15, 
         30, 5)))
  3: .marg(mod = mod, var_interest = var_interest, data = data, weights = weights, ...)
  4: lapply(data, function(x) {
         df_levels <- at_transforms(model_df = x, at_list = gen_at_list(df = x, var_interest = var_interest, 
             at_var_interest = at_var_interest))
         pred_se(df_levels = df_levels, model = mod, type = type, base_rn = base_rn, vcov_mat = vcov_mat, 
             weights = weights, link_func = NULL, deriv_func = NULL)
     })
  5: FUN(X[[i]], ...)
  6: pred_se(df_levels = df_levels, model = mod, type = type, base_rn = base_rn, vcov_mat = vcov_mat, 
         weights = weights, link_func = NULL, deriv_func = NULL)
  7: pred_se.glm(df_levels = df_levels, model = mod, type = type, base_rn = base_rn, vcov_mat = vcov_mat, 
         weights = weights, link_func = NULL, deriv_func = NULL)
  8: .pred_se(model = model, deriv_func = model$family$mu.eta, link_func = model$family$linkinv, 
         ...)
  9: calc_pred_se(vcov_mat, jacobs)
  10: diag(jac %*% vcov_model %*% t(jac))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 303 SKIPPED: 0 FAILED: 1
  1. Error: Collinear cols treated right (@test_glm.R#288) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    1.6Mb
    libs   3.4Mb
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    libs  18.3Mb
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  10.7Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   4.4Mb
Found the following significant warnings:
  IPCATree.h:692:23: warning: ‘IPCATree<double>::stop’ will be initialized after [-Wreorder]
  IPCATree.h:689:16: warning:   ‘double IPCATree<double>::epsilon’ [-Wreorder]
  IPCATree.h:781:5: warning:   when initialized here [-Wreorder]
  IPCATree.h:696:19: warning: ‘IPCATree<double>::splitStrategy’ will be initialized after [-Wreorder]
  IPCATree.h:690:18: warning:   ‘unsigned int IPCATree<double>::minPoints’ [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-devel/mph.Rcheck/00install.out’ for details.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Found the following significant warnings:
  recursion.h:22:7: warning: ‘class_tree::K’ will be initialized after [-Wreorder]
  recursion.h:21:13: warning:   ‘arma::vec class_tree::nu_vec’ [-Wreorder]
  recursion.cpp:9:1: warning:   when initialized here [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-devel/MRS.Rcheck/00install.out’ for details.
Found the following significant warnings:
  DE.c:128:36: warning: ‘snprintf’ output truncated before the last format character [-Wformat-truncation=]
  DE.c:301:40: warning: ‘snprintf’ output truncated before the last format character [-Wformat-truncation=]
  DE.c:322:34: warning: ‘snprintf’ output truncated before the last format character [-Wformat-truncation=]
See ‘/data/gannet/ripley/R/packages/tests-devel/MSCMT.Rcheck/00install.out’ for details.
installed size is 41.7Mb
  sub-directories of 1Mb or more:
    libs  41.4Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is 67.3Mb
  sub-directories of 1Mb or more:
    libs  67.1Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.7Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpdvgNP3’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpdvgNP3’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpdvgNP3’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpdvgNP3’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpdvgNP3’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpdvgNP3’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpdvgNP3’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpdvgNP3’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpdvgNP3’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpdvgNP3’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpdvgNP3’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpdvgNP3’, resetting
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   7.4Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   7.9Mb
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    R              3.4Mb
    classic-bugs   1.6Mb
    include        5.8Mb
    tests          1.2Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.1Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs  15.3Mb
File ‘nws/R/zzz.R’:
  .onLoad calls:
    require(methods)

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

blendOptions: warning in assign(names[i], new[[i]], env = options):
  partial argument match of 'env' to 'envir'
docall: warning in get(as.character(fun), env = .GlobalEnv, mode =
  "function"): partial argument match of 'env' to 'envir'
logMsg: no visible global function definition for ‘flush.console’
nwsPkgInfo: no visible global function definition for
  ‘packageDescription’
initialize,nwsServer: no visible global function definition for
  ‘make.socket’
initialize,nwsServer: no visible global function definition for
  ‘close.socket’
Undefined global functions or variables:
  close.socket flush.console make.socket packageDescription
Consider adding
  importFrom("utils", "close.socket", "flush.console", "make.socket",
             "packageDescription")
to your NAMESPACE file.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    help   2.2Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/ODMconverter.Rcheck/ODMconverter/extdata’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/ODMconverter.Rcheck/ODMconverter/extdata’, resetting
installed size is 87.6Mb
  sub-directories of 1Mb or more:
    libs  87.2Mb
mapvar: no visible global function definition for ‘data’
mapvar: no visible binding for global variable ‘state.fips’
mapvar: no visible global function definition for ‘rgb’
mapvar: no visible global function definition for ‘rect’
mapvar: no visible global function definition for ‘text’
rowScrape: no visible global function definition for ‘tail’
rowScrape: no visible global function definition for ‘head’
scrapeTable: no visible binding for global variable ‘tail’
Undefined global functions or variables:
  data head rect rgb state.fips tail text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "rect", "text")
  importFrom("utils", "data", "head", "tail")
to your NAMESPACE file.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/opefimor.Rcheck/opefimor/book’, resetting
installed size is 153.5Mb
  sub-directories of 1Mb or more:
    R         2.3Mb
    libs    143.7Mb
    models    4.7Mb
Compilation used the following non-portable flag(s):
  ‘-Wno-deprecated-declarations’ ‘-Wno-ignored-attributes’
  ‘-Wno-int-in-bool-context’ ‘-Wno-misleading-indentation’
  ‘-Wno-pragmas’ ‘-Wno-unknown-pragmas’ ‘-Wno-unused-function’
  ‘-Wno-unused-local-typedefs’ ‘-Wno-unused-parameter’ ‘-Wvla’
including flag(s) suppressing warnings
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      5.8Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   5.0Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   3.4Mb
Found the following significant warnings:
  pads_circle_pack.cpp:233:6: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=]
See ‘/data/gannet/ripley/R/packages/tests-devel/packcircles.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Found the following significant warnings:
  Warning: CHARACTER expression at (1) is being truncated (6/1) [-Wcharacter-truncation]
  Warning: CHARACTER expression will be truncated in assignment (1/9) at (1) [-Wcharacter-truncation]
  Warning: CHARACTER expression will be truncated in assignment (1/19) at (1) [-Wcharacter-truncation]
  Warning: CHARACTER expression will be truncated in assignment (1/16) at (1) [-Wcharacter-truncation]
  Warning: CHARACTER expression will be truncated in assignment (1/12) at (1) [-Wcharacter-truncation]
See ‘/data/gannet/ripley/R/packages/tests-devel/pbdSLAP.Rcheck/00install.out’ for details.
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    lib  12.5Mb
Found the following significant warnings:
  R_zmq_utility.c:34:24: warning: ‘sprintf’ writing a terminating nul past the end of the destination [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/pbdZMQ.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.3Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/PBSmodelling.Rcheck/PBSmodelling/examples’, resetting
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.6Mb
    libs      1.4Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   2.1Mb
    libs   6.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Found the following significant warnings:
  sparse.c:926:16: warning: self-comparison always evaluates to false [-Wtautological-compare]
See ‘/data/gannet/ripley/R/packages/tests-devel/PET.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/PGICA.Rcheck/Sim’, resetting
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   1.7Mb
installed size is 35.5Mb
  sub-directories of 1Mb or more:
    libs  34.8Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 27.7Mb
  sub-directories of 1Mb or more:
    libs  27.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   2.9Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   1.6Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   7.0Mb
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   6.4Mb
    libs      6.0Mb
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    libs  21.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   2.8Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   3.3Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.4Mb
Found the following significant warnings:
  gaussianProcesses/GaussianProcess.h:66:7: warning: ‘GaussianProcess::Observations’ will be initialized after [-Wreorder]
  gaussianProcesses/GaussianProcess.h:64:22: warning:   ‘CovarianceFunction& GaussianProcess::covFunc’ [-Wreorder]
  gaussianProcesses/GaussianProcess.cpp:3:1: warning:   when initialized here [-Wreorder]
  gaussianProcesses/GaussianProcess.h:64:22: warning: ‘GaussianProcess::covFunc’ will be initialized after [-Wreorder]
  gaussianProcesses/GaussianProcess.cpp:6:12: warning:   base ‘ForwardModel’ [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-devel/psgp.Rcheck/00install.out’ for details.
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    libs  24.3Mb
installed size is 66.8Mb
  sub-directories of 1Mb or more:
    libs   56.6Mb
    local   9.4Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    contrib   3.8Mb
    doc       2.9Mb
    libs      1.2Mb
Compilation used the following non-portable flag(s):
  ‘-W’
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   6.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    Output   2.2Mb
    bin      2.9Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/r2lh.Rcheck/tmp’, resetting
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   4.7Mb
.disableThreads: no visible global function definition for
  ‘stopCluster’
.enableThreads: no visible global function definition for ‘detectCores’
.enableThreads: no visible global function definition for
  ‘makePSOCKcluster’
.enableThreads: no visible global function definition for
  ‘clusterExport’
.enableThreads: no visible global function definition for ‘clusterCall’
.forwardSelection: no visible binding for global variable ‘var’
.forwardSelection: no visible global function definition for ‘glm’
.forwardSelection: no visible global function definition for ‘formula’
.forwardSelection: no visible global function definition for ‘binomial’
.forwardSelection: no visible global function definition for ‘lm’
.forwardSelection: no visible global function definition for ‘predict’
.predict.internal: no visible global function definition for ‘predict’
randomGLM: no visible binding for global variable ‘cor’
randomGLM: no visible binding for global variable ‘sd’
randomGLM: no visible global function definition for ‘var’
thinRandomGLM: no visible global function definition for ‘glm’
thinRandomGLM: no visible global function definition for ‘binomial’
thinRandomGLM: no visible global function definition for ‘lm’
Undefined global functions or variables:
  binomial clusterCall clusterExport cor detectCores formula glm lm
  makePSOCKcluster predict sd stopCluster var
Consider adding
  importFrom("stats", "binomial", "cor", "formula", "glm", "lm",
             "predict", "sd", "var")
to your NAMESPACE file.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs   3.4Mb
installed size is 30.2Mb
  sub-directories of 1Mb or more:
    libs  28.9Mb
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    blp    7.1Mb
    libs   9.1Mb
Found the following significant warnings:
  intersection.cc:384:1: warning: ‘%g’ directive writing 12 bytes into a region of size between 0 and 41 [-Wformat-overflow=]
  intersection.cc:384:1: warning: ‘%g’ directive writing 12 bytes into a region of size between 0 and 42 [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/RCALI.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/RchivalTag.Rcheck/RchivalTag/example_files’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/RchivalTag.Rcheck/RchivalTag/example_files’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/RchivalTag.Rcheck/RchivalTag/example_files’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/RchivalTag.Rcheck/RchivalTag/example_files’, resetting
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    include   5.1Mb
    libs      1.9Mb
Error in re-building vignettes:
  ...
Latexmk: This is Latexmk, John Collins, 12 Dec. 2017, version: 4.54c.
Error in rmultinom(n, size, prob) : NA in probability vector
Error in rmultinomC(n, size, prob) : NAs not allowed in probability
Error in rmultinom(n, size, prob) : no positive probabilities
Error in rmultinomC(n, size, prob) : Not enough positive probabilities
Error : Only CSC, COO and CSR matrices from SciPy are supported.
dimnames(.) <- NULL:  translated to 
dimnames(.) <- list(NULL,NULL)  <==>  unname(.)
dimnames(.) <- NULL:  translated to 
dimnames(.) <- list(NULL,NULL)  <==>  unname(.)
Error in asSpMat(lm) : lgCMatrix is not supported.
Error in asSpMat(L) : lgTMatrix is not supported.
dimnames(.) <- NULL:  translated to 
dimnames(.) <- list(NULL,NULL)  <==>  unname(.)
Error in asSpMat(nm) : ngCMatrix is not supported.
Error in asSpMat(ngt) : ngTMatrix is not supported.
Error in asSpMat(nM) : ntTMatrix is not supported.
Error in asSpMat(nsc) : nsCMatrix is not supported.
Error in asSpMat(ldi) : ldiMatrix is not supported.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RcppArmadillo-unitTests.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

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

! Emergency stop.
<read *> 
         
l.7 \setmargrb
              {0.75in}{0.75in}{0.75in}{0.75in}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is 28.0Mb
  sub-directories of 1Mb or more:
    include  25.5Mb
    libs      2.3Mb
installed size is 32.3Mb
  sub-directories of 1Mb or more:
    include   7.8Mb
    libs     23.8Mb
installed size is 81.2Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib      62.5Mb
    libs     16.6Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    include   7.0Mb
    libs      6.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib       3.1Mb
Compilation used the following non-portable flag(s):
  ‘-Wno-non-virtual-dtor’ ‘-Wno-parentheses’
including flag(s) suppressing warnings
installed size is 57.4Mb
  sub-directories of 1Mb or more:
    include   8.9Mb
    libs     48.3Mb
installed size is 170.6Mb
  sub-directories of 1Mb or more:
    include    4.6Mb
    lib      129.6Mb
    libs      36.2Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Running ‘testthat.R’ [96s/136s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rdomains)
  > 
  > test_check("rdomains")
  ── 1. Error: dmoz cat (@test-dmoz-cat.R#5)  ────────────────────────────────────
  HTTP error 404.
  1: get_dmoz_data() at testthat/test-dmoz-cat.R:5
  2: curl_download("https://github.com/soodoku/domain_classifier/blob/master/rdomains/data-raw/dmoz/dmoz_domain_category.zip?raw=true", 
         tmp)
  
  Shallalist Data saved to the following destination: ./ 
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2 SKIPPED: 0 FAILED: 1
  1. Error: dmoz cat (@test-dmoz-cat.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  11.0Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
xy: warning in assign(xname, X, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
xy: warning in assign(yname, y, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
bestmods: no visible global function definition for ‘abline’
bestmods: no visible global function definition for ‘axis’
bestmods: no visible global function definition for ‘lines’
cic: no visible global function definition for ‘lsfit’
cic: no visible global function definition for ‘var’
cvic: no visible global function definition for ‘lsfit’
cvic: no visible global function definition for ‘lm’
eic: no visible global function definition for ‘lsfit’
eic: no visible global function definition for ‘lm’
ic.min: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘var’
xy: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline axis lines lm lsfit rnorm var
Consider adding
  importFrom("graphics", "abline", "axis", "lines")
  importFrom("stats", "lm", "lsfit", "rnorm", "var")
to your NAMESPACE file.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   4.6Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   5.9Mb
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  15.3Mb
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    libs  22.1Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is 84.7Mb
  sub-directories of 1Mb or more:
    libs  83.9Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      2.4Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc     3.1Mb
    fonts   1.5Mb
    libs    2.6Mb
installed size is 25.0Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    help  10.5Mb
    libs  10.8Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-devel/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’,
    ‘R_GlobalContext’
File ‘rJava/libs/rJava.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  readPEDfile.c:321:74: warning: ‘%s’ directive output may be truncated writing up to 63 bytes into a region of size between 46 and 109 [-Wformat-truncation=]
See ‘/data/gannet/ripley/R/packages/tests-devel/rJPSGCS.Rcheck/00install.out’ for details.
Found the following significant warnings:
  LASlib/laswriter_las.cpp:126:6: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  LASzip/laszip.cpp:275:6: warning: ‘ bytes’ directive writing 6 bytes into a region of size between 5 and 18 [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/rlas.Rcheck/00install.out’ for details.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Found the following significant warnings:
  newmat5.cpp:525:69: warning: throw will always call terminate() [-Wterminate]
See ‘/data/gannet/ripley/R/packages/tests-devel/Rmixmod.Rcheck/00install.out’ for details.
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  14.8Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
installed size is 21.5Mb
  sub-directories of 1Mb or more:
    libs  21.2Mb
installed size is 97.7Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     95.6Mb
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    libs  19.0Mb
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    libs  20.9Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   6.4Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Found the following significant warnings:
  rph_tfbs.c:811:26: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 9 [-Wformat-truncation=]
See ‘/data/gannet/ripley/R/packages/tests-devel/rphast.Rcheck/00install.out’ for details.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/RPPanalyzer.Rcheck/RPPanalyzer/extdata’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/RPPanalyzer.Rcheck/RPPanalyzer/extdata’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/RPPanalyzer.Rcheck/RPPanalyzer/extdata’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/RPPanalyzer.Rcheck/RPPanalyzer/extdata’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/RPPanalyzer.Rcheck/RPPanalyzer/extdata’, resetting
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rprojroot)
  > 
  > test_check("rprojroot")
  Error in readRDS(pfile) : 
    cannot read unreleased workspace version 3 written by experimental R 3.5.0
  Calls: cat ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
  Execution halted
  ── 1. Failure: thisfile works with Rscript (@test-thisfile.R#12)  ──────────────
  "scripts/thisfile-cat.R" not equal to res[[length(res)]].
  1/1 mismatches
  x[1]: "scripts/thisfile-cat.R"
  y[1]: "WARNING: ignoring environment value of R_HOME"
  
  Error in readRDS(pfile) : 
    cannot read unreleased workspace version 3 written by experimental R 3.5.0
  Calls: cat ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
  Execution halted
  ── 2. Failure: thisfile works with R (@test-thisfile.R#19)  ────────────────────
  "scripts/thisfile-cat.R" not equal to res[[length(res)]].
  1/1 mismatches
  x[1]: "scripts/thisfile-cat.R"
  y[1]: "WARNING: ignoring environment value of R_HOME"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 76 SKIPPED: 4 FAILED: 2
  1. Failure: thisfile works with Rscript (@test-thisfile.R#12) 
  2. Failure: thisfile works with R (@test-thisfile.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  11.1Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpbkjGkh’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpbkjGkh’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpbkjGkh’, resetting
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-devel/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’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    libs  15.1Mb
installed size is 50.7Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  49.2Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   2.7Mb
installed size is 150.7Mb
  sub-directories of 1Mb or more:
    doc     2.4Mb
    libs  146.7Mb
installed size is 251.8Mb
  sub-directories of 1Mb or more:
    libs  249.4Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
Math.Sym: no visible binding for global variable ‘transtab’
jythonStart: no visible global function definition for ‘.jinit’
jythonStart: no visible global function definition for ‘.jnew’
jythonStart: no visible binding for global variable ‘.Jython’
sympy: no visible binding for global variable ‘.Jython’
sympy: no visible global function definition for ‘.jstrVal’
sympyStart: no visible binding for global variable ‘.Jython’
Undefined global functions or variables:
  .Jython .jinit .jnew .jstrVal transtab
Found the following significant warnings:
  rph_tfbs.c:811:26: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 9 [-Wformat-truncation=]
See ‘/data/gannet/ripley/R/packages/tests-devel/rtfbs.Rcheck/00install.out’ for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       2.7Mb
    projects   2.3Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is 45.0Mb
  sub-directories of 1Mb or more:
    libs  44.3Mb
installed size is 49.4Mb
  sub-directories of 1Mb or more:
    libs  48.6Mb
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
    test  19.6Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs    8.0Mb
    yacas   1.5Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Found the following significant warnings:
  BGPscan.h:63:10: warning: ‘BGPscan::m_beta_alt’ will be initialized after [-Wreorder]
  BGPscan.h:49:15: warning:   ‘arma::uword BGPscan::m_inc_idx’ [-Wreorder]
  BGPscan.h:96:8: warning:   when initialized here [-Wreorder]
  USTscan.h:28:15: warning: ‘USTscanbase<arma::Mat<unsigned int>, unsigned int>::m_counts’ will be initialized after [-Wreorder]
  USTscan.h:23:15: warning:   ‘arma::uword USTscanbase<arma::Mat<unsigned int>, unsigned int>::m_num_locs’ [-Wreorder]
  USTscan.h:62:8: warning:   when initialized here [-Wreorder]
  USTscan.h:30:15: warning: ‘USTscanbase<arma::Mat<unsigned int>, unsigned int>::m_zone_lengths’ will be initialized after [-Wreorder]
  USTscan.h:26:15: warning:   ‘bool USTscanbase<arma::Mat<unsigned int>, unsigned int>::m_store_everything’ [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-devel/scanstatistics.Rcheck/00install.out’ for details.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
prime.factor: no visible global function definition for ‘data’
prime.factor: no visible binding for global variable ‘primlist’
Undefined global functions or variables:
  data primlist
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   2.1Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is 23.0Mb
  sub-directories of 1Mb or more:
    doc    6.0Mb
    libs  16.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Found the following significant warnings:
  Warning: namespace ‘Biobase’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/Seurat.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    doc     10.7Mb
    libs     5.8Mb
    sqlite   1.5Mb
Found the following significant warnings:
  data/data_set.h:79:25: warning: ‘data_set::xpMat_’ will be initialized after [-Wreorder]
  data/data_set.h:64:7: warning:   ‘arma::mat data_set::Y’ [-Wreorder]
  data/data_set.h:23:3: warning:   when initialized here [-Wreorder]
  ./learn-rate/onedim_learn_rate.h:30:10: warning: ‘onedim_learn_rate::scale_’ will be initialized after [-Wreorder]
  ./learn-rate/onedim_learn_rate.h:27:10: warning:   ‘double onedim_learn_rate::gamma_’ [-Wreorder]
  ./learn-rate/onedim_learn_rate.h:18:3: warning:   when initialized here [-Wreorder]
  ./learn-rate/ddim_learn_rate.h:51:10: warning: ‘ddim_learn_rate::eta_’ will be initialized after [-Wreorder]
  ./learn-rate/ddim_learn_rate.h:48:10: warning:   ‘double ddim_learn_rate::a_’ [-Wreorder]
  ./learn-rate/ddim_learn_rate.h:24:3: warning:   when initialized here [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-devel/sgd.Rcheck/00install.out’ for details.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  11.1Mb
Found the following significant warnings:
  expression.h:80:10: warning: ‘ev3::Operand::exponent’ will be initialized after [-Wreorder]
  expression.h:58:7: warning:   ‘int ev3::Operand::dependency’ [-Wreorder]
  expression.cpp:271:1: warning:   when initialized here [-Wreorder]
  expression.cpp:276:1: warning:   when initialized here [-Wreorder]
  expression.cpp:281:1: warning:   when initialized here [-Wreorder]
  expression.cpp:286:1: warning:   when initialized here [-Wreorder]
  expression.h:83:11: warning: ‘ev3::Operand::depexponent’ will be initialized after [-Wreorder]
  expression.cpp:317:1: warning:   when initialized here [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-devel/simplr.Rcheck/00install.out’ for details.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.4Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Found the following significant warnings:
  NelderMead.c:140:24: warning: ‘%5d’ directive writing between 5 and 10 bytes into a region of size 6 [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/sme.Rcheck/00install.out’ for details.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   5.9Mb
installed size is 34.9Mb
  sub-directories of 1Mb or more:
    libs  33.8Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    R      4.9Mb
    doc    4.7Mb
    help   4.9Mb
    libs   2.2Mb
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  24.2Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   9.1Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs  13.4Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/Rtmpe5J0Ys’, resetting
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    include   9.1Mb
    lib       1.7Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpersMq8’, resetting
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.0Mb
Running ‘testthat.R’ [8s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(subprocess)
  > 
  > # See for more details:
  > # https://github.com/hadley/testthat/issues/144
  > # https://github.com/hadley/testthat/issues/86
  > # https://github.com/luckyrandom/cmaker/commit/b85813ac2b7aef69932eca8fbb4fa0ec225e0af0
  > #
  > # When R CMD check runs tests, it sets R_TESTS. When the tests
  > # themeselves run R CMD xxxx, as is the case with the tests in
  > # devtools, having R_TESTS set causes errors because it confuses
  > # the R subprocesses. Unsetting it here avoids those problems.
  > #
  > # We need this because we spawn child R processes and they get very
  > # confused if this variable (R_TESTS) is present in their environment.
  > Sys.setenv("R_TESTS" = "")
  > 
  > test_check("subprocess")
  ── 1. Error: child process is terminated in Linux (@test-termination.R#85)  ────
  is_process_handle(handle) is not TRUE
  1: expect_true(wait_until_appears(child_id)) at testthat/test-termination.R:85
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: wait_until_appears(child_id)
  5: process_wait(handle, TIMEOUT_IMMEDIATE) at /data/gannet/ripley/R/packages/tests-devel/subprocess.Rcheck/tests/testthat/helper-processes.R:58
  6: stopifnot(is_process_handle(handle))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 71 SKIPPED: 2 FAILED: 1
  1. Error: child process is terminated in Linux (@test-termination.R#85) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  RMcrt.h:80:13: warning: ‘extendedleaps::rmdata::gdt’ will be initialized after [-Wreorder]
  RMcrt.h:76:10: warning:   ‘bool extendedleaps::rmdata::unreliable’ [-Wreorder]
  RMcrt.cpp:19:1: warning:   when initialized here [-Wreorder]
  RVcrt.h:101:18: warning: ‘extendedleaps::rvdata::e’ will be initialized after [-Wreorder]
  RVcrt.h:99:10: warning:   ‘bool extendedleaps::rvdata::unreliable’ [-Wreorder]
  RVcrt.cpp:36:1: warning:   when initialized here [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-devel/subselect.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   1.7Mb
installed size is 60.5Mb
  sub-directories of 1Mb or more:
    libs  59.7Mb
Running examples in ‘svMisc-Ex.R’ failed
The error most likely occurred in:

> ### Name: toRjson
> ### Title: Convert R object to and from RJSON specification
> ### Aliases: toRjson evalRjson listToJson
> ### Keywords: utilities
> 
> ### ** Examples
> 
> ## A complex R object
> Robj <- structure(list(
+ 	a = as.double(c(1:5, 6)),
+ 	LETTERS,
+ 	c = c(c1 = 4.5, c2 = 7.8, c3 = Inf, c4 = -Inf, NA, c6 = NaN),
+ 	c(TRUE, FALSE, NA),
+ 	e = factor(c("a", "b", "a")),
+ 	f = "this is a \"string\"\nwith\tspecial chars",
+ 	g = matrix(rnorm(4), ncol = 2),
+ 	`h&'$@` = data.frame(x = 1:3, y = rnorm(3),
+ 		fact = factor(c("b", "a", "b"))),
+ 	i = Sys.Date(),
+     j = list(1:5, y = "another item")),
+     comment = "My comment\n\"",
+     anAttrib = 1:10,
+     anotherAttrib = list(TRUE, y = 1:4))
> 
> ## Convert to simplest RJSON, without attributes
> Rjson1 <- toRjson(Robj)
> Rjson1
[1] list(c(1., 2., 3., 4., 5., 6.), c("A", "B", "C", "D", "E", "F",                              
[2] "G", "H", "I", "J", "K", "L", "M", "N", "O", "P", "Q", "R", "S",                             
[3] "T", "U", "V", "W", "X", "Y", "Z"), c(4.5, 7.8, Inf, -Inf, NA,                               
[4] NaN), c(TRUE, FALSE, NA), c("a", "b", "a"), "this is a \\"string\\"\\nwith\\tspecial chars", 
[5]     c(-0.626453810742332, 0.183643324222082, -0.835628612410047,                             
[6]     1.59528080213779), list(seq(1, 3), c(0.329507771815361, -0.820468384118015,              
[7]     0.487429052428485), c("b", "a", "b")), "2017-12-21", list(                               
[8]         seq(1, 5), "another item"))                                                          
> evalRjson(Rjson1)
Error in .getClassesFromCache(Class) : 
  class should be either a character-string name or a class definition
Calls: evalRjson ... new -> getClass -> getClassDef -> .getClassesFromCache
Execution halted
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: GNU Extension: Different type kinds at (1)
  Warning: GNU Extension: initialization of common block variable ‘iset’ in DATA statement at (1)
  Warning: GNU Extension: Variable ‘iset’ at (1) is in COMMON but only in BLOCK DATA initialization is allowed
  Warning: GNU Extension: Missing comma at (1)
  Warning: CHARACTER expression will be truncated in assignment (10/13) at (1) [-Wcharacter-truncation]
  Warning: ‘pst_kg’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘burn_frlb’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘harveff’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘frac_harvk’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘cnop’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘hi_ovr’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘lai_init’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘orig_tnylda’ is used uninitialized in this function [-Wuninitialized]
  Warning: CHARACTER expression will be truncated in assignment (1/3) at (1) [-Wcharacter-truncation]
  Warning: ‘fr_curb’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-devel/SWATmodel.Rcheck/00install.out’ for details.
Found the following significant warnings:
  sybilSBML.c:2236:32: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=]
  sybilSBML.c:2247:34: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/sybilSBML.Rcheck/00install.out’ for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/taxlist.Rcheck/taxlist/cyperus’, resetting
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.9Mb
    libs   1.2Mb
installed size is 32.7Mb
  sub-directories of 1Mb or more:
    libs  31.5Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    apps   2.6Mb
    libs   2.0Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.5Mb
    libs   6.7Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/Rtmp2ZSxNm’, resetting
  Warning: working directory was changed to ‘/tmp/Rtmp2ZSxNm’, resetting
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    examples  13.4Mb
    include    3.0Mb
installed size is 25.4Mb
  sub-directories of 1Mb or more:
    libs  25.3Mb
installed size is 36.1Mb
  sub-directories of 1Mb or more:
    libs  35.7Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/trib.Rcheck/trib/exdata/tribometer’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/trib.Rcheck/trib/exdata/tribometer’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/trib.Rcheck/trib/exdata/profile’, resetting
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/trib.Rcheck/trib/exdata/profile’, resetting
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmprsZu94/treePos/2017_12_21/run’, resetting
installed size is 25.1Mb
  sub-directories of 1Mb or more:
    doc         2.2Mb
    dummydata   1.4Mb
    libs       20.6Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.0Mb
Found the following significant warnings:
  libunrtf/convert.c:1397:21: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=]
See ‘/data/gannet/ripley/R/packages/tests-devel/unrtf.Rcheck/00install.out’ for details.
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
Found the following significant warnings:
  convert_util.cpp:299:20: warning: null destination pointer [-Wformat-overflow=]
  convert_util.cpp:307:20: warning: null destination pointer [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/VariABEL.Rcheck/00install.out’ for details.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
Found the following significant warnings:
  EM.c:386:25: warning: ‘sprintf’ writing a terminating nul past the end of the destination [-Wformat-overflow=]
  EM.c:391:25: warning: ‘sprintf’ writing a terminating nul past the end of the destination [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/VBmix.Rcheck/00install.out’ for details.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is 26.8Mb
  sub-directories of 1Mb or more:
    libs  26.4Mb
installed size is 48.3Mb
  sub-directories of 1Mb or more:
    libs  47.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpXg2sWm’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpXg2sWm’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpXg2sWm’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpXg2sWm’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpXg2sWm’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpXg2sWm’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpXg2sWm’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpXg2sWm’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpXg2sWm’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpXg2sWm’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpXg2sWm’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpXg2sWm’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpXg2sWm’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpXg2sWm’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpXg2sWm’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpXg2sWm’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpXg2sWm’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpXg2sWm’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpXg2sWm’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpXg2sWm’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpXg2sWm’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpXg2sWm’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpXg2sWm’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpXg2sWm’, resetting
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
Bundesliga.Mannschaft: no visible global function definition for ‘data’
Bundesliga.Mannschaft: no visible binding for global variable
  ‘Bundesliga’
Bundesliga.Tabelle: no visible global function definition for ‘data’
Bundesliga.Tabelle: no visible binding for global variable ‘Bundesliga’
Bundesliga.XML: no visible global function definition for ‘data’
Bundesliga.XML: no visible binding for global variable ‘Bundesliga’
sens.spec: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Found the following significant warnings:
  assp/asspfio.c:528:31: warning: ‘%s’ directive writing up to 3 bytes into a region of size between 0 and 11 [-Wformat-overflow=]
  assp/fmt.c:989:24: warning: ‘+.2e ’ directive writing 5 bytes into a region of size between 0 and 13 [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/wrassp.Rcheck/00install.out’ for details.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    exampleData   1.6Mb
    examples      4.6Mb
Running examples in ‘xtractomatic-Ex.R’ failed
The error most likely occurred in:

> ### Name: xtracto_3D
> ### Title: Extract environmental data in a 3-D bounding box using ERDDAP.
> ### Aliases: xtracto_3D
> 
> ### ** Examples
> 
> xpos <- c(230, 231)
> ypos <- c(40, 41)
> tpos <- c('2006-05-05', '2006-05-06')
> extract <- xtracto_3D(xpos, ypos, tpos, 'ncdcOisst2Agg')
Error in getfileCoords(dataStruct) : object 'udtime' not found
Calls: xtracto_3D -> getfileCoords
Execution halted
Packages in Depends field not imported from:
  'Rglpk' 'corrplot' 'lattice' 'rgl'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
multiplot: no visible global function definition for 'rainbow'
multiplot: no visible global function definition for 'plot'
multiplot: no visible global function definition for 'text'
multiplot: no visible global function definition for 'lines'
multiplot: no visible global function definition for 'par'
plot.abf2: no visible global function definition for 'plot'
plot.abf2: no visible global function definition for 'abline'
plot.abf2: no visible global function definition for 'text'
plot.abf2split: no visible global function definition for 'plot'
Undefined global functions or variables:
  abline lines par plot rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "par", "plot", "text")
to your NAMESPACE file.
fillCSVData: no visible global function definition for 'read.table'
fillData: no visible global function definition for 'edit'
plotGraphs: no visible global function definition for 'par'
plotGraphs: no visible global function definition for 'plot'
plotGraphs: no visible global function definition for 'lines'
plotGraphs: no visible global function definition for 'legend'
plotGraphs: no visible global function definition for 'dev.new'
Undefined global functions or variables:
  dev.new edit legend lines par plot read.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "legend", "lines", "par", "plot")
  importFrom("utils", "edit", "read.table")
to your NAMESPACE file.
print.funlinWLS: no visible global function definition for 'pchisq'
print.linML: no visible global function definition for 'pchisq'
print.loglinML: no visible global function definition for 'pchisq'
print.satMarML: no visible global function definition for 'pchisq'
print.satMcarWLS: no visible global function definition for 'pchisq'
summary.funlinWLS: no visible global function definition for 'pchisq'
summary.linML: no visible global function definition for 'pchisq'
summary.loglinML: no visible global function definition for 'pchisq'
summary.satMarML: no visible global function definition for 'pchisq'
summary.satMcarWLS: no visible global function definition for 'pchisq'
summary.waldTest: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
Package in Depends field not imported from: 'MASS'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
acm: no visible global function definition for 'read.table'
clusters: no visible global function definition for 'write.matrix'
clusters: no visible global function definition for 'dev.new'
clusters: no visible global function definition for 'par'
clusters: no visible global function definition for 'hist'
clusters: no visible global function definition for 'legend'
clusters: no visible global function definition for 'pdf'
clusters: no visible global function definition for 'dev.off'
erra: no visible global function definition for 'read.table'
erra: no visible global function definition for 'pbeta'
Undefined global functions or variables:
  dev.new dev.off hist legend par pbeta pdf read.table write.matrix
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf")
  importFrom("graphics", "hist", "legend", "par")
  importFrom("stats", "pbeta")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'library' or 'require' call to 'mvtnorm' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Aggregate: no visible global function definition for 'aggregate'
Aggregate: no visible binding for global variable 'tail'
Aggregate: no visible binding for global variable 'var'
cocktailEnsemble: no visible global function definition for 'glm'
cocktailEnsemble: no visible global function definition for 'binomial'
cocktailEnsemble: no visible global function definition for 'step'
cocktailEnsemble: no visible binding for global variable 'na.omit'
imputeMissings : <anonymous>: no visible global function definition for
  'median'
predict.cocktailEnsemble: no visible global function definition for
  'predict'
Undefined global functions or variables:
  aggregate binomial glm median na.omit predict step tail var
Consider adding
  importFrom("stats", "aggregate", "binomial", "glm", "median",
             "na.omit", "predict", "step", "var")
  importFrom("utils", "tail")
to your NAMESPACE file.
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    R  13.6Mb
.amdai.initparam: no visible global function definition for 'cov'
.amdat.initiparam: no visible global function definition for 'cov'
amdai: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'SemiPar' 'nlme'
  Please remove these calls from your code.
asp: no visible global function definition for 'as.formula'
asp: no visible global function definition for 'var'
aspm: no visible binding for global variable 'X.Declan'
aspm: no visible binding for global variable 'Z.Jaida'
aspm: no visible binding for global variable 'group.vec.Handan'
aspm: no visible global function definition for 'as.formula'
aspm: no visible global function definition for 'glm'
aspm: no visible global function definition for 'binomial'
aspm: no visible global function definition for 'poisson'
Undefined global functions or variables:
  X.Declan Z.Jaida as.formula binomial glm group.vec.Handan poisson var
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "poisson", "var")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'MASS' 'Matrix'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'Rcpp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Depends: includes the non-default packages:
  'Matrix' 'coda' 'mvtnorm' 'MCMCpack' 'spatstat' 'parallel'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' calls to packages already attached by Depends:
  'MCMCpack' 'Matrix' 'coda' 'mvtnorm' 'parallel' 'spatstat'
  Please remove these calls from your code.
Package in Depends field not imported from: 'lattice'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
critical.values: no visible global function definition for 'rnorm'
critical.values: no visible global function definition for 'quantile'
mandel.test: no visible global function definition for 'qf'
mtukey.test : p.test: no visible global function definition for 'qf'
mtukey.test: no visible binding for global variable 'quantile'
mtukey.test: no visible global function definition for 'rnorm'
tukey.test: no visible global function definition for 'qf'
Undefined global functions or variables:
  qf quantile rnorm
Consider adding
  importFrom("stats", "qf", "quantile", "rnorm")
to your NAMESPACE file.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data       2.7Mb
    pictures   2.1Mb
ADM3: no visible global function definition for 'read.table'
ADM3: no visible global function definition for 'write.table'
dLRs: no visible global function definition for 'IQR'
dLRs: no visible global function definition for 'na.omit'
dLRs: no visible global function definition for 'qnorm'
plotADM3: no visible global function definition for 'plot'
plotADM3: no visible global function definition for 'abline'
plotADM3: no visible global function definition for 'segments'
Undefined global functions or variables:
  IQR abline na.omit plot qnorm read.table segments write.table
Consider adding
  importFrom("graphics", "abline", "plot", "segments")
  importFrom("stats", "IQR", "na.omit", "qnorm")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
bayescan: no visible global function definition for 'shortPathName'
Undefined global functions or variables:
  shortPathName
Consider adding
  importFrom("utils", "shortPathName")
to your NAMESPACE file.
aftgee: no visible global function definition for 'model.extract'
aftgee: no visible global function definition for 'model.matrix'
aftgee: no visible global function definition for 'lm'
aftgee: no visible global function definition for 'vcov'
aftgee.fit: no visible global function definition for 'lm'
aftgee.fit: no visible global function definition for 'rexp'
aftgee.fit: no visible global function definition for 'var'
aftsrr: no visible global function definition for 'model.extract'
aftsrr: no visible global function definition for 'model.matrix'
aftsrr.fit: no visible global function definition for 'lm'
aftsrr.fit: no visible global function definition for 'rexp'
aftsrr.fit: no visible global function definition for 'var'
getSmoothSuv: no visible global function definition for 'pnorm'
print.summary.aftgee: no visible global function definition for
  'printCoefmat'
print.summary.aftsrr: no visible global function definition for
  'printCoefmat'
solveGehan: no visible global function definition for 'nlm'
summary.aftgee: no visible global function definition for 'pnorm'
summary.aftsrr: no visible global function definition for 'pnorm'
viEmp: no visible global function definition for 'rexp'
viEmp: no visible global function definition for 'rnorm'
viEmp: no visible global function definition for 'var'
zlFun: no visible global function definition for 'lm'
Undefined global functions or variables:
  lm model.extract model.matrix nlm pnorm printCoefmat rexp rnorm var
  vcov
Consider adding
  importFrom("stats", "lm", "model.extract", "model.matrix", "nlm",
             "pnorm", "printCoefmat", "rexp", "rnorm", "var", "vcov")
to your NAMESPACE file.
closure_total_fair: no visible global function definition for 'is'
closure_transitive: no visible global function definition for 'is'
de_transitive: no visible global function definition for 'is'
get_equivalence_classes: no visible global function definition for 'is'
get_incomparable_pairs: no visible global function definition for 'is'
get_independent_sets: no visible global function definition for 'is'
is_reflexive: no visible global function definition for 'is'
is_total: no visible global function definition for 'is'
is_transitive: no visible global function definition for 'is'
pareto2_estimate_mle: no visible global function definition for
  'uniroot'
pareto2_test_f: no visible global function definition for 'qf'
pareto2_test_f: no visible global function definition for 'pf'
plot.citfun: no visible global function definition for 'plot'
plot.citfun: no visible global function definition for 'par'
plot.citfun: no visible global function definition for 'segments'
plot.citfun: no visible global function definition for 'points'
plot_producer: no visible global function definition for 'plot'
plot_producer: no visible global function definition for 'par'
plot_producer: no visible global function definition for 'segments'
plot_producer: no visible global function definition for 'points'
rpareto2: no visible global function definition for 'runif'
Undefined global functions or variables:
  is par pf plot points qf runif segments uniroot
Consider adding
  importFrom("graphics", "par", "plot", "points", "segments")
  importFrom("methods", "is")
  importFrom("stats", "pf", "qf", "runif", "uniroot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
IIR: no visible global function definition for 'qnorm'
TIR: no visible global function definition for 'qnorm'
agreement: no visible global function definition for 'var'
agreement: no visible global function definition for 'pchisq'
agreement: no visible global function definition for 'dnorm'
agreement: no visible global function definition for 'qnorm'
html.report: no visible global function definition for 'plot'
plot.report: no visible global function definition for 'plot'
plot.report: no visible global function definition for 'axis'
plot.report: no visible global function definition for 'points'
unified.agreement: no visible global function definition for 'lm'
unified.agreement: no visible global function definition for 'qnorm'
unified.agreement: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  axis dnorm lm pchisq plot pnorm points qnorm var
Consider adding
  importFrom("graphics", "axis", "plot", "points")
  importFrom("stats", "dnorm", "lm", "pchisq", "pnorm", "qnorm", "var")
to your NAMESPACE file.
Package in Depends field not imported from: 'XML'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Namespace with empty importFrom: 'survival'
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'survival'
A package should be listed in only one of these fields.
backfit.cox.interaction: no visible global function definition for
  'coxph'
backfit.lm.interaction: no visible global function definition for 'lm'
backfit.logistic.interaction: no visible global function definition for
  'glm'
backfit.logistic.main: no visible global function definition for 'glm'
cox.interaction: no visible global function definition for 'coxph'
cv.cox.interaction: no visible global function definition for 'coxph'
cv.cox.main: no visible global function definition for 'coxph'
cv.lm.interaction: no visible global function definition for 'lm'
cv.lm.main: no visible global function definition for 'lm'
cv.logistic.interaction: no visible global function definition for
  'glm'
cv.logistic.main: no visible global function definition for 'glm'
lm.interaction: no visible global function definition for 'lm'
logistic.interaction: no visible global function definition for 'glm'
logistic.main: no visible global function definition for 'glm'
Undefined global functions or variables:
  coxph glm lm
Consider adding
  importFrom("stats", "glm", "lm")
to your NAMESPACE file.
dke.fun.default: no visible global function definition for 'hist'
kef: no visible global function definition for 'dbinom'
kef: no visible global function definition for 'dgamma'
kef: no visible global function definition for 'dlnorm'
plot.dke.fun: no visible global function definition for 'hist'
plot.dke.fun: no visible global function definition for 'lines'
plot.hcvc.fun1d: no visible global function definition for
  'plot.default'
plot.hcvd.fun1d: no visible global function definition for
  'plot.default'
plot.kern.fun1d: no visible global function definition for
  'plot.default'
plot.kpmfe.fun1d: no visible global function definition for
  'plot.default'
plot.reg.fun1d: no visible global function definition for
  'plot.default'
simp_int: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx dbinom dgamma dlnorm hist lines plot.default
Consider adding
  importFrom("graphics", "hist", "lines", "plot.default")
  importFrom("stats", "approx", "dbinom", "dgamma", "dlnorm")
to your NAMESPACE file.
'library' or 'require' call to 'stats' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
akmeans: no visible global function definition for 'kmeans'
Undefined global functions or variables:
  kmeans
Consider adding
  importFrom("stats", "kmeans")
to your NAMESPACE file.
adpbar: no visible global function definition for 'optim'
alabama: no visible global function definition for 'optim'
auglag: no visible global function definition for 'modifyList'
auglag1: no visible global function definition for 'optim'
auglag1: no visible global function definition for 'nlminb'
auglag2: no visible global function definition for 'optim'
auglag2: no visible global function definition for 'nlminb'
auglag3: no visible global function definition for 'optim'
auglag3: no visible global function definition for 'nlminb'
augpen: no visible global function definition for 'optim'
constrOptim.nl: no visible global function definition for 'modifyList'
Undefined global functions or variables:
  modifyList nlminb optim
Consider adding
  importFrom("stats", "nlminb", "optim")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
eval.blockdesign: no visible global function definition for
  'model.matrix'
eval.design: no visible global function definition for 'model.matrix'
expand.formula: no visible global function definition for 'as.formula'
model.matrix.formula: no visible global function definition for
  'model.matrix.default'
model.matrix.terms: no visible global function definition for
  'model.matrix.default'
optBlock : set.factors: no visible global function definition for 'C'
optBlock : remove.nesting: no visible global function definition for
  'as.formula'
optBlock: no visible global function definition for 'formula'
optBlock: no visible global function definition for 'model.matrix'
optFederov: no visible global function definition for 'formula'
optFederov: no visible global function definition for 'model.matrix'
optMonteCarlo : RandomLevels: no visible global function definition for
  'runif'
optMonteCarlo : RandomMixture: no visible global function definition
  for 'rexp'
optMonteCarlo : expand: no visible global function definition for
  'model.matrix'
optMonteCarlo: no visible global function definition for 'as.formula'
Undefined global functions or variables:
  C as.formula formula model.matrix model.matrix.default rexp runif
Consider adding
  importFrom("stats", "C", "as.formula", "formula", "model.matrix",
             "model.matrix.default", "rexp", "runif")
to your NAMESPACE file.
hierarchical: no visible global function definition for 'terms'
hierarchical: no visible global function definition for 'loglin'
hierarchical: no visible global function definition for 'dmultinom'
markov: no visible global function definition for 'download.file'
metropolis: no visible global function definition for 'runif'
mpolyListToMat : <anonymous>: no visible global function definition for
  'runif'
polyOptim: no visible global function definition for 'deriv'
print.hierarchical: no visible binding for global variable 'sd'
spectral : summarize: no visible global function definition for 'sd'
subsets : <anonymous>: no visible global function definition for
  'combn'
Undefined global functions or variables:
  combn deriv dmultinom download.file loglin runif sd terms
Consider adding
  importFrom("stats", "deriv", "dmultinom", "loglin", "runif", "sd",
             "terms")
  importFrom("utils", "combn", "download.file")
to your NAMESPACE file.
gascuel: no visible global function definition for 'optim'
Undefined global functions or variables:
  optim
Consider adding
  importFrom("stats", "optim")
to your NAMESPACE file.
allanVarSelect: no visible global function definition for 'read.csv'
fitvbiglm: no visible global function definition for 'read.csv'
fitvbiglm: no visible global function definition for 'update'
getbestchunksize: no visible global function definition for 'read.csv'
getbestchunksize: no visible global function definition for
  'object.size'
predictvbiglm: no visible global function definition for 'read.csv'
predictvbiglm: no visible global function definition for 'predict'
predictvbiglm: no visible global function definition for
  'weighted.mean'
readinbigdata : <anonymous>: no visible global function definition for
  'read.csv'
Undefined global functions or variables:
  object.size predict read.csv update weighted.mean
Consider adding
  importFrom("stats", "predict", "update", "weighted.mean")
  importFrom("utils", "object.size", "read.csv")
to your NAMESPACE file.
amCSV.amCluster: no visible global function definition for 'write.csv'
amCSV.amPairwise: no visible global function definition for 'write.csv'
amCSV.amUnique: no visible global function definition for 'write.csv'
amCluster: no visible global function definition for 'hclust'
amCluster: no visible global function definition for 'as.dist'
amHTML.amCluster: no visible global function definition for 'browseURL'
amHTML.amPairwise: no visible global function definition for
  'browseURL'
amHTML.amUnique: no visible global function definition for 'browseURL'
amUniqueProfile: no visible global function definition for 'layout'
amUniqueProfile: no visible global function definition for 'par'
amUniqueProfile: no visible global function definition for
  'plot.default'
amUniqueProfile: no visible global function definition for 'points'
amUniqueProfile: no visible global function definition for 'lines'
amUniqueProfile: no visible global function definition for 'arrows'
amUniqueProfile: no visible global function definition for 'text'
amUniqueProfile: no visible global function definition for 'legend'
Undefined global functions or variables:
  arrows as.dist browseURL hclust layout legend lines par plot.default
  points text write.csv
Consider adding
  importFrom("graphics", "arrows", "layout", "legend", "lines", "par",
             "plot.default", "points", "text")
  importFrom("stats", "as.dist", "hclust")
  importFrom("utils", "browseURL", "write.csv")
to your NAMESPACE file.
batch.possSpells.fnc: no visible binding for global variable 'words'
possSpells.fnc: no visible binding for global variable 'len.phons'
possSpells.fnc: no visible binding for global variable 'phon1'
possSpells.fnc: no visible binding for global variable 'len.total'
possSpells.fnc: no visible binding for global variable 'poss.spells'
Undefined global functions or variables:
  len.phons len.total phon1 poss.spells words
Package in Depends field not imported from: 'car'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' calls which should be '::':
  'car:::bcPower' 'car:::bootCase' 'car:::deltaMethod'
  'car:::infIndexPlot' 'car:::invResPlot' 'car:::invTranEstimate'
  'car:::invTranPlot' 'car:::marginalModelPlot' 'car:::outlierTest'
  'car:::powerTransform' 'car:::residualPlot' 'car:::residualPlots'
  'car:::testTransform'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'car:::residCurvTest' 'car:::tukeyNonaddTest'
  See the note in ?`:::` about the use of this operator.
alr4Web: no visible global function definition for 'browseURL'
print.summary.lm: no visible binding for global variable 'quantile'
print.summary.lm: no visible global function definition for 'quantile'
print.summary.lm: no visible global function definition for
  'printCoefmat'
print.summary.lm: no visible global function definition for 'naprint'
print.summary.lm: no visible global function definition for 'pf'
print.summary.lm: no visible global function definition for 'symnum'
Undefined global functions or variables:
  browseURL naprint pf printCoefmat quantile symnum
Consider adding
  importFrom("stats", "naprint", "pf", "printCoefmat", "quantile",
             "symnum")
  importFrom("utils", "browseURL")
to your NAMESPACE file.
'library' or 'require' call to 'Biobase' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
EXP.step: no visible global function definition for 'rgamma'
EXP.step: no visible global function definition for 'rnorm'
MAX.step: no visible global function definition for 'uniroot'
Norm.GMedian: no visible binding for global variable 'median'
RNASeq.Data.Gene: no visible binding for global variable 'quantile'
decom.initial: no visible global function definition for 'kmeans'
decom.initial: no visible global function definition for 'quantile'
decom.initial: no visible global function definition for 'var'
dispersion.nb.QL: no visible binding for global variable 'quantile'
est.mu.nb.mle: no visible global function definition for 'runif'
est.v.nb.QL: no visible global function definition for 'runif'
pdf2grid: no visible global function definition for 'dnorm'
pdf2grid: no visible global function definition for 'dgamma'
prior.grid: no visible global function definition for 'sd'
prior.grid: no visible global function definition for 'dnorm'
test.AMAP: no visible global function definition for 'rgamma'
test.AMAP: no visible global function definition for 'rnorm'
test.AMAP: no visible global function definition for 'quantile'
Undefined global functions or variables:
  dgamma dnorm kmeans median quantile rgamma rnorm runif sd uniroot var
Consider adding
  importFrom("stats", "dgamma", "dnorm", "kmeans", "median", "quantile",
             "rgamma", "rnorm", "runif", "sd", "uniroot", "var")
to your NAMESPACE file.
Checking should be performed on sources prepared by 'R CMD build'.
amltest: no visible global function definition for 'var'
amltest: no visible global function definition for 'optim'
amltest: no visible global function definition for 'lm'
cleanclust: no visible global function definition for 'cor'
cleanclust: no visible global function definition for 'hclust'
cleanclust: no visible global function definition for 'as.dist'
cleanclust: no visible global function definition for 'cutree'
Undefined global functions or variables:
  as.dist cor cutree hclust lm optim var
Consider adding
  importFrom("stats", "as.dist", "cor", "cutree", "hclust", "lm",
             "optim", "var")
to your NAMESPACE file.
AMOEBA : Classi: no visible global function definition for 'sd'
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
random.init.MLPneuron: no visible global function definition for
  'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Analyz.loadSteps,Analyz: no visible global function definition for
  'read.csv'
Undefined global functions or variables:
  read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'discretization' 'foreign' 'functional' 'stringr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
aode: no visible global function definition for 'Compose'
mdl: no visible global function definition for 'cutPoints'
setVar: no visible global function definition for 'Compose'
Undefined global functions or variables:
  Compose cutPoints
andrews: no visible global function definition for 'plot.new'
andrews: no visible global function definition for 'plot.window'
andrews: no visible global function definition for 'title'
andrews: no visible global function definition for 'axis'
andrews: no visible global function definition for 'box'
andrews: no visible global function definition for 'lines'
andrews: no visible global function definition for 'rainbow'
andrews: no visible global function definition for 'hsv'
selectand: no visible global function definition for 'lines'
Undefined global functions or variables:
  axis box hsv lines plot.new plot.window rainbow title
Consider adding
  importFrom("grDevices", "hsv", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "title")
to your NAMESPACE file.
plot,ANFIS: no visible binding for global variable 'X'
plotMF,ANFIS : <anonymous>: no visible global function definition for
  'lines'
plotMFs,ANFIS: no visible global function definition for 'par'
Undefined global functions or variables:
  X lines par
Consider adding
  importFrom("graphics", "lines", "par")
to your NAMESPACE file.
GetTotalValues: no visible global function definition for 'rgamma'
GetTotalValues: no visible global function definition for 'runif'
MakeAnglers: no visible global function definition for 'runif'
MakeAnglers: no visible global function definition for 'rgamma'
Undefined global functions or variables:
  rgamma runif
Consider adding
  importFrom("stats", "rgamma", "runif")
to your NAMESPACE file.
'library' or 'require' call to 'tcltk' which was already attached by Depends.
  Please remove these calls from your code.
annot : annotlist: no visible global function definition for
  'read.table'
annot : annotlist: no visible global function definition for
  'write.table'
annot: no visible global function definition for 'flush.console'
annot: no visible global function definition for 'read.table'
annot: no visible global function definition for 'choose.dir'
Undefined global functions or variables:
  choose.dir flush.console read.table write.table
Consider adding
  importFrom("utils", "choose.dir", "flush.console", "read.table",
             "write.table")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from 'anoint' for: 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
installed size is 35.3Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
aw_map: no visible global function definition for 'browseURL'
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
'library' or 'require' call to 'boot' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
varbin: no visible global function definition for 'boot'
Undefined global functions or variables:
  boot
'library' or 'require' call to 'boot' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'boot' 'lme4' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' call to 'tkrplot' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
TSPM: no visible global function definition for 'glm'
TSPM: no visible binding for global variable 'poisson'
TSPM: no visible global function definition for 'hatvalues'
TSPM: no visible global function definition for 'residuals'
TSPM: no visible global function definition for 'deviance'
TSPM: no visible global function definition for 'qchisq'
TSPM: no visible global function definition for 'qf'
TSPM: no visible global function definition for 'pf'
TSPM: no visible global function definition for 'pchisq'
TSPM: no visible global function definition for 'p.adjust'
norm.inttable: no visible global function definition for 'median'
norm.inttable : <anonymous>: no visible global function definition for
  'quantile'
saint_permF: no visible global function definition for 'read.table'
saint_permF: no visible global function definition for 'write.table'
saint_permF: no visible global function definition for 'write.csv2'
tspm_apms: no visible global function definition for 'read.table'
varFilter : <anonymous>: no visible global function definition for
  'median'
varFilter: no visible global function definition for 'median'
varFilter: no visible global function definition for 'quantile'
Undefined global functions or variables:
  deviance glm hatvalues median p.adjust pchisq pf poisson qchisq qf
  quantile read.table residuals write.csv2 write.table
Consider adding
  importFrom("stats", "deviance", "glm", "hatvalues", "median",
             "p.adjust", "pchisq", "pf", "poisson", "qchisq", "qf",
             "quantile", "residuals")
  importFrom("utils", "read.table", "write.csv2", "write.table")
to your NAMESPACE file.
apple: no visible global function definition for 'ginv'
apple: no visible global function definition for 'runif'
deri: no visible global function definition for 'ginv'
logit: no visible global function definition for 'qlogis'
plot.apple: no visible global function definition for 'matplot'
plot.apple: no visible global function definition for 'lines'
y.app: no visible global function definition for 'ginv'
Undefined global functions or variables:
  ginv lines matplot qlogis runif
Consider adding
  importFrom("graphics", "lines", "matplot")
  importFrom("stats", "qlogis", "runif")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'ellipse' 'lattice'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
bookTheme: no visible global function definition for 'trellis.par.set'
easyBoundaryFunc: no visible global function definition for 'runif'
getPackages: no visible global function definition for
  'install.packages'
permuteRelief: no visible binding for global variable 'sd'
quadBoundaryFunc: no visible global function definition for 'runif'
transparentTheme: no visible global function definition for 'rgb'
transparentTheme: no visible global function definition for
  'trellis.par.set'
upperp: no visible global function definition for 'ellipse'
upperp: no visible global function definition for 'panel.xyplot'
upperp: no visible global function definition for 'trellis.par.get'
Undefined global functions or variables:
  ellipse install.packages panel.xyplot rgb runif sd trellis.par.get
  trellis.par.set
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "runif", "sd")
  importFrom("utils", "install.packages")
to your NAMESPACE file.
Package in Depends field not imported from: 'emulator'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Afun: no visible global function definition for 'corr.matrix'
betahat.app.H: no visible global function definition for 'quad.form'
betahat.app.H: no visible global function definition for
  'quad.form.inv'
cdash.fun: no visible global function definition for 'quad.3form'
cdash.fun: no visible global function definition for 'quad.form'
generate.toy.observations : delta: no visible global function
  definition for 'rmvnorm'
generate.toy.observations : delta: no visible global function
  definition for 'corr.matrix'
object: no visible global function definition for 'quad.form'
opt.1: no visible global function definition for 'optim'
opt.gt.1: no visible global function definition for 'optim'
subsets.fun : select: no visible global function definition for
  'rbinom'
Undefined global functions or variables:
  corr.matrix optim quad.3form quad.form quad.form.inv rbinom rmvnorm
Consider adding
  importFrom("stats", "optim", "rbinom")
to your NAMESPACE file.
runAPSIM: warning in scan(reports_file[i], "", sep = "", skip =
  length(temp), nline = 1): partial argument match of 'nline' to
  'nlines'
runAPSIM: no visible global function definition for 'write.table'
runAPSIM: no visible global function definition for 'read.table'
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
kristen.colors: no visible global function definition for
  'colorRampPalette'
kristen.colors: no visible global function definition for 'grey'
plot3d.points: no visible global function definition for 'heat.colors'
plot3d.points: no visible global function definition for 'plot'
ragged.image: no visible global function definition for 'heat.colors'
ragged.image: no visible global function definition for 'image'
scatterplot.density: no visible global function definition for 'grey'
scatterplot.density: no visible global function definition for 'image'
scatterplot.density: no visible global function definition for 'abline'
scatterplot.density: no visible global function definition for 'lm'
scatterplot.density: no visible global function definition for 'legend'
vertical.image.legend: no visible global function definition for 'par'
vertical.image.legend: no visible global function definition for
  'image'
vertical.image.legend: no visible global function definition for 'axis'
vertical.image.legend: no visible global function definition for 'box'
Undefined global functions or variables:
  abline axis box colorRampPalette grey heat.colors image legend lm par
  plot
Consider adding
  importFrom("grDevices", "colorRampPalette", "grey", "heat.colors")
  importFrom("graphics", "abline", "axis", "box", "image", "legend",
             "par", "plot")
  importFrom("stats", "lm")
to your NAMESPACE file.
aqDayOfWeekStat: no visible global function definition for 'index'
aqDropHour: no visible global function definition for 'index'
aqFilterOHLCSD: no visible binding for global variable 'sd'
aqHourIndex: no visible global function definition for 'index'
aqHourlyStat: no visible global function definition for 'index'
aqLoadOHLC: no visible global function definition for 'read.csv'
aqLoadSeriesField: no visible global function definition for 'read.csv'
aqLoadXtsFromCsv: no visible global function definition for 'read.csv2'
aqLoadYahooEOD: no visible global function definition for 'read.csv'
aqSaveXtsToCsv: no visible global function definition for 'write.csv2'
aqStoreSeriesField: no visible global function definition for 'index'
aqStoreSeriesField: no visible global function definition for
  'capture.output'
aqStoreSeriesField: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  capture.output index read.csv read.csv2 sd write.csv2 write.table
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "capture.output", "read.csv", "read.csv2",
             "write.csv2", "write.table")
to your NAMESPACE file.
AR1seg_func: no visible global function definition for 'median'
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'MASS' 'TSP'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
ardec: no visible global function definition for 'filter'
ardec.lm: no visible global function definition for 'ar'
ardec.lm: no visible global function definition for 'lm'
Undefined global functions or variables:
  ar filter lm
Consider adding
  importFrom("stats", "ar", "filter", "lm")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/ArfimaMLM.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'AffymetrixDataTestFiles'
Packages suggested but not available for checking:
  'sfit' 'expectile' 'HaarSeg' 'mpcbs'
binarize.array: no visible binding for global variable 'sd'
mskmeans: no visible global function definition for 'kmeans'
Undefined global functions or variables:
  kmeans sd
Consider adding
  importFrom("stats", "kmeans", "sd")
to your NAMESPACE file.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.5Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    bin   12.0Mb
    misc   2.1Mb
Package suggested but not available for checking: 'cacheSweave'
Warning: no function found corresponding to methods exports from 'ascii' for: 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
'library' or 'require' calls in package code:
  'cacheSweave' 'weaver'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'utils:::RtangleSetup'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'survival:::survmean' 'utils:::.SweaveValidFilenameRegexp'
  'utils:::RtangleFinish' 'utils:::RtangleRuncode'
  'utils:::SweaveParseOptions'
  See the note in ?`:::` about the use of this operator.
Unavailable namespace imported from by a ':::' call: 'cacheSweave'
  See the note in ?`:::` about the use of this operator.
S3 methods shown with full name in documentation object 'cbind.ascii':
  'cbind.ascii'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Packages which this enhances but not available for checking:
  'REBayes' 'Rmosek'
NeedsCompilation field should likely be 'yes'
'library' or 'require' calls to packages already attached by Depends:
  'Hmisc' 'splancs'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'Hmisc' 'shapefiles' 'splancs'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ASP.Score: no visible global function definition for 'pnorm'
Graphs.Bayesian: no visible global function definition for 'dev.new'
colorhex: no visible global function definition for 'gray'
colorhex: no visible global function definition for 'rgb'
Undefined global functions or variables:
  dev.new gray pnorm rgb
Consider adding
  importFrom("grDevices", "dev.new", "gray", "rgb")
  importFrom("stats", "pnorm")
to your NAMESPACE file.
Package which this enhances but not available for checking: 'asreml'
':::' call which should be '::': 'assertive.base:::print_and_capture'
  See the note in ?`:::` about the use of this operator.
Running examples in 'assist-Ex.R' failed
The error most likely occurred in:

> ### Name: anova.ssr
> ### Title: Testing a Non-parametric Function Fitted via Smoothing Splines
> ### Aliases: anova.ssr
> ### Keywords: file
> 
> ### ** Examples
> 
> data(acid)
> 
> # fit a partial thin-plate spline
> temp <- ssr(ph~t1+x1+x2, rk=tp(t1), data=acid, spar="m")
At line 1992 of file rkpk1.f
Fortran runtime error: Index '2' of dimension 1 of array 'jpvt' above upper bound of 1
Package in Depends field not imported from: 'mvtnorm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CALPHA: no visible global function definition for 'dbinom'
CALPHA: no visible global function definition for 'pchisq'
CAST: no visible global function definition for 'fisher.test'
CAST: no visible global function definition for 'chisq.test'
CMC: no visible global function definition for 'pf'
MULTI: no visible global function definition for 'complete.cases'
RVT1: no visible global function definition for 'pchisq'
RVT2: no visible global function definition for 'pchisq'
RWAS: no visible global function definition for 'pnorm'
SKAT: no visible global function definition for 'dbeta'
SKAT: no visible global function definition for 'pchisq'
TTEST: no visible global function definition for 'complete.cases'
TTEST: no visible global function definition for 'pf'
WST: no visible global function definition for 'mvfft'
WST: no visible global function definition for 'pnorm'
my_cmc_method: no visible global function definition for
  'complete.cases'
my_getUV: no visible global function definition for 'complete.cases'
my_orwss_method: no visible global function definition for 'sd'
my_rarecov_method: no visible global function definition for
  'chisq.test'
my_rbt_method: no visible global function definition for 'ppois'
my_score_method: no visible global function definition for 'pchisq'
my_ssu_method: no visible global function definition for 'pchisq'
my_ssuw_method: no visible global function definition for 'pchisq'
my_sum_method: no visible global function definition for 'pchisq'
my_uminp_method: no visible global function definition for 'pchisq'
my_uminp_method: no visible global function definition for 'pmvnorm'
Undefined global functions or variables:
  chisq.test complete.cases dbeta dbinom fisher.test mvfft pchisq pf
  pmvnorm pnorm ppois sd
Consider adding
  importFrom("stats", "chisq.test", "complete.cases", "dbeta", "dbinom",
             "fisher.test", "mvfft", "pchisq", "pf", "pnorm", "ppois",
             "sd")
to your NAMESPACE file.
beamDiskOverlap: no visible global function definition for 'integrate'
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
fm_unred: no visible global function definition for 'spline'
galage: no visible global function definition for 'integrate'
lumdist: no visible global function definition for 'integrate'
Undefined global functions or variables:
  integrate spline
Consider adding
  importFrom("stats", "integrate", "spline")
to your NAMESPACE file.
VPC.graph : findQuantile: no visible global function definition for
  'quantile'
VPC.graph : findQuantileCI : <anonymous>: no visible global function
  definition for 'quantile'
asVPC.binW: no visible global function definition for 'median'
asVPC.binW : <anonymous>: no visible global function definition for
  'quantile'
asVPC.binW: no visible global function definition for 'quantile'
asVPC.distanceW: no visible global function definition for 'median'
asVPC.distanceW : <anonymous>: no visible global function definition
  for 'quantile'
asVPC.distanceW: no visible global function definition for 'quantile'
makeCOVbin: no visible global function definition for 'quantile'
makeCOVbin: no visible global function definition for 'median'
read_Simdata: no visible global function definition for 'read.table'
Undefined global functions or variables:
  median quantile read.table
Consider adding
  importFrom("stats", "median", "quantile")
  importFrom("utils", "read.table")
to your NAMESPACE file.
asymp.test.default: no visible global function definition for 'var'
asymp.test.default: no visible global function definition for 'pnorm'
asymp.test.default: no visible global function definition for 'qnorm'
asymp.test.formula: no visible global function definition for 'terms'
seDMean.default: no visible global function definition for 'var'
seDMeanG.default: no visible global function definition for 'var'
seDVar.default: no visible global function definition for 'var'
seMean.default: no visible global function definition for 'var'
seRMean.default: no visible global function definition for 'var'
seRVar.default: no visible global function definition for 'var'
seVar.default: no visible global function definition for 'var'
Undefined global functions or variables:
  pnorm qnorm terms var
Consider adding
  importFrom("stats", "pnorm", "qnorm", "terms", "var")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/AtelieR.Rcheck/00install.out' for details.
get.est.ATT: no visible global function definition for 'tail'
get.est.MT: no visible global function definition for 'tail'
get.est.simple: no visible global function definition for 'tail'
newton.r: no visible global function definition for 'tail'
plot.ATE: no visible global function definition for 'par'
plot.ATE: no visible global function definition for 'plot'
plot.ATE: no visible global function definition for 'axis'
plot.ATE: no visible global function definition for 'abline'
plot.ATE: no visible global function definition for 'lines'
plot.ATE: no visible global function definition for 'legend'
plot.ATE: no visible global function definition for 'points'
print.summary.ATE: no visible global function definition for
  'printCoefmat'
summary.ATE: no visible global function definition for 'qnorm'
summary.ATE: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  abline axis legend lines par plot pnorm points printCoefmat qnorm
  tail
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "plot", "points")
  importFrom("stats", "pnorm", "printCoefmat", "qnorm")
  importFrom("utils", "tail")
to your NAMESPACE file.
atmcmc : rmvtnorm: no visible global function definition for 'rnorm'
atmcmc: no visible global function definition for 'rnorm'
atmcmc: no visible global function definition for 'runif'
atmcmc: no visible global function definition for 'par'
atmcmc: no visible global function definition for 'lm'
atmcmc: no visible global function definition for 'lines'
atmcmc: no visible global function definition for 'var'
atmcmc: no visible global function definition for 'cov'
atmcmc: no visible global function definition for 'quantile'
atmcmc: no visible global function definition for 'sd'
plotmcmc: no visible global function definition for 'pdf'
plotmcmc: no visible global function definition for 'par'
plotmcmc: no visible global function definition for 'dev.new'
plotmcmc: no visible global function definition for 'png'
plotmcmc: no visible global function definition for 'hist'
plotmcmc: no visible global function definition for 'dev.off'
plotmcmc: no visible global function definition for 'plot'
plotmcmc: no visible global function definition for 'lines'
Undefined global functions or variables:
  cov dev.new dev.off hist lines lm par pdf plot png quantile rnorm
  runif sd var
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf", "png")
  importFrom("graphics", "hist", "lines", "par", "plot")
  importFrom("stats", "cov", "lm", "quantile", "rnorm", "runif", "sd",
             "var")
to your NAMESPACE file.
LHSdesign: no visible global function definition for 'qnorm'
LHSdesign: no visible global function definition for 'qunif'
LHSdesign: no visible global function definition for 'qt'
MCdesign: no visible global function definition for 'rnorm'
MCdesign: no visible global function definition for 'runif'
MCdesign: no visible global function definition for 'rt'
Undefined global functions or variables:
  qnorm qt qunif rnorm rt runif
Consider adding
  importFrom("stats", "qnorm", "qt", "qunif", "rnorm", "rt", "runif")
to your NAMESPACE file.
PlotAtm.lin : scale_image: no visible global function definition for
  'heat.colors'
PlotAtm.lin : scale_image: no visible global function definition for
  'par'
PlotAtm.lin : scale_image: no visible global function definition for
  'sd'
PlotAtm.lin : scale_image: no visible global function definition for
  'approx'
PlotAtm.lin : scale_image: no visible global function definition for
  'image'
PlotAtm.lin : scale_image: no visible global function definition for
  'axis'
PlotAtm.lin : scale_image: no visible global function definition for
  'mtext'
PlotAtm.lin: no visible global function definition for 'arrows'
PlotAtm.lin: no visible global function definition for 'text'
PlotAtm.lin: no visible global function definition for 'polygon'
sky.colors: no visible global function definition for 'rgb'
Undefined global functions or variables:
  approx arrows axis heat.colors image mtext par polygon rgb sd text
Consider adding
  importFrom("grDevices", "heat.colors", "rgb")
  importFrom("graphics", "arrows", "axis", "image", "mtext", "par",
             "polygon", "text")
  importFrom("stats", "approx", "sd")
to your NAMESPACE file.
parse_response: no visible global function definition for 'read.csv'
Undefined global functions or variables:
  read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
attribrisk: no visible global function definition for 'terms'
attribrisk: no visible global function definition for '.getXlevels'
attribrisk: no visible global function definition for 'model.response'
attribrisk: no visible global function definition for 'model.weights'
attribrisk: no visible global function definition for 'model.offset'
attribrisk: no visible global function definition for 'model.matrix'
attribrisk: no visible global function definition for 'model.frame'
attribrisk.fit: no visible global function definition for 'glm.fit'
attribrisk.fit: no visible global function definition for 'binomial'
attribrisk.fit: no visible global function definition for 'glm.control'
attribrisk.fit: no visible global function definition for 'coef'
attribrisk.fit: no visible global function definition for
  'coefficients'
attribrisk_boot: no visible global function definition for 'var'
print.attribrisk: no visible global function definition for 'qnorm'
summary.attribrisk: no visible global function definition for 'hasArg'
summary.attribrisk: no visible global function definition for 'var'
Undefined global functions or variables:
  .getXlevels binomial coef coefficients glm.control glm.fit hasArg
  model.frame model.matrix model.offset model.response model.weights
  qnorm terms var
Consider adding
  importFrom("methods", "hasArg")
  importFrom("stats", ".getXlevels", "binomial", "coef", "coefficients",
             "glm.control", "glm.fit", "model.frame", "model.matrix",
             "model.offset", "model.response", "model.weights", "qnorm",
             "terms", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
plot.AUC: no visible global function definition for 'plot'
plot.AUC: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines plot
Consider adding
  importFrom("graphics", "lines", "plot")
to your NAMESPACE file.
AUCRFcv: no visible global function definition for 'predict'
plot.AUCRF: no visible global function definition for 'par'
plot.AUCRF: no visible global function definition for 'dotchart'
plot.AUCRF: no visible global function definition for 'title'
plot.AUCRF: no visible global function definition for 'text'
Undefined global functions or variables:
  dotchart par predict text title
Consider adding
  importFrom("graphics", "dotchart", "par", "text", "title")
  importFrom("stats", "predict")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'RJSONIO' 'hexbin' 'plotrix'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
audioHist: no visible global function definition for 'hist'
audioHist: no visible global function definition for 'rescale'
audioHist: no visible global function definition for 'toJSON'
audioScatter: no visible binding for global variable 'formula'
audioScatter: no visible global function definition for 'hexbinplot'
audioScatter: no visible global function definition for 'cor'
audioScatter: no visible global function definition for 'toJSON'
audioSplom: no visible global function definition for 'hexplom'
audioSplom: no visible binding for global variable 'BTY'
audioSplom: no visible binding for global variable 'panel.hexboxplot'
audioSplom: no visible global function definition for 'combn'
audioSplom : <anonymous>: no visible global function definition for
  'cor'
audioSplom : <anonymous>: no visible global function definition for
  'toJSON'
audiolyzRcheck: no visible global function definition for
  'download.file'
audiolyzRcheck: no visible global function definition for 'unzip'
matricize: no visible global function definition for 'hexbin'
panel.audiolyzR: no visible global function definition for
  'panel.hexbinplot'
Undefined global functions or variables:
  BTY combn cor download.file formula hexbin hexbinplot hexplom hist
  panel.hexbinplot panel.hexboxplot rescale toJSON unzip
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "cor", "formula")
  importFrom("utils", "combn", "download.file", "unzip")
to your NAMESPACE file.
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.5/audio.Rcheck/00install.out' for details.
simulateD: no visible global function definition for 'rgamma'
simulateT: no visible global function definition for 'runif'
simulateT: no visible global function definition for 'rbeta'
simulateT: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  rbeta rbinom rgamma runif
Consider adding
  importFrom("stats", "rbeta", "rbinom", "rgamma", "runif")
to your NAMESPACE file.
Package which this enhances but not available for checking: 'rPython'
'library' or 'require' calls in package code:
  'ggplot2' 'gpclib' 'maptools'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
gLog.ep: no visible global function definition for 'quantile'
gedestp: no visible global function definition for 'na.omit'
gedestp: no visible global function definition for 'optim'
gets.mean: no visible global function definition for 'start'
gets.mean: no visible global function definition for 'end'
gets.mean: no visible global function definition for 'window'
gets.mean: no visible global function definition for 'pt'
gets.mean: no visible global function definition for 'Box.test'
gets.mean: no visible global function definition for 'pchisq'
gets.vol: no visible global function definition for 'start'
gets.vol: no visible global function definition for 'end'
gets.vol: no visible global function definition for 'window'
gets.vol: no visible global function definition for 'pt'
gets.vol: no visible global function definition for 'Box.test'
gets.vol: no visible global function definition for 'pchisq'
jb.test: no visible global function definition for 'pchisq'
skewness.test: no visible global function definition for 'pchisq'
sm: no visible global function definition for 'start'
sm: no visible global function definition for 'end'
sm: no visible global function definition for 'window'
sm: no visible global function definition for 'pt'
sm: no visible global function definition for 'pchisq'
sm: no visible global function definition for 'Box.test'
Undefined global functions or variables:
  Box.test end na.omit optim pchisq pt quantile start window
Consider adding
  importFrom("stats", "Box.test", "end", "na.omit", "optim", "pchisq",
             "pt", "quantile", "start", "window")
to your NAMESPACE file.
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
                 ".", call. = FALSE)
         mock(name = name, env = env, new = eval(new_values[[qual_name]], eval_env, eval_env))
     })
  4: FUN(X[[i]], ...)
  5: stop("Can't mock functions in base packages (", pkg_name, ")", call. = FALSE)
  
  == testthat results  ===========================================================
  OK: 448 SKIPPED: 0 FAILED: 4
  1. Error: autovar function returns hello world (@test_autovar.r#14) 
  2. Error: model_score calls its subfunctions correctly for AIC (@test_model_score.r#50) 
  3. Error: model_score calls its subfunctions correctly for BIC (@test_model_score.r#81) 
  4. Error: select_valid_masks calls bitwAnd correctly (@test_select_valid_masks.r#15) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
                 ".", call. = FALSE)
         mock(name = name, env = env, new = eval(new_values[[qual_name]], eval_env, eval_env))
     })
  4: FUN(X[[i]], ...)
  5: stop("Can't mock functions in base packages (", pkg_name, ")", call. = FALSE)
  
