Combi: no visible global function definition for 'new'
barplotMixCluster: no visible global function definition for 'is'
barplotMixCluster: no visible global function definition for 'par'
barplotMixCluster: no visible global function definition for 'lines'
barplotMixCluster: no visible global function definition for 'text'
barplotMixCluster: no visible global function definition for 'title'
barplotMixCluster: no visible global function definition for 'mtext'
histMixCluster: no visible global function definition for 'is'
histMixCluster: no visible global function definition for 'par'
histMixCluster: no visible global function definition for 'dnorm'
histMixCluster: no visible global function definition for 'lines'
mixmodEntPlot: no visible global function definition for 'par'
mixmodEntPlot: no visible global function definition for 'lines'
mixmodEntPlot: no visible global function definition for 'axis'
mixmodEntPlot: no visible global function definition for 'title'
mixmodEntPlot: no visible binding for global variable 'par'
plot,MixmodCombi: no visible global function definition for 'par'
plot,MixmodCombi: no visible global function definition for 'plot.new'
plot,MixmodCombi: no visible global function definition for 'title'
Undefined global functions or variables:
  axis dnorm is lines mtext new par plot.new text title
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "par", "plot.new",
             "text", "title")
  importFrom("methods", "is", "new")
  importFrom("stats", "dnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Warning in gzfile(file, "rb") :
  cannot open compressed file 'd:/RCompile/CRANpkg/lib/3.4/lattice/Meta/Rd.rds', probable reason 'Permission denied'
Error in gzfile(file, "rb") : cannot open the connection
Calls: <Anonymous> -> lapply -> FUN -> readRDS -> gzfile
Execution halted
.pLGP_qvec: no visible global function definition for 'ppois'
.qLGP_pvec: no visible global function definition for 'qpois'
.rLGP.failsafe: no visible global function definition for 'runif'
.subdmg: no visible global function definition for 'dbinom'
dnegbin: no visible global function definition for 'dnbinom'
pLGP: no visible global function definition for 'ppois'
qLGP: no visible global function definition for 'qpois'
rLGP: no visible global function definition for 'rpois'
rLGP: no visible global function definition for 'rnorm'
rLGP: no visible global function definition for 'runif'
rbinegbin: no visible global function definition for 'rnbinom'
rmanaclash: no visible global function definition for 'rbinom'
rmanaclash: no visible global function definition for 'runif'
Undefined global functions or variables:
  dbinom dnbinom ppois qpois rbinom rnbinom rnorm rpois runif
Consider adding
  importFrom("stats", "dbinom", "dnbinom", "ppois", "qpois", "rbinom",
             "rnbinom", "rnorm", "rpois", "runif")
to your NAMESPACE file.
predict.MOA_trainedmodel: no visible global function definition for
  'delete.response'
predict.MOA_trainedmodel: no visible global function definition for
  'model.frame'
trainMOA: no visible binding for global variable 'na.exclude'
Undefined global functions or variables:
  delete.response model.frame na.exclude
Consider adding
  importFrom("stats", "delete.response", "model.frame", "na.exclude")
to your NAMESPACE file.
dbGetDistinct,RMongo-character-character-character: no visible global
  function definition for 'read.table'
dbGetQueryForKeys,RMongo-character-character-character-numeric-numeric:
  no visible global function definition for 'read.csv'
Undefined global functions or variables:
  read.csv read.table
Consider adding
  importFrom("utils", "read.csv", "read.table")
to your NAMESPACE file.
CoeffYWeq: no visible global function definition for 'index'
fitdistrForPrecipitation: no visible global function definition for
  'fitdistr'
generate.CCGammaObject: no visible binding for global variable 'rnorm'
generate.CCGammaObject: no visible global function definition for
  'pnorm'
generate.YuleWalkerCoefficientBlockmatrices: no visible binding for
  global variable 'rnorm'
generate.YuleWalkerCoefficientBlockmatricesPerEachMonth: no visible
  binding for global variable 'rnorm'
generatePrecipitationAmount: no visible global function definition for
  'str'
omega_inv: no visible global function definition for 'uniroot'
qqfit: no visible binding for global variable 'qexp'
qqfit: no visible global function definition for 'ecdf'
Undefined global functions or variables:
  ecdf fitdistr index pnorm qexp rnorm str uniroot
Consider adding
  importFrom("stats", "ecdf", "pnorm", "qexp", "rnorm", "uniroot")
  importFrom("utils", "str")
to your NAMESPACE file.
rms.pval: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
dWishartSpike: no visible global function definition for 'dnorm'
pWishartSpike: no visible global function definition for 'pnorm'
qWishartSpike: no visible global function definition for 'qnorm'
rWishartSpike: no visible global function definition for 'qnorm'
rmp: no visible global function definition for 'runif'
rtw: no visible global function definition for 'runif'
Undefined global functions or variables:
  dnorm pnorm qnorm runif
Consider adding
  importFrom("stats", "dnorm", "pnorm", "qnorm", "runif")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'DESeq' 'seqinr' 'topGO'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.isPath: no visible global function definition for 'tail'
.isPath: no visible global function definition for 'head'
navGraph : <anonymous>: no visible global function definition for
  'tail'
navGraph : <anonymous>: no visible global function definition for 'sd'
navGraph: no visible global function definition for 'colors'
ng_image_array_gray : <anonymous>: no visible global function
  definition for 'grey'
scagGraph: no visible global function definition for 'quantile'
closeViz,NG_Viz2DAxis: no visible global function definition for
  'dev.off'
initializeViz,NG_Viz2DAxis: no visible global function definition for
  'dev.new'
initializeViz,NG_Viz2DAxis: no visible global function definition for
  'dev.cur'
plot,NG_graph-ANY: no visible global function definition for 'box'
plot,NG_graph-ANY: no visible global function definition for 'axis'
plot,NG_graph-ANY: no visible global function definition for 'points'
plot,NG_graph-ANY: no visible global function definition for 'text'
plot,NG_graph-ANY: no visible global function definition for 'segments'
updateViz,NG_Viz2DAxis: no visible global function definition for
  'dev.set'
Undefined global functions or variables:
  axis box colors dev.cur dev.new dev.off dev.set grey head points
  quantile sd segments tail text
Consider adding
  importFrom("grDevices", "colors", "dev.cur", "dev.new", "dev.off",
             "dev.set", "grey")
  importFrom("graphics", "axis", "box", "points", "segments", "text")
  importFrom("stats", "quantile", "sd")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
getOccurrences: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.4/progress/include/RProgress.h:172:27: warning: ISO C++ forbids variable length array 'bar' [-Wvla]
  d:/RCompile/CRANpkg/lib/3.4/progress/include/RProgress.h:220:26: warning: ISO C++ forbids variable length array 'spaces' [-Wvla]
See 'd:/Rcompile/CRANpkg/local/3.4/rncl.Rcheck/00install.out' for details.
.collapse: no visible global function definition for 'head'
RNGinfo: no visible global function definition for 'setNames'
RNGlibs: no visible global function definition for 'tail'
RNGseq : <anonymous>: no visible global function definition for
  'nextRNGStream'
RNGseq: no visible global function definition for 'nextRNGStream'
RNGseq_seed: no visible global function definition for 'runif'
RNGseq_seed: no visible global function definition for 'nextRNGStream'
checkRNG: no visible global function definition for 'checkTrue'
nextRNG: no visible global function definition for 'runif'
.setRNG,numeric: no visible global function definition for 'runif'
Undefined global functions or variables:
  checkTrue head nextRNGStream runif setNames tail
Consider adding
  importFrom("stats", "runif", "setNames")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
well19937.validate: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      5.2Mb
Nnls.trimW : fun1: no visible global function definition for 'runif'
initM: no visible global function definition for 'runif'
rnmf: no visible global function definition for 'txtProgressBar'
rnmf: no visible global function definition for 'setTxtProgressBar'
see: no visible global function definition for 'heat.colors'
see: no visible global function definition for 'colorRampPalette'
see: no visible global function definition for 'grey'
see: no visible global function definition for 'par'
see: no visible global function definition for 'image'
see: no visible global function definition for 'mtext'
simtum: no visible global function definition for 'runif'
simtum: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  colorRampPalette grey heat.colors image mtext par rnorm runif
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("grDevices", "colorRampPalette", "grey", "heat.colors")
  importFrom("graphics", "image", "mtext", "par")
  importFrom("stats", "rnorm", "runif")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'robustbase' 'sfsmisc'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.BuildPartial: no visible global function definition for 'as.formula'
.BuildPartial: no visible global function definition for 'residuals'
.PairwiseCorrelation : .Standardize : <anonymous>: no visible global
  function definition for 'na.omit'
.PairwiseCorrelation : .Standardize: no visible binding for global
  variable 'median'
.PairwiseCorrelation: no visible global function definition for
  'complete.cases'
.yw: no visible global function definition for 'toeplitz'
FastQn: no visible global function definition for 'median'
FastQn: no visible global function definition for 'mad'
fqn: no visible global function definition for 'median'
fqn: no visible global function definition for 'mad'
psdcor: no visible global function definition for 'posdefify'
psdcor: no visible global function definition for 'nearcor'
robar: no visible global function definition for 'frequency'
robcor: no visible global function definition for 'covMcd'
s_FastQn: no visible global function definition for 'median'
Undefined global functions or variables:
  as.formula complete.cases covMcd frequency mad median na.omit nearcor
  posdefify residuals toeplitz
Consider adding
  importFrom("stats", "as.formula", "complete.cases", "frequency", "mad",
             "median", "na.omit", "residuals", "toeplitz")
to your NAMESPACE file.
QD2coef.f: no visible global function definition for 'ppoints'
QD2coef.f: no visible global function definition for 'lsfit'
QD2funC.f: no visible global function definition for 'ppoints'
QD2funC.f: no visible global function definition for 'lsfit'
gminit: no visible global function definition for 'var'
lywalg: no visible global function definition for 'median'
qloggamma: no visible global function definition for 'qgamma'
qloggamma: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  lsfit median ppoints qgamma qnorm var
Consider adding
  importFrom("stats", "lsfit", "median", "ppoints", "qgamma", "qnorm",
             "var")
to your NAMESPACE file.
Package in Depends field not imported from: 'ROptRegTS'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
RobRSVD: no visible global function definition for 'median'
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
See 'd:/Rcompile/CRANpkg/local/3.4/RobustEM.Rcheck/00install.out' for details.
cluster_em_outlier: no visible global function definition for 'qchisq'
jth_dsty: no visible global function definition for 'mahalanobis'
k_means: no visible global function definition for 'kmeans'
mix_rcm: no visible global function definition for 'median'
Undefined global functions or variables:
  kmeans mahalanobis median qchisq
Consider adding
  importFrom("stats", "kmeans", "mahalanobis", "median", "qchisq")
to your NAMESPACE file.
'LinkingTo' for
  'mgcv' 'robustbase'
are unused as they have no 'include' directory
Packages in Depends field not imported from:
  'Rcpp' 'RcppArmadillo' 'mgcv' 'robustbase'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GIC: no visible global function definition for 'integrate'
QM.poisson: no visible global function definition for 'ppois'
QM.poisson: no visible global function definition for 'dpois'
cplot.robustgam: no visible global function definition for 'plot'
expect.poisson: no visible global function definition for 'dpois'
expect.poisson: no visible global function definition for 'ppois'
pred.robustgam: no visible global function definition for
  'Predict.matrix'
robust.sigma: no visible global function definition for 'median'
robustgam: no visible global function definition for 's'
robustgam: no visible global function definition for
  'smooth.construct.tp.smooth.spec'
robustgam: no visible global function definition for
  'smooth.construct.cr.smooth.spec'
robustgam: no visible global function definition for
  'smooth.construct.ps.smooth.spec'
robustgam : w.fun: no visible global function definition for 'covMcd'
robustgam.GIC.optim: no visible global function definition for 'optim'
robustgam.crossval : w.fun: no visible global function definition for
  'covMcd'
robustgam.crossval: no visible global function definition for
  'integrate'
smooth.construct.tr.smooth.spec: no visible global function definition
  for 'quantile'
w.binomial: no visible global function definition for 'pbinom'
w.poisson: no visible global function definition for 'ppois'
Undefined global functions or variables:
  Predict.matrix covMcd dpois integrate median optim pbinom plot ppois
  quantile s smooth.construct.cr.smooth.spec
  smooth.construct.ps.smooth.spec smooth.construct.tp.smooth.spec
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dpois", "integrate", "median", "optim", "pbinom",
             "ppois", "quantile")
to your NAMESPACE file.
aggregateRanks: no visible binding for global variable 'median'
aggregateRanks: no visible global function definition for 'pnorm'
betaScores: no visible global function definition for 'pbeta'
correctBetaPvaluesExact: no visible binding for global variable 'qbeta'
thresholdBetaScore: no visible global function definition for 'pbeta'
Undefined global functions or variables:
  median pbeta pnorm qbeta
Consider adding
  importFrom("stats", "median", "pbeta", "pnorm", "qbeta")
to your NAMESPACE file.
Package in Depends field not imported from: 'robustbase'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages in Depends field not imported from:
  'penalized' 'splines' 'survival' 'survivalROC'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
boot.ROC: no visible global function definition for 'qnorm'
boot.ROC: no visible global function definition for 'penalized'
boot.ROC: no visible global function definition for 'coefficients'
boot.ROC: no visible global function definition for 'sd'
boot.ROC: no visible global function definition for 'optL1'
boot.ROCt: no visible global function definition for 'qnorm'
boot.ROCt: no visible global function definition for 'penalized'
boot.ROCt: no visible global function definition for 'Surv'
boot.ROCt: no visible global function definition for 'coefficients'
boot.ROCt: no visible global function definition for 'sd'
boot.ROCt: no visible global function definition for 'survivalROC'
boot.ROCt: no visible global function definition for 'optL1'
Undefined global functions or variables:
  Surv coefficients optL1 penalized qnorm sd survivalROC
Consider adding
  importFrom("stats", "coefficients", "qnorm", "sd")
to your NAMESPACE file.
'library' or 'require' call to 'ROCR' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'ROCR'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
o.rocc: warning in factor(pr, level = c(0, 1)): partial argument match
  of 'level' to 'levels'
p.rocc: warning in factor(pr, level = c(0, 1)): partial argument match
  of 'level' to 'levels'
o.rocc: no visible global function definition for 'prediction'
o.rocc: no visible global function definition for 'performance'
o.rocc: no visible global function definition for 'binom.test'
tr.rocc: no visible global function definition for 'prediction'
tr.rocc: no visible global function definition for 'performance'
Undefined global functions or variables:
  binom.test performance prediction
Consider adding
  importFrom("stats", "binom.test")
to your NAMESPACE file.
NPROCwoGS: no visible global function definition for 'quantile'
NPROCwoGS : rdirichlet: no visible global function definition for
  'rgamma'
NPROCwoGS: no visible global function definition for 'rbinom'
NPROCwoGS: no visible global function definition for 'rbeta'
NPROCwoGS: no visible binding for global variable 'quantile'
Undefined global functions or variables:
  quantile rbeta rbinom rgamma
Consider adding
  importFrom("stats", "quantile", "rbeta", "rbinom", "rgamma")
to your NAMESPACE file.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'RODBC'
A package should be listed in only one of these fields.
'library' or 'require' call to 'RODBC' which was already attached by Depends.
  Please remove these calls from your code.
Package required but not available: 'Rcplex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package which this enhances but not available for checking: 'ROI.plugin.cplex'
ROSE.eval: no visible global function definition for 'methods'
ROSE.eval: no visible binding for global variable 'model.frame'
ROSE.eval: no visible binding for global variable 'predict'
adj.formula: no visible global function definition for 'terms'
adj.formula: no visible global function definition for 'as.formula'
omnibus.balancing: no visible binding for global variable 'model.frame'
ou.sampl: no visible global function definition for 'rbinom'
over.sampl: no visible global function definition for 'rbinom'
plot.roc.inner: no visible global function definition for 'plot'
roc.curve: no visible global function definition for 'lines'
roc.curve: no visible global function definition for 'abline'
rose.real: no visible binding for global variable 'sd'
rose.real: no visible global function definition for 'sd'
rose.real: no visible global function definition for 'rnorm'
rose.sampl: no visible global function definition for 'rbinom'
under.sampl: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  abline as.formula lines methods model.frame plot predict rbinom rnorm
  sd terms
Consider adding
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "as.formula", "model.frame", "predict", "rbinom",
             "rnorm", "sd", "terms")
  importFrom("utils", "methods")
to your NAMESPACE file.
predict.rotationForest: no visible global function definition for
  'predict'
rotationForest: no visible global function definition for 'princomp'
Undefined global functions or variables:
  predict princomp
Consider adding
  importFrom("stats", "predict", "princomp")
to your NAMESPACE file.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.1Mb
bestFM: no visible global function definition for 'data'
gaRoth: no visible global function definition for 'data'
ros: no visible global function definition for 'na.omit'
rosunc: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  data na.omit rnorm
Consider adding
  importFrom("stats", "na.omit", "rnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
mfix : m4m: no visible global function definition for 'median'
rrfa: no visible global function definition for 'predict'
rrfb: no visible global function definition for 'predict'
rrfc1: no visible global function definition for 'predict'
rrfc2: no visible global function definition for 'predict'
rrfc3: no visible global function definition for 'predict'
rrfc4: no visible global function definition for 'predict'
rrfc5 : regdat: no visible global function definition for 'predict'
rrfc5 : regdat: no visible global function definition for 'glm'
rrfc5: no visible global function definition for 'predict'
rrfc6: no visible global function definition for 'predict'
rrfc7: no visible global function definition for 'predict'
rrfd: no visible global function definition for 'predict'
rrfe : rdms: no visible global function definition for 'rbinom'
rrfe: no visible global function definition for 'predict'
Undefined global functions or variables:
  glm median predict rbinom
Consider adding
  importFrom("stats", "glm", "median", "predict", "rbinom")
to your NAMESPACE file.
.computeValueReduct: no visible global function definition for 'combn'
.findAllReductsFromCore: no visible global function definition for
  'combn'
.findFirstReductsFromCore: no visible global function definition for
  'combn'
.findSmallestReductFamilyFromCore: no visible global function
  definition for 'combn'
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
royston.test: no visible global function definition for 'shapiro.test'
royston.test: no visible global function definition for 'cor'
royston.test: no visible global function definition for 'qnorm'
royston.test: no visible global function definition for 'pnorm'
royston.test: no visible global function definition for 'cov'
royston.test: no visible global function definition for 'mahalanobis'
royston.test: no visible global function definition for 'qqplot'
royston.test: no visible global function definition for 'qchisq'
royston.test: no visible global function definition for 'ppoints'
royston.test: no visible global function definition for 'abline'
royston.test: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  abline cor cov mahalanobis pchisq pnorm ppoints qchisq qnorm qqplot
  shapiro.test
Consider adding
  importFrom("graphics", "abline")
  importFrom("stats", "cor", "cov", "mahalanobis", "pchisq", "pnorm",
             "ppoints", "qchisq", "qnorm", "qqplot", "shapiro.test")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'MASS' 'RandomFields' 'akima' 'denstrip' 'geoR' 'lattice' 'maps'
  'mgcv' 'rgl' 'sm' 'tkrplot'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'tcltk'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package in Depends field not imported from: 'hash'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
P: no visible global function definition for 'has.key'
get_rand_int: no visible global function definition for 'runif'
last: no visible global function definition for 'tail'
rand_partitions: no visible global function definition for 'hash'
Undefined global functions or variables:
  has.key hash runif tail
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "tail")
to your NAMESPACE file.
evalMedian: no visible global function definition for 'xtabs'
evalMode: no visible global function definition for 'xtabs'
rpartScore: no visible global function definition for 'model.extract'
rpartScore: no visible global function definition for 'var'
rpartScore: no visible binding for global variable 'var'
splitAbs: no visible global function definition for 'xtabs'
Undefined global functions or variables:
  model.extract var xtabs
Consider adding
  importFrom("stats", "model.extract", "var", "xtabs")
to your NAMESPACE file.
'library' or 'require' call to 'RODBC' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
rpart.rules.push: no visible global function definition for 'sqlSave'
rpart.rules.table : <anonymous>: no visible global function definition
  for 'setNames'
rpart.subrules.table : <anonymous>: no visible global function
  definition for 'setNames'
Undefined global functions or variables:
  setNames sqlSave
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'survival'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'MASS' 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GenerateData: no visible global function definition for 'mvrnorm'
GetVarImp : FitPenalizedModel: no visible global function definition
  for 'clogit'
Undefined global functions or variables:
  clogit mvrnorm
cell.density.default: no visible binding for global variable
  'universalConstants'
conect.pdb: no visible binding for global variable 'elements'
masses.default: no visible binding for global variable 'elements'
toSymbols.character: no visible binding for global variable 'elements'
toSymbols.integer: no visible binding for global variable 'elements'
visualize.coords: no visible binding for global variable 'elements'
visualize.coords: no visible binding for global variable 'rgb'
Undefined global functions or variables:
  elements rgb universalConstants
Consider adding
  importFrom("grDevices", "rgb")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/rpg.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   2.8Mb
Files in the 'vignettes' directory newer than all files in 'inst/doc':
  'NEWS.html'
Files in the 'vignettes' directory but no files in 'inst/doc':
  'TNRSVignette.pdf', 'rPlantVignette.pdf'
Package has no Sweave vignette sources and no VignetteBuilder field.
postgresqlImportFile: no visible global function definition for
  'count.fields'
postgresqlImportFile: no visible global function definition for
  'read.table'
Undefined global functions or variables:
  count.fields read.table
Consider adding
  importFrom("utils", "count.fields", "read.table")
to your NAMESPACE file.
but_last: no visible global function definition for 'head'
first: no visible global function definition for 'head'
last: no visible global function definition for 'tail'
preview_frames: no visible global function definition for 'str'
print.EprimeFrame: no visible global function definition for 'str'
print.FrameList: no visible global function definition for 'str'
Undefined global functions or variables:
  head str tail
Consider adding
  importFrom("utils", "head", "str", "tail")
to your NAMESPACE file.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
print.pbDevices: no visible global function definition for 'str'
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
to your NAMESPACE file.
rpygeo.geoprocessor: warning in system(py.call, invisible = TRUE,
  minimize = TRUE, wait = wait): partial argument match of 'minimize'
  to 'minimized'
Package which this enhances but not available for checking: 'rjpod'
Found the following significant warnings:
  d:/RCompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:824:13: warning: this decimal constant is unsigned only in ISO C90
  d:/RCompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:842:13: warning: this decimal constant is unsigned only in ISO C90
  d:/RCompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomlosslatentmodel.hpp:84:13: warning: this decimal constant is unsigned only in ISO C90
  d:/Rcompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:824:13: warning: this decimal constant is unsigned only in ISO C90
  d:/Rcompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:842:13: warning: this decimal constant is unsigned only in ISO C90
  d:/Rcompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomlosslatentmodel.hpp:84:13: warning: this decimal constant is unsigned only in ISO C90
See 'd:/Rcompile/CRANpkg/local/3.4/RQuantLib.Rcheck/00install.out' for details.
installed size is 23.2Mb
  sub-directories of 1Mb or more:
    libs  22.8Mb
plot.rmas: no visible global function definition for 'rainbow'
plot.tmatrix: no visible global function definition for 'rainbow'
plot.tmatrix: no visible global function definition for 'dev.new'
Undefined global functions or variables:
  dev.new rainbow
Consider adding
  importFrom("grDevices", "dev.new", "rainbow")
to your NAMESPACE file.
rrBlupM6: no visible global function definition for 'optimize'
Undefined global functions or variables:
  optimize
Consider adding
  importFrom("stats", "optimize")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'glasso' 'matrixcalc' 'mvoutlier' 'pcaPP'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
rrest: no visible binding for global variable 'glasso'
rrest: no visible global function definition for 'pcout'
rrest: no visible global function definition for 'var'
rrest: no visible global function definition for 'mahalanobis'
rrlda : centerObservations: no visible global function definition for
  'l1median_NLM'
rrlda : df.L2glasso: no visible global function definition for
  'duplication.matrix'
rrlda : alt.df.L2glasso: no visible global function definition for
  'lower.triangle'
Undefined global functions or variables:
  duplication.matrix glasso l1median_NLM lower.triangle mahalanobis
  pcout var
Consider adding
  importFrom("stats", "mahalanobis", "var")
to your NAMESPACE file.
'library' or 'require' call to 'robustbase' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.computekappa: no visible global function definition for 'pnorm'
.computekappa: no visible global function definition for 'dnorm'
.initmethod : <anonymous>: no visible global function definition for
  'median'
.initmethod: no visible global function definition for 'model.matrix'
.mspe: no visible global function definition for 'rnorm'
.mspe : <anonymous>: no visible global function definition for 'rnorm'
makedata: no visible global function definition for 'rnorm'
makedata : addraneff: no visible global function definition for 'rnorm'
plot.meanssaemodel: no visible global function definition for 'par'
plot.meanssaemodel: no visible global function definition for 'plot'
plot.meanssaemodel: no visible global function definition for 'lines'
plot.meanssaemodel: no visible global function definition for 'axis'
plot.meanssaemodel: no visible global function definition for 'grid'
plot.meanssaemodel: no visible global function definition for 'box'
plot.meanssaemodel: no visible global function definition for 'legend'
plot.meanssaemodel: no visible global function definition for 'arrows'
saemodel: no visible global function definition for 'model.frame'
saemodel: no visible global function definition for 'model.response'
saemodel: no visible global function definition for 'model.matrix'
summary.fitsaemodel: no visible global function definition for 'pt'
summary.fitsaemodel: no visible global function definition for
  'printCoefmat'
Undefined global functions or variables:
  arrows axis box dnorm grid legend lines median model.frame
  model.matrix model.response par plot pnorm printCoefmat pt rnorm
Consider adding
  importFrom("graphics", "arrows", "axis", "box", "grid", "legend",
             "lines", "par", "plot")
  importFrom("stats", "dnorm", "median", "model.frame", "model.matrix",
             "model.response", "pnorm", "printCoefmat", "pt", "rnorm")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/RSAGA.Rcheck/00install.out' for details.
checkArgs: no visible global function definition for 'count.fields'
checkArgs: no visible global function definition for 'read.table'
estimateHap: no visible global function definition for 'read.table'
estimateHap: no visible global function definition for 'write.table'
plot.treeoutput: no visible global function definition for 'par'
plot.treeoutput: no visible global function definition for 'layout'
plot.treeoutput: no visible global function definition for 'barplot'
plot.treeoutput: no visible global function definition for 'plot'
plot.treeoutput: no visible global function definition for 'lines'
plot.treeoutput: no visible global function definition for 'lowess'
readArgs: no visible global function definition for 'read.table'
readOutput: no visible global function definition for 'read.table'
readTrees: no visible global function definition for 'count.fields'
restartRun: no visible global function definition for 'count.fields'
setWeights: no visible global function definition for 'write.table'
writeTreeoutput: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  barplot count.fields layout lines lowess par plot read.table
  write.table
Consider adding
  importFrom("graphics", "barplot", "layout", "lines", "par", "plot")
  importFrom("stats", "lowess")
  importFrom("utils", "count.fields", "read.table", "write.table")
to your NAMESPACE file.
stripslash: no visible global function definition for 'tail'
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
f_cal_chk_f: no visible global function definition for 'qf'
f_main: no visible binding for global variable 'median'
f_main: no visible binding for global variable 'sd'
f_main: no visible global function definition for 'write.table'
f_main_p: no visible global function definition for 'write.table'
f_main_p: no visible global function definition for 'runif'
get_random_filename: no visible global function definition for 'runif'
rSCA.correlation: no visible global function definition for
  'read.table'
rSCA.correlation: no visible global function definition for 'read.csv'
rSCA.correlation: no visible global function definition for 'cor'
rSCA.inference: no visible global function definition for 'read.table'
rSCA.inference: no visible global function definition for 'read.csv'
rSCA.inference: no visible global function definition for 'na.omit'
rSCA.missing: no visible global function definition for 'read.table'
rSCA.missing: no visible global function definition for 'read.csv'
rSCA.modeling: no visible global function definition for 'read.table'
rSCA.modeling: no visible global function definition for 'read.csv'
rSCA.modeling: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  cor median na.omit qf read.csv read.table runif sd write.table
Consider adding
  importFrom("stats", "cor", "median", "na.omit", "qf", "runif", "sd")
  importFrom("utils", "read.csv", "read.table", "write.table")
to your NAMESPACE file.
Found the following significant warnings:
  rproxy_impl.c:295:3: warning: ISO C forbids nested functions [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/3.4/rscproxy.Rcheck/00install.out' for details.
convexhull: no visible global function definition for 'chull'
convexhull: no visible global function definition for 'rnorm'
drawcompletegraph: no visible global function definition for 'plot'
drawcompletegraph: no visible global function definition for 'segments'
getbag: no visible global function definition for 'plot'
getbag: no visible global function definition for 'chull'
getbag: no visible global function definition for 'polygon'
getbag: no visible global function definition for 'points'
inflate: no visible global function definition for 'rnorm'
rsmed: no visible global function definition for 'runif'
rsplot: no visible global function definition for 'plot'
rsplot: no visible global function definition for 'chull'
rsplot: no visible global function definition for 'polygon'
rsplot: no visible global function definition for 'points'
rsrings: no visible global function definition for 'plot'
rsrings: no visible global function definition for 'chull'
rsrings: no visible global function definition for 'polygon'
rsrings: no visible global function definition for 'points'
rstinterval: no visible global function definition for 'plot'
rstinterval: no visible global function definition for 'runif'
rstinterval: no visible global function definition for 'rnorm'
rstinterval: no visible global function definition for 'chull'
rstinterval: no visible global function definition for 'polygon'
Undefined global functions or variables:
  chull plot points polygon rnorm runif segments
Consider adding
  importFrom("grDevices", "chull")
  importFrom("graphics", "plot", "points", "polygon", "segments")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
rsem: no visible global function definition for 'write.table'
rsem.Ascov: no visible global function definition for 'qchisq'
rsem.Ascov: no visible global function definition for 'pchisq'
rsem.emmusig: no visible global function definition for 'na.omit'
rsem.emmusig: no visible global function definition for 'qchisq'
rsem.emmusig: no visible global function definition for 'pchisq'
rsem.fit: no visible global function definition for 'pchisq'
rsem.fit: no visible global function definition for 'pf'
rsem.print : print.estimate: no visible global function definition for
  'pnorm'
rsem.weight: no visible global function definition for 'qchisq'
rsem.weight: no visible global function definition for 'pchisq'
semdiag.call.eqs: no visible global function definition for
  'write.table'
semdiag.read.eqs: no visible global function definition for 'read.fwf'
Undefined global functions or variables:
  na.omit pchisq pf pnorm qchisq read.fwf write.table
Consider adding
  importFrom("stats", "na.omit", "pchisq", "pf", "pnorm", "qchisq")
  importFrom("utils", "read.fwf", "write.table")
to your NAMESPACE file.
Found the following significant warnings:
   #warning Please include winsock2.h before windows.h
  qap_decode.c:200:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:200:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:55: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:60: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.4/Rserve.Rcheck/00install.out' for details.
Rserve: no visible global function definition for 'shortPathName'
Undefined global functions or variables:
  shortPathName
Consider adding
  importFrom("utils", "shortPathName")
to your NAMESPACE file.
addNoisyCopies: no visible global function definition for 'rnorm'
eta: no visible global function definition for 'var'
gaussClassifier: no visible global function definition for 'runif'
getSigma: no visible global function definition for 'sd'
getSigma: no visible binding for global variable 'sd'
sfaClassify: no visible global function definition for 'rainbow'
sfaClassify: no visible global function definition for 'par'
sfaClassify: no visible global function definition for 'plot'
sfaClassify: no visible global function definition for 'points'
sfaClassify: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines par plot points rainbow rnorm runif sd var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "lines", "par", "plot", "points")
  importFrom("stats", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
Depends: includes the non-default packages:
  'biwt' 'cairoDevice' 'fBasics' 'gplots' 'gWidgets' 'gWidgetsRGtk2'
  'minerva' 'parmigene' 'stringr' 'snowfall'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' calls to packages already attached by Depends:
  'grDevices' 'snowfall'
  Please remove these calls from your code.
'library' or 'require' call to 'ctc' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'biwt' 'cairoDevice' 'fBasics' 'gWidgets' 'gWidgetsRGtk2' 'gplots'
  'minerva' 'parmigene' 'snowfall' 'stringr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' calls in package code:
  'MASS' 'codetools' 'lattice' 'network' 'parallel' 'tcltk' 'xtable'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: 'utils:::edit.data.frame'
  See the note in ?`:::` about the use of this operator.
filterSD: no visible binding for global variable 'sd'
filterSD: no visible global function definition for 'quantile'
fit_lasso: no visible global function definition for 'coef'
fit_prlasso: no visible global function definition for 'coef'
rsig: no visible binding for global variable 'mclapply'
rsig.all: no visible binding for global variable 'mclapply'
rsig.all : <anonymous>: no visible global function definition for
  'flush.console'
rsig.all : <anonymous>: no visible global function definition for
  'predict'
Undefined global functions or variables:
  coef flush.console mclapply predict quantile sd
Consider adding
  importFrom("stats", "coef", "predict", "quantile", "sd")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
composeMosaicFromImageRandom: no visible global function definition for
  'runif'
composeMosaicFromImageRegular: no visible global function definition
  for 'runif'
computeStatisticalQuantitiesTile: no visible global function definition
  for 'median'
createLibraryIndexDataFrame: no visible global function definition for
  'write.table'
getCloseMatch: no visible global function definition for 'runif'
Undefined global functions or variables:
  median runif write.table
Consider adding
  importFrom("stats", "median", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file.
negbin.pow : negbin.disp: no visible global function definition for
  'rpois'
negbin.pow : negbin.disp: no visible global function definition for
  'rnbinom'
negbin.pow : inner.fcn: no visible global function definition for
  'na.omit'
negbin.pow : inner.fcn: no visible global function definition for
  'quantile'
negbin.pow: no visible global function definition for 'txtProgressBar'
negbin.pow: no visible global function definition for
  'setTxtProgressBar'
poiss.pow : inner.fcn: no visible global function definition for
  'rpois'
poiss.pow : inner.fcn: no visible global function definition for
  'quantile'
poiss.pow: no visible global function definition for 'txtProgressBar'
poiss.pow: no visible global function definition for
  'setTxtProgressBar'
Undefined global functions or variables:
  na.omit quantile rnbinom rpois setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit", "quantile", "rnbinom", "rpois")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   8.4Mb
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:

======== End of example output (where/before crash/hang up occured ?) ========
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
exoplantname: no visible global function definition for 'URLencode'
localgroupname: no visible global function definition for 'URLencode'
starname: no visible global function definition for 'URLencode'
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
rbing.O2: no visible global function definition for 'runif'
rbing.O2: no visible global function definition for 'rbeta'
rbing.O2: no visible global function definition for 'rbinom'
rbing.Op: no visible global function definition for 'rnorm'
rbing.Op: no visible global function definition for 'rbinom'
rbing.Op: no visible global function definition for 'runif'
rbmf.O2: no visible global function definition for 'runif'
rmf.matrix: no visible global function definition for 'runif'
rmf.vector: no visible global function definition for 'rnorm'
rmf.vector: no visible global function definition for 'rbinom'
rustiefel: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rbeta rbinom rnorm runif
Consider adding
  importFrom("stats", "rbeta", "rbinom", "rnorm", "runif")
to your NAMESPACE file.
Package in Depends field not imported from: 'plyr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
RStorm: no visible global function definition for 'alply'
Undefined global functions or variables:
  alply
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    Lib  11.5Mb
Math.Sym: no visible binding for global variable 'transtab'
jythonStart: no visible global function definition for '.jinit'
jythonStart: no visible global function definition for '.jnew'
jythonStart: no visible binding for global variable '.Jython'
sympy: no visible binding for global variable '.Jython'
sympy: no visible global function definition for '.jstrVal'
sympyStart: no visible binding for global variable '.Jython'
Undefined global functions or variables:
  .Jython .jinit .jnew .jstrVal transtab
barplot.rtconnect: no visible global function definition for 'rainbow'
barplot.rtconnect: no visible global function definition for 'text'
plot.rtconnect: no visible global function definition for 'par'
plot.rtconnect: no visible global function definition for 'plot'
plot.rtconnect: no visible global function definition for 'axis.Date'
rtconnect: no visible global function definition for 'read.table'
Undefined global functions or variables:
  axis.Date par plot rainbow read.table text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis.Date", "par", "plot", "text")
  importFrom("utils", "read.table")
to your NAMESPACE file.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
classify_model: no visible global function definition for 'predict'
cross_validate: no visible global function definition for 'predict'
read_data: no visible global function definition for 'read.csv'
read_data: no visible global function definition for 'read.delim'
Undefined global functions or variables:
  predict read.csv read.delim
Consider adding
  importFrom("stats", "predict")
  importFrom("utils", "read.csv", "read.delim")
to your NAMESPACE file.
plotGLCM: no visible global function definition for 'plot'
plotGLCM: no visible global function definition for 'points'
Undefined global functions or variables:
  plot points
Consider adding
  importFrom("graphics", "plot", "points")
to your NAMESPACE file.
.forest.plot: no visible global function definition for 'par'
.forest.plot: no visible global function definition for 'plot'
.forest.plot: no visible global function definition for 'abline'
.forest.plot: no visible global function definition for 'arrows'
.forest.plot: no visible global function definition for 'points'
.forest.plot.scale: no visible global function definition for 'par'
.forest.plot.scale: no visible global function definition for 'plot'
.forest.plot.scale: no visible global function definition for 'axTicks'
.forest.plot.scale : <anonymous>: no visible global function definition
  for 'lines'
.forest.plot.scale: no visible global function definition for 'lines'
.forest.plot.scale: no visible global function definition for 'text'
.rtf.plot: no visible global function definition for 'png'
.rtf.plot: no visible global function definition for 'dev.off'
.rtf.trellis.object: no visible global function definition for 'png'
.rtf.trellis.object: no visible global function definition for
  'dev.off'
addSessionInfo.RTF: no visible global function definition for
  'sessionInfo'
Undefined global functions or variables:
  abline arrows axTicks dev.off lines par plot png points sessionInfo
  text
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "abline", "arrows", "axTicks", "lines", "par",
             "plot", "points", "text")
  importFrom("utils", "sessionInfo")
to your NAMESPACE file.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   2.0Mb
animated_county_unemployment_choropleth: no visible global function
  definition for 'data'
animated_state_unemployment_choropleth: no visible global function
  definition for 'data'
build_county_df: no visible global function definition for 'data'
build_state_df: no visible global function definition for 'data'
county_unemployment_choropleth: no visible global function definition
  for 'data'
get_county_unemployment_df: no visible global function definition for
  'read.fwf'
get_county_unemployment_df: no visible global function definition for
  'data'
state_unemployment_choropleth: no visible global function definition
  for 'data'
Undefined global functions or variables:
  data read.fwf
Consider adding
  importFrom("utils", "data", "read.fwf")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'Runuran' 'cairoDevice' 'gWidgets' 'gWidgetsRGtk2' 'rvgtest'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: 'utils:::.getHelpFile'
  See the note in ?`:::` about the use of this operator.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
HapMendlianCheck: no visible global function definition for
  'write.table'
rvPDT.test.sub: no visible global function definition for 'pnorm'
whap.prehap: no visible global function definition for 'write.table'
whap.prehap: no visible global function definition for 'read.table'
Undefined global functions or variables:
  pnorm read.table write.table
Consider adding
  importFrom("stats", "pnorm")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
'library' or 'require' call to 'pixmap' which was already attached by Depends.
  Please remove these calls from your code.
rvideopoker: warning in rp.radiogroup(mypanel, var =
  state$penny.nickel.quarter.dollar, initval = 1, values = c(1, 5, 25,
  100), title = "Bet (in Cents)", action = setbet): partial argument
  match of 'var' to 'variable'
rvideopoker: warning in rp.slider(mypanel, var = state$no.of.credits,
  from = 1, to = 5, initval = 1, title = "How many Credits?",
  resolution = 1, action = creditset, showvalue = TRUE): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC1, action = card1check, title = "Keep Card 1?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC2, action = card2check, title = "Keep Card 2?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC3, action = card3check, title = "Keep Card 3?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC4, action = card4check, title = "Keep Card 4?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC5, action = card5check, title = "Keep Card 5?"): partial
  argument match of 'var' to 'variable'
rvideopoker : plotFrame: no visible global function definition for
  'par'
rvideopoker : showBack: no visible global function definition for
  'title'
rvideopoker : showCardsInitially: no visible global function definition
  for 'title'
Undefined global functions or variables:
  par title
Consider adding
  importFrom("graphics", "par", "title")
to your NAMESPACE file.
Package suggested but not available for checking: 'gpuR'
Package in Depends field not imported from: 'parallel'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' calls which should be '::':
  'base:::ifelse' 'base:::mapply' 'graphics:::abline' 'stats:::cor'
  'stats:::cov' 'stats:::rbeta' 'stats:::rbinom' 'stats:::rcauchy'
  'stats:::rchisq' 'stats:::rexp' 'stats:::rgamma' 'stats:::rhyper'
  'stats:::rmultinom' 'stats:::rpois' 'stats:::rt' 'stats:::runif'
  See the note in ?`:::` about the use of this operator.
Found the following significant warnings:
  Warning: GNU Extension: Different type kinds at (1)
See 'd:/Rcompile/CRANpkg/local/3.4/rvsel.Rcheck/00install.out' for details.
lc_TDT: no visible global function definition for 'pchisq'
rvTDT: no visible global function definition for 'dbeta'
Undefined global functions or variables:
  dbeta pchisq
Consider adding
  importFrom("stats", "dbeta", "pchisq")
to your NAMESPACE file.
LASSO: no visible global function definition for 'lm'
LASSO: no visible global function definition for 'anova'
LASSO: no visible global function definition for 'glm'
LASSO: no visible global function definition for 'pchisq'
LASSO : <anonymous>: no visible global function definition for
  'extractAIC'
PCR : <anonymous>: no visible global function definition for 'cor'
PLS : <anonymous>: no visible global function definition for 'cor'
RR : RRscore: no visible binding for global variable 'sd'
SPLS: no visible global function definition for 'lm'
SPLS: no visible global function definition for 'anova'
SPLS : <anonymous>: no visible global function definition for
  'extractAIC'
VTWOD : getScores: no visible global function definition for 'sd'
VTWOD : getScores: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  anova cor extractAIC glm lm pchisq pnorm sd
Consider adding
  importFrom("stats", "anova", "cor", "extractAIC", "glm", "lm",
             "pchisq", "pnorm", "sd")
to your NAMESPACE file.
check_ISO_code: no visible binding for global variable 'NoAm_country'
check_ISO_code: no visible binding for global variable 'SoAm_country'
check_ISO_code: no visible binding for global variable 'Oceana_country'
check_ISO_code: no visible binding for global variable 'Africa_country'
check_ISO_code: no visible binding for global variable 'Asia_country'
check_ISO_code: no visible binding for global variable 'Eur_country'
climate_map: no visible binding for global variable 'data'
date_correct: no visible global function definition for 'tail'
Undefined global functions or variables:
  Africa_country Asia_country Eur_country NoAm_country Oceana_country
  SoAm_country data tail
Consider adding
  importFrom("utils", "data", "tail")
to your NAMESPACE file.
RWBP.default: no visible global function definition for 'na.omit'
RWBP.default: no visible global function definition for 'kmeans'
RWBP.formula: no visible global function definition for 'model.extract'
plot.RWBP: no visible global function definition for 'plot'
predict.RWBP: no visible global function definition for 'head'
Undefined global functions or variables:
  head kmeans model.extract na.omit plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "kmeans", "model.extract", "na.omit")
  importFrom("utils", "head")
to your NAMESPACE file.
weblogo: no visible global function definition for 'browseURL'
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
wiener_plot: no visible global function definition for 'density'
wiener_plot: no visible global function definition for 'par'
wiener_plot: no visible global function definition for 'plot'
wiener_plot: no visible global function definition for 'rug'
wiener_plot: no visible global function definition for 'mtext'
Undefined global functions or variables:
  density mtext par plot rug
Consider adding
  importFrom("graphics", "mtext", "par", "plot", "rug")
  importFrom("stats", "density")
to your NAMESPACE file.
File 'RWinEdt/R/zzz.R':
  .onAttach calls:
    writeLines(edtFile, con = send2RedtLoc)
    writeLines(edtFile, con = send2RedtLoc)