  == testthat results  ===========================================================
  OK: 448 SKIPPED: 0 FAILED: 4
  1. Error: autovar function returns hello world (@test_autovar.r#14) 
  2. Error: model_score calls its subfunctions correctly for AIC (@test_model_score.r#50) 
  3. Error: model_score calls its subfunctions correctly for BIC (@test_model_score.r#81) 
  4. Error: select_valid_masks calls bitwAnd correctly (@test_select_valid_masks.r#15) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 67.3Mb
  sub-directories of 1Mb or more:
    java  67.2Mb
best: no visible global function definition for 'optim'
randomboards: no visible global function definition for 'runif'
randomprobs: no visible global function definition for 'runif'
Undefined global functions or variables:
  optim runif
Consider adding
  importFrom("stats", "optim", "runif")
to your NAMESPACE file.
File 'aylmer/libs/i386/aylmer.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'aylmer.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'aylmer.o'
File 'aylmer/libs/x64/aylmer.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'aylmer.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'aylmer.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
CRexp_set: no visible global function definition for 'runif'
b6e6rl: no visible global function definition for 'runif'
derand_RL: no visible global function definition for 'runif'
derandexp_RL: no visible global function definition for 'runif'
nahvyb_expt: no visible global function definition for 'runif'
roulete: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
.generateTransform: no visible global function definition for 'sd'
.generateUnitHyperCube: no visible global function definition for
  'runif'
.makeBoundedSingleStep: no visible global function definition for
  'runif'
.makeBoundedStep: no visible global function definition for 'runif'
.makeStep: no visible global function definition for 'runif'
.staircaseSampling: no visible global function definition for 'runif'
GaussianPrior: no visible global function definition for 'qnorm'
LogNormalPrior: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  qnorm runif sd
Consider adding
  importFrom("stats", "qnorm", "runif", "sd")
to your NAMESPACE file.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   8.9Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.8Mb
BACprior.CV: no visible global function definition for 'na.fail'
BACprior.CV: no visible global function definition for 'plot'
BACprior.CV: no visible global function definition for 'abline'
BACprior.boot: no visible global function definition for 'na.fail'
BACprior.boot: no visible global function definition for 'plot'
BACprior.boot: no visible global function definition for 'abline'
BACprior.lm: no visible global function definition for 'na.fail'
BACprior.lm: no visible global function definition for 'coef'
BACprior.lm: no visible global function definition for 'vcov'
Undefined global functions or variables:
  abline coef na.fail plot vcov
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("stats", "coef", "na.fail", "vcov")
to your NAMESPACE file.
'library' or 'require' call to 'mvtnorm' which was already attached by Depends.
  Please remove these calls from your code.
bagging: no visible global function definition for 'predict'
samme: no visible global function definition for 'predict'
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
best_binomial_bandit : f: no visible global function definition for
  'dbeta'
best_binomial_bandit : f: no visible global function definition for
  'pbeta'
best_binomial_bandit: no visible global function definition for
  'integrate'
best_poisson_bandit : f: no visible global function definition for
  'dgamma'
best_poisson_bandit : f: no visible global function definition for
  'pgamma'
best_poisson_bandit: no visible global function definition for
  'integrate'
deseasonalized_trend: no visible global function definition for
  'predict'
distribution_estimate: no visible global function definition for
  'quantile'
distribution_estimate: no visible global function definition for
  'qbeta'
significance_analysis: no visible global function definition for
  'prop.test'
sim_post: no visible global function definition for 'rbeta'
summarize_metrics: no visible global function definition for 'median'
summarize_metrics: no visible global function definition for
  'prop.test'
Undefined global functions or variables:
  dbeta dgamma integrate median pbeta pgamma predict prop.test qbeta
  quantile rbeta
Consider adding
  importFrom("stats", "dbeta", "dgamma", "integrate", "median", "pbeta",
             "pgamma", "predict", "prop.test", "qbeta", "quantile",
             "rbeta")
to your NAMESPACE file.
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    libs  33.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/bapred.Rcheck/00install.out' for details.
'library' or 'require' calls to packages already attached by Depends:
  'grid' 'lattice'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'grid' 'lattice'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
barcode: no visible global function definition for 'unit'
barcode: no visible global function definition for 'grid.newpage'
barcode: no visible global function definition for 'grid.text'
barcode: no visible global function definition for 'gpar'
barcode: no visible global function definition for 'pushViewport'
barcode: no visible global function definition for 'viewport'
barcode: no visible global function definition for 'convertHeight'
barcode: no visible global function definition for 'convertWidth'
barcode: no visible global function definition for 'grid.rect'
barcode: no visible global function definition for 'popViewport'
barcode.panel: no visible global function definition for 'unit'
barcode.panel: no visible global function definition for 'hist'
barcode.panel: no visible global function definition for 'pushViewport'
barcode.panel: no visible global function definition for 'viewport'
barcode.panel: no visible global function definition for 'grid.xaxis'
barcode.panel: no visible global function definition for 'gpar'
barcode.panel: no visible global function definition for 'grid.text'
barcode.panel: no visible global function definition for 'popViewport'
barcode.panel: no visible global function definition for
  'grid.segments'
barcode.panel: no visible global function definition for 'grid.points'
Undefined global functions or variables:
  convertHeight convertWidth gpar grid.newpage grid.points grid.rect
  grid.segments grid.text grid.xaxis hist popViewport pushViewport unit
  viewport
Consider adding
  importFrom("graphics", "hist")
to your NAMESPACE file.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.8Mb
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == testthat results  ===========================================================
  OK: 104 SKIPPED: 0 FAILED: 70
  1. Failure: encode and decode on random strings (@test_base32.R#10) 
  2. Failure: encode and decode on random strings (@test_base32.R#10) 
  3. Failure: encode and decode on random strings (@test_base32.R#10) 
  4. Failure: encode and decode on random strings (@test_base32.R#10) 
  5. Failure: encode and decode on random strings (@test_base32.R#10) 
  6. Failure: encode and decode on random strings (@test_base32.R#10) 
  7. Failure: encode and decode on random strings (@test_base32.R#10) 
  8. Failure: encode and decode on random strings (@test_base32.R#10) 
  9. Failure: encode and decode on random strings (@test_base32.R#10) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == testthat results  ===========================================================
  OK: 104 SKIPPED: 0 FAILED: 70
  1. Failure: encode and decode on random strings (@test_base32.R#10) 
  2. Failure: encode and decode on random strings (@test_base32.R#10) 
  3. Failure: encode and decode on random strings (@test_base32.R#10) 
  4. Failure: encode and decode on random strings (@test_base32.R#10) 
  5. Failure: encode and decode on random strings (@test_base32.R#10) 
  6. Failure: encode and decode on random strings (@test_base32.R#10) 
  7. Failure: encode and decode on random strings (@test_base32.R#10) 
  8. Failure: encode and decode on random strings (@test_base32.R#10) 
  9. Failure: encode and decode on random strings (@test_base32.R#10) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Packages which this enhances but not available for checking:
  'doMC' 'rPython'
'library' or 'require' call to 'hwriter' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to 'parallel' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
':::' call which should be '::': 'parallel:::detectCores'
  See the note in ?`:::` about the use of this operator.
asyncRunCommands: no visible global function definition for 'runif'
mergeCsv: no visible global function definition for 'read.csv'
mergeCsv: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  read.csv runif write.csv
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
Package suggested but not available for checking: 'doMC'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/BayClone2.Rcheck/00install.out' for details.
bridge.nmix.R: no visible global function definition for 'rnorm'
draw.alpha: no visible global function definition for 'runif'
draw.alpha: no visible global function definition for 'dbeta'
draw.alpha.2: no visible global function definition for 'runif'
draw.beta.2: no visible global function definition for 'runif'
draw.sig2: no visible global function definition for 'rgamma'
draw.tau: no visible global function definition for 'rgamma'
draw.u: no visible global function definition for 'runif'
draw.w: no visible global function definition for 'runif'
draw.w: no visible global function definition for 'rgamma'
draw.w.marg: no visible global function definition for 'runif'
draw.w.marg: no visible global function definition for 'rgamma'
trace.beta: no visible global function definition for 'plot'
trace.beta: no visible global function definition for 'lines'
trace.beta: no visible global function definition for 'legend'
trace.beta.mcmc: no visible global function definition for 'sd'
trace.beta.mcmc: no visible binding for global variable 'sd'
trace.beta.mcmc: no visible global function definition for 'plot'
trace.beta.mcmc: no visible global function definition for 'title'
trace.beta.mcmc: no visible global function definition for 'hsv'
trace.beta.mcmc: no visible global function definition for 'lines'
trace.beta.mcmc: no visible global function definition for 'points'
Undefined global functions or variables:
  dbeta hsv legend lines plot points rgamma rnorm runif sd title
Consider adding
  importFrom("grDevices", "hsv")
  importFrom("graphics", "legend", "lines", "plot", "points", "title")
  importFrom("stats", "dbeta", "rgamma", "rnorm", "runif", "sd")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/bayesCL.Rcheck/00install.out' for details.
FECRT: no visible global function definition for 'pdf'
FECRT: no visible global function definition for 'hist'
FECRT: no visible global function definition for 'abline'
FECRT: no visible global function definition for 'dev.off'
FECRT.analysis: no visible global function definition for 'pdf'
FECRT.analysis: no visible global function definition for 'hist'
FECRT.analysis: no visible global function definition for 'abline'
FECRT.analysis: no visible global function definition for 'dev.off'
fecrt: no visible global function definition for 'pdf'
fecrt: no visible global function definition for 'hist'
fecrt: no visible global function definition for 'abline'
fecrt: no visible global function definition for 'dev.off'
fecrt.analysis: no visible global function definition for 'pdf'
fecrt.analysis: no visible global function definition for 'hist'
fecrt.analysis: no visible global function definition for 'abline'
fecrt.analysis: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  abline dev.off hist pdf
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "hist")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/bayesDem.Rcheck/00install.out' for details.
BMAnimalTrack: no visible global function definition for 'nlm'
BMAnimalTrack: no visible global function definition for 'qnorm'
dataSim: no visible global function definition for 'rnorm'
rBBridge: no visible global function definition for 'rnorm'
rBMotion: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  nlm qnorm rnorm
Consider adding
  importFrom("stats", "nlm", "qnorm", "rnorm")
to your NAMESPACE file.
BayesianbetaregEst: no visible global function definition for 'runif'
BayesianbetaregEst: no visible global function definition for 'as.ts'
BayesianbetaregEst: no visible global function definition for 'dev.new'
BayesianbetaregEst: no visible global function definition for 'ts.plot'
BayesianbetaregEst: no visible binding for global variable 'sd'
BayesianbetaregEst: no visible global function definition for
  'quantile'
betaresiduals : lt: no visible global function definition for 'dbeta'
diagnostics: no visible global function definition for 'plot'
diagnostics: no visible global function definition for 'abline'
diagnostics: no visible global function definition for 'qqnorm'
diagnostics: no visible global function definition for 'qqline'
dpostb: no visible global function definition for 'dbeta'
dpostg: no visible global function definition for 'dbeta'
plotresiduals: no visible global function definition for 'plot'
print.summary.Bayesianbetareg: no visible global function definition
  for 'printCoefmat'
summary.Bayesianbetareg: no visible global function definition for
  'coef'
Undefined global functions or variables:
  abline as.ts coef dbeta dev.new plot printCoefmat qqline qqnorm
  quantile runif sd ts.plot
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "plot")
  importFrom("stats", "as.ts", "coef", "dbeta", "printCoefmat", "qqline",
             "qqnorm", "quantile", "runif", "sd", "ts.plot")
to your NAMESPACE file.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Depends: includes the non-default packages:
  'gplots' 'xtable' 'mnormt' 'MASS' 'bayesm' 'boa' 'e1071' 'gtools'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  'MASS' 'bayesm' 'boa' 'e1071' 'gplots' 'gtools' 'mnormt' 'xtable'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   4.1Mb
noninform_prior : a : f1: no visible global function definition for
  'pbeta'
noninform_prior : a : f1: no visible global function definition for
  'dbeta'
noninform_prior : a: no visible global function definition for
  'integrate'
noninform_prior: no visible global function definition for 'rbeta'
noninform_prior: no visible global function definition for 'optim'
postNullFun : b : f1: no visible global function definition for 'pbeta'
postNullFun : b : f1: no visible global function definition for 'dbeta'
postNullFun : b: no visible global function definition for 'integrate'
prior_prob : a : f1: no visible global function definition for 'pbeta'
prior_prob : a : f1: no visible global function definition for 'dbeta'
prior_prob : a: no visible global function definition for 'integrate'
Undefined global functions or variables:
  dbeta integrate optim pbeta rbeta
Consider adding
  importFrom("stats", "dbeta", "integrate", "optim", "pbeta", "rbeta")
to your NAMESPACE file.
MHratioPopPref: no visible global function definition for 'runif'
MratioPopMult: no visible global function definition for 'dunif'
MratioPopMult: no visible global function definition for 'runif'
bayesPref: no visible global function definition for 'runif'
calcP: no visible global function definition for 'dunif'
calcP: no visible global function definition for 'dmultinom'
calcdic: no visible global function definition for 'median'
calcdic: no visible binding for global variable 'median'
calcdic: no visible global function definition for 'dmultinom'
calcdicExtern: no visible global function definition for 'median'
calcdicExtern: no visible global function definition for 'dmultinom'
calcdicExtern: no visible binding for global variable 'median'
credibleIntervals: no visible global function definition for 'quantile'
prefPlot: no visible global function definition for 'postscript'
prefPlot: no visible global function definition for 'plot'
prefPlot: no visible global function definition for 'lines'
prefPlot: no visible global function definition for 'density'
prefPlot: no visible global function definition for 'median'
prefPlot: no visible global function definition for 'legend'
prefPlot: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  density dev.off dmultinom dunif legend lines median plot postscript
  quantile runif
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "density", "dmultinom", "dunif", "median",
             "quantile", "runif")
to your NAMESPACE file.
BayesFH: no visible global function definition for 'rnorm'
BayesFH: no visible global function definition for 'rgamma'
BayesSAE: no visible global function definition for 'runif'
BayesSAE: no visible global function definition for 'as.formula'
BayesSAE: no visible global function definition for 'terms'
BayesSAE: no visible global function definition for 'delete.response'
BayesSAE: no visible global function definition for 'model.response'
BayesSAE: no visible global function definition for 'model.matrix'
BayesSAE: no visible global function definition for 'coef'
BayesSAE: no visible global function definition for 'lm'
BayesSFH: no visible global function definition for 'rnorm'
BayesSFH: no visible global function definition for 'runif'
BayesSFH: no visible global function definition for 'rgamma'
BayesSYC: no visible global function definition for 'rnorm'
BayesSYC: no visible global function definition for 'runif'
BayesSYC: no visible global function definition for 'rgamma'
BayesUFH: no visible global function definition for 'rnorm'
BayesUFH: no visible global function definition for 'rgamma'
BayesUYC: no visible global function definition for 'rnorm'
BayesUYC: no visible global function definition for 'rgamma'
BayesYC: no visible global function definition for 'rnorm'
BayesYC: no visible global function definition for 'rgamma'
model.compare: no visible global function definition for 'dnorm'
print.summary.BayesSAE: no visible global function definition for
  'printCoefmat'
replication: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  as.formula coef delete.response dnorm lm model.matrix model.response
  printCoefmat rgamma rnorm runif terms
Consider adding
  importFrom("stats", "as.formula", "coef", "delete.response", "dnorm",
             "lm", "model.matrix", "model.response", "printCoefmat",
             "rgamma", "rnorm", "runif", "terms")
to your NAMESPACE file.
Found the following Makefile(s) without a final LF:
  src/Makevars
Some 'make' programs ignore lines not ending in LF.
File 'BayesSAE/libs/i386/BayesSAE.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'HBsae.o'
File 'BayesSAE/libs/x64/BayesSAE.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'HBsae.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
mlike.alt.g.AR: no visible global function definition for 'integrate'
mlike.alt.gtheta.AR: no visible global function definition for 'dbeta'
mlike.null.AR: no visible global function definition for 'dbeta'
multilevel.Gibbs.AR: no visible global function definition for
  'txtProgressBar'
multilevel.Gibbs.AR : pbFun: no visible global function definition for
  'setTxtProgressBar'
trendtest.Gibbs.AR: no visible global function definition for
  'txtProgressBar'
trendtest.Gibbs.AR : pbFun: no visible global function definition for
  'setTxtProgressBar'
trendtest.Gibbs.AR: no visible global function definition for 'dcauchy'
trendtest.Gibbs.AR: no visible global function definition for 'pcauchy'
trendtest.MC.AR: no visible global function definition for
  'txtProgressBar'
trendtest.MC.AR : pbFun: no visible global function definition for
  'setTxtProgressBar'
trendtest.nullMargLikeAR: no visible global function definition for
  'integrate'
ttest.Gibbs.AR: no visible global function definition for
  'txtProgressBar'
ttest.Gibbs.AR : pbFun: no visible global function definition for
  'setTxtProgressBar'
ttest.Gibbs.AR: no visible global function definition for 'dcauchy'
ttest.Gibbs.AR: no visible global function definition for 'pcauchy'
ttest.MCGQ.AR: no visible global function definition for 'integrate'
Undefined global functions or variables:
  dbeta dcauchy integrate pcauchy setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "dbeta", "dcauchy", "integrate", "pcauchy")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'MASS' 'combinat' 'gplots' 'mnormt'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bayes.regress: no visible binding for global variable 'var'
bayesregressB1S1: no visible global function definition for 'rgamma'
bayesregressB1S2: no visible global function definition for 'rgamma'
bayesregressB2S1: no visible global function definition for 'rgamma'
bayesregressB2S2: no visible global function definition for 'rgamma'
bayesregressB3S1: no visible global function definition for 'rWishart'
bayesregressB3S1: no visible global function definition for 'rgamma'
bayesregressB3S2: no visible global function definition for 'rWishart'
bayesregressB3S2: no visible global function definition for 'rgamma'
Undefined global functions or variables:
  rWishart rgamma var
Consider adding
  importFrom("stats", "rWishart", "rgamma", "var")
to your NAMESPACE file.
Depends: includes the non-default packages:
  'lme4' 'MASS' 'VGAM' 'mvtnorm' 'matrixcalc' 'coda'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/Bayesthresh.Rcheck/00install.out' for details.
validate: no visible binding for global variable 'qnorm'
validate: no visible global function definition for 'pchisq'
validate: no visible global function definition for 'qnorm'
validate: no visible global function definition for 'plot'
validate: no visible global function definition for 'axis'
validate: no visible global function definition for 'points'
validate: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline axis pchisq plot points qnorm
Consider adding
  importFrom("graphics", "abline", "axis", "plot", "points")
  importFrom("stats", "pchisq", "qnorm")
to your NAMESPACE file.
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
Found the following file(s) containing GNU extensions:
  src/Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section 'Writing portable packages' in
the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: 'boa:::boa.getparms'
  See the note in ?`:::` about the use of this operator.
File 'BayHap/libs/i386/BayHap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'mcmc.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'mcmc.o'
File 'BayHap/libs/x64/BayHap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'mcmc.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'mcmc.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'library' or 'require' call to 'coda' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
'library' or 'require' call to 'mvnmle' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
BilogData: no visible global function definition for 'write.table'
CohensD.rawData: no visible global function definition for 'var'
EtaSq: no visible global function definition for 'summary.aov'
HedgesG.rawData: no visible global function definition for 'var'
LittleMCAR: no visible global function definition for 'mlest'
LittleMCAR: no visible global function definition for 'pchisq'
PseudoR2: no visible global function definition for 'predict'
Undefined global functions or variables:
  mlest pchisq predict summary.aov var write.table
Consider adding
  importFrom("stats", "pchisq", "predict", "summary.aov", "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'fields' 'poibin' 'rjags'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
BMR.plot: no visible global function definition for 'heat.colors'
BMR.plot: no visible global function definition for 'image.plot'
BMR.plot: no visible global function definition for 'title'
BMR.plot: no visible global function definition for 'mtext'
BMR.plot: no visible global function definition for 'par'
baysic.data: no visible global function definition for 'layout'
baysic.data: no visible global function definition for 'barplot'
baysic.data: no visible global function definition for 'rainbow'
baysic.fit: no visible global function definition for 'jags.model'
baysic.fit: no visible global function definition for 'update'
baysic.fit: no visible global function definition for 'coda.samples'
baysic.test: no visible global function definition for 'ppois'
baysic.test : <anonymous>: no visible global function definition for
  'ppoibin'
baysic.test: no visible global function definition for 'pbinom'
fuzzy.FDR.approx: no visible global function definition for 'p.adjust'
fuzzy.FDR.approx: no visible global function definition for 'runif'
Undefined global functions or variables:
  barplot coda.samples heat.colors image.plot jags.model layout mtext
  p.adjust par pbinom ppoibin ppois rainbow runif title update
Consider adding
  importFrom("grDevices", "heat.colors", "rainbow")
  importFrom("graphics", "barplot", "layout", "mtext", "par", "title")
  importFrom("stats", "p.adjust", "pbinom", "ppois", "runif", "update")
to your NAMESPACE file.
BAYSTAR: no visible global function definition for 'median'
BAYSTAR: no visible global function definition for 'ar'
BAYSTAR: no visible global function definition for 'quantile'
BAYSTAR: no visible global function definition for 'dev.new'
BAYSTAR: no visible global function definition for 'ts.plot'
BAYSTAR: no visible global function definition for 'title'
BAYSTAR: no visible global function definition for 'par'
BAYSTAR: no visible global function definition for 'plot.ts'
BAYSTAR: no visible global function definition for 'lines'
BAYSTAR: no visible global function definition for 'acf'
TAR.lagd: no visible global function definition for 'runif'
TAR.sigma: no visible global function definition for 'rgamma'
TAR.simu: no visible global function definition for 'rnorm'
TAR.summary: no visible global function definition for 'quantile'
TAR.summary: no visible global function definition for 'sd'
TAR.thres: no visible global function definition for 'rnorm'
TAR.thres: no visible global function definition for 'runif'
Undefined global functions or variables:
  acf ar dev.new lines median par plot.ts quantile rgamma rnorm runif
  sd title ts.plot
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "lines", "par", "title")
  importFrom("stats", "acf", "ar", "median", "plot.ts", "quantile",
             "rgamma", "rnorm", "runif", "sd", "ts.plot")
to your NAMESPACE file.
Package in Depends field not imported from: 'splines'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
LaplaceMetropolis_admkr: no visible binding for global variable
  'median'
LaplaceMetropolis_admkr: no visible global function definition for
  'mad'
LaplaceMetropolis_gaussian: no visible binding for global variable
  'median'
LaplaceMetropolis_gaussian: no visible global function definition for
  'mad'
cost_admkr: no visible global function definition for 'sd'
cov_chol: no visible global function definition for 'qchisq'
cov_chol_admkr: no visible global function definition for 'qchisq'
gibbs_admkr_erro: no visible global function definition for 'rnorm'
gibbs_admkr_erro: no visible global function definition for 'runif'
gibbs_admkr_nw: no visible global function definition for 'qnorm'
gibbs_admkr_nw: no visible global function definition for 'rnorm'
gibbs_admkr_nw: no visible global function definition for 'runif'
loglikelihood_admkr: no visible global function definition for 'sd'
margin_like_admkr: no visible global function definition for 'sd'
np_gibbs: no visible global function definition for 'qnorm'
np_gibbs: no visible global function definition for 'rnorm'
np_gibbs: no visible global function definition for 'runif'
np_gibbs: no visible global function definition for 'rgamma'
Undefined global functions or variables:
  mad median qchisq qnorm rgamma rnorm runif sd
Consider adding
  importFrom("stats", "mad", "median", "qchisq", "qnorm", "rgamma",
             "rnorm", "runif", "sd")
to your NAMESPACE file.
bbmm.contour: no visible global function definition for 'na.omit'
bbmm.contour: no visible global function definition for 'optimize'
bbmm.contour: no visible global function definition for 'contour'
bbmm.contour: no visible global function definition for 'points'
bbmm.contour: no visible global function definition for 'lines'
brownian.bridge: no visible global function definition for 'sd'
brownian.motion.variance: no visible global function definition for
  'optimize'
Undefined global functions or variables:
  contour lines na.omit optimize points sd
Consider adding
  importFrom("graphics", "contour", "lines", "points")
  importFrom("stats", "na.omit", "optimize", "sd")
to your NAMESPACE file.
bbo: no visible global function definition for 'runif'
bbo: no visible global function definition for 'tail'
plot.bbo: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot runif tail
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
  importFrom("utils", "tail")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'HI' 'lme4' 'locfit' 'secr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
BBRecap: no visible global function definition for 'optimize'
BBRecap: no visible global function definition for 'arms'
BBRecap: no visible global function definition for 'median'
BBRecap : HPD.interval: no visible global function definition for
  'density'
BBRecap : HPD.interval: no visible global function definition for
  'quantile'
BBRecap.custom.part: no visible global function definition for
  'optimize'
LBRecap: no visible global function definition for 'findbars'
LBRecap: no visible global function definition for 'as.formula'
LBRecap: no visible global function definition for 'glm'
LBRecap: no visible global function definition for 'binomial'
LBRecap: no visible global function definition for 'glmer'
LBRecap: no visible global function definition for 'logLik'
LBRecap: no visible global function definition for 'coef'
LBRecap: no visible global function definition for 'na.omit'
LBRecap: no visible global function definition for 'fixef'
LBRecap: no visible global function definition for 'ranef'
LBRecap: no visible global function definition for 'qnorm'
LBRecap: no visible global function definition for 'plot'
LBRecap: no visible global function definition for 'points'
LBRecap: no visible global function definition for 'axis'
LBRecap: no visible global function definition for 'abline'
LBRecap.custom.part: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  abline arms as.formula axis binomial coef density findbars fixef glm
  glmer logLik median na.omit optimize plot points qnorm quantile ranef
Consider adding
  importFrom("graphics", "abline", "axis", "plot", "points")
  importFrom("stats", "as.formula", "binomial", "coef", "density", "glm",
             "logLik", "median", "na.omit", "optimize", "qnorm",
             "quantile")
to your NAMESPACE file.
'library' or 'require' call to 'rgl' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
pairs.bce : panel.cor: no visible global function definition for 'text'
pairs.bce : panel.cor: no visible global function definition for 'cor'
pairs.bce : panel.hist: no visible global function definition for 'par'
pairs.bce : panel.hist: no visible global function definition for
  'hist'
pairs.bce : panel.hist: no visible global function definition for
  'rect'
pairs.bce: no visible global function definition for 'pairs'
panel.cor: no visible global function definition for 'par'
panel.cor: no visible global function definition for 'cor'
panel.cor: no visible global function definition for 'strwidth'
panel.cor: no visible global function definition for 'text'
rdirichlet2: no visible global function definition for 'rgamma'
summary.bce: no visible global function definition for 'cov'
summary.bce: no visible binding for global variable 'sd'
summary.bce: no visible binding for global variable 'quantile'
Undefined global functions or variables:
  cor cov hist pairs par quantile rect rgamma sd strwidth text
Consider adding
  importFrom("graphics", "hist", "pairs", "par", "rect", "strwidth",
             "text")
  importFrom("stats", "cor", "cov", "quantile", "rgamma", "sd")
to your NAMESPACE file.
Packages suggested but not available for checking: 'bcmaps.rdata' 'doMC'
check.summary: no visible global function definition for 'sd'
risk.summary: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  sd write.csv
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
plot.cvsvd: no visible binding for global variable 'sd'
plot.cvsvd: no visible global function definition for 'plot'
plot.cvsvd: no visible global function definition for 'lines'
plot.cvsvd: no visible global function definition for 'segments'
plot.cvsvd: no visible global function definition for 'points'
print.cvsvd: no visible binding for global variable 'sd'
summary.cvsvd: no visible binding for global variable 'sd'
Undefined global functions or variables:
  lines plot points sd segments
Consider adding
  importFrom("graphics", "lines", "plot", "points", "segments")
  importFrom("stats", "sd")
to your NAMESPACE file.
mise: no visible global function definition for 'integrate'
density,BrVitale : density.vitale : <anonymous>: no visible global
  function definition for 'dbeta'
density,Chen99Kernel : <anonymous>: no visible global function
  definition for 'dbeta'
density,HirukawaJLNKernel : <anonymous>: no visible global function
  definition for 'dbeta'
density,MicroBetaChen99Kernel : <anonymous>: no visible global function
  definition for 'dbeta'
density,Vitale : <anonymous>: no visible global function definition for
  'dbeta'
distribution,BernsteinPolynomials : <anonymous>: no visible global
  function definition for 'integrate'
distribution,KernelDensity : <anonymous>: no visible global function
  definition for 'integrate'
print,BoundedDensity: no visible global function definition for 'str'
print,KernelDensity: no visible global function definition for 'str'
rsample,BoundedDensity: no visible global function definition for
  'runif'
setNormalizationConst,MacroBetaChen99Kernel: no visible global function
  definition for 'integrate'
setNormalizationConst,MacroBetaHirukawaTSKernel: no visible global
  function definition for 'integrate'
setNormalizationConstant,MacroBetaHirukawaJLNKernel: no visible global
  function definition for 'integrate'
setNormalizationConstants,MicroBetaChen99Kernel :
  density.kernelFunction: no visible global function definition for
  'dbeta'
setNormalizationConstants,MicroBetaChen99Kernel : <anonymous>: no
  visible global function definition for 'integrate'
show,BoundedDensity: no visible global function definition for 'str'
show,KernelDensity: no visible global function definition for 'str'
Undefined global functions or variables:
  dbeta integrate runif str
Consider adding
  importFrom("stats", "dbeta", "integrate", "runif")
  importFrom("utils", "str")
to your NAMESPACE file.
BDtest: no visible global function definition for 'binom.test'
CIlnpv: no visible global function definition for 'qnorm'
CIlnpvak: no visible global function definition for 'qnorm'
CIlppv: no visible global function definition for 'qnorm'
CIlppvak: no visible global function definition for 'qnorm'
CIpvBI: no visible global function definition for 'rbeta'
CIpvBI: no visible global function definition for 'quantile'
CIpvBI: no visible global function definition for 'median'
CIpvBII: no visible global function definition for 'rbeta'
CIpvBII: no visible global function definition for 'quantile'
CIpvBII: no visible global function definition for 'median'
nNPV: no visible global function definition for 'qnorm'
nPPV: no visible global function definition for 'qnorm'
plotnPV: no visible global function definition for 'na.omit'
plotnPV: no visible global function definition for 'lines'
plotnPV2 : defplot: no visible global function definition for 'plot'
plotnPV2 : defplot: no visible global function definition for 'lines'
plotnPV2: no visible global function definition for 'par'
plotnPV2: no visible global function definition for 'layout'
simPV: no visible global function definition for 'rbinom'
simPV: no visible global function definition for 'quantile'
Undefined global functions or variables:
  binom.test layout lines median na.omit par plot qnorm quantile rbeta
  rbinom
Consider adding
  importFrom("graphics", "layout", "lines", "par", "plot")
  importFrom("stats", "binom.test", "median", "na.omit", "qnorm",
             "quantile", "rbeta", "rbinom")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'RColorBrewer' 'beadarray'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
beadtypeFilter: no visible global function definition for 'na.omit'
beadtypeFilter: no visible global function definition for 'exprs'
beadtypeFilter: no visible global function definition for 'se.exprs'
beadtypeFilter: no visible global function definition for 'beadNum'
beadtypeFilter: no visible global function definition for 'fData'
emCDF: no visible global function definition for 'brewer.pal'
emCDF: no visible global function definition for 'plot'
emCDF: no visible global function definition for 'ecdf'
emCDF: no visible global function definition for 'legend'
emCDF: no visible global function definition for 'lines'
emCDF: no visible global function definition for 'text'
emCDF: no visible global function definition for 'reshape'
iccFun : <anonymous>: no visible global function definition for
  'quantile'
varianceplot: no visible global function definition for 'reshape'
varianceplot: no visible global function definition for 'plot'
varianceplot: no visible global function definition for 'points'
varianceplot: no visible global function definition for 'legend'
Undefined global functions or variables:
  beadNum brewer.pal ecdf exprs fData legend lines na.omit plot points
  quantile reshape se.exprs text
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points", "text")
  importFrom("stats", "ecdf", "na.omit", "quantile", "reshape")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/beadarrayMSV.Rcheck/00install.out' for details.
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/math/special_functions/detail/bernoulli_details.hpp:128:36: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/math/special_functions/detail/bernoulli_details.hpp:152:9: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.5/beanz.Rcheck/00install.out' for details.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
beep: no visible global function definition for 'download.file'
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
'library' or 'require' call to 'multcomp' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
beqi2: no visible global function definition for 'na.omit'
beqi2: no visible global function definition for 'browseURL'
readAMBI: no visible global function definition for 'read.csv'
readBEQI: no visible global function definition for 'read.csv'
readERF: no visible global function definition for 'read.csv'
readTWN: no visible global function definition for 'read.csv'
read_ITI_FIBI: no visible global function definition for 'read.csv'
Undefined global functions or variables:
  browseURL na.omit read.csv
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "browseURL", "read.csv")
to your NAMESPACE file.
'library' or 'require' call to 'MASS' which was already attached by Depends.
  Please remove these calls from your code.
ber: no visible global function definition for 'model.matrix'
ber: no visible global function definition for 'as.formula'
ber_bg: no visible global function definition for 'model.matrix'
ber_bg: no visible global function definition for 'as.formula'
combat_np: no visible global function definition for 'as.formula'
combat_np: no visible global function definition for 'model.matrix'
combat_p: no visible global function definition for 'as.formula'
combat_p: no visible global function definition for 'model.matrix'
combat_p: no visible binding for global variable 'var'
combat_p: no visible global function definition for 'par'
combat_p: no visible global function definition for 'density'
combat_p: no visible global function definition for 'plot'
combat_p: no visible global function definition for 'lines'
combat_p: no visible global function definition for 'dnorm'
combat_p: no visible global function definition for 'qqnorm'
combat_p: no visible global function definition for 'qqline'
combat_p: no visible global function definition for 'rgamma'
combat_p: no visible global function definition for 'qqplot'
combat_p: no visible global function definition for 'title'
mean_centering: no visible global function definition for
  'model.matrix'
standardization: no visible global function definition for
  'model.matrix'
Undefined global functions or variables:
  as.formula density dnorm lines model.matrix par plot qqline qqnorm
  qqplot rgamma title var
Consider adding
  importFrom("graphics", "lines", "par", "plot", "title")
  importFrom("stats", "as.formula", "density", "dnorm", "model.matrix",
             "qqline", "qqnorm", "qqplot", "rgamma", "var")
to your NAMESPACE file.
Package in Depends field not imported from: 'Rmpfr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bI: no visible global function definition for 'is'
bI: no visible global function definition for 'mpfr'
bI: no visible binding for global variable 'slot'
bI: no visible global function definition for 'as'
Undefined global functions or variables:
  as is mpfr slot
Consider adding
  importFrom("methods", "as", "is", "slot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
betafam: no visible global function definition for 'pnorm'
betafam: no visible global function definition for 'pchisq'
betafam: no visible global function definition for 'lm'
betafam: no visible global function definition for 'coefficients'
betafam: no visible global function definition for 'glm.fit'
betafam: no visible global function definition for 'gaussian'
betafam: no visible global function definition for 'glmnet'
Undefined global functions or variables:
  coefficients gaussian glm.fit glmnet lm pchisq pnorm
Consider adding
  importFrom("stats", "coefficients", "gaussian", "glm.fit", "lm",
             "pchisq", "pnorm")
to your NAMESPACE file.
'library' or 'require' call to 'vegan' which was already attached by Depends.
  Please remove these calls from your code.
S3 methods shown with full name in documentation object 'cca.pertables':
  'cca.pertables'

S3 methods shown with full name in documentation object 'rda.pertables':
  'rda.pertables'

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.
betas.lm: no visible binding for global variable 'sd'
betas.lm: no visible global function definition for 'sd'
my.wtd.var: no visible global function definition for 'var'
Undefined global functions or variables:
  sd var
Consider adding
  importFrom("stats", "sd", "var")
to your NAMESPACE file.
bezierArcLength: no visible global function definition for 'sd'
bezierArcLength: no visible global function definition for 'lm'
bezierCurveFit: no visible global function definition for 'nls'
bezierCurveFit: no visible global function definition for 'nls.control'
bezierCurveFit: no visible global function definition for 'lm'
bezierCurveFit: no visible global function definition for 'na.omit'
pointsOnBezier: no visible global function definition for 'optim'
Undefined global functions or variables:
  lm na.omit nls nls.control optim sd
Consider adding
  importFrom("stats", "lm", "na.omit", "nls", "nls.control", "optim",
             "sd")
to your NAMESPACE file.
binommh.default : log_lik: no visible global function definition for
  'dbinom'
binommh.default: no visible global function definition for 'dbinom'
binommh.default: no visible global function definition for 'runif'
binommh.formula: no visible global function definition for
  'model.frame'
binommh.formula: no visible global function definition for
  'model.matrix'
binommh.formula: no visible global function definition for
  'model.response'
expmh.default : log_lik: no visible global function definition for
  'dexp'
expmh.default: no visible global function definition for 'dexp'
expmh.default: no visible global function definition for 'runif'
expmh.formula: no visible global function definition for 'model.frame'
expmh.formula: no visible global function definition for 'model.matrix'
expmh.formula: no visible global function definition for
  'model.response'
poissmh.default : log_lik: no visible global function definition for
  'dpois'
poissmh.default: no visible global function definition for 'dpois'
poissmh.default: no visible global function definition for 'runif'
poissmh.formula: no visible global function definition for
  'model.frame'
poissmh.formula: no visible global function definition for
  'model.matrix'
poissmh.formula: no visible global function definition for
  'model.response'
Undefined global functions or variables:
  dbinom dexp dpois model.frame model.matrix model.response runif
Consider adding
  importFrom("stats", "dbinom", "dexp", "dpois", "model.frame",
             "model.matrix", "model.response", "runif")
to your NAMESPACE file.
block.gibbs: no visible global function definition for 'rmultinom'
rdirichlet: no visible global function definition for 'rgamma'
Undefined global functions or variables:
  rgamma rmultinom
Consider adding
  importFrom("stats", "rgamma", "rmultinom")
to your NAMESPACE file.
global: no visible global function definition for 'par'
global: no visible global function definition for 'runif'
global: no visible global function definition for 'cov'
mymcmc: no visible global function definition for 'par'
mymcmc: no visible global function definition for 'rnorm'
mymcmc: no visible global function definition for 'runif'
mymcmc: no visible global function definition for 'cov'
mymcmc: no visible global function definition for 'lines'
plkhci: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  cov lines par qchisq rnorm runif
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "cov", "qchisq", "rnorm", "runif")
to your NAMESPACE file.
installed size is 139.8Mb
  sub-directories of 1Mb or more:
    include  138.8Mb
Package in Depends field not imported from: 'betareg'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bias: no visible global function definition for 'predict'
bias: no visible global function definition for 'pnorm'
bias: no visible global function definition for 'model.matrix'
Undefined global functions or variables:
  model.matrix pnorm predict
Consider adding
  importFrom("stats", "model.matrix", "pnorm", "predict")
to your NAMESPACE file.
BiDimRegression: no visible global function definition for 'lm'
BiDimRegression: no visible global function definition for 'pf'
print.BiDimRegression: no visible global function definition for
  'printCoefmat'
print.summary.BiDimRegression: no visible global function definition
  for 'printCoefmat'
Undefined global functions or variables:
  lm pf printCoefmat
Consider adding
  importFrom("stats", "lm", "pf", "printCoefmat")
to your NAMESPACE file.
'library' or 'require' call to 'mvtnorm' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'Rcpp' 'mvtnorm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File 'bifactorial/libs/i386/bifactorial.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'misc.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'krit.o', 'pv.o'
File 'bifactorial/libs/x64/bifactorial.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'misc.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'krit.o', 'pv.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
anon_matrix: no visible global function definition for
  'filebacked.big.matrix'
anon_matrix: no visible global function definition for 'capture.output'
finalize_anon_matrix: no visible global function definition for
  'capture.output'
Undefined global functions or variables:
  capture.output filebacked.big.matrix
Consider adding
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'DBI' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bigglm.RODBC: no visible global function definition for 'odbcQuery'
bigglm.RODBC : chunk: no visible global function definition for
  'odbcQuery'
bigglm.RODBC : chunk: no visible global function definition for
  'sqlGetResults'
bigglm,ANY-DBIConnection: no visible global function definition for
  'dbSendQuery'
bigglm,ANY-DBIConnection: no visible global function definition for
  'dbClearResult'
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for 'dbClearResult'
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for 'dbSendQuery'
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for 'fetch'
Undefined global functions or variables:
  dbClearResult dbSendQuery fetch odbcQuery sqlGetResults
Package which this enhances but not available for checking: 'synchronicity'
Package unavailable to check Rd xrefs: 'synchronicity'
quickModel: no visible global function definition for 'tail'
quickSource: no visible global function definition for 'write.table'
Undefined global functions or variables:
  tail write.table
Consider adding
  importFrom("utils", "tail", "write.table")
to your NAMESPACE file.
bigRR: no visible global function definition for 'gaussian'
bigRR.default: no visible global function definition for 'gaussian'
bigRR.formula: no visible global function definition for 'gaussian'
bigRR.formula: no visible global function definition for 'as.formula'
bigRR.formula: no visible global function definition for 'model.frame'
bigRR.formula: no visible global function definition for 'model.matrix'
bigRR.formula: no visible global function definition for
  'model.response'
bigRR_update: no visible global function definition for 'gaussian'
hugeRR: no visible global function definition for 'gaussian'
hugeRR_update: no visible global function definition for 'gaussian'
plot.bigRR: no visible global function definition for 'par'
plot.bigRR: no visible global function definition for 'plot'
plot.bigRR: no visible global function definition for 'rgb'
Undefined global functions or variables:
  as.formula gaussian model.frame model.matrix model.response par plot
  rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "par", "plot")
  importFrom("stats", "as.formula", "gaussian", "model.frame",
             "model.matrix", "model.response")
to your NAMESPACE file.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      2.6Mb
Packages in Depends field not imported from:
  'gbm' 'glmnet' 'randomForest' 'tree'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
LDCAEst: no visible global function definition for 'glmnet'
cv.LDCA: no visible global function definition for 'cv.glmnet'
predict.LDCA: no visible global function definition for 'predict'
predict.cv.LDCA: no visible global function definition for 'predict'
predict.tsp.gbm: no visible global function definition for 'predict'
predict.tsp.randomForest: no visible global function definition for
  'predict'
predict.tsp.tree: no visible global function definition for 'predict'
tsp.gbm: no visible global function definition for 'gbm.fit'
tsp.randomForest: no visible global function definition for
  'randomForest'
tsp.tree: no visible global function definition for 'tree.control'
tsp.tree: no visible global function definition for 'tree'
Undefined global functions or variables:
  cv.glmnet gbm.fit glmnet predict randomForest tree tree.control
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   3.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
plot,bild-missing: no visible global function definition for
  'dev.interactive'
plot,bild-missing: no visible global function definition for
  'devAskNewPage'
plot,bild-missing: no visible global function definition for
  'extendrange'
Undefined global functions or variables:
  dev.interactive devAskNewPage extendrange
Consider adding
  importFrom("grDevices", "dev.interactive", "devAskNewPage",
             "extendrange")
to your NAMESPACE file.
chisq.sim.factory : chisq.sim.func: no visible global function
  definition for 'chisq.test'
rmultnom: no visible global function definition for 'runif'
Undefined global functions or variables:
  chisq.test runif
Consider adding
  importFrom("stats", "chisq.test", "runif")
to your NAMESPACE file.
commonprob2sigma: no visible global function definition for 'approxfun'
rmvbin: no visible global function definition for 'qnorm'
simul.commonprob: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  approxfun qnorm
Consider adding
  importFrom("stats", "approxfun", "qnorm")
to your NAMESPACE file.
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
             stop("Function ", name, " not found in environment ", environmentName(env), 
                 ".", call. = FALSE)
         mock(name = name, env = env, new = eval(new_values[[qual_name]], eval_env, eval_env))
     })
  4: FUN(X[[i]], ...)
  5: stop("Can't mock functions in base packages (", pkg_name, ")", call. = FALSE)
  
  == testthat results  ===========================================================
  OK: 26 SKIPPED: 0 FAILED: 3
  1. Error: canDownloadFiles (@test-download_files.R#9) 
  2. Error: canReturnEmptyDFWhenEmptyDownloadFiles (@test-download_files.R#27) 
  3. Error: canProcessYaml (@test-process_yaml.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Mtoquant: no visible global function definition for 'qnorm'
NHS: no visible global function definition for 'qnorm'
NHS : WilsonScore: no visible global function definition for 'qnorm'
binMto.formula: no visible global function definition for 'model.frame'
plot.binMto: no visible global function definition for 'plot.new'
plot.binMto: no visible global function definition for 'par'
plot.binMto: no visible global function definition for 'strwidth'
plot.binMto: no visible global function definition for 'axis'
plot.binMto: no visible global function definition for 'box'
plot.binMto: no visible global function definition for 'segments'
plot.binMto: no visible global function definition for 'points'
plot.binMto: no visible global function definition for 'abline'
simPowerI: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  abline axis box model.frame par plot.new points qnorm rbinom segments
  strwidth
Consider adding
  importFrom("graphics", "abline", "axis", "box", "par", "plot.new",
             "points", "segments", "strwidth")
  importFrom("stats", "model.frame", "qnorm", "rbinom")
to your NAMESPACE file.
bin_ps: no visible global function definition for 'runif'
bin_ps: no visible global function definition for 'dbinom'
draw_i: no visible global function definition for 'runif'
Undefined global functions or variables:
  dbinom runif
Consider adding
  importFrom("stats", "dbinom", "runif")
to your NAMESPACE file.
IndivdRUMIndMH: no visible global function definition for
  'flush.console'
dRUMAuxMix: no visible global function definition for 'flush.console'
dRUMHAM: no visible global function definition for 'flush.console'
dRUMIndMH: no visible global function definition for 'flush.console'
print.binomlogit: no visible global function definition for 'is'
summary.binomlogit: no visible global function definition for 'is'
Undefined global functions or variables:
  flush.console is
Consider adding
  importFrom("methods", "is")
  importFrom("utils", "flush.console")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' calls in package code:
  'ggplot2' 'lattice' 'polynom' 'tcltk'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
bins.quantiles: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
Running examples in 'binst-Ex.R' failed
The error most likely occurred in:

> ### Name: create_breaks
> ### Title: A convenience functon for creating breaks with various methods.
> ### Aliases: create_breaks
> 
> ### ** Examples
> 
> kmeans_breaks <- create_breaks(1:10)
> create_bins(1:10, kmeans_breaks)
 [1] 1 1 1 2 2 2 3 3 3 3
> 
> # passing the k means parameter "centers" = 4
> kmeans_breaks <- create_breaks(1:10, list(centers=4))
> create_bins(1:10, kmeans_breaks)
 [1] 1 1 1 1 2 2 2 3 3 3
> 
> entropy_breaks <- create_breaks(1:10, rep(c(1,2), each = 5), method="entropy")
> create_bins(1:10, entropy_breaks)
 [1] 1 1 1 1 1 2 2 2 2 2
> 
> dt_breaks <- create_breaks(iris$Sepal.Length, iris$Species, method="dt")
Error in extree_data(formula = y ~ x, data = list(x = c(5.1, 4.9, 4.7,  : 
  could not find function "extree_data"
Calls: create_breaks ... create_dtbreaks -> do.call -> <Anonymous> -> eval -> eval
Execution halted
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
     2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
     2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 
     3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 
     3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L)), row.names = c(NA, -150L), class = "data.frame"))
  10: eval(mf, parent.frame())
  11: eval(mf, parent.frame())
  
  == testthat results  ===========================================================
  OK: 22 SKIPPED: 0 FAILED: 3
  1. Error: using decision trees partykit (@test_dt.R#4) 
  2. Error: using decision trees partykit with controls works (@test_dt.R#10) 
  3. Error: NAs removed in create_breaks correctly (@test_nasremoved.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
'library' or 'require' calls to packages already attached by Depends:
  'ape' 'cladoRcpp' 'phylobase' 'rexpokit'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'ape' 'cladoRcpp' 'methods' 'phylobase' 'rexpokit'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' calls which should be '::':
  'ape:::floating.pie.asp' 'cladoRcpp:::areas_list_to_states_list_old'
  See the note in ?`:::` about the use of this operator.
Running 'testthat.R' [22s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
     })(list("try-error", "character"), structure(function (conn, x, ...) 
     standardGeneric("dbQuoteString"), generic = structure("dbQuoteString", package = "DBI"), package = "DBI", group = list(), valueClass = character(0), signature = c("conn", 
     "x"), default = `\001NULL\001`, skeleton = (function (conn, x, ...) 
     stop("invalid call in method dispatch to 'dbQuoteString' (no default method)", domain = NA))(conn, 
         x, ...), class = structure("standardGeneric", package = "methods")), <environment>)
  17: stop(gettextf("unable to find an inherited method for function %s for signature %s", 
         sQuote(fdef@generic), sQuote(cnames)), domain = NA)
  