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
getcolors: no visible global function definition for 'rainbow'
lines.rief: no visible global function definition for 'lines.default'
lines.riif: no visible global function definition for 'lines.default'
lines.rirf: no visible global function definition for 'lines.default'
plot.ifile: no visible global function definition for 'plot'
plot.rief: no visible global function definition for 'plot.default'
plot.rief: no visible global function definition for 'lines'
plot.riif: no visible global function definition for 'plot.default'
plot.riif: no visible global function definition for 'lines'
plot.rirf: no visible global function definition for 'plot.default'
plot.rirf: no visible global function definition for 'lines'
plot.rtef: no visible global function definition for 'plot.default'
plot.rtif: no visible global function definition for 'plot.default'
plot.rtrf: no visible global function definition for 'plot.default'
read.ifile: no visible global function definition for 'read.table'
read.pfile: no visible global function definition for 'read.table'
write.wdat: no visible global function definition for 'write.table'
Undefined global functions or variables:
  lines lines.default plot plot.default rainbow read.table write.table
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "lines", "lines.default", "plot",
             "plot.default")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
.dwt: no visible global function definition for 'median'
.udwt: no visible global function definition for 'median'
plotSignalTransformation: no visible global function definition for
  'plot'
plotSignalTransformation: no visible global function definition for
  'box'
plotSignalTransformation: no visible global function definition for
  'axis'
plotSignalTransformation: no visible global function definition for
  'lines'
plotSignalTransformation: no visible global function definition for
  'legend'
Undefined global functions or variables:
  axis box legend lines median plot
Consider adding
  importFrom("graphics", "axis", "box", "legend", "lines", "plot")
  importFrom("stats", "median")
to your NAMESPACE file.
Analyze: no visible global function definition for 'runif'
Analyze: no visible global function definition for 'mcmc'
Analyze: no visible global function definition for 'varnames<-'
AnalyzeWithExitPoll: no visible global function definition for 'runif'
AnalyzeWithExitPoll: no visible global function definition for 'mcmc'
AnalyzeWithExitPoll: no visible global function definition for
  'varnames<-'
Tune: no visible global function definition for 'runif'
TuneWithExitPoll: no visible global function definition for 'runif'
form.mcmc.object: no visible global function definition for
  'varnames<-'
gendata.ep : rdirichlet: no visible global function definition for
  'rgamma'
gendata.ep : rwish: no visible global function definition for 'rchisq'
gendata.ep : rwish: no visible global function definition for 'rnorm'
gendata.ep: no visible global function definition for 'rpois'
gendata.ep: no visible global function definition for 'runif'
gendata.ep: no visible global function definition for 'rmultinom'
gendata.ep: no visible global function definition for 'cov2cor'
gq.summary: no visible global function definition for 'mcmc.list'
gq.summary: no visible global function definition for 'mcmc'
gq_diagnostics: no visible global function definition for 'mcmc.list'
gq_diagnostics: no visible global function definition for 'mcmc'
gq_diagnostics: no visible global function definition for 'gelman.diag'
gq_diagnostics: no visible global function definition for 'geweke.diag'
gq_diagnostics: no visible global function definition for 'heidel.diag'
gq_diagnostics: no visible global function definition for
  'autocorr.diag'
Undefined global functions or variables:
  autocorr.diag cov2cor gelman.diag geweke.diag heidel.diag mcmc
  mcmc.list rchisq rgamma rmultinom rnorm rpois runif varnames<-
Consider adding
  importFrom("stats", "cov2cor", "rchisq", "rgamma", "rmultinom",
             "rnorm", "rpois", "runif")
to your NAMESPACE file.
Package in Depends field not imported from: 'lars'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/Ryacas.Rcheck/00install.out' for details.
'library' or 'require' call to 'vcd' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'foreign' 'ggplot2' 'grid' 'psych'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: 'foreign:::adQuote'
  See the note in ?`:::` about the use of this operator.
.onAttach: no visible global function definition for 'winMenuAdd'
.onAttach: no visible global function definition for 'winMenuAddItem'
calc.hist.breaks: no visible global function definition for
  'nclass.Sturges'
calc.hist.breaks: no visible global function definition for 'nclass.FD'
calc.hist.breaks: no visible global function definition for
  'nclass.scott'
check.class: no visible global function definition for 'as.formula'
gtkColorSelectionForPlotGetColor: no visible global function definition
  for 'rgb'
gtkColorSelectionWidgetNew: no visible global function definition for
  'colors'
gtkFileChooserDialogFilteredActivate: no visible binding for global
  variable 'theme_grey'
localize: no visible global function definition for 'localeToCharset'
summary.CrossTable : twoDimTable: no visible global function definition
  for 'addmargins'
summary.CrossTable: no visible global function definition for
  'assocstats'
write.spss: no visible global function definition for 'write.table'
write.stata: no visible global function definition for 'write.table'
Undefined global functions or variables:
  addmargins as.formula assocstats colors localeToCharset nclass.FD
  nclass.Sturges nclass.scott rgb theme_grey winMenuAdd winMenuAddItem
  write.table
Consider adding
  importFrom("grDevices", "colors", "nclass.FD", "nclass.Sturges",
             "nclass.scott", "rgb")
  importFrom("stats", "addmargins", "as.formula")
  importFrom("utils", "localeToCharset", "winMenuAdd", "winMenuAddItem",
             "write.table")
to your NAMESPACE file.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    sample_data   3.2Mb
calculate.summary: no visible global function definition for 'sd'
detect.saccades: no visible global function definition for 'median'
diagnostic.plot: no visible global function definition for 'dev.new'
diagnostic.plot: no visible global function definition for 'par'
diagnostic.plot: no visible global function definition for 'recordPlot'
diagnostic.plot: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  dev.new dev.off median par recordPlot sd
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "recordPlot")
  importFrom("graphics", "par")
  importFrom("stats", "median", "sd")
to your NAMESPACE file.
eblupDyn: no visible global function definition for 'model.frame'
eblupDyn: no visible global function definition for 'model.matrix'
eblupDyn: no visible global function definition for 'pnorm'
eblupRY: no visible global function definition for 'model.frame'
eblupRY: no visible global function definition for 'model.matrix'
eblupRY: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  model.frame model.matrix pnorm
Consider adding
  importFrom("stats", "model.frame", "model.matrix", "pnorm")
to your NAMESPACE file.
SAENET.nnet: no visible global function definition for 'as.formula'
SAENET.nnet: no visible global function definition for 'rnorm'
SAENET.train: no visible global function definition for 'predict'
Undefined global functions or variables:
  as.formula predict rnorm
Consider adding
  importFrom("stats", "as.formula", "predict", "rnorm")
to your NAMESPACE file.
fit.saery.AR1: no visible global function definition for 'qnorm'
fit.saery.MA1: no visible global function definition for 'qnorm'
fit.saery.indep: no visible global function definition for 'qnorm'
mse.saery.boot.AR1.typeI: no visible global function definition for
  'rnorm'
mse.saery.boot.AR1.typeI: no visible global function definition for
  'write.table'
mse.saery.boot.AR1.typeII: no visible global function definition for
  'rnorm'
mse.saery.boot.AR1.typeII: no visible global function definition for
  'write.table'
mse.saery.boot.MA1.typeI: no visible global function definition for
  'rnorm'
mse.saery.boot.MA1.typeI: no visible global function definition for
  'write.table'
mse.saery.boot.MA1.typeII: no visible global function definition for
  'rnorm'
mse.saery.boot.MA1.typeII: no visible global function definition for
  'write.table'
plot.saery: no visible global function definition for 'devAskNewPage'
plot.saery: no visible global function definition for 'par'
plot.saery: no visible global function definition for 'plot'
plot.saery: no visible global function definition for 'abline'
plot.saery: no visible global function definition for 'title'
plot.saery: no visible global function definition for 'axis'
plot.saery: no visible global function definition for 'lines'
plot.saery: no visible global function definition for 'legend'
pvalue: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  abline axis devAskNewPage legend lines par plot pnorm qnorm rnorm
  title write.table
Consider adding
  importFrom("grDevices", "devAskNewPage")
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "plot", "title")
  importFrom("stats", "pnorm", "qnorm", "rnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Package in Depends field not imported from: 'lpSolveAPI'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
glm: no visible binding for global variable 'gaussian'
glm: no visible global function definition for 'glm.control'
glm: no visible global function definition for 'model.response'
glm: no visible global function definition for 'is.empty.model'
glm: no visible global function definition for 'model.matrix'
glm: no visible global function definition for 'model.weights'
glm: no visible global function definition for 'model.offset'
glm: no visible global function definition for 'model.extract'
glm: no visible global function definition for 'glm.fit'
glm: no visible global function definition for '.getXlevels'
separator: no visible global function definition for 'make.lp'
separator: no visible global function definition for 'set.column'
separator: no visible global function definition for 'set.rhs'
separator: no visible global function definition for 'set.constr.type'
separator: no visible global function definition for 'set.objfn'
separator: no visible global function definition for 'set.bounds'
separator: no visible global function definition for 'lp.control'
separator: no visible global function definition for 'get.variables'
separator: no visible global function definition for 'set.basis'
separator: no visible global function definition for
  'get.dual.solution'
Undefined global functions or variables:
  .getXlevels gaussian get.dual.solution get.variables glm.control
  glm.fit is.empty.model lp.control make.lp model.extract model.matrix
  model.offset model.response model.weights set.basis set.bounds
  set.column set.constr.type set.objfn set.rhs
Consider adding
  importFrom("stats", ".getXlevels", "gaussian", "glm.control",
             "glm.fit", "is.empty.model", "model.extract",
             "model.matrix", "model.offset", "model.response",
             "model.weights")
to your NAMESPACE file.
plot.safidesign: no visible global function definition for 'par'
plot.safidesign: no visible global function definition for 'matplot'
plot.safidesign: no visible global function definition for 'axis'
plot.safimodel : plot.coef: no visible global function definition for
  'colorRampPalette'
plot.safimodel : plot.coef: no visible global function definition for
  'barplot'
plot.safimodel : plot.coef: no visible global function definition for
  'axis'
plot.safimodel : plot.coef: no visible global function definition for
  'abline'
plot.safimodel : plot.coef: no visible global function definition for
  'box'
plot.safimodel: no visible global function definition for 'par'
safiModel: no visible global function definition for 'lm'
Undefined global functions or variables:
  abline axis barplot box colorRampPalette lm matplot par
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "abline", "axis", "barplot", "box", "matplot",
             "par")
  importFrom("stats", "lm")
to your NAMESPACE file.
propdiff.acc: no visible global function definition for 'rbeta'
propdiff.acc: no visible global function definition for 'rbinom'
propdiff.acc: no visible global function definition for 'pbeta'
propdiff.alc: no visible global function definition for 'rbeta'
propdiff.alc: no visible global function definition for 'rbinom'
propdiff.alc: no visible global function definition for 'qbeta'
propdiff.freq: no visible global function definition for 'qnorm'
propdiff.mblacc: no visible global function definition for 'rbeta'
propdiff.mblacc: no visible global function definition for 'rbinom'
propdiff.mblacc: no visible global function definition for 'pbeta'
propdiff.mblalc: no visible global function definition for 'rbeta'
propdiff.mblalc: no visible global function definition for 'rbinom'
propdiff.mblalc: no visible global function definition for 'qbeta'
propdiff.mblmodwoc: no visible global function definition for 'qchisq'
propdiff.mblmodwoc: no visible global function definition for 'pbeta'
propdiff.mblwoc: no visible global function definition for 'pbeta'
propdiff.modwoc: no visible global function definition for 'qchisq'
propdiff.modwoc: no visible global function definition for 'pbeta'
propdiff.woc: no visible global function definition for 'pbeta'
Undefined global functions or variables:
  pbeta qbeta qchisq qnorm rbeta rbinom
Consider adding
  importFrom("stats", "pbeta", "qbeta", "qchisq", "qnorm", "rbeta",
             "rbinom")
to your NAMESPACE file.
plot.samEL: no visible global function definition for 'matplot'
plot.samHL: no visible global function definition for 'matplot'
plot.samLL: no visible global function definition for 'matplot'
plot.samQL: no visible global function definition for 'matplot'
predict.samEL: no visible global function definition for 'ns'
predict.samHL: no visible global function definition for 'ns'
predict.samLL: no visible global function definition for 'ns'
predict.samQL: no visible global function definition for 'ns'
samEL: no visible global function definition for 'ns'
samHL: no visible global function definition for 'ns'
samHL: no visible binding for global variable 'median'
samLL: no visible global function definition for 'ns'
samQL: no visible global function definition for 'ns'
Undefined global functions or variables:
  matplot median ns
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "median")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'impute' 'matrixStats'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'impute' 'matrixStats'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
S3 methods shown with full name in documentation object 'samr-internal':
  'plot.SAMoutput' 'print.SAMoutput'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
GraphBinaryForestPlot: no visible global function definition for
  'abline'
GraphBinaryForestPlot: no visible global function definition for 'text'
GraphContinuousForestPlot: no visible global function definition for
  'abline'
GraphContinuousForestPlot: no visible global function definition for
  'text'
ImputeBinaryEvents: no visible global function definition for 'rbinom'
ImputeSMD: no visible global function definition for 'rnorm'
funnelplot: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline rbinom rnorm text
Consider adding
  importFrom("graphics", "abline", "text")
  importFrom("stats", "rbinom", "rnorm")
to your NAMESPACE file.
generate.sample.core: no visible global function definition for
  'predict'
mdh: no visible global function definition for 'model.frame'
mdh: no visible binding for global variable 'na.fail'
mdh: no visible global function definition for '.getXlevels'
mdh: no visible global function definition for 'quantile'
mdh: no visible global function definition for 'hist'
predict.mdh: no visible global function definition for 'model.frame'
samur: no visible global function definition for 'predict'
Undefined global functions or variables:
  .getXlevels hist model.frame na.fail predict quantile
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", ".getXlevels", "model.frame", "na.fail", "predict",
             "quantile")
to your NAMESPACE file.
.run_chunk: no visible global function definition for 'capture.output'
install_sand_packages: no visible global function definition for
  'packageDescription'
set_chapter: no visible global function definition for 'sessionInfo'
Undefined global functions or variables:
  capture.output packageDescription sessionInfo
Consider adding
  importFrom("utils", "capture.output", "packageDescription",
             "sessionInfo")
to your NAMESPACE file.
download.sas7bdat.sources : <anonymous>: no visible global function
  definition for 'download.file'
generate.sas7bdat.source: no visible global function definition for
  'download.file'
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
parse.SAScii: no visible binding for global variable 'end'
parse.SAScii: no visible binding for global variable 'start'
read.SAScii: no visible global function definition for 'download.file'
read.SAScii: no visible global function definition for 'unzip'
read.SAScii: no visible global function definition for 'read.fwf'
read.SAScii: no visible global function definition for 'capture.output'
Undefined global functions or variables:
  capture.output download.file end read.fwf start unzip
Consider adding
  importFrom("stats", "end", "start")
  importFrom("utils", "capture.output", "download.file", "read.fwf",
             "unzip")
to your NAMESPACE file.
SASPECT: no visible global function definition for 'dbinom'
my.SOnePro: missing arguments not allowed in calls to 'c'
my.ttest: no visible global function definition for 'var'
Undefined global functions or variables:
  dbinom var
Consider adding
  importFrom("stats", "dbinom", "var")
to your NAMESPACE file.
loads: no visible global function definition for 'untar'
saves: no visible global function definition for 'tar'
Undefined global functions or variables:
  tar untar
Consider adding
  importFrom("utils", "tar", "untar")
to your NAMESPACE file.
clogistCalc: no visible global function definition for 'model.matrix'
clogistCalc: no visible global function definition for 'glm.fit'
clogistCalc: no visible global function definition for 'binomial'
clogistInfo : all.not.equal: no visible global function definition for
  'var'
geeUOmega: no visible global function definition for 'model.extract'
geeUOmega: no visible global function definition for 'model.matrix'
geeUOmega: no visible binding for global variable 'contrasts'
mgee: no visible binding for global variable 'gaussian'
sawsCalc: no visible global function definition for 'pf'
sawsCalc: no visible global function definition for 'qt'
Undefined global functions or variables:
  binomial contrasts gaussian glm.fit model.extract model.matrix pf qt
  var
Consider adding
  importFrom("stats", "binomial", "contrasts", "gaussian", "glm.fit",
             "model.extract", "model.matrix", "pf", "qt", "var")
to your NAMESPACE file.
K: no visible global function definition for 'dnorm'
sBF: no visible global function definition for 'density'
sBF: no visible global function definition for 'txtProgressBar'
sBF: no visible global function definition for 'setTxtProgressBar'
Undefined global functions or variables:
  density dnorm setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "density", "dnorm")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
plot.psgc: no visible global function definition for 'par'
plot.psgc: no visible global function definition for 'barplot'
plot.psgc: no visible global function definition for 'hist'
plotci.sA: no visible global function definition for 'par'
plotci.sA: no visible global function definition for 'plot'
plotci.sA: no visible global function definition for 'points'
plotci.sA: no visible global function definition for 'segments'
plotci.sA: no visible global function definition for 'abline'
plotci.sA: no visible global function definition for 'axis'
qM.sM: no visible binding for global variable 'quantile'
rwish: no visible global function definition for 'rnorm'
sbgcop.mcmc: no visible global function definition for 'qnorm'
sbgcop.mcmc: no visible global function definition for 'rnorm'
sbgcop.mcmc: no visible global function definition for 'cov'
sbgcop.mcmc: no visible global function definition for 'runif'
sbgcop.mcmc: no visible global function definition for 'pnorm'
sbgcop.mcmc: no visible global function definition for 'quantile'
summary.psgc: no visible global function definition for 'acf'
Undefined global functions or variables:
  abline acf axis barplot cov hist par plot pnorm points qnorm quantile
  rnorm runif segments
Consider adding
  importFrom("graphics", "abline", "axis", "barplot", "hist", "par",
             "plot", "points", "segments")
  importFrom("stats", "acf", "cov", "pnorm", "qnorm", "quantile",
             "rnorm", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  d:/Compiler/gcc-4.9.3/local330/include/gmp-x64.h:140:23: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/Compiler/gcc-4.9.3/local330/include/gmp-x64.h:141:14: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.4/sbrl.Rcheck/00install.out' for details.
fitSBSA: no visible binding for global variable 'var'
fitSBSA: no visible global function definition for 'var'
fitSBSA: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  qnorm var
Consider adding
  importFrom("stats", "qnorm", "var")
to your NAMESPACE file.
ChooseBest: no visible global function definition for 'head'
GetScores: no visible global function definition for 'write.table'
ReportTable: no visible binding for global variable 'sd'
ReportTable: no visible global function definition for 'write.table'
Undefined global functions or variables:
  head sd write.table
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "head", "write.table")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'MASS' 'lars'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
lse: no visible global function definition for 'lm'
predict.scalreg: no visible global function definition for 'fitted'
slassoEst: no visible global function definition for 'qnorm'
slassoEst: no visible global function definition for 'lars'
slassoEst: no visible global function definition for 'predict.lars'
Undefined global functions or variables:
  fitted lars lm predict.lars qnorm
Consider adding
  importFrom("stats", "fitted", "lm", "qnorm")
to your NAMESPACE file.
importCol: no visible global function definition for 'packageVersion'
importMCMC : getL: no visible global function definition for
  'read.table'
importMCMC : getP: no visible global function definition for
  'read.table'
importMCMC : getB: no visible global function definition for
  'read.table'
importMCMC : getR: no visible global function definition for
  'read.table'
importProj : getPolicies: no visible global function definition for
  'read.table'
importProj : getYears: no visible global function definition for
  'read.table'
importProj : getB: no visible global function definition for
  'read.table'
importProj : getY: no visible global function definition for
  'read.table'
iterate : summaryN: no visible binding for global variable 'median'
iterate : summarySigmaI: no visible binding for global variable
  'median'
plotLA: no visible global function definition for 'aggregate'
plotN: no visible global function definition for 'aggregate'
Undefined global functions or variables:
  aggregate median packageVersion read.table
Consider adding
  importFrom("stats", "aggregate", "median")
  importFrom("utils", "packageVersion", "read.table")
to your NAMESPACE file.
plot.scair: no visible global function definition for 'par'
plot.scair: no visible global function definition for 'plot'
plot.scair: no visible global function definition for 'points'
plot.scar: no visible global function definition for 'par'
plot.scar: no visible global function definition for 'plot'
plot.scar: no visible global function definition for 'points'
predict.scair: no visible global function definition for 'approx'
predict.scar: no visible global function definition for 'approx'
scair: no visible global function definition for 'gaussian'
scair: no visible global function definition for 'runif'
scair: no visible global function definition for 'rnorm'
scar: no visible global function definition for 'gaussian'
scar: no visible global function definition for 'glm.fit'
scar: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx gaussian glm.fit par plot points rnorm runif
Consider adding
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "approx", "gaussian", "glm.fit", "rnorm", "runif")
to your NAMESPACE file.
prime.factor: no visible global function definition for 'data'
prime.factor: no visible binding for global variable 'primlist'
Undefined global functions or variables:
  data primlist
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
futuresplot: no visible global function definition for 'rainbow'
plot.schwartz2f.fit: no visible global function definition for
  'colorRampPalette'
plot.schwartz2f.fit: no visible global function definition for
  'rainbow'
plot,schwartz2f.fit-missing: no visible global function definition for
  'colorRampPalette'
plot,schwartz2f.fit-missing: no visible global function definition for
  'rainbow'
Undefined global functions or variables:
  colorRampPalette rainbow
Consider adding
  importFrom("grDevices", "colorRampPalette", "rainbow")
to your NAMESPACE file.
c,scidbdf: warning in build_dim_schema(x, newname = j): partial
  argument match of 'newname' to 'newnames'
.format: no visible global function definition for 'capture.output'
.scidbstr: no visible global function definition for 'capture.output'
glm.fit_scidb: no visible global function definition for 'gaussian'
glm.fit_scidb: no visible global function definition for 'pnorm'
glm_scidb: no visible global function definition for 'gaussian'
glm_scidb: no visible global function definition for 'as.formula'
iqiter : nextEl: no visible global function definition for 'read.table'
iquery: no visible global function definition for 'read.table'
model_scidb: no visible global function definition for 'as.formula'
model_scidb: no visible global function definition for 'terms'
model_scidb: no visible global function definition for 'drop.terms'
predict.glm_scidb: no visible global function definition for 'coef'
print.glm_scidb: no visible global function definition for 'coef'
summary.glm_scidb: no visible global function definition for 'coef'
glm.fit,scidb-ANY-MNSN: no visible global function definition for
  'gaussian'
glm.fit,scidb-ANY-MNSN: no visible global function definition for
  'pnorm'
glm,ANY-ANY-scidbdf: no visible global function definition for
  'gaussian'
glm,ANY-ANY-scidbdf: no visible global function definition for
  'as.formula'
image,scidb: no visible global function definition for 'axis'
Undefined global functions or variables:
  as.formula axis capture.output coef drop.terms gaussian pnorm
  read.table terms
Consider adding
  importFrom("graphics", "axis")
  importFrom("stats", "as.formula", "coef", "drop.terms", "gaussian",
             "pnorm", "terms")
  importFrom("utils", "capture.output", "read.table")
to your NAMESPACE file.
'library' or 'require' call to 'QUIC' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
scio.cv: no visible global function definition for 'cov'
scio.refit: no visible global function definition for 'QUIC'
Undefined global functions or variables:
  QUIC cov
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
bargraph.CI: no visible global function definition for 'barplot'
bargraph.CI: no visible global function definition for 'arrows'
bargraph.CI: no visible global function definition for 'gray.colors'
lineplot.CI : int.plot: no visible global function definition for 'par'
lineplot.CI : int.plot: no visible global function definition for
  'matplot'
lineplot.CI : int.plot : axisInt: no visible global function definition
  for 'axis'
lineplot.CI : int.plot: no visible global function definition for
  'text'
lineplot.CI: no visible global function definition for 'plot'
lineplot.CI: no visible global function definition for 'axis'
lineplot.CI: no visible global function definition for 'arrows'
lineplot.CI: no visible global function definition for 'points'
Undefined global functions or variables:
  arrows axis barplot gray.colors matplot par plot points text
Consider adding
  importFrom("grDevices", "gray.colors")
  importFrom("graphics", "arrows", "axis", "barplot", "matplot", "par",
             "plot", "points", "text")
to your NAMESPACE file.
ES: no visible global function definition for 'read.table'
ES: no visible global function definition for 'sd'
ES: no visible global function definition for 'var'
ES: no visible global function definition for 'median'
combine: no visible global function definition for 'read.table'
Undefined global functions or variables:
  median read.table sd var
Consider adding
  importFrom("stats", "median", "sd", "var")
  importFrom("utils", "read.table")
to your NAMESPACE file.
score.GGUM: no visible global function definition for 'dnorm'
score.GGUM: no visible global function definition for 'hist'
score.GGUM: no visible global function definition for 'write.table'
Undefined global functions or variables:
  dnorm hist write.table
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "dnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file.
CreatePssm: no visible binding for global variable 'training'
Undefined global functions or variables:
  training
bdecomp : <anonymous>: no visible global function definition for 'var'
betafam: no visible global function definition for 'integrate'
calcscore.formula: no visible global function definition for
  'model.response'
plotscore: no visible binding for global variable 'plot'
plotscore: no visible global function definition for 'lines'
Undefined global functions or variables:
  integrate lines model.response plot var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "integrate", "model.response", "var")
to your NAMESPACE file.
plot.SK: no visible global function definition for 'plot'
plot.SK: no visible global function definition for 'segments'
plot.SK: no visible global function definition for 'axis'
plot.SK: no visible global function definition for 'mtext'
Undefined global functions or variables:
  axis mtext plot segments
Consider adding
  importFrom("graphics", "axis", "mtext", "plot", "segments")
to your NAMESPACE file.
Newsboy: no visible global function definition for 'qnorm'
Newsboy: no visible global function definition for 'dnorm'
Newsboy: no visible global function definition for 'pnorm'
SCperf: no visible global function definition for 'ARMAtoMA'
SCperf: no visible global function definition for 'qnorm'
SSL: no visible global function definition for 'qnorm'
SSL: no visible global function definition for 'ARMAtoMA'
Undefined global functions or variables:
  ARMAtoMA dnorm pnorm qnorm
Consider adding
  importFrom("stats", "ARMAtoMA", "dnorm", "pnorm", "qnorm")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'RCurl' 'XML'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'RCurl' 'XML'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
scrape: no visible global function definition for 'getURLAsynchronous'
scrape: no visible global function definition for 'runif'
scrape: no visible global function definition for 'capture.output'
scrape: no visible binding for global variable 'xmlParse'
scrape: no visible binding for global variable 'htmlParse'
Undefined global functions or variables:
  capture.output getURLAsynchronous htmlParse runif xmlParse
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'MASS' 'oligoClasses'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
lahiri.design: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
estimateTimeToComputeTargetDefinition: no visible global function
  definition for 'flush.console'
estimateTimeToComputeTargetDefinition: no visible global function
  definition for 'combn'
initialize,sdcTargetDefinitionClass: no visible global function
  definition for 'flush.console'
initialize,sdcTargetDefinitionClass: no visible global function
  definition for 'combn'
initialize,sdcTargetDefinitionClass: no visible global function
  definition for 'quantile'
initialize,sdcTargetMatrixClass: no visible global function definition
  for 'flush.console'
Undefined global functions or variables:
  combn flush.console quantile
Consider adding
  importFrom("stats", "quantile")
  importFrom("utils", "combn", "flush.console")
to your NAMESPACE file.
Error in re-building vignettes:
  ...

Loading required package: mgcv
Loading required package: nlme

Attaching package: 'nlme'

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

    getData

This is mgcv 1.8-16. For overview type 'help("mgcv-package")'.
Loading required package: glmnet
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-5

Loading required package: earth
Loading required package: plotmo
Loading required package: plotrix
Loading required package: TeachingDemos
Loading required package: rJava
Quitting from lines 45-52 (quick_sdm.Rmd) 
Error: processing vignette 'quick_sdm.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
Execution halted
'library' or 'require' calls in package code:
  'raster' 'sp'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
sealasso: no visible global function definition for 'lars'
weight.calc: no visible global function definition for 'lars'
Undefined global functions or variables:
  lars
adx: no visible global function definition for 'abline'
adx: no visible global function definition for 'legend'
dx: no visible global function definition for 'abline'
dx: no visible global function definition for 'legend'
maxd: no visible global function definition for 'abline'
maxd: no visible global function definition for 'legend'
pc: no visible global function definition for 'rainbow'
pc: no visible global function definition for 'plot'
pc: no visible global function definition for 'abline'
pc: no visible global function definition for 'legend'
pc: no visible global function definition for 'points'
pcu: no visible global function definition for 'rainbow'
pcu: no visible global function definition for 'plot'
pcu: no visible global function definition for 'abline'
pcu: no visible global function definition for 'legend'
pcu: no visible global function definition for 'points'
rmsd: no visible global function definition for 'abline'
rmsd: no visible global function definition for 'legend'
rsd: no visible global function definition for 'abline'
rsd: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline legend plot points rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "legend", "plot", "points")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'NADA' 'lubridate' 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package in Depends field not imported from: 'JM'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SEchart: no visible global function definition for 'plot'
SEchart: no visible global function definition for 'rect'
SEchart: no visible global function definition for 'par'
SEchart: no visible global function definition for 'grid'
SEchart: no visible global function definition for 'axis'
SEchart: no visible global function definition for 'text'
SEchart: no visible global function definition for 'lines'
SEchart: no visible global function definition for 'heat.colors'
SEchart: no visible global function definition for 'topo.colors'
SEchart: no visible global function definition for 'cm.colors'
SEchart: no visible global function definition for 'terrain.colors'
SEchart: no visible global function definition for 'gray.colors'
SEchart: no visible global function definition for 'rainbow'
SEchart: no visible global function definition for 'points'
SEchart: no visible global function definition for 'legend'
Undefined global functions or variables:
  axis cm.colors gray.colors grid heat.colors legend lines par plot
  points rainbow rect terrain.colors text topo.colors
Consider adding
  importFrom("grDevices", "cm.colors", "gray.colors", "heat.colors",
             "rainbow", "terrain.colors", "topo.colors")
  importFrom("graphics", "axis", "grid", "legend", "lines", "par",
             "plot", "points", "rect", "text")
to your NAMESPACE file.
fdc2s: no visible global function definition for 'lm'
fdc3s: no visible global function definition for 'lm'
fds2s: no visible global function definition for 'lm'
fds3s: no visible global function definition for 'lm'
Undefined global functions or variables:
  lm
Consider adding
  importFrom("stats", "lm")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'car' 'sgeostat' 'spatstat'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.read.SeerStatTXT: no visible global function definition for
  'read.table'
.write.SeerStatTXT: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.5Mb
'library' or 'require' calls in package code:
  'rgdal' 'spdep' 'spgrass6'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.use.spgrass6: no visible global function definition for 'listw2mat'
.use.spgrass6: no visible global function definition for 'sn2listw'
conprof: no visible global function definition for 'axis'
conprof: no visible global function definition for 'lines'
isp: no visible global function definition for 'combn'
points.SegLocal: no visible global function definition for 'points'
Undefined global functions or variables:
  axis combn lines listw2mat points sn2listw
Consider adding
  importFrom("graphics", "axis", "lines", "points")
  importFrom("utils", "combn")
to your NAMESPACE file.
get.infectiousness: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  qchisq
Consider adding
  importFrom("stats", "qchisq")
to your NAMESPACE file.
Files in the 'vignettes' directory but no files in 'inst/doc':
  'INSTRUCTION.Rmd'
Package has no Sweave vignette sources and no VignetteBuilder field.
get_statistics_from_file: no visible global function definition for
  'read.csv'
glm_anova: no visible global function definition for 'aov'
glm_anova: no visible global function definition for 'glm'
glm_anova: no visible global function definition for 'gaussian'
glm_anova: no visible global function definition for 'anova'
glm_anova: no visible global function definition for 'quasipoisson'
glm_anova: no visible global function definition for 'sd'
glm_anova: no visible global function definition for 'p.adjust'
ttest_cohens_d: no visible global function definition for 't.test'
ttest_cohens_d: no visible global function definition for 'sd'
Undefined global functions or variables:
  anova aov gaussian glm p.adjust quasipoisson read.csv sd t.test
Consider adding
  importFrom("stats", "anova", "aov", "gaussian", "glm", "p.adjust",
             "quasipoisson", "sd", "t.test")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
predict.SEL: warning in splineDesign(newdata, knots = knts, ord =
  object$nord, deriv = rep(deriv, length(newdata)), outer.ok = TRUE):
  partial argument match of 'deriv' to 'derivs'
getbinPost: no visible binding for global variable 'dbeta'
getbinPost: no visible binding for global variable 'pbeta'
getbinPost : fu: no visible global function definition for 'dbinom'
getbinPost : fu: no visible global function definition for 'predict'
getbinPost: no visible global function definition for 'integrate'
getbinPost: no visible global function definition for 'splinefun'
int.funct: no visible global function definition for 'integrate'
int.funct2: no visible global function definition for 'integrate'
min.abs: no visible global function definition for 'uniroot'
plot.SEL: no visible global function definition for 'plot'
print.SEL: no visible global function definition for 'integrate'
print.summary.SEL : foo1: no visible global function definition for
  'predict'
print.summary.SEL : foo2: no visible global function definition for
  'predict'
print.summary.SEL: no visible global function definition for
  'integrate'
quantSEL: no visible global function definition for 'predict'
quantSEL: no visible global function definition for 'splinefun'
rvSEL: no visible global function definition for 'runif'
Undefined global functions or variables:
  dbeta dbinom integrate pbeta plot predict runif splinefun uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dbeta", "dbinom", "integrate", "pbeta", "predict",
             "runif", "splinefun", "uniroot")
to your NAMESPACE file.
Package in Depends field not imported from: 'sem'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages in Depends field not imported from:
  'datautils' 'irlba'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
computeKernel: no visible binding for global variable 'sd'
computeKernel: no visible global function definition for 'dist'
computeKernel: no visible global function definition for 'quantile'
computeProjectionFromKernel : <anonymous>: no visible global function
  definition for 'irlba'
distortions: no visible binding for global variable 'sd'
distortions: no visible global function definition for 'dist'
Undefined global functions or variables:
  dist irlba quantile sd
Consider adding
  importFrom("stats", "dist", "quantile", "sd")
to your NAMESPACE file.
ChiSquaredLRTest: no visible global function definition for 'na.omit'
ChiSquaredLRTest: no visible global function definition for 'cov'
ChiSquaredLRTest: no visible global function definition for 'dmvnorm'
ChiSquaredLRTest: no visible global function definition for 'pchisq'
NormalTheoryLRTest: no visible global function definition for 'na.omit'
NormalTheoryLRTest: no visible global function definition for 'cov'
NormalTheoryLRTest: no visible global function definition for 'dmvnorm'
NormalTheoryLRTest: no visible global function definition for 'sd'
NormalTheoryLRTest: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  cov dmvnorm na.omit pchisq pnorm sd
Consider adding
  importFrom("stats", "cov", "na.omit", "pchisq", "pnorm", "sd")
to your NAMESPACE file.
'library' or 'require' call to 'MplusAutomation' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
'library' or 'require' calls in package code:
  'XML' 'boot' 'sem'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  'boot:::const' 'stats:::AIC.logLik' 'stats:::BIC.logLik'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'addPath.plsm' 'endogenous' 'predecessors' 'qSquared' 'reorder'
  'resempls' 'residuals.sempls'
efficiencies.semsfa: no visible global function definition for 'dnorm'
efficiencies.semsfa: no visible global function definition for 'pnorm'
fan: no visible global function definition for 'pnorm'
plot.semsfa: no visible global function definition for 'hist'
plot.semsfa: no visible global function definition for 'plot'
plot.semsfa: no visible global function definition for 'density'
semsfa: no visible global function definition for 'residuals'
semsfa: no visible global function definition for 'loess'
semsfa: no visible global function definition for 'optimize'
semsfa: no visible global function definition for 'pnorm'
semsfa: no visible binding for global variable 'sd'
summary.semsfa: no visible global function definition for 'pt'
summary.semsfa: no visible global function definition for
  'printCoefmat'
Undefined global functions or variables:
  density dnorm hist loess optimize plot pnorm printCoefmat pt
  residuals sd
Consider adding
  importFrom("graphics", "hist", "plot")
  importFrom("stats", "density", "dnorm", "loess", "optimize", "pnorm",
             "printCoefmat", "pt", "residuals", "sd")
to your NAMESPACE file.
.plot_attachment: no visible global function definition for 'dev.off'
.update_list: no visible global function definition for 'modifyList'
mime_part.data.frame: no visible global function definition for
  'write.table'
mime_part.ggplot: no visible binding for global variable 'pdf'
mime_part.matrix: no visible global function definition for
  'write.table'
mime_part.trellis: no visible binding for global variable 'pdf'
Undefined global functions or variables:
  dev.off modifyList pdf write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("utils", "modifyList", "write.table")
to your NAMESPACE file.
'library' or 'require' call to 'rtiff' which was already attached by Depends.
  Please remove these calls from your code.
gconv: no visible global function definition for 'convolve'
sens.analysis.aberrant.rank: no visible global function definition for
  'pnorm'
sens.analysis.mh: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  convolve pnorm
Consider adding
  importFrom("stats", "convolve", "pnorm")
to your NAMESPACE file.
mscorev: no visible global function definition for 'quantile'
senmwCI : funcCI: no visible global function definition for 'qnorm'
senmwCI : funcCI2: no visible global function definition for 'qnorm'
separable1k: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm qnorm quantile
Consider adding
  importFrom("stats", "pnorm", "qnorm", "quantile")
to your NAMESPACE file.
plot.sensitivity.2.0d: no visible global function definition for 'gray'
sensitivitySGD: no visible global function definition for 'tail'
sensitivitySGL: no visible global function definition for 'tail'
Undefined global functions or variables:
  gray tail
Consider adding
  importFrom("grDevices", "gray")
  importFrom("utils", "tail")
to your NAMESPACE file.
separationplot: no visible global function definition for 'dev.new'
separationplot: no visible global function definition for 'pdf'
separationplot: no visible global function definition for 'par'
separationplot: no visible global function definition for 'plot'
separationplot: no visible global function definition for 'title'
separationplot: no visible global function definition for 'segments'
separationplot: no visible global function definition for 'rect'
separationplot: no visible global function definition for 'points'
separationplot: no visible global function definition for 'lines'
separationplot: no visible global function definition for
  'colorRampPalette'
separationplot: no visible global function definition for 'layout'
separationplot: no visible global function definition for 'plot.new'
separationplot: no visible global function definition for 'legend'
separationplot: no visible global function definition for 'dev.off'
separationplot: no visible global function definition for 'locator'
sp.categorical: no visible global function definition for 'dev.new'
sp.categorical: no visible global function definition for 'pdf'
sp.categorical: no visible global function definition for 'par'
sp.categorical: no visible global function definition for 'layout'
sp.categorical: no visible global function definition for 'plot'
sp.categorical: no visible global function definition for 'text'
sp.categorical: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  colorRampPalette dev.new dev.off layout legend lines locator par pdf
  plot plot.new points rect segments text title
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.new", "dev.off",
             "pdf")
  importFrom("graphics", "layout", "legend", "lines", "locator", "par",
             "plot", "plot.new", "points", "rect", "segments", "text",
             "title")
to your NAMESPACE file.
GammaDist: no visible binding for global variable 'rgamma'
VEpowerPP: no visible global function definition for 'qnorm'
applyStopRules: no visible global function definition for 'qnorm'
finalLogRankTest: no visible global function definition for 'qnorm'
finalLogRankTest: no visible global function definition for 'pchisq'
generateDropout: no visible global function definition for 'rexp'
generateEnrollment: no visible global function definition for 'rpois'
generateEnrollment: no visible global function definition for 'runif'
generateInfection: no visible global function definition for 'rexp'
generateInfection : <anonymous>: no visible global function definition
  for 'rexp'
getAlphaPerTest: no visible global function definition for 'uniroot'
getHarmBound: no visible global function definition for 'dbinom'
getHarmBound: no visible global function definition for 'write.csv'
getTreatmentAssignment : <anonymous>: no visible global function
  definition for 'runif'
getTreatmentAssignment: no visible global function definition for
  'runif'
simTrial: no visible global function definition for 'runif'
sumTrialOneTrtArm: no visible global function definition for 'quantile'
testVE: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  dbinom pchisq qnorm quantile rexp rgamma rpois runif uniroot
  write.csv
Consider adding
  importFrom("stats", "dbinom", "pchisq", "qnorm", "quantile", "rexp",
             "rgamma", "rpois", "runif", "uniroot")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.6Mb
Unexported objects imported by ':::' calls:
  'igraph:::.igraph.shapes' 'igraph:::i.get.arrow.mode'
  'igraph:::i.parse.plot.params' 'igraph:::igraph.Arrows'
  'igraph:::igraph.check.shapes' 'igraph:::igraph.polygon'
  See the note in ?`:::` about the use of this operator.
plotenz : addmark: no visible global function definition for 'par'
plotenz : addmark: no visible global function definition for 'plot'
plotenz : addmark: no visible global function definition for 'text'
plotenz : addmark: no visible global function definition for 'segments'
plotenz : addband: no visible global function definition for 'segments'
plotenz : addband: no visible global function definition for 'text'
plotenz: no visible global function definition for 'layout'
plotenz: no visible global function definition for 'text'
plotenz: no visible global function definition for 'dev.new'
Undefined global functions or variables:
  dev.new layout par plot segments text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "layout", "par", "plot", "segments", "text")
to your NAMESPACE file.
capture: no visible binding for global variable 'resultText'
restore.session: no visible binding for global variable
  '.save.session.packages'
restore.session: no visible binding for global variable
  '.save.session.search'
save.session: no visible global function definition for 'dev.list'
save.session: no visible binding for '<<-' assignment to
  '.save.session.search'
save.session: no visible binding for '<<-' assignment to
  '.save.session.packages'
Undefined global functions or variables:
  .save.session.packages .save.session.search dev.list resultText
Consider adding
  importFrom("grDevices", "dev.list")
to your NAMESPACE file.
setpath: no visible global function definition for 'cov'
setpath: no visible global function definition for 'median'
setpath: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  cov median pchisq
Consider adding
  importFrom("stats", "cov", "median", "pchisq")
to your NAMESPACE file.
random.number.test: no visible global function definition for 'runif'
random.number.test: no visible global function definition for 'rnorm'
setRNG: no visible global function definition for 'runif'
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
'library' or 'require' call to 'graphics' which was already attached by Depends.
  Please remove these calls from your code.
severity: no visible global function definition for 'qnorm'
severity: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
L_exp: no visible global function definition for 'pnorm'
L_hNV: no visible global function definition for 'pnorm'
L_trunc: no visible global function definition for 'pnorm'
L_trunc_mufest: no visible global function definition for 'pnorm'
dgp: no visible global function definition for 'runif'
dgp: no visible global function definition for 'rnorm'
eff.sfa: no visible global function definition for 'predict'
fitted.sfa: no visible global function definition for 'predict'
predict.sfa: no visible global function definition for 'coef'
print.sfa: no visible global function definition for 'coef'
residuals.sfa: no visible global function definition for 'fitted'
sfa: no visible global function definition for 'model.frame'
sfa: no visible global function definition for 'model.response'
sfa.fit: no visible global function definition for 'lm'
sfa.fit: no visible global function definition for 'resid'
sfa.fit: no visible global function definition for 'var'
sfa.fit: no visible global function definition for 'optim'
summary.sfa: no visible global function definition for 'logLik'
summary.sfa: no visible global function definition for 'pchisq'
te.eff.sfa: no visible global function definition for 'residuals'
te.eff.sfa: no visible global function definition for 'pnorm'
u.sfa: no visible global function definition for 'residuals'
u.sfa: no visible global function definition for 'dnorm'
u.sfa: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  coef dnorm fitted lm logLik model.frame model.response optim pchisq
  pnorm predict resid residuals rnorm runif var
Consider adding
  importFrom("stats", "coef", "dnorm", "fitted", "lm", "logLik",
             "model.frame", "model.response", "optim", "pchisq", "pnorm",
             "predict", "resid", "residuals", "rnorm", "runif", "var")
to your NAMESPACE file.
installed size is 64.6Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    gdal   3.2Mb
    libs  51.7Mb
    proj   5.0Mb
Error in re-building vignettes:
  ...
Quitting from lines 137-138 (sf2.Rmd) 
Error: processing vignette 'sf2.Rmd' failed with diagnostics:
Could not guess driver for d:\RCompile\CRANpkg\local\3.4\sf.Rcheck\vign_test\sf\vignettes\nc.shp
Execution halted
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.4/BH/include/boost/unordered/detail/buckets.hpp:586:29: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.4/BH/include/boost/unordered/detail/buckets.hpp:591:38: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.4/sgd.Rcheck/00install.out' for details.
coxCrossVal: no visible binding for global variable 'sd'
error.bars: no visible global function definition for 'segments'
linCrossVal: no visible binding for global variable 'sd'
logitCrossVal: no visible binding for global variable 'sd'
plot.cv.SGL: no visible global function definition for 'points'
Undefined global functions or variables:
  points sd segments
Consider adding
  importFrom("graphics", "points", "segments")
  importFrom("stats", "sd")
to your NAMESPACE file.
.computePStar: no visible global function definition for 'uniroot'
plotBoundary: no visible global function definition for
  'scale_y_continuous'
Undefined global functions or variables:
  scale_y_continuous uniroot
Consider adding
  importFrom("stats", "uniroot")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'Matrix' 'fields'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
distLaplacian: no visible global function definition for 'sparseMatrix'
gmdDeflation: no visible global function definition for 'rnorm'
laplacian: no visible global function definition for 'sparseMatrix'
Undefined global functions or variables:
  rnorm sparseMatrix
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   7.7Mb
amse: no visible global function definition for 'na.omit'
arb: no visible global function definition for 'na.omit'
rdatagen: no visible global function definition for 'qnorm'
rdatagen: no visible global function definition for 'pbinom'
rdatagen: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  na.omit pbinom pnorm qnorm
Consider adding
  importFrom("stats", "na.omit", "pbinom", "pnorm", "qnorm")
to your NAMESPACE file.
UQnormalize.count: no visible binding for global variable 'quantile'
plotNScores: no visible global function definition for 'par'
plotNScores: no visible global function definition for 'hist'
plotNScores: no visible global function definition for 'title'
plotScores: no visible global function definition for 'par'
plotScores: no visible global function definition for 'hist'
plotScores: no visible global function definition for 'title'
sgRSEA: no visible binding for global variable 'sd'
sgRSEA: no visible global function definition for 'p.adjust'
sgRSEA.mean: no visible binding for global variable 'sd'
sgRSEA.mean: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  hist p.adjust par quantile sd title
Consider adding
  importFrom("graphics", "hist", "par", "title")
  importFrom("stats", "p.adjust", "quantile", "sd")
to your NAMESPACE file.
'library' or 'require' call to 'foreign' which was already attached by Depends.
  Please remove these calls from your code.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/shapes.Rcheck/00install.out' for details.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    www   9.5Mb
popify: no visible global function definition for 'runif'
tipify: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    www   6.2Mb
get_selected_names: no visible global function definition for 'tail'
get_selected_names: no visible global function definition for 'head'
Undefined global functions or variables:
  head tail
Consider adding
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
shrink.estim: no visible global function definition for 'cov'
shrink.estim: no visible global function definition for 'cor'
shrink.estim: no visible global function definition for 'cov2cor'
targetCor: no visible global function definition for 'cor.test'
targetCor: no visible global function definition for 'cor'
targetCor: no visible global function definition for 'sd'
targetCor: no visible global function definition for 'cov'
targetD: no visible binding for global variable 'var'
targetF: no visible global function definition for 'cov'
targetF: no visible global function definition for 'cor'
targetG: no visible global function definition for 'cor'
targetG: no visible global function definition for 'sd'
targetG: no visible global function definition for 'cov'
targetGpos: no visible global function definition for 'cor'
targetGpos: no visible global function definition for 'sd'
targetGpos: no visible global function definition for 'cov'
targetGstar: no visible global function definition for 'cor'
targetGstar: no visible global function definition for 'sd'
targetGstar: no visible global function definition for 'cov'
Undefined global functions or variables:
  cor cor.test cov cov2cor sd var
Consider adding
  importFrom("stats", "cor", "cor.test", "cov", "cov2cor", "sd", "var")
to your NAMESPACE file.
.params: no visible binding for global variable 'URLencode'
.params: no visible global function definition for 'URLencode'
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
load_fonts: no visible global function definition for 'unzip'
Undefined global functions or variables:
  unzip
Consider adding
  importFrom("utils", "unzip")
to your NAMESPACE file.
footpoint.nodes: no visible global function definition for
  'coordinates'
nt.connect: no visible global function definition for 'bbox'
nt.connect: no visible global function definition for 'plot.new'
nt.connect: no visible global function definition for 'plot.window'
nt.connect: no visible global function definition for 'title'
nt.connect: no visible global function definition for 'rainbow'
nt.connect: no visible global function definition for 'slot'
nt.connect: no visible global function definition for
  'as.SpatialLines.SLDF'
nt.connect: no visible global function definition for 'lines'
nt.connect: no visible global function definition for
  'SpatialLinesDataFrame'
points2network: no visible global function definition for 'is'
ptsinnt.view: no visible global function definition for 'bbox'
ptsinnt.view: no visible global function definition for 'plot'
ptsinnt.view: no visible global function definition for 'points'
ptsinnt.view: no visible global function definition for 'lines'
ptsinnt.view: no visible global function definition for 'legend'
readshpnw: no visible global function definition for 'is'
readshpnw: no visible global function definition for 'coordinates'
Undefined global functions or variables:
  SpatialLinesDataFrame as.SpatialLines.SLDF bbox coordinates is legend
  lines plot plot.new plot.window points rainbow slot title
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend", "lines", "plot", "plot.new",
             "plot.window", "points", "title")
  importFrom("methods", "is", "slot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Depends: includes the non-default packages:
  'hdrcde' 'coda' 'MASS' 'bayesm' 'mnormt' 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  'MASS' 'bayesm' 'coda' 'hdrcde' 'mnormt' 'spatstat'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages in Depends field not imported from:
  'ade4' 'corpcor'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
filter.PCA.default: no visible global function definition for
  'princomp'
filter.mRMR.default: no visible global function definition for
  'discretize'
gaussian.default: no visible global function definition for 'cov'
gaussian.default: no visible global function definition for
  'cov.shrink'
plot.verify.cv: no visible global function definition for 'plot'
plot.verify.cv: no visible global function definition for 'points'
plot.verify.ho: no visible global function definition for 'plot'
plot.verify.ho: no visible global function definition for 'points'
plot.verify.loo: no visible global function definition for 'plot'
plot.verify.loo: no visible global function definition for 'points'
predict.dpa1: no visible global function definition for 'cor'
predict.filter.PCA: no visible global function definition for 'predict'
predict.filter.RegressionTreeFilter: no visible global function
  definition for 'is.struct'
predict.filter.RegressionTreeFilter: no visible global function
  definition for 'var'
simulator.Simple1: no visible global function definition for 'rnorm'
verify.ho.default: no visible global function definition for 'predict'
verify.loo.default: no visible global function definition for 'predict'
Undefined global functions or variables:
  cor cov cov.shrink discretize is.struct plot points predict princomp
  rnorm var
Consider adding
  importFrom("graphics", "plot", "points")
  importFrom("stats", "cor", "cov", "predict", "princomp", "rnorm",
             "var")
to your NAMESPACE file.
dSepAdji: no visible global function definition for 'as'
dag2cpdagAdj: no visible global function definition for 'as'
randomDAG: no visible global function definition for 'rbinom'
structIntervDist: no visible global function definition for 'as'
Undefined global functions or variables:
  as rbinom
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "rbinom")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
plot.std: no visible global function definition for 'rainbow'
plot.std: no visible global function definition for 'legend'
read.std: no visible global function definition for 'read.table'
std: no visible global function definition for 'na.exclude'
Undefined global functions or variables:
  legend na.exclude rainbow read.table
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend")
  importFrom("stats", "na.exclude")
  importFrom("utils", "read.table")
to your NAMESPACE file.
.cluster: no visible global function definition for 'kmeans'
.plot.sigclust: no visible global function definition for 'par'
.plot.sigclust: no visible global function definition for 'density'
.plot.sigclust: no visible global function definition for 'runif'
.plot.sigclust: no visible global function definition for 'dnorm'
.plot.sigclust: no visible global function definition for 'lines'
.plot.sigclust: no visible global function definition for 'points'
.plot.sigclust: no visible global function definition for 'title'
.plot.sigclust: no visible global function definition for 'text'
.plot.sigclust: no visible global function definition for 'qnorm'
.plot.sigclust: no visible global function definition for 'abline'
.plot.sigclust: no visible global function definition for 'quantile'
.plot.sigclust: no visible global function definition for 'legend'
.simnull: no visible global function definition for 'rnorm'
.vareigen: no visible global function definition for 'mad'
.vareigen: no visible global function definition for 'cov'
sigclust: no visible global function definition for 'sd'
sigclust: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  abline cov density dnorm kmeans legend lines mad par pnorm points
  qnorm quantile rnorm runif sd text title
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "points",
             "text", "title")
  importFrom("stats", "cov", "density", "dnorm", "kmeans", "mad",
             "pnorm", "qnorm", "quantile", "rnorm", "runif", "sd")
to your NAMESPACE file.
Sight.Est: no visible global function definition for 'glm'
Sight.Est: no visible global function definition for 'binomial'
Sight.Est: no visible global function definition for 'coef'
Sight.Est: no visible global function definition for 'terms'
Sight.Est: no visible binding for global variable 'binomial'
covtheta: no visible global function definition for 'cov'
print.sightest: no visible global function definition for 'qnorm'
summary.sightest: no visible global function definition for 'qnorm'
vardiff: no visible global function definition for 'vcov'
vardiff: no visible global function definition for 'coef'
vardiff: no visible global function definition for 'terms'
varlog.lam: no visible global function definition for 'vcov'
varlog.lam: no visible global function definition for 'coef'
varlog.lam: no visible global function definition for 'terms'
Undefined global functions or variables:
  binomial coef cov glm qnorm terms vcov
Consider adding
  importFrom("stats", "binomial", "coef", "cov", "glm", "qnorm", "terms",
             "vcov")
to your NAMESPACE file.
plot.intersect: no visible global function definition for 'points'
plot.intersect: no visible global function definition for 'plot'
plot.receiver: no visible global function definition for 'points'
plot.receiver: no visible global function definition for 'plot'
plot.receiver: no visible global function definition for 'segments'
plot.transmitter: no visible global function definition for 'points'
plot.transmitter: no visible global function definition for 'plot'
plot.transmitter: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines plot points segments
Consider adding
  importFrom("graphics", "lines", "plot", "points", "segments")
to your NAMESPACE file.
signmedian.test: no visible global function definition for 'median'
signmedian.test: no visible global function definition for 'binom.test'
signmedian.test: no visible global function definition for 'pbinom'
signmedian.test: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  binom.test median pbinom pnorm
Consider adding
  importFrom("stats", "binom.test", "median", "pbinom", "pnorm")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'gdata' 'splines'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.SII: no visible global function definition for 'plot'
plot.SII: no visible global function definition for 'lines'
plot.SII: no visible global function definition for 'abline'
plot.SII: no visible global function definition for 'legend'
sii : approx.l: no visible global function definition for 'approx'
sii.excel: no visible global function definition for 'predict'
sii.excel : approx.l: no visible global function definition for
  'approx'
Undefined global functions or variables:
  abline approx legend lines plot predict
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "plot")
  importFrom("stats", "approx", "predict")
to your NAMESPACE file.
SCIrp: no visible binding for global variable 'median'
WYht: no visible global function definition for 'lm'
WYht: no visible global function definition for 'residuals'
WYht: no visible global function definition for 'coefficients'
WYht: no visible global function definition for 'quantile'
mcpHill : alignfunc: no visible global function definition for 'lm'
mcpHill : alignfunc: no visible global function definition for
  'predict'
mcpHill : funcA: no visible global function definition for 'lm'
mcpHill : funcA: no visible global function definition for 'residuals'
mcpHill : tstatshort: no visible global function definition for 'lm'
mcpHill : tstatshort: no visible global function definition for
  'coefficients'
mcpHill : tstatshort: no visible global function definition for
  'residuals'
tsht: no visible global function definition for 'quantile'
Undefined global functions or variables:
  coefficients lm median predict quantile residuals
Consider adding
  importFrom("stats", "coefficients", "lm", "median", "predict",
             "quantile", "residuals")
to your NAMESPACE file.
mainalg,mmctestres: no visible global function definition for 'hist'
Undefined global functions or variables:
  hist
Consider adding
  importFrom("graphics", "hist")
to your NAMESPACE file.
linearextrapolation: no visible global function definition for 'coef'
linearextrapolation: no visible global function definition for 'lm'
plotsimexaft: no visible global function definition for 'plot'
plotsimexaft: no visible global function definition for 'lm'
plotsimexaft: no visible global function definition for 'predict'
plotsimexaft: no visible global function definition for 'lines'
plotsimexaft: no visible global function definition for 'points'
plotsimexaft: no visible global function definition for 'legend'
print.simexaft: no visible global function definition for 'coef'
quadraticextrapolation: no visible global function definition for
  'coef'
quadraticextrapolation: no visible global function definition for 'lm'
simexaft: no visible global function definition for 'terms'
simexaft: no visible global function definition for 'rnorm'
simexaft: no visible binding for global variable 'var'
simexaft: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  coef legend lines lm plot pnorm points predict rnorm terms var
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points")
  importFrom("stats", "coef", "lm", "pnorm", "predict", "rnorm", "terms",
             "var")
to your NAMESPACE file.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'construct.s' 'extract.covmat'
getFormula: no visible global function definition for 'as.formula'
internalSimXyplot : f: no visible global function definition for
  'median'
runSimulation: no visible global function definition for 'runif'
setup: no visible global function definition for 'runif'
clusterSetup,ANY-data.frame-SampleControl: no visible binding for
  global variable 'cnam'
clusterSetup,ANY-data.frame-TwoStageControl: no visible binding for
  global variable 'cnam'
initialize,DCARContControl: no visible binding for global variable
  'rnorm'
initialize,DataControl: no visible binding for global variable 'rnorm'
Undefined global functions or variables:
  as.formula cnam median rnorm runif
Consider adding
  importFrom("stats", "as.formula", "median", "rnorm", "runif")
to your NAMESPACE file.
cumallcausehr: no visible global function definition for 'integrate'
plotbe: no visible global function definition for 'plot'
plotbe: no visible global function definition for 'lines'
plotbe: no visible global function definition for 'legend'
plotcph: no visible global function definition for 'confint'
plotcph: no visible global function definition for 'plot'
plotcph: no visible global function definition for 'abline'
plotcph: no visible global function definition for 'axis'
plotcph: no visible global function definition for 'polygon'
plotcph: no visible global function definition for 'lines'
plotnae: no visible global function definition for 'plot'
simCR: no visible global function definition for 'rnorm'
simEBMT: no visible global function definition for 'model.matrix'
simexit: no visible global function definition for 'runif'
simexitinner: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  abline axis confint integrate legend lines model.matrix plot polygon
  rnorm runif uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "plot",
             "polygon")
  importFrom("stats", "confint", "integrate", "model.matrix", "rnorm",
             "runif", "uniroot")
to your NAMESPACE file.
'library' or 'require' call to 'boot' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'boot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File 'simpleboot/R/zzz.R':
  .onLoad calls:
    require(boot)

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

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
randInitializeWeights: no visible global function definition for
  'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Files in the 'vignettes' directory but no files in 'inst/doc':
  'usingSimpleRCache.Rmd'
Package has no Sweave vignette sources and no VignetteBuilder field.
'library' or 'require' calls not declared from:
  'LiblineaR' 'microbenchmark' 'simPopulation' 'stringr'
Running 'cpp_sa.r' [8s]
Running the tests in 'tests/cpp_sa.r' failed.
Last 13 lines of output:
  > min.temp <- 10^-2
  > sample <- TRUE
  > parallel <- TRUE
  > verbose <- FALSE
  > 
  > sourceCpp("src/calibPop.cpp") 
  Error in sourceCpp("src/calibPop.cpp") : 
    file not found: 'd:/Rcompile/CRANpkg/local/3.4/simPop.Rcheck/tests_i386/src/calibPop.cpp'
  Calls: sourceCpp -> .Call
  In addition: Warning messages:
  1: In normalizePath(path.expand(path), winslash, mustWork) :
    path[1]="src": Das System kann die angegebene Datei nicht finden
  2: In normalizePath(path.expand(path), winslash, mustWork) :
    path[1]="src/calibPop.cpp": Das System kann den angegebenen Pfad nicht finden
  Execution halted
Running 'cpp_sa.r' [9s]
Running the tests in 'tests/cpp_sa.r' failed.
Last 13 lines of output:
  > min.temp <- 10^-2
  > sample <- TRUE
  > parallel <- TRUE
  > verbose <- FALSE
  > 
  > sourceCpp("src/calibPop.cpp") 
  Error in sourceCpp("src/calibPop.cpp") : 
    file not found: 'd:/Rcompile/CRANpkg/local/3.4/simPop.Rcheck/tests_x64/src/calibPop.cpp'
  Calls: sourceCpp -> .Call
  In addition: Warning messages:
  1: In normalizePath(path.expand(path), winslash, mustWork) :
    path[1]="src": Das System kann die angegebene Datei nicht finden
  2: In normalizePath(path.expand(path), winslash, mustWork) :
    path[1]="src/calibPop.cpp": Das System kann den angegebenen Pfad nicht finden
  Execution halted
Package in Depends field not imported from: 'mclust'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Simpsons: no visible global function definition for 'Mclust'
Simpsons: no visible global function definition for 'lm'
Simpsons: no visible global function definition for 'plot'
Simpsons: no visible global function definition for 'abline'
Simpsons: no visible global function definition for 'par'
Simpsons: no visible global function definition for 'legend'
Simpsons: no visible global function definition for 'txtProgressBar'
Simpsons: no visible global function definition for 'setTxtProgressBar'
Simpsons: no visible global function definition for 'quantile'
plot.Simpson: no visible global function definition for 'plot'
plot.Simpson: no visible global function definition for 'lm'
plot.Simpson: no visible global function definition for 'abline'
plot.Simpson: no visible global function definition for 'par'
plot.Simpson: no visible global function definition for 'legend'
Undefined global functions or variables:
  Mclust abline legend lm par plot quantile setTxtProgressBar
  txtProgressBar
Consider adding
  importFrom("graphics", "abline", "legend", "par", "plot")
  importFrom("stats", "lm", "quantile")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
simrel: no visible global function definition for 'runif'
simrel: no visible global function definition for 'rnorm'
simrelplot: no visible global function definition for 'par'
simrelplot: no visible global function definition for 'layout'
simrelplot: no visible global function definition for 'devAskNewPage'
simrelplot: no visible global function definition for 'dev.hold'
simrelplot: no visible global function definition for 'plot'
simrelplot: no visible global function definition for 'abline'
simrelplot: no visible global function definition for 'dev.flush'
simrelplot: no visible global function definition for 'points'
simrelplot: no visible global function definition for 'axis'
simrelplot: no visible global function definition for 'mtext'
simrelplot: no visible global function definition for 'box'
simrelplot: no visible global function definition for 'cov'
Undefined global functions or variables:
  abline axis box cov dev.flush dev.hold devAskNewPage layout mtext par
  plot points rnorm runif
Consider adding
  importFrom("grDevices", "dev.flush", "dev.hold", "devAskNewPage")
  importFrom("graphics", "abline", "axis", "box", "layout", "mtext",
             "par", "plot", "points")
  importFrom("stats", "cov", "rnorm", "runif")
to your NAMESPACE file.
Found the following hidden files and directories:
  vignettes/.Rhistory
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'abind' 'svUnit'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
simSummary: no visible global function definition for 'abind'
simSummary_unitTests: no visible global function definition for
  'clearLog'
simSummary_unitTests: no visible global function definition for
  'runTest'
simSummary_unitTests: no visible global function definition for
  'svSuite'
simSummary_unitTests: no visible global function definition for 'Log'
simSummary_unitTests: no visible global function definition for 'stats'
simSummary_unitTests: no visible global function definition for
  'metadata'
simSummary_unitTests: no visible global function definition for
  'errorLog'
Undefined global functions or variables:
  Log abind clearLog errorLog metadata runTest stats svSuite
evalGrids: no visible global function definition for 'sessionInfo'
meanAndNormCI: no visible global function definition for 'sd'
Undefined global functions or variables:
  sd sessionInfo
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "sessionInfo")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-5

Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Quitting from lines 56-66 (elastic-net.Rmd) 
Shutting down cluster.
Error: processing vignette 'elastic-net.Rmd' failed with diagnostics:
one node produced an error: Could not find file d:/RCompile/CRANpkg/local/3.4/simulator.Rcheck/vign_test/simulator/vignettes/files/slm/k_10/n_100/p_50/rho_0.8/snr_2/model.Rdata
Execution halted
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.
cvskda: no visible global function definition for 'detectCores'
cvskda: no visible global function definition for 'makeCluster'
cvskda: no visible global function definition for 'clusterApplyLB'
cvskda: no visible global function definition for 'mclapply'
cvskda: no visible global function definition for 'stopCluster'
Undefined global functions or variables:
  clusterApplyLB detectCores makeCluster mclapply stopCluster
dskt: no visible global function definition for 'dt'
pskt: no visible global function definition for 'pt'
qskt: no visible global function definition for 'qt'
rskt: no visible global function definition for 'runif'
Undefined global functions or variables:
  dt pt qt runif
Consider adding
  importFrom("stats", "dt", "pt", "qt", "runif")
to your NAMESPACE file.
Package which this enhances but not available for checking: 'kmndirs'
Unavailable namespace imported from by a ':::' call: 'kmndirs'
  See the note in ?`:::` about the use of this operator.
plot.sla: no visible global function definition for 'title'
plot.sla: no visible global function definition for 'abline'
print.sla: no visible global function definition for 'coef'
sla.default: no visible global function definition for 'lm'
sla.default: no visible global function definition for 'anova'
Undefined global functions or variables:
  abline anova coef lm title
Consider adding
  importFrom("graphics", "abline", "title")
  importFrom("stats", "anova", "coef", "lm")
to your NAMESPACE file.
slcestimates: no visible global function definition for 'par'
slcestimates: no visible global function definition for 'plot'
slcestimates: no visible global function definition for 'abline'
slcestimates: no visible global function definition for 'lines'
slcestimates: no visible global function definition for 'axis'
slcestimates: no visible global function definition for 'points'
slcestimates: no visible global function definition for 'title'
Undefined global functions or variables:
  abline axis lines par plot points title
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "par", "plot",
             "points", "title")
to your NAMESPACE file.
cvsmac: no visible global function definition for 'predict'
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
File 'smco/R/smco.R':
  .onAttach calls:
    cat(paste("This is smco package", version, "\n"))

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

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

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

.MHUpdateFuncGen.PF : MHUpdateFunc: no visible global function
  definition for 'runif'
MarkovSwitchingFuncGenerator : generateNextStreamsFunc: no visible
  global function definition for 'runif'
MarkovSwitchingFuncGenerator: no visible global function definition for
  'rnorm'
MarkovSwitchingFuncGenerator: no visible global function definition for
  'runif'
MarkovSwitchingFuncGenerator : logObsDensFunc: no visible global
  function definition for 'dnorm'
MarkovSwitchingFuncGenerator : propagateFunc: no visible global
  function definition for 'dnorm'
MarkovSwitchingFuncGenerator : propagateFunc: no visible global
  function definition for 'runif'
Undefined global functions or variables:
  dnorm rnorm runif
Consider adding
  importFrom("stats", "dnorm", "rnorm", "runif")
to your NAMESPACE file.
em: no visible global function definition for 'coxph'
em: no visible global function definition for 'optim'
plotpredictsmcure: no visible global function definition for 'plot'
plotpredictsmcure: no visible global function definition for 'matplot'
plotpredictsmcure: no visible global function definition for 'lines'
smcure: no visible binding for global variable 'na.omit'
smcure: no visible global function definition for 'model.frame'
smcure: no visible global function definition for 'model.extract'
smcure: no visible global function definition for 'model.matrix'
smcure: no visible global function definition for 'coxph'
smcure: no visible global function definition for 'survreg'
smcure: no visible binding for global variable 'var'
smcure: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  coxph lines matplot model.extract model.frame model.matrix na.omit
  optim plot pnorm survreg var
Consider adding
  importFrom("graphics", "lines", "matplot", "plot")
  importFrom("stats", "model.extract", "model.frame", "model.matrix",
             "na.omit", "optim", "pnorm", "var")
to your NAMESPACE file.
branching.resample: no visible global function definition for 'rbinom'
cov.weights: no visible global function definition for 'var'
inverse.cdf.weights: no visible global function definition for 'runif'
multinomial.resample: no visible global function definition for 'runif'
stratified.resample: no visible global function definition for 'runif'
systematic.resample: no visible global function definition for 'runif'
Undefined global functions or variables:
  rbinom runif var
Consider adding
  importFrom("stats", "rbinom", "runif", "var")
to your NAMESPACE file.
'library' or 'require' call to 'proxy' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'proxy' 'tm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
normalize: no visible binding for global variable 'sd'
simDic: no visible global function definition for 'simil'
simDoc: no visible global function definition for 'simil'
Undefined global functions or variables:
  sd simil
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Grad.sph: no visible global function definition for 'dist'
IMDS: no visible global function definition for 'cmdscale'
IMDS: no visible global function definition for 'as.dist'
IMDS: no visible global function definition for 'runif'
IMDS: no visible global function definition for 'optim'
idistSph: no visible global function definition for 'dist'
obj.sph: no visible global function definition for 'dist'
plot.imds: no visible binding for global variable 'lines'
plot.imds: no visible global function definition for 'plot'
plot.imds: no visible global function definition for 'text'
plot.imds: no visible global function definition for 'rect'
Undefined global functions or variables:
  as.dist cmdscale dist lines optim plot rect runif text
Consider adding
  importFrom("graphics", "lines", "plot", "rect", "text")
  importFrom("stats", "as.dist", "cmdscale", "dist", "optim", "runif")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'lattice' 'splines'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'lattice' 'splines'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
getRoughnessMatrix: no visible global function definition for 'ns'
plotSmeDiagnostic: no visible global function definition for 'layout'
plotSmeDiagnostic: no visible global function definition for 'plot'
plotSmeModel: no visible global function definition for 'plot'
plotSmeModel: no visible global function definition for 'lines'
plotSmeModel: no visible global function definition for 'col2rgb'
plotSmeModel: no visible global function definition for 'polygon'
plotSmeModel: no visible global function definition for 'rgb'
plotSmeRaw: no visible global function definition for 'xyplot'
plotSmeRaw : <anonymous>: no visible global function definition for
  'panel.xyplot'
plotSmeRaw : <anonymous>: no visible global function definition for
  'panel.lines'
sme.default: no visible global function definition for 'ns'
sme.list: no visible binding for global variable 'ns'
sme.list : <anonymous>: no visible global function definition for 'ns'
vcov.sme: no visible global function definition for 'ns'
Undefined global functions or variables:
  col2rgb layout lines ns panel.lines panel.xyplot plot polygon rgb
  xyplot
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
  importFrom("graphics", "layout", "lines", "plot", "polygon")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'ggplot2' 'reshape'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'corpcor' 'ggplot2' 'reshape'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Warning: GNU Extension: Symbol 'ntt' is used before it is typed at (1)
See 'd:/Rcompile/CRANpkg/local/3.4/smint.Rcheck/00install.out' for details.
'library' or 'require' calls in package code:
  'MASS' 'survival'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
lines.SmithWilsonYieldCurve: no visible global function definition for
  'lines'
plot.SmithWilsonYieldCurve: no visible global function definition for
  'plot'
points.SmithWilsonYieldCurve: no visible global function definition for
  'points'
Undefined global functions or variables:
  lines plot points
Consider adding
  importFrom("graphics", "lines", "plot", "points")
to your NAMESPACE file.
Fourier2d: no visible global function definition for 'fft'
kernel2dsmooth: no visible global function definition for 'fft'
Undefined global functions or variables:
  fft
Consider adding
  importFrom("stats", "fft")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'akima' 'misc3d' 'rgl' 'rpanel' 'tkrplot'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
dNMR: no visible global function definition for 'pnorm'
dNMR: no visible global function definition for 'dnorm'
pNMR: no visible global function definition for 'pnorm'
pNMR: no visible global function definition for 'dnorm'
rMR: no visible global function definition for 'rnorm'
rMR: no visible global function definition for 'rchisq'
Undefined global functions or variables:
  dnorm pnorm rchisq rnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm", "rchisq", "rnorm")
to your NAMESPACE file.
SMVar.paired : <anonymous>: no visible global function definition for
  'var'
SMVar.paired: no visible global function definition for 'var'
SMVar.paired: no visible global function definition for 'pt'
SMVar.paired: no visible global function definition for 'p.adjust'
SMVar.paired: no visible global function definition for 'write.table'
SMVar.unpaired : <anonymous>: no visible global function definition for
  'var'
SMVar.unpaired: no visible global function definition for 'var'
SMVar.unpaired: no visible global function definition for 'pt'
SMVar.unpaired: no visible global function definition for 'p.adjust'
SMVar.unpaired: no visible global function definition for 'write.table'
Undefined global functions or variables:
  p.adjust pt var write.table
Consider adding
  importFrom("stats", "p.adjust", "pt", "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
affinityMatrix: no visible global function definition for 'dnorm'
displayClusters: no visible global function definition for 'image'
displayClusters: no visible global function definition for 'grey'
displayClustersWithHeatmap: no visible global function definition for
  'median'
displayClustersWithHeatmap: no visible global function definition for
  'heatmap'
Undefined global functions or variables:
  dnorm grey heatmap image median
Consider adding
  importFrom("grDevices", "grey")
  importFrom("graphics", "image")
  importFrom("stats", "dnorm", "heatmap", "median")
to your NAMESPACE file.
sclust: no visible global function definition for 'var'
snipEM: no visible global function definition for 'cov'
stEM: no visible global function definition for 'cov'
stEM: no visible global function definition for 'quantile'
Undefined global functions or variables:
  cov quantile var
Consider adding
  importFrom("stats", "cov", "quantile", "var")
to your NAMESPACE file.
Package in Depends field not imported from: 'snow'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
KS.test: no visible global function definition for 'quantile'
KS.test : Fgaus: no visible global function definition for 'pnorm'
KS.test: no visible global function definition for 'setNames'
cs.test: no visible global function definition for 'pbinom'
cs.test: no visible global function definition for 'pnorm'
cs.test: no visible global function definition for 'setNames'
kde: no visible global function definition for 'quantile'
kde : Fgaus: no visible global function definition for 'pnorm'
kde: no visible global function definition for 'par'
kre: no visible global function definition for 'quantile'
kre: no visible global function definition for 'lines'
ns.test: no visible global function definition for 'complete.cases'
ns.test: no visible global function definition for 'qnorm'
ns.test: no visible global function definition for 'pnorm'
ns.test: no visible global function definition for 'pchisq'
ns.test: no visible global function definition for 'setNames'
ns.test: no visible global function definition for 'qt'
quant.test: no visible global function definition for 'complete.cases'
quant.test: no visible global function definition for 'pbinom'
quant.test: no visible global function definition for 'pnorm'
quant.test: no visible global function definition for 'setNames'
quant.test: no visible global function definition for 'quantile'
quant.test: no visible global function definition for 'phyper'
runs.test: no visible global function definition for 'median'
runs.test: no visible global function definition for 'setNames'
runs.test: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  complete.cases lines median par pbinom pchisq phyper pnorm qnorm qt
  quantile setNames
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "complete.cases", "median", "pbinom", "pchisq",
             "phyper", "pnorm", "qnorm", "qt", "quantile", "setNames")
to your NAMESPACE file.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'mvtnorm' 'combinat'
A package should be listed in only one of these fields.
chisq.test.a: no visible global function definition for 'chisq.test'
maxsel: no visible global function definition for 'complete.cases'
maxsel.asymp.test: no visible global function definition for
  'complete.cases'
Undefined global functions or variables:
  chisq.test complete.cases
Consider adding
  importFrom("stats", "chisq.test", "complete.cases")
to your NAMESPACE file.
MDSplot: no visible global function definition for 'par'
MDSplot: no visible global function definition for 'rainbow'
MDSplot: no visible global function definition for 'plot'
MDSplot: no visible global function definition for 'pairs'
classCenter : <anonymous>: no visible binding for global variable
  'median'
grow.snpRF: no visible global function definition for 'update'
na.roughfix.data.frame : roughfix: no visible global function
  definition for 'median'
na.roughfix.default: no visible global function definition for 'median'
outlier.default: no visible global function definition for 'median'
outlier.default: no visible global function definition for 'mad'
plot.margin: no visible global function definition for
  'installed.packages'
plot.margin: no visible global function definition for 'rainbow'
plot.margin: no visible global function definition for 'plot.default'
plot.snpRF: no visible global function definition for 'matplot'
tuneSnpRF: no visible global function definition for 'axis'
varImpPlot: no visible global function definition for 'par'
varImpPlot: no visible global function definition for 'dotchart'
varImpPlot: no visible global function definition for 'mtext'
Undefined global functions or variables:
  axis dotchart installed.packages mad matplot median mtext pairs par
  plot plot.default rainbow update
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "dotchart", "matplot", "mtext", "pairs",
             "par", "plot", "plot.default")
  importFrom("stats", "mad", "median", "update")
  importFrom("utils", "installed.packages")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'Biostrings' 'GenomicRanges' 'IRanges' 'Rsamtools'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
calculate.areas: no visible global function definition for 'runif'
calculate.gradedareas: no visible global function definition for
  'rnorm'
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from 'SoDA' for: 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Missing or unexported object: 'base::WHAT'
Packages in Depends field not imported from:
  'MASS' 'magic' 'ppls' 'psych'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
get.hnx.B.initialW: no visible global function definition for
  'normalize.vector'
get.hnx.B.initialW: no visible global function definition for 'adiag'
hclust.wrap: no visible global function definition for 'hclust'
hclust.wrap: no visible global function definition for 'dist'
hclust.wrap: no visible global function definition for 'cutree'
my.normdata.gen: no visible global function definition for 'mvrnorm'
my.normdata.gen: no visible global function definition for 'rnorm'
odc.clust: no visible binding for global variable 'kmeans'
odc.cv: no visible global function definition for 'ginv'
odc.optimallambda2: no visible global function definition for 'tr'
odc.optimallambda2: no visible global function definition for 'ginv'
odc.optimallambda2: no visible binding for global variable 'sd'
sodc.clust: no visible binding for global variable 'kmeans'
Undefined global functions or variables:
  adiag cutree dist ginv hclust kmeans mvrnorm normalize.vector rnorm
  sd tr
Consider adding
  importFrom("stats", "cutree", "dist", "hclust", "kmeans", "rnorm",
             "sd")
to your NAMESPACE file.
hsvScale: no visible global function definition for 'hsv'
plotConcentric: no visible global function definition for 'plot'
plotConcentric: no visible global function definition for 'points'
plotConcentric: no visible global function definition for 'legend'
plotPoints: no visible global function definition for 'plot'
plotStress: no visible global function definition for 'plot'
plotStress: no visible global function definition for 'polygon'
plotStress: no visible global function definition for 'points'
Undefined global functions or variables:
  hsv legend plot points polygon
Consider adding
  importFrom("grDevices", "hsv")
  importFrom("graphics", "legend", "plot", "points", "polygon")
to your NAMESPACE file.
HardKMeansDemo: no visible global function definition for
  'graphics.off'
HardKMeansDemo: no visible global function definition for 'plot'
HardKMeansDemo: no visible global function definition for 'points'
initializeMeansMatrix: no visible global function definition for
  'runif'
initializeMeansMatrix: no visible global function definition for 'dist'
normalizeMatrix: no visible global function definition for 'sd'
plotRoughKMeans: no visible global function definition for
  'graphics.off'
plotRoughKMeans: no visible global function definition for 'plot'
plotRoughKMeans: no visible global function definition for 'points'
Undefined global functions or variables:
  dist graphics.off plot points runif sd
Consider adding
  importFrom("grDevices", "graphics.off")
  importFrom("graphics", "plot", "points")
  importFrom("stats", "dist", "runif", "sd")
to your NAMESPACE file.
Ssimpute.als: no visible global function definition for 'rnorm'
Ssvd.als: no visible global function definition for 'rnorm'
cs.default: no visible binding for global variable 'weighted.mean'
simpute.als: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm weighted.mean
Consider adding
  importFrom("stats", "rnorm", "weighted.mean")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'aqp' 'lattice' 'methods' 'munsell' 'splancs'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' calls in package code:
  'chemometrics' 'spatstat'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.soma: no visible global function definition for 'plot'
soma: no visible global function definition for 'runif'
Undefined global functions or variables:
  plot runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
to your NAMESPACE file.
bm: no visible global function definition for 'rnorm'
bm: no visible global function definition for 'ts'
fbm: no visible global function definition for 'fft'
fbm: no visible global function definition for 'rnorm'
fbm: no visible global function definition for 'ts'
gbm: no visible global function definition for 'rnorm'
gbm: no visible global function definition for 'ts'
Undefined global functions or variables:
  fft rnorm ts
Consider adding
  importFrom("stats", "fft", "rnorm", "ts")
to your NAMESPACE file.
getAlpha: no visible global function definition for 'pbinom'
kfweOrd: no visible global function definition for 'qnbinom'
Undefined global functions or variables:
  pbinom qnbinom
Consider adding
  importFrom("stats", "pbinom", "qnbinom")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from 'someMTP' for: 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
'library' or 'require' call to 'hexbin' which was already attached by Depends.
  Please remove these calls from your code.
hexbinpie: no visible global function definition for 'quantile'
hexbinpie: no visible global function definition for 'polygon'
hexbinpie: no visible global function definition for 'text'
makehexbinplot: no visible global function definition for 'rainbow'
makehexbinplot: no visible global function definition for 'col2rgb'
makehexbinplot: no visible global function definition for 'edit'
makehexbinplot: no visible global function definition for 'dev.new'
makehexbinplot: no visible global function definition for 'plot.new'
makehexbinplot: no visible global function definition for 'plot.window'
makehexbinplot: no visible global function definition for 'box'
makehexbinplot: no visible global function definition for 'axis'
makehexbinplot: no visible global function definition for 'legend'
som.plot: no visible global function definition for 'read.table'
Undefined global functions or variables:
  axis box col2rgb dev.new edit legend plot.new plot.window polygon
  quantile rainbow read.table text
Consider adding
  importFrom("grDevices", "col2rgb", "dev.new", "rainbow")
  importFrom("graphics", "axis", "box", "legend", "plot.new",
             "plot.window", "polygon", "text")
  importFrom("stats", "quantile")
  importFrom("utils", "edit", "read.table")
to your NAMESPACE file.
dfrag: no visible global function definition for 'qgeom'
dfrag: no visible global function definition for 'plogis'
dfrag: no visible global function definition for 'dgeom'
estAbund: no visible global function definition for 'xtabs'
mmN : <anonymous>: no visible global function definition for 'uniroot'
pfrag: no visible global function definition for 'qgeom'
phi.deriv.default: no visible global function definition for
  'model.matrix'
phi.deriv.default: no visible binding for global variable 'sd'
phi.update.default: no visible global function definition for 'glm'
phi.update.default: no visible binding for global variable
  'quasipoisson'
phi.update.default: no visible global function definition for 'predict'
phi.update.lframe: no visible global function definition for 'glm'
phi.update.lframe: no visible binding for global variable
  'quasipoisson'
phi.update.lframe: no visible global function definition for 'predict'
pr.y.given.x : <anonymous>: no visible global function definition for
  'dpois'
pr.y.given.x : <anonymous> : <anonymous>: no visible global function
  definition for 'dpois'
pr.y.given.x : <anonymous>: no visible global function definition for
  'convolve'
qfrag: no visible global function definition for 'qgeom'
rfrag: no visible global function definition for 'qgeom'
simSonic: no visible global function definition for 'rpois'
Undefined global functions or variables:
  convolve dgeom dpois glm model.matrix plogis predict qgeom
  quasipoisson rpois sd uniroot xtabs
Consider adding
  importFrom("stats", "convolve", "dgeom", "dpois", "glm",
             "model.matrix", "plogis", "predict", "qgeom",
             "quasipoisson", "rpois", "sd", "uniroot", "xtabs")
to your NAMESPACE file.
plot.soo_function: no visible global function definition for
  'terrain.colors'
plot.soo_function: no visible binding for global variable 'image'
plot.soo_function: no visible binding for global variable 'contour'
plot3d: no visible global function definition for 'persp3d'
plot3d: no visible global function definition for 'terrain.colors'
random_parameters.soo_function: no visible global function definition
  for 'runif'
random_rotation_matrix: no visible global function definition for
  'runif'
Undefined global functions or variables:
  contour image persp3d runif terrain.colors
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "contour", "image")
  importFrom("stats", "runif")
to your NAMESPACE file.
simdata_contaminated : <anonymous>: no visible global function
  definition for 'rbinom'
simdata_uniform : multivariate_uniform : <anonymous>: no visible global
  function definition for 'runif'
which_min: no visible global function definition for 'head'
which_min: no visible global function definition for 'tail'
Undefined global functions or variables:
  head rbinom runif tail
Consider adding
  importFrom("stats", "rbinom", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
convert_municipality_names: no visible global function definition for
  'read.csv'
regression_plot: no visible binding for global variable 'loess'
regression_plot: no visible global function definition for
  'colorRampPalette'
regression_plot: no visible global function definition for
  'loess.control'
regression_plot: no visible global function definition for 'predict'
regression_plot : <anonymous>: no visible global function definition
  for 'quantile'
regression_plot : <anonymous>: no visible global function definition
  for 'pnorm'
regression_plot: no visible global function definition for
  'flush.console'
regression_plot: no visible global function definition for 'density'
Undefined global functions or variables:
  colorRampPalette density flush.console loess loess.control pnorm
  predict quantile read.csv
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "density", "loess", "loess.control", "pnorm",
             "predict", "quantile")
  importFrom("utils", "flush.console", "read.csv")
to your NAMESPACE file.
'library' or 'require' call to 'rgdal' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
analyzeSP23Design: no visible global function definition for 'plot'
exploreSP23Design: no visible global function definition for
  'txtProgressBar'
exploreSP23Design: no visible global function definition for
  'setTxtProgressBar'
generateClinicalTrialData : <anonymous>: no visible global function
  definition for 'runif'
generateClinicalTrialData: no visible global function definition for
  'rbinom'
generateClinicalTrialData: no visible global function definition for
  'rexp'
mHP.b : crossingProbDiff: no visible global function definition for
  'pnorm'
mHP.b : crossingProbDiff: no visible global function definition for
  'Miwa'
mHP.b: no visible global function definition for 'qnorm'
mHP.b: no visible global function definition for 'uniroot'
mHP.c : crossingProbDiff: no visible global function definition for
  'Miwa'
mHP.c: no visible global function definition for 'uniroot'
mHP.c: no visible global function definition for 'qnorm'
performInterimLook: no visible global function definition for 'optim'
performInterimLook: no visible global function definition for
  'constrOptim'
performInterimLook: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  Miwa constrOptim optim plot pnorm qnorm rbinom rexp runif
  setTxtProgressBar txtProgressBar uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "constrOptim", "optim", "pnorm", "qnorm", "rbinom",
             "rexp", "runif", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
SPA: no visible global function definition for 'var'
Score.Test.Interact: no visible global function definition for 'pchisq'
Score.Test.Overall: no visible global function definition for 'var'
Score.Test.Overall: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  pchisq var
Consider adding
  importFrom("stats", "pchisq", "var")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'glasso' 'limSolve'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
glasso.miss: no visible global function definition for 'cov'
glasso.miss: no visible global function definition for 'glasso'
glasso.miss: no visible global function definition for 'Solve'
space.miss: no visible global function definition for 'Solve'
Undefined global functions or variables:
  Solve cov glasso
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
'library' or 'require' call to 'Matrix' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'Matrix' 'igraph' 'splines'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GenPar: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'Rcpp' 'colorspace' 'picante'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: 'fastshp'
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.
Found the following significant warnings:
  Warning: GNU Extension: Different type kinds at (1)
See 'd:/Rcompile/CRANpkg/local/3.4/spanr.Rcheck/00install.out' for details.
span: no visible global function definition for 'complete.cases'
spanr: no visible global function definition for 'model.frame'
spanr: no visible global function definition for 'complete.cases'
spanr.hull: no visible global function definition for 'par'
spanr.hull: no visible global function definition for 'plot.new'
spanr.hull: no visible global function definition for 'plot.window'
spanr.hull: no visible global function definition for 'axis'
spanr.hull: no visible global function definition for 'title'
spanr.hull: no visible global function definition for 'points'
spanr.hull: no visible global function definition for 'lines'
spanr.hull: no visible global function definition for 'abline'
spanr.hull: no visible global function definition for 'text'
spanr.hull: no visible global function definition for 'segments'
spanr.hull: no visible global function definition for 'box'
Undefined global functions or variables:
  abline axis box complete.cases lines model.frame par plot.new
  plot.window points segments text title
Consider adding
  importFrom("graphics", "abline", "axis", "box", "lines", "par",
             "plot.new", "plot.window", "points", "segments", "text",
             "title")
  importFrom("stats", "complete.cases", "model.frame")
to your NAMESPACE file.
plot.spa: no visible global function definition for 'plot'
plot.spa: no visible global function definition for 'lines'
plot.spa: no visible global function definition for 'points'
plot.spa: no visible global function definition for 'gray'
plot.spa: no visible global function definition for 'box'
predict.spa: no visible global function definition for 'fitted'
predict.spa: no visible global function definition for 'coef'
spa.gcv: no visible global function definition for 'density'
spa.gcv: no visible global function definition for 'quantile'
spa.sim: no visible global function definition for 'runif'
spa.sim: no visible global function definition for 'rnorm'
spa.sim: no visible global function definition for 'rbinom'
update.spa: no visible global function definition for 'quantile'
Undefined global functions or variables:
  box coef density fitted gray lines plot points quantile rbinom rnorm
  runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "box", "lines", "plot", "points")
  importFrom("stats", "coef", "density", "fitted", "quantile", "rbinom",
             "rnorm", "runif")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'RCurl' 'XML'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SPARQL : <anonymous>: no visible global function definition for
  'URLencode'
SPARQL: no visible binding for global variable 'getURL'
SPARQL: no visible global function definition for 'URLencode'
SPARQL: no visible binding for global variable 'xmlParse'
SPARQL: no visible global function definition for 'getNodeSet'
SPARQL: no visible global function definition for 'xpathApply'
SPARQL: no visible binding for global variable 'postForm'
get_attr: no visible global function definition for 'getNodeSet'
get_attr : <anonymous> : <anonymous>: no visible global function
  definition for 'getNodeSet'
get_attr : <anonymous> : <anonymous>: no visible global function
  definition for 'xmlDoc'
get_value: no visible global function definition for 'xmlDoc'
get_value: no visible global function definition for 'xpathSApply'
get_value: no visible binding for global variable 'xmlValue'
get_value: no visible global function definition for 'xpathApply'
get_value: no visible binding for global variable 'xmlGetAttr'
readCSVstring: no visible global function definition for 'read.csv'
readTSVstring: no visible global function definition for 'read.delim'
Undefined global functions or variables:
  URLencode getNodeSet getURL postForm read.csv read.delim xmlDoc
  xmlGetAttr xmlParse xmlValue xpathApply xpathSApply
Consider adding
  importFrom("utils", "URLencode", "read.csv", "read.delim")
to your NAMESPACE file.
f.I2.cont: no visible global function definition for 'combn'
f.I2.dich: no visible global function definition for 'combn'
f.pstar.cont: no visible global function definition for 'combn'
f.pstar.dich: no visible global function definition for 'combn'
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
image.matrixBC: no visible global function definition for 'dev.new'
image.matrixBC: no visible global function definition for 'image'
image.matrixBC: no visible global function definition for 'heat.colors'
image.matrixBC: no visible global function definition for 'axis'
image.matrixBC: no visible global function definition for 'title'
image.sparseBC: no visible global function definition for 'dev.new'
image.sparseBC: no visible global function definition for 'image'
image.sparseBC: no visible global function definition for 'heat.colors'
image.sparseBC: no visible global function definition for 'axis'
image.sparseBC: no visible global function definition for 'tail'
image.sparseBC: no visible global function definition for 'title'
matrixBC: no visible global function definition for 'kmeans'
sparseBC: no visible global function definition for 'kmeans'
sparseBC.choosekr: no visible global function definition for 'kmeans'
sparseBC.choosekr: no visible binding for global variable 'sd'
Undefined global functions or variables:
  axis dev.new heat.colors image kmeans sd tail title
Consider adding
  importFrom("grDevices", "dev.new", "heat.colors")
  importFrom("graphics", "axis", "image", "title")
  importFrom("stats", "kmeans", "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
Running 'testthat.r' [0s]
Running the tests in 'tests/testthat.r' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
rmvn.sparse: no visible global function definition for 'rnorm'
rmvn.sparse: no visible global function definition for 'as'
Undefined global functions or variables:
  as rnorm
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "rnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Clarketest: no visible global function definition for 'pbinom'
Clarketest: no visible global function definition for 'qbinom'
DIC: no visible global function definition for 'model.matrix'
LogLike: no visible global function definition for 'model.matrix'
Vuongtest: no visible global function definition for 'var'
Vuongtest: no visible global function definition for 'qnorm'
Vuongtest: no visible global function definition for 'pnorm'
est.sc: no visible global function definition for 'model.matrix'
gpind: no visible global function definition for 'rgamma'
nbind: no visible global function definition for 'rgamma'
poiind: no visible global function definition for 'rgamma'
zigpind: no visible global function definition for 'rbinom'
zigpind: no visible global function definition for 'rgamma'
zipind: no visible global function definition for 'rbinom'
zipind: no visible global function definition for 'rgamma'
Undefined global functions or variables:
  model.matrix pbinom pnorm qbinom qnorm rbinom rgamma var
Consider adding
  importFrom("stats", "model.matrix", "pbinom", "pnorm", "qbinom",
             "qnorm", "rbinom", "rgamma", "var")
to your NAMESPACE file.
gev.impute: no visible global function definition for 'rnorm'
gev.init: no visible global function definition for 'rbinom'
gev.init: no visible global function definition for 'var'
gev.init: no visible global function definition for 'optimize'
gev.logscore: no visible global function definition for 'density'
gev.logscore: no visible global function definition for 'splinefun'
gev.update.M: no visible global function definition for 'runif'
gev.update.hyper: no visible global function definition for 'rgamma'
gev.update.lambda: no visible global function definition for 'rnorm'
gev.update.lambda: no visible global function definition for 'dgamma'
gev.update.lambda: no visible global function definition for 'dnorm'
gev.update.lambda: no visible global function definition for 'runif'
gev.update.tau.kappa: no visible global function definition for 'rnorm'
gev.update.tau.kappa: no visible global function definition for 'dnorm'
gev.update.tau.kappa: no visible global function definition for 'runif'
gev.update.tau.mu: no visible global function definition for 'rnorm'
gev.update.tau.mu: no visible global function definition for 'dnorm'
gev.update.tau.mu: no visible global function definition for 'runif'
gev.update.tau.xi: no visible global function definition for 'rnorm'
gev.update.tau.xi: no visible global function definition for 'dnorm'
gev.update.tau.xi: no visible global function definition for 'runif'
gev.update.theta: no visible global function definition for 'rnorm'
gp.like.lambda: no visible global function definition for 'dgamma'
Undefined global functions or variables:
  density dgamma dnorm optimize rbinom rgamma rnorm runif splinefun var
Consider adding
  importFrom("stats", "density", "dgamma", "dnorm", "optimize", "rbinom",
             "rgamma", "rnorm", "runif", "splinefun", "var")
to your NAMESPACE file.
codisp: no visible global function definition for 'complete.cases'
cor.spatial: no visible global function definition for 'complete.cases'
modified.ttest: no visible global function definition for
  'complete.cases'
modified.ttest: no visible global function definition for 'cor'
plot.codisp: no visible global function definition for 'plot'
plot.codisp: no visible global function definition for 'title'
Undefined global functions or variables:
  complete.cases cor plot title
Consider adding
  importFrom("graphics", "plot", "title")
  importFrom("stats", "complete.cases", "cor")
to your NAMESPACE file.
I2BR: no visible global function definition for 'pnorm'
I2SmD2: no visible global function definition for 'pnorm'
IBR: no visible global function definition for 'pnorm'
ISmD2: no visible global function definition for 'pnorm'
MestimatorBR: no visible global function definition for 'optim'
MestimatorSmith: no visible global function definition for 'optim'
psidotBR: no visible global function definition for 'dnorm'
psidotBR: no visible global function definition for 'pnorm'
psidotSmD2: no visible global function definition for 'dnorm'
psidotSmD2: no visible global function definition for 'pnorm'
tailBRInt: no visible global function definition for 'pnorm'
tailSmithInt: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dnorm optim pnorm
Consider adding
  importFrom("stats", "dnorm", "optim", "pnorm")
to your NAMESPACE file.
bbox_to_SpatialPolygons: no visible global function definition for
  'CRS'
bbox_to_SpatialPolygons: no visible global function definition for
  'Polygon'
bbox_to_SpatialPolygons: no visible global function definition for
  'Polygons'
bbox_to_SpatialPolygons: no visible global function definition for
  'SpatialPolygons'
list.raster.files: no visible global function definition for 'CRS'
list.raster.files: no visible global function definition for
  'spTransform'
list.raster.files: no visible global function definition for
  'SpatialPolygonsDataFrame'
list.raster.files: no visible global function definition for 'spChFIDs'
predict_rasterEngine : predict.rasterEngine_function: no visible global
  function definition for 'complete.cases'
projectRaster_rigorous : chunk_function: no visible global function
  definition for 'spTransform'
projectRaster_rigorous : chunk_function: no visible global function
  definition for 'CRS'
spatial_sync_raster: no visible global function definition for 'bbox'
spatial_sync_vector: no visible global function definition for
  'spTransform'
spatial_sync_vector: no visible global function definition for 'CRS'
Undefined global functions or variables:
  CRS Polygon Polygons SpatialPolygons SpatialPolygonsDataFrame bbox
  complete.cases spChFIDs spTransform
Consider adding
  importFrom("stats", "complete.cases")
to your NAMESPACE file.
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.4/RcppParallel/include/tthread/tinythread.h:632:14: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.4/RcppParallel/include/tbb/tbb_stddef.h:463:37: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.4/RcppParallel/include/tbb/atomic.h:29:30: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.4/RcppParallel/include/tbb/tick_count.h:42:14: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.4/RcppParallel/include/tbb/tick_count.h:43:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.4/RcppParallel/include/tbb/tick_count.h:75:21: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.4/RcppParallel/include/tbb/tick_count.h:102:10: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.4/RcppParallel/include/tbb/tick_count.h:80:37: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.4/RcppParallel/include/tbb/tick_count.h:127:30: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.4/SpatMCA.Rcheck/00install.out' for details.
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.4/RcppParallel/include/tthread/tinythread.h:632:14: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.4/SpatPCA.Rcheck/00install.out' for details.
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    R      4.8Mb
    data   3.4Mb
    doc    4.6Mb
    help   5.0Mb
    libs   1.2Mb
GenerateCliquesCovariance: no visible global function definition for
  'rnorm'
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    1.5Mb
    etc    1.7Mb
bartlett: no visible global function definition for 'pchisq'
local.rbfdot: no visible binding for global variable 'sd'
local.rbfdot: no visible global function definition for 'dist'
local.rbfdot : <anonymous>: no visible global function definition for
  'median'
speccalt: no visible global function definition for 'kmeans'
Undefined global functions or variables:
  dist kmeans median pchisq sd
Consider adding
  importFrom("stats", "dist", "kmeans", "median", "pchisq", "sd")
to your NAMESPACE file.
ChaoBunge: no visible global function definition for 'qnorm'
ChaoLee1992: no visible global function definition for 'qnorm'
Pmix: no visible global function definition for 'dpois'
PmixSCon: no visible global function definition for 'dbeta'
bootPCG: no visible global function definition for 'flush.console'
bootPCG: no visible global function definition for 'quantile'
bootPnpmle: no visible global function definition for 'flush.console'
bootPnpmle: no visible global function definition for 'quantile'
bootUnpmle: no visible global function definition for 'flush.console'
bootUnpmle: no visible global function definition for 'quantile'
chao1984: no visible global function definition for 'qnorm'
jackknife: no visible global function definition for 'dbinom'
jackknife: no visible global function definition for 'qnorm'
pcg: no visible global function definition for 'flush.console'
unpmle: no visible global function definition for 'flush.console'
untrunPmix: no visible global function definition for 'dpois'
Undefined global functions or variables:
  dbeta dbinom dpois flush.console qnorm quantile
Consider adding
  importFrom("stats", "dbeta", "dbinom", "dpois", "qnorm", "quantile")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
randomCorrelations: no visible global function definition for 'cor'
specGlm : <anonymous>: no visible global function definition for 'coef'
specLm : <anonymous>: no visible global function definition for 'coef'
Undefined global functions or variables:
  coef cor
Consider adding
  importFrom("stats", "coef", "cor")
to your NAMESPACE file.
Missing or unexported object: 'ChemoSpec::readJDX'
'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.
'library' or 'require' call to 'ROCR' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'ROCR' 'rpart'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/sphereplot.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
See 'd:/Rcompile/CRANpkg/local/3.4/SpherWave.Rcheck/00install.out' for details.
lambda.global: no visible global function definition for 'mad'
lambda.global: no visible global function definition for 'quantile'
lambda.global: no visible global function definition for 'qnorm'
lambda.global: no visible global function definition for 'pnorm'
ls.comp: no visible global function definition for 'lsfit'
modterritory: no visible global function definition for 'median'
newgotterritory: no visible global function definition for 'median'
newterritory: no visible global function definition for 'median'
ridge.comp: no visible global function definition for 'lsfit'
ridge.diacomp: no visible global function definition for 'ls.diag'
sw.plot: no visible global function definition for 'par'
sw.plot: no visible global function definition for 'plot'
sw.plot: no visible global function definition for 'points'
sw.plot: no visible global function definition for 'image'
sw.plot: no visible global function definition for 'axis'
sw.plot: no visible global function definition for 'legend'
sw.plot: no visible global function definition for 'box'
sw.plot: no visible global function definition for 'title'
thresh.level: no visible global function definition for 'na.omit'
thresh.level: no visible global function definition for 'mad'
thresh.level: no visible global function definition for 'qnorm'
thresh.level: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  axis box image legend ls.diag lsfit mad median na.omit par plot pnorm
  points qnorm quantile title
Consider adding
  importFrom("graphics", "axis", "box", "image", "legend", "par", "plot",
             "points", "title")
  importFrom("stats", "ls.diag", "lsfit", "mad", "median", "na.omit",
             "pnorm", "qnorm", "quantile")
to your NAMESPACE file.
Running examples in 'spider-Ex.R' failed
The error most likely occurred in:

> ### Name: seqStat
> ### Title: Sequence statistics
> ### Aliases: seqStat
> ### Keywords: Barcoding Utilities
> 
> ### ** Examples
> 
> data(anoteropsis)
> seqStat(anoteropsis)
Error in checkDNA(x, gapsAsMissing = TRUE) : object 'output' not found
Calls: seqStat -> sapply -> lapply -> FUN -> checkDNA
Execution halted
Packages in Depends field not imported from:
  'lars' 'parallel' 'randomForest'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' call to 'quadprog' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'quadprog'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SPIn: no visible global function definition for 'density'
SPIn: no visible global function definition for 'quantile'
SPIn: no visible global function definition for 'solve.QP'
bootSPIn: no visible global function definition for 'runif'
plot.SPIn: no visible global function definition for 'hist'
plot.SPIn: no visible global function definition for 'lines'
plot.SPIn: no visible global function definition for 'text'
plot.SPIn: no visible global function definition for 'quantile'
plot.SPIn: no visible global function definition for 'legend'
Undefined global functions or variables:
  density hist legend lines quantile runif solve.QP text
Consider adding
  importFrom("graphics", "hist", "legend", "lines", "text")
  importFrom("stats", "density", "quantile", "runif")
to your NAMESPACE file.
spi: no visible global function definition for 'read.table'
spi: no visible global function definition for 'ecdf'
spi: no visible global function definition for 'qnorm'
spi: no visible global function definition for 'colorRampPalette'
spi: no visible global function definition for 'filled.contour'
spi: no visible global function definition for 'axis'
Undefined global functions or variables:
  axis colorRampPalette ecdf filled.contour qnorm read.table
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "filled.contour")
  importFrom("stats", "ecdf", "qnorm")
  importFrom("utils", "read.table")
to your NAMESPACE file.
NoSep: no visible global function definition for 'setNames'
Reshape: no visible global function definition for 'setNames'
Reshape: no visible global function definition for 'reshape'
read.concat: no visible global function definition for 'count.fields'
read.concat: no visible global function definition for 'read.table'
Undefined global functions or variables:
  count.fields read.table reshape setNames
Consider adding
  importFrom("stats", "reshape", "setNames")
  importFrom("utils", "count.fields", "read.table")
to your NAMESPACE file.
R2.global: no visible global function definition for 'var'
calculer.var.exp: no visible global function definition for 'var'
creer.noeud: no visible global function definition for 'var'
ponderer.classe: no visible global function definition for 'var'
ponderer.classe: no visible global function definition for 'cov'
spodt: no visible global function definition for 'model.frame'
spodt.tree: no visible global function definition for 'plot.new'
spodt.tree: no visible global function definition for 'par'
spodt.tree: no visible global function definition for 'plot.window'
spodt.tree: no visible global function definition for 'text'
spodt.tree: no visible global function definition for 'segments'
test.spodt: no visible global function definition for 'model.frame'
test.spodt: no visible global function definition for 'hist'
test.spodt: no visible global function definition for 'abline'
tracer.noeud: no visible global function definition for 'text'
tracer.noeud: no visible global function definition for 'segments'
Undefined global functions or variables:
  abline cov hist model.frame par plot.new plot.window segments text
  var
Consider adding
  importFrom("graphics", "abline", "hist", "par", "plot.new",
             "plot.window", "segments", "text")
  importFrom("stats", "cov", "model.frame", "var")
to your NAMESPACE file.
ffmpeg version N-34549-g13b7781, Copyright (c) 2000-2011 the FFmpeg developers
  built on Nov  6 2011 22:02:08 with gcc 4.6.1
  configuration: --enable-gpl --enable-version3 --disable-w32threads --enable-runtime-cpudetect --enable-avisynth --enable-bzlib --enable-frei0r --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libfreetype --enable-libgsm --enable-libmp3lame --enable-libopenjpeg --enable-librtmp --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvo-aacenc --enable-libvo-amrwbenc --enable-libvorbis --enable-libvpx --enable-libx264 --enable-libxavs --enable-libxvid --enable-zlib
  libavutil    51. 24. 0 / 51. 24. 0
  libavcodec   53. 28. 0 / 53. 28. 0
  libavformat  53. 19. 0 / 53. 19. 0
  libavdevice  53.  4. 0 / 53.  4. 0
  libavfilter   2. 47. 0 /  2. 47. 0
  libswscale    2.  1. 0 /  2.  1. 0
  libpostproc  51.  2. 0 / 51.  2. 0
ffmpeg version N-34549-g13b7781, Copyright (c) 2000-2011 the FFmpeg developers
  built on Nov  6 2011 22:02:08 with gcc 4.6.1
  configuration: --enable-gpl --enable-version3 --disable-w32threads --enable-runtime-cpudetect --enable-avisynth --enable-bzlib --enable-frei0r --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libfreetype --enable-libgsm --enable-libmp3lame --enable-libopenjpeg --enable-librtmp --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvo-aacenc --enable-libvo-amrwbenc --enable-libvorbis --enable-libvpx --enable-libx264 --enable-libxavs --enable-libxvid --enable-zlib
  libavutil    51. 24. 0 / 51. 24. 0
  libavcodec   53. 28. 0 / 53. 28. 0
  libavformat  53. 19. 0 / 53. 19. 0
  libavdevice  53.  4. 0 / 53.  4. 0
  libavfilter   2. 47. 0 /  2. 47. 0
  libswscale    2.  1. 0 /  2.  1. 0
  libpostproc  51.  2. 0 / 51.  2. 0
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
ffmpeg version N-34549-g13b7781, Copyright (c) 2000-2011 the FFmpeg developers
  built on Nov  6 2011 22:02:08 with gcc 4.6.1
  configuration: --enable-gpl --enable-version3 --disable-w32threads --enable-runtime-cpudetect --enable-avisynth --enable-bzlib --enable-frei0r --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libfreetype --enable-libgsm --enable-libmp3lame --enable-libopenjpeg --enable-librtmp --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvo-aacenc --enable-libvo-amrwbenc --enable-libvorbis --enable-libvpx --enable-libx264 --enable-libxavs --enable-libxvid --enable-zlib
  libavutil    51. 24. 0 / 51. 24. 0
  libavcodec   53. 28. 0 / 53. 28. 0
  libavformat  53. 19. 0 / 53. 19. 0
  libavdevice  53.  4. 0 / 53.  4. 0
  libavfilter   2. 47. 0 /  2. 47. 0
  libswscale    2.  1. 0 /  2.  1. 0
  libpostproc  51.  2. 0 / 51.  2. 0
The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
ffmpeg version N-34549-g13b7781, Copyright (c) 2000-2011 the FFmpeg developers
  built on Nov  6 2011 22:02:08 with gcc 4.6.1
  configuration: --enable-gpl --enable-version3 --disable-w32threads --enable-runtime-cpudetect --enable-avisynth --enable-bzlib --enable-frei0r --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libfreetype --enable-libgsm --enable-libmp3lame --enable-libopenjpeg --enable-librtmp --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvo-aacenc --enable-libvo-amrwbenc --enable-libvorbis --enable-libvpx --enable-libx264 --enable-libxavs --enable-libxvid --enable-zlib
  libavutil    51. 24. 0 / 51. 24. 0
  libavcodec   53. 28. 0 / 53. 28. 0
  libavformat  53. 19. 0 / 53. 19. 0
  libavdevice  53.  4. 0 / 53.  4. 0
  libavfilter   2. 47. 0 /  2. 47. 0
  libswscale    2.  1. 0 /  2.  1. 0
  libpostproc  51.  2. 0 / 51.  2. 0
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
ffmpeg version N-34549-g13b7781, Copyright (c) 2000-2011 the FFmpeg developers
  built on Nov  6 2011 22:02:08 with gcc 4.6.1
  configuration: --enable-gpl --enable-version3 --disable-w32threads --enable-runtime-cpudetect --enable-avisynth --enable-bzlib --enable-frei0r --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libfreetype --enable-libgsm --enable-libmp3lame --enable-libopenjpeg --enable-librtmp --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvo-aacenc --enable-libvo-amrwbenc --enable-libvorbis --enable-libvpx --enable-libx264 --enable-libxavs --enable-libxvid --enable-zlib
  libavutil    51. 24. 0 / 51. 24. 0
  libavcodec   53. 28. 0 / 53. 28. 0
  libavformat  53. 19. 0 / 53. 19. 0
  libavdevice  53.  4. 0 / 53.  4. 0
  libavfilter   2. 47. 0 /  2. 47. 0
  libswscale    2.  1. 0 /  2.  1. 0
  libpostproc  51.  2. 0 / 51.  2. 0
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
ffmpeg version N-34549-g13b7781, Copyright (c) 2000-2011 the FFmpeg developers
  built on Nov  6 2011 22:02:08 with gcc 4.6.1
  configuration: --enable-gpl --enable-version3 --disable-w32threads --enable-runtime-cpudetect --enable-avisynth --enable-bzlib --enable-frei0r --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libfreetype --enable-libgsm --enable-libmp3lame --enable-libopenjpeg --enable-librtmp --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvo-aacenc --enable-libvo-amrwbenc --enable-libvorbis --enable-libvpx --enable-libx264 --enable-libxavs --enable-libxvid --enable-zlib
  libavutil    51. 24. 0 / 51. 24. 0
  libavcodec   53. 28. 0 / 53. 28. 0
  libavformat  53. 19. 0 / 53. 19. 0
  libavdevice  53.  4. 0 / 53.  4. 0
  libavfilter   2. 47. 0 /  2. 47. 0
  libswscale    2.  1. 0 /  2.  1. 0
  libpostproc  51.  2. 0 / 51.  2. 0
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.
Ell.Theta: no visible global function definition for 'ell.theta'
confid.int.theta: no visible global function definition for 'qchisq'
confid.int.theta : sim.c: no visible global function definition for
  'runif'
confid.int.theta: no visible global function definition for 'quantile'
dd.est: no visible global function definition for 'ecdf'
ks.sporm : Simul: no visible global function definition for 'runif'
ks.stat: no visible global function definition for 'ecdf'
plotor: no visible global function definition for 'ecdf'
plotor: no visible global function definition for 'plot'
test.theta: no visible global function definition for 'ecdf'
test.theta : sim: no visible global function definition for 'runif'
Undefined global functions or variables:
  ecdf ell.theta plot qchisq quantile runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "ecdf", "qchisq", "quantile", "runif")
to your NAMESPACE file.
fetch_NBAPlayerStatistics: no visible global function definition for
  'read.table'
Undefined global functions or variables:
  read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
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.
Found the following significant warnings:
  Warning: GNU Extension: Symbol 'k' is used before it is typed at (1)
See 'd:/Rcompile/CRANpkg/local/3.4/spsmooth.Rcheck/00install.out' for details.
.dpssToEigenvalues: no visible global function definition for 'mvfft'
smooth.construct.sp.smooth.spec: no visible global function definition
  for 'str'
Undefined global functions or variables:
  mvfft str
Consider adding
  importFrom("stats", "mvfft")
  importFrom("utils", "str")
to your NAMESPACE file.
plotThin: no visible global function definition for 'par'
plotThin: no visible global function definition for 'dev.interactive'
plotThin: no visible global function definition for 'plot'
plotThin: no visible global function definition for 'hist'
thin: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  dev.interactive hist par plot write.csv
Consider adding
  importFrom("grDevices", "dev.interactive")
  importFrom("graphics", "hist", "par", "plot")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
.GameSPT: no visible global function definition for 'runif'
.GameSPT: no visible global function definition for 'points'
.GameST: no visible global function definition for 'runif'
.GameST: no visible global function definition for 'points'
.arc: no visible global function definition for 'lines'
.ptpedal: no visible global function definition for 'polygon'
.sptpedal2: no visible global function definition for 'segments'
.sptpedal3: no visible global function definition for 'polygon'
.sptpedal4: no visible global function definition for 'polygon'
chaos.spt: no visible global function definition for 'plot'
chaos.spt: no visible global function definition for 'polygon'
chaos.spt: no visible global function definition for 'runif'
chaos.spt: no visible global function definition for 'points'
chaos.st: no visible global function definition for 'plot'
chaos.st: no visible global function definition for 'polygon'
chaos.st: no visible global function definition for 'runif'
chaos.st: no visible global function definition for 'points'
plot.spt: no visible global function definition for 'plot'
plot.spt: no visible global function definition for 'polygon'
plot.st: no visible global function definition for 'plot'
plot.st: no visible global function definition for 'polygon'
Undefined global functions or variables:
  lines plot points polygon runif segments
Consider adding
  importFrom("graphics", "lines", "plot", "points", "polygon",
             "segments")
  importFrom("stats", "runif")
to your NAMESPACE file.
CMCSimulation: no visible global function definition for 'rexp'
CMCSimulation: no visible global function definition for 'plot'
CMCSimulation: no visible global function definition for 'axis'
booking_clerkMC: no visible global function definition for 'runif'
booking_clerkMC: no visible global function definition for 'rexp'
fixedpoint_show: no visible global function definition for 'plot'
fixedpoint_show: no visible global function definition for 'lines'
mean.trapTransect: no visible global function definition for
  'weighted.mean'
newtonraphson_show: no visible global function definition for 'plot'
newtonraphson_show: no visible global function definition for 'lines'
print.transectHolder: no visible global function definition for 'str'
print.trapTransect: no visible global function definition for 'str'
sd.transectHolder: no visible global function definition for 'sd'
simulate.transectHolder: no visible global function definition for
  'runif'
Undefined global functions or variables:
  axis lines plot rexp runif sd str weighted.mean
Consider adding
  importFrom("graphics", "axis", "lines", "plot")
  importFrom("stats", "rexp", "runif", "sd", "weighted.mean")
  importFrom("utils", "str")
to your NAMESPACE file.
sGda : <anonymous>: no visible global function definition for 'cov'
sortgene: no visible global function definition for 'model.matrix'
Undefined global functions or variables:
  cov model.matrix
Consider adding
  importFrom("stats", "cov", "model.matrix")
to your NAMESPACE file.
'library' or 'require' call to 'tcltk' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
read.csv.sql: no visible global function definition for 'download.file'
sqldf: no visible global function definition for 'modifyList'
sqldf: no visible global function definition for 'head'
Undefined global functions or variables:
  download.file head modifyList
Consider adding
  importFrom("utils", "download.file", "head", "modifyList")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'RJDBC' 'RMySQL' 'RODBC' 'RPostgreSQL' 'RSQLite' 'tcltk'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
cacheQuery: no visible global function definition for 'read.csv'
cacheQuery: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  read.csv write.csv
Consider adding
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
SQN: no visible binding for global variable 'median'
SQN: no visible global function definition for 'quantile'
SQN.demo.data: no visible global function definition for 'rnorm'
mix.qn: no visible global function definition for 'ecdf'
mix.qn: no visible global function definition for 'quantile'
Undefined global functions or variables:
  ecdf median quantile rnorm
Consider adding
  importFrom("stats", "ecdf", "median", "quantile", "rnorm")
to your NAMESPACE file.
plot.srafit: no visible global function definition for 'layout'
plot.srafit: no visible global function definition for 'par'
sraData : vartruncGauss : ff: no visible global function definition for
  'dnorm'
sraData : vartruncGauss : ff: no visible global function definition for
  'pnorm'
sraData : vartruncGauss: no visible global function definition for
  'uniroot'
sraPlotMean: no visible global function definition for 'axis'
sraPlotMean: no visible global function definition for 'points'
sraPlotMean: no visible global function definition for 'lines'
sraPlotMeanResid: no visible global function definition for 'axis'
sraPlotMeanResid: no visible global function definition for 'abline'
sraPlotMeanResid: no visible global function definition for 'points'
sraPlotVar: no visible global function definition for 'axis'
sraPlotVar: no visible global function definition for 'points'
sraPlotVar: no visible global function definition for 'lines'
sraPlotVarResid: no visible global function definition for 'axis'
sraPlotVarResid: no visible global function definition for 'abline'
sraPlotVarResid: no visible global function definition for 'points'
sraPlotlegend: no visible global function definition for 'legend'
sraStartingvalues : sraStartingvalues.mu0: no visible global function
  definition for 'rnorm'
sraStartingvalues : sraStartingvalues.logvarA0: no visible global
  function definition for 'rnorm'
sraStartingvalues : sraStartingvalues.logvarE0: no visible global
  function definition for 'rnorm'
sraStartingvalues: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  abline axis dnorm layout legend lines par pnorm points rnorm uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "layout", "legend", "lines",
             "par", "points")
  importFrom("stats", "dnorm", "pnorm", "rnorm", "uniroot")
to your NAMESPACE file.
draw.srd: no visible global function definition for 'complete.cases'
draw.srd: no visible global function definition for 'runif'
draw.srd: no visible global function definition for 'arrows'
draw.srd: no visible global function definition for 'text'
draw.srd: no visible global function definition for 'segments'
draw.srd.enc: no visible global function definition for 'par'
draw.srd.enc: no visible global function definition for 'plot.new'
draw.srd.enc: no visible global function definition for 'plot.window'
draw.srd.enc: no visible global function definition for 'rgb'
draw.srd.enc: no visible global function definition for 'polygon'
draw.srd.enc: no visible global function definition for 'pchisq'
draw.srd.enc: no visible global function definition for 'text'
draw.srd.enc: no visible global function definition for 'title'
draw.srd.enc: no visible global function definition for 'arrows'
drawcell: no visible global function definition for 'polygon'
drawcell: no visible global function definition for 'segments'
rotate.srd: no visible global function definition for 'devAskNewPage'
srd: no visible global function definition for 'devAskNewPage'
Undefined global functions or variables:
  arrows complete.cases devAskNewPage par pchisq plot.new plot.window
  polygon rgb runif segments text title
Consider adding
  importFrom("grDevices", "devAskNewPage", "rgb")
  importFrom("graphics", "arrows", "par", "plot.new", "plot.window",
             "polygon", "segments", "text", "title")
  importFrom("stats", "complete.cases", "pchisq", "runif")
to your NAMESPACE file.
Found the following hidden files and directories:
  .Rapp.history
  inst/script/.Rapp.history
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
File 'sROC/R/onload.R':
  .onLoad calls:
    packageStartupMessage("sROC 0.1-2 loaded")

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

AUC : TrapezInt: no visible global function definition for 'approx'
AUC : SimpsonInt: no visible global function definition for 'approx'
CI.CDF: no visible global function definition for 'qnorm'
bw.CDF: no visible global function definition for 'sd'
bw.CDF: no visible global function definition for 'IQR'
bw.CDF.pi: no visible global function definition for 'sd'
bw.CDF.pi: no visible global function definition for 'bw.nrd0'
bw.CDF.pi: no visible global function definition for 'bw.nrd'
bw.CDF.pi: no visible global function definition for 'bw.ucv'
bw.CDF.pi: no visible global function definition for 'bw.bcv'
bw.CDF.pi: no visible global function definition for 'bw.SJ'
bw.CDF.pi: no visible global function definition for 'IQR'
plot.CDF: no visible global function definition for 'plot.default'
plot.CDF: no visible global function definition for 'lines'
plot.CDF: no visible global function definition for 'polygon'
plot.ROC: no visible global function definition for 'plot.default'
plot.ROC: no visible global function definition for 'abline'
Undefined global functions or variables:
  IQR abline approx bw.SJ bw.bcv bw.nrd bw.nrd0 bw.ucv lines
  plot.default polygon qnorm sd
Consider adding
  importFrom("graphics", "abline", "lines", "plot.default", "polygon")
  importFrom("stats", "IQR", "approx", "bw.SJ", "bw.bcv", "bw.nrd",
             "bw.nrd0", "bw.ucv", "qnorm", "sd")
to your NAMESPACE file.
ssd : correction_method_D: no visible global function definition for
  'rnorm'
ssd : generate_bootstrap: no visible global function definition for
  'rmultinom'
ssd : bootstrap_method: no visible global function definition for
  'median'
ssd : bootstrap_method: no visible global function definition for
  'quantile'
ssd : unbalanced_generate_bootstrap: no visible global function
  definition for 'rmultinom'
ssd : unbalanced_bootstrap_method: no visible global function
  definition for 'median'
ssd : unbalanced_bootstrap_method: no visible global function
  definition for 'quantile'
ssd: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  median qchisq quantile rmultinom rnorm
Consider adding
  importFrom("stats", "median", "qchisq", "quantile", "rmultinom",
             "rnorm")
to your NAMESPACE file.
L_hNV: no visible global function definition for 'pnorm'
L_hNV_rho: no visible global function definition for 'pnorm'
eff.ssfa: no visible global function definition for 'pnorm'
plot_fitted: no visible global function definition for 'lines'
plot_moran: no visible global function definition for 'residuals'
print.summary.ssfa: no visible global function definition for
  'printCoefmat'
ssfa: no visible global function definition for 'model.frame'
ssfa: no visible global function definition for 'model.response'
ssfa.fit: no visible global function definition for 'lm'
ssfa.fit: no visible global function definition for 'var'
ssfa.fit: no visible global function definition for 'logLik'
summary.ssfa: no visible global function definition for 'pnorm'
summary.ssfa: no visible global function definition for 'logLik'
summary.ssfa: no visible global function definition for 'pchisq'
summary.ssfa: no visible binding for global variable 'df'
u.ssfa: no visible global function definition for 'dnorm'
u.ssfa: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  df dnorm lines lm logLik model.frame model.response pchisq pnorm
  printCoefmat residuals var
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "df", "dnorm", "lm", "logLik", "model.frame",
             "model.response", "pchisq", "pnorm", "printCoefmat",
             "residuals", "var")
to your NAMESPACE file.
Package in Depends field not imported from: 'survey'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fit.model: no visible global function definition for 'hadamard'
Undefined global functions or variables:
  hadamard
sslCoTrain: no visible global function definition for 'predict'
sslSelfTrain: no visible global function definition for 'predict'
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
map.world: no visible global function definition for 'par'
map.world: no visible global function definition for 'plot.new'
map.world: no visible global function definition for 'plot.window'
map.world: no visible global function definition for 'lines'
map.world: no visible global function definition for 'title'
map.world: no visible global function definition for 'axis'
map.world: no visible global function definition for 'box'
plot.smooth.sspline: no visible global function definition for
  'predict'
plot.smooth.sspline: no visible global function definition for
  'filled.contour'
plot.smooth.sspline: no visible binding for global variable
  'terrain.colors'
plot.smooth.sspline: no visible global function definition for 'title'
plot.smooth.sspline: no visible global function definition for 'axis'
station: no visible binding for global variable 'WTdiff'
station: no visible global function definition for 'points'
Undefined global functions or variables:
  WTdiff axis box filled.contour lines par plot.new plot.window points
  predict terrain.colors title
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "axis", "box", "filled.contour", "lines", "par",
             "plot.new", "plot.window", "points", "title")
  importFrom("stats", "predict")
to your NAMESPACE file.
calcgroup : probtotrating: no visible global function definition for
  'convolve'
enterratdata: no visible global function definition for 'edit'
gplot.SSrat: no visible global function definition for 'par'
gplot.SSrat: no visible global function definition for 'plot'
gplot.SSrat: no visible global function definition for 'legend'
Undefined global functions or variables:
  convolve edit legend par plot
Consider adding
  importFrom("graphics", "legend", "par", "plot")
  importFrom("stats", "convolve")
  importFrom("utils", "edit")
to your NAMESPACE file.
SS.ID: no visible global function definition for 'var'
SS.sim.chol: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm var
Consider adding
  importFrom("stats", "rnorm", "var")
to your NAMESPACE file.
error.est : <anonymous>: no visible global function definition for
  'median'
holm.robust: no visible global function definition for 'pnorm'
holm.robust: no visible global function definition for 'median'
holm.robust: no visible global function definition for 'mad'
huberize: no visible global function definition for 'quantile'
ssvd.initial: no visible global function definition for 'mad'
ssvd.iter.thresh: no visible global function definition for 'mad'
Undefined global functions or variables:
  mad median pnorm quantile
Consider adding
  importFrom("stats", "mad", "median", "pnorm", "quantile")
to your NAMESPACE file.
optimal_cutoff: no visible global function definition for 'tail'
plot.stabsel: no visible global function definition for 'hcl'
plot.stabsel: no visible global function definition for 'par'
plot.stabsel: no visible global function definition for 'matplot'
plot.stabsel: no visible global function definition for 'abline'
plot.stabsel: no visible global function definition for 'axis'
plot.stabsel: no visible global function definition for 'plot'
plot.stabsel: no visible global function definition for 'tail'
plot.stabsel: no visible global function definition for 'points'
Undefined global functions or variables:
  abline axis hcl matplot par plot points tail
Consider adding
  importFrom("grDevices", "hcl")
  importFrom("graphics", "abline", "axis", "matplot", "par", "plot",
             "points")
  importFrom("utils", "tail")
to your NAMESPACE file.
.ls.objects: no visible binding for global variable 'object.size'
Undefined global functions or variables:
  object.size
Consider adding
  importFrom("utils", "object.size")
to your NAMESPACE file.
.expandLevels: no visible global function definition for 'na.omit'
.ffStack: no visible global function definition for 'na.omit'
.ffffStack: no visible global function definition for 'na.omit'
Stack : <anonymous>: no visible global function definition for
  'na.omit'
ffStack,ffdf-data.frame: no visible global function definition for
  'na.omit'
ffStack,ffdf-ffdf: no visible global function definition for 'na.omit'
ffStack,ffdf-list: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
genericPlot: no visible global function definition for 'dev.new'
genericPlot: no visible global function definition for 'par'
genericPlot: no visible global function definition for 'rainbow'
genericPlot: no visible global function definition for 'plot'
genericPlot: no visible global function definition for 'lines'
genericPlot: no visible global function definition for 'legend'
genericPlot: no visible global function definition for 'dev.copy2pdf'
genericPlot: no visible global function definition for 'dev.copy2eps'
genericPlot: no visible global function definition for 'dev.print'
genericPlot: no visible binding for global variable 'png'
genericPlot: no visible binding for global variable 'tiff'
plotStrains: no visible global function definition for 'rainbow'
plotStrains: no visible global function definition for 'dev.new'
plotStrains: no visible global function definition for 'par'
plotStrains: no visible global function definition for 'plot'
plotStrains: no visible global function definition for 'lines'
plotStrains: no visible global function definition for 'legend'
plotStrains: no visible global function definition for 'dev.copy2pdf'
plotStrains: no visible global function definition for 'dev.copy2eps'
plotStrains: no visible global function definition for 'dev.print'
plotStrains: no visible binding for global variable 'png'
plotStrains: no visible binding for global variable 'tiff'
Undefined global functions or variables:
  dev.copy2eps dev.copy2pdf dev.new dev.print legend lines par plot png
  rainbow tiff
Consider adding
  importFrom("grDevices", "dev.copy2eps", "dev.copy2pdf", "dev.new",
             "dev.print", "png", "rainbow", "tiff")
  importFrom("graphics", "legend", "lines", "par", "plot")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'np' 'sp'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'np' 'sp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
stkde: no visible global function definition for 'npudensbw'
stkde: no visible global function definition for 'npudens'
stkde: no visible global function definition for 'quantile'
stkde: no visible global function definition for 'heat.colors'
stkde: no visible global function definition for 'par'
stkde: no visible global function definition for 'image'
stkde: no visible global function definition for 'contour'
stkde.base: no visible global function definition for 'npudensbw'
stkde.base: no visible global function definition for 'npudens'
stkde.sig: no visible global function definition for 'SpatialPoints'
stkde.sig: no visible global function definition for 'spsample'
stkde.sig: no visible global function definition for 'bbox'
stkde.sig: no visible global function definition for 'quantile'
stkde.sig: no visible global function definition for 'heat.colors'
stkde.sig: no visible global function definition for 'par'
stkde.sig: no visible global function definition for 'image'
stkde.sig: no visible global function definition for 'contour'
Undefined global functions or variables:
  SpatialPoints bbox contour heat.colors image npudens npudensbw par
  quantile spsample
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "contour", "image", "par")
  importFrom("stats", "quantile")
to your NAMESPACE file.
find.names: no visible global function definition for 'na.omit'
generate.names: no visible global function definition for 'na.omit'
standardize.countrynames: no visible global function definition for
  'data'
standardize.names: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    include   8.2Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   5.0Mb
'library' or 'require' call to 'codetools' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'codetools' 'gss'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following hidden files and directories:
  inst/.Renviron.d
  inst/.Rprofile.d
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
Warning: no function found corresponding to methods exports from 'stashR' for: 'initialize'

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

Probably some imports need to be declared in the NAMESPACE file.
cacheVersionFile: no visible global function definition for
  'download.file'
getdata: no visible global function definition for 'download.file'
copyDB,localDB: no visible global function definition for 'new'
initialize,localDB: no visible global function definition for
  'callNextMethod'
initialize,remoteDB: no visible global function definition for
  'callNextMethod'
Undefined global functions or variables:
  callNextMethod download.file new
Consider adding
  importFrom("methods", "callNextMethod", "new")
  importFrom("utils", "download.file")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running 'tests.R' [2s]
Running the tests in 'tests/tests.R' failed.
Last 13 lines of output:
  > ## Test objects of class 'remoteDB'
  > ## These tests will fail (within a 'try()') if Internet connectivity
  > ## is not available
  > 
  > myurl <- "http://www.biostat.jhsph.edu/MCAPS/data_v0.3/"
  > 
  > ## create a 'remoteDB' object ##
  > db <- new("remoteDB", url= myurl, dir = dir, name= "MCAPS")
  Error in download.file(rpath, versionFile(db, where = "local"), mode = "w",  : 
    cannot open URL 'http://www.biostat.jhsph.edu/MCAPS/data_v0.3/version'
  Calls: new ... initialize -> initialize -> cacheVersionFile -> download.file
  In addition: Warning message:
  In download.file(rpath, versionFile(db, where = "local"), mode = "w",  :
    cannot open URL 'http://www.biostat.jhsph.edu/MCAPS/data_v0.3/version': HTTP status was '404 Not Found'
  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.
Found the following significant warnings:
  decTreeImpFuncCpp.cpp:1677:42: warning: unknown escape sequence: '\040'
See 'd:/Rcompile/CRANpkg/local/3.4/StatMethRank.Rcheck/00install.out' for details.
inspect: no visible global function definition for 'par'
inspect: no visible global function definition for 'abline'
inspect: no visible global function definition for 'lines'
inspect: no visible global function definition for 'points'
plotfit: no visible global function definition for 'dev.off'
plotfit: no visible global function definition for 'par'
plotfit: no visible global function definition for 'lines'
plotfit: no visible global function definition for 'points'
plotfit: no visible global function definition for 'legend'
plothill: no visible global function definition for 'par'
plothill: no visible global function definition for 'abline'
plothill: no visible global function definition for 'points'
plotmultifit: no visible global function definition for 'par'
plotmultifit: no visible global function definition for 'lines'
plotmultifit: no visible global function definition for 'points'
plotmultifit: no visible global function definition for 'pexp'
plotmultifit: no visible global function definition for 'plnorm'
plotmultifit: no visible global function definition for 'ppois'
plotmultifit: no visible global function definition for 'legend'
plotols: no visible global function definition for 'dev.off'
plotols: no visible global function definition for 'lm'
plotols: no visible global function definition for 'par'
plotols: no visible global function definition for 'abline'
plotols: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline dev.off legend lines lm par pexp plnorm points ppois
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("graphics", "abline", "legend", "lines", "par", "points")
  importFrom("stats", "lm", "pexp", "plnorm", "ppois")
to your NAMESPACE file.
getStp: no visible global function definition for 'lm'
plot.steeptest: no visible global function definition for 'plot'
plot.steeptest: no visible global function definition for 'axis'
plot.steeptest: no visible global function definition for 'box'
plot.steeptest: no visible global function definition for 'lm'
plot.steeptest: no visible global function definition for 'abline'
plot.steeptest: no visible global function definition for 'legend'
plot.steeptest: no visible global function definition for
  'as.graphicsAnnot'
steeptest: no visible global function definition for 'lm'
summary.steeptest: no visible global function definition for 'var'
summary.steeptest: no visible global function definition for 'quantile'
Undefined global functions or variables:
  abline as.graphicsAnnot axis box legend lm plot quantile var
Consider adding
  importFrom("grDevices", "as.graphicsAnnot")
  importFrom("graphics", "abline", "axis", "box", "legend", "plot")
  importFrom("stats", "lm", "quantile", "var")
to your NAMESPACE file.
Stem.Bootstrap: no visible global function definition for 'runif'
filtering: no visible global function definition for 'is.ts'
filtering: no visible global function definition for 'ts'
filtering: no visible global function definition for 'start'
filtering: no visible global function definition for 'end'
filtering: no visible global function definition for 'frequency'
kalman: no visible global function definition for 'ts'
smoothing: no visible global function definition for 'is.ts'
smoothing: no visible global function definition for 'ts'
smoothing: no visible global function definition for 'start'
smoothing: no visible global function definition for 'end'
smoothing: no visible global function definition for 'frequency'
Undefined global functions or variables:
  end frequency is.ts runif start ts
Consider adding
  importFrom("stats", "end", "frequency", "is.ts", "runif", "start",
             "ts")
to your NAMESPACE file.
cv.step.plr: no visible global function definition for 'binomial'
cv.step.plr: no visible global function definition for 'predict'
cv.step.plr: no visible binding for global variable 'var'
plr: no visible global function definition for 'binomial'
predict.stepplr: no visible global function definition for 'predict'
summary.plr: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  binomial pnorm predict var
Consider adding
  importFrom("stats", "binomial", "pnorm", "predict", "var")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'plr-internal':
  'anova.stepplr' 'print.plr' 'print.stepplr' 'summary.plr'
  'summary.stepplr'

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

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
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.
initialize.emul: no visible global function definition for 'lm'
make.ranges: no visible global function definition for 'lm'
optimize.emul: no visible global function definition for 'nlminb'
optimize.emul: no visible global function definition for 'runif'
rsurface.plot: no visible global function definition for 'par'
rsurface.plot: no visible global function definition for
  'filled.contour'
rsurface.plot: no visible binding for global variable 'topo.colors'
rsurface.plot: no visible global function definition for 'title'
test.all: no visible global function definition for 'par'
test.all: no visible global function definition for 'plot'
test.all: no visible global function definition for 'lines'
test.csv: no visible global function definition for 'plot.default'
test.csv: no visible global function definition for 'lines'
Undefined global functions or variables:
  filled.contour lines lm nlminb par plot plot.default runif title
  topo.colors
Consider adding
  importFrom("grDevices", "topo.colors")
  importFrom("graphics", "filled.contour", "lines", "par", "plot",
             "plot.default", "title")
  importFrom("stats", "lm", "nlminb", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
See 'd:/Rcompile/CRANpkg/local/3.4/stima.Rcheck/00install.out' for details.
bos.cat2: no visible global function definition for 'resid'
bos.cat2: no visible global function definition for 'lm'
plot.rt: no visible global function definition for 'plot'
plot.rt: no visible global function definition for 'text'
plot.rt: no visible global function definition for 'rect'
plot.rt: no visible global function definition for 'title'
plot.rt: no visible global function definition for 'par'
stdata: no visible binding for global variable 'var'
stima: no visible global function definition for 'fitted'
stima: no visible global function definition for 'lm'
stima: no visible global function definition for 'anova'
stima: no visible global function definition for 'predict'
stima: no visible global function definition for 'cor'
stima: no visible global function definition for 'as.formula'
stima: no visible global function definition for 'step'
Undefined global functions or variables:
  anova as.formula cor fitted lm par plot predict rect resid step text
  title var
Consider adding
  importFrom("graphics", "par", "plot", "rect", "text", "title")
  importFrom("stats", "anova", "as.formula", "cor", "fitted", "lm",
             "predict", "resid", "step", "var")
to your NAMESPACE file.
na.stinterp.default: no visible global function definition for 'time'
na.stinterp.default: no visible global function definition for
  'na.omit'
Undefined global functions or variables:
  na.omit time
Consider adding
  importFrom("stats", "na.omit", "time")
to your NAMESPACE file.
ConstructMPst: no visible global function definition for 'na.omit'
ConstructMPst: no visible global function definition for
  'txtProgressBar'
ConstructMPst: no visible global function definition for
  'setTxtProgressBar'
MedianPolishM.default : Res: no visible binding for global variable
  'median'
MedianPolishM.default: no visible binding for global variable 'median'
MedianPolishM.default: no visible global function definition for
  'median'
Mpplot: no visible global function definition for 'layout'
Mpplot: no visible global function definition for 'plot'
Mpplot: no visible global function definition for 'text'
Mpplot: no visible global function definition for 'axis'
Mpplot: no visible global function definition for 'mtext'
print.plot.MedianPolishM: no visible global function definition for
  'layout'
print.plot.MedianPolishM: no visible global function definition for
  'stripchart'
print.plot.MedianPolishM: no visible global function definition for
  'ts.plot'
print.plot.MedianPolishM: no visible global function definition for
  'plot'
print.plot.MedianPolishM: no visible global function definition for
  'legend'
removetrendMPst: no visible global function definition for
  'txtProgressBar'
removetrendMPst: no visible global function definition for
  'setTxtProgressBar'
splineMPST: no visible global function definition for 'na.omit'
splineMPST: no visible global function definition for 'txtProgressBar'
splineMPST: no visible global function definition for
  'setTxtProgressBar'
Undefined global functions or variables:
  axis layout legend median mtext na.omit plot setTxtProgressBar
  stripchart text ts.plot txtProgressBar
Consider adding
  importFrom("graphics", "axis", "layout", "legend", "mtext", "plot",
             "stripchart", "text")
  importFrom("stats", "median", "na.omit", "ts.plot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.4/RcppParallel/include/tthread/tinythread.h:632:14: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.4/StMoSim.Rcheck/00install.out' for details.
myQQNorm: no visible global function definition for 'mad'
myQQNorm: no visible global function definition for 'qnorm'
myQQNorm: no visible global function definition for 'plot'
myQQNorm: no visible global function definition for 'matlines'
myQQNorm: no visible global function definition for 'points'
myQQNorm: no visible global function definition for 'qqline'
myQQNorm: no visible global function definition for 'box'
qqnormSim,lm: no visible global function definition for 'resid'
Undefined global functions or variables:
  box mad matlines plot points qnorm qqline resid
Consider adding
  importFrom("graphics", "box", "matlines", "plot", "points")
  importFrom("stats", "mad", "qnorm", "qqline", "resid")
to your NAMESPACE file.
sharpe: no visible global function definition for 'sd'
sortino: no visible global function definition for 'sd'
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Namespace with empty importFrom: 'tcltk2'
DetailOpLines: no visible global function definition for
  'tkProgressBar'
DetailOpLines: no visible global function definition for
  'setTkProgressBar'
MultiTrainWithInventory: no visible global function definition for
  'tkProgressBar'
MultiTrainWithInventory: no visible global function definition for
  'setTkProgressBar'
SimHistory: no visible global function definition for 'tkProgressBar'
SimHistory: no visible global function definition for
  'setTkProgressBar'
Undefined global functions or variables:
  setTkProgressBar tkProgressBar
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
See 'd:/Rcompile/CRANpkg/local/3.4/stpp.Rcheck/00install.out' for details.
'library' or 'require' calls in package code:
  'rgl' 'rpanel'
  Please use :: or requireNamespace() instead.
  See section 'Suggested 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.
.rdirichlet: no visible global function definition for 'rgamma'
DGobj.simul.mechanistic: no visible global function definition for
  'rbinom'
DGobj.simul.mechanistic: no visible global function definition for
  'rpois'
DGobj.simul.mechanistic: no visible global function definition for
  'par'
DGobj.simul.mechanistic: no visible global function definition for
  'plot'
DGobj.simul.mechanistic: no visible global function definition for
  'mtext'
DGobj.simul.mechanistic: no visible global function definition for
  'box'
DGobj.simul.regression: no visible global function definition for
  'rnorm'
DGobj.simul.regression: no visible global function definition for
  'rmultinom'
DGobj.simul.regression: no visible global function definition for 'par'
DGobj.simul.regression: no visible global function definition for
  'plot'
ranking.strains: no visible global function definition for 'lm'
ranking.strains: no visible global function definition for 'par'
ranking.strains: no visible global function definition for 'plot'
ranking.strains: no visible global function definition for 'points'
ranking.strains: no visible global function definition for 'hist'
ranking.strains: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline box hist lm mtext par plot points rbinom rgamma rmultinom
  rnorm rpois
Consider adding
  importFrom("graphics", "abline", "box", "hist", "mtext", "par", "plot",
             "points")
  importFrom("stats", "lm", "rbinom", "rgamma", "rmultinom", "rnorm",
             "rpois")
to your NAMESPACE file.
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.
add_b1_takenone: no visible global function definition for 'quantile'
plot.strata: no visible global function definition for 'layout'
plot.strata: no visible global function definition for 'par'
plot.strata: no visible global function definition for 'hist'
plot.strata: no visible global function definition for 'rgb'
plot.strata: no visible global function definition for 'abline'
plot.strata: no visible global function definition for 'text'
plot.strata: no visible global function definition for 'mtext'
robust_initpbh: no visible global function definition for 'var'
strata.LH: no visible global function definition for 'combn'
strata.LH: no visible global function definition for 'quantile'
Undefined global functions or variables:
  abline combn hist layout mtext par quantile rgb text var
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "abline", "hist", "layout", "mtext", "par",
             "text")
  importFrom("stats", "quantile", "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
HRatio: no visible global function definition for 'qnorm'
icweib: no visible global function definition for 'model.frame'
icweib: no visible binding for global variable 'na.pass'
icweib: no visible global function definition for 'complete.cases'
icweib: no visible global function definition for 'model.matrix'
icweib: no visible global function definition for 'optim'
icweib: no visible global function definition for 'pchisq'
icweib: no visible global function definition for 'pnorm'
plot.icweib : getstat: no visible global function definition for
  'qnorm'
plot.icweib: no visible global function definition for 'plot'
plot.icweib: no visible global function definition for 'lines'
plot.icweib: no visible global function definition for 'legend'
print.icweib: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  complete.cases legend lines model.frame model.matrix na.pass optim
  pchisq plot pnorm qnorm
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "complete.cases", "model.frame", "model.matrix",
             "na.pass", "optim", "pchisq", "pnorm", "qnorm")
to your NAMESPACE file.
'library' or 'require' call to 'ROAuth' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
RMSEA : lower.lambda: no visible global function definition for
  'pchisq'
RMSEA: no visible global function definition for 'uniroot'
RMSEA : upper.lambda: no visible global function definition for
  'pchisq'
RMSEA: no visible global function definition for 'pchisq'
boot.lavaan: no visible global function definition for 'cov'
boot.lavaan: no visible binding for global variable 'sd'
factanal.prcomp: no visible global function definition for 'princomp'
fit.nlminb: no visible global function definition for 'nlminb'
fit.nlminb: no visible global function definition for 'pchisq'
pval: no visible global function definition for 'pnorm'
rmnorm : <anonymous>: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  cov nlminb pchisq pnorm princomp rnorm sd uniroot
Consider adding
  importFrom("stats", "cov", "nlminb", "pchisq", "pnorm", "princomp",
             "rnorm", "sd", "uniroot")
to your NAMESPACE file.
installed size is 33.9Mb
  sub-directories of 1Mb or more:
    libs  33.3Mb
breakpoints.formula: no visible global function definition for
  '%dopar%'
breakpoints.formula: no visible binding for global variable 'i'
efpFunctional: multiple local function definitions for 'plotProcess'
  with different formal arguments
mefp.efp: multiple local function definitions for 'computeEmpProc' with
  different formal arguments
sctest.default: no visible global function definition for 'tail'
Undefined global functions or variables:
  %dopar% i tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
PlotHypTree: no visible global function definition for 'browseURL'
treePValues: no visible global function definition for 'lm'
treePValues: no visible global function definition for 'pf'
plot,GBH-ANY: no visible binding for global variable 'sorted.hyp'
plot,GBH-ANY: no visible binding for global variable 'pval'
plot,GBH-ANY: no visible binding for global variable 'group'
plot,GBH-ANY: no visible binding for global variable 'type'
Undefined global functions or variables:
  browseURL group lm pf pval sorted.hyp type
Consider adding
  importFrom("stats", "lm", "pf")
  importFrom("utils", "browseURL")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from 'stsm.class' for: 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
stsm.model: no visible global function definition for 'is.ts'
stsm.model: no visible global function definition for 'var'
stsm.model: no visible global function definition for 'frequency'
stsm.model: no visible global function definition for 'na.omit'
stsm.model: no visible global function definition for 'fft'
stsm.model: no visible global function definition for 'new'
stsm.sgf: no visible global function definition for 'frequency'
char2numeric,stsm: no visible global function definition for
  'frequency'
set.cpar,stsm: no visible global function definition for 'validObject'
set.nopars,stsm: no visible global function definition for
  'validObject'
set.pars,stsm: no visible global function definition for 'validObject'
transPars,stsm: no visible global function definition for 'var'
Undefined global functions or variables:
  fft frequency is.ts na.omit new validObject var
Consider adding
  importFrom("methods", "new", "validObject")
  importFrom("stats", "fft", "frequency", "is.ts", "na.omit", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
SubLasso: no visible global function definition for 'predict'
SubLasso: no visible global function definition for 'coef'
SubLasso: no visible global function definition for 'dev.new'
SubLasso: no visible global function definition for 'cor'
SubLasso: no visible global function definition for 'boxplot'
predict.sublasso: no visible global function definition for 'predict'
Undefined global functions or variables:
  boxplot coef cor dev.new predict
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "boxplot")
  importFrom("stats", "coef", "cor", "predict")
to your NAMESPACE file.
identifyGraph: no visible global function definition for 'phyper'
mytriangle: no visible global function definition for 'symbols'
plotGraph: no visible global function definition for 'par'
plotGraph: no visible global function definition for 'plot'
updateOrgEnvir: no visible global function definition for 'read.table'
Undefined global functions or variables:
  par phyper plot read.table symbols
Consider adding
  importFrom("graphics", "par", "plot", "symbols")
  importFrom("stats", "phyper")
  importFrom("utils", "read.table")
to your NAMESPACE file.
predict.subsemble: no visible global function definition for 'predict'
predict.subsemble: no visible binding for global variable 'family'
subsemble: no visible global function definition for 'gaussian'
subsemble: no visible global function definition for 'detectCores'
subsemble : .make_Z_l: no visible global function definition for
  'parSapply'
subsemble : .make_Z_l: no visible global function definition for
  'makeCluster'
subsemble : .make_Z_l: no visible global function definition for
  'stopCluster'
subsemble: no visible global function definition for 'parSapply'
subsemble: no visible global function definition for 'makeCluster'
subsemble: no visible global function definition for 'stopCluster'
subsemble: no visible global function definition for 'predict'
Undefined global functions or variables:
  detectCores family gaussian makeCluster parSapply predict stopCluster
Consider adding
  importFrom("stats", "family", "gaussian", "predict")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'ROCR' 'penalized'
  Please remove these calls from your code.
ELF: no visible global function definition for 'pt'
ELF: no visible global function definition for 'qnorm'
ELF: no visible global function definition for 'lm'
ELF: no visible global function definition for 'lowess'
ELF: no visible global function definition for 'dnorm'
ELF: no visible global function definition for 'approx'
subtype: no visible global function definition for 'runif'
subtype: no visible global function definition for 'hclust'
subtype: no visible global function definition for 'dist'
subtype: no visible global function definition for 'cutree'
subtype: no visible global function definition for 'pt'
subtype: no visible global function definition for 'heatmap'
test_subtype_only: no visible global function definition for 'pt'
test_subtype_only: no visible global function definition for 'survdiff'
test_subtype_only: no visible global function definition for 'survfit'
test_subtype_only: no visible global function definition for 'title'
ufun: no visible global function definition for 'dnorm'
ufun: no visible global function definition for 'lowess'
Undefined global functions or variables:
  approx cutree dist dnorm hclust heatmap lm lowess pt qnorm runif
  survdiff survfit title
Consider adding
  importFrom("graphics", "title")
  importFrom("stats", "approx", "cutree", "dist", "dnorm", "hclust",
             "heatmap", "lm", "lowess", "pt", "qnorm", "runif")
to your NAMESPACE file.
playSudoku : replot: no visible global function definition for 'par'
playSudoku : replot: no visible global function definition for 'plot'
playSudoku : replot: no visible global function definition for
  'segments'
playSudoku : replot: no visible global function definition for 'text'
playSudoku: no visible global function definition for 'tktoplevel'
playSudoku: no visible global function definition for 'tkwm.title'
playSudoku: no visible global function definition for 'tkrplot'
playSudoku: no visible global function definition for 'tktext'
playSudoku: no visible global function definition for 'tkscrollbar'
playSudoku : <anonymous>: no visible global function definition for
  'tkyview'
playSudoku: no visible global function definition for 'tkconfigure'
playSudoku : <anonymous>: no visible global function definition for
  'tkset'
playSudoku: no visible global function definition for 'tkpack'
playSudoku: no visible global function definition for 'tcl'
playSudoku: no visible global function definition for 'tkcget'
playSudoku : showz: no visible global function definition for
  'tkrreplot'
playSudoku : type: no visible global function definition for 'tkinsert'
playSudoku : type: no visible global function definition for 'tksee'
playSudoku : kb: no visible global function definition for 'tkdestroy'
playSudoku: no visible global function definition for
  'getGraphicsEvent'
playSudoku: no visible global function definition for 'tkbind'
playSudoku: no visible global function definition for 'tkwait.window'
Undefined global functions or variables:
  getGraphicsEvent par plot segments tcl text tkbind tkcget tkconfigure
  tkdestroy tkinsert tkpack tkrplot tkrreplot tkscrollbar tksee tkset
  tktext tktoplevel tkwait.window tkwm.title tkyview
Consider adding
  importFrom("grDevices", "getGraphicsEvent")
  importFrom("graphics", "par", "plot", "segments", "text")
to your NAMESPACE file.
SUE.fitted.values: no visible global function definition for
  'model.frame'
SUE.lm: no visible global function definition for 'model.frame'
SUE.lm: no visible global function definition for 'lm'
SUE.lm: no visible global function definition for 'anova'
SUE.plot: no visible global function definition for 'plot'
SUE.residuals: no visible global function definition for 'model.frame'
parameters : para2: no visible global function definition for 'uniroot'
parameters: no visible global function definition for 'optimize'
parameters: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  anova lm model.frame optimize plot uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "anova", "lm", "model.frame", "optimize",
             "uniroot")
to your NAMESPACE file.
MCMCCV: no visible global function definition for 'rnorm'
MLCVGauss: no visible global function definition for 'runif'
MLCVGauss: no visible global function definition for 'optim'
SimSunderData: no visible global function definition for 'runif'
SimSunderData: no visible global function definition for 'dist'
SimSunderData: no visible global function definition for 'rnorm'
SimSunderData: no visible global function definition for 'qgamma'
SimSunderData: no visible global function definition for 'pnorm'
SimSunderData: no visible global function definition for 'rmultinom'
Undefined global functions or variables:
  dist optim pnorm qgamma rmultinom rnorm runif
Consider adding
  importFrom("stats", "dist", "optim", "pnorm", "qgamma", "rmultinom",
             "rnorm", "runif")
to your NAMESPACE file.
sunter: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
supcluster : itgamma: no visible global function definition for
  'rgamma'
supcluster : itgamma: no visible global function definition for
  'dgamma'
supcluster : itgamma: no visible global function definition for 'runif'
supcluster : itbeta: no visible global function definition for 'rnorm'
supcluster : itbeta: no visible global function definition for 'runif'
supcluster : itj: no visible global function definition for 'dmultinom'
supcluster: no visible global function definition for 'kmeans'
tab1: no visible global function definition for 'image'
tab1: no visible global function definition for 'gray'
tab1: no visible global function definition for 'var'
Undefined global functions or variables:
  dgamma dmultinom gray image kmeans rgamma rnorm runif var
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "image")
  importFrom("stats", "dgamma", "dmultinom", "kmeans", "rgamma", "rnorm",
             "runif", "var")
to your NAMESPACE file.
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.
print.bws.count: no visible binding for global variable 'sd'
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
GG2.boot: no visible global function definition for 'integrate'
KM2.pert: no visible global function definition for 'rexp'
pbc.sample: no visible binding for global variable 'pbc'
plot.surv2sample: no visible global function definition for 'plot'
q95: no visible global function definition for 'quantile'
rmstaug: no visible global function definition for 'lm'
rmstaug: no visible global function definition for 'glm'
rmstaug: no visible global function definition for 'pchisq'
rmstreg: no visible global function definition for 'lm'
rmstreg: no visible global function definition for 'glm'
rmstreg: no visible global function definition for 'pchisq'
surv2sample: no visible binding for global variable 'sd'
surv2sample: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  glm integrate lm pbc pchisq plot pnorm quantile rexp sd
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "glm", "integrate", "lm", "pchisq", "pnorm",
             "quantile", "rexp", "sd")
to your NAMESPACE file.
Est.Var.CCH.trueweights: no visible binding for global variable 'var'
getEstimatesSP: no visible global function definition for 'quantile'
getEstimatesSP: no visible global function definition for 'resid'
prepareDataNP: no visible global function definition for
  'complete.cases'
prepareDataSP: no visible global function definition for
  'complete.cases'
processRawOutput: no visible global function definition for 'qnorm'
survAM.estimate: no visible global function definition for 'median'
survAM.estimate: no visible binding for global variable 'sd'
Undefined global functions or variables:
  complete.cases median qnorm quantile resid sd var
Consider adding
  importFrom("stats", "complete.cases", "median", "qnorm", "quantile",
             "resid", "sd", "var")
to your NAMESPACE file.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

plot.survAUC: no visible global function definition for 'plot'
plot.survAUC: no visible global function definition for 'lines'
plot.survErr: no visible global function definition for 'plot'
plot.survErr: no visible global function definition for 'lines'
schemper: no visible global function definition for 'predict'
schemper: no visible global function definition for 'survfit'
schemper: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx lines plot predict survfit
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "approx", "predict")
to your NAMESPACE file.
Est.PH: no visible global function definition for 'coxph'
Inf.Cval: no visible global function definition for 'rexp'
Inf.Cval: no visible global function definition for 'var'
Inf.Cval.Delta: no visible global function definition for 'rexp'
Inf.Cval.Delta: no visible global function definition for 'var'
cvC: no visible global function definition for 'coxph'
cvC: no visible global function definition for 'weighted.mean'
Undefined global functions or variables:
  coxph rexp var weighted.mean
Consider adding
  importFrom("stats", "rexp", "var", "weighted.mean")
to your NAMESPACE file.
pearson: no visible global function definition for 'cor'
plot.survcorr: no visible global function definition for 'pnorm'
plot.survcorr: no visible global function definition for 'par'
plot.survcorr: no visible global function definition for 'plot'
plot.survcorr: no visible global function definition for 'points'
survcorr: no visible global function definition for 'model.frame'
survcorr: no visible global function definition for 'qnorm'
survcorr: no visible global function definition for 'runif'
survcorr: no visible global function definition for 'pnorm'
survcorr: no visible global function definition for 'var'
survcorr: no visible global function definition for 'qt'
Undefined global functions or variables:
  cor model.frame par plot pnorm points qnorm qt runif var
Consider adding
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "cor", "model.frame", "pnorm", "qnorm", "qt",
             "runif", "var")
to your NAMESPACE file.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   1.6Mb
dropout : <anonymous>: no visible global function definition for
  'na.omit'
encToInt: no visible global function definition for 'localeToCharset'
intToEnc: no visible global function definition for 'localeToCharset'
Undefined global functions or variables:
  localeToCharset na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "localeToCharset")
to your NAMESPACE file.
'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.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.5Mb
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').
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
See 'd:/Rcompile/CRANpkg/local/3.4/survrec.Rcheck/00install.out' for details.
lines.survfitr: no visible global function definition for 'lines'
plot.survfitr: no visible global function definition for 'plot'
plot.survfitr: no visible global function definition for 'lines'
plot.survfitr: no visible global function definition for 'qnorm'
print.survfitr : pfun: no visible global function definition for
  'median'
survdiffr: no visible global function definition for 'runif'
survdiffr: no visible global function definition for 'terms'
survdiffr: no visible global function definition for 'model.extract'
survfitr: no visible global function definition for 'terms'
survfitr: no visible global function definition for 'model.extract'
Undefined global functions or variables:
  lines median model.extract plot qnorm runif terms
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "median", "model.extract", "qnorm", "runif",
             "terms")
to your NAMESPACE file.
plot.rmst2: no visible global function definition for 'par'
plot.rmst2: no visible global function definition for 'plot'
plot.rmst2: no visible global function definition for 'polygon'
plot.rmst2: no visible global function definition for 'lines'
rmst1: no visible global function definition for 'qnorm'
rmst2: no visible global function definition for 'qnorm'
rmst2: no visible global function definition for 'pnorm'
rmst2.sample.data: no visible global function definition for 'data'
rmst2reg: no visible global function definition for 'lm'
rmst2reg: no visible global function definition for 'glm'
rmst2reg: no visible global function definition for 'pchisq'
rmst2reg: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  data glm lines lm par pchisq plot pnorm polygon qnorm
Consider adding
  importFrom("graphics", "lines", "par", "plot", "polygon")
  importFrom("stats", "glm", "lm", "pchisq", "pnorm", "qnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
fitModel: no visible global function definition for 'var'
fitModel: no visible global function definition for 'cov'
svpls: no visible global function definition for 'pt'
Undefined global functions or variables:
  cov pt var
Consider adding
  importFrom("stats", "cov", "pt", "var")
to your NAMESPACE file.
dlgMessage.tcltkGUI: no visible global function definition for 'alarm'
dlgMessage.tcltkGUI: no visible global function definition for
  'bringToTop'
Undefined global functions or variables:
  alarm bringToTop
Consider adding
  importFrom("grDevices", "bringToTop")
  importFrom("utils", "alarm")
to your NAMESPACE file.
svd3dplot: no visible global function definition for 'wireframe'
svd3dplot: no visible global function definition for 'levelplot'
Undefined global functions or variables:
  levelplot wireframe
startHttpServer : <anonymous> : Rjsonp: no visible global function
  definition for 'localeToCharset'
Undefined global functions or variables:
  localeToCharset
Consider adding
  importFrom("utils", "localeToCharset")
to your NAMESPACE file.
.onAttach : svBrowser: no visible global function definition for
  'browseURL'
.onAttach: no visible global function definition for 'loadhistory'
Undefined global functions or variables:
  browseURL loadhistory
Consider adding
  importFrom("utils", "browseURL", "loadhistory")
to your NAMESPACE file.
completion : finalize : <anonymous>: no visible global function
  definition for 'existsFunction'
listMethods: no visible global function definition for 'findFunction'
tempvar: no visible global function definition for 'runif'
Undefined global functions or variables:
  existsFunction findFunction runif
Consider adding
  importFrom("methods", "existsFunction", "findFunction")
  importFrom("stats", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
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.
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.
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'amap' 'gplots' 'impute'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'MASS' 'amap' 'gplots' 'impute'
  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)
See 'd:/Rcompile/CRANpkg/local/3.4/SWATmodel.Rcheck/00install.out' for details.
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    libs  25.5Mb
readSWAT: no visible global function definition for 'read.fortran'
runSWAT2005: no visible global function definition for 'read.fortran'
runSWAT2009: no visible global function definition for 'read.fortran'
runSWAT2012: no visible global function definition for 'read.fortran'
Undefined global functions or variables:
  read.fortran
Consider adding
  importFrom("utils", "read.fortran")
to your NAMESPACE file.
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').
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
symbol: no visible global function definition for 'plot.new'
symbol: no visible global function definition for 'plot.window'
symbol: no visible global function definition for 'axis'
symbol: no visible global function definition for 'box'
symbol: no visible global function definition for 'title'
symbol: no visible global function definition for 'rainbow'
symbol: no visible global function definition for 'hsv'
symbol: no visible global function definition for 'rect'
symbol: no visible global function definition for 'polygon'
symbol: no visible global function definition for 'lines'
symbol: no visible global function definition for 'text'
Undefined global functions or variables:
  axis box hsv lines plot.new plot.window polygon rainbow rect text
  title
Consider adding
  importFrom("grDevices", "hsv", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "polygon", "rect", "text", "title")
to your NAMESPACE file.
integrate.polynomial : f: no visible global function definition for
  'dmvnorm'
Undefined global functions or variables:
  dmvnorm
Package in Depends field not imported from: 'fields'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cwt_fw: no visible global function definition for 'fft'
cwt_iw: no visible global function definition for 'fft'
est_riskshrink_thresh: no visible global function definition for
  'median'
Undefined global functions or variables:
  fft median
Consider adding
  importFrom("stats", "fft", "median")
to your NAMESPACE file.
ProgressBAR: no visible global function definition for 'txtProgressBar'
ProgressBAR: no visible global function definition for
  'setTxtProgressBar'
cor.matrix: no visible global function definition for 'cor'
cor.matrix.partial: no visible global function definition for 'cor'
optimal: no visible global function definition for 'combn'
optimal: no visible global function definition for 'cor'
Undefined global functions or variables:
  combn cor setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "cor")
  importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'RCurl' 'RJSONIO'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' calls to packages already attached by Depends:
  'tcltk' 'tkrplot'
  Please remove these calls from your code.
Namespaces with empty importFrom:
  'Rcpp' 'methods'
mainNetFunction: no visible global function definition for 'png'
mainNetFunction: no visible global function definition for 'plot'
mainNetFunction: no visible global function definition for 'lines'
mainNetFunction: no visible global function definition for 'legend'
mainNetFunction: no visible global function definition for 'dev.off'
plotPR: no visible global function definition for 'plot'
plotROC: no visible global function definition for 'plot'
plotROC: no visible global function definition for 'lines'
simulatedData: no visible global function definition for 'rpois'
simulatedData : <anonymous>: no visible global function definition for
  'rpois'
simulatedData : rlognormpois: no visible global function definition for
  'rnorm'
simulatedData : rlognormpois: no visible global function definition for
  'rpois'
Undefined global functions or variables:
  dev.off legend lines plot png rnorm rpois
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "rnorm", "rpois")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'LowRankQP' 'rgenoud'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
fn.V: no visible global function definition for 'LowRankQP'
gaps.plot: no visible global function definition for 'abline'
path.plot: no visible global function definition for 'lines'
path.plot: no visible global function definition for 'abline'
path.plot: no visible global function definition for 'legend'
synth: no visible binding for global variable 'sd'
synth: no visible binding for global variable 'var'
synth: no visible global function definition for 'LowRankQP'
Undefined global functions or variables:
  LowRankQP abline legend lines sd var
Consider adding
  importFrom("graphics", "abline", "legend", "lines")
  importFrom("stats", "sd", "var")
to your NAMESPACE file.
.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.
'library' or 'require' call to 'grid' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to 'perturb' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'grid'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cellgram: no visible global function definition for 'grid.rect'
cellgram: no visible global function definition for 'gpar'
cellgram: no visible global function definition for 'grid.segments'
cellgram: no visible global function definition for 'grid.circle'
cellgram: no visible global function definition for 'grid.polygon'
cellgram: no visible global function definition for 'grid.text'
cellgram: no visible global function definition for 'unit'
compare: no visible global function definition for 'sd'
tableplot.colldiag: no visible global function definition for
  'colldiag'
tableplot.colldiag: no visible global function definition for 'xtabs'
tableplot.default: no visible global function definition for
  'grid.newpage'
tableplot.default: no visible global function definition for
  'grid.layout'
tableplot.default: no visible global function definition for 'unit'
tableplot.default: no visible global function definition for
  'pushViewport'
tableplot.default: no visible global function definition for 'viewport'
tableplot.default: no visible global function definition for
  'grid.text'
tableplot.default: no visible global function definition for
  'upViewport'
tableplot.default: no visible global function definition for 'gpar'
tableplot.default: no visible global function definition for
  'grid.rect'
tableplot.default: no visible global function definition for
  'popViewport'
Undefined global functions or variables:
  colldiag gpar grid.circle grid.layout grid.newpage grid.polygon
  grid.rect grid.segments grid.text popViewport pushViewport sd unit
  upViewport viewport xtabs
Consider adding
  importFrom("stats", "sd", "xtabs")
to your NAMESPACE file.
TCRsink: no visible global function definition for 'head'
Undefined global functions or variables:
  head
Consider adding
  importFrom("utils", "head")
to your NAMESPACE file.
itabplot : <anonymous>: no visible global function definition for
  'capture.output'
itabplot: no visible global function definition for 'browseURL'
Undefined global functions or variables:
  browseURL capture.output
Consider adding
  importFrom("utils", "browseURL", "capture.output")
to your NAMESPACE file.
plot.tabu: no visible global function definition for 'image'
plot.tabu: no visible global function definition for 'gray'
plot.tabu: no visible global function definition for 'par'
plot.tabu: no visible global function definition for 'layout'
plot.tabu: no visible global function definition for 'plot'
Undefined global functions or variables:
  gray image layout par plot
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "image", "layout", "par", "plot")
to your NAMESPACE file.
NANOVA.test: no visible global function definition for 'ecdf'
NANOVA.test2: no visible global function definition for 'ecdf'
NANOVA.test3: no visible global function definition for 'ecdf'
fdr.table: no visible global function definition for 'median'
fdr.table: no visible global function definition for 'quantile'
gene.classifier1: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  ecdf median quantile write.table
Consider adding
  importFrom("stats", "ecdf", "median", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'gdata' 'ggplot2' 'grid' 'lattice' 'xtable'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
AnalyzeLVZ: no visible global function definition for 'approx'
ConvP2Vdepthinv: no visible global function definition for 'approx'
DistSummary: no visible global function definition for 'heat.colors'
Earthplot: no visible global function definition for 'heat.colors'
Earthplot: no visible global function definition for 'par'
Earthplot: no visible global function definition for 'plot'
Earthplot: no visible global function definition for 'approx'
Earthplot: no visible global function definition for 'image'
Earthplot: no visible binding for global variable 'lines'
FindRoots: no visible global function definition for 'uniroot'
InterpModel: no visible global function definition for 'approx'
LinInterp: no visible global function definition for 'approx'
PolarPlot: no visible binding for global variable 'plot'
Rayfan: no visible binding for global variable 'lines'
polaraxis: no visible global function definition for 'text'
Undefined global functions or variables:
  approx heat.colors image lines par plot text uniroot
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "image", "lines", "par", "plot", "text")
  importFrom("stats", "approx", "uniroot")
to your NAMESPACE file.
end.TawnyPortfolio: no visible global function definition for 'end'
start.TawnyPortfolio: no visible global function definition for 'start'
Undefined global functions or variables:
  end start
Consider adding
  importFrom("stats", "end", "start")
to your NAMESPACE file.
BootTree: no visible global function definition for 'hclust'
BootTree: no visible global function definition for 'dist'
BootTree: no visible global function definition for 'as.dist'
BootTree: no visible global function definition for 'cor'
BootTree: no visible binding for global variable 'var'
Pgpd: no visible global function definition for 'optim'
Pgpd : <anonymous>: no visible global function definition for 'optim'
Pgpd: no visible global function definition for 'var'
Pgpd: no visible global function definition for 'rnorm'
Pgpd: no visible global function definition for 'quantile'
Pvalue: no visible global function definition for 'rnorm'
SigTree: no visible global function definition for 'data'
TreeStat: no visible global function definition for 'hclust'
TreeStat: no visible global function definition for 'as.dist'
TreeStat: no visible global function definition for 'dist'
TreeStat: no visible global function definition for 'cor'
plot.best: no visible global function definition for 'hclust'
plot.best: no visible global function definition for 'as.dist'
plot.best: no visible global function definition for 'dist'
plot.best: no visible global function definition for 'cor'
plot.best: no visible global function definition for 'plot'
treetext: no visible global function definition for 'par'
treetext: no visible global function definition for 'text'
Undefined global functions or variables:
  as.dist cor data dist hclust optim par plot quantile rnorm text var
Consider adding
  importFrom("graphics", "par", "plot", "text")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "optim",
             "quantile", "rnorm", "var")
  importFrom("utils", "data")
to your NAMESPACE file.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.9Mb
    libs   1.4Mb
cluster_cutoff_at_first_empty_bin: no visible global function
  definition for 'hist'
mapper1D: no visible global function definition for 'dist'
mapper1D: no visible global function definition for 'as.dist'
mapper1D: no visible global function definition for 'hclust'
mapper1D: no visible global function definition for 'cutree'
mapper2D: no visible global function definition for 'dist'
mapper2D: no visible global function definition for 'as.dist'
mapper2D: no visible global function definition for 'hclust'
mapper2D: no visible global function definition for 'cutree'
Undefined global functions or variables:
  as.dist cutree dist hclust hist
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "as.dist", "cutree", "dist", "hclust")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'RSEIS' 'pracma' 'signal'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
E.2SI: no visible binding for global variable 'var'
E.2SI: no visible global function definition for 'var'
E.BE: no visible global function definition for 'var'
E.Beta: no visible global function definition for 'var'
E.PO: no visible global function definition for 'var'
E.PPS: no visible global function definition for 'var'
E.SI: no visible global function definition for 'var'
E.STPPS: no visible global function definition for 'var'
E.STSI: no visible global function definition for 'var'
E.STpiPS: no visible global function definition for 'var'
E.SY: no visible global function definition for 'var'
E.WR: no visible global function definition for 'var'
E.piPS: no visible global function definition for 'var'
GREG.SI: no visible global function definition for 'var'
S.BE: no visible global function definition for 'runif'
S.PO: no visible global function definition for 'runif'
S.PPS: no visible global function definition for 'runif'
S.SI: no visible global function definition for 'runif'
S.STPPS: no visible global function definition for 'runif'
S.WR: no visible global function definition for 'rbinom'
S.piPS: no visible global function definition for 'runif'
p.WR: no visible global function definition for 'dmultinom'
Undefined global functions or variables:
  dmultinom rbinom runif var
Consider adding
  importFrom("stats", "dmultinom", "rbinom", "runif", "var")
to your NAMESPACE file.
TeachNet: no visible global function definition for 'predict'
createWeights1: no visible global function definition for 'rnorm'
createWeights2: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  predict rnorm
Consider adding
  importFrom("stats", "predict", "rnorm")
to your NAMESPACE file.
aniplotevents: no visible global function definition for 'plot'
aniplotevents: no visible global function definition for 'lines'
cbfs: no visible global function definition for 'rnorm'
cbfs: no visible global function definition for 'runif'
cbfs_red: no visible global function definition for 'arima.sim'
cbfs_red: no visible global function definition for 'runif'
eventCluster: no visible global function definition for 'princomp'
eventCluster: no visible global function definition for 'kmeans'
measures: no visible global function definition for 'sd'
measures: no visible global function definition for 'var'
measures: no visible global function definition for 'PP.test'
noiseTests: no visible global function definition for 'Box.test'
noiseTests: no visible global function definition for 'PP.test'
noiseTests: no visible global function definition for 'ar'
plotevents: no visible global function definition for 'plot'
plotevents: no visible global function definition for 'lines'
ur.za.fast : roll: no visible global function definition for 'coef'
ur.za.fast : roll: no visible global function definition for 'lm'
Undefined global functions or variables:
  Box.test PP.test ar arima.sim coef kmeans lines lm plot princomp
  rnorm runif sd var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "Box.test", "PP.test", "ar", "arima.sim", "coef",
             "kmeans", "lm", "princomp", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'mean.tensor':
  'mean.tensor'

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
TER.deesc.1.B : A1.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.1.B : A1.f: no visible binding for global variable 'ID'
TER.deesc.1.B : A2.n.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.1.B : A2.n.f: no visible binding for global variable 'ID'
TER.deesc.1.B: no visible binding for '<<-' assignment to 'ID'
TER.deesc.1.B: no visible binding for global variable 'ID'
TER.deesc.A.B : A1.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : A1.f: no visible binding for global variable 'ID'
TER.deesc.A.B : A3.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : A3.f: no visible binding for global variable 'ID'
TER.deesc.A.B : A2.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : A2.f: no visible binding for global variable 'ID'
TER.deesc.A.B : B1.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : B1.f: no visible binding for global variable 'ID'
TER.deesc.A.B: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B: no visible binding for global variable 'ID'
Undefined global functions or variables:
  ID
Depends: includes the non-default packages:
  'grid' 'quadprog' 'maps' 'maptools' 'mapdata' 'dichromat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  'dichromat' 'grid' 'mapdata' 'maps' 'maptools' 'quadprog'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 43.4Mb
  sub-directories of 1Mb or more:
    libs      12.4Mb
    tessdata  30.9Mb
Packages in Depends field not imported from:
  'boot' 'survrec'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    3.5Mb
    libs   2.2Mb
phyper_right: no visible global function definition for 'dhyper'
progression: no visible global function definition for 'density'
progression: no visible global function definition for 'plot'
progression: no visible global function definition for 'points'
progression: no visible global function definition for 'legend'
progression: no visible global function definition for 'text'
specificities.distribution.plot: no visible global function definition
  for 'dhyper'
specificities.distribution.plot: no visible global function definition
  for 'plot'
specificities.distribution.plot: no visible global function definition
  for 'Axis'
specificities.distribution.plot: no visible global function definition
  for 'arrows'
specificities.distribution.plot: no visible global function definition
  for 'text'
specificities.distribution.plot: no visible global function definition
  for 'title'
specificities.probabilities.vector: no visible global function
  definition for 'phyper'
Undefined global functions or variables:
  Axis arrows density dhyper legend phyper plot points text title
Consider adding
  importFrom("graphics", "Axis", "arrows", "legend", "plot", "points",
             "text", "title")
  importFrom("stats", "density", "dhyper", "phyper")
to your NAMESPACE file.
.dea_create_model: no visible global function definition for
  'getSrcFilename'
.wMean: no visible global function definition for 'weighted.mean'
Undefined global functions or variables:
  getSrcFilename weighted.mean
Consider adding
  importFrom("stats", "weighted.mean")
  importFrom("utils", "getSrcFilename")
to your NAMESPACE file.
transfer: no visible global function definition for 'rgamma'
transfer: no visible global function definition for 'rnorm'
transfer: no visible global function definition for 'rnbinom'
transfer: no visible global function definition for 'rpois'
transfer: no visible global function definition for 'rbinom'
transfer: no visible global function definition for 'runif'
plot,transfer: no visible global function definition for 'barplot'
plot,transfer: no visible global function definition for 'axis'
plot,transfer: no visible global function definition for 'par'
plot,transfer: no visible global function definition for 'hist'
Undefined global functions or variables:
  axis barplot hist par rbinom rgamma rnbinom rnorm rpois runif
Consider adding
  importFrom("graphics", "axis", "barplot", "hist", "par")
  importFrom("stats", "rbinom", "rgamma", "rnbinom", "rnorm", "rpois",
             "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Matrix.h:27:18: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.4/TFMPvalue.Rcheck/00install.out' for details.
ParseTrueFX: no visible global function definition for 'read.csv'
TrueFXRef: no visible global function definition for 'download.file'
TrueFXRef: no visible global function definition for 'browseURL'
Undefined global functions or variables:
  browseURL download.file read.csv
Consider adding
  importFrom("utils", "browseURL", "download.file", "read.csv")
to your NAMESPACE file.
'library' or 'require' call to 'zoo' which was already attached by Depends.
  Please remove these calls from your code.
Thinknum: no visible global function definition for 'URLencode'
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
coef_traceplot: no visible global function definition for 'rainbow'
coef_traceplot: no visible global function definition for 'plot'
coef_traceplot: no visible global function definition for 'abline'
coef_traceplot : <anonymous>: no visible global function definition for
  'lines'
coef_traceplot: no visible global function definition for 'text'
ee.GEE.aux : <anonymous>: no visible global function definition for
  'combn'
Undefined global functions or variables:
  abline combn lines plot rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "plot", "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
summary.tsls: no visible global function definition for 'printCoefmat'
threesls: no visible global function definition for 'cor'
threesls: no visible global function definition for 'pt'
tsls.formula: no visible global function definition for 'model.matrix'
tsls.formula: no visible global function definition for
  'model.response'
Undefined global functions or variables:
  cor model.matrix model.response printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.matrix", "model.response",
             "printCoefmat", "pt")
to your NAMESPACE file.
.LoadTickDataHK: no visible global function definition for 'read.csv'
.LoadTickDataSHSZ: no visible global function definition for 'read.csv'
DrawDown: no visible global function definition for 'na.omit'
PerformanceReport: no visible global function definition for
  'aggregate'
PerformanceReport: no visible global function definition for 'sd'
Undefined global functions or variables:
  aggregate na.omit read.csv sd
Consider adding
  importFrom("stats", "aggregate", "na.omit", "sd")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
newTiddler: no visible global function definition for 'new'
twImage: no visible global function definition for 'new'
twLink: no visible global function definition for 'new'
twList: no visible global function definition for 'new'
twTable: no visible global function definition for 'new'
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
read_json: no visible global function definition for 'tail'
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Files in the 'vignettes' directory newer than same file in 'inst/doc':
  'introduction-to-tidyjson.Rmd'
Running 'test-all.r' [0s]
Running the tests in 'tests/test-all.r' failed.
Complete output:
  > library(testthat)
  > test_check("jplyr")
  Loading required package: jplyr
  Error in loadNamespace(name) : there is no package called 'jplyr'
  Calls: test_check ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
  In addition: Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'jplyr'
  Execution halted
plot.tight.clust: no visible global function definition for 'hclust'
plot.tight.clust: no visible global function definition for 'dist'
plot.tight.clust: no visible global function definition for 'image'
plot.tight.clust: no visible global function definition for
  'colorRampPalette'
plot.tight.clust: no visible global function definition for 'axis'
plot.tight.clust: no visible global function definition for 'lines'
tight.clust : find.candidates : kmeans.classify: no visible global
  function definition for 'kmeans'
write.tight.clust: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  axis colorRampPalette dist hclust image kmeans lines write.table
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "image", "lines")
  importFrom("stats", "dist", "hclust", "kmeans")
  importFrom("utils", "write.table")
to your NAMESPACE file.
.viterbiTrainingEmission,contHMM-list-list: no visible global function
  definition for 'var'
sampleObs,tDist-numeric: no visible global function definition for 'rt'
Undefined global functions or variables:
  rt var
Consider adding
  importFrom("stats", "rt", "var")
to your NAMESPACE file.
'library' or 'require' call to 'ggplot2' 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: 'microbenchmark'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
determine_replications: no visible global function definition for
  'microbenchmark'
do_timeit: no visible global function definition for 'Rprof'
do_timeit: no visible global function definition for 'summaryRprof'
mean.timeit: no visible global function definition for 'aggregate'
plot.timeit: no visible global function definition for 'ggplot'
plot.timeit: no visible global function definition for 'aes'
plot.timeit: no visible global function definition for 'geom_boxplot'
plot.timeit: no visible global function definition for 'geom_point'
plot.timeit: no visible global function definition for 'xlab'
plot.timeit: no visible global function definition for 'ylab'
plot.timeit: no visible global function definition for 'ggtitle'
plot.timeit: no visible global function definition for 'coord_flip'
timeit: no visible binding for global variable 'median'
Undefined global functions or variables:
  Rprof aes aggregate coord_flip geom_boxplot geom_point ggplot ggtitle
  median microbenchmark summaryRprof xlab ylab
Consider adding
  importFrom("stats", "aggregate", "median")
  importFrom("utils", "Rprof", "summaryRprof")
to your NAMESPACE file.
'library' or 'require' call to 'shiny' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'ggplot2'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
timeline: no visible global function definition for 'ggplot'
timeline: no visible global function definition for 'geom_segment'
timeline: no visible global function definition for 'aes_string'
timeline: no visible global function definition for 'geom_rect'
timeline: no visible global function definition for 'geom_text'
timeline: no visible global function definition for 'theme'
timeline: no visible global function definition for 'element_blank'
timeline: no visible global function definition for 'xlab'
timeline: no visible global function definition for 'ylab'
timeline: no visible global function definition for 'xlim'
timeline: no visible global function definition for
  'scale_y_continuous'
timeline: no visible global function definition for 'geom_point'
timeline: no visible global function definition for 'scale_color_grey'
timeline: no visible global function definition for 'geom_hline'
Undefined global functions or variables:
  aes_string element_blank geom_hline geom_point geom_rect geom_segment
  geom_text ggplot scale_color_grey scale_y_continuous theme xlab xlim
  ylab
density.tm: no visible global function definition for 'density'
mu.mle: no visible global function definition for 'optimize'
pophistory.tm: no visible binding for global variable 'quantile'
quantile.tm: no visible global function definition for 'quantile'
sample.pop: no visible global function definition for 'runif'
summary.tm: no visible global function definition for 'quantile'
Undefined global functions or variables:
  density optimize quantile runif
Consider adding
  importFrom("stats", "density", "optimize", "quantile", "runif")
to your NAMESPACE file.
generatelatencies: no visible binding for global variable 'allNames'
generatetimedeltas: no visible global function definition for 'head'
generatetimedeltas: no visible global function definition for 'tail'
generatevertexedgelist : <anonymous>: no visible global function
  definition for 'head'
generatevertexedgelist : <anonymous>: no visible global function
  definition for 'tail'
plotnetworkslices: no visible global function definition for 'par'
plotnetworkslices: no visible global function definition for 'text'
plottanet: no visible global function definition for 'plot'
plottonet: no visible global function definition for 'plot'
shortesttimepath : <anonymous>: no visible global function definition
  for 'tail'
Undefined global functions or variables:
  allNames head par plot tail text
Consider adding
  importFrom("graphics", "par", "plot", "text")
  importFrom("methods", "allNames")
  importFrom("utils", "head", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' calls in package code:
  'ggplot2' 'plyr'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'Matrix' 'lubridate' 'timeDate'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
is.Bizday: no visible global function definition for 'isWeekday'
plotCalendarHeatmap: no visible global function definition for 'ddply'
plotCalendarHeatmap: no visible global function definition for '.'
plotCalendarHeatmap: no visible binding for global variable 'year'
plotCalendarHeatmap: no visible binding for global variable 'month'
plotCalendarHeatmap: no visible binding for global variable 'week'
plotCalendarHeatmap: no visible global function definition for 'ggplot'
plotCalendarHeatmap: no visible global function definition for 'aes'
plotCalendarHeatmap: no visible binding for global variable 'monthweek'
plotCalendarHeatmap: no visible binding for global variable 'weekday'
plotCalendarHeatmap: no visible global function definition for
  'geom_tile'
plotCalendarHeatmap: no visible global function definition for
  'facet_grid'
plotCalendarHeatmap: no visible global function definition for
  'scale_fill_gradientn'
projectDate: no visible global function definition for 'holidayNYSE'
projectDate: no visible global function definition for
  'sparse.model.matrix'
Undefined global functions or variables:
  . aes ddply facet_grid geom_tile ggplot holidayNYSE isWeekday month
  monthweek scale_fill_gradientn sparse.model.matrix week weekday year
boot_autocov: no visible global function definition for 'is.ts'
boot_autocov: no visible global function definition for 'tsboot'
boot_autocov: no visible global function definition for 'quantile'
boot_autocov: no visible global function definition for 'par'
boot_autocov: no visible global function definition for 'frequency'
boot_autocov: no visible global function definition for 'polygon'
boot_autocov: no visible global function definition for 'lines'
boot_autocov: no visible global function definition for 'abline'
boot_autocov: no visible global function definition for 'acf'
boot_spec: no visible global function definition for 'is.ts'
boot_spec: no visible global function definition for 'tsboot'
boot_spec: no visible global function definition for 'spec.pgram'
boot_spec: no visible global function definition for 'quantile'
boot_spec: no visible global function definition for 'polygon'
boot_spec: no visible global function definition for 'lines'
redraw: no visible global function definition for 'spec.pgram'
statistic: no visible global function definition for 'acf'
Undefined global functions or variables:
  abline acf frequency is.ts lines par polygon quantile spec.pgram
  tsboot
Consider adding
  importFrom("graphics", "abline", "lines", "par", "polygon")
  importFrom("stats", "acf", "frequency", "is.ts", "quantile",
             "spec.pgram")
to your NAMESPACE file.
createHstore.ts: no visible global function definition for 'time'
exploreDb : <anonymous>: no visible global function definition for
  'plot'
exportTsList : <anonymous>: no visible global function definition for
  'time'
exportTsList: no visible global function definition for 'write.csv2'
importTsList: no visible global function definition for 'read.csv2'
importTsList : <anonymous>: no visible global function definition for
  'as.ts'
plot.tslist: no visible global function definition for 'plot'
plot.tslist : <anonymous>: no visible global function definition for
  'time'
plot.tslist: no visible global function definition for 'par'
plot.tslist: no visible global function definition for 'legend'
readTimeSeries : <anonymous>: no visible global function definition for
  'ts'
resolveOverlap: no visible global function definition for 'is.ts'
resolveOverlap: no visible global function definition for 'frequency'
resolveOverlap: no visible global function definition for 'time'
resolveOverlap: no visible global function definition for 'ts'
storeTimeSeries: no visible binding for global variable 'frequency'
zooLikeDateConvert: no visible global function definition for 'time'
zooLikeDateConvert: no visible global function definition for
  'frequency'
zooLikeDateConvert: no visible global function definition for 'cycle'
Undefined global functions or variables:
  as.ts cycle frequency is.ts legend par plot read.csv2 time ts
  write.csv2
Consider adding
  importFrom("graphics", "legend", "par", "plot")
  importFrom("stats", "as.ts", "cycle", "frequency", "is.ts", "time",
             "ts")
  importFrom("utils", "read.csv2", "write.csv2")
to your NAMESPACE file.
author.search: no visible binding for global variable 'na.omit'
reference.list: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
drawGraph: no visible global function definition for 'pdf'
drawGraph: no visible global function definition for 'par'
drawGraph: no visible global function definition for 'plot'
drawGraph: no visible global function definition for 'segments'
drawGraph: no visible global function definition for 'lines'
drawGraph: no visible global function definition for 'text'
drawGraph: no visible global function definition for 'dev.off'
drugRank: no visible global function definition for 'aggregate'
floating2: no visible global function definition for 'cor'
timma: no visible global function definition for 'median'
timma: no visible global function definition for 'write.table'
Undefined global functions or variables:
  aggregate cor dev.off lines median par pdf plot segments text
  write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "plot", "segments", "text")
  importFrom("stats", "aggregate", "cor", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'ExPosition' 'InPosition' 'TExPosition' 'prettyGraphs'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
adjustableTierChart: no visible global function definition for
  'postscript'
adjustableTierChart: no visible global function definition for
  'dev.off'
barplot2: no visible global function definition for 'grey.colors'
barplot2: no visible global function definition for 'dev.hold'
barplot2: no visible global function definition for 'dev.flush'
nberShade.ggplot: no visible global function definition for
  'extendrange'
scatterPlot: no visible global function definition for 'xy.coords'
screenPage: no visible global function definition for 'dev.list'
setColors: no visible global function definition for 'palette'
ymdShade: no visible global function definition for 'grey'
ymdXy: no visible global function definition for 'dev.cur'
Undefined global functions or variables:
  dev.cur dev.flush dev.hold dev.list dev.off extendrange grey
  grey.colors palette postscript xy.coords
Consider adding
  importFrom("grDevices", "dev.cur", "dev.flush", "dev.hold", "dev.list",
             "dev.off", "extendrange", "grey", "grey.colors", "palette",
             "postscript", "xy.coords")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'boot' 'lattice' 'splines' 'tcltk'
  Please remove these calls from your code.
ls.tree: no visible global function definition for 'lm'
ls.tree: no visible global function definition for 'coef'
Undefined global functions or variables:
  coef lm
Consider adding
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'rgl' 'tcltk'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.my.tkdev: no visible global function definition for 'win.metafile'
tkpersp : draw: no visible global function definition for 'par'
tkpersp : draw: no visible global function definition for 'persp'
Undefined global functions or variables:
  par persp win.metafile
Consider adding
  importFrom("grDevices", "win.metafile")
  importFrom("graphics", "par", "persp")
to your NAMESPACE file.
FLXmclust.Density: no visible global function definition for 'dmvnorm'
FLXmclust.Estimate: no visible global function definition for 'flexmix'
FLXmclust.Estimate: no visible global function definition for
  'FLXmclust'
coefmclust: no visible global function definition for 'parameters'
flexmix.Density: no visible global function definition for
  'model.matrix'
flexmix.Density: no visible global function definition for
  'model.response'
flexmix.Density: no visible global function definition for
  'model.frame'
flexmix.Density: no visible global function definition for 'dnorm'
flexmix.Density: no visible global function definition for 'dpois'
flexmix.Density: no visible global function definition for 'dbinom'
flexmix.Estimate: no visible global function definition for 'flexmix'
flexmix.Estimate: no visible global function definition for 'FLXglm'
tleplot,TLE-data.frame: no visible global function definition for
  'legend'
Undefined global functions or variables:
  FLXglm FLXmclust dbinom dmvnorm dnorm dpois flexmix legend
  model.frame model.matrix model.response parameters
Consider adding
  importFrom("graphics", "legend")
  importFrom("stats", "dbinom", "dnorm", "dpois", "model.frame",
             "model.matrix", "model.response")
to your NAMESPACE file.
'library' or 'require' call to 'mvtnorm' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'mvtnorm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
EMN: no visible global function definition for 'dmvnorm'
EMN: no visible global function definition for 'pmvnorm'
EMT: no visible global function definition for 'GenzBretz'
EMT: no visible global function definition for 'dmvt'
EMT: no visible global function definition for 'pmvt'
MomemNT: no visible global function definition for 'pnorm'
MomemNT: no visible global function definition for 'dnorm'
MomemNT: no visible global function definition for 'pmvnorm'
MomemNT: no visible global function definition for 'dmvnorm'
TT.moment: no visible global function definition for 'GenzBretz'
TT.moment: no visible global function definition for 'pmvt'
TT.moment: no visible global function definition for 'dt'
TT.moment: no visible global function definition for 'pt'
TT.moment: no visible global function definition for 'dmvt'
cdfNI: no visible global function definition for 'pnorm'
cdfNI: no visible global function definition for 'pt'
inits: no visible global function definition for 'lm'
Undefined global functions or variables:
  GenzBretz dmvnorm dmvt dnorm dt lm pmvnorm pmvt pnorm pt
Consider adding
  importFrom("stats", "dnorm", "dt", "lm", "pnorm", "pt")
to your NAMESPACE file.
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    examples  19.1Mb
    include    2.9Mb
search_collection: no visible global function definition for
  'URLencode'
search_company: no visible global function definition for 'URLencode'
search_keyword: no visible global function definition for 'URLencode'
search_list: no visible global function definition for 'URLencode'
search_movie: no visible global function definition for 'URLencode'
search_multi: no visible global function definition for 'URLencode'
search_person: no visible global function definition for 'URLencode'
search_tv: no visible global function definition for 'URLencode'
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
extractContentDOM: no visible global function definition for
  'capture.output'
extractHTMLStrip: no visible global function definition for
  'capture.output'
Undefined global functions or variables:
  capture.output
Consider adding
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'Rcampdf' 'Rpoppler' 'tm.lexicon.GeneralInquirer'
Package unavailable to check Rd xrefs: 'Rpoppler'
flowlength: no visible global function definition for 'is'
river: no visible global function definition for 'is'
sinkfill: no visible global function definition for 'is'
subcatch: no visible global function definition for 'is'
topidx: no visible global function definition for 'is'
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Tosls.formula: no visible global function definition for 'model.matrix'
Tosls.formula: no visible global function definition for
  'model.response'
summary: no visible global function definition for 'coef'
summary: no visible global function definition for 'pt'
Undefined global functions or variables:
  coef model.matrix model.response pt
Consider adding
  importFrom("stats", "coef", "model.matrix", "model.response", "pt")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'Cairo' 'RGtk2' 'colorspace' 'gWidgets' 'tourr'
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'TeachingDemos' 'ash'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'Cairo' 'RGtk2' 'colorspace' 'gWidgets' 'tourr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' calls in package code:
  'TeachingDemos' 'ash'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
ConfA: no visible global function definition for 'qf'
EstM2Sn: no visible global function definition for 'nlm'
EstM2Sn: no visible global function definition for 'qnorm'
TV.model: no visible global function definition for 'dev.new'
TV.model: no visible global function definition for 'points'
betaBino: no visible global function definition for 'pbinom'
doseD: no visible global function definition for 'lm'
doseD: no visible global function definition for 'dev.new'
doseD: no visible global function definition for 'par'
doseD: no visible global function definition for 'plot'
doseD: no visible global function definition for 'axTicks'
doseD: no visible global function definition for 'axis'
doseD: no visible global function definition for 'lines'
doseD: no visible global function definition for 'abline'
doseD: no visible global function definition for 'legend'
setD: no visible global function definition for 'dev.new'
setD: no visible global function definition for 'par'
setD: no visible global function definition for 'pbinom'
setD: no visible global function definition for 'abline'
setD: no visible global function definition for 'axis'
setD: no visible global function definition for 'rect'
setD: no visible global function definition for 'lines'
setD: no visible global function definition for 'text'
setD: no visible global function definition for 'axTicks'
setD: no visible global function definition for 'legend'
spoD : spoD_A: no visible global function definition for 'chisq.test'
Undefined global functions or variables:
  abline axTicks axis chisq.test dev.new legend lines lm nlm par pbinom
  plot points qf qnorm rect text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axTicks", "axis", "legend", "lines",
             "par", "plot", "points", "rect", "text")
  importFrom("stats", "chisq.test", "lm", "nlm", "pbinom", "qf", "qnorm")
to your NAMESPACE file.
align1d : obj: no visible global function definition for 'dist'
align2d : obj: no visible global function definition for 'dist'
align2d : pen: no visible global function definition for 'dist'
align2d: no visible global function definition for 'dist'
sumt: no visible global function definition for 'optim'
tpe1d: no visible global function definition for 'hclust'
tpe2d: no visible global function definition for 'hclust'
tpe2d: no visible global function definition for 'cmdscale'
Undefined global functions or variables:
  cmdscale dist hclust optim
Consider adding
  importFrom("stats", "cmdscale", "dist", "hclust", "optim")
to your NAMESPACE file.
Package in Depends field not imported from: 'lgtdl'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ci.plot: no visible global function definition for 'gaussian'
ci.plot: no visible global function definition for 'qnorm'
ci.plot: no visible global function definition for 'plot'
ci.plot: no visible global function definition for 'lines'
cst.fit.ff: no visible global function definition for 'pnorm'
cstfit.1: no visible global function definition for 'var'
gof.test.boots.pf: no visible binding for global variable 'sd'
gof.test.int.1.ff: no visible global function definition for 'quantile'
gof.test.int.1.ff: no visible global function definition for 'var'
gof.test.int.ff: no visible global function definition for 'pnorm'
gofTest: no visible binding for global variable 'sd'
plotGof: no visible global function definition for 'plot'
plotGof : <anonymous>: no visible global function definition for
  'lines'
plotGof: no visible global function definition for 'lines'
sig.test.int.1.ff: no visible global function definition for 'quantile'
sig.test.int.1.ff: no visible global function definition for 'var'
sig.test.int.ff: no visible global function definition for 'pnorm'
test.boots.1: no visible binding for global variable 'sd'
tpr: no visible global function definition for 'poisson'
tpr: no visible global function definition for 'glm.fit'
tpr: no visible global function definition for 'coef'
tpr: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx coef gaussian glm.fit lines plot pnorm poisson qnorm quantile
  sd var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "approx", "coef", "gaussian", "glm.fit", "pnorm",
             "poisson", "qnorm", "quantile", "sd", "var")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: ggplot2

Attaching package: 'trackeR'

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

    append

Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=57.157231,-2.104296&zoom=13&size=640x640&scale=2&maptype=terrain&sensor=false
Quitting from lines 90-91 (TourDetrackeR.Rmd) 
Error: processing vignette 'TourDetrackeR.Rmd' failed with diagnostics:
map grabbing failed - see details in ?get_openstreetmap.
Execution halted
DeadReckoning: no visible global function definition for 'filter'
DeadReckoning: no visible global function definition for 'approx'
DeadReckoning: no visible global function definition for 'lm'
Mapper: no visible global function definition for 'colorRampPalette'
Mapper: no visible global function definition for 'terrain.colors'
Mapper: no visible global function definition for 'points'
Mapper: no visible global function definition for 'axis'
Standardize: no visible global function definition for 'lm'
Undefined global functions or variables:
  approx axis colorRampPalette filter lm points terrain.colors
Consider adding
  importFrom("grDevices", "colorRampPalette", "terrain.colors")
  importFrom("graphics", "axis", "points")
  importFrom("stats", "approx", "filter", "lm")
to your NAMESPACE file.
microsoftTranslate: no visible global function definition for
  'URLencode'
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
rtrapezoid: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
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.
mytree.asymmetric.age: no visible global function definition for
  'capture.output'
mytree.asymmetric.age: no visible global function definition for
  'collapse.singles'
mytree.asymmetric.age: no visible global function definition for
  'drop.fossil'
mytree.asymmetric.taxa: no visible global function definition for
  'capture.output'
mytree.asymmetric.taxa: no visible global function definition for
  'collapse.singles'
mytree.asymmetric.taxa: no visible global function definition for
  'drop.fossil'
mytree.symmetric.age: no visible global function definition for
  'capture.output'
mytree.symmetric.age: no visible global function definition for
  'collapse.singles'
mytree.symmetric.age: no visible global function definition for
  'drop.fossil'
mytree.symmetric.taxa: no visible global function definition for
  'capture.output'
mytree.symmetric.taxa: no visible global function definition for
  'collapse.singles'
mytree.symmetric.taxa: no visible global function definition for
  'drop.fossil'
Undefined global functions or variables:
  capture.output collapse.singles drop.fossil
Consider adding
  importFrom("utils", "capture.output")
to your NAMESPACE file.
plot.trifield: no visible global function definition for 'topo.colors'
plot.trifield: no visible global function definition for 'plot'
plot.trifield: no visible global function definition for 'image'
plot.trifield: no visible global function definition for 'contour'
plot.trifield: no visible global function definition for 'text'
ternary.legend: no visible global function definition for 'arrows'
ternary.legend: no visible global function definition for 'text'
triaxes: no visible global function definition for 'lines'
tribox: no visible global function definition for 'polygon'
Undefined global functions or variables:
  arrows contour image lines plot polygon text topo.colors
Consider adding
  importFrom("grDevices", "topo.colors")
  importFrom("graphics", "arrows", "contour", "image", "lines", "plot",
             "polygon", "text")
to your NAMESPACE file.
'library' or 'require' call to 'fpc' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.tkm: no visible global function definition for 'plotcluster'
plot.tkm: no visible global function definition for 'plot'
plot.tkm: no visible global function definition for 'points'
plot.tkm: no visible global function definition for 'lines'
plot.tkm: no visible global function definition for 'discrcoord'
Undefined global functions or variables:
  discrcoord lines plot plotcluster points
Consider adding
  importFrom("graphics", "lines", "plot", "points")
to your NAMESPACE file.
cinbag: no visible global function definition for 'var'
trimTrees: no visible global function definition for 'predict'
Undefined global functions or variables:
  predict var
Consider adding
  importFrom("stats", "predict", "var")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'gtools' 'mgcv'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'gtools' 'mgcv' 'msm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
HtoGp: no visible global function definition for 'odd'
HtoGp: no visible global function definition for 'even'
plot.pirls.gam: no visible global function definition for 'par'
plot.pirls.gam: no visible global function definition for 'plot'
plot.pirls.gam: no visible global function definition for 'title'
plot.pirls.gam: no visible global function definition for 'lines'
plot.pirls.gam: no visible global function definition for 'rug'
plot.pirls.gam: no visible global function definition for 'mtext'
test.trioGxE: no visible global function definition for 'write.table'
trioGxE: no visible global function definition for 'quantile'
trioGxE: no visible global function definition for 'qtnorm'
trioplot: no visible global function definition for 'quantile'
trioplot: no visible global function definition for 'formula'
trioplot: no visible global function definition for 'gam'
trioplot: no visible global function definition for 'binomial'
Undefined global functions or variables:
  binomial even formula gam lines mtext odd par plot qtnorm quantile
  rug title write.table
Consider adding
  importFrom("graphics", "lines", "mtext", "par", "plot", "rug", "title")
  importFrom("stats", "binomial", "formula", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/TROM.Rcheck/00install.out' for details.
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.
binary.hess: no visible global function definition for 'as'
trust.optim: no visible global function definition for 'as'
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' calls to packages already attached by Depends:
  'leaps' 'locfit' 'mgcv'
  Please remove these calls from your code.
':::' calls which should be '::':
  'stats:::ARMAacf' 'stats:::acf' 'stats:::arima'
  See the note in ?`:::` about the use of this operator.
dmvnb: no visible global function definition for 'dbinom'
drvts: no visible global function definition for 'dnorm'
drvts: no visible global function definition for 'dbinom'
dsvts: no visible global function definition for 'dnorm'
rescale: no visible global function definition for 'qlogis'
rescale: no visible global function definition for 'plogis'
tslogl: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dbinom dnorm plogis qlogis
Consider adding
  importFrom("stats", "dbinom", "dnorm", "plogis", "qlogis")
to your NAMESPACE file.
tfDetails: no visible global function definition for 'start'
tfDetails: no visible global function definition for 'end'
Undefined global functions or variables:
  end start
Consider adding
  importFrom("stats", "end", "start")
to your NAMESPACE file.
Running 'test_code.r' [1s]
Running the tests in 'tests/test_code.r' failed.
Last 13 lines of output:
  +     scoring(fit)
  +   }
  +   if(interv){
  +     interv_test(fit, tau=floor(n/2), delta=0.8, external=FALSE, est_interv=TRUE, ...)
  +     interv_detect(fit, taus=floor(0.45*n):ceiling(0.55*n), delta=0.8, B=3, ...)
  +     interv_multiple(fit, taus=floor(0.45*n):ceiling(0.55*n), deltas=c(0,1), B=3, final.control_bootstrap=NULL, ...)
  +   }
  +   return(TRUE)
  + }
  > 
  > checkfit(model=list(past_obs=1, past_mean=1), param=list(intercept=2, past_obs=0.4, past_mean=0.3), startestims=TRUE, extended=TRUE)
  Error in tsglm.sim(n = n, param = param, model = model, xreg = xreg, link = link,  : 
    could not find function "tsglm.sim"
  Calls: checkfit
  Execution halted
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.
Error in re-building vignettes:
  ...
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "Guide.tex" --max-iterations=20 -I "D:/RCompile/recent/R/share/texmf/tex/latex" -I "D:/RCompile/recent/R/share/texmf/bibtex/bst"' had status 1
Error in find_vignette_product(name, by = "texi2pdf", engine = engine) : 
  Failed to locate the 'texi2pdf' output file (by engine 'utils::Sweave') for vignette with name 'Guide'. The following files exist in directory '.': 'Guide.Stex', 'Guide.tex'
Calls: buildVignettes -> find_vignette_product
Execution halted
Package in Depends field not imported from: 'deSolve'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
vintageMap: no visible global function definition for 'read.table'
TSget,character-TSfameLocalConnection: no visible global function
  definition for 'as.ts'
TSget,character-TSfameLocalConnection: no visible global function
  definition for 'zoo'
TSget,character-TSfameLocalConnection: no visible global function
  definition for 'frequency'
TSget,character-TSfameServerConnection: no visible global function
  definition for 'as.ts'
TSget,character-TSfameServerConnection: no visible global function
  definition for 'zoo'
TSget,character-TSfameServerConnection: no visible global function
  definition for 'frequency'
Undefined global functions or variables:
  as.ts frequency read.table zoo
Consider adding
  importFrom("stats", "as.ts", "frequency")
  importFrom("utils", "read.table")
to your NAMESPACE file.
DstandardizedLoadings.TSFmodel: no visible global function definition
  for 'cov'
FAfitStats.TSFmodel: no visible global function definition for 'cov'
FAfitStats.default: no visible global function definition for 'cor'
FAfitStats.default: no visible global function definition for
  'factanal'
FAfitStats.default: no visible global function definition for 'pchisq'
FAmodelFitStats: no visible global function definition for 'pchisq'
checkResiduals.TSFmodel: no visible global function definition for
  'cov'
distribution.factorsEstEval: no visible global function definition for
  'par'
distribution.factorsEstEval: no visible binding for global variable
  'par'
distribution.factorsEstEval: no visible global function definition for
  'density'
distribution.factorsEstEval: no visible global function definition for
  'matplot'
distribution.factorsEstEval: no visible global function definition for
  'title'
summary.TSFmodel: no visible global function definition for 'start'
summary.TSFmodel: no visible global function definition for 'end'
Undefined global functions or variables:
  cor cov density end factanal matplot par pchisq start title
Consider adding
  importFrom("graphics", "matplot", "par", "title")
  importFrom("stats", "cor", "cov", "density", "end", "factanal",
             "pchisq", "start")
to your NAMESPACE file.
Func.SAX: no visible global function definition for 'sd'
Func.SAX: no visible global function definition for 'qnorm'
Func.matrix: no visible global function definition for 'qnorm'
Func.motif: no visible global function definition for 'sd'
Func.motif: no visible global function definition for 'na.omit'
Func.motif: no visible global function definition for 'combn'
Func.motif.multivariate: no visible global function definition for
  'txtProgressBar'
Func.motif.multivariate: no visible global function definition for
  'setTxtProgressBar'
Undefined global functions or variables:
  combn na.omit qnorm sd setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit", "qnorm", "sd")
  importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
dLag : dlag.f: no visible global function definition for
  'complete.cases'
distmat: no visible global function definition for 'dist'
fitCity: no visible global function definition for 'glm.control'
fitCity: no visible global function definition for 'terms'
ldmvnorm: no visible global function definition for 'mahalanobis'
lspline: no visible global function definition for 'quantile'
plot.tsdecomp: no visible global function definition for 'par'
plot.tsdecomp: no visible global function definition for 'plot'
setupFormula: no visible global function definition for 'as.formula'
spatialgibbs: no visible global function definition for 'rnorm'
spatialgibbs: no visible global function definition for 'rgamma'
spatialgibbs: no visible global function definition for 'runif'
tsdecomp: no visible global function definition for 'fft'
Undefined global functions or variables:
  as.formula complete.cases dist fft glm.control mahalanobis par plot
  quantile rgamma rnorm runif terms
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "as.formula", "complete.cases", "dist", "fft",
             "glm.control", "mahalanobis", "quantile", "rgamma", "rnorm",
             "runif", "terms")
to your NAMESPACE file.
covTranspose11: warning in glasso(sc, 2 * rhoc/n, wi.init = gc$wi,
  w.init = gc$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
covTranspose11: warning in glasso(sr, 2 * rhor/p, wi.init = gr$wi,
  w.init = gr$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
.help.ESS: no visible global function definition for 'index.search'
TransSphere : ttin: no visible global function definition for 't.test'
TransSphere: no visible global function definition for 'sd'
TransSphere: no visible global function definition for 'quantile'
TransSphere: no visible global function definition for 'pt'
Undefined global functions or variables:
  index.search pt quantile sd t.test
Consider adding
  importFrom("stats", "pt", "quantile", "sd", "t.test")
to your NAMESPACE file.
arimainterp: no visible binding for global variable 'head'
arimainterp: no visible binding for global variable 'na.omit'
arimainterp: no visible binding for global variable 'tail'
arimapar: no visible binding for global variable 'na.omit'
arimapar: no visible global function definition for 'tail'
arimapred: no visible binding for global variable 'na.omit'
arimapred: no visible global function definition for 'predict'
marimapar: no visible binding for global variable 'na.omit'
marimapred: no visible binding for global variable 'na.omit'
plotarimapred: no visible global function definition for 'plot'
plotarimapred: no visible global function definition for 'lines'
Undefined global functions or variables:
  head lines na.omit plot predict tail
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "na.omit", "predict")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
TSgetSQL: no visible global function definition for 'ts'
TSputSQL: no visible global function definition for 'is.ts'
TSputSQL: no visible global function definition for 'frequency'
TSputSQL: no visible global function definition for 'time'
TSquery: no visible global function definition for 'ts'
Undefined global functions or variables:
  frequency is.ts time ts
Consider adding
  importFrom("stats", "frequency", "is.ts", "time", "ts")
to your NAMESPACE file.
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.
http.connection: no visible global function definition for 'setNames'
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'gsl' 'igraph' 'snowfall'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
accelerate: no visible global function definition for 'modifyList'
boxplot.turbosim: no visible global function definition for 'par'
boxplot.turbosim: no visible global function definition for 'axis'
boxplot.turbosim: no visible global function definition for 'mtext'
dataprof.turbosim: no visible global function definition for 'quantile'
dataprof.turbosim: no visible global function definition for 'par'
dataprof.turbosim: no visible global function definition for 'plot'
dataprof.turbosim: no visible global function definition for 'lines'
dataprof.turbosim: no visible global function definition for 'segments'
dataprof.turbosim: no visible global function definition for 'legend'
line.search: no visible global function definition for 'optimize'
pairs.turbosim: no visible global function definition for 'par'
pairs.turbosim: no visible global function definition for 'plot'
pairs.turbosim: no visible global function definition for 'legend'
pairs.turbosim: no visible global function definition for 'axis'
pairs.turbosim: no visible global function definition for 'title'
pairs.turbosim: no visible global function definition for 'coef'
pairs.turbosim: no visible global function definition for 'abline'
pairs.turbosim: no visible global function definition for 'text'
plot.turbo: no visible global function definition for 'plot'
plot.turbo: no visible global function definition for 'lines'
plot.turbo: no visible global function definition for 'legend'
turboSim: no visible binding for global variable 'par'
turboem: no visible global function definition for 'modifyList'
Undefined global functions or variables:
  abline axis coef legend lines modifyList mtext optimize par plot
  quantile segments text title
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "mtext",
             "par", "plot", "segments", "text", "title")
  importFrom("stats", "coef", "optimize", "quantile")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
turf: no visible global function definition for 'read.table'
turf: no visible global function definition for 'flush.console'
turf.combos: no visible global function definition for 'combn'
Undefined global functions or variables:
  combn flush.console read.table
Consider adding
  importFrom("utils", "combn", "flush.console", "read.table")
to your NAMESPACE file.
turtle_param: no visible global function definition for 'col2rgb'
Undefined global functions or variables:
  col2rgb
Consider adding
  importFrom("grDevices", "col2rgb")
to your NAMESPACE file.
TwoCop: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
condnorm: no visible global function definition for 'pnorm'
condnorm: no visible global function definition for 'dnorm'
find.p.joint: no visible global function definition for 'integrate'
find.p.joint.alt: no visible global function definition for 'integrate'
termsInt: no visible global function definition for 'pnorm'
termsInt.alt: no visible global function definition for 'pnorm'
twoStageNull: no visible global function definition for 'qnorm'
twoStageNull: no visible global function definition for 'optimize'
twoStagePower: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dnorm integrate optimize pnorm qnorm
Consider adding
  importFrom("stats", "dnorm", "integrate", "optimize", "pnorm", "qnorm")
to your NAMESPACE file.
txtacf: no visible binding for global variable 'na.fail'
txtacf: no visible global function definition for 'acf'
txtboxplot : <anonymous>: no visible global function definition for
  'boxplot.stats'
txtboxplot: no visible global function definition for 'boxplot.stats'
txtdensity: no visible global function definition for 'density'
Undefined global functions or variables:
  acf boxplot.stats density na.fail
Consider adding
  importFrom("grDevices", "boxplot.stats")
  importFrom("stats", "acf", "density", "na.fail")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/uaparserjs.Rcheck/00install.out' for details.
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.
ubRacing : predCandidate: no visible global function definition for
  'predict'
ubRacing : aux2.friedman.edit: no visible global function definition
  for 'pchisq'
ubRacing : aux2.friedman.edit: no visible global function definition
  for 'qt'
ubRacing : aux.friedman.edit: no visible global function definition for
  'wilcox.test'
ubRacing : aux.ttest.edit: no visible global function definition for
  't.test'
ubRacing : aux.ttest.edit: no visible global function definition for
  'p.adjust'
ubRacing : idFolds: no visible global function definition for
  'quantile'
ubRacing: no visible binding for global variable 'sd'
ubSmoteExs: no visible global function definition for 'runif'
Undefined global functions or variables:
  p.adjust pchisq predict qt quantile runif sd t.test wilcox.test
Consider adding
  importFrom("stats", "p.adjust", "pchisq", "predict", "qt", "quantile",
             "runif", "sd", "t.test", "wilcox.test")
to your NAMESPACE file.
med: no visible global function definition for 'quantile'
uh: no visible global function definition for 'mad'
uh.bu: no visible global function definition for 'mad'
Undefined global functions or variables:
  mad quantile
Consider adding
  importFrom("stats", "mad", "quantile")
to your NAMESPACE file.
permute.rows: no visible global function definition for 'runif'
uniCox: no visible global function definition for 'quantile'
uniCoxCV: no visible global function definition for 'quantile'
uniCoxCV: no visible global function definition for 'coxph'
uniCoxCV: no visible binding for global variable 'var'
Undefined global functions or variables:
  coxph quantile runif var
Consider adding
  importFrom("stats", "quantile", "runif", "var")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'predict.uniCox':
  'predict.uniCox'

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
dudewicz.unif.test: no visible global function definition for 'runif'
frosini.unif.test: no visible global function definition for 'runif'
hegazy.unif.test: no visible global function definition for 'runif'
kolmogorov.unif.test: no visible global function definition for 'runif'
kuiper.unif.test: no visible global function definition for 'runif'
neyman.unif.test: no visible global function definition for 'runif'
quesenberry.unif.test: no visible global function definition for
  'runif'
sarkadi.unif.test: no visible global function definition for 'runif'
sherman.unif.test: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
cumcount: no visible global function definition for 'setNames'
uniqtag: no visible global function definition for 'setNames'
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
ok: 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.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   1.7Mb
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.
UPMASKfile: no visible global function definition for 'read.table'
UPMASKfile: no visible global function definition for 'write.table'
analyse_randomKde2d: no visible global function definition for 'hist'
analyse_randomKde2d: no visible global function definition for 'lines'
analyse_randomKde2d_AutoCalibrated: no visible global function
  definition for 'hist'
analyse_randomKde2d_AutoCalibrated: no visible global function
  definition for 'lines'
create_randomKde2d: no visible global function definition for 'image'
create_randomKde2d: no visible global function definition for 'points'
getStarsAtHighestDensityRegion: no visible global function definition
  for 'rgb'
getStarsAtHighestDensityRegion: no visible global function definition
  for 'dev.new'
getStarsAtHighestDensityRegion: no visible global function definition
  for 'plot'
getStarsAtHighestDensityRegion: no visible global function definition
  for 'image'
getStarsAtHighestDensityRegion: no visible global function definition
  for 'contour'
getStarsAtHighestDensityRegion: no visible global function definition
  for 'points'
innerLoop: no visible global function definition for 'dev.new'
innerLoop: no visible global function definition for 'par'
innerLoop: no visible global function definition for 'pairs'
innerLoop: no visible global function definition for 'rainbow'
kde2dForSubset: no visible global function definition for 'image'
kde2dForSubset: no visible global function definition for 'points'
Undefined global functions or variables:
  contour dev.new hist image lines pairs par plot points rainbow
  read.table rgb write.table
Consider adding
  importFrom("grDevices", "dev.new", "rainbow", "rgb")
  importFrom("graphics", "contour", "hist", "image", "lines", "pairs",
             "par", "plot", "points")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
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.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
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.
histw: no visible global function definition for 'plot.new'
histw: no visible global function definition for 'plot.window'
histw: no visible global function definition for 'axis'
histw: no visible global function definition for 'rect'
histw: no visible global function definition for 'lines'
uwham.boot: no visible binding for global variable 'var'
Undefined global functions or variables:
  axis lines plot.new plot.window rect var
Consider adding
  importFrom("graphics", "axis", "lines", "plot.new", "plot.window",
             "rect")
  importFrom("stats", "var")
to your NAMESPACE file.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
'library' or 'require' call to 'foreach' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'foreach'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
constant.post.9mo: no visible global function definition for 'pexp'
ll.coverage.optim.const.post.9m: no visible global function definition
  for 'dexp'
make.sample.pop: no visible global function definition for 'runif'
mcmc.converge: no visible global function definition for 'par'
mcmc.converge: no visible global function definition for 'plot'
mcmc.converge: no visible global function definition for 'points'
mcmc.converge: no visible global function definition for 'density'
mcmc.converge: no visible global function definition for 'lines'
mcmc.converge : <anonymous>: no visible global function definition for
  'sd'
mcmc.estimate : run.chain: no visible global function definition for
  'dexp'
mcmc.estimate : run.chain: no visible global function definition for
  'rnorm'
mcmc.estimate : run.chain: no visible global function definition for
  'runif'
mcmc.estimate : run.chain: no visible global function definition for
  'par'
mcmc.estimate : run.chain: no visible global function definition for
  'plot'
mcmc.estimate: no visible global function definition for '%dopar%'
mcmc.estimate: no visible global function definition for 'foreach'
sim.n.vacc.sample.pop : <anonymous>: no visible global function
  definition for 'runif'
vaccinate.sample.pop: no visible global function definition for 'runif'
Undefined global functions or variables:
  %dopar% density dexp foreach lines par pexp plot points rnorm runif
  sd
Consider adding
  importFrom("graphics", "lines", "par", "plot", "points")
  importFrom("stats", "density", "dexp", "pexp", "rnorm", "runif", "sd")
to your NAMESPACE file.
Running 'coverageTest.r' [0s]
Running the tests in 'tests/coverageTest.r' failed.
Last 13 lines of output:
  > #*  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
  > #*  
  > #*  $Id: coverageTest.r 378 2012-01-27 02:35:09Z ken $
  > #*  ----------------------------------------------------------------------------
  > 
  > 
  > # TBD: Add file header
  > # TBD: Do I need some 'library( pkg )' or 'source( file )' calls here???
  > 
  > 
  > # source( "../tests/testUtils.r" )
  > source( getTestPaths("vacem","tests/testUtils.r") )
  Error in source(getTestPaths("vacem", "tests/testUtils.r")) : 
    could not find function "getTestPaths"
  Execution halted
Packages suggested but not available for checking: 'vaers' 'vaersND'
Files in the 'vignettes' directory but no files in 'inst/doc':
  'demo.cc.R', 'demo.cd.R', 'demo.cfw.R', 'demo.cytokine.R',
    'demo.leukemia.R', 'demo.qtl.R'
Package has no Sweave vignette sources and no VignetteBuilder field.
varComp.fit: no visible binding for global variable 'combn'
varComp.fit: no visible global function definition for 'plot'
varComp.fit: no visible global function definition for 'abline'
wchibarsq: no visible global function definition for 'combn'
Undefined global functions or variables:
  abline combn plot
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("utils", "combn")
to your NAMESPACE file.
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.
withoutmixture,VSLCMresultsContinuous: no visible global function
  definition for 'sd'
withoutmixture,VSLCMresultsContinuous: no visible global function
  definition for 'dnorm'
Undefined global functions or variables:
  dnorm sd
Consider adding
  importFrom("stats", "dnorm", "sd")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'MASS' 'strucchange'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
black_scholes: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
burdenPlot: no visible global function definition for 'density'
burdenPlot: no visible global function definition for 'axis'
burdenPlot: no visible global function definition for 'points'
burdenPlot: no visible global function definition for 'lines'
burdenPlot: no visible global function definition for 'abline'
burdenPlot: no visible global function definition for 'text'
burdenPlot: no visible global function definition for 'sd'
burdenPlot: no visible global function definition for 'segments'
vbdm: no visible global function definition for 'var'
vbdm: no visible global function definition for 'pchisq'
vbdmR : run_discrete_mixture_vanilla: no visible global function
  definition for 'var'
vbdmR: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  abline axis density lines pchisq points sd segments text var
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "points", "segments",
             "text")
  importFrom("stats", "density", "pchisq", "sd", "var")
to your NAMESPACE file.
compute_KL : rtnorm: no visible global function definition for 'runif'
compute_KL : rtnorm: no visible global function definition for 'dnorm'
compute_KL: no visible global function definition for 'qnorm'
compute_KL: no visible global function definition for 'dnorm'
compute_KL: no visible global function definition for 'pnorm'
compute_KL: no visible global function definition for 'var'
compute_KL: no visible global function definition for 'rbinom'
compute_KL: no visible global function definition for 'rnorm'
compute_KL: no visible global function definition for 'sd'
vbsr: no visible global function definition for 'qchisq'
vbsr: no visible global function definition for 'var'
vbsr: no visible global function definition for 'pchisq'
vbsr: no visible global function definition for 'sd'
vbsr: no visible binding for global variable 'sd'
Undefined global functions or variables:
  dnorm pchisq pnorm qchisq qnorm rbinom rnorm runif sd var
Consider adding
  importFrom("stats", "dnorm", "pchisq", "pnorm", "qchisq", "qnorm",
             "rbinom", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   2.2Mb
cv.vda.le.default: no visible global function definition for 'predict'
cv.vda.r.default: no visible global function definition for 'predict'
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
Compare2FDS: no visible global function definition for 'runif'
Compare2FDS: no visible global function definition for 'lm'
Compare2FDS: no visible global function definition for 'model.matrix'
Compare2FDS: no visible global function definition for 'plot'
Compare2FDS: no visible global function definition for 'abline'
Compare2FDS: no visible global function definition for 'lines'
Compare2FDS: no visible global function definition for 'text'
Compare2Vdg: no visible global function definition for 'par'
Compare2Vdg: no visible global function definition for 'plot'
Compare2Vdg: no visible global function definition for 'lines'
Compare2Vdg: no visible global function definition for 'legend'
FDSPlot: no visible global function definition for 'runif'
FDSPlot: no visible global function definition for 'lm'
FDSPlot: no visible global function definition for 'model.matrix'
FDSPlot: no visible global function definition for 'plot'
FDSPlot: no visible global function definition for 'abline'
Vdgraph: no visible global function definition for 'par'
Vdgraph: no visible global function definition for 'plot'
Vdgraph: no visible global function definition for 'lines'
Vdgraph: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline legend lines lm model.matrix par plot runif text
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "plot",
             "text")
  importFrom("stats", "lm", "model.matrix", "runif")
to your NAMESPACE file.
calculateParameters,AffineTransformation: no visible global function
  definition for 'lm'
calculateParameters,AffineTransformation: no visible global function
  definition for 'coef'
calculateParameters,SimilarityTransformation: no visible global
  function definition for 'lm'
calculateParameters,SimilarityTransformation: no visible global
  function definition for 'coef'
plotGridTransformation,Cartesian2DCoordinateTransformation: no visible
  global function definition for 'points'
plotGridTransformation,Cartesian2DCoordinateTransformation: no visible
  global function definition for 'legend'
Undefined global functions or variables:
  coef legend lm points
Consider adding
  importFrom("graphics", "legend", "points")
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
vsetdiff : <anonymous>: no visible global function definition for
  'head'
Undefined global functions or variables:
  head
Consider adding
  importFrom("utils", "head")
to your NAMESPACE file.
DrawDensity3D: no visible global function definition for 'colorRamp'
DrawDensity3D: no visible global function definition for 'rgb'
ReadFromFile3D: no visible global function definition for 'read.table'
Undefined global functions or variables:
  colorRamp read.table rgb
Consider adding
  importFrom("grDevices", "colorRamp", "rgb")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'library' or 'require' call to 'stats' which was already attached by Depends.
  Please remove these calls from your code.
plot.VennDiagram : <anonymous>: no visible global function definition
  for 'hcl'
plot.VennDiagram: no visible global function definition for 'plot.new'
plot.VennDiagram: no visible global function definition for
  'plot.window'
plot.VennDiagram: no visible global function definition for 'col2rgb'
plot.VennDiagram: no visible global function definition for 'rgb'
plot.VennDiagram: no visible global function definition for 'polygon'
plot.VennDiagram: no visible global function definition for 'text'
plot.VennDiagram: no visible global function definition for 'title'
Undefined global functions or variables:
  col2rgb hcl plot.new plot.window polygon rgb text title
Consider adding
  importFrom("grDevices", "col2rgb", "hcl", "rgb")
  importFrom("graphics", "plot.new", "plot.window", "polygon", "text",
             "title")
to your NAMESPACE file.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.2Mb
    help   2.6Mb
    libs   1.2Mb
vif: no visible global function definition for 'sd'
vif: no visible global function definition for 'lm'
vif: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  lm pnorm sd
Consider adding
  importFrom("stats", "lm", "pnorm", "sd")
to your NAMESPACE file.
hyperpara: no visible binding for global variable 'var'
hyperpara: no visible global function definition for 'hist'
Undefined global functions or variables:
  hist var
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "var")
to your NAMESPACE file.
panel.meansdplot : meansdplot.stats: no visible global function
  definition for 'sd'
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Package in Depends field not imported from: 'sm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
vioplot: no visible global function definition for 'quantile'
vioplot: no visible global function definition for 'median'
vioplot: no visible global function definition for 'plot.new'
vioplot: no visible global function definition for 'plot.window'
vioplot: no visible global function definition for 'axis'
vioplot: no visible global function definition for 'box'
vioplot: no visible global function definition for 'polygon'
vioplot: no visible global function definition for 'lines'
vioplot: no visible global function definition for 'rect'
vioplot: no visible global function definition for 'points'
Undefined global functions or variables:
  axis box lines median plot.new plot.window points polygon quantile
  rect
Consider adding
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "points", "polygon", "rect")
  importFrom("stats", "median", "quantile")
to your NAMESPACE file.
viopoints.default: no visible global function definition for 'par'
viopoints.default: no visible global function definition for 'plot.new'
viopoints.default: no visible global function definition for
  'plot.window'
viopoints.default: no visible global function definition for 'axis'
viopoints.default: no visible global function definition for 'arrows'
viopoints.default: no visible global function definition for
  'getFromNamespace'
viopoints.default: no visible global function definition for 'title'
viopoints.default: no visible global function definition for 'box'
Undefined global functions or variables:
  arrows axis box getFromNamespace par plot.new plot.window title
Consider adding
  importFrom("graphics", "arrows", "axis", "box", "par", "plot.new",
             "plot.window", "title")
  importFrom("utils", "getFromNamespace")
to your NAMESPACE file.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc           3.6Mb
    htmlwidgets   3.5Mb
visualize.continuous: no visible global function definition for 'plot'
visualize.continuous: no visible global function definition for
  'polygon'
visualize.continuous: no visible global function definition for 'axis'
visualize.continuous: no visible global function definition for 'mtext'
visualize.continuous: no visible global function definition for 'title'
visualize.discrete: no visible global function definition for 'barplot'
visualize.discrete: no visible global function definition for 'axis'
visualize.discrete: no visible global function definition for 'mtext'
visualize.discrete: no visible global function definition for 'title'
Undefined global functions or variables:
  axis barplot mtext plot polygon title
Consider adding
  importFrom("graphics", "axis", "barplot", "mtext", "plot", "polygon",
             "title")
to your NAMESPACE file.
Decile.Plot: no visible global function definition for 'barplot'
Decile.Plot: no visible global function definition for 'axis'
Sliding.Window: no visible global function definition for 'plot'
Sliding.Window: no visible global function definition for 'lines'
Sliding.Window: no visible global function definition for 'legend'
Undefined global functions or variables:
  axis barplot legend lines plot
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines", "plot")
to your NAMESPACE file.
RCplot: no visible global function definition for 'residuals'
RCplot: no visible global function definition for 'predict'
RCplot: no visible global function definition for 'par'
RCplot: no visible global function definition for 'plot.new'
RCplot: no visible global function definition for 'plot.window'
RCplot: no visible global function definition for 'strwidth'
RCplot: no visible global function definition for 'plot'
RCplot: no visible global function definition for 'abline'
RCplot: no visible global function definition for 'text'
RCplot: no visible global function definition for 'mtext'
fitted.vlmc: no visible global function definition for 'predict'
print.vlmc: no visible global function definition for 'AIC'
residuals.vlmc: no visible global function definition for 'predict'
simulate.vlmc: no visible global function definition for 'runif'
summary.vlmc: no visible global function definition for 'predict'
vlmc: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  AIC abline mtext par plot plot.new plot.window predict qchisq
  residuals runif strwidth text
Consider adding
  importFrom("graphics", "abline", "mtext", "par", "plot", "plot.new",
             "plot.window", "strwidth", "text")
  importFrom("stats", "AIC", "predict", "qchisq", "residuals", "runif")
to your NAMESPACE file.
voss1d: no visible global function definition for 'approx'
voss1d: no visible global function definition for 'rnorm'
voss1g: no visible global function definition for 'dchisq'
voss1g: no visible global function definition for 'approx'
voss1g: no visible global function definition for 'rnorm'
voss2d: no visible global function definition for 'rnorm'
voss2g: no visible global function definition for 'dchisq'
voss2g: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  approx dchisq rnorm
Consider adding
  importFrom("stats", "approx", "dchisq", "rnorm")
to your NAMESPACE file.
add.spread.vowelplot: no visible global function definition for
  'points'
add.spread.vowelplot: no visible binding for global variable 'mtext'
add.spread.vowelplot: no visible global function definition for 'lines'
add.spread.vowelplot: no visible global function definition for
  'prcomp'
add.spread.vowelplot: no visible global function definition for
  'arrows'
add.spread.vowelplot: no visible global function definition for
  'legend'
add.spread.vowelplot: no visible global function definition for 'text'
add.vowelplot: no visible global function definition for 'points'
add.vowelplot: no visible binding for global variable 'mtext'
add.vowelplot: no visible global function definition for 'arrows'
add.vowelplot: no visible global function definition for 'text'
compute.medians: no visible global function definition for 'median'
compute.sds: no visible global function definition for 'sd'
load.vowels: no visible global function definition for 'read.table'
norm.lobanov: no visible global function definition for 'sd'
vowelplot: no visible global function definition for 'plot'
vowelplot: no visible global function definition for 'legend'
vowelplot: no visible global function definition for 'arrows'
vowelplot: no visible global function definition for 'text'
Undefined global functions or variables:
  arrows legend lines median mtext plot points prcomp read.table sd
  text
Consider adding
  importFrom("graphics", "arrows", "legend", "lines", "mtext", "plot",
             "points", "text")
  importFrom("stats", "median", "prcomp", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'library' or 'require' call to 'raster' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
level: no visible global function definition for 'quantile'
obj.rec: no visible global function definition for 'txtProgressBar'
obj.rec: no visible global function definition for 'setTxtProgressBar'
project: no visible global function definition for 'aggregate'
raster.proj: no visible global function definition for 'quantile'
raster.proj: no visible global function definition for 'rasterFromXYZ'
raster.proj: no visible global function definition for 'plot.new'
raster.proj: no visible global function definition for 'plot'
raster.proj: no visible global function definition for 'legend'
sub.obj: no visible global function definition for 'aggregate'
sub.obj: no visible global function definition for 'txtProgressBar'
sub.obj: no visible global function definition for 'setTxtProgressBar'
surface: no visible global function definition for 'quantile'
Undefined global functions or variables:
  aggregate legend plot plot.new quantile rasterFromXYZ
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "legend", "plot", "plot.new")
  importFrom("stats", "aggregate", "quantile")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
'library' or 'require' call to 'misc3d' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.vscc: no visible global function definition for 'rainbow'
plot.vscc: no visible global function definition for 'pairs'
Undefined global functions or variables:
  pairs rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "pairs")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'lattice' 'latticeExtra' 'stringdist'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ald: no visible global function definition for 'detectCores'
ald: no visible global function definition for 'mclapply'
coltheart.N: no visible global function definition for 'detectCores'
coltheart.N: no visible global function definition for 'mclapply'
hamming.distance: no visible global function definition for
  'stringdist'
ldknn: no visible global function definition for 'detectCores'
ldknn: no visible global function definition for 'mclapply'
ldknn.odds: no visible global function definition for 'glm'
ldknn.odds: no visible binding for global variable 'binomial'
ldknn.odds: no visible global function definition for 'coefficients'
levenshtein.damerau.distance: no visible global function definition for
  'stringdist'
levenshtein.distance: no visible global function definition for
  'stringdist'
plot.ldknn.run: no visible global function definition for 'histogram'
plot.ldknn.run: no visible global function definition for
  'theEconomist.theme'
plot.ldknn.run: no visible global function definition for 'xyplot'
plot.ldknn.run: no visible global function definition for 'as.layer'
Undefined global functions or variables:
  as.layer binomial coefficients detectCores glm histogram mclapply
  stringdist theEconomist.theme xyplot
Consider adding
  importFrom("stats", "binomial", "coefficients", "glm")
to your NAMESPACE file.
Package in Depends field not imported from: 'Rcpp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
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.
wave.multiple.correlation: no visible global function definition for
  'qnorm'
Undefined global functions or variables:
  qnorm
Consider adding
  importFrom("stats", "qnorm")
to your NAMESPACE file.
changepoints.sbs: no visible global function definition for 'mad'
changepoints.wbs: no visible global function definition for 'var'
changepoints.wbs: no visible global function definition for 'quantile'
plot.sbs: no visible global function definition for 'ts.plot'
plot.sbs: no visible global function definition for 'lines'
plot.sbs: no visible global function definition for 'title'
random.intervals: no visible global function definition for 'runif'
sbs.default: no visible global function definition for 'var'
wbs.default: no visible global function definition for 'var'
Undefined global functions or variables:
  lines mad quantile runif title ts.plot var
Consider adding
  importFrom("graphics", "lines", "title")
  importFrom("stats", "mad", "quantile", "runif", "ts.plot", "var")
to your NAMESPACE file.
onesamplemeantest: no visible global function definition for 'pnorm'
twosamplemeantest: no visible global function definition for 'pnorm'
wcq: no visible global function definition for 'var'
wcq: no visible global function definition for 'pnorm'
wcq.fdrc: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  p.adjust pnorm var
Consider adding
  importFrom("stats", "p.adjust", "pnorm", "var")
to your NAMESPACE file.
Package in Depends field not imported from: 'RJSONIO'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
WDI: no visible binding for global variable 'WDI_data'
WDIcache: no visible global function definition for 'fromJSON'
WDIsearch: no visible binding for global variable 'WDI_data'
Undefined global functions or variables:
  WDI_data fromJSON
cleanAndSubsetDetailedData: no visible global function definition for
  'read.csv'
cleanAndSubsetObtainedData: no visible global function definition for
  'read.csv'
getStationCode: no visible binding for global variable
  'USAirportWeatherStations'
getStationCode: no visible binding for global variable 'IntlWxStations'
getWeatherForDate: no visible global function definition for
  'write.csv'
Undefined global functions or variables:
  IntlWxStations USAirportWeatherStations read.csv write.csv
Consider adding
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
File 'webvis/R/zzz.R':
  .onLoad calls:
    print("Welcome to the webvis pacakge.")

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

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

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Weighted.Box.test: no visible global function definition for 'acf'
Weighted.Box.test: no visible binding for global variable 'na.pass'
Weighted.Box.test: no visible global function definition for 'pgamma'
Weighted.Box.test: no visible global function definition for 'pchisq'
Weighted.LM.test: no visible global function definition for 'acf'
Weighted.LM.test: no visible binding for global variable 'na.pass'
Weighted.LM.test: no visible global function definition for 'pgamma'
Undefined global functions or variables:
  acf na.pass pchisq pgamma
Consider adding
  importFrom("stats", "acf", "na.pass", "pchisq", "pgamma")
to your NAMESPACE file.
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').
plot.whatif: no visible global function definition for 'na.fail'
plot.whatif : do.plot: no visible global function definition for
  'lines'
plot.whatif : do.plot: no visible global function definition for
  'lowess'
plot.whatif: no visible global function definition for 'postscript'
plot.whatif: no visible global function definition for 'plot'
plot.whatif: no visible global function definition for 'dev.off'
whatif: no visible global function definition for 'read.table'
whatif: no visible global function definition for 'complete.cases'
whatif: no visible global function definition for 'terms'
whatif: no visible global function definition for 'model.matrix'
whatif: no visible global function definition for 'model.frame'
whatif: no visible global function definition for 'update.formula'
whatif: no visible global function definition for 'na.omit'
whatif: no visible global function definition for 'na.fail'
Undefined global functions or variables:
  complete.cases dev.off lines lowess model.frame model.matrix na.fail
  na.omit plot postscript read.table terms update.formula
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "complete.cases", "lowess", "model.frame",
             "model.matrix", "na.fail", "na.omit", "terms",
             "update.formula")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Files in the 'vignettes' directory newer than all files in 'inst/doc':
  'gk.bib', 'gkpubs.bib', 'whatif.pdf', 'whatif.tex'
Package has no Sweave vignette sources and no VignetteBuilder field.
'library' or 'require' call to 'markdown' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
download_img_data: no visible global function definition for
  'download.file'
smooth_hist: no visible global function definition for 'quantile'
whitestripe: no visible global function definition for 'hist'
whitestripe: no visible global function definition for 'quantile'
whitestripe: no visible global function definition for 'sd'
whitestripe_norm: no visible global function definition for 'sd'
Undefined global functions or variables:
  download.file hist quantile sd
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "quantile", "sd")
  importFrom("utils", "download.file")
to your NAMESPACE file.
Found the following significant warnings:
  tabix/knetfile.c:438:5: warning: ISO C does not support the 'I64' ms_printf length modifier [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/3.4/WhopGenome.Rcheck/00install.out' for details.
Running examples in 'WhopGenome-Ex.R' failed
The error most likely occurred in:

> ### Name: fai_close
> ### Title: Closes a file previously opened with fai_open
> ### Aliases: fai_close
> 
> ### ** Examples
> 
> 
> ##
> ##	Example :
> ##
> faifile  <- system.file("extdata", "ex.fasta", package = "WhopGenome")
> faifh <- fai_open( faifile )
> stopifnot( faifh != NULL )
Error in faifh != NULL : 
  comparison (2) is possible only for atomic and list types
Calls: stopifnot
Execution halted
dlog.norm: no visible global function definition for 'rnorm'
fun.load.hals.a: no visible global function definition for 'sfExport'
fun.load.hals.a: no visible global function definition for 'sfLibrary'
fun.load.hals.fill: no visible global function definition for
  'sfExport'
fun.load.hals.fill: no visible global function definition for
  'sfLibrary'
fun.load.widals.a: no visible global function definition for 'sfExport'
fun.load.widals.a: no visible global function definition for
  'sfLibrary'
fun.load.widals.fill: no visible global function definition for
  'sfExport'
fun.load.widals.fill: no visible global function definition for
  'sfLibrary'
unif.mh: no visible global function definition for 'runif'
Undefined global functions or variables:
  rnorm runif sfExport sfLibrary
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'genefilter' 'parallel'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.onAttach: no visible global function definition for
  'packageDescription'
.relax.cvcompute: no visible binding for global variable
  'weighted.mean'
.relax.widenet.cv.elnet: no visible global function definition for
  'predict'
.relax.widenet.cv.elnet: no visible binding for global variable
  'weighted.mean'
.relax.widenet.cv.lognet: no visible global function definition for
  'predict'
.relax.widenet.cv.lognet: no visible binding for global variable
  'weighted.mean'
.widenet.cv.elnet: no visible global function definition for 'predict'
.widenet.cv.elnet: no visible binding for global variable
  'weighted.mean'
.widenet.cv.lognet: no visible global function definition for 'predict'
.widenet.cv.lognet: no visible binding for global variable
  'weighted.mean'
predict.widenet: no visible global function definition for 'predict'
screen.cor : <anonymous>: no visible global function definition for
  'var'
screen.cor : <anonymous>: no visible global function definition for
  'cor.test'
screen.ttest: no visible global function definition for 'colttests'
widenet: no visible global function definition for 'mc.reset.stream'
widenet: no visible global function definition for 'mclapply'
widenet: no visible global function definition for 'predict'
Undefined global functions or variables:
  colttests cor.test mc.reset.stream mclapply packageDescription
  predict var weighted.mean
Consider adding
  importFrom("stats", "cor.test", "predict", "var", "weighted.mean")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
Bundesliga.Mannschaft: no visible global function definition for 'data'
Bundesliga.Mannschaft: no visible binding for global variable
  'Bundesliga'
Bundesliga.Tabelle: no visible global function definition for 'data'
Bundesliga.Tabelle: no visible binding for global variable 'Bundesliga'
Bundesliga.XML: no visible global function definition for 'data'
Bundesliga.XML: no visible binding for global variable 'Bundesliga'
sens.spec: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
wilcox.selection.split: no visible global function definition for
  'pnorm'
wilcox.test2: no visible global function definition for 'wilcox.test'
Undefined global functions or variables:
  pnorm wilcox.test
Consider adding
  importFrom("stats", "pnorm", "wilcox.test")
to your NAMESPACE file.
Cs: no visible global function definition for 'wilcox.test'
Don: no visible global function definition for 'points'
Don: no visible global function definition for 'chisq.test'
Lixn: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  chisq.test pchisq points wilcox.test
Consider adding
  importFrom("graphics", "points")
  importFrom("stats", "chisq.test", "pchisq", "wilcox.test")
to your NAMESPACE file.
plotTrait: no visible global function definition for 'plot'
plotTrait: no visible global function definition for 'points'
plotTrait: no visible global function definition for 'legend'
test.windex: no visible global function definition for 'hist'
test.windex: no visible global function definition for 'abline'
test.windex: no visible global function definition for 'legend'
windex: no visible global function definition for 'sd'
windex: no visible global function definition for 'var'
windex: no visible global function definition for 'dist'
windex: no visible global function definition for 'quantile'
Undefined global functions or variables:
  abline dist hist legend plot points quantile sd var
Consider adding
  importFrom("graphics", "abline", "hist", "legend", "plot", "points")
  importFrom("stats", "dist", "quantile", "sd", "var")
to your NAMESPACE file.
.__A__.1 : <anonymous>: no visible binding for global variable '.hwnd'
Undefined global functions or variables:
  .hwnd
Unexported objects imported by ':::' calls:
  'circular:::DensityCircularRad' 'circular:::DvonmisesRad'
  'circular:::DwrappednormalRad' 'circular:::MlevonmisesRad'
  'circular:::MlewrappednormalRad'
  See the note in ?`:::` about the use of this operator.
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.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    5.0Mb
    libs   1.4Mb
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  3: A$visualize()
  4: DiagrammeR::create_nodes
  5: getExportedValue(pkg, name)
  6: stop(gettextf("'%s' is not an exported object from 'namespace:%s'", name, getNamespaceName(ns)), 
         call. = FALSE, domain = NA)
  
  testthat results ================================================================
  OK: 132 SKIPPED: 0 FAILED: 4
  1. Error: visualization of empty automat works (@test-automat.R#131) 
  2. Error: visualization without set state works (@test-automat.R#139) 
  3. Error: visualization with implicit state works (@test-automat.R#148) 
  4. Error: visualization works (@test-automat.R#163) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/word.alignment.Rcheck/00install.out' for details.
'library' or 'require' call to 'tm' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'plyr' 'reshape2'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
wordmatch: no visible global function definition for 'llply'
wordmatch : <anonymous>: no visible global function definition for
  'llply'
wordmatch: no visible global function definition for 'melt'
wordmatch: no visible global function definition for 'count'
Undefined global functions or variables:
  count llply melt
pickList : <anonymous>: no visible global function definition for
  'na.omit'
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Running examples in 'wPerm-Ex.R' failed
The error most likely occurred in:

> ### Name: perm.oneway.anova
> ### Title: Permutation One-Way ANOVA Test
> ### Aliases: perm.oneway.anova
> 
> ### ** Examples
> 
> # Last year's energy consumptions, to the nearest 10 million BTU, for
> # independent random samples of households in the four U.S. regions.
> data("energy")
> str(energy)
'data.frame':	20 obs. of  2 variables:
 $ ENERGY: int  13 8 11 12 11 15 10 16 11 13 ...
 $ REGION: Factor w/ 4 levels "Midwest","Northeast",..: 2 2 2 2 2 1 1 1 1 1 ...
> attach(energy)
> 
> # Permutation one-way ANOVA to decide whether the energy distributions
> # have systematically larger values in some U.S. regions than in others.
> # Regions ordered to Northeast, Midwest, South, and West; 999 replications.
> perm.oneway.anova(ENERGY, REGION, ford = c(2,1,3,4), R = 999)
Error in lengths(x) : 'dimnames' must be a list
Calls: perm.oneway.anova ... stack.default -> rep -> rep.factor -> NextMethod -> lengths
Execution halted
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.6Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data  11.1Mb
Found the following significant warnings:
  assp/asspfio.c:632:11: warning: ISO C does not support the 'I64' ms_printf length modifier [-Wformat=]
  assp/asspfio.c:638:10: warning: ISO C does not support the 'I64' ms_printf length modifier [-Wformat=]
  assp/asspfio.c:664:10: warning: ISO C does not support the 'I64' ms_printf length modifier [-Wformat=]
  assp/asspfio.c:670:10: warning: ISO C does not support the 'I64' ms_printf length modifier [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/3.4/wrassp.Rcheck/00install.out' for details.
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.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
quadplot: no visible global function definition for 'median'
xgobi: no visible global function definition for 'write.table'
Undefined global functions or variables:
  median write.table
Consider adding
  importFrom("stats", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
XHWE: no visible global function definition for 'read.table'
result: no visible global function definition for 'pchisq'
result: no visible global function definition for 'rbinom'
result: no visible global function definition for 'rmultinom'
Undefined global functions or variables:
  pchisq rbinom read.table rmultinom
Consider adding
  importFrom("stats", "pchisq", "rbinom", "rmultinom")
  importFrom("utils", "read.table")
to your NAMESPACE file.
.xssfcolor: no visible global function definition for 'col2rgb'
Undefined global functions or variables:
  col2rgb
Consider adding
  importFrom("grDevices", "col2rgb")
to your NAMESPACE file.
R5.value.default: no visible binding for global variable 'data.table'
R5.value.default: no visible global function definition for
  'as.data.table'
R5.value.parse: no visible binding for global variable 'data.table'
R5.value.parse: no visible global function definition for
  'is.data.table'
R5.value.parse: no visible global function definition for
  'as.data.table'
stampme: no visible global function definition for 'flush.console'
stampmsg: no visible global function definition for 'flush.console'
write.data.table: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  as.data.table data.table flush.console is.data.table write.table
Consider adding
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE file.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    exampleData   1.3Mb
    examples      4.5Mb
    libs          4.2Mb
newXMLDoc: no visible binding for global variable 'doc'
source: no visible binding for global variable 'use_file'
xmlFlatListTree : f: no visible binding for global variable 'nodeNames'
xmlFlatListTree : f: no visible binding for global variable 'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'nodeSet'
xmlFlatListTree : addNode: no visible binding for global variable
  'nodeSet'
xmlFlatListTree : addNode: no visible binding for global variable 'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'nodeNames'
xmlFlatListTree : addNode: no visible binding for global variable
  'nodeNames'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'parentCount'
xmlFlatListTree : addNode: no visible binding for global variable
  'parentCount'
xmlFlatListTree : <anonymous>: no visible binding for global variable
  'e'
xmlFlatTree : <anonymous>: no visible binding for global variable 'e'
[[,XMLCodeFile: possible error in updateIds(doc, save = x): unused
  argument (save = x)
Undefined global functions or variables:
  doc e idx nodeNames nodeSet parentCount use_file
LPGM: no visible global function definition for 'flush.console'
PGM: no visible global function definition for 'flush.console'
PGM.path.neighborhood: no visible global function definition for
  'runif'
PGMSim: no visible global function definition for 'rpois'
PGMSim: no visible global function definition for 'par'
WPGMSim: no visible global function definition for 'rpois'
XMRF.Sim: no visible global function definition for 'cov2cor'
XMRF.Sim: no visible global function definition for 'rbinom'
XMRF.Sim: no visible global function definition for 'rnorm'
glm.generic: no visible global function definition for 'flush.console'
mymult: no visible global function definition for 'rmultinom'
plot.GMS: no visible global function definition for 'pdf'
plot.GMS: no visible global function definition for 'dev.off'
plotNet: no visible global function definition for 'pdf'
plotNet: no visible global function definition for 'dev.off'
print.GMS: no visible global function definition for 'str'
processSeq: no visible binding for global variable 'quantile'
processSeq: no visible binding for global variable 'var'
processSeq: no visible global function definition for 'ks.test'
rmpois : <anonymous>: no visible global function definition for 'rpois'
Undefined global functions or variables:
  cov2cor dev.off flush.console ks.test par pdf quantile rbinom
  rmultinom rnorm rpois runif str var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par")
  importFrom("stats", "cov2cor", "ks.test", "quantile", "rbinom",
             "rmultinom", "rnorm", "rpois", "runif", "var")
  importFrom("utils", "flush.console", "str")
to your NAMESPACE file.
Package required but not available: 'rPython'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' calls in package code:
  'chron' 'fts' 'its' 'timeDate' 'timeSeries' 'tseries'
  Please use :: or requireNamespace() instead.
  See section 'Suggested 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').
.NS.estimator: no visible global function definition for 'lm'
.NS.estimator: no visible global function definition for 'coef'
.NS.estimator: no visible global function definition for 'na.omit'
.NS.estimator: no visible global function definition for 'resid'
.NSS.estimator: no visible global function definition for 'lm'
.NSS.estimator: no visible global function definition for 'coef'
.NSS.estimator: no visible global function definition for 'na.omit'
.NSS.estimator: no visible global function definition for 'resid'
NSrates: no visible global function definition for 'time'
Nelson.Siegel: no visible global function definition for 'optimize'
Srates: no visible global function definition for 'time'
Svensson: no visible global function definition for 'median'
Svensson: no visible global function definition for 'optimize'
Undefined global functions or variables:
  coef lm median na.omit optimize resid time
Consider adding
  importFrom("stats", "coef", "lm", "median", "na.omit", "optimize",
             "resid", "time")
to your NAMESPACE file.
kmeansN: no visible global function definition for 'kmeans'
kmeansN: no visible global function definition for 'aggregate'
kmeansN2: no visible global function definition for 'aggregate'
kmeansN2: no visible binding for global variable 'sd'
Undefined global functions or variables:
  aggregate kmeans sd
Consider adding
  importFrom("stats", "aggregate", "kmeans", "sd")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'deSolve' 'triangle'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
piczoeppritz: no visible global function definition for 'locator'
piczoeppritz: no visible global function definition for 'rect'
piczoeppritz: no visible global function definition for 'grey'
piczoeppritz: no visible global function definition for 'segments'
piczoeppritz: no visible global function definition for 'arrows'
piczoeppritz: no visible global function definition for 'text'
plotzoeppritz: no visible global function definition for 'plot'
plotzoeppritz: no visible global function definition for 'par'
plotzoeppritz: no visible global function definition for 'lines'
plotzoeppritz: no visible global function definition for 'abline'
plotzoeppritz: no visible global function definition for 'grey'
plotzoeppritz: no visible global function definition for 'strheight'
plotzoeppritz: no visible global function definition for 'text'
plotzoeppritz: no visible global function definition for 'legend'
pzoeppritz: no visible global function definition for 'par'
pzoeppritz: no visible global function definition for 'plot'
pzoeppritz: no visible global function definition for 'title'
pzoeppritz: no visible global function definition for 'text'
Undefined global functions or variables:
  abline arrows grey legend lines locator par plot rect segments
  strheight text title
Consider adding
  importFrom("grDevices", "grey")
  importFrom("graphics", "abline", "arrows", "legend", "lines",
             "locator", "par", "plot", "rect", "segments", "strheight",
             "text", "title")
to your NAMESPACE file.
ztable.glm: no visible global function definition for 'confint'
ztable.glm: no visible global function definition for 'coef'
ztable.nls: no visible global function definition for 'formula'
Undefined global functions or variables:
  coef confint formula
Consider adding
  importFrom("stats", "coef", "confint", "formula")
to your NAMESPACE file.
confint.zyp: no visible global function definition for 'qnorm'
confint.zyp: no visible global function definition for 'var'
zyp.sen: no visible global function definition for 'terms'
zyp.sen: no visible global function definition for 'median'
zyp.trend.csv: no visible global function definition for 'read.csv'
zyp.trend.csv: no visible global function definition for 'write.csv'
zyp.yuepilon: no visible global function definition for 'acf'
zyp.yuepilon: no visible binding for global variable 'na.pass'
zyp.yuepilon: no visible global function definition for 'confint'
zyp.yuepilon: no visible global function definition for 'lm'
zyp.zhang: no visible global function definition for 'acf'
zyp.zhang: no visible binding for global variable 'na.pass'
zyp.zhang: no visible global function definition for 'confint'
zyp.zhang: no visible global function definition for 'lm'
Undefined global functions or variables:
  acf confint lm median na.pass qnorm read.csv terms var write.csv
Consider adding
  importFrom("stats", "acf", "confint", "lm", "median", "na.pass",
             "qnorm", "terms", "var")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
Running examples in ‘ActuDistns-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dgumbeld
> ### Title: Gumbel pdf
> ### Aliases: dgumbeld
> ### Keywords: Gumbel distribution
> 
> ### ** Examples
> x=runif(10,min=0,max=1)
> y=dgumbeld(x)
Error in dgumbel(x, mu = mu, sigma = sigma) : 
  unused arguments (mu = mu, sigma = sigma)
Calls: dgumbeld -> ifelse -> dgumbel
Execution halted
Found the following significant warnings:
  Warning: namespace ‘unmarked’ is not available and has been replaced
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/AMModels.Rcheck/00install.out’ for details.
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/audio.Rcheck/00install.out’ for details.
Running ‘test-all.R’ [0s/0s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  
  Failed -------------------------------------------------------------------------
  1. Error: samme returns a character vector of predicted classes (@test_samme.R#6) 
  Need at least two classes to do classification.
  1: samme(activity ~ ., train, test, 3, ntree = 5, trace = F) at /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/bagRboostR/tests/test_samme.R:6
  2: randomForest(formula, data = t, do.trace = trace, ntree = ntree, mtry = mtry)
  3: randomForest.formula(formula, data = t, do.trace = trace, ntree = ntree, mtry = mtry)
  4: randomForest.default(m, y, ...)
  5: stop("Need at least two classes to do classification.")
  
  DONE ===========================================================================
  Error: Test failures
  In addition: Warning message:
  Placing tests in `inst/tests/` is deprecated. Please use `tests/testthat/` instead 
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: BiSEp
Loading required package: mclust
Package 'mclust' version 5.2.1
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: GOSemSim

GOSemSim v2.0.3  For help: https://guangchuangyu.github.io/GOSemSim

If you use GOSemSim in published research, please cite:
Guangchuang Yu, Fei Li, Yide Qin, Xiaochen Bo, Yibo Wu, Shengqi Wang. GOSemSim: an R package for measuring semantic similarity among GO terms and gene products Bioinformatics 2010, 26(7):976-978

'select()' returned many:1 mapping between keys and columns

Error: processing vignette ‘BiSEp.Snw’ failed with diagnostics:
 chunk 16 (label = packages) 
Error in mgeneSim(unG5, ont = "MF", organism = "human") : 
  unused arguments (ont = "MF", organism = "human")
Execution halted
Error in re-building vignettes:
  ...
! Dimension too large.
\fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa 
                                                  \fb@putboxa #1\fb@afterfra...
l.8929 \end{kframe}
                   
! Dimension too large.
\fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa 
                                                  \fb@putboxa #1\fb@afterfra...
l.8929 \end{kframe}
                   
! Dimension too large.
\fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa 
                                                  \fb@putboxa #1\fb@afterfra...
l.8929 \end{kframe}
                   
! Dimension too large.
\fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa 
                                                  \fb@putboxa #1\fb@afterfra...
l.8929 \end{kframe}
                   
! Dimension too large.
\fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa 
                                                  \fb@putboxa #1\fb@a
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/deeplearning.Rcheck/00install.out’ for details.
Running ‘has-devel.R’ [1s/1s]
  Running ‘test-that.R’ [28s/30s]
Running the tests in ‘tests/test-that.R’ failed.
Last 13 lines of output:
  5: as.vector(object)
  6: find_topic("foofoo")
  7: find_pkg_topic(path, topic)
  8: topic_index(pkg)
  9: build_topic_index(pkg)
  10: invert(lapply(rds, aliases))
  
  Updating collate directive in  /tmp/Rtmp9xWrPG/testCollateOrder/DESCRIPTION 
  
  testthat results ================================================================
  OK: 377 SKIPPED: 10 FAILED: 1
  1. Error: help and ? find files for devtools-loaded packages (@test-help.r#45) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/DNAprofiles.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-patched-gcc/Work/PKGS/FastRWeb.Rcheck/00install.out’ for details.
Running examples in ‘fheatmap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name:  Column Annotations 
> ### Title: Annotations of columns in "fheatmap_data"
> ### Aliases: ' annotation_col '
> ### Keywords: annotation_col
> 
> ### ** Examples
> 
> data(annotation_col)
> fheatmap(fheatmap_data,annotation_col=annotation_col)
Error in theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),  : 
  formal argument "plot.margin" matched by multiple actual arguments
Calls: fheatmap -> draw_tree -> theme_blank -> theme
Execution halted
Running examples in ‘gapfill-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Image
> ### Title: Image Panels
> ### Aliases: Image
> 
> ### ** Examples
> 
> Image(ndvi)
Error in theme(line = element_blank(), strip.background = element_rect(fill = "white",  : 
  formal argument "line" matched by multiple actual arguments
Calls: Image -> theme
Execution halted
Running ‘run-all.R’ [9s/9s]
Running the tests in ‘tests/run-all.R’ failed.
Last 13 lines of output:
  2: compare(object, expected, ...)
  3: Image(ndvi)
  4: theme(line = element_blank(), strip.background = element_rect(fill = "white", color = "white"), 
         strip.text.x = element_text(), strip.text.y = element_text(), axis.ticks = element_blank(), 
         axis.text.x = element_blank(), axis.text.y = element_blank(), axis.title.x = element_blank(), 
         axis.title.y = element_blank(), line = element_blank(), legend.position = "right", 
         panel.border = element_blank(), plot.margin = unit(c(1, 1, 1, 1), "mm"), panel.margin = unit(2, 
             "mm"))
  
  testthat results ================================================================
  OK: 859 SKIPPED: 0 FAILED: 1
  1. Error: Image (@test-Image.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Authors@R field gives persons with no valid roles:
  Mark S.
        Handcock Developer <handcock@stat.ucla.edu>
  Michael S.
        Rendall Developer <mrendall@rand.org>
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/HydeNet.Rcheck/00install.out’ for details.
Found the following significant warnings:
   # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/igraph.Rcheck/00install.out’ for details.
Running examples in ‘imfr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: imf_codes
> ### Title: Retrieve individual database codes
> ### Aliases: imf_codes
> 
> ### ** Examples
> 
> # Retrieve indicators from BOP database
> test = imf_codes(codelist = 'CL_INDICATOR_BOP')

Downloading: 550 B     
Downloading: 550 B     
Downloading: 550 B     
Downloading: 550 B     
Downloading: 550 B     
Downloading: 550 B     Error: lexical error: invalid char in json text.
                                       <html xmlns="http://www.w3.org/
                     (right here) ------^
Execution halted
Running ‘testthat.R’ [0s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  # of Infringing URLs:  19
  # of Copyrighted URLs: 11
  
  1. Failure: Search Works (@tests.R#28) -----------------------------------------
  length(s2) not equal to 2.
  1/1 mismatches
  [1] 1 - 2 == -1
  
  
  testthat results ================================================================
  OK: 4 SKIPPED: 0 FAILED: 1
  1. Failure: Search Works (@tests.R#28) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘mcglm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: anova.mcglm
> ### Title: Anova Tables
> ### Aliases: anova.mcglm
> 
> ### ** Examples
> 
> x1 <- seq(-1, 1, l = 100)
> x2 <- gl(5, 20)
> beta <- c(5, 0, -2, -1, 1, 2)
> X <- model.matrix(~ x1 + x2)
> set.seed(123)
> y <- rnorm(100, mean = X%*%beta, sd = 1)
> data = data.frame("y" = y, "x1" = x1, "x2" = x2)
> fit.anova <- mcglm(c(y ~ x1 + x2), list(mc_id(data)), data = data)
Automatic initial values selected. 
Error in rep(1:n_resp, information$n_betas) : invalid 'times' argument
> anova(fit.anova)
Error in UseMethod("anova") : 
  no applicable method for 'anova' applied to an object of class "try-error"
Calls: anova
Execution halted
Error in re-building vignettes:
  ...
----------------------------------------------------------------------
  mcglm: Multivariate Covariance Generalized Linear Models

  For support, collaboration or bug report, visit: 
    https://github.com/wbonat/mcglm

  mcglm version 0.3.0 (build on 2016-06-06) is now loaded.
----------------------------------------------------------------------
Loading required package: Matrix
Error in rep(1:n_resp, information$n_betas) : invalid ‘times’ argument
Quitting from lines 116-118 (GLMExamples.Rmd) 
Error: processing vignette ‘GLMExamples.Rmd’ failed with diagnostics:
$ operator is invalid for atomic vectors
Execution halted
Running ‘run-base.R’ [292s/290s]
Running the tests in ‘tests/run-base.R’ failed.
Last 13 lines of output:
  testthat results ================================================================
  OK: 2349 SKIPPED: 1 FAILED: 15
  1. Error: downsample wrapper works with xgboost, we had issue #492 (@test_base_downsample.R#38) 
  2. Failure: generateCalibrationData (@test_base_generateCalibration.R#55) 
  3. Failure: generateCalibrationData (@test_base_generateCalibration.R#57) 
  4. Failure: plotFilterValues (@test_base_generateFilterValuesData.R#72) 
  5. Failure: plotFilterValues (@test_base_generateFilterValuesData.R#74) 
  6. Failure: generateLearningCurve (@test_base_generateLearningCurve.R#46) 
  7. Failure: generateLearningCurve (@test_base_generateLearningCurve.R#48) 
  8. Failure: generatePartialDependenceData (@test_base_generatePartialDependence.R#216) 
  9. Failure: generatePartialDependenceData (@test_base_generatePartialDependence.R#219) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  3    z_pos nist_testbed_GF_Agie_1<Device>:path_pos_z<PATH_POSITION>
  Normalized Distance: 27.4341489022279
  Error: `mapped_plot` not equal to lazyLoadDBfetch(c(36521L, 321L), datafile, compressed, envhook).
  Component "layers": Component 1: Component 3: Component 2: Modes of target, current: function, environment
  Component "layers": Component 1: Component 3: Component 2: target, current do not match when deparsed
  Component "layers": Component 1: Component 7: Component 2: Modes of target, current: function, environment
  Component "layers": Component 1: Component 7: Component 2: target, current do not match when deparsed
  Component "layers": Component 1: Component 9: Component 2: Modes of target, current: function, environment
  Component "layers": Component 1: Component 9: Component 2: target, current do not match when deparsed
  Component "layers": Component 1: Component 12: Modes of target, current: function, environment
  Component "layers": Component 1: Component 12: target, current do not match when deparsed
  Component "layers": Component 2: Component 3: Component 2: Modes of target, current: fun
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  7: readoqcsv(system.file("extdata", "testdata.csv", package = "OptiQuantR"))
  8: `$<-`(`*tmp*`, "id", value = 1:11)
  9: `$<-.data.table`(`*tmp*`, "id", value = 1:11)
  10: `$<-.data.frame`(x, name, value)
  11: stop(sprintf(ngettext(N, "replacement has %d row, data has %d", "replacement has %d rows, data has %d"), 
         N, nrows), domain = NA)
  
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 3
  1. Error: output has 17 columns (@test_tableproperties.R#27) 
  2. Error: output has the right column names (@test_tableproperties.R#31) 
  3. Error: output is of class data.frame & data.table (@test_tableproperties.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  testthat results ================================================================
  OK: 154 SKIPPED: 0 FAILED: 12
  1. Failure: createTable (@test-poplite.R#252) 
  2. Failure: createTable (@test-poplite.R#252) 
  3. Failure: createTable (@test-poplite.R#252) 
  4. Failure: createTable (@test-poplite.R#252) 
  5. Failure: insertStatement (@test-poplite.R#330) 
  6. Failure: insertStatement (@test-poplite.R#350) 
  7. Failure: insertStatement (@test-poplite.R#330) 
  8. Failure: insertStatement (@test-poplite.R#350) 
  9. Failure: insertStatement (@test-poplite.R#330) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Error: evaluation nested too deeply: infinite recursion / options(expressions=)?
Execution halted
LastFirstDiscreteSparse: Error while checking: evaluation nested too
  deeply: infinite recursion / options(expressions=)?
Found the following significant warnings:
  Warning: replacing previous import ‘ape::complement’ by ‘Biostrings::complement’ when loading ‘RADami’
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RADami.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API call to R: ‘R_GlobalContext’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  libjson/Source/JSONGlobals.h:43:50: warning: invoking macro json_global_decl argument 3: empty macro arguments are undefined in ISO C++98 [-Wpedantic]
  libjson/Source/JSONGlobals.h:44:49: warning: invoking macro json_global_decl argument 3: empty macro arguments are undefined in ISO C++98 [-Wpedantic]
  JSONValidator.cpp:394:105: warning: invoking macro JSON_ASSERT_SAFE argument 3: empty macro arguments are undefined in ISO C++98 [-Wpedantic]
  JSONValidator.cpp:397:104: warning: invoking macro JSON_ASSERT_SAFE argument 3: empty macro arguments are undefined in ISO C++98 [-Wpedantic]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RJSONIO.Rcheck/00install.out’ for details.
Running ‘RMongo-Ex.R’ [2s/1s]
Running the tests in ‘tests/RMongo-Ex.R’ failed.
Last 13 lines of output:
  +   dbRemoveQuery(mongo, "test_data", '{}')
  +   dbDisconnect(mongo)
  +   
  +   # print(length(output))
  +   print(as.character(output[1]))
  + 
  +   checkEquals("{ \"_id\" : \"bar\"}", as.character(output[1]))
  +   # checkEquals("bar", as.character(output[1]))
  + }
  > 
  > test.dbInsertDocument()
  Error in .jcall(rmongo.object@javaMongo, "S", "dbInsertDocument", collection,  : 
    com.mongodb.MongoException$Network: Write operation to server /127.0.0.1:27017 failed on database test
  Calls: test.dbInsertDocument ... dbInsertDocument -> dbInsertDocument -> .jcall -> .jcheck -> .Call
  Execution halted
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: S3 methods ‘[.xml_missing’, ‘[.xml_nodeset’, ‘[[.xml_missing’, ‘xml_attr<-.xml_missing’, ‘xml_attr<-.xml_node’, ‘xml_attr<-.xml_nodeset’, ‘xml_attrs<-.xml_missing’, ‘xml_attrs<-.xml_node’, ‘xml_attrs<-.xml_nodeset’, ‘xml_name<-.xml_missing’, ‘xml_name<-.xml_node’, ‘xml_name<-.xml_nodeset’, ‘xml_text<-.xml_missing’, ‘xml_text<-.xml_node’, ‘xml_text<-.xml_nodeset’, ‘as.character.xml_document’, ‘as.character.xml_missing’, ‘as.character.xml_node’, ‘as.character.xml_nodeset’, ‘as_list.xml_missing’, ‘as_list.xml_node’, ‘as_list.xml_nodeset’, ‘as_xml_document.character’, ‘as_xml_document.connection’, ‘as_xml_document.list’, ‘as_xml_document.raw’, ‘as_xml_document.response’, ‘as_xml_document.xml_document’, ‘as_xml_document.xml_node’, ‘as_xml_document.xml_nodeset’, ‘format.xml_node’, ‘is.na.xml_missing’, ‘is.na.xml_node’, ‘is.na.xml_nodeset’, ‘nodeset_apply.x [... truncated]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/selectr.Rcheck/00install.out’ for details.
Running examples in ‘sidier-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: double.plot
> ### Title: Haplotype and population networks including mutations and
> ###   haplotype frequencies.
> ### Aliases: double.plot
> 
> ### ** Examples
> 
> cat(">Population1_sequence1",
+ "TTATAAAATCTA----TAGC",
+ ">Population1_sequence2",
+ "TAAT----TCTA----TAAC",
+ ">Population1_sequence3",
+ "TTATAAAAATTA----TAGC",
+ ">Population1_sequence4",
+ "TAAT----TCTA----TAAC",
+ ">Population2_sequence1",
+ "TTAT----TCGAGGGGTAGC",
+ ">Population2_sequence2",
+ "TAAT----TCTA----TAAC",
+ ">Population2_sequence3",
+ "TTATAAAA--------TAGC",
+ ">Population2_sequence4",
+ "TTAT----TCGAGGGGTAGC",
+ ">Population3_sequence1",
+ "TTAT----TCGA----TAGC",
+ ">Population3_sequence2",
+ "TTAT----TCGA----TAGC",
+ ">Population3_sequence3",
+ "TTAT----TCGA----TAGC",
+ ">Population3_sequence4",
+ "TTAT----TCGA----TAGC",
+      file = "ex2.fas", sep = "\n")
> library(ape)
> double.plot(align=read.dna(file="ex2.fas",format="fasta"))
Warning in pie.network(align = align, indel.method = indel.method, substitution.model = substitution.model,  :
  Population names defined by algorithm between character 1 and the first symbol '_' in sequences name.
Error in rep(colnames(pop2)[which(pop2 != 0)], pop2[which(pop2 != 0)]) : 
  invalid 'times' argument
Calls: double.plot -> pie.network -> pop.dist
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 170-174 (pairwiseSNHT.Rnw) 
Error: processing vignette ‘pairwiseSNHT.Rnw’ failed with diagnostics:
invalid ‘times’ argument
Execution halted
newXMLDoc: no visible binding for global variable ‘doc’
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
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   5.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 70-71 (ACSN-vignette.Rmd) 
Error: processing vignette 'ACSN-vignette.Rmd' failed with diagnostics:
the table must have a header (column names)
Execution halted
Running examples in ‘ActuDistns-Ex.R’ failed
The error most likely occurred in:

> ### Name: dgumbeld
> ### Title: Gumbel pdf
> ### Aliases: dgumbeld
> ### Keywords: Gumbel distribution
> 
> ### ** Examples
> x=runif(10,min=0,max=1)
> y=dgumbeld(x)
Error in dgumbel(x, mu = mu, sigma = sigma) : 
  unused arguments (mu = mu, sigma = sigma)
Calls: dgumbeld -> ifelse -> dgumbel
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data       2.8Mb
    pictures   2.5Mb
Running ‘testthat.R’ [29s/48s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > suppressPackageStartupMessages(library(adegenet))
  > test_check("adegenet")
  
   *** caught segfault ***
  address 6000000, cause 'memory not mapped'
Package suggested but not available for checking: ‘microbenchmark’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 15-19 (ALA4R.Rmd) 
Error: processing vignette 'ALA4R.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    data  15.5Mb
installed size is 35.5Mb
  sub-directories of 1Mb or more:
    R  35.4Mb
Running ‘allFormats.R’
Running the tests in ‘tests/allFormats.R’ failed.
Complete output:
  > options(digits.secs=6, width=70)
  > 
  > library(anytime)
  > 
  > ref <- format(as.POSIXct(c("2016-09-01 10:11:12", "2016-09-01 10:11:12.345678"),
  +                          "%Y-%m-%d %H:%M:%0S"))
  Warning messages:
  1: In strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
    unknown timezone '%Y-%m-%d %H:%M:%0S'
  2: In as.POSIXct.POSIXlt(x) : unknown timezone '%Y-%m-%d %H:%M:%0S'
  3: In strptime(x, f, tz = tz) : unknown timezone '%Y-%m-%d %H:%M:%0S'
  4: In as.POSIXct.POSIXlt(as.POSIXlt(x, tz, ...), tz, ...) :
    unknown timezone '%Y-%m-%d %H:%M:%0S'
  5: In as.POSIXlt.POSIXct(x, tz) : unknown timezone '%Y-%m-%d %H:%M:%0S'
  > 
  > 
  > stopifnot(ref == format(anytime(c("2016-09-01 10:11:12", "2016-09-01 10:11:12.345678"))))
  Error: ref == format(anytime(c("2016-09-01 10:11:12", "2016-09-01 10:11:12.345678"))) are not all TRUE
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 17-67 (performance.Rmd) 
Error: processing vignette 'performance.Rmd' failed with diagnostics:
there is no package called 'microbenchmark'
Execution halted
Package suggested but not available for checking: ‘kebabs’
Package required but not available: ‘geoR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘AR1seg-Ex.R’ failed
The error most likely occurred in:

> ### Name: AR1seg-package
> ### Title: Segmentation of an AR(1) Gaussian process
> ### Aliases: AR1seg-package AR1seg
> 
> ### ** Examples
> 
> library(AR1seg)
> data(y)
> res=AR1seg_func(y,Kmax=15,rho=TRUE)
Error in cumsum(datasize)[breaks[k, 1:k]] : 
  only 0's may be mixed with negative subscripts
Calls: AR1seg_func -> Segmentor -> Segmentor.default
Execution halted
Package suggested but not available for checking: ‘pdInfoBuilder’
Packages suggested but not available for checking:
  ‘EBImage’ ‘sfit’ ‘expectile’ ‘HaarSeg’ ‘mpcbs’
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 16-27 (Benchmarks.Rmd) 
Error: processing vignette 'Benchmarks.Rmd' failed with diagnostics:
there is no package called 'microbenchmark'
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/BayesFM.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/ripley/R/packages/tests32/bayesImageS.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R     1.7Mb
    doc   2.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 2-14 (./children/SETTINGS-knitr.txt) 
Quitting from lines NA-14 (./children/SETTINGS-knitr.txt) 
Error: processing vignette 'MCMC-diagnostics.Rmd' failed with diagnostics:
object 'params' not found
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.7Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/BCSub.Rcheck/00install.out’ for details.
installed size is 117.7Mb
  sub-directories of 1Mb or more:
    include  117.6Mb
Running examples in ‘BigQuic-Ex.R’ failed
The error most likely occurred in:

> ### 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 fffffff8, 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 ...
Error in re-building vignettes:
  ...
Loading required package: BiSEp
Loading required package: mclust
Package 'mclust' version 5.2.1
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: GOSemSim

GOSemSim v2.0.3  For help: https://guangchuangyu.github.io/GOSemSim

If you use GOSemSim in published research, please cite:
Guangchuang Yu, Fei Li, Yide Qin, Xiaochen Bo, Yibo Wu, Shengqi Wang. GOSemSim: an R package for measuring semantic similarity among GO terms and gene products Bioinformatics 2010, 26(7):976-978

'select()' returned many:1 mapping between keys and columns

Error: processing vignette 'BiSEp.Snw' failed with diagnostics:
 chunk 16 (label = packages) 
Error in mgeneSim(unG5, ont = "MF", organism = "human") : 
  unused arguments (ont = "MF", organism = "human")
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 40-46 (profiling.Rmd) 
Error: processing vignette 'profiling.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Invalid maximum heap size: -Xmx4G
The specified size exceeds the maximum representable size.
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘gtools’ ‘knitr’ ‘nnet’ ‘parallel’ ‘rJava’ ‘reshape’
  ‘rmarkdown’ ‘shinyjs’
  All declared Imports should be used.
Missing or unexported object: ‘xgboost::predict’
File ‘BMN/libs/BMN.so’:
  Found ‘__1cDstdEcout_’, 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.
Installation failed.
See ‘/home/ripley/R/packages/tests32/bootTimeInference.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 67-80 (benchmarks.Rmd) 
Error: processing vignette 'benchmarks.Rmd' failed with diagnostics:
there is no package called 'microbenchmark'
Execution halted
Package which this enhances but not available for checking: ‘FastRWeb’
Installation failed.
See ‘/home/ripley/R/packages/tests32/CampaR1.Rcheck/00install.out’ for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data     1.8Mb
    models   2.3Mb
Package required but not available: ‘V8’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   6.2Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extdata   9.8Mb
Found the following significant warnings:
  "cec_r.c", line 192: warning: improper pointer/integer combination: op "="
  "cec_r.c", line 267: warning: improper pointer/integer combination: op ":"
See ‘/home/ripley/R/packages/tests32/CEC.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 160-170 (checkmate.Rmd) 
Error: processing vignette 'checkmate.Rmd' failed with diagnostics:
there is no package called 'microbenchmark'
Execution halted
installed size is 60.0Mb
  sub-directories of 1Mb or more:
    data  60.0Mb
Package suggested but not available for checking: ‘js’
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    extdata  12.5Mb
Running ‘testthat.R’ [90m/45m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ClusterR)
  Loading required package: gtools
  > 
  > test_check("ClusterR")
  Error: C stack usage  106913796 is too close to the limit
  Warning: stack imbalance in '$', 150 then 155
  Warning: stack imbalance in '{', 146 then 149
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
terminate called after throwing an instance of 'std::logic_error'
  what():  Mat::elem(): index out of bounds
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
    pdf   2.8Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data     3.8Mb
    exdata   5.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    java   5.2Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    app   2.9Mb
    doc   2.2Mb
Package suggested but not available for checking: ‘RandomFields’
Package unavailable to check Rd xrefs: ‘RandomFields’
Running examples in ‘CompRandFld-Ex.R’ failed
The error most likely occurred in:

> ### Name: Covariogram
> ### Title: Computes covariance, variogram and extremal coefficient
> ###   functions
> ### Aliases: Covariogram
> ### Keywords: Composite
> 
> ### ** Examples
> 
> library(CompRandFld)
> library(RandomFields)
Error in library(RandomFields) : 
  there is no package called ‘RandomFields’
Execution halted
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data      6.5Mb
    extdata   2.8Mb
Package required but not available: ‘RandomFields’

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

> ### Name: coocnet
> ### Title: coocnet
> ### Aliases: coocnet
> 
> ### ** Examples
> 
> cooccurNetwork  = coocnet(dataFile=getexample(dataType="protein"), dataType="protein")
reading file......
completed. (10,329)
preprocess file......Error in if (pred >= memsize * alpha || ncol > 150 || (nrow > 30000 &  : 
  missing value where TRUE/FALSE needed
Calls: coocnet ... cooccur.dataprepreprocess.preprocess -> inmemoryflag
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 176-178 (Extending-cooccurNet.Rmd) 
Error: processing vignette 'Extending-cooccurNet.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 775-800 (CopulaDTA_Vignette.Rmd) 
Error: processing vignette 'CopulaDTA_Vignette.Rmd' failed with diagnostics:
formal argument "axis.title.y" matched by multiple actual arguments
Execution halted
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   7.4Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/corehunter.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/ripley/R/packages/tests32/csp.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Observations with missing time information found - removing 1 rows
Discrete time points created:  3
Warning:  measures of time dependent predictor 1 occurring at final measurement occasion removed, as they have no time to impact processes
Extracting first non-missing value for time independent predictors
imputedefs==FALSE (default, recommended) so setting observations with no time value to NA
Running ctsemCarefulFit with 16 parameters

 *** caught segfault ***
address 8, cause 'memory not mapped'
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 50-109 (cubature.Rmd) 
Error: processing vignette 'cubature.Rmd' failed with diagnostics:
there is no package called 'microbenchmark'
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/CuCubes.Rcheck/00install.out’ for details.
installed size is 32.2Mb
  sub-directories of 1Mb or more:
    extdata  32.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 177-179 (cycling_data_analysis.Rmd) 
Error: processing vignette 'cycling_data_analysis.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 27-38 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running ‘testthat.R’ [17s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(DataExplorer)
  > 
  > test_check("DataExplorer")
  1. Error: test if report is generated (@test-generate-report.r#8) --------------
  pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  1: GenerateReport(iris, output_file = file_name, output_dir = dir_name, quiet = TRUE) at testthat/test-generate-report.r:8
  2: render(input = report_dir, output_file = output_file, output_dir = output_dir, intermediates_dir = output_dir, 
         params = list(data = input_data, fun_options = list()), ...)
  3: pandoc_available(required_pandoc, error = TRUE)
  4: stop(paste(msg, collapse = " "), call. = FALSE)
  
  testthat results ================================================================
  OK: 34 SKIPPED: 0 FAILED: 1
  1. Error: test if report is generated (@test-generate-report.r#8) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot625429334c8a.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot625429334c8a.png': No such file or directory
Quitting from lines 512-515 (data.tree.Rmd) 
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    sample_data   3.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.9Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/deeplearning.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Rcpp

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Joining, by = "gene"
Joining, by = "cell"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "cell"
Joining, by = c("cell", "capture")
Have 35 cells after filtering
Joining, by = "cell"
Have 20 genes after filtering
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "cell"
Joining, by = c("cell", "capture")
Loading pre-compiled model from /home/ripley/R/Lib32/DeLorean/extdata/exact-sizes.rds
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    2.0Mb
    help   1.3Mb
Packages suggested but not available for checking:
  ‘gurobi’ ‘Rcplex’ ‘Rsymphony’
Package unavailable to check Rd xrefs: ‘Rmosek’
Installation failed.
See ‘/home/ripley/R/packages/tests32/deTestSet.Rcheck/00install.out’ for details.
Running ‘has-devel.R’
  Running ‘test-that.R’ [251s/253s]
Running the tests in ‘tests/test-that.R’ failed.
Complete output:
  > library(testthat)
  > test_check("devtools")
  Loading required package: devtools
  1. Error: help and ? find files for devtools-loaded packages (@test-help.r#45) -
  invalid 'times' argument
  1: expect_true(!is.null(find_topic("foofoo"))) at testthat/test-help.r:45
  2: expect(identical(as.vector(object), TRUE), sprintf("%s isn't true.", lab), info = info)
  3: as.expectation(exp, ..., srcref = srcref)
  4: identical(as.vector(object), TRUE)
  5: as.vector(object)
  6: find_topic("foofoo")
  7: find_pkg_topic(path, topic)
  8: topic_index(pkg)
  9: build_topic_index(pkg)
  10: invert(lapply(rds, aliases))
  
  Updating collate directive in  /tmp/RtmpcPaiVD/testCollateOrder/DESCRIPTION 
  
  testthat results ================================================================
  OK: 377 SKIPPED: 10 FAILED: 1
  1. Error: help and ? find files for devtools-loaded packages (@test-help.r#45) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/dfphase1.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘DiagrammeRsvg’ ‘rsvg’
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    extdata       2.5Mb
    htmlwidgets   5.0Mb
    img           3.4Mb
Package required but not available: ‘deTestSet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    2.2Mb
Error in re-building vignettes:
  ...
Warning in buildVignettes(dir = "/home/ripley/R/packages/tests32/dMod.Rcheck/vign_test/dMod") :
  Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/framework.Rmd’
(Is a VignetteBuilder field missing?)
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: cOde
Loading required package: trust
Loading required package: ggplot2
Loading required package: stringr

Attaching package: 'dMod'

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

    profile

"jak-stat.c", line 6: zero or negative subscript
"jak-stat.c", line 7: zero or negative subscript
cc: acomp failed for jak-stat.c
make: Fatal error: Command failed for target `jak-stat.o'
Current working directory /home/ripley/R/packages/tests32/dMod.Rcheck/vign_test/dMod/vignettes
Warning: running command '/home/ripley/R/cc/bin/R CMD SHLIB jak-stat.c' had status 1 and error message 'Illegal seek'
"jak-stat_s.c", line 6: zero or negative subscript
"jak-stat_s.c", line 7: zero or negative subscript
cc: acomp failed for jak-stat_s.c
make: Fatal error: Command failed for target `jak-stat_s.o'
Current working directory /home/ripley/R/packages/tests32/dMod.Rcheck/vign_test/dMod/vignettes
Warning: running command '/home/ripley/R/cc/bin/R CMD SHLIB jak-stat_s.c' had status 1 and error message 'Illegal seek'
Quitting from lines 71-81 (dMod.Rmd) 
Error: processing vignette 'dMod.Rmd' failed with diagnostics:
unable to load shared object '/home/ripley/R/packages/tests32/dMod.Rcheck/vign_test/dMod/vignettes/jak-stat_s.so':
  ld.so.1: R: fatal: /home/ripley/R/packages/tests32/dMod.Rcheck/vign_test/dMod/vignettes/jak-stat_s.so: open failed: No such file or directory
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/DNAprofiles.Rcheck/00install.out’ for details.
Running examples in ‘docopulae-Ex.R’ failed
The error most likely occurred in:

> ### Name: rowmatch
> ### Title: Row Matching
> ### Aliases: rowmatch
> 
> ### ** Examples
> 
> a = as.matrix(expand.grid(as.double(2:3), as.double(3:6)))
> a = a[sample(nrow(a)),]
> a
     Var1 Var2
[1,]    2    4
[2,]    3    6
[3,]    3    4
[4,]    2    5
[5,]    2    3
[6,]    2    6
[7,]    3    3
[8,]    3    5
> 
> b = as.matrix(expand.grid(as.double(3:4), as.double(2:5)))
> b = b[sample(nrow(b)),]
> b
     Var1 Var2
[1,]    4    4
[2,]    3    2
[3,]    4    2
[4,]    3    5
[5,]    3    3
[6,]    4    5
[7,]    4    3
[8,]    3    4
> 
> i = rowmatch(a, b)
Error in ordt[i] : subscript too large for 32-bit R
Calls: rowmatch
Execution halted
Running ‘testthat.R’ [127s/127s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(docopulae)
  > 
  > test_check("docopulae")
  1. Error: rowmatch works in trivial cases (@test_base.R#255) -------------------
  subscript too large for 32-bit R
  1: expect_equal(rowmatch(b, a), as.integer(c(NA, NA))) at testthat/test_base.R:255
  2: compare(object, expected, ...)
  3: rowmatch(b, a)
  
  2. Error: rowmatch works for a random example (@test_base.R#279) ---------------
  subscript too large for 32-bit R
  1: rowmatch(x, s) at testthat/test_base.R:279
  
  testthat results ================================================================
  OK: 142 SKIPPED: 0 FAILED: 2
  1. Error: rowmatch works in trivial cases (@test_base.R#255) 
  2. Error: rowmatch works for a random example (@test_base.R#279) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘rgbif’
Packages suggested but not available for checking:
  ‘RMySQL’ ‘microbenchmark’
Packages unavailable to check Rd xrefs: ‘microbenchmark’, ‘RMySQL’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 23-25 (DT.Rmd) 
Error: processing vignette 'DT.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    models   4.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   2.2Mb
Error in re-building vignettes:
  ...
Loading required package: foreign
This is vegdata 0.9

No Turbowin installation path found. 

############################################################
Turboveg root directory is set to "/tmp/RtmpAcaWk3"
If you want to change this use: options(tv_home="<path_to_your_Turbowin_root>")
############################################################
Quitting from lines 51-61 (eHOF.Rnw) 
Error: processing vignette 'eHOF.Rnw' failed with diagnostics:
unsupported conversion from 'CP437' to ''
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    examples   4.9Mb
Running examples in ‘elementR-Ex.R’ failed
The error most likely occurred in:

> ### Name: elementR_project
> ### Title: Object elementR_project
> ### Aliases: elementR_project
> 
> ### ** Examples
> 
> ## create a new elementR_repStandard object based on the "filePath" 
> ## from a folder containing sample replicate
> 
> filePath <- system.file("Example_Session", package="elementR")
> 
> exampleProject <- elementR_project$new(filePath)

 *** caught segfault ***
address f02bc, cause 'invalid permissions'
Running ‘testthat.R’ [150s/150s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(emdi)
  Loading required package: maptools
  Loading required package: sp
  Checking rgeos availability: FALSE
   	Note: when rgeos is not available, polygon geometry 	computations in maptools depend on gpclib,
   	which has a restricted licence. It is disabled by default;
   	to enable gpclib, type gpclibPermit()
  > 
  > test_check("emdi")
  
   Bootstrap started                                                                        
   Bootstrap completed                                                                      1. Failure: Does parametric_bootstrap return the benchmark results? (@test_mse_estimation.R#44) 
  MSE[, "Quantile_10"] not equal to as.numeric(as.character(ebp_MSE_bc[, "quant10"])).
  5/5 mismatches (average diff: 0.0552)
  [1]  187158 -  187158 == -0.011422
  [2]   94721 -   94721 ==  0.000952
  [3]  610685 -  610685 == -0.048113
  [4]  355750 -  355750 ==  0.024758
  [5] 1737092 - 1737092 == -0.190909
  
  
  testthat results ================================================================
  OK: 19 SKIPPED: 0 FAILED: 1
  1. Failure: Does parametric_bootstrap return the benchmark results? (@test_mse_estimation.R#44) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘emIRT-Ex.R’ failed
The error most likely occurred in:

> ### Name: dynIRT
> ### Title: Dynamic IRT estimation via Variational Inference
> ### Aliases: dynIRT
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> 
> ### Replication of Martin-Quinn Judicial Ideology Scores
> ### Based on July 23, 2014 (2014 Release 01) release of the Supreme Court Database
> ### Start values and priors based on replication code provided by Kevin Quinn
> 
> data(mq_data)
> 
> ## Estimate dynamic variational model using dynIRT()
> lout <- dynIRT(.data = mq_data$data.mq,
+                     .starts = mq_data$cur.mq,
+                     .priors = mq_data$priors.mq,
+                     .control = {list(
+                     threads = 1,
+                     verbose = TRUE,
+                     thresh = 1e-6,
+ 		    maxit=500
+                     )})

==================== 
dynIRT: Dynamic IRT via Variational Inference


error: Mat::init(): size is fixed and hence cannot be changedterminate called after throwing an instance of 'std::logic_error'
  what():  Mat::init(): size is fixed and hence cannot be changed
installed size is  7.5Mb
  sub-directories of 1Mb or more:
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    xsd   5.9Mb
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  ...
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sh: +RTS:  not found
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Execution halted
Package suggested but not available for checking: ‘ggtree’
Error in re-building vignettes:
  ...
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Execution halted
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installed size is  7.9Mb
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    help   3.3Mb
Package suggested but not available for checking: ‘RCytoscape’
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installed size is  5.3Mb
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    help   1.0Mb
installed size is 11.7Mb
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Running examples in ‘expm-Ex.R’ failed
The error most likely occurred in:

> ### Name: logm
> ### Title: Matrix Logarithm
> ### Aliases: logm
> ### Keywords: algebra math
> 
> ### ** Examples
> 
> m <- diag(2)
> logm(m)
     [,1] [,2]
[1,]    0    0
[2,]    0    0
> expm(logm(m))
     [,1] [,2]
[1,]    1    0
[2,]    0    1
> 
> ## Here, logm() is barely defined, and Higham08 has needed an amendment
> ## in order for not to loop forever:
> D0 <- diag(x=c(1, 0.))
> (L. <- logm(D0))
Warning in logm.Higham08(x) :
  Inverse scaling did not work (t = 1).
The matrix logarithm may not exist for this matrix.Setting m = 3 arbitrarily.
     [,1]     [,2]
[1,]    0        0
[2,]    0 -9576994
> stopifnot( all.equal(D0, expm(L.)) )
> 
> ## A matrix for which clearly no logm(.) exists:
> (m <- cbind(1:2, 1))
     [,1] [,2]
[1,]    1    1
[2,]    2    1
> (l.m <- logm(m)) ## all NA
Warning in sqrt(S[ij, ij]) : NaNs produced
Error in solve.default(X[ii, ii] + X[ij, ij], S[ii, ij] - sumU) : 
  system is computationally singular: reciprocal condition number = 0
Calls: logm ... logm.Higham08 -> rootS -> solve -> solve -> solve.default
Execution halted
Running examples in ‘ExtDist-Ex.R’ failed
The error most likely occurred in:

> ### Name: eval.estimation
> ### Title: Parameter Estimation Evaluation.
> ### Aliases: eval.estimation
> 
> ### ** Examples
> 
> eval.estimation(rdist=rNormal,edist=eNormal,n = 100, rep.num = 50,
+ params = list(mean = 1,sd = 5))
Error : Hessian function might be wrong - check it! 

Error : Hessian function might be wrong - check it! 

Error : Hessian function might be wrong - check it! 

Error : Hessian function might be wrong - check it! 

Error : Hessian function might be wrong - check it! 

Error : Hessian function might be wrong - check it! 

Error in eval(expr, envir, enclos) : object 'value' not found
Calls: eval.estimation ... edist -> wmle -> with -> with.default -> eval -> eval
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/FactoRizationMachines.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘Rserve’
Installation failed.
See ‘/home/ripley/R/packages/tests32/FastRWeb.Rcheck/00install.out’ for details.
Running examples in ‘fheatmap-Ex.R’ failed
The error most likely occurred in:

> ### Name:  Column Annotations 
> ### Title: Annotations of columns in "fheatmap_data"
> ### Aliases: ' annotation_col '
> ### Keywords: annotation_col
> 
> ### ** Examples
> 
> data(annotation_col)
> fheatmap(fheatmap_data,annotation_col=annotation_col)
Error in theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),  : 
  formal argument "plot.margin" matched by multiple actual arguments
Calls: fheatmap -> draw_tree -> theme_blank -> theme
Execution halted
Error in re-building vignettes:
  ...
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  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 2-23 (Best_Prectices.Rmd) 
Error: processing vignette 'Best_Prectices.Rmd' failed with diagnostics:
could not find function "doc_date"
Execution halted
Packages suggested but not available for checking:
  ‘microbenchmark’ ‘multipanelfigure’
Installation failed.
See ‘/home/ripley/R/packages/tests32/FLSSS.Rcheck/00install.out’ for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    fonts   6.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    fonts   7.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 168-169 (formattable-data-frame.Rmd) 
Error: processing vignette 'formattable-data-frame.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running examples in ‘fractaldim-Ex.R’ failed
The error most likely occurred in:

> ### Name: fd.estim.method
> ### Title: Estimation of Fractal Dimension via Specific Methods
> ### Aliases: fd.estim.method fd.estim.variation fd.estim.variogram
> ###   fd.estim.madogram fd.estim.rodogram fd.estim.genton fd.estim.incr1
> ###   fd.estim.hallwood fd.estim.boxcount fd.estim.periodogram
> ###   fd.estim.dctII fd.estim.wavelet fd.estim.transect.var
> ###   fd.estim.transect.incr1 fd.estim.isotropic fd.estim.squareincr
> ###   fd.estim.filter1
> ### Keywords: ts spatial
> 
> ### ** Examples
> 
> library(RandomFields)
Error in library(RandomFields) : 
  there is no package called ‘RandomFields’
Execution halted
Running ‘run_tests.R’
Running the tests in ‘tests/run_tests.R’ failed.
Complete output:
  > library(fractaldim)
  Loading required package: abind
  > library(RandomFields)
  Error in library(RandomFields) : 
    there is no package called 'RandomFields'
  Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R   5.8Mb
Package unavailable to check Rd xrefs: ‘RMark’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 90-102 (sparse_matrices.Rmd) 
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there is no package called 'microbenchmark'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
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Quitting from lines 604-605 (futureheatwaves.Rmd) 
Error: processing vignette 'futureheatwaves.Rmd' failed with diagnostics:
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Execution halted
Package suggested but not available for checking: ‘geoR’
Package suggested but not available for checking: ‘R2BayesX’
Running examples in ‘gamsel-Ex.R’ failed
The error most likely occurred in:

> ### Name: gamsel
> ### Title: Fit Regularization Path for Gaussian or Binomial Generalized
> ###   Additive Model
> ### Aliases: gamsel
> ### Keywords: regression smooth nonparametric
> 
> ### ** Examples
> 
> data=gendata(n=500,p=12,k.lin=3,k.nonlin=3,deg=8,sigma=0.5)
> attach(data)
> bases=pseudo.bases(X,degree=10,df=6)
> # Gaussian gam
> gamsel.out=gamsel(X,y,bases=bases)
> par(mfrow=c(1,2),mar=c(5,4,3,1))
> summary(gamsel.out)
> gamsel.cv=cv.gamsel(X,y,bases=bases)
> par(mfrow=c(1,1))
> plot(gamsel.cv)
> par(mfrow=c(3,4))
> plot(gamsel.out,newx=X,index=20)
> # Binomial model
> gamsel.out=gamsel(X,yb,family="binomial")
> par(mfrow=c(1,2),mar=c(5,4,3,1))
> summary(gamsel.out)

 *** caught segfault ***
address 1000, cause 'memory not mapped'
Running examples in ‘gapfill-Ex.R’ failed
The error most likely occurred in:

> ### Name: Image
> ### Title: Image Panels
> ### Aliases: Image
> 
> ### ** Examples
> 
> Image(ndvi)
Error in theme(line = element_blank(), strip.background = element_rect(fill = "white",  : 
  formal argument "line" matched by multiple actual arguments
Calls: Image -> theme
Execution halted
Running ‘run-all.R’ [139s/139s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check('gapfill')
  Loading required package: gapfill
  Loading required package: ggplot2
  1. Error: Image (@test-Image.R#5) ----------------------------------------------
  formal argument "line" matched by multiple actual arguments
  1: expect_equal(class(Image(ndvi)), c("gg", "ggplot")) at testthat/test-Image.R:5
  2: compare(object, expected, ...)
  3: Image(ndvi)
  4: theme(line = element_blank(), strip.background = element_rect(fill = "white", color = "white"), 
         strip.text.x = element_text(), strip.text.y = element_text(), axis.ticks = element_blank(), 
         axis.text.x = element_blank(), axis.text.y = element_blank(), axis.title.x = element_blank(), 
         axis.title.y = element_blank(), line = element_blank(), legend.position = "right", 
         panel.border = element_blank(), plot.margin = unit(c(1, 1, 1, 1), "mm"), panel.margin = unit(2, 
             "mm"))
  
  testthat results ================================================================
  OK: 859 SKIPPED: 0 FAILED: 1
  1. Error: Image (@test-Image.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    data    3.8Mb
    doc     3.1Mb
    tests   2.6Mb
Error in re-building vignettes:
  ...
Warning in packageDescription("gputools") :
  no package 'gputools' was found
Error: processing vignette 'gcbd.Rnw' failed with diagnostics:
at gcbd.Rnw:860, subscript out of bounds
Execution halted
Package unavailable to check Rd xrefs: ‘gcmr’
Installation failed.
See ‘/home/ripley/R/packages/tests32/gdpc.Rcheck/00install.out’ for details.
Running ‘test-all.R’
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > library(sp)
  > library(gstat)
  > library(geoR)
  Error in library(geoR) : there is no package called 'geoR'
  Execution halted
Running ‘testthat.R’ [23s/23s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(GeneralTree)
  Loading required package: R6
  > 
  > test_check("GeneralTree")
  1. Error: plotting a tree works (@test_plot.R#64) ------------------------------
  'create_nodes' is not an exported object from 'namespace:DiagrammeR'
  1: expect_identical(plot(tree)$x$diagram, diagram) at testthat/test_plot.R:64
  2: identical(object, expected)
  3: plot(tree)
  4: plot.GeneralTree(tree)
  5: generate_grViz(x, ...)
  6: do.call(DiagrammeR::create_nodes, create_nodes_call)
  7: DiagrammeR::create_nodes
  8: getExportedValue(pkg, name)
  9: stop(gettextf("'%s' is not an exported object from 'namespace:%s'", name, getNamespaceName(ns)), 
         call. = FALSE, domain = NA)
  
  testthat results ================================================================
  OK: 118 SKIPPED: 0 FAILED: 1
  1. Error: plotting a tree works (@test_plot.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 102-103 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
'create_nodes' is not an exported object from 'namespace:DiagrammeR'
Execution halted
installed size is  5.9Mb
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    exdata   5.3Mb
Package suggested but not available for checking: ‘reactome.db’
Packages suggested but not available for checking: ‘geoR’ ‘geoRglm’
Package suggested but not available for checking: ‘geojsonlint’
Package unavailable to check Rd xrefs: ‘geojsonlint’
Running examples in ‘geojson-Ex.R’ failed
The error most likely occurred in:

> ### Name: as.geojson
> ### Title: Geojson class
> ### Aliases: as.geojson as.geojson,SpatialLines-method
> ###   as.geojson,SpatialLinesDataFrame-method
> ###   as.geojson,SpatialPoints-method
> ###   as.geojson,SpatialPointsDataFrame-method
> ###   as.geojson,SpatialPolygons-method
> ###   as.geojson,SpatialPolygonsDataFrame-method
> ###   as.geojson,character-method as.geojson,geojson-method
> ###   as.geojson,json-method
> 
> ### ** Examples
> 
> # character
> as.geojson(geojson_data$featurecollection_point)
<geojson> 
  type:  FeatureCollection 
Warning: 'geojsonlint' not installed, skipping GeoJSON linting
Error in if (checkforpkg("geojsonlint")) { : 
  argument is not interpretable as logical
Calls: <Anonymous> ... geo_bbox.geojson -> geo_bbox -> geo_bbox.character -> hint_geojson
Execution halted
Running ‘test-all.R’
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  > library("geojson")
  
  Attaching package: 'geojson'
  
  The following object is masked from 'package:graphics':
  
      polygon
  
  > test_check("geojson")
  1. Error: geo_bbox works - Point input (@test-geo_bbox.R#5) --------------------
  argument is not interpretable as logical
  1: point(x) at testthat/test-geo_bbox.R:5
  2: point.character(x)
  3: hint_geojson(x)
  
  2. Error: geo_bbox works - Point input (@test-geo_bbox.R#16) -------------------
  argument is not interpretable as logical
  1: multipoint(x) at testthat/test-geo_bbox.R:16
  2: multipoint.character(x)
  3: hint_geojson(x)
  
  Error in if (checkforpkg("geojsonlint")) { : 
    argument is not interpretable as logical
  Calls: test_check ... eval -> eval -> point -> point.character -> hint_geojson
  In addition: Warning message:
  'geojsonlint' not installed, skipping GeoJSON linting 
  testthat results ================================================================
  OK: 36 SKIPPED: 0 FAILED: 2
  1. Error: geo_bbox works - Point input (@test-geo_bbox.R#5) 
  2. Error: geo_bbox works - Point input (@test-geo_bbox.R#16) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'geojson'

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

    polygon

Warning: 'geojsonlint' not installed, skipping GeoJSON linting
Quitting from lines 30-44 (geojson-operations.Rmd) 
Error: processing vignette 'geojson-operations.Rmd' failed with diagnostics:
argument is not interpretable as logical
Execution halted
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    data  27.2Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Packages required but not available: ‘constrainedKriging’ ‘RandomFields’

Package suggested but not available for checking: ‘geoR’

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

Package suggested but not available for checking: ‘geoRglm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘geoR’ ‘RandomFields’

Package which this enhances but not available for checking: ‘INLA’
Packages unavailable to check Rd xrefs: ‘RandomFields’, ‘geoR’
Running ‘testthat.R’ [10s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(gesis)
  > 
  > test_check("gesis")
  1. Failure: get_study_groups() works (@test-availability.R#6) ------------------
  nrow(groups) is not strictly more than 0. Difference: 0
  
  
  testthat results ================================================================
  OK: 3 SKIPPED: 0 FAILED: 1
  1. Failure: get_study_groups() works (@test-availability.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 60-61 (gesis.Rmd) 
Error: processing vignette 'gesis.Rmd' failed with diagnostics:
invalid 'description' argument
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.2Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/ggdmc.Rcheck/00install.out’ for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘readr’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra
Warning: Ignoring unknown aesthetics: data_id, tooltip
Warning: Ignoring unknown aesthetics: data_id, tooltip
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot2fa132805e4b.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot2fa132805e4b.png': No such file or directory
Quitting from lines 28-33 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot1a3e52981b9f.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot1a3e52981b9f.png': No such file or directory
Quitting from lines 13-27 (an_introduction.Rmd) 
Error: processing vignette 'an_introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running ‘testthat.R’ [133s/133s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ggplot2)
  > 
  > test_check("ggplot2")
  1. Failure: inherits timezone from data (@test-scale-date.R#18) ----------------
  sc$timezone not equal to NULL.
  Types not compatible: character vs NULL
  
  
  testthat results ================================================================
  OK: 778 SKIPPED: 0 FAILED: 1
  1. Failure: inherits timezone from data (@test-scale-date.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 125-126 (ggsdc.Rmd) 
Error: processing vignette 'ggsdc.Rmd' failed with diagnostics:
Process terminated
Execution halted
Packages which this enhances but not available for checking:
  ‘geoRglm’ ‘BRugs’
Package unavailable to check Rd xrefs: ‘geoRglm’
Running ‘testthat.R’ [505s/505s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(glmmsr)
  > 
  > test_check("glmmsr")
  1. Error: nSL = 0 gives similar result to Laplace (@test_fit.R#116) ------------
  std::bad_alloc
  1: glmm(response ~ covariate + (1 | cluster) + (1 | group), data = three_level, family = binomial, 
         method = "SR", control = list(nSL = 0), verbose = 0) at testthat/test_fit.R:116
  2: find_lfun_glmm_internal(modfr, method = method, control = con)
  3: find_lfun_SR(modfr, devfun_lme4, nSL = control$nSL, nAGQ = control$nAGQ)
  4: (function (value) 
     {
         if (missing(value)) {
             calibration_parameters__n_sparse_levels__get(self)
         }
         else {
             calibration_parameters__n_sparse_levels__set(self, value)
         }
     })(quote(0))
  5: calibration_parameters__n_sparse_levels__set(self, value)
  
  testthat results ================================================================
  OK: 76 SKIPPED: 0 FAILED: 1
  1. Error: nSL = 0 gives similar result to Laplace (@test_fit.R#116) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: lme4
Loading required package: Matrix
Quitting from lines 373-389 (glmmsr-vignette.Rmd) 
Error: processing vignette 'glmmsr-vignette.Rmd' failed with diagnostics:
std::bad_alloc
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/gmwm.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘pdftools’
Installation failed.
See ‘/home/ripley/R/packages/tests32/goldi.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in genoud(fn = criterion, nvars = d, max = TRUE, pop.size = optimcontrol$pop.size,  :
  Stopped because hard maximum generation limit was hit.
##  rgenoud (Version 5.7-12.4, Build Date: 2015-07-19)
##  See http://sekhon.berkeley.edu/rgenoud for additional documentation.
##  Please cite software as:
##   Walter Mebane, Jr. and Jasjeet S. Sekhon. 2011.
##   ``Genetic Optimization Using Derivatives: The rgenoud package for R.''
##   Journal of Statistical Software, 42(11): 1-26. 
##

This is randtoolbox. For overview, type 'help("randtoolbox")'.
Package suggested but not available for checking: ‘Sxslt’
Running examples in ‘gsl-Ex.R’ failed
The error most likely occurred in:

> ### Name: multimin
> ### Title: Function minimization
> ### Aliases: Multimin multimin multimin.init multimin.iterate
> ###   multimin.restart multimin.fminimizer.size
> ### Keywords: array
> 
> ### ** Examples
> 
> # The Rosenbrock function:
> x0 <- c(-1.2, 1)
> f <- function(x) (1 - x[1])^2 + 100 * (x[2] - x[1]^2)^2
> df <- function(x) c(-2*(1 - x[1]) + 100 * 2 * (x[2] - x[1]^2) * (-2*x[1]),
+                     100 * 2 * (x[2] - x[1]^2))
> 
> # The simple way to call multimin.
> state <- multimin(x0, f, df)
> print(state$x)
[1] 0.999997 0.999994
> 
> # The fine-control way to call multimin.
> state <- multimin.init(x0, f, df, method="conjugate-fr")
> for (i in 1:200)
+ 	state <- multimin.iterate(state)

 *** caught segfault ***
address 20, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
installed size is 64.0Mb
  sub-directories of 1Mb or more:
    java  62.5Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   9.5Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 122-128 (Basic_use.Rmd) 
Error: processing vignette 'Basic_use.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running examples in ‘haven-Ex.R’ failed
The error most likely occurred in:

> ### Name: read_dta
> ### Title: Read and write Stata DTA files.
> ### Aliases: read_dta read_stata write_dta
> 
> ### ** Examples
> 
> path <- system.file("examples", "iris.dta", package = "haven")
> read_dta(path)
Error in df_parse_dta_file(spec, encoding) : 
  Failed to parse /home/ripley/R/Lib32/haven/examples/iris.dta: Invalid file, or file has unsupported features.
Calls: read_dta -> df_parse_dta_file -> .Call
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: plotly
Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Loading required package: viridis

---------------------
Welcome to heatmaply version 0.6.0
Type ?heatmaply for the main documentation.
The github page is: https://github.com/talgalili/heatmaply/

Suggestions and bug-reports can be submitted at: https://github.com/talgalili/heatmaply/issues
Or contact: <tal.galili@gmail.com>

	To suppress this message use:  suppressPackageStartupMessages(library(heatmaply))
---------------------

Quitting from lines 83-85 (heatmaply.Rmd) 
Error: processing vignette 'heatmaply.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 58-81 (replicating-highcharts-demos.Rmd) 
Error: processing vignette 'replicating-highcharts-demos.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package which this enhances but not available for checking: ‘RProtoBuf’
Package unavailable to check Rd xrefs: ‘RProtoBuf’
Running examples in ‘HLSM-Ex.R’ failed
The error most likely occurred in:

> ### Name: HLSMrandomEF
> ### Title: Function to run the MCMC sampler in random effects model (and
> ###   HLSMfixedEF for fixed effects model)
> ### Aliases: HLSMrandomEF HLSMfixedEF print.HLSM print.summary.HLSM
> ###   summary.HLSM getIntercept getAlpha getLS getLikelihood getBeta
> 
> ### ** Examples
> 
> 
> library(HLSM)
> 
> #Set values for the inputs of the function
> priors = NULL
> tune = NULL
> initialVals = NULL
> niter = 10
> 
> #Random effect HLSM on Pitt and Spillane data
> random.fit = HLSMrandomEF(Y = ps.advice.mat,FullX = ps.edge.vars.mat,
+ 	initialVals = initialVals,priors = priors,
+ 	tune = tune,tuneIn = FALSE,dd = 2,niter = niter,
+ 	intervention = 0)

 *** caught segfault ***
address 82000000, cause 'memory not mapped'

Traceback:
 1: base::.Call(.NAME, ...)
 2: .Call("R_igraph_graph_adjacency", adjmatrix, as.numeric(mode),     PACKAGE = "igraph")
 3: graph.adjacency.dense(adjmatrix, mode = mode, weighted = weighted,     diag = diag)
 4: graph.adjacency(Y[[tt]])
 5: FUN(X[[i]], ...)
 6: lapply(1:KK, function(tt) {    g = graph.adjacency(Y[[tt]])    ss = shortest.paths(g)    ss[ss > 4] = 4    Z0 = cmdscale(ss, k = dd)    dimnames(Z0)[[1]] = dimnames(YY[[tt]])[[1]]    return(Z0)})
 7: HLSMrandomEF(Y = ps.advice.mat, FullX = ps.edge.vars.mat, initialVals = initialVals,     priors = priors, tune = tune, tuneIn = FALSE, dd = 2, niter = niter,     intervention = 0)
An irrecoverable exception occurred. R is aborting now ...
Package required but not available: ‘bamsignals’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   2.7Mb
Running ‘test-all.R’
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > library(htmltools)
  > 
  > test_check("htmltools")
  Error in grepl("\n", lines, fixed = TRUE) : invalid multibyte string at '<f0><9f><98><8e>', making sure it's UTF-8 encoded on all platforms.'
  Calls: test_check ... with_reporter -> force -> source_file -> srcfilecopy -> grepl
  testthat results ================================================================
  OK: 146 SKIPPED: 0 FAILED: 0
  Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
trying URL 'https://arxiv.org/e-print/1406.4806v1'
Content type 'application/x-eprint-tar' length 29273 bytes (28 KB)
==================================================
downloaded 28 KB

Quitting from lines 79-82 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
there is no package called 'pdftools'
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/HydeNet.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
installed size is  6.4Mb
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    data   6.4Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   1.9Mb
    doc    2.3Mb
Running examples in ‘icenReg-Ex.R’ failed
The error most likely occurred in:

> ### Name: simIC_weib
> ### Title: Simulates interval censored data from regression model with a
> ###   Weibull baseline
> ### Aliases: simIC_weib
> 
> ### ** Examples
> 
> set.seed(1)
> sim_data <- simIC_weib(n = 500, b1 = .3, b2 = -.3, model = 'ph', 
+                       shape = 2, scale = 2, inspections = 6, 
+                       inspectLength = 1)
> #simulates data from a cox-ph with beta weibull distribution.
> 
> diag_covar(Surv(l, u, type = 'interval2') ~ x1 + x2, 
+            data = sim_data, model = 'po')
> diag_covar(Surv(l, u, type = 'interval2') ~ x1 + x2,
+            data = sim_data, model = 'ph')
Error in ans[isOk] <- log(-log(x[isOk])) : 
  NAs are not allowed in subscripted assignments
Calls: diag_covar -> diag_covar -> s_trans
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error in (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  : 
  there is no package called 'states2k'
Quitting from lines 24-109 (US-Engineering-Weather-Map.Rmd) 
Error: processing vignette 'US-Engineering-Weather-Map.Rmd' failed with diagnostics:
object 'states2k_map' not found
Execution halted
Running examples in ‘ifa-Ex.R’ failed
The error most likely occurred in:

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

 *** caught segfault ***
address 9, cause 'memory not mapped'

Traceback:
 1: grepl("\\.[^.]+\\.(gz|bz2|xz)$", x)
 2: fileExt(file)
 3: data(memory)
An irrecoverable exception occurred. R is aborting now ...
Error in re-building vignettes:
  ...
Quitting from lines 1343-1398 (pritikin-schmidt.Rnw) 
Error: processing vignette 'pritikin-schmidt.Rnw' failed with diagnostics:
Fit not achieved
Execution halted
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    help   1.3Mb
    libs   5.6Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/imager.Rcheck/00install.out’ for details.
Running examples in ‘IntegratedMRF-Ex.R’ failed
The error most likely occurred in:

> ### Name: CombPredict
> ### Title: Integrated Prediction of Testing samples using Combination
> ###   Weights from integrated RF or MRF model
> ### Aliases: CombPredict
> 
> ### ** Examples
> 
> library(IntegratedMRF)
> data(Dream_Dataset)
> Tree=1
> Feature=1
> Leaf=5
> Confidence=80
> finalX=Dream_Dataset[[1]]
> Cell=Dream_Dataset[[2]]
> Y_train_Dream=Dream_Dataset[[3]]
> Y_train_cell=Dream_Dataset[[4]]
> Y_test=Dream_Dataset[[5]]
> Y_test_cell=Dream_Dataset[[6]]
> Drug=c(1,2,3)
> Y_train_Drug=matrix(Y_train_Dream[,Drug],ncol=length(Drug))
> Result=Combination(finalX,Y_train_Drug,Cell,Y_train_cell,Tree,Feature,Leaf,Confidence)

 *** caught segfault ***
address 27a000, cause 'memory not mapped'
Error in re-building vignettes:
  ...
Loading required package: gdistance
Loading required package: raster
Loading required package: sp
Loading required package: igraph

Attaching package: 'igraph'

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

    union

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

    decompose, spectrum

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

    union

Loading required package: Matrix

Attaching package: 'gdistance'

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

    normalize


Error: processing vignette 'ipdw.Rnw' failed with diagnostics:
 chunk 2 (label = ipdw-1) 
Error in library("geoR") : there is no package called 'geoR'
Execution halted
installed size is  6.9Mb
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    data   6.7Mb
Running examples in ‘iqspr-Ex.R’ failed
The error most likely occurred in:

> ### Name: QSPRpred-class
> ### Title: QSPRpredictor class
> ### Aliases: QSPRpred QSPRpred-class
> 
> ### ** Examples
> 
> data(qspr.data)
> smis <- paste(qspr.data[,1])
> ty <- qspr.data[,c(2,5)]
> trainidx <- sample(1:nrow(qspr.data), 5000)
> testidx <- (1:nrow(qspr.data))[-trainidx][1:100]
> 
> data(qsprpred_EG_5k) 
> ## same as run => qsprpred_EG_5k <- 
> 
> #-----arguments
> #smis: SMILES string set (character vector) for training
> #y: property sets (matrix) for training  
> #v_ymin: minimum value of target properties
> #v_ymax: maximum value of target properties
> #v_descriptor: function transforming SMILES strings to feature matrix 
> #v_fpnames: character vectors indicating finger print used in the descriptor
> #w0: matrix representing prior mean of coeffients in linear regression model
> #V0_inv: matrix representing the prior variance of coeffients in linear regression model
> #a0: numeric value representing the location parameter in gamma prior 
> #b0: numeric value representing the shape parameter in gamma prior 
> #------
> 
> predictions <- qsprpred_EG_5k$qspr_predx(smis[testidx])  

get fingerprint graph from SMILES strings          
Error in .jcall("org/guha/rcdk/util/Misc", "Ljava/lang/Object;", "getProperty",  : 
  RcallMethod: cannot determine object class
Calls: <Anonymous> ... lapply -> FUN -> get.property -> .jcall -> .External
Execution halted
File ‘itree/libs/itree.so’:
  Found ‘printf’, possibly from ‘printf’ (C)
    Objects: ‘xval.o’, ‘xval_penalty.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.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 114-116 (JacobiEigen.Rmd) 
Error: processing vignette 'JacobiEigen.Rmd' failed with diagnostics:
there is no package called 'microbenchmark'
Execution halted
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    dict  19.5Mb
Package suggested but not available for checking: ‘RProtoBuf’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: MASS
Loading required package: boot

Attaching package: 'boot'

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

    aml

Loading required package: lattice

Attaching package: 'lattice'

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

    melanoma

Loading required package: statmod
Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLSX' (Excel 2007+) files.

gdata: Run the function 'installXLSXsupport()'
gdata: to automatically download and install the perl
gdata: libaries needed to support Excel XLS and XLSX formats.

Attaching package: 'gdata'

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

    nobs

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

    object.size

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

    startsWith
installed size is  6.6Mb
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Running examples in ‘lakemorpho-Ex.R’ failed
The error most likely occurred in:

> ### Name: lakeMajorAxisLength
> ### Title: Calculate the length of the major axis for lake
> ### Aliases: lakeMajorAxisLength
> 
> ### ** Examples
> 
> data(lakes)
> lakeMajorAxisLength(inputLM)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘coordinates’ for signature ‘"numeric"’
Calls: lakeMajorAxisLength ... lapply -> Lines -> is -> Line -> coordinates -> <Anonymous>
Execution halted
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    R      1.4Mb
    doc    2.6Mb
    help   1.2Mb
installed size is  6.6Mb
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    doc            1.2Mb
    testdata       2.3Mb
    vignettedata   2.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: `legend.margin` must be specified using `margin()`. For the old behavior use legend.spacing
largeVis was compiled with 32-bit types. This will limit the size of the datasets it can process. Consider recompiling with -DARMA_64BIT_WORD
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Warning: `legend.margin` must be specified using `margin()`. For the old behavior use legend.spacing
Error: C stack usage  151210780 is too close to the limit
Quitting from lines 195-219 (momentumandusedata.Rmd) 
Error: processing vignette 'momentumandusedata.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/LatentREGpp.Rcheck/00install.out’ for details.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    geojson  11.5Mb
File ‘leaps/libs/leaps.so’:
  Found ‘__f90_esfw’, possibly from ‘print’ (Fortran), ‘write’
    (Fortran)
    Object: ‘leaps.o’
  Found ‘__f90_eslw’, possibly from ‘print’ (Fortran), ‘write’
    (Fortran)
    Object: ‘leaps.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 26.0Mb
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    extdata   1.7Mb
    libs     23.8Mb
Running examples in ‘lidR-Ex.R’ failed
The error most likely occurred in:

> ### Name: as.raster.lasmetrics
> ### Title: Transform a 'lasmetrics' object into a spatial 'RasterLayer'
> ###   object
> ### Aliases: as.raster.lasmetrics
> 
> ### ** Examples
> 
> LASfile <- system.file("extdata", "Megaplot.laz", package="lidR")
> lidar = readLAS(LASfile)
Error: ERROR: '%s' after %u of %u points> 
> meanHeight = grid_metrics(lidar, mean(Z))
Error: First argument is not a LAS object
Execution halted
Error in re-building vignettes:
  ...

 *** caught segfault ***
address 1c00000, cause 'memory not mapped'
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 107-108 (lingtypology.Rmd) 
Error: processing vignette 'lingtypology.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R          1.3Mb
    doc        2.1Mb
    testdata   1.7Mb
Package suggested but not available for checking: ‘Rsymphony’
Packages required but not available: ‘geoR’ ‘RandomFields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 60-67 (quick-start.Rmd) 
Error: processing vignette 'quick-start.Rmd' failed with diagnostics:
error reading from connection
Execution halted
Running ‘testthat.R’ [110s/110s]
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. Error: interval handles POSIXlt inputs (@test-intervals.R#86) ---------------
  invalid 'tz' value
  1: expect_equal(interval(t1, t2), new("Interval", 18316800, start = as.POSIXct("2007-01-01", 
         tz = "UTC"), tzone = "UTC")) at testthat/test-intervals.R:86
  2: compare(object, expected, ...)
  3: interval(t1, t2)
  4: as.POSIXct(start, tz = tzone)
  5: as.POSIXct.POSIXlt(start, tz = tzone)
  
  testthat results ================================================================
  OK: 2152 SKIPPED: 0 FAILED: 1
  1. Error: interval handles POSIXlt inputs (@test-intervals.R#86) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘lvnet-Ex.R’ failed
The error most likely occurred in:

> ### Name: lav2lvnet
> ### Title: Convert lavaan model to lvnet model matrices
> ### Aliases: lav2lvnet
> 
> ### ** Examples
> 
> library("lavaan")
This is lavaan 0.5-22
lavaan is BETA software! Please report any bugs.

Attaching package: ‘lavaan’

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

    vech

> 
> # Load dataset:
> data(HolzingerSwineford1939)
> Data <- HolzingerSwineford1939[,7:15]
> 
> # lavaan model
> HS.model <- '
+ visual  =~ x1 + x2 + x3
+ textual =~ x4 + x5 + x6
+ speed   =~ x7 + x8 + x9 '
> 
> # fit via lavaan:
> lavFit <- cfa(HS.model, HolzingerSwineford1939[7:15],std.lv=TRUE)
> 
> # Fit via lvnet:
> mod <- lav2lvnet(HS.model, HolzingerSwineford1939[7:15])
> lvnetFit <- lvnet(Data, lambda = mod$lambda, psi = mod$psi)
Error: The job for model 'model' exited abnormally with the error message: Non-conformable matrices [(9 x 3) and (9 x 3)] in Matrix Multiply.
Execution halted
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    base_files   6.5Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Warning in arrange_impl(.data, dots) :
  '.Random.seed' is not an integer vector but of type 'NULL', so ignored
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot50a13dc81c.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot50a13dc81c.png': No such file or directory
Quitting from lines 95-96 (manhattanly.Rmd) 
Error: processing vignette 'manhattanly.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/ManifoldOptim.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot4d95298b7181.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot4d95298b7181.png': No such file or directory
Quitting from lines 63-70 (manipulateWidgets.Rmd) 
Error: processing vignette 'manipulateWidgets.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
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Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Rcpp
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 72-86 (matchingR-performance.Rmd) 
Error: processing vignette 'matchingR-performance.Rmd' failed with diagnostics:
there is no package called 'microbenchmark'
Execution halted
Running examples in ‘mcglm-Ex.R’ failed
The error most likely occurred in:

> ### Name: anova.mcglm
> ### Title: Anova Tables
> ### Aliases: anova.mcglm
> 
> ### ** Examples
> 
> x1 <- seq(-1, 1, l = 100)
> x2 <- gl(5, 20)
> beta <- c(5, 0, -2, -1, 1, 2)
> X <- model.matrix(~ x1 + x2)
> set.seed(123)
> y <- rnorm(100, mean = X%*%beta, sd = 1)
> data = data.frame("y" = y, "x1" = x1, "x2" = x2)
> fit.anova <- mcglm(c(y ~ x1 + x2), list(mc_id(data)), data = data)
Automatic initial values selected. 
Error in rep(1:n_resp, information$n_betas) : invalid 'times' argument
> anova(fit.anova)
Error in UseMethod("anova") : 
  no applicable method for 'anova' applied to an object of class "try-error"
Calls: anova
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
----------------------------------------------------------------------
  mcglm: Multivariate Covariance Generalized Linear Models

  For support, collaboration or bug report, visit: 
    https://github.com/wbonat/mcglm

  mcglm version 0.3.0 (build on 2016-06-06) is now loaded.
----------------------------------------------------------------------
Loading required package: Matrix
Error in rep(1:n_resp, information$n_betas) : invalid 'times' argument
Quitting from lines 116-118 (GLMExamples.Rmd) 
Error: processing vignette 'GLMExamples.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
Execution halted
Running examples in ‘mcPAFit-Ex.R’ failed
The error most likely occurred in:

> ### Name: mcPAFit
> ### Title: estimates the Preferential Attachment function in a temporal
> ###   complex network without temporal information.
> ### Aliases: mcPAFit
> ### Keywords: package Preferential Attachment function Markov chain Monte
> ###   Carlo Gibbs sampling missing timeline
> 
> ### ** Examples
> 
> library(mcPAFit)
> N      <- 1000 #number of nodes in the network 
> M      <- 500  #number of needed sample
> lag   <-  1
> start <-  100
> 
> data   <- create_sim_data(N = N, alpha = 1)
> write.table(data$random[,1:2], row.names = FALSE,
+             col.names = FALSE, file = "input.txt")
> system.time(mcPAFit(file_name = "input.txt",burn_in = 0, s = 5, skip = 1, 
+             needed_sample = M, G = 20,only_active_node = 1, random = 0))
terminate called after throwing an instance of 'std::out_of_range'
  what():  vector::_M_range_check: __n (which is 15) >= this->size() (which is 0)
Installation failed.
See ‘/home/ripley/R/packages/tests32/medSTC.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: arm
Loading required package: MASS
Loading required package: Matrix
Loading required package: lme4

arm (Version 1.9-3, built: 2016-11-21)

Working directory is /home/ripley/R/packages/tests32/merTools.Rcheck/vign_test/merTools/vignettes

Loading required package: dplyr

Attaching package: 'dplyr'

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

    select

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: Rcpp
rstanarm (Version 2.13.1, packaged: 2016-11-20 16:59:31 UTC)
- Do not expect the default priors to remain the same in future rstanarm versions.
Thus, R scripts should specify priors explicitly, even if they are just the defaults.
- For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores())
Running examples in ‘metaSEM-Ex.R’ failed
The error most likely occurred in:

> ### Name: BCG
> ### Title: Dataset on the Effectiveness of the BCG Vaccine for Preventing
> ###   Tuberculosis
> ### Aliases: BCG
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(BCG)
> 
> ## Univariate meta-analysis on the log of the odds ratio
> summary( meta(y=ln_OR, v=v_ln_OR, data=BCG,
+               x=cbind(scale(Latitude,scale=FALSE),
+               scale(Year,scale=FALSE))) )
Error in running mxModel:
<simpleError: The job for model 'Meta analysis with ML' exited abnormally with the error message: Non-conformable matrices [(1 x 3) and (1 x 3)] in Matrix Multiply.>
Warning: The job for model 'Meta analysis with ML' exited abnormally with the error message: Non-conformable matrices [(1 x 3) and (1 x 3)] in Matrix Multiply.
Error: $ operator is invalid for atomic vectors
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/MethyBayes.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mhde_article.tex' failed.
Messages:
/usr/local/bin/texi2dvi: biber failed
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   4.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 48-63 (compiled_models.Rmd) 
Error: processing vignette 'compiled_models.Rmd' failed with diagnostics:
there is no package called 'microbenchmark'
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   5.2Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
Package which this enhances but not available for checking: ‘MonetDBLite’
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   7.1Mb
Packages suggested but not available for checking: ‘geojsonio’ ‘rmapshaper’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   2.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 30-37 (msaR.Rmd) 
Error: processing vignette 'msaR.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/MultiBD.Rcheck/00install.out’ for details.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    java  14.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    2.4Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    extdata  16.3Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.5Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
Packages suggested but not available for checking: ‘graphite’ ‘NFPdata’
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
Error in re-building vignettes:
  ...
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

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

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

    IQR, mad, xtabs

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

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

Loading required package: graphite
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'graphite'
Quitting from lines 198-206 (NFP.Rnw) 
Error: processing vignette 'NFP.Rnw' failed with diagnostics:
could not find function "pathways"
Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R         2.5Mb
    include   3.2Mb
Running ‘anova.gls.R’
  Running ‘augPred_lab.R’ [261s/261s]
  Running ‘augPredmissing.R’
  Running ‘coef.R’
  Comparing ‘coef.Rout’ to ‘coef.Rout.save’ ... OK
  Running ‘contrMat.R’
  Running ‘data.frame.R’
  Running ‘deparse.R’
  Running ‘fitted.R’
  Running ‘getData.R’
  Running ‘gls.R’
  Running ‘lmList.R’
  Running ‘lme.R’ [31s/31s]
  Comparing ‘lme.Rout’ to ‘lme.Rout.save’ ... OK
  Running ‘missing.R’
  Comparing ‘missing.Rout’ to ‘missing.Rout.save’ ... OK
  Running ‘nlme.R’
  Running ‘nlme2.R’ [13s/13s]
  Running ‘predict.lme.R’
  Running ‘sigma-fixed-etc.R’ [134s/138s]
Running the tests in ‘tests/sigma-fixed-etc.R’ failed.
Last 13 lines of output:
  +     all.equal(fixef(t6.fix.ML.lme),
  +               c("(Intercept)"= 24.009565, "I(age - 11)"= 0.64760432), tol= 1e-7)
  +     ,
  +     all.equal(sM6$tTable[,"Std.Error"],
  +               c("(Intercept)"= 0.426561, "I(age - 11)"= 0.066832), tol = 5e-5)
  +     ,
  +     all.equal(aM6[,"F-value"], c(3162.47, 93.8969), tol = 5e-5)
  +     ,
  +     all.equal(iM6$varStruct["Female",],
  + 	      c(lower = 0.51230063,
  + 		est.  = 0.65065925,
  + 		upper = 0.82638482), tol = 5e-5)
  + )
  Error: all.equal(iM6$varStruct["Female", ], c(lower = 0.51230063, est. = 0.65065925,  .... is not TRUE
  Execution halted
Running ‘test-all.R’ [17s/17s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > if(require("testthat", quietly = TRUE)) {
  +     test_check("nloptr")
  + } else {
  +     print( "package 'testthat' not available, cannot run unit tests" )
  + }
  Loading required package: nloptr
  1. Failure: Test NLopt tutorial example with NLOPT_LN_COBYLA with gradient information. (@test-example.R#101) 
  res1$solution not equal to `solution.opt`.
  2/2 mismatches (average diff: 0.00818)
  [1] 0.328 - 0.333 == -0.00572
  [2] 0.307 - 0.296 ==  0.01064
  
  
  Error: nlopt_add_inequality_mconstraint returned NLOPT_INVALID_ARGS.
  2. Failure: Test HS023. (@test-hs023.R#90) -------------------------------------
  res$solution not equal to `solution.opt`.
  1/2 mismatches
  [1] 3 - 1 == 2
  
  
  3. Failure: Test HS023. (@test-hs023.R#95) -------------------------------------
  all(eval_g_ineq(res$solution)$constr <= res$options$tol_constraints_ineq) isn't true.
  
  
  testthat results ================================================================
  OK: 40 SKIPPED: 0 FAILED: 3
  1. Failure: Test NLopt tutorial example with NLOPT_LN_COBYLA with gradient information. (@test-example.R#101) 
  2. Failure: Test HS023. (@test-hs023.R#90) 
  3. Failure: Test HS023. (@test-hs023.R#95) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    data      4.4Mb
    doc       1.2Mb
    reports   3.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'vignette_get_nltt_values.Rmd' failed with diagnostics:
(converted from warning) Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/nortestARMA.Rcheck/00install.out’ for details.
installed size is 39.1Mb
  sub-directories of 1Mb or more:
    extdata  39.0Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
File ‘oblique.tree/libs/oblique.tree.so’:
  Found ‘__f90_esfw’, possibly from ‘print’ (Fortran), ‘write’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R            1.5Mb
    test_files   4.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    help   2.1Mb
Packages suggested but not available for checking: ‘RAppArmor’ ‘feather’
Installation failed.
See ‘/home/ripley/R/packages/tests32/OpenMx.Rcheck/00install.out’ for details.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    java     1.3Mb
    models   6.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    nifti   4.1Mb
Running examples in ‘P2C2M-Ex.R’ failed
The error most likely occurred in:

> ### Name: p2c2m.complete
> ### Title: Execute the complete P2C2M pipeline via a single command
> ### Aliases: p2c2m.complete
> 
> ### ** Examples
> 
> ## Example of the minimal data requirements to run P2C2M
> 
> # The absolute path to the input directory is set
> inPath <- system.file("extdata", "sim.E.003.small/", package="P2C2M")
> 
> # The name of the xml-file generated by BEAUTi and located in 
> # "inPath" is set
> inFile <- "sim.E.003.small.xml"
> 
> # Posterior predictive simulations with a setting of 2 simulation 
> # replicates are preformed
> sim.E.003.small <- p2c2m.complete(inPath, inFile, num.reps=2, save.metadata=TRUE)
Error in python.exec(code, get.exception) : cannot import name izip
Calls: p2c2m.complete -> p2c2m.readstarb -> <Anonymous> -> python.exec
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data        1.6Mb
    localdata   3.1Mb
Info message:
Couldn't find 'pandoc'!
Pandoc version is set to '1.16', use `set_pandoc_version` to change the settings if necessary.
File ‘ParallelForest/libs/ParallelForest.so’:
  Found ‘__f90_esfw’, possibly from ‘print’ (Fortran), ‘write’
    (Fortran)
    Object: ‘classification.o’
  Found ‘__f90_eslw’, possibly from ‘print’ (Fortran), ‘write’
    (Fortran)
    Object: ‘classification.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.
Packages which this enhances but not available for checking:
  ‘remoter’ ‘pbdCS’
Package which this enhances but not available for checking: ‘remoter’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    1.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc        1.6Mb
    examples   1.8Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      2.8Mb
    data   2.4Mb
Running examples in ‘pcalg-Ex.R’ failed
The error most likely occurred in:

> ### Name: unifDAG
> ### Title: Uniform Sampling of Directed Acyclic Graphs (DAG)
> ### Aliases: unifDAG unifDAG.approx
> ### Keywords: graphs models
> 
> ### ** Examples
> 
> # require("Rgraphviz")
> set.seed(123)
> dag1 <- unifDAG(n=10)
GNU MP: Cannot allocate memory (size=4)
installed size is 27.1Mb
  sub-directories of 1Mb or more:
    libs  26.4Mb
Packages suggested but not available for checking: ‘geoR’ ‘georob’
Packages unavailable to check Rd xrefs: ‘geoR’, ‘RandomFields’, ‘georob’
Running examples in ‘pedometrics-Ex.R’ failed
The error most likely occurred in:

> ### Name: vgmICP
> ### Title: Initial covariance parameters (ICP)
> ### Aliases: vgmICP
> 
> ### ** Examples
> 
> data(meuse, package = "sp")
> icp <- vgmICP(z = log(meuse$copper), coords = meuse[, 1:2])
Error: Package(s) needed for this function to work but notinstalled: georob geoR
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      4.5Mb
    data   3.1Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/pETM.Rcheck/00install.out’ for details.
File ‘PET/libs/PET.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘art.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘art.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.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
ERROR: Duplicated records found in prim.key field
ERROR: NULL records found in prim.key field
OK: No duplicated records found in prim.key field
OK: No NULL records found in prim.key field
Quitting from lines 754-768 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
there is no package called 'microbenchmark'
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
Package suggested but not available for checking: ‘OCplus’
Package unavailable to check Rd xrefs: ‘OCplus’
Package suggested but not available for checking: ‘ReportingTools’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   6.4Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Running examples in ‘poppr-Ex.R’ failed
The error most likely occurred in:

> ### Name: bitwise.dist
> ### Title: Calculate a dissimilarity distance matrix for SNP data.
> ### Aliases: bitwise.dist
> 
> ### ** Examples
> 
> set.seed(999)
> x <- glSim(n.ind = 10, n.snp.nonstruc = 5e2, n.snp.struc = 5e2, ploidy = 2)

 *** caught segfault ***
address 7400000, cause 'memory not mapped'
Running ‘test-all.R’ [37s/46s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > options(poppr.debug = TRUE)
  > test_check("poppr")
  Loading required package: poppr
  Loading required package: adegenet
  Loading required package: ade4
  
     /// adegenet 2.0.1 is loaded ////////////
  
     > overview: '?adegenet'
     > tutorials/doc/questions: 'adegenetWeb()' 
     > bug reports/feature requests: adegenetIssues()
  
  
  This is poppr version 2.3.0. To get started, type package?poppr
  OMP parallel support: available
  
   *** caught segfault ***
  address 7000000, cause 'memory not mapped'
Running ‘testthat.R’ [35s/35s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(popprxl)
  Loading required package: poppr
  Loading required package: adegenet
  Loading required package: ade4
  
     /// adegenet 2.0.1 is loaded ////////////
  
     > overview: '?adegenet'
     > tutorials/doc/questions: 'adegenetWeb()' 
     > bug reports/feature requests: adegenetIssues()
  
  
  This is poppr version 2.3.0. To get started, type package?poppr
  OMP parallel support: available
  
  popprxl is loaded. Use read.genalexcel() to read in your data.
  
  > 
  > test_check("popprxl")
  1. Error: Geographic data can be imported (@test-import.R#34) ------------------
  Number of samples (Row 1, Column B) is not numeric. 
    I found: NA 
  1: read.genalexcel(geox, sheet = 1, geo = TRUE, genclone = FALSE) at testthat/test-import.R:34
  2: stop(msg)
  
  testthat results ================================================================
  OK: 8 SKIPPED: 0 FAILED: 1
  1. Error: Geographic data can be imported (@test-import.R#34) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘ROI.plugin.symphony’
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    java   5.6Mb
File ‘powell/libs/powell.so’:
  Found ‘printf’, possibly from ‘printf’ (C)
    Object: ‘powell.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package unavailable to check Rd xrefs: ‘microbenchmark’
Installation failed.
See ‘/home/ripley/R/packages/tests32/preseqR.Rcheck/00install.out’ for details.
Package required but not available: ‘geoR’

Package suggested but not available for checking: ‘INLA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 31-43 (PRISMA.Rmd) 
Error: processing vignette 'PRISMA.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/ProFit.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    dict   5.3Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc        3.7Mb
    examples   2.5Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.3Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/pystr.Rcheck/00install.out’ for details.
Running examples in ‘qgraph-Ex.R’ failed
The error most likely occurred in:

> ### Name: centrality_auto
> ### Title: Automatic centrality statistics of graphs
> ### Aliases: centrality_auto
> ### Keywords: graphs centrality
> 
> ### ** Examples
> 
> set.seed(1)
> adj <- matrix(sample(0:1,10^2,TRUE,prob=c(0.8,0.2)),nrow=10,ncol=10)
> Q <- qgraph(adj)
> centrality_auto(Q) 
Node 1, Reach 9, Total 9
Node 2, Reach 9, Total 18
Node 3, Reach 1, Total 19
Node 4, Reach 9, Total 28
Node 5, Reach 9, Total 37
Node 6, Reach 9, Total 46
Node 7, Reach 9, Total 55
Node 8, Reach 9, Total 64
Node 9, Reach 10, Total 74
Node 10, Reach 9, Total 83

 *** caught segfault ***
address 86800000, cause 'memory not mapped'

Traceback:
 1: base::.Call(.NAME, ...)
 2: .Call("R_igraph_graph_adjacency", adjmatrix, as.numeric(mode),     PACKAGE = "igraph")
 3: graph.adjacency.dense(adjmatrix, mode = mode, weighted = weighted,     diag = diag)
 4: graph.adjacency(adjmatrix = abs(1/x), mode = ifelse(directed.gr,     "directed", "undirected"), weighted = (if (weighted.gr) TRUE),     diag = FALSE)
 5: centrality_auto(Q)
An irrecoverable exception occurred. R is aborting now ...
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    data  12.9Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    contrib   3.7Mb
    doc       3.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 66-100 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 92-106 (wilcox1973.Rmd) 
Error: processing vignette 'wilcox1973.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.7Mb
Packages suggested but not available for checking: ‘RMySQL’ ‘its’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: Removed 16 rows containing missing values (geom_point).
Warning: Removed 16 rows containing missing values (geom_point).
Quitting from lines 141-142 (Use_case.Rmd) 
Error: processing vignette 'Use_case.Rmd' failed with diagnostics:
the table must have a header (column names)
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 16-31 (Performance.Rmd) 
Error: processing vignette 'Performance.Rmd' failed with diagnostics:
there is no package called 'microbenchmark'
Execution halted
Found the following significant warnings:
  Warning: replacing previous import ‘ape::complement’ by ‘Biostrings::complement’ when loading ‘RADami’
See ‘/home/ripley/R/packages/tests32/RADami.Rcheck/00install.out’ for details.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    app   6.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    extdata   1.5Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    htmlwidgets   6.6Mb
Running examples in ‘ramidst-Ex.R’ failed
The error most likely occurred in:

> ### Name: dbn_generator
> ### Title: Generates a random dynamic Bayesian network
> ### Aliases: dbn_generator
> 
> ### ** Examples
> 
> d <- dbn_generator(3,2,2)
Error in .jfindClass(as.character(class)) : class not found
Calls: dbn_generator -> J -> jclassName -> .jfindClass
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/RandomFields.Rcheck/00install.out’ for details.
Found the following significant warnings:
  "randomForestSRC.c", line 11363: warning: improper pointer/integer combination: arg #2
See ‘/home/ripley/R/packages/tests32/randomForestSRC.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’
Package required but not available: ‘RandomFields’

Packages suggested but not available for checking: ‘gurobi’ ‘rgurobi’

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

> ### Name: RArcInfo
> ### Title: RArcInfo
> ### Aliases: RArcInfo
> ### Keywords: file
> 
> ### ** Examples
> 
> 
> #See example(plotpoly) for another example
> 
> library(RArcInfo)
> 
> datadir<-system.file("exampleData",package="RArcInfo")
> infodir<-system.file("exampleData","info",package="RArcInfo")
> coveragedir<-system.file("exampleData","wetlands",package="RArcInfo")
> 
> #get.bnddata needs the last slash...
> infodir<-paste(c(infodir,"/"), collapse="")
> 
> #List all the tables
> 
> covnames<-get.namesofcoverages(datadir)
> tablenames<-get.tablenames(infodir)
> 
> 
> #Display the name of the table and its fields
> for(i in 1:length(tablenames[[1]]))
+ {
+ 	print(c("Table: ",tablenames$TableName[i]))
+ 
+ 	fields<-get.tablefields(infodir,tablenames$TableName[i])
+ 	print("Fields")
+ 	for(j in 1:length(fields))
+ 		print(fields[[j]][1])
+ 
+ 	#Get the data
+ 	if(i==1)
+ 		tabledata<-get.tabledata(infodir,tablenames$TableName[i])
+ 	else
+ 		tabledata<-c(tabledata, get.tabledata(infodir,tablenames$TableName[i]) )
+ }
[1] "Table: "                          "WETLANDS.BND                    "
Error in get.tablefields(infodir, tablenames$TableName[i]) : 
  ERROR 3: Attempt to read past EOF in /home/ripley/R/Lib32/RArcInfo/exampleData/info/arc0000.nit.
Calls: get.tablefields -> .Call
Execution halted
Running ‘valencia.R’
  Running ‘wetlands.R’
Running the tests in ‘tests/wetlands.R’ failed.
Complete output:
  > library(RArcInfo)
  Loading required package: RColorBrewer
  > 
  > datadir<-system.file("exampleData",package="RArcInfo")
  > infodir<-system.file("exampleData","info",package="RArcInfo")
  > coveragedir<-system.file("exampleData","wetlands",package="RArcInfo")
  > 
  > #get.bnddata needs the last slash...
  > infodir<-paste(c(infodir,"/"), collapse="")
  > 
  > #List all the tables
  > 
  > covnames<-get.namesofcoverages(datadir)
  > tablenames<-get.tablenames(infodir)
  > 
  > 
  > #Display the name of the table and its filds
  > for(i in 1:length(tablenames[[1]]))
  + {
  + 	print(c("Table: ",tablenames$TableName[i]))
  + 
  + 	fields<-get.tablefields(infodir,tablenames$TableName[i])
  + 	print("Fields")
  + 	for(j in 1:length(fields))
  + 		print(fields[[j]][1])
  + 
  + 	#Get the data
  + 	if(i==1)
  + 		tabledata<-get.tabledata(infodir,tablenames$TableName[i])
  + 	else
  + 		tabledata<-c(tabledata, get.tabledata(infodir,tablenames$TableName[i]) )
  + }
  [1] "Table: "                          "WETLANDS.BND                    "
  Error in get.tablefields(infodir, tablenames$TableName[i]) : 
    ERROR 3: Attempt to read past EOF in /home/ripley/R/Lib32/RArcInfo/exampleData/info/arc0000.nit.
  Calls: get.tablefields -> .Call
  Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    etc    2.2Mb
    po     1.5Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/rCBA.Rcheck/00install.out’ for details.
Running examples in ‘rcdk-Ex.R’ failed
The error most likely occurred in:

> ### Name: eval.desc
> ### Title: Evaluate a Molecular Descriptor
> ### Aliases: eval.desc
> ### Keywords: programming
> 
> ### ** Examples
> 
> smiles <- c('CCC', 'c1ccccc1', 'CC(=O)C')
> mols <- sapply(smiles, parse.smiles)
> 
> dnames <- get.desc.names('constitutional')
Error in .jcall("org/guha/rcdk/descriptors/DescriptorUtilities", "[Ljava/lang/String;",  : 
  RcallMethod: cannot determine object class
Calls: get.desc.names -> .jcall -> .External
Execution halted
Error in re-building vignettes:
  ...
Loading required package: fingerprint

Error: processing vignette 'rcdk.Rnw' failed with diagnostics:
 chunk 11 
Error in .jcall("org/guha/rcdk/util/Misc", "S", "getSmiles", molecule,  : 
  RcallMethod: cannot determine object class
Execution halted
Running examples in ‘rchallenge-Ex.R’ failed
The error most likely occurred in:

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

```{r}
library(rchallenge)
```
<link rel="stylesheet" 
 href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css">
`r icon("fa-user")`
`r icon("fa-user fa-lg")`
`r icon("fa-user fa-2x")`
`r icon("fa-user fa-3x")`
`r icon("fa-user fa-3x fa-border")`
> rmarkdown::render(file)
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 336-337 (RClone_qmsevpops.Rmd) 
Error: processing vignette 'RClone_qmsevpops.Rmd' failed with diagnostics:
the table must have a header (column names)
Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   4.4Mb
    po    2.2Mb
Running examples in ‘RcppCCTZ-Ex.R’ failed
The error most likely occurred in:

> ### Name: toTz
> ### Title: Shift datetime object from one timezone to another
> ### Aliases: toTz
> 
> ### ** Examples
> 
> toTz(Sys.time(), "America/New_York", "Europe/London")
Error in toTz(Sys.time(), "America/New_York", "Europe/London") : 
  Bad 'from' timezone
Calls: toTz -> .Call
Execution halted
Running ‘simpleTests.R’
Running the tests in ‘tests/simpleTests.R’ failed.
Complete output:
  > 
  > library(RcppCCTZ)
  > 
  > ord <- "America/Chicago"
  > lax <- "America/Los_Angeles"
  > lga <- "America/New_York"
  > htr <- "Europe/London"
  > utc <- "UTC"
  > 
  > now <- ISOdatetime(2016, 11, 29, 12, 00, 00, tz="UTC")
  > 
  > format(toTz(now, utc, lax), tz=lax)
  /usr/share/zoneinfo/America/Los_Angeles: No such file or directory
  Error in toTz(now, utc, lax) : Bad 'to' timezone
  Calls: format -> toTz -> .Call
  Execution halted
Running examples in ‘RcppGetconf-Ex.R’ failed
The error most likely occurred in:

> ### Name: getAll
> ### Title: Return all System Configuration Settings
> ### Aliases: getAll
> 
> ### ** Examples
> 
> head(getAll(), 30)
Error in getAll() : Memory allocation error
Calls: head -> getAll -> .Call
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/RcppHoney.Rcheck/00install.out’ for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    include   1.5Mb
    lib       3.0Mb
    libs      1.0Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc       2.2Mb
    include   6.5Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    include   3.7Mb
    lib       6.0Mb
    libs      1.6Mb
Package suggested but not available for checking: ‘V8’
Running ‘testthat.R’ [15s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(readr)
  > 
  > test_check("readr")
  1. Failure: locale affects am/pm (@test-parsing-datetime.R#173) ----------------
  `a` not equal to `b`.
  Attributes: < Names: 1 string mismatch >
  Attributes: < Length mismatch: comparison on first 2 components >
  Attributes: < Component 2: Modes: character, list >
  Attributes: < Component 2: Lengths: 1, 4 >
  Attributes: < Component 2: names for current but not for target >
  Attributes: < Component 2: Attributes: < target is NULL, current is list > >
  Attributes: < Component 2: target is character, current is tbl_df >
  'is.NA' value mismatch: 1 in current 0 in target
  
  
  testthat results ================================================================
  OK: 406 SKIPPED: 2 FAILED: 1
  1. Failure: locale affects am/pm (@test-parsing-datetime.R#173) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘readxl-Ex.R’ failed
The error most likely occurred in:

> ### Name: excel_sheets
> ### Title: List all sheets in an excel spreadsheet.
> ### Aliases: excel_sheets
> 
> ### ** Examples
> 
> excel_sheets(system.file("extdata/datasets.xlsx", package = "readxl"))
[1] "iris"     "mtcars"   "chickwts" "quakes"  
> excel_sheets(system.file("extdata/datasets.xls", package = "readxl"))
[1] "iris"     "mtcars"   "chickwts" "quakes"  
> 
> # To load all sheets in a workbook, use lapply
> path <- system.file("extdata/datasets.xls", package = "readxl")
> lapply(excel_sheets(path), read_excel, path = path)

 *** caught segfault ***
address 307b460, cause 'memory not mapped'
Installation failed.
See ‘/home/ripley/R/packages/tests32/redist.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘Rsymphony’

Package which this enhances but not available for checking: ‘Rcplex’
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    java   6.0Mb
Running examples in ‘reprex-Ex.R’ failed
The error most likely occurred in:

> ### Name: un-reprex
> ### Title: Un-render a reprex
> ### Aliases: un-reprex reprex_invert reprex_clean reprex_rescue
> 
> ### ** Examples
> 
> ## a rendered reprex can be inverted, at least approximately
> x <- reprex({
+   #' Some text
+   #+ chunk-label-and-options-cannot-be-recovered, message = TRUE
+   (x <- 1:4)
+   #' More text
+   y <- 2:5
+   x + y
+ }, show = FALSE)
Error in reprex_(r_file) : 
Cannot render this code.
Error : pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Calls: reprex -> reprex_
Execution halted
Running examples in ‘respirometry-Ex.R’ failed
The error most likely occurred in:

> ### Name: calc_MO2
> ### Title: Calculate metabolic rate
> ### Aliases: calc_MO2
> 
> ### ** Examples
> 
> # get O2 data
> file <- system.file('extdata', 'witrox_file.txt', package = 'respirometry')
> o2_data <- na.omit(import_witrox(file, split_channels = TRUE)$CH_4)
Warning in strsplit(raw, split = "\r\n", fixed = T) :
  input string 1 is invalid UTF-8
Error in grep("Date &Time [", f[1:20], fixed = TRUE):length(f) : 
  argument of length 0
Calls: na.omit -> import_witrox
Execution halted
Found the following significant warnings:
  Warning: iteration 7 invokes undefined behavior [-Waggressive-loop-optimizations]
See ‘/home/ripley/R/packages/tests32/rexpokit.Rcheck/00install.out’ for details.
Package unavailable to check Rd xrefs: ‘Rsymphony’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc     2.2Mb
    fonts   1.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 79-84 (WebGL.Rmd) 
Error: processing vignette 'WebGL.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages suggested but not available for checking:
  ‘hyperdraw’ ‘hypergraph’ ‘rggobi’
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    extra  10.2Mb
installed size is 23.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help  10.6Mb
    libs   9.0Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc   9.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 34-47 (intro_rhandsontable.Rmd) 
Error: processing vignette 'intro_rhandsontable.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘feather’
Running examples in ‘rio-Ex.R’ failed
The error most likely occurred in:

> ### Name: gather_attrs
> ### Title: Gather attributes from data.frame variables
> ### Aliases: gather_attrs
> 
> ### ** Examples
> 
> e <- import("http://www.stata-press.com/data/r13/auto.dta")
Error in df_parse_dta_file(spec, encoding) : 
  Failed to parse /tmp/RtmplHayrs/file248b14dd2378.dta: Invalid file, or file has unsupported features.
Calls: import ... convert_attributes -> read_dta -> df_parse_dta_file -> .Call
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
Note: information on .o files is not available
File ‘/home/ripley/R/Lib32/rJava/libs/rJava.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API call to R: ‘R_GlobalContext’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    java  11.2Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    datasets   9.0Mb
installed size is 46.8Mb
  sub-directories of 1Mb or more:
    exe  46.7Mb
Running examples in ‘RKEEL-Ex.R’ failed
The error most likely occurred in:

> ### Name: Alatasetal_A
> ### Title: Alatasetal_A KEEL Association Rules Algorithm
> ### Aliases: Alatasetal_A R6_Alatasetal_A
> ### Keywords: association rules
> 
> ### ** Examples
> 
> 
> #Load KEEL dataset iris
> dat<-loadKeelDataset("iris")
/home/ripley/R/Lib32/RKEELdata/datasets/> 
> #Create algorithm
> algorithm <- Alatasetal_A(dat)
> 
> #Run algorithm
> algorithm$run()
Executing algorithm...
/tmp/Rtmp5eai9Z/experiment_2017-01-11_09-39-402656/results/KEELToPMML/TSTAlatasetal_A/result0s0file0.pmml
Error! Error in private$readOutputs(paste0(private$mainPath, "/results/KEELToPMML/TST", : Results were not stored. Execution error.
> 
> #Rules in format arules
> algorithm$rules
NULL
> 
> #Show a number of rules
> algorithm$showRules(2)
Error! Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘inspect’ for signature ‘"NULL"’
> 
> #Return a data.frame with all interest measures of set rules
> algorithm$getInterestMeasures()
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘quality’ for signature ‘"NULL"’
Calls: <Anonymous> -> <Anonymous> -> <Anonymous>
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data      1.0Mb
    extdata   3.1Mb
Running examples in ‘Rlibeemd-Ex.R’ failed
The error most likely occurred in:

> ### Name: ceemdan
> ### Title: CEEMDAN decomposition
> ### Aliases: ceemdan
> 
> ### ** Examples
> 
> imfs <- ceemdan(UKgas, threads = 1)
Error reported by gsl_linalg_solve_tridiag: tried to divide by zero
> # trend extraction
> ts.plot(UKgas, imfs[, ncol(imfs)], col = 1:2, 
+         main = "Quarterly UK gas consumption", ylab = "Million therms")
> 
> # CEEMDAN for logarithmic demand, note that increasing ensemble size 
> # will produce smoother results
> imfs <- ceemdan(log(UKgas), ensemble_size = 50, threads = 1)
Error reported by gsl_linalg_solve_tridiag: tried to divide by zero
> plot(ts.union("log(obs)" = log(UKgas), Seasonal = imfs[, 1], 
+      Irregular = rowSums(imfs[, 2:5]), Trend = imfs[, 6]), 
+      main = "Quarterly UK gas consumption")
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Error in plot.window(...) : need finite 'ylim' values
Calls: plot ... plotts -> plot.default -> localWindow -> plot.window
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    rmd   6.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    java   4.6Mb
File ‘RMC/libs/RMC.so’:
  Found ‘__1cDstdEcout_’, possibly from ‘std::cout’ (C++)
    Objects: ‘RMC.o’, ‘predict.o’
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘ap.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rmetasim/libs/rmetasim.so’:
  Found ‘__1cDstdEcout_’, possibly from ‘std::cout’ (C++)
    Objects: ‘Democlass.o’, ‘Landscape.o’, ‘PackedIndividual.o’,
      ‘rmetasim.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.
Package suggested but not available for checking: ‘RDRToolbox’
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    java  12.7Mb
Packages suggested but not available for checking: ‘rrdf’ ‘Sxslt’
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    R  10.1Mb
Package unavailable to check Rd xrefs: ‘StatDA’
Package suggested but not available for checking: ‘ROI.plugin.symphony’

Package which this enhances but not available for checking: ‘ROI.plugin.cplex’
Installation failed.
See ‘/home/ripley/R/packages/tests32/rootWishart.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘geoR’ ‘RandomFields’
Installation failed.
See ‘/home/ripley/R/packages/tests32/rpg.Rcheck/00install.out’ for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   4.9Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/Rserve.Rcheck/00install.out’ for details.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   4.8Mb
Running examples in ‘rstanarm-Ex.R’ failed
The error most likely occurred in:

> ### Name: example_model
> ### Title: Example model
> ### Aliases: example_model
> 
> ### ** Examples
> 
> example_model <- 
+   stan_glmer(cbind(incidence, size - incidence) ~ size + period + (1|herd),
+              data = lme4::cbpp, family = binomial,
+              # this next line is only to keep the example small in size!
+              chains = 2, cores = 1, seed = 12345, iter = 500)

SAMPLING FOR MODEL 'binomial' NOW (CHAIN 1).
Running ‘testthat.R’ [31s/40s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Part of the rstanarm package for estimating model parameters
  > # Copyright (C) 2015 Trustees of Columbia University
  > # 
  > # This program is free software; you can redistribute it and/or
  > # modify it under the terms of the GNU General Public License
  > # as published by the Free Software Foundation; either version 3
  > # of the License, or (at your option) any later version.
  > # 
  > # This program is distributed in the hope that it will be useful,
  > # but WITHOUT ANY WARRANTY; without even the implied warranty of
  > # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  > # GNU General Public License for more details.
  > # 
  > # You should have received a copy of the GNU General Public License
  > # along with this program; if not, write to the Free Software
  > # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  > 
  > library(testthat)
  > library(rstanarm)
  Loading required package: Rcpp
  rstanarm (Version 2.13.1, packaged: 2016-11-20 16:59:31 UTC)
  - Do not expect the default priors to remain the same in future rstanarm versions.
  Thus, R scripts should specify priors explicitly, even if they are just the defaults.
  - For execution on a local, multicore CPU with excess RAM we recommend calling
  options(mc.cores = parallel::detectCores())
  
  Attaching package: 'rstanarm'
  
  The following object is masked from 'package:testthat':
  
      compare
  
  > Sys.unsetenv("R_TESTS")
  > example(example_model)
  
  exmpl_> example_model <- 
  exmpl_+   stan_glmer(cbind(incidence, size - incidence) ~ size + period + (1|herd),
  exmpl_+              data = lme4::cbpp, family = binomial,
  exmpl_+              # this next line is only to keep the example small in size!
  exmpl_+              chains = 2, cores = 1, seed = 12345, iter = 500)
  
  SAMPLING FOR MODEL 'binomial' NOW (CHAIN 1).
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 2-7 (./children/SETTINGS-knitr.txt) 
Quitting from lines NA-7 (./children/SETTINGS-knitr.txt) 
Error: processing vignette 'aov.Rmd' failed with diagnostics:
object 'params' not found
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs        4.1Mb
    unitTests   1.0Mb
File ‘Rsundials/libs/Rsundials.so’:
  Found ‘printf’, possibly from ‘printf’ (C)
    Objects: ‘nvector_serial.o’, ‘sundials_band.o’,
      ‘sundials_smalldense.o’
  Found ‘putchar’, possibly from ‘putchar’ (C)
    Objects: ‘nvector_serial.o’, ‘sundials_band.o’,
      ‘sundials_smalldense.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 46-54 (trie_usage.Rmd) 
Error: processing vignette 'trie_usage.Rmd' failed with diagnostics:
there is no package called 'microbenchmark'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 116-126 (using_rucrdtw.Rmd) 
Error: processing vignette 'using_rucrdtw.Rmd' failed with diagnostics:
there is no package called 'microbenchmark'
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    include   5.7Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java  10.6Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/rwirelesscom.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Running examples in ‘RxnSim-Ex.R’ failed
The error most likely occurred in:

> ### Name: RxnSim-package
> ### Title: Functions to compute chemical reaction and molecular similarity
> ### Aliases: RxnSim-package RxnSim rxnsim
> 
> ### ** Examples
> 
> ## Not run: Reaction similarity
> rs.compute('CCCO>>CCC=O', 'CC(O)C>>CC(=O)C')
Error in .jcall("org/guha/rcdk/util/Misc", "Ljava/lang/Object;", "getProperty",  : 
  RcallMethod: cannot determine object class
Calls: rs.compute ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/rzmq.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/ripley/R/packages/tests32/s2.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 34-35 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 149-195 (schumaker.Rmd) 
Error: processing vignette 'schumaker.Rmd' failed with diagnostics:
there is no package called 'microbenchmark'
Execution halted
Found the following executable files:
  vignettes/Indices_cache/html/Ceara-election_0d515408b54fd6997da9c38a8521d02a.rdb
  vignettes/SciencesPo_cache/html/Ceara-election_ecf5fc665d12287cb4f45d6dfb91d746.rdb
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
Running examples in ‘SDraw-Ex.R’ failed
The error most likely occurred in:

> ### Name: grts.line
> ### Title: Draw a equi-probable GRTS sample from a linear (line) resource.
> ### Aliases: grts.line
> ### Keywords: design survey
> 
> ### ** Examples
> 
> 
> # Draw sample
> HI.sample <- grts.line(HI.coast,100,50)
Error in spsurvey::grts(design = Equaldsgn, DesignID = "Site", type.frame = sframe.type,  : 
  
A little-endian processor is required for the grts function.
Calls: grts.line -> grts.equi -> <Anonymous>
Execution halted
Running examples in ‘Segmentor3IsBack-Ex.R’ failed
The error most likely occurred in:

> ### Name: BestSegmentation
> ### Title: BestSegmentation
> ### Aliases: BestSegmentation
> ### Keywords: R-package PDPA Segmentation
> 
> ### ** Examples
> 
> require(Segmentor3IsBack);
> N=2000 
> x=rnbinom(3*N,size=1.3,prob=rep(c(0.7,0.2,0.01),each=N));
> res=Segmentor(data=x,model=3,Kmax=10, keep=TRUE);  
Error in cumsum(datasize)[breaks[k, 1:k]] : 
  only 0's may be mixed with negative subscripts
Calls: Segmentor -> Segmentor.default
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data        1.7Mb
    sequences   2.1Mb
Running examples in ‘seqminer-Ex.R’ failed
The error most likely occurred in:

> ### Name: tabix.read.table
> ### Title: Read tabix file, similar to running tabix in command line.
> ### Aliases: tabix.read.table
> 
> ### ** Examples
> 
> fileName = system.file("vcf/all.anno.filtered.extract.vcf.gz", package = "seqminer")
> snp <- tabix.read.table(fileName, "1:196623337-196632470")
[ti_index_load] wrong magic number.
[ti_index_load] fail to load the index: /home/ripley/R/Lib32/seqminer/vcf/all.anno.filtered.extract.vcf.gz.tbi
Cannot open specified tabix file: /home/ripley/R/Lib32/seqminer/vcf/all.anno.filtered.extract.vcf.gz
[ti_index_load] wrong magic number.
[ti_index_load] fail to load the index: /home/ripley/R/Lib32/seqminer/vcf/all.anno.filtered.extract.vcf.gz.tbi
Cannot open specified tabix file: /home/ripley/R/Lib32/seqminer/vcf/all.anno.filtered.extract.vcf.gz
Error in strsplit(body, "\t") : non-character argument
Calls: tabix.read.table -> do.call -> strsplit
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    www   9.9Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    www   7.1Mb
Running examples in ‘sidier-Ex.R’ failed
The error most likely occurred in:

> ### Name: double.plot
> ### Title: Haplotype and population networks including mutations and
> ###   haplotype frequencies.
> ### Aliases: double.plot
> 
> ### ** Examples
> 
> cat(">Population1_sequence1",
+ "TTATAAAATCTA----TAGC",
+ ">Population1_sequence2",
+ "TAAT----TCTA----TAAC",
+ ">Population1_sequence3",
+ "TTATAAAAATTA----TAGC",
+ ">Population1_sequence4",
+ "TAAT----TCTA----TAAC",
+ ">Population2_sequence1",
+ "TTAT----TCGAGGGGTAGC",
+ ">Population2_sequence2",
+ "TAAT----TCTA----TAAC",
+ ">Population2_sequence3",
+ "TTATAAAA--------TAGC",
+ ">Population2_sequence4",
+ "TTAT----TCGAGGGGTAGC",
+ ">Population3_sequence1",
+ "TTAT----TCGA----TAGC",
+ ">Population3_sequence2",
+ "TTAT----TCGA----TAGC",
+ ">Population3_sequence3",
+ "TTAT----TCGA----TAGC",
+ ">Population3_sequence4",
+ "TTAT----TCGA----TAGC",
+      file = "ex2.fas", sep = "\n")
> library(ape)
> double.plot(align=read.dna(file="ex2.fas",format="fasta"))
Warning in pie.network(align = align, indel.method = indel.method, substitution.model = substitution.model,  :
  Population names defined by algorithm between character 1 and the first symbol '_' in sequences name.
Error in rep(colnames(pop2)[which(pop2 != 0)], pop2[which(pop2 != 0)]) : 
  invalid 'times' argument
Calls: double.plot -> pie.network -> pop.dist
Execution halted
Running examples in ‘simba-Ex.R’ failed
The error most likely occurred in:

> ### Name: hexgrid
> ### Title: Produces the nodes of an equidistant grid.
> ### Aliases: hexgrid
> ### Keywords: methods datagen
> 
> ### ** Examples
> 
> ## produces a grid with r=400:    
> test.grd <- hexgrid(456000, 7356700, r=400)
> ## for plotting the following is recommended as it preserves 
> ## real positions:
> library(geoR)
Error in library(geoR) : there is no package called ‘geoR’
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.7Mb
Error in re-building vignettes:
  ...
Loading required package: fingerprint

Error: processing vignette 'SimuChemPC_vignette.Rnw' failed with diagnostics:
 chunk 2 
Error in .jcall("org/guha/rcdk/util/Misc", "[Lorg/openscience/cdk/interfaces/IAtomContainer;",  : 
  RcallMethod: cannot determine object class
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 74-76 (smapr-vignette.Rmd) 
Error: processing vignette 'smapr-vignette.Rmd' failed with diagnostics:
object 'westBoundLongitude' not found
Execution halted
Running ‘testthat.R’ [112s/89s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # setting R_TESTS to empty string because of
  > # https://github.com/hadley/testthat/issues/144
  > # https://github.com/hadley/testthat/issues/86
  > # revert this when that issue in R is fixed.
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(Smisc)
  > 
  > # There shouldn't be any files in the tmp folder
  > unlink("testthat/tmp", recursive = TRUE, force = TRUE)
  > dir.create("testthat/tmp")
  > 
  > test_check("Smisc")
  1. Failure: dkbinom() sums to 1 (@test_dkbinom.R#61) ---------------------------
  `x1` not equal to 1.
  1/1 mismatches
  [1] 1 - 1 == 1.11e-15
  
  
  testthat results ================================================================
  OK: 275 SKIPPED: 0 FAILED: 1
  1. Failure: dkbinom() sums to 1 (@test_dkbinom.R#61) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/SnakeCharmR.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Quitting from lines 170-174 (pairwiseSNHT.Rnw) 
Error: processing vignette 'pairwiseSNHT.Rnw' failed with diagnostics:
invalid 'times' argument
Execution halted
Running examples in ‘soil.spec-Ex.R’ failed
The error most likely occurred in:

> ### Name: read.opus-method
> ### Title: Reads binary OPUS files containing spectroscopy
> ### Aliases: read.opus read.opus,character-method read.opus,list-method
> ### Keywords: methods
> 
> ### ** Examples
> 
> ## Original binary Opus files:
> pth = system.file(package = "soil.spec")
> lst <- as.list(list.files(path=pth, pattern="*.0$", full.names=TRUE))
> file.info(lst[[1]])
                                                 size isdir mode
/home/ripley/R/Lib32/soil.spec/icr_087266_B2.0 167196 FALSE  644
                                                             mtime
/home/ripley/R/Lib32/soil.spec/icr_087266_B2.0 2016-12-25 03:49:58
                                                             ctime
/home/ripley/R/Lib32/soil.spec/icr_087266_B2.0 2016-12-25 03:51:26
                                                             atime uid gid
/home/ripley/R/Lib32/soil.spec/icr_087266_B2.0 2016-12-25 23:46:24 501   1
                                                uname grname
/home/ripley/R/Lib32/soil.spec/icr_087266_B2.0 ripley  other
> xx <- read.opus(lst)
Error in seq.default(lxv, fxv, (fxv - lxv)/(NPT1 - 1)) : 
  wrong sign in 'by' argument
Calls: read.opus ... read.opus -> lapply -> FUN -> rev -> seq -> seq.default
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.0Mb
Package required but not available: ‘RandomFields’

Package suggested but not available for checking: ‘fastshp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot33637396a8d.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot33637396a8d.png': No such file or directory
Quitting from lines 20-30 (intro_sparkline.Rmd) 
Error: processing vignette 'intro_sparkline.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running examples in ‘sparsesvd-Ex.R’ failed
The error most likely occurred in:

> ### Name: sparsesvd
> ### Title: Singular Value Decomposition of a Sparse Matrix.
> ### Aliases: sparsesvd
> 
> ### ** Examples
> 
> M <- rbind(
+   c(20, 10, 15,  0,  2),
+   c(10,  5,  8,  1,  0),
+   c( 0,  1,  2,  6,  3),
+   c( 1,  0,  0, 10,  5))
> M <- Matrix::Matrix(M, sparse=TRUE)
> print(M)
4 x 5 sparse Matrix of class "dgCMatrix"
                  
[1,] 20 10 15  . 2
[2,] 10  5  8  1 .
[3,]  .  1  2  6 3
[4,]  1  .  . 10 5
> 
> res <- sparsesvd(M, rank=2L) # compute first 2 singular components

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

Traceback:
 1: .Call(svdLAS2_, dim(M), M@i, M@p, M@x, as.integer(rank), as.double(tol *     c(-1, 1)), as.double(kappa))
 2: sparsesvd(M, rank = 2L)
An irrecoverable exception occurred. R is aborting now ...
Running ‘formats.R’ [15s/20s]
Running the tests in ‘tests/formats.R’ failed.
Complete output:
  > ## any sparse matrix format that inherits from dMatrix should work
  > library(sparsesvd)
  > library(Matrix)
  > 
  > M <- rbind(
  +   c(20, 10, 15,  0,  2),
  +   c(10,  5,  8,  1,  0),
  +   c( 0,  1,  2,  6,  3),
  +   c( 1,  0,  0, 10,  5))
  > 
  > res1 <- sparsesvd(as(M, "dgCMatrix")) # standard format (column-compressed)
  
   *** caught segfault ***
  address 4, cause 'memory not mapped'
  
  Traceback:
   1: .Call(svdLAS2_, dim(M), M@i, M@p, M@x, as.integer(rank), as.double(tol *     c(-1, 1)), as.double(kappa))
   2: sparsesvd(as(M, "dgCMatrix"))
  An irrecoverable exception occurred. R is aborting now ...
Running examples in ‘SpatialPack-Ex.R’ failed
The error most likely occurred in:

> ### Name: codisp
> ### Title: Codispersion Coefficient
> ### Aliases: codisp
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> ## This example uses the camg data set, available in the geoR Package
> ## (Ribeiro and Diggle, 2001).
> 
> ## required to loading the camg data set from geoR package 
> library(geoR)
Error in library(geoR) : there is no package called ‘geoR’
Execution halted
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    R      4.2Mb
    data   3.5Mb
    doc    4.9Mb
    help   5.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    1.7Mb
    etc    2.0Mb
sh: -version:  not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
sh: -version:  not found
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
sh: -version:  not found
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
sh: -version:  not found
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
sh: -version:  not found
sh: -version:  not found
sh: -version:  not found
sh: -version:  not found
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Installation failed.
See ‘/home/ripley/R/packages/tests32/sprint.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: sp

Version 3.3 of the spsurvey package was loaded successfully.


Error: processing vignette 'Area_Design.Rnw' failed with diagnostics:
 chunk 1 (label = processor) 
Error in eval(expr, envir, enclos) : 
A little-endian processor is required for this vignette.
Execution halted
Package which this enhances but not available for checking: ‘RMySQL’
Running examples in ‘StAMPP-Ex.R’ failed
The error most likely occurred in:

> ### Name: stamppFst
> ### Title: Fst Computation
> ### Aliases: stamppFst
> 
> ### ** Examples
> 
> # import genotype data and convert to allele frequecies 
> data(potato.mini, package="StAMPP")
> potato.freq <- stamppConvert(potato.mini, "r")
> 
> # Calculate pairwise Fst values between each population
> potato.fst <- stamppFst(potato.freq, 100, 95, 1)

 *** caught segfault ***
address 8, cause 'memory not mapped'
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    include   5.7Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   5.5Mb
File ‘stepPlr/libs/stepPlr.so’:
  Found ‘__f90_esfw’, possibly from ‘print’ (Fortran), ‘write’
    (Fortran)
    Object: ‘cg_descent.o’
  Found ‘__f90_eslw’, possibly from ‘print’ (Fortran), ‘write’
    (Fortran)
    Object: ‘cg_descent.o’
  Found ‘__f90_stop’, possibly from ‘stop’ (Fortran)
    Object: ‘cg_descent.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 480-491 (drivers.Rmd) 
Error: processing vignette 'drivers.Rmd' failed with diagnostics:
there is no package called 'microbenchmark'
Execution halted
Packages suggested but not available for checking: ‘tmap’ ‘tmaptools’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 108-113 (introducing-stplanr.Rmd) 
Error: processing vignette 'introducing-stplanr.Rmd' failed with diagnostics:
there is no package called 'tmap'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: mice
Loading required package: Rcpp
mice 2.25 2015-11-09
Loading required package: sas7bdat
Loading required package: nloptr
Loading required package: survival
installed size is 31.9Mb
  sub-directories of 1Mb or more:
    libs  31.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 61-64 (stRvignette.Rmd) 
Error: processing vignette 'stRvignette.Rmd' failed with diagnostics:
Process terminated
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/subprocess.Rcheck/00install.out’ for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    help   1.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.8Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
File ‘survrec/libs/survrec.so’:
  Found ‘rand_’, possibly from ‘rand’ (Fortran)
    Object: ‘bootstrap.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.
Running examples in ‘svd-Ex.R’ failed
The error most likely occurred in:

> ### Name: extmat
> ### Title: External matrices operations.
> ### Aliases: is.extmat extmat.ncol extmat.nrow extmat ematmul
> 
> ### ** Examples
> 
> ## Not run: 
> ##D library(Matrix)
> ##D f <- function(v) as.numeric(A %*% v) # Convert Matrix object back to vector
> ##D tf <- function(v) as.numeric(tA %*% v) # Convert Matrix object back to vector
> ##D 
> ##D e <- new.env()
> ##D assign("A", USCounties, e)
> ##D assign("tA", t(USCounties), e)
> ##D environment(f) <- e
> ##D environment(tf) <- e
> ##D 
> ##D m <-extmat(f, tf, nrow(USCounties), ncol(USCounties))
> ##D system.time(v1 <- propack.svd(m, neig = 10))
> ##D #   user  system elapsed 
> ##D #  0.252   0.007   0.259 
> ##D system.time(v2 <- propack.svd(as.matrix(USCounties), neig = 10))
> ##D #   user  system elapsed 
> ##D #  8.563   0.027   8.590 
> ## End(Not run)
> 
> # The largest eigenvalue and the corresponding eigenvector of a Hilbert matrix
> h <- outer(1:5000, 1:5000, function(i, j) 1 / (i + j - 1))
> v1 <- trlan.eigen(h, neig = 1)
> # Same, but using complex numbers
> v2 <- ztrlan.eigen(h, neig = 1)

 *** caught segfault ***
address 4000, cause 'memory not mapped'

Traceback:
 1: .Call("ztrlan_eigen", X, neig, opts, lambda, U)
 2: ztrlan.eigen(h, neig = 1)
An irrecoverable exception occurred. R is aborting now ...
File ‘svmpath/libs/svmpath.so’:
  Found ‘__f90_esfw’, possibly from ‘print’ (Fortran), ‘write’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’

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.
Installation failed.
See ‘/home/ripley/R/packages/tests32/sybilSBML.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/ripley/R/packages/tests32/TauStar.Rcheck/00install.out’ for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    3.9Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    3.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    rda    4.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 65-72 (tibble.Rmd) 
Error: processing vignette 'tibble.Rmd' failed with diagnostics:
there is no package called 'microbenchmark'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

sh: nproc:  not found
Quitting from lines 111-116 (Tigger-Vignette.Rmd) 
Error: processing vignette 'Tigger-Vignette.Rmd' failed with diagnostics:
error in running command: 'Illegal seek'
Execution halted
Package suggested but not available for checking: ‘rmapshaper’
Running examples in ‘TimeMachine-Ex.R’ failed
The error most likely occurred in:

> ### Name: mu.mle
> ### Title: Maximum-Likelihood Estimation of the Mutation Rate
> ### Aliases: mu.mle
> 
> ### ** Examples
> 
> # Load example dataset
> data(pdm)
> transitions <- full.transitions(pdm$unitary.transitions, pdm$loci)
> pi <- stationary.dist(transitions)
> 
> mu.int <- c(0.1, 10)
> samples <- 10
> 
> # MLE of the mutation rate for a single target population size
> n <- 10
> mle.res <- mu.mle(transitions, pi, pdm$population, n, mu.int, samples)
Error: C stack usage  75501764 is too close to the limit
Execution halted
Running ‘simple.R’
Running the tests in ‘tests/simple.R’ failed.
Complete output:
  > 
  > ## run in the R session temp.dir. which gets cleaned
  > setwd(tempdir())                        
  > 
  > ## process html -- should work everywhere
  > file.copy(system.file("examples", "simpleHtml.Rmd", package="tint"), "simpleHtml.Rmd")
  [1] TRUE
  > rmarkdown::render("simpleHtml.Rmd")
  Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  Execution halted
Running examples in ‘TPmsm-Ex.R’ failed
The error most likely occurred in:

> ### Name: image.TPCmsm
> ### Title: image method for a TPCmsm object
> ### Aliases: image.TPCmsm
> ### Keywords: hplot methods multivariate survival
> 
> ### ** Examples
> 
> # Set the number of threads
> nth <- setThreadsTP(2)
> 
> # Create survTP object
> data(heartTP)
> heartTP_obj <- with( heartTP, survTP(time1, event1, Stime, event, age=age) )
> 
> # Compute LIN conditional transition probabilities with confidence band
> TPCmsm_obj <- transLIN(heartTP_obj, s=57, t=310, x=0, conf=TRUE, n.boot=100,
+ method.boot="basic")

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

Traceback:
 1: .Call(Rf_BtoTPCmsm, lst, UT, UX, s, t, x, statenames, as.integer(nboot),     conflevel, methodboot, PACKAGE = "TPmsm")
 2: BtoTPCmsm(lst, UT, UX, s, t, xi, state.names, n.boot, conf.level,     method.boot)
 3: TransBoot.TPC(object, s, t, state.names, n.boot, conf.level,     method.boot, xi, ...)
 4: TransBoot(object, s, t, state.names, n.boot, conf.level, method.boot,     xi, ...)
 5: TransMethod.TPC(object, s, t, state.names, conf, n.boot, conf.level,     method.boot, xi = x, bw = bw, window = window, methodweights = method.weights,     ...)
 6: TransMethod(object, s, t, state.names, conf, n.boot, conf.level,     method.boot, xi = x, bw = bw, window = window, methodweights = method.weights,     ...)
 7: transLIN(heartTP_obj, s = 57, t = 310, x = 0, conf = TRUE, n.boot = 100,     method.boot = "basic")
An irrecoverable exception occurred. R is aborting now ...
File ‘tpr/libs/tpr.so’:
  Found ‘__1cDstdEcerr_’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    2.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: ggplot2

Attaching package: 'trackeR'

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

    append

Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=57.157231,-2.104296&zoom=13&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false
Quitting from lines 96-97 (TourDetrackeR.Rmd) 
Error: processing vignette 'TourDetrackeR.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/treeHFM.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ape
Loading required package: ade4
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
negative edges length changed to 0!
Quitting from lines 115-133 (DengueVignette.Rmd) 
Error: processing vignette 'DengueVignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘TSMySQL’
Package suggested but not available for checking: ‘gcmr’
Error in re-building vignettes:
  ...
Loading required package: splines
Loading required package: gamlss.data
Loading required package: gamlss.dist
Loading required package: MASS
Loading required package: nlme
Loading required package: parallel
 **********   GAMLSS Version 5.0-1  ********** 
For more on GAMLSS look at http://www.gamlss.org/
Type gamlssNews() to see new features/changes/bug fixes.

GAMLSS-RS iteration 1: Global Deviance = 803.7 
GAMLSS-RS iteration 2: Global Deviance = 803.7 
GAMLSS-RS iteration 3: Global Deviance = 803.7 
GAMLSS-RS iteration 1: Global Deviance = 805.6 
GAMLSS-RS iteration 2: Global Deviance = 805.6 
GAMLSS-RS iteration 3: Global Deviance = 805.6 
Loading required package: stats4

Attaching package: 'VGAM'

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

    ps

Loading required package: tseries
Loading required package: quantmod
Loading required package: xts
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: TTR

Attaching package: 'TTR'

The following object is masked from 'package:gamlss.dist':

    DPO

Version 0.4-0 included new data defaults. See ?getSymbols.
Warning in vglm.fitter(x = x, y = y, w = w, offset = offset, Xm2 = Xm2,  :
  iterations terminated because half-step sizes are very small
Warning in vglm.fitter(x = x, y = y, w = w, offset = offset, Xm2 = Xm2,  :
  some quantities such as z, residuals, SEs may be inaccurate due to convergence at a half-step

Error: processing vignette 'tsglm.Rnw' failed with diagnostics:
 chunk 40 (label = gcmr-package) 
Error in library("gcmr") : there is no package called 'gcmr'
Execution halted
Packages suggested but not available for checking: ‘TSMySQL’ ‘RMySQL’
Packages unavailable to check Rd xrefs: ‘TSMySQL’, ‘RMySQL’
Package unavailable to check Rd xrefs: ‘TSMySQL’
Package required but not available: ‘OpenMx’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc   8.2Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/uroot.Rcheck/00install.out’ for details.
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    data  14.9Mb
installed size is 29.8Mb
  sub-directories of 1Mb or more:
    data  29.1Mb
Packages suggested but not available for checking:
  ‘microbenchmark’ ‘RMySQL’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'purrr'

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

    contains, order_by

Quitting from lines 280-302 (valr.Rmd) 
Error: processing vignette 'valr.Rmd' failed with diagnostics:
there is no package called 'microbenchmark'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 24-36 (intro_to_vegalite.Rmd) 
Error: processing vignette 'intro_to_vegalite.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    1.3Mb
    help   2.7Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc           3.8Mb
    htmlwidgets   3.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 22-27 (Introduction-to-visNetwork.Rmd) 
Error: processing vignette 'Introduction-to-visNetwork.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    extdata  11.3Mb
Found the following significant warnings:
  "predict.c", line 112: warning: improper pointer/integer combination: op "<"
See ‘/home/ripley/R/packages/tests32/VLMC.Rcheck/00install.out’ for details.
Running examples in ‘walkr-Ex.R’ failed
The error most likely occurred in:

> ### Name: complete_solution
> ### Title: Complete Solution
> ### Aliases: complete_solution
> 
> ### ** Examples
> 
> A <- matrix(1, ncol = 3)
> b <- 0.5
> complete_solution(A, b)

 *** caught segfault ***
address 4c00000, cause 'memory not mapped'
Running ‘test-all.R’ [23s/31s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("walkr")
  Loading required package: walkr
  Loading required package: ggplot2
  
   *** caught segfault ***
  address fa912000, cause 'memory not mapped'
Error in re-building vignettes:
  ...
Loading required package: ggplot2

 *** caught segfault ***
address 5000000, cause 'memory not mapped'
Installation failed.
See ‘/home/ripley/R/packages/tests32/wand.Rcheck/00install.out’ for details.
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc  12.3Mb
Package suggested but not available for checking: ‘iptools’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 96-98 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running examples in ‘webuse-Ex.R’ failed
The error most likely occurred in:

> ### Name: webuse
> ### Title: webuse
> ### Aliases: webuse webuselist webuse-package
> 
> ### ** Examples
> 
> webuse("auto")
Error in df_parse_dta_raw(spec, encoding) : 
  Failed to parse file: Invalid file, or file has unsupported features.
Calls: webuse -> read_dta -> df_parse_dta_raw -> .Call
Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/Wmisc.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 37-39 (wordcloud.Rmd) 
Error: processing vignette 'wordcloud.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    data  13.4Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  11.9Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    data  14.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 597-620 (wrswoR.Rmd) 
Error: processing vignette 'wrswoR.Rmd' failed with diagnostics:
package 'microbenchmark' not found
Execution halted
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    java  17.5Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    java   4.9Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    java  10.9Mb
Found the following significant warnings:
  "NodeGC.c", line 385: warning: improper pointer/integer combination: op "=="
See ‘/home/ripley/R/packages/tests32/XML.Rcheck/00install.out’ for details.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    exampleData   1.5Mb
    examples      4.6Mb
Running examples in ‘XRJulia-Ex.R’ failed
The error most likely occurred in:

> ### Name: JuliaFunction-class
> ### Title: Proxy Objects in R for Julia Functions
> ### Aliases: JuliaFunction JuliaFunction-class
> ###   initialize,JuliaFunction-method
> 
> ### ** Examples
> 
> if(findJulia(test = TRUE)) {
+   set.seed(228)
+   x <- matrix(rnorm(1000),20,5)
+   xm <- juliaSend(x)
+   svdJ <- JuliaFunction("svdfact")
+   sxm <- svdJ(xm)
+   sxm
+ }
sh: no:  not found

Error in .Object$initialize(...) : 
  Unable to start Julia connection on port 1251: all connections are in use
Calls: juliaSend ... <Anonymous> -> new -> initialize -> initialize -> <Anonymous>
Execution halted
Running examples in ‘XRPython-Ex.R’ failed
The error most likely occurred in:

> ### Name: RPython
> ### Title: An Evaluator for the Python Interface.
> ### Aliases: RPython
> 
> ### ** Examples
> 
> ev <- RPython()
> xx <- ev$Eval("[1, %s, 5]", pi)
Error in python.exec(expr) : 'dict' object has no attribute 'has_key'
Calls: <Anonymous> -> ServerEval -> python.exec
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/xyz.Rcheck/00install.out’ for details.
Running examples in ‘anametrix-Ex.R’ failed
The error most likely occurred in:

> ### Name: authenticate
> ### Title: authenticate
> ### Aliases: authenticate
> 
> ### ** Examples
> 
> username <- "demo.user@demoanametrix.com"
> password <- "password"
> auth     <- authenticate("https://demo.anametrix.com/api", username, password)
Failed to authenticate with Anametrix API 
Error: Connection timed out after 100010 milliseconds 
Error in xmlTreeParse(resp) : object 'resp' not found
Calls: authenticate -> xmlTreeParse
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 31-44 (apcluster.Rnw) 
Error: processing vignette 'apcluster.Rnw' failed with diagnostics:
there is no package called 'kebabs'
Execution halted
Packages suggested but not available for checking: ‘cacheSweave’ ‘weaver’
Error in re-building vignettes:
  ...
Warning in summary.cross(cross) :
  Some markers at the same position on chr 1B1,1D,2B,2D1,3A,3B,3D,4A,5A,5B,5D,6D,7A,7B,7D; use jittermap().
Warning in summary.cross(cross) :
  Some chromosomes > 1000 cM in length; there may be a problem with the genetic map.
  (Perhaps it is in basepairs?)
Warning in summary.cross(cross) :
  Some markers at the same position on chr L.1,L.2,L.3,L.4,L.5,L.6,L.7,L.8,L.9; use jittermap().
Warning in heatMap(mapBC6, chr = c("L.3", "L.5", "L.8", "L.9"), lmax = 70) :
  Running est.rf.
Warning in summary.cross(cross) :
  Some markers at the same position on chr L.1,L.2,L.3,L.4,L.5,L.6,L.7; use jittermap().
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in predictExtrapUp(alpha, lambda, beta, predictPositionsRescaled[depthIndRange],  :
  Unable to find suitable chronologies for top of core - truncated to date of extraction
Warning in predictExtrapUp(alpha, lambda, beta, predictPositionsRescaled[depthIndRange],  :
  Unable to find suitable chronologies for top of core - truncated to date of extraction
Warning in predictExtrapUp(alpha, lambda, beta, predictPositionsRescaled[depthIndRange],  :
  Unable to find suitable chronologies for top of core - truncated to date of extraction
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is 117.6Mb
  sub-directories of 1Mb or more:
    include  117.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 471-483 (the_clusterR_package.Rmd) 
Error: processing vignette 'the_clusterR_package.Rmd' failed with diagnostics:
std::bad_alloc
Execution halted
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   7.4Mb
Error in re-building vignettes:
  ...
Observations with missing time information found - removing 1 rows
Discrete time points created:  3
Warning:  measures of time dependent predictor 1 occurring at final measurement occasion removed, as they have no time to impact processes
Extracting first non-missing value for time independent predictors
imputedefs==FALSE (default, recommended) so setting observations with no time value to NA
Running ctsemCarefulFit with 16 parameters

Begin fit attempt 1 of at maximum 16 tries

 Lowest minimum so far:  30875.4163174822

 OpenMx status code 6 not in list of acceptable status codes, 0
 OpenMx status code 6 not in list of acceptable status codes, 0
Error in eigen(fit$output$calculatedHessian, symmetric = T, only.values = T) : 
  infinite or missing values in 'x'

 Eigenvalues of Hessian could not be calculated

Begin fit attempt 2 of at maximum 16 tries

 *** caught segfault ***
address 0, cause 'memory not mapped'
Error in runHelper(model, frontendStart, intervals, silent, suppressWarnings,  : 
  Requested improper value (2, 1) from (1, 1) matrix
Warning: stack imbalance in '<-', 234 then 235
Warning: stack imbalance in 'lapply', 250 then 251
Running ‘testthat.R’ [16s/40s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(curl)
  > 
  > test_check("curl")
  This is libcurl version 7.48.0 with OpenSSL/1.0.1t 
  Using test server: https://http2bin.org 
  1. Failure: Keep-Alive (@test-handle.R#31) -------------------------------------
  any(grepl("existing connection", req)) isn't true.
  
  
  TLSv1.2 (OUT), TLS alert, Client hello (1):
  testthat results ================================================================
  OK: 122 SKIPPED: 0 FAILED: 1
  1. Failure: Keep-Alive (@test-handle.R#31) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(DataExplorer)
  > 
  > test_check("DataExplorer")
  1. Error: test if report is generated (@test-generate-report.r#8) --------------
  pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  1: GenerateReport(iris, output_file = file_name, output_dir = dir_name, quiet = TRUE) at testthat/test-generate-report.r:8
  2: render(input = report_dir, output_file = output_file, output_dir = output_dir, intermediates_dir = output_dir, 
         params = list(data = input_data, fun_options = list()), ...)
  3: pandoc_available(required_pandoc, error = TRUE)
  4: stop(paste(msg, collapse = " "), call. = FALSE)
  
  testthat results ================================================================
  OK: 34 SKIPPED: 0 FAILED: 1
  1. Error: test if report is generated (@test-generate-report.r#8) 
  
  Error: testthat unit tests failed
  Execution halted
ToGraphViz: no visible binding for global variable ‘create_nodes’
ToGraphViz: possible error in create_graph(nodes, edges, graph_attrs =
  graphAttributes, node_attrs = nodeAttributes, edge_attrs =
  edgeAttributes): unused arguments (graph_attrs = graphAttributes,
  node_attrs = nodeAttributes, edge_attrs = edgeAttributes)
Undefined global functions or variables:
  create_nodes
Running examples in ‘data.tree-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot.Node
> ### Title: Plot a graph, or get a graphviz dot representation of the tree
> ### Aliases: GetDefaultTooltip SetEdgeStyle SetGraphStyle SetNodeStyle
> ###   ToGraphViz plot.Node
> 
> ### ** Examples
> 
> data(acme)
> SetGraphStyle(acme, rankdir = "TB")
> SetEdgeStyle(acme, arrowhead = "vee", color = "grey35", penwidth = 2)
> #per default, Node style attributes will be inherited:
> SetNodeStyle(acme, style = "filled,rounded", shape = "box", fillcolor = "GreenYellow", 
+              fontname = "helvetica", tooltip = GetDefaultTooltip)
> SetNodeStyle(acme$IT, fillcolor = "LightBlue", penwidth = "5px")
> #inheritance can be avoided:
> SetNodeStyle(acme$Accounting, inherit = FALSE, fillcolor = "Thistle", 
+              fontcolor = "Firebrick", tooltip = "This is the accounting department")
> SetEdgeStyle(acme$Research$`New Labs`, 
+              color = "red", 
+              label = "Focus!", 
+              penwidth = 3, 
+              fontcolor = "red")
> #use Do to set style on specific nodes:
> Do(acme$leaves, function(node) SetNodeStyle(node, shape = "egg"))
> plot(acme)
Error in do.call(create_nodes, myargs) : object 'create_nodes' not found
Calls: plot -> plot.Node -> ToGraphViz -> do.call
Execution halted
Running ‘testthat.R’ [15s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("data.tree")
  Loading required package: data.tree
  1. Error: grViz (@test-draw.R#18) ----------------------------------------------
  object 'create_nodes' not found
  1: ToGraphViz(acme, direction = "descend", pruneFun = function(x) x$level < 3) at testthat/test-draw.R:18
  2: do.call(create_nodes, myargs)
  
  2. Error: grViz single attribute (@test-draw.R#27) -----------------------------
  object 'create_nodes' not found
  1: ToGraphViz(acme) at testthat/test-draw.R:27
  2: do.call(create_nodes, myargs)
  
  3. Error: grViz single attribute names not uniuqe (@test-draw.R#67) ------------
  object 'create_nodes' not found
  1: ToGraphViz(mytree) at testthat/test-draw.R:67
  2: do.call(create_nodes, myargs)
  
                            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: 0 FAILED: 3
  1. Error: grViz (@test-draw.R#18) 
  2. Error: grViz single attribute (@test-draw.R#27) 
  3. Error: grViz single attribute names not uniuqe (@test-draw.R#67) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot36be674d9e0.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot36be674d9e0.png': No such file or directory
Quitting from lines 512-515 (data.tree.Rmd) 
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running ‘has-devel.R’
  Running ‘test-that.R’ [71s/102s]
Running the tests in ‘tests/test-that.R’ failed.
Complete output:
  > library(testthat)
  > test_check("devtools")
  Loading required package: devtools
  1. Error: help and ? find files for devtools-loaded packages (@test-help.r#45) -
  invalid 'times' argument
  1: expect_true(!is.null(find_topic("foofoo"))) at testthat/test-help.r:45
  2: expect(identical(as.vector(object), TRUE), sprintf("%s isn't true.", lab), info = info)
  3: as.expectation(exp, ..., srcref = srcref)
  4: identical(as.vector(object), TRUE)
  5: as.vector(object)
  6: find_topic("foofoo")
  7: find_pkg_topic(path, topic)
  8: topic_index(pkg)
  9: build_topic_index(pkg)
  10: invert(lapply(rds, aliases))
  
  Updating collate directive in  /tmp/RtmpFEaynS/testCollateOrder/DESCRIPTION 
  
  testthat results ================================================================
  OK: 377 SKIPPED: 10 FAILED: 1
  1. Error: help and ? find files for devtools-loaded packages (@test-help.r#45) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘DPpackage/libs/DPpackage.so’:
  Found ‘__f90_esuw’, possibly from ‘write’ (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDBDPdensity.o’, ‘LDDPdensity.o’,
      ‘LDDPsurvival.o’, ‘LDPDdoublyintsba.o’, ‘LDTFPdensity.o’,
      ‘LDTFPglmmpois.o’, ‘LDTFPsurvival.o’, ‘PSgamgam.o’,
      ‘PSgamgauss.o’, ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.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.
Error in re-building vignettes:
  ...
Loading required package: foreign
This is vegdata 0.9

No Turbowin installation path found. 

############################################################
Turboveg root directory is set to "/tmp/Rtmpo9aiUB"
If you want to change this use: options(tv_home="<path_to_your_Turbowin_root>")
############################################################
Quitting from lines 51-61 (eHOF.Rnw) 
Error: processing vignette 'eHOF.Rnw' failed with diagnostics:
unsupported conversion from 'CP437' to ''
Execution halted
Running ‘testthat.R’ [18s/24s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > if (packageVersion("testthat") >= "0.9.1") {
  +   library(testthat)
  +   test_check("emil")
  + }
  Loading required package: emil
  
  Attaching package: 'emil'
  
  The following object is masked from 'package:base':
  
      mode
  
  1. Error: glmnet (@test-methods.r#23) ------------------------------------------
  dim(X) must have a positive length
  1: fit_glmnet(iris[-5], iris$Species) at testthat/test-methods.r:23
  2: glmnet::cv.glmnet(x, y, family = family, nfolds = nfolds, foldid = foldid, alpha = alpha, 
         lambda = lambda, ...)
  3: apply(nz, 1, median)
  4: stop("dim(X) must have a positive length")
  
  testthat results ================================================================
  OK: 182 SKIPPED: 0 FAILED: 1
  1. Error: glmnet (@test-methods.r#23) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘emIRT-Ex.R’ failed
The error most likely occurred in:

> ### Name: dynIRT
> ### Title: Dynamic IRT estimation via Variational Inference
> ### Aliases: dynIRT
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> 
> ### Replication of Martin-Quinn Judicial Ideology Scores
> ### Based on July 23, 2014 (2014 Release 01) release of the Supreme Court Database
> ### Start values and priors based on replication code provided by Kevin Quinn
> 
> data(mq_data)
> 
> ## Estimate dynamic variational model using dynIRT()
> lout <- dynIRT(.data = mq_data$data.mq,
+                     .starts = mq_data$cur.mq,
+                     .priors = mq_data$priors.mq,
+                     .control = {list(
+                     threads = 1,
+                     verbose = TRUE,
+                     thresh = 1e-6,
+ 		    maxit=500
+                     )})

==================== 
dynIRT: Dynamic IRT via Variational Inference


error: Mat::init(): size is fixed and hence cannot be changed
terminate called after throwing an instance of 'std::logic_error'
  what():  Mat::init(): size is fixed and hence cannot be changed
Running examples in ‘fBasics-Ex.R’ failed
The error most likely occurred in:

> ### Name: akimaInterp
> ### Title: Bivariate Spline Interpolation
> ### Aliases: akimaInterp akimaInterpp
> ### Keywords: programming
> 
> ### ** Examples
>  
> ## akimaInterp -
>    # Akima Interpolation:    
>    if (require(akima)) {
+      set.seed(1953)
+      x = runif(999) - 0.5
+      y = runif(999) - 0.5
+      z = cos(2*pi*(x^2+y^2))
+      ans = akimaInterp(x, y, z, gridPoints = 41, extrap = FALSE)
+      persp(ans, theta = -40, phi = 30, col = "steelblue",
+         xlab = "x", ylab = "y", zlab = "z")
+      contour(ans)
+    }
Loading required package: akima
Warning in akima::interp.new(x, y, z, xo, yo, linear = FALSE, ncp = NULL,  :
  interp.new() is deprecated, use interp()
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Error in persp.default(ans, theta = -40, phi = 30, col = "steelblue",  : 
  invalid 'z' limits
Calls: persp -> persp.default
Execution halted
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
Running examples in ‘gamsel-Ex.R’ failed
The error most likely occurred in:

> ### Name: gamsel
> ### Title: Fit Regularization Path for Gaussian or Binomial Generalized
> ###   Additive Model
> ### Aliases: gamsel
> ### Keywords: regression smooth nonparametric
> 
> ### ** Examples
> 
> data=gendata(n=500,p=12,k.lin=3,k.nonlin=3,deg=8,sigma=0.5)
> attach(data)
> bases=pseudo.bases(X,degree=10,df=6)
> # Gaussian gam
> gamsel.out=gamsel(X,y,bases=bases)
> par(mfrow=c(1,2),mar=c(5,4,3,1))
> summary(gamsel.out)
> gamsel.cv=cv.gamsel(X,y,bases=bases)
> par(mfrow=c(1,1))
> plot(gamsel.cv)
> par(mfrow=c(3,4))
> plot(gamsel.out,newx=X,index=20)
> # Binomial model
> gamsel.out=gamsel(X,yb,family="binomial")

 *** caught segfault ***
address 663c83f1, cause 'memory not mapped'

Traceback:
 1: .Call("gamselFit", y, X, U, tol, degrees, D_mat, gamma, psi,     family_id, max_iter, lambda, num_lambda, as.integer(traceit))
 2: gamsel(X, yb, family = "binomial")
An irrecoverable exception occurred. R is aborting now ...
Running ‘run-all.R’ [20s/23s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check('gapfill')
  Loading required package: gapfill
  Loading required package: ggplot2
  1. Error: Image (@test-Image.R#5) ----------------------------------------------
  formal argument "line" matched by multiple actual arguments
  1: expect_equal(class(Image(ndvi)), c("gg", "ggplot")) at testthat/test-Image.R:5
  2: compare(object, expected, ...)
  3: Image(ndvi)
  4: theme(line = element_blank(), strip.background = element_rect(fill = "white", color = "white"), 
         strip.text.x = element_text(), strip.text.y = element_text(), axis.ticks = element_blank(), 
         axis.text.x = element_blank(), axis.text.y = element_blank(), axis.title.x = element_blank(), 
         axis.title.y = element_blank(), line = element_blank(), legend.position = "right", 
         panel.border = element_blank(), plot.margin = unit(c(1, 1, 1, 1), "mm"), panel.margin = unit(2, 
             "mm"))
  
  testthat results ================================================================
  OK: 859 SKIPPED: 0 FAILED: 1
  1. Error: Image (@test-Image.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc        1.5Mb
    examples   1.7Mb
    vign       1.4Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra
Warning: Ignoring unknown aesthetics: data_id, tooltip
Warning: Ignoring unknown aesthetics: data_id, tooltip
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot1bcc46781c34.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot1bcc46781c34.png': No such file or directory
Quitting from lines 28-33 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot54895f3c12b5.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot54895f3c12b5.png': No such file or directory
Quitting from lines 13-27 (an_introduction.Rmd) 
Error: processing vignette 'an_introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running ‘testthat.R’ [23s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ggplot2)
  > 
  > test_check("ggplot2")
  1. Failure: inherits timezone from data (@test-scale-date.R#18) ----------------
  sc$timezone not equal to NULL.
  Types not compatible: character vs NULL
  
  
  testthat results ================================================================
  OK: 778 SKIPPED: 0 FAILED: 1
  1. Failure: inherits timezone from data (@test-scale-date.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
Running examples in ‘IAPWS95-Ex.R’ failed
The error most likely occurred in:

> ### Name: TDh
> ### Title: Temperature, Function of Density and Enthalpy
> ### Aliases: TDh
> 
> ### ** Examples
> 
> D <- 838.025
> h <- 977.181624
> TDh(D,h)
Running examples in ‘ifa-Ex.R’ failed
The error most likely occurred in:

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

 *** caught segfault ***
address a61a78f8, cause 'memory not mapped'

Traceback:
 1: sub(".*\\.", "", x)
 2: fileExt(file)
 3: data(memory)
An irrecoverable exception occurred. R is aborting now ...
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    help   1.3Mb
    libs   7.1Mb
installed size is 209.2Mb
  sub-directories of 1Mb or more:
    extdata  208.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   5.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: `legend.margin` must be specified using `margin()`. For the old behavior use legend.spacing
largeVis was compiled with 32-bit types. This will limit the size of the datasets it can process. Consider recompiling with -DARMA_64BIT_WORD
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Warning: `legend.margin` must be specified using `margin()`. For the old behavior use legend.spacing
Error: C stack usage  242970384 is too close to the limit
Warning: stack imbalance in '.Call', 267 then 265
Warning: stack imbalance in '{', 264 then 262
Warning: stack imbalance in '<-', 257 then 255
terminate called after throwing an instance of 'std::logic_error'
  what():  Mat::col(): index out of bounds
installed size is 26.2Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs     24.0Mb
Running ‘testthat.R’ [20s/23s]
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. Error: interval handles POSIXlt inputs (@test-intervals.R#86) ---------------
  invalid 'tz' value
  1: expect_equal(interval(t1, t2), new("Interval", 18316800, start = as.POSIXct("2007-01-01", 
         tz = "UTC"), tzone = "UTC")) at testthat/test-intervals.R:86
  2: compare(object, expected, ...)
  3: interval(t1, t2)
  4: as.POSIXct(start, tz = tzone)
  5: as.POSIXct.POSIXlt(start, tz = tzone)
  
  testthat results ================================================================
  OK: 2152 SKIPPED: 0 FAILED: 1
  1. Error: interval handles POSIXlt inputs (@test-intervals.R#86) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Warning in arrange_impl(.data, dots) :
  '.Random.seed' is not an integer vector but of type 'NULL', so ignored
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot1142d244043.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot1142d244043.png': No such file or directory
Quitting from lines 95-96 (manhattanly.Rmd) 
Error: processing vignette 'manhattanly.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot732011545ef2.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot732011545ef2.png': No such file or directory
Quitting from lines 63-70 (manipulateWidgets.Rmd) 
Error: processing vignette 'manipulateWidgets.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.0Mb
Running examples in ‘mcPAFit-Ex.R’ failed
The error most likely occurred in:

> ### Name: mcPAFit
> ### Title: estimates the Preferential Attachment function in a temporal
> ###   complex network without temporal information.
> ### Aliases: mcPAFit
> ### Keywords: package Preferential Attachment function Markov chain Monte
> ###   Carlo Gibbs sampling missing timeline
> 
> ### ** Examples
> 
> library(mcPAFit)
> N      <- 1000 #number of nodes in the network 
> M      <- 500  #number of needed sample
> lag   <-  1
> start <-  100
> 
> data   <- create_sim_data(N = N, alpha = 1)
> write.table(data$random[,1:2], row.names = FALSE,
+             col.names = FALSE, file = "input.txt")
> system.time(mcPAFit(file_name = "input.txt",burn_in = 0, s = 5, skip = 1, 
+             needed_sample = M, G = 20,only_active_node = 1, random = 0))
terminate called after throwing an instance of 'std::out_of_range'
  what():  vector::_M_range_check: __n (which is 161132824) >= this->size() (which is 20)
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
installed size is 191.2Mb
  sub-directories of 1Mb or more:
    libs  190.9Mb
Error in re-building vignettes:
  ...
Loading required package: alphahull
Loading required package: rgl
Loading required package: Rvcg
Quitting from lines 56-57 (molaR_vignette.Rmd) 
Error: processing vignette 'molaR_vignette.Rmd' failed with diagnostics:
alpha adjustment required
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R         2.5Mb
    include   3.2Mb
Running ‘test-all.R’
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > if(require("testthat", quietly = TRUE)) {
  +     test_check("nloptr")
  + } else {
  +     print( "package 'testthat' not available, cannot run unit tests" )
  + }
  Loading required package: nloptr
  1. Failure: Test NLopt tutorial example with NLOPT_LN_COBYLA with gradient information. (@test-example.R#101) 
  res1$solution not equal to `solution.opt`.
  2/2 mismatches (average diff: 0.00818)
  [1] 0.328 - 0.333 == -0.00572
  [2] 0.307 - 0.296 ==  0.01064
  
  
  testthat results ================================================================
  OK: 42 SKIPPED: 0 FAILED: 1
  1. Failure: Test NLopt tutorial example with NLOPT_LN_COBYLA with gradient information. (@test-example.R#101) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘run-all.R’ [31s/35s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > #  Copyright 2013 Christian Sigg
  > #
  > #  This program is free software; you can redistribute it and/or modify
  > #  it under the terms of the GNU General Public License as published by
  > #  the Free Software Foundation; either version 2 of the License, or
  > #  (at your option) any later version.
  > #
  > #  This program is distributed in the hope that it will be useful,
  > #  but WITHOUT ANY WARRANTY; without even the implied warranty of
  > #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  > #  GNU General Public License for more details.
  > #
  > #  A copy of the GNU General Public License is available at
  > #  http://www.r-project.org/Licenses/
  > 
  > library(testthat)
  > library(MASS)
  > library(glmnet)
  Loading required package: Matrix
  Loading required package: foreach
  Loaded glmnet 2.0-5
  
  > library(nscancor)
  > 
  > test_check("nscancor")
  1. Error: non-negative sparse CCA correlation equivalence (@test_acor.R#73) ----
  v collapsed to the zero vector, try relaxing the constraints
  1: equiv(10, 5) at testthat/test_acor.R:73
  2: nscancor(X, Y, xpredict = xpredict, ypredict = xpredict) at testthat/test_acor.R:70
  3: nscc_inner(X, Xp, Y, Yp, xpredict, ypredict, cc, iter_tol, iter_max, verbosity)
  4: stop("v collapsed to the zero vector, try relaxing the constraints")
  
  testthat results ================================================================
  OK: 83 SKIPPED: 0 FAILED: 1
  1. Error: non-negative sparse CCA correlation equivalence (@test_acor.R#73) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘oblique.tree-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot.trim.sequence
> ### Title: Plot a Trim Sequence
> ### Aliases: plot.trim.sequence
> ### Keywords: tree
> 
> ### ** Examples
> 
> #grow an oblique tree
> data(Pima.tr, package="MASS")
> ob.tree <- oblique.tree(	type~.,
+ 				Pima.tr,
+ 				oblique.splits="only",
+ 				variable.selection="model.selection.aic")
> 
> #look at the tree
> plot(ob.tree);text(ob.tree)
> 
> #and its trim sequence
> plot(trim.oblique.tree(ob.tree))
Error in list.of.node.names.to.prune[[list.index]] : 
  subscript