  == testthat results  ===========================================================
  OK: 116 SKIPPED: 1 FAILED: 2
  1. Error: Gene Ontology tag retrieval (@test-tags-go.r#10) 
  2. Error: Gene Ontology tag substitution (@test-tags-go.r#19) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 70-73 (Functional_Annotation.Rmd) 
Error: processing vignette 'Functional_Annotation.Rmd' failed with diagnostics:
The given dataset:  hsapiens_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets() function.
Execution halted
'library' or 'require' call to 'MGRASTer' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.onAttach: no visible global function definition for 'packageVersion'
biom.matrix: no visible global function definition for 'packageVersion'
Undefined global functions or variables:
  packageVersion
Consider adding
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
extractPDB : atom.select : sel.txt2nums: no visible global function
  definition for 'na.omit'
extractPDB : read.pdb: no visible global function definition for
  'na.omit'
mat.read: no visible global function definition for 'read.table'
mat.write: no visible global function definition for 'write.table'
scpcp: no visible global function definition for 'pgamma'
sim : sim.func: no visible global function definition for 'write.table'
simc: no visible global function definition for 'write.table'
simc : simc.func: no visible global function definition for
  'write.table'
sims: no visible global function definition for 'write.table'
sims : sims.func: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  na.omit pgamma read.table write.table
Consider adding
  importFrom("stats", "na.omit", "pgamma")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning in buildVignettes(dir = "d:/Rcompile/CRANpkg/local/3.5/biorxivr.Rcheck/vign_test/biorxivr") :
  Files named as vignettes but with no recognized vignette engine:
   'vignettes/index.Rmd'
(Is a VignetteBuilder field missing?)
Quitting from lines 17-20 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
failed to load external entity "http://www.biorxiv.org/search/Ecology?page=0"
Execution halted
binom.ci : bc: no visible global function definition for 'qf'
binom.ci : bc: no visible global function definition for 'qnorm'
cvar: no visible global function definition for 'sd'
eta2: no visible global function definition for 'lm'
eta2: no visible global function definition for 'as.formula'
gg_qqplot: no visible binding for global variable 'qnorm'
gg_qqplot: no visible global function definition for 'quantile'
panel.hist: no visible global function definition for 'par'
panel.hist: no visible global function definition for 'hist'
panel.hist: no visible global function definition for 'rect'
plotcdf2: no visible global function definition for 'colorRampPalette'
plotcdf2 : jet.colors: no visible global function definition for 'gray'
plotcdf2: no visible global function definition for 'persp'
poi.ci: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  as.formula colorRampPalette gray hist lm par persp qchisq qf qnorm
  quantile rect sd
Consider adding
  importFrom("grDevices", "colorRampPalette", "gray")
  importFrom("graphics", "hist", "par", "persp", "rect")
  importFrom("stats", "as.formula", "lm", "qchisq", "qf", "qnorm",
             "quantile", "sd")
to your NAMESPACE file.
Depends: includes the non-default packages:
  'colorspace' 'deldir' 'rgl' 'tcltk' 'tcltk2' 'tkrplot'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
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.
plot.BIPOD: no visible global function definition for 'par'
plot.BIPOD: no visible global function definition for 'matplot'
plot.BIPOD: no visible global function definition for 'abline'
plot.BIPOD: no visible global function definition for 'plot'
plot.BIPOD: no visible global function definition for 'density'
plot.BIPOD: no visible global function definition for 'curve'
plot.BIPOD: no visible global function definition for 'dlnorm'
plot.BIPOD: no visible global function definition for 'dnorm'
plot.BIPOD: no visible global function definition for 'acf'
plot.BIPOD: no visible global function definition for 'pairs'
plot.BIPOD : standfun: no visible global function definition for 'sd'
plot.BIPOD: no visible global function definition for 'sd'
plot.BIPOD: no visible global function definition for 'points'
plot.BIPOD: no visible global function definition for 'tail'
plot.BIPOD: no visible global function definition for 'matlines'
plot.BIPOD: no visible binding for global variable 'quantile'
plot.BIPOD: no visible global function definition for 'lines'
Undefined global functions or variables:
  abline acf curve density dlnorm dnorm lines matlines matplot pairs
  par plot points quantile sd tail
Consider adding
  importFrom("graphics", "abline", "curve", "lines", "matlines",
             "matplot", "pairs", "par", "plot", "points")
  importFrom("stats", "acf", "density", "dlnorm", "dnorm", "quantile",
             "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
aveslope: no visible global function definition for 'pbeta'
bisoreg : <anonymous>: no visible global function definition for
  'pbeta'
bisoreg: no visible global function definition for 'rgamma'
bisoreg: no visible global function definition for 'rbeta'
bisoreg: no visible global function definition for 'rnorm'
bisoreg: no visible global function definition for 'rbinom'
bisoreg: no visible global function definition for 'dnorm'
bisoreg: no visible global function definition for 'var'
fitted.biso : <anonymous>: no visible global function definition for
  'median'
get.W : <anonymous>: no visible global function definition for 'pbeta'
loess.wrapper : theta.fit: no visible global function definition for
  'loess'
loess.wrapper : theta.predict: no visible global function definition
  for 'predict'
loess.wrapper: no visible global function definition for 'loess'
nd2004 : initfun: no visible global function definition for 'rnorm'
nd2004 : initfun: no visible global function definition for 'rgamma'
plot.biso: no visible global function definition for 'plot'
plot.biso : <anonymous>: no visible global function definition for
  'quantile'
plot.biso: no visible global function definition for 'polygon'
plot.biso: no visible global function definition for 'gray'
plot.biso: no visible global function definition for 'points'
plot.biso : <anonymous>: no visible global function definition for
  'median'
plot.biso: no visible global function definition for 'lines'
summary.biso: no visible binding for global variable 'fivenum'
Undefined global functions or variables:
  dnorm fivenum gray lines loess median pbeta plot points polygon
  predict quantile rbeta rbinom rgamma rnorm var
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "lines", "plot", "points", "polygon")
  importFrom("stats", "dnorm", "fivenum", "loess", "median", "pbeta",
             "predict", "quantile", "rbeta", "rbinom", "rgamma", "rnorm",
             "var")
to your NAMESPACE file.
bivarcalcn: no visible global function definition for 'qnorm'
bivarcalcn: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
biwt.cor: no visible global function definition for 'covMcd'
biwt.cor: no visible binding for global variable 'mad'
biwt.est: no visible global function definition for 'covMcd'
biwt.est: no visible global function definition for 'mahalanobis'
chi.int: no visible global function definition for 'pchisq'
chi.int.p: no visible global function definition for 'dchisq'
chi.int2: no visible global function definition for 'pchisq'
chi.int2.p: no visible global function definition for 'dchisq'
rejpt.bw: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  covMcd dchisq mad mahalanobis pchisq
Consider adding
  importFrom("stats", "dchisq", "mad", "mahalanobis", "pchisq")
to your NAMESPACE file.
install_blat: no visible global function definition for 'download.file'
install_blat: no visible global function definition for 'unzip'
Undefined global functions or variables:
  download.file unzip
Consider adding
  importFrom("utils", "download.file", "unzip")
to your NAMESPACE file.
blighty: no visible global function definition for 'par'
blighty: no visible global function definition for 'polygon'
blighty: no visible global function definition for 'points'
blighty: no visible global function definition for 'box'
blighty: no visible global function definition for 'axis'
blighty: no visible global function definition for 'abline'
map.scale: no visible global function definition for 'locator'
map.scale: no visible global function definition for 'segments'
map.scale: no visible global function definition for 'text'
north.pointer: no visible global function definition for 'locator'
north.pointer: no visible global function definition for 'text'
north.pointer: no visible global function definition for 'arrows'
north.pointer: no visible global function definition for 'segments'
sqlimits: no visible global function definition for 'frame'
sqlimits: no visible global function definition for 'par'
Undefined global functions or variables:
  abline arrows axis box frame locator par points polygon segments text
Consider adding
  importFrom("graphics", "abline", "arrows", "axis", "box", "frame",
             "locator", "par", "points", "polygon", "segments", "text")
to your NAMESPACE file.
Package suggested but not available for checking: 'bigrf'
Missing or unexported object: 'xgboost::predict'
bglmer: no visible global function definition for 'packageVersion'
getBglmerDevianceFunctionBody: no visible global function definition
  for 'packageVersion'
getParInfo : <anonymous>: no visible global function definition for
  'sd'
makeRefitDevFun: no visible global function definition for
  'packageVersion'
mkBglmerDevfun: no visible global function definition for
  'packageVersion'
namedList: no visible global function definition for 'setNames'
refit.bmerMod: no visible global function definition for
  'packageVersion'
refit.bmerMod: no visible global function definition for 'model.frame'
refit.bmerMod: no visible global function definition for 'family'
refit.bmerMod: no visible global function definition for 'getCall'
Undefined global functions or variables:
  family getCall model.frame packageVersion sd setNames
Consider adding
  importFrom("stats", "family", "getCall", "model.frame", "sd",
             "setNames")
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
blockMessage : <anonymous>: no visible global function definition for
  'head'
blockMessage: no visible global function definition for 'head'
blockMessage: no visible global function definition for 'tail'
Undefined global functions or variables:
  head tail
Consider adding
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'plot.mat':
  'plot.mat' 'plot.mat.nm'

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  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
blockmodelskmeans: no visible global function definition for 'dist'
matrixplot: no visible global function definition for 'image'
matrixplot: no visible global function definition for 'hsv'
matrixplot: no visible global function definition for 'axis'
Undefined global functions or variables:
  axis dist hsv image
Consider adding
  importFrom("grDevices", "hsv")
  importFrom("graphics", "axis", "image")
  importFrom("stats", "dist")
to your NAMESPACE file.
plotblockrand: no visible global function definition for 'pdf'
plotblockrand: no visible global function definition for 'dev.off'
plotblockrand: no visible global function definition for 'par'
plotblockrand: no visible global function definition for 'plot.new'
plotblockrand: no visible global function definition for 'strheight'
plotblockrand: no visible global function definition for 'strwidth'
plotblockrand: no visible global function definition for 'text'
plotblockrand: no visible global function definition for 'lines'
Undefined global functions or variables:
  dev.off lines par pdf plot.new strheight strwidth text
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "plot.new", "strheight",
             "strwidth", "text")
to your NAMESPACE file.
BLR: no visible global function definition for 'weighted.mean'
BLR: no visible global function definition for 'var'
BLR: no visible global function definition for 'model.matrix'
BLR: no visible global function definition for 'rnorm'
BLR: no visible global function definition for 'rchisq'
BLR: no visible global function definition for 'rgamma'
BLR: no visible global function definition for 'dnorm'
dLambda: no visible global function definition for 'dgamma'
dScaledInvChisq: no visible global function definition for 'dchisq'
metropLambda: no visible global function definition for 'rgamma'
metropLambda: no visible global function definition for 'dexp'
metropLambda: no visible global function definition for 'dbeta'
metropLambda: no visible global function definition for 'dgamma'
metropLambda: no visible global function definition for 'runif'
Undefined global functions or variables:
  dbeta dchisq dexp dgamma dnorm model.matrix rchisq rgamma rnorm runif
  var weighted.mean
Consider adding
  importFrom("stats", "dbeta", "dchisq", "dexp", "dgamma", "dnorm",
             "model.matrix", "rchisq", "rgamma", "rnorm", "runif", "var",
             "weighted.mean")
to your NAMESPACE file.
Package in Depends field not imported from: 'drc'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bmd: no visible global function definition for 'qnorm'
bmd: no visible global function definition for 'predict'
bmd: no visible global function definition for 'LL.2'
bmd: no visible global function definition for 'LN.2'
bmd: no visible global function definition for 'W1.2'
bmd: no visible global function definition for 'W2.2'
bmd: no visible global function definition for 'LL.5'
bmd: no visible global function definition for 'LN.4'
bmd: no visible global function definition for 'W1.4'
bmd: no visible global function definition for 'W2.4'
bmd: no visible global function definition for 'FPL.4'
bmd: no visible global function definition for 'maED'
bmd: no visible global function definition for 'ED'
Undefined global functions or variables:
  ED FPL.4 LL.2 LL.5 LN.2 LN.4 W1.2 W1.4 W2.2 W2.4 maED predict qnorm
Consider adding
  importFrom("stats", "predict", "qnorm")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'Amelia' 'MASS' 'lavaan' 'sem' 'snowfall'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' calls to packages already attached by Depends:
  'coda' 'functional' 'plyr'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'coda' 'functional' 'plyr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
HDistNoSize: no visible global function definition for 'density'
HDistSize: no visible global function definition for 'density'
bmkconverge: no visible global function definition for 'Compose'
bmksensitive: no visible global function definition for 'Compose'
bmksummary: no visible global function definition for 'Compose'
bmksummary: no visible global function definition for 'Curry'
bmksummary: no visible binding for global variable 'quantile'
bmksummary : std.error: no visible global function definition for 'var'
bmksummary: no visible global function definition for 'mcmc'
bmksummary: no visible global function definition for 'mcmc.list'
bmksummary: no visible global function definition for 'median'
bmksummary: no visible global function definition for 'effectiveSize'
bmksummary: no visible global function definition for 'gelman.diag'
Undefined global functions or variables:
  Compose Curry density effectiveSize gelman.diag mcmc mcmc.list median
  quantile var
Consider adding
  importFrom("stats", "density", "median", "quantile", "var")
to your NAMESPACE file.
bmmix : LL.y: no visible global function definition for 'dmultinom'
bmmix : LL.x : <anonymous>: no visible global function definition for
  'dmultinom'
bmmix : LPrior.alpha: no visible global function definition for 'dexp'
bmmix : alpha.move: no visible global function definition for 'rnorm'
bmmix : alpha.move: no visible global function definition for 'runif'
bmmix : phi.move: no visible global function definition for 'rnorm'
bmmix : phi.move: no visible global function definition for 'runif'
bmmix: no visible global function definition for 'read.table'
Undefined global functions or variables:
  dexp dmultinom read.table rnorm runif
Consider adding
  importFrom("stats", "dexp", "dmultinom", "rnorm", "runif")
  importFrom("utils", "read.table")
to your NAMESPACE file.
GibbsIteration: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  rbinom
Consider adding
  importFrom("stats", "rbinom")
to your NAMESPACE file.
File 'BMN/libs/i386/BMN.dll':
  Found '_ZSt4cout', possibly from 'std::cout' (C++)
    Objects: 'JunctionTree.o', 'pseudoLikelihood.o'
File 'BMN/libs/x64/BMN.dll':
  Found '_ZSt4cout', possibly from 'std::cout' (C++)
    Objects: 'JunctionTree.o', 'pseudoLikelihood.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
make_topology: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
bnlr: no visible global function definition for 'dnorm'
bnlr: no visible global function definition for 'runif'
chainsum : <anonymous>: no visible global function definition for
  'quantile'
infocrit: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm quantile runif
Consider adding
  importFrom("stats", "dnorm", "quantile", "runif")
to your NAMESPACE file.
clusterplots: no visible global function definition for 'par'
clusterplots: no visible global function definition for 'rainbow'
clusterplots: no visible global function definition for 'plot'
clusterplots: no visible global function definition for 'axis'
clusterplots: no visible global function definition for 'lines'
diagplots: no visible global function definition for 'par'
diagplots: no visible global function definition for 'plot'
diagplots: no visible global function definition for 'hist'
tseriesca: no visible global function definition for 'rgamma'
tseriesca: no visible global function definition for 'runif'
tseriesca: no visible global function definition for 'dbeta'
tseriesca: no visible global function definition for 'dgamma'
tseriescm: no visible global function definition for 'rgamma'
tseriescm: no visible global function definition for 'runif'
tseriescm: no visible global function definition for 'dbeta'
tseriescm: no visible global function definition for 'dgamma'
tseriescq: no visible global function definition for 'rgamma'
tseriescq: no visible global function definition for 'runif'
tseriescq: no visible global function definition for 'dbeta'
tseriescq: no visible global function definition for 'dgamma'
Undefined global functions or variables:
  axis dbeta dgamma hist lines par plot rainbow rgamma runif
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "hist", "lines", "par", "plot")
  importFrom("stats", "dbeta", "dgamma", "rgamma", "runif")
to your NAMESPACE file.
BOGest: no visible global function definition for 'read.table'
BOGstat: no visible global function definition for 'phyper'
BOGstat: no visible global function definition for 'wilcox.test'
BOGstat: no visible global function definition for 'p.adjust'
gseaplot: no visible global function definition for 'par'
gseaplot: no visible global function definition for 'plot'
gseaplot: no visible global function definition for 'points'
gseaplot: no visible global function definition for 'axis'
gseaplot: no visible global function definition for 'segments'
hgplot: no visible global function definition for 'par'
hgplot: no visible global function definition for 'barplot'
Undefined global functions or variables:
  axis barplot p.adjust par phyper plot points read.table segments
  wilcox.test
Consider adding
  importFrom("graphics", "axis", "barplot", "par", "plot", "points",
             "segments")
  importFrom("stats", "p.adjust", "phyper", "wilcox.test")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/BonEV.Rcheck/00install.out' for details.
print.boolprob: no visible global function definition for 'plot'
print.boolprof: no visible global function definition for 'plot'
start_msg: no visible global function definition for
  'packageDescription'
Undefined global functions or variables:
  packageDescription plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
Found the following non-portable file paths:
  Boom/inst/include/Models/Hierarchical/PosteriorSamplers/HierarchicalGaussianRegressionAsisSampler.hpp
  Boom/inst/include/Models/PointProcess/PosteriorSamplers/HomogeneousPoissonProcessPosteriorSampler.hpp
  Boom/inst/include/Models/PointProcess/PosteriorSamplers/MarkovModulatedPoissonProcessPosteriorSampler.hpp

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section 'Package structure' in the 'Writing R Extensions' manual.
installed size is 72.2Mb
  sub-directories of 1Mb or more:
    include   2.9Mb
    lib      69.0Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
boostBackend: no visible global function definition for 'model.frame'
findFormulaIn: no visible global function definition for 'as.formula'
kFoldCV: no visible binding for global variable 'par'
predictResponseFromWeightedAverage: no visible global function
  definition for 'weighted.mean'
print.boostr: no visible global function definition for 'str'
Undefined global functions or variables:
  as.formula model.frame par str weighted.mean
Consider adding
  importFrom("graphics", "par")
  importFrom("stats", "as.formula", "model.frame", "weighted.mean")
  importFrom("utils", "str")
to your NAMESPACE file.
'library' or 'require' call to 'lpSolveAPI' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'genetics' 'lpSolveAPI'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
alleleEnrichment: no visible binding for global variable 'na.omit'
alleleEnrichment: no visible binding for global variable 'na.pass'
alleleEnrichment: no visible global function definition for
  'write.table'
alleleEnrichment.data.alleles: no visible binding for global variable
  'na.omit'
alleleEnrichment.data.alleles: no visible binding for global variable
  'na.pass'
alleleEnrichment.data.alleles : <anonymous>: no visible global function
  definition for 'allele.count'
alleleEnrichment.data.alleles: no visible global function definition
  for 'runif'
alleleEnrichment.data.pheno: no visible global function definition for
  'read.table'
alleleEnrichment.lp: no visible global function definition for
  'make.lp'
alleleEnrichment.lp : <anonymous>: no visible global function
  definition for 'set.column'
alleleEnrichment.lp : <anonymous>: no visible global function
  definition for 'set.type'
alleleEnrichment.lp: no visible global function definition for
  'set.objfn'
alleleEnrichment.lp: no visible global function definition for
  'set.constr.type'
alleleEnrichment.lp: no visible global function definition for
  'set.rhs'
alleleEnrichment.lp: no visible global function definition for
  'lp.control'
alleleEnrichment.lp: no visible global function definition for
  'get.variables'
getGenotypes : <anonymous>: no visible global function definition for
  'genotype'
getRefAlleles: no visible global function definition for 'read.table'
getSnpWeights: no visible global function definition for 'read.table'
readMapfile: no visible global function definition for 'read.table'
Undefined global functions or variables:
  allele.count genotype get.variables lp.control make.lp na.omit
  na.pass read.table runif set.column set.constr.type set.objfn set.rhs
  set.type write.table
Consider adding
  importFrom("stats", "na.omit", "na.pass", "runif")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
specdens: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
boot.stepAIC: no visible global function definition for 'update'
boot.stepAIC: no visible binding for global variable 'coef'
boot.stepAIC : <anonymous>: no visible global function definition for
  'anova'
boot.stepAIC: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  anova coef pnorm update
Consider adding
  importFrom("stats", "anova", "coef", "pnorm", "update")
to your NAMESPACE file.
bootSVD: no visible global function definition for 'object.size'
bootSVD : <anonymous> : <anonymous>: no visible global function
  definition for 'quantile'
bootSVD_LD: no visible global function definition for 'txtProgressBar'
bootSVD_LD: no visible global function definition for
  'setTxtProgressBar'
genQ: no visible global function definition for 'rnorm'
getHDpercentiles : <anonymous>: no visible global function definition
  for 'quantile'
getMomentsAndMomentCI: no visible binding for global variable 'var'
os: no visible global function definition for 'object.size'
simEEG: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  object.size quantile rnorm setTxtProgressBar txtProgressBar var
Consider adding
  importFrom("stats", "quantile", "rnorm", "var")
  importFrom("utils", "object.size", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file.
boottol: no visible global function definition for 'setNames'
boottol : shift: no visible global function definition for 'tail'
boottol : shift: no visible global function definition for 'head'
boottol: no visible global function definition for 'na.omit'
vastol: no visible global function definition for 'setNames'
vastol: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  head na.omit setNames tail
Consider adding
  importFrom("stats", "na.omit", "setNames")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
boxplotdou.formula: no visible global function definition for
  'model.frame'
bxpdou: no visible global function definition for 'rainbow'
bxpdou.abox: no visible global function definition for 'rect'
bxpdou.abox: no visible global function definition for 'segments'
bxpdou.abox: no visible global function definition for 'points'
bxpdou.boxplot.stat: no visible global function definition for
  'boxplot'
bxpdou.sheer.color: no visible global function definition for
  'adjustcolor'
bxpdou.stats: no visible global function definition for 'formula'
do.call.with.par: no visible global function definition for
  'modifyList'
only.graphic.pars: no visible global function definition for 'par'
Undefined global functions or variables:
  adjustcolor boxplot formula model.frame modifyList par points rainbow
  rect segments
Consider adding
  importFrom("grDevices", "adjustcolor", "rainbow")
  importFrom("graphics", "boxplot", "par", "points", "rect", "segments")
  importFrom("stats", "formula", "model.frame")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
bPeaksAnalysis: no visible global function definition for 'write.table'
dataReading: no visible global function definition for 'read.table'
dataSmoothing: no visible global function definition for 'filter'
peakDetection: no visible global function definition for 'quantile'
peakDetection: no visible global function definition for 'pdf'
peakDetection: no visible global function definition for 'par'
peakDetection: no visible global function definition for 'plot'
peakDetection: no visible global function definition for 'text'
peakDetection: no visible global function definition for 'abline'
peakDetection: no visible global function definition for 'points'
peakDetection: no visible global function definition for 'dev.off'
peakDetection: no visible global function definition for 'write.table'
peakDrawing: no visible global function definition for 'par'
peakDrawing: no visible global function definition for 'plot'
peakDrawing: no visible global function definition for 'abline'
peakLocation: no visible global function definition for 'read.table'
peakLocation: no visible global function definition for 'pdf'
peakLocation: no visible global function definition for 'barplot'
peakLocation: no visible global function definition for 'dev.off'
peakLocation: no visible global function definition for 'write.table'
Undefined global functions or variables:
  abline barplot dev.off filter par pdf plot points quantile read.table
  text write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "barplot", "par", "plot", "points",
             "text")
  importFrom("stats", "filter", "quantile")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
M0: no visible global function definition for 'fft'
M1: no visible global function definition for 'fft'
bpk: no visible binding for global variable 'dnorm'
bpkde: no visible binding for global variable 'dnorm'
bpkde: no visible binding for global variable 'bw.SJ'
bpkde: no visible global function definition for 'rnorm'
bpkde: no visible global function definition for 'fft'
bpkde: no visible global function definition for 'optimize'
contour.discretize.kernel: no visible global function definition for
  'contour.default'
contour.mvkde: no visible global function definition for
  'contour.default'
image.discretize.kernel: no visible global function definition for
  'image.default'
image.discretize.kernel: no visible global function definition for
  'gray'
image.mvkde: no visible global function definition for 'image.default'
image.mvkde: no visible global function definition for 'gray'
image.mvlinbin: no visible global function definition for 'image'
image.mvlinbin: no visible global function definition for 'gray'
plot.discretize.kernel: no visible global function definition for
  'mtext'
plot.discretize.kernel: no visible global function definition for 'par'
plot.mvkde: no visible global function definition for 'mtext'
plot.mvkde: no visible global function definition for 'par'
plot.mvlinbin: no visible global function definition for 'plot'
plot.mvlinbin: no visible global function definition for 'mtext'
plot.mvlinbin: no visible global function definition for 'par'
Undefined global functions or variables:
  bw.SJ contour.default dnorm fft gray image image.default mtext
  optimize par plot rnorm
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "contour.default", "image", "image.default",
             "mtext", "par", "plot")
  importFrom("stats", "bw.SJ", "dnorm", "fft", "optimize", "rnorm")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/brainGraph.Rcheck/00install.out' for details.
Package in Depends field not imported from: 'waveslim'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

const.cor.list: no visible global function definition for
  'wave.correlation'
const.var.list: no visible global function definition for
  'wave.variance'
fitting: no visible global function definition for 'hist'
fitting: no visible global function definition for 'nlm'
fitting: no visible global function definition for 'write.table'
p.value.compute: no visible global function definition for 'pnorm'
p.value.compute: no visible global function definition for 'pt'
random.attack: no visible global function definition for 'runif'
read.convert_1_2: no visible global function definition for
  'read.table'
read.cor.txt: no visible global function definition for 'read.table'
read.var.txt: no visible global function definition for 'read.table'
save.cor.txt: no visible global function definition for 'write.table'
save.var.txt: no visible global function definition for 'write.table'
sim.equadist: no visible global function definition for 'write.table'
small.world: no visible global function definition for 'dist'
small.world: no visible global function definition for 'write.table'
wave.trans: no visible global function definition for 'dwt'
wave.trans: no visible global function definition for 'modwt'
wave.trans: no visible global function definition for 'brick.wall'
Undefined global functions or variables:
  brick.wall dist dwt hist modwt nlm pnorm pt read.table runif
  wave.correlation wave.variance write.table
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "dist", "nlm", "pnorm", "pt", "runif")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
File 'brainwaver/libs/i386/brainwaver.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'connexity_small_world.o'
File 'brainwaver/libs/x64/brainwaver.dll':
  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 the system RNG.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
apply.breaks: no visible binding for global variable 'median'
break.clust: no visible global function definition for 'plot'
break.clust: no visible global function definition for 'median'
breakage.plot: no visible binding for global variable 'median'
breakage.plot: no visible global function definition for 'plot'
breakage.plot: no visible global function definition for 'abline'
breakage.plot: no visible global function definition for 'lm'
find.bottom: no visible global function definition for 'filter'
fit.breakage: no visible global function definition for 'optim'
fit.breakage: no visible global function definition for 'plot'
fit.breakage: no visible global function definition for 'points'
fit.sensitivity.plot: no visible global function definition for
  'contour'
fit.sensitivity.plot: no visible global function definition for
  'points'
fit.sensitivity.plot: no visible global function definition for 'text'
Undefined global functions or variables:
  abline contour filter lm median optim plot points text
Consider adding
  importFrom("graphics", "abline", "contour", "plot", "points", "text")
  importFrom("stats", "filter", "lm", "median", "optim")
to your NAMESPACE file.
Running 'test-all.R' [51s]
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
  > #test_check("breathtestcore", filter = "plot_breathtestfit")
  > test_check("breathtestcore")
  Loading required package: breathtestcore
  -- 1. Failure: read_iris_csv returns with funny identification cleans up (@test_
  iconv(f$study) not equal to "GE-flüssig".
  1/1 mismatches
  x[1]: "GE-flÃ¼ssig"
  y[1]: "GE-flüssig"
  
  == testthat results  ===========================================================
  OK: 351 SKIPPED: 4 FAILED: 1
  1. Failure: read_iris_csv returns with funny identification cleans up (@test_read_iris_csv.R#51) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     2.2Mb
    doc   2.4Mb
plot,ANY-brob: no visible global function definition for 'plot.default'
plot,ANY-glub: no visible global function definition for 'plot.default'
plot,brob-ANY: no visible global function definition for 'plot.default'
plot,brob-missing: no visible global function definition for
  'plot.default'
plot,glub-ANY: no visible global function definition for 'plot.default'
plot,glub-missing: no visible global function definition for
  'plot.default'
Undefined global functions or variables:
  plot.default
Consider adding
  importFrom("graphics", "plot.default")
to your NAMESPACE file.
Foreign function calls to a different package:
  .C("CharArray", ..., PACKAGE = "libOpenBUGS")
  .C("CmdInterpreter", ..., PACKAGE = "libOpenBUGS")
  .C("Integer", ..., PACKAGE = "libOpenBUGS")
  .C("RealArray", ..., PACKAGE = "libOpenBUGS")
  .C("SetTempDir", ..., PACKAGE = "libOpenBUGS")
  .C("SetWorkingDir", ..., PACKAGE = "libOpenBUGS")
Undeclared package in foreign function calls:
   'libOpenBUGS'
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
BOOTSimpsonD : BSimpson: no visible global function definition for
  'estSimpsonf'
BOOTSimpsonR : BSimpson: no visible global function definition for
  'estSimpsonf'
CIGLM: no visible global function definition for 'confint'
CIGLM: no visible global function definition for 'univariate_calpha'
CIGLM: no visible global function definition for 'adjusted_calpha'
CInp.default : <anonymous>: no visible global function definition for
  'quantile'
CInp.default: no visible binding for global variable 'median'
R2Bugsdat1w: no visible global function definition for 'model.frame'
R2Bugsdat1w: no visible global function definition for 'model.matrix'
R2Bugsdat1w.data.frame: no visible global function definition for
  'as.formula'
R2Bugsdat1w.data.frame: no visible global function definition for
  'model.frame'
R2Bugsdat1w.data.frame: no visible global function definition for
  'model.matrix'
SCSnp.default: no visible binding for global variable 'median'
modelparm.gamlss: no visible binding for global variable 'coef'
modelparm.gamlss: no visible binding for global variable 'vcov'
modelparm.geeglm: no visible binding for global variable 'coef'
modelparm.geeglm: no visible binding for global variable 'vcov'
simplesimint: no visible global function definition for 'cov2cor'
summary.simplesimint: no visible global function definition for
  'cov2cor'
Undefined global functions or variables:
  adjusted_calpha as.formula coef confint cov2cor estSimpsonf median
  model.frame model.matrix quantile univariate_calpha vcov
Consider adding
  importFrom("stats", "as.formula", "coef", "confint", "cov2cor",
             "median", "model.frame", "model.matrix", "quantile", "vcov")
to your NAMESPACE file.
BSGS.Sample: no visible global function definition for 'rgamma'
BSGS.Simple: no visible global function definition for 'rgamma'
CompWiseGibbs: no visible global function definition for 'runif'
CompWiseGibbs: no visible global function definition for 'rnorm'
CompWiseGibbsSMP: no visible global function definition for 'rbinom'
CompWiseGibbsSMP: no visible global function definition for 'runif'
CompWiseGibbsSMP: no visible global function definition for 'rnorm'
CompWiseGibbsSimple: no visible global function definition for 'runif'
CompWiseGibbsSimple: no visible global function definition for 'rnorm'
CompWiseGibbsSimple: no visible global function definition for 'rgamma'
GroupMH: no visible global function definition for 'runif'
GroupZ.MH: no visible global function definition for 'runif'
Undefined global functions or variables:
  rbinom rgamma rnorm runif
Consider adding
  importFrom("stats", "rbinom", "rgamma", "rnorm", "runif")
to your NAMESPACE file.
bs.design: no visible global function definition for 'spline.des'
bshazard.default: no visible global function definition for
  'model.frame'
bshazard.default: no visible global function definition for
  'model.matrix'
bshazard.default: no visible global function definition for
  'model.response'
bshazard_fit: no visible global function definition for 'aggregate'
bspois: no visible global function definition for 'dpois'
bspois: no visible global function definition for 'var'
bspois: no visible global function definition for 'qnorm'
lines.bshazard: no visible global function definition for 'lines'
plot.bshazard: no visible global function definition for 'plot'
plot.bshazard: no visible global function definition for 'lines'
print.bshazard: no visible global function definition for 'aggregate'
Undefined global functions or variables:
  aggregate dpois lines model.frame model.matrix model.response plot
  qnorm spline.des var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "aggregate", "dpois", "model.frame",
             "model.matrix", "model.response", "qnorm", "var")
to your NAMESPACE file.
LenthPlot: no visible global function definition for 'grey'
plot.BsProb : spikes: no visible global function definition for 'grey'
Undefined global functions or variables:
  grey
Consider adding
  importFrom("grDevices", "grey")
to your NAMESPACE file.
plot.bspec: no visible global function definition for 'par'
plot.bspec: no visible global function definition for 'plot'
plot.bspec: no visible global function definition for 'matlines'
plot.bspec: no visible global function definition for 'points'
plot.bspec: no visible global function definition for 'axis'
plot.bspec: no visible global function definition for 'mtext'
plot.bspec: no visible global function definition for 'axTicks'
plot.bspec: no visible global function definition for 'box'
plot.bspecACF: no visible global function definition for 'plot'
plot.bspecACF: no visible global function definition for 'abline'
plot.bspecACF: no visible global function definition for 'matlines'
Undefined global functions or variables:
  abline axTicks axis box matlines mtext par plot points
Consider adding
  importFrom("graphics", "abline", "axTicks", "axis", "box", "matlines",
             "mtext", "par", "plot", "points")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'VGAM' 'quadprog' 'quantreg'
  Please remove these calls from your code.
dqreg: no visible binding for global variable 'median'
dqreg: no visible global function definition for 'median'
log_pdf : q0: no visible global function definition for 'qnorm'
log_pdf : d0: no visible global function definition for 'dnorm'
log_pdf : q0: no visible global function definition for 'qt'
log_pdf : d0: no visible global function definition for 'dt'
log_pdf : q0: no visible global function definition for 'qweibull'
log_pdf : d0: no visible global function definition for 'dweibull'
log_pdf : q0: no visible global function definition for 'qgamma'
log_pdf : d0: no visible global function definition for 'dgamma'
make.B: no visible global function definition for 'qnorm'
make.B: no visible global function definition for 'qweibull'
make.B: no visible global function definition for 'qgamma'
qr_plot: no visible global function definition for 'gray'
qr_plot: no visible binding for global variable 'quantile'
qr_plot: no visible global function definition for 'polygon'
qr_plot: no visible global function definition for 'lines'
qreg: no visible global function definition for 'sd'
qreg: no visible global function definition for 'lm'
qreg: no visible global function definition for 'var'
qreg_spline: no visible global function definition for 'rnorm'
qreg_spline: no visible global function definition for 'var'
qreg_spline: no visible binding for global variable 'quantile'
rootfind: no visible global function definition for 'runif'
Undefined global functions or variables:
  dgamma dnorm dt dweibull gray lines lm median polygon qgamma qnorm qt
  quantile qweibull rnorm runif sd var
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "lines", "polygon")
  importFrom("stats", "dgamma", "dnorm", "dt", "dweibull", "lm",
             "median", "qgamma", "qnorm", "qt", "quantile", "qweibull",
             "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
The following directory looks like a leftover from 'knitr':
  'figure'
Please remove from your package.
alpha.proxy: no visible global function definition for 'filled.contour'
alpha.proxy: no visible global function definition for 'axis'
alpha.proxy: no visible global function definition for 'contour'
factor.model.stat: no visible global function definition for 'quantile'
factor.model.stat: no visible global function definition for 'lsfit'
partial.rainbow: no visible binding for global variable 'rainbow'
var.shrink.eqcor: no visible global function definition for 'var'
var.shrink.eqcor: no visible global function definition for 'quantile'
var.shrink.eqcor: no visible global function definition for 'cov2cor'
Undefined global functions or variables:
  axis contour cov2cor filled.contour lsfit quantile rainbow var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "contour", "filled.contour")
  importFrom("stats", "cov2cor", "lsfit", "quantile", "var")
to your NAMESPACE file.
plot.bursts: no visible global function definition for 'plot'
plot.bursts: no visible global function definition for 'axis'
plot.bursts: no visible global function definition for 'arrows'
Undefined global functions or variables:
  arrows axis plot
Consider adding
  importFrom("graphics", "arrows", "axis", "plot")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'haplo.stats' 'msm'
  Please remove these calls from your code.
fitBVS: no visible global function definition for 'qnorm'
fitBVS: no visible global function definition for 'model.matrix'
fitBVS: no visible global function definition for 'as.formula'
fitBVS: no visible global function definition for 'glm'
fitBVS: no visible global function definition for 'deviance'
fitBVS: no visible global function definition for 'pnorm'
plotBVS: no visible global function definition for 'par'
plotBVS: no visible global function definition for 'image'
plotBVS: no visible global function definition for 'axis'
sampleBVS: no visible global function definition for 'qnorm'
sampleBVS: no visible global function definition for 'pnorm'
sampleBVS: no visible global function definition for 'runif'
summaryBVS: no visible global function definition for 'qnorm'
summaryBVS : inc.prob: no visible global function definition for
  'pnorm'
summaryBVS: no visible global function definition for 'pnorm'
summaryBVS: no visible global function definition for 'model.matrix'
Undefined global functions or variables:
  as.formula axis deviance glm image model.matrix par pnorm qnorm runif
Consider adding
  importFrom("graphics", "axis", "image", "par")
  importFrom("stats", "as.formula", "deviance", "glm", "model.matrix",
             "pnorm", "qnorm", "runif")
to your NAMESPACE file.
makemim: no visible global function definition for 'cor'
sigtestMTC: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  cor p.adjust
Consider adding
  importFrom("stats", "cor", "p.adjust")
to your NAMESPACE file.
cabootcrs: no visible global function definition for 'read.table'
cabootcrs: no visible global function definition for 'rmultinom'
cabootcrs: no visible global function definition for 'rpois'
plotca : plotonepic: no visible global function definition for 'qchisq'
plotca : plotonepic: no visible global function definition for
  'dev.new'
plotca : plotonepic: no visible global function definition for 'plot'
plotca : plotonepic: no visible global function definition for 'points'
plotca : plotonepic: no visible global function definition for 'abline'
plotca : plotonepic: no visible global function definition for 'legend'
plotca : plotonepic: no visible global function definition for 'title'
plotca : plotonepic: no visible global function definition for 'lines'
plotca : plotonepic: no visible global function definition for 'text'
plotca: no visible global function definition for 'colours'
plotca: no visible global function definition for 'rainbow'
plotca: no visible global function definition for 'read.table'
Undefined global functions or variables:
  abline colours dev.new legend lines plot points qchisq rainbow
  read.table rmultinom rpois text title
Consider adding
  importFrom("grDevices", "colours", "dev.new", "rainbow")
  importFrom("graphics", "abline", "legend", "lines", "plot", "points",
             "text", "title")
  importFrom("stats", "qchisq", "rmultinom", "rpois")
  importFrom("utils", "read.table")
to your NAMESPACE file.
bcMer: no visible global function definition for 'family'
biasCorrectionBernoulli: no visible global function definition for
  'qlogis'
biasCorrectionBernoulli : <anonymous>: no visible global function
  definition for 'qlogis'
biasCorrectionGaussian: no visible global function definition for
  'model.matrix'
cAIC: no visible global function definition for 'family'
conditionalBootstrap: no visible global function definition for
  'simulate'
conditionalBootstrap : <anonymous>: no visible global function
  definition for 'predict'
conditionalBootstrap: no visible global function definition for 'sigma'
deleteZeroComponents: no visible global function definition for 'lm'
deleteZeroComponents: no visible global function definition for
  'formula'
deleteZeroComponents: no visible global function definition for
  'model.frame'
deleteZeroComponents: no visible global function definition for 'terms'
deleteZeroComponents: no visible global function definition for
  'reformulate'
getcondLL: no visible global function definition for 'family'
getcondLL: no visible global function definition for 'dbinom'
getcondLL: no visible global function definition for 'dpois'
getcondLL: no visible global function definition for 'dnorm'
getcondLL: no visible global function definition for 'sigma'
Undefined global functions or variables:
  dbinom dnorm dpois family formula lm model.frame model.matrix predict
  qlogis reformulate sigma simulate terms
Consider adding
  importFrom("stats", "dbinom", "dnorm", "dpois", "family", "formula",
             "lm", "model.frame", "model.matrix", "predict", "qlogis",
             "reformulate", "sigma", "simulate", "terms")
to your NAMESPACE file.
---- unloading
Warning message:
.onUnload failed in unloadNamespace() for 'cairoDevice', details:
  call: .C("cleanupGTK", PACKAGE = "cairoDevice")
  error: "cleanupGTK" not available for .C() for package "cairoDevice"
Error in inDL(x, as.logical(local), as.logical(now), ...) : 
  unable to load shared object 'd:/RCompile/CRANpkg/lib/3.5/cairoDevice/libs/x64/cairoDevice.dll':
  LoadLibrary failure:  Die angegebene Prozedur wurde nicht gefunden.

Warning in fun(libname, pkgname) :
  Failed to load cairoDevice, attempting to install itError in inDL(x, as.logical(local), as.logical(now), ...) : 
  unable to load shared object 'd:/RCompile/CRANpkg/lib/3.5/cairoDevice/libs/x64/cairoDevice.dll':
  LoadLibrary failure:  Die angegebene Prozedur wurde nicht gefunden.



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 in inDL(x, as.logical(local), as.logical(now), ...) : 
  unable to load shared object 'd:/RCompile/CRANpkg/lib/3.5/cairoDevice/libs/x64/cairoDevice.dll':
  LoadLibrary failure:  Die angegebene Prozedur wurde nicht gefunden.

Please install GTK+ from http://ftp.gnome.org/pub/gnome/binaries/win64/gtk+/2.22/gtk+-bundle_2.22.1-20101229_win64.zip
If the package still does not load, please ensure that GTK+ is installed and that it is on your PATH environment variable
IN ANY CASE, RESTART R BEFORE TRYING TO LOAD THE PACKAGE AGAIN
Warning message:
In fun(libname, pkgname) :
  Failed to load cairoDevice, attempting to install itError in inDL(x, as.logical(local), as.logical(now), ...) : 
  unable to load shared object 'd:/RCompile/CRANpkg/lib/3.5/cairoDevice/libs/x64/cairoDevice.dll':
  LoadLibrary failure:  Die angegebene Prozedur wurde nicht gefunden.



It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
Error in inDL(x, as.logical(local), as.logical(now), ...) : 
  unable to load shared object 'd:/RCompile/CRANpkg/lib/3.5/cairoDevice/libs/x64/cairoDevice.dll':
  LoadLibrary failure:  Die angegebene Prozedur wurde nicht gefunden.
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()
Error in .C("do_Cairo", as.numeric(width), as.numeric(height), as.numeric(pointsize),  : 
  "do_Cairo" not available for .C() for package "cairoDevice"
Calls: Cairo -> .C
Execution halted
makemar : predictions: no visible global function definition for
  'rbinom'
mice.impute.rfcat : <anonymous>: no visible global function definition
  for 'predict'
mice.impute.rfcont: no visible global function definition for 'predict'
mice.impute.rfcont: no visible global function definition for 'rnorm'
simdata: no visible global function definition for 'rbinom'
simdata: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  predict rbinom rnorm
Consider adding
  importFrom("stats", "predict", "rbinom", "rnorm")
to your NAMESPACE file.
calibrate: no visible global function definition for 'lines'
calibrate: no visible global function definition for 'text'
canocor: no visible global function definition for 'cor'
circle: no visible global function definition for 'points'
dlines: no visible global function definition for 'lines'
origin: no visible global function definition for 'par'
origin: no visible global function definition for 'lines'
rda: no visible global function definition for 'cor'
rda: no visible global function definition for 'princomp'
rda: no visible global function definition for 'var'
textxy: no visible global function definition for 'text'
Undefined global functions or variables:
  cor lines par points princomp text var
Consider adding
  importFrom("graphics", "lines", "par", "points", "text")
  importFrom("stats", "cor", "princomp", "var")
to your NAMESPACE file.
EK.eqn10.supp: no visible global function definition for 'integrate'
MH: no visible global function definition for 'rmvnorm'
MH: no visible global function definition for 'runif'
computer.model: no visible global function definition for 'rmvnorm'
create.new.toy.datasets: no visible global function definition for
  'rnorm'
model.inadequacy: no visible global function definition for 'rmvnorm'
prob.psi1: no visible global function definition for 'dmvnorm'
prob.psi2: no visible global function definition for 'dmvnorm'
prob.theta: no visible global function definition for 'dmvnorm'
sample.theta: no visible global function definition for 'rmvnorm'
stage1: no visible global function definition for 'optim'
stage2: no visible global function definition for 'optim'
stage3: no visible global function definition for 'optim'
Undefined global functions or variables:
  dmvnorm integrate optim rmvnorm rnorm runif
Consider adding
  importFrom("stats", "integrate", "optim", "rnorm", "runif")
to your NAMESPACE file.
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
         env <- asNamespace(pkg_name)
         if (!exists(name, envir = env, mode = "function")) 
             stop("Function ", name, " not found in environment ", environmentName(env), 
                 ".", call. = FALSE)
         mock(name = name, env = env, new = eval(new_values[[qual_name]], eval_env, eval_env))
     })
  4: FUN(X[[i]], ...)
  5: stop("Can't mock functions in base packages (", pkg_name, ")", call. = FALSE)
  
  == testthat results  ===========================================================
  OK: 28 SKIPPED: 0 FAILED: 1
  1. Error: debugger is called (@test-error.R#45) 
  
  Error: testthat unit tests failed
  Execution halted
File 'camel/libs/i386/camel.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'SFGen.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'SFGen.o'
File 'camel/libs/x64/camel.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'SFGen.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'SFGen.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
CAM: no visible global function definition for 'object.size'
CAM: no visible global function definition for 'as'
computeScoreMat: no visible global function definition for 'combn'
computeScoreMat: no visible global function definition for 'var'
computeScoreMatParallel: no visible global function definition for
  'var'
selLm: no visible global function definition for 'lm'
selLm: no visible global function definition for 'coef'
train_gam: no visible global function definition for 'formula'
train_lasso: no visible global function definition for 'predict'
train_linear: no visible global function definition for 'lm'
Undefined global functions or variables:
  as coef combn formula lm object.size predict var
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "coef", "formula", "lm", "predict", "var")
  importFrom("utils", "combn", "object.size")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
bootstrapCapwire: no visible global function definition for 'quantile'
drawCapRatesBeta : <anonymous>: no visible global function definition
  for 'rbeta'
drawCapRatesExp : <anonymous>: no visible global function definition
  for 'rexp'
drawCapRatesGamma : <anonymous>: no visible global function definition
  for 'rgamma'
drawCapRatesGeom : <anonymous>: no visible global function definition
  for 'rgeom'
drawCapRatesUnif : <anonymous>: no visible global function definition
  for 'runif'
partitionCountData : find.3.way.partitions: no visible global function
  definition for 'dmultinom'
Undefined global functions or variables:
  dmultinom quantile rbeta rexp rgamma rgeom runif
Consider adding
  importFrom("stats", "dmultinom", "quantile", "rbeta", "rexp", "rgamma",
             "rgeom", "runif")
to your NAMESPACE file.
Sub.pair: no visible global function definition for 'qnorm'
as.record: no visible global function definition for 'capture.output'
estN: no visible global function definition for 'sd'
estN: no visible global function definition for 'qnorm'
estN.bootstrap: no visible global function definition for 'runif'
Undefined global functions or variables:
  capture.output qnorm runif sd
Consider adding
  importFrom("stats", "qnorm", "runif", "sd")
  importFrom("utils", "capture.output")
to your NAMESPACE file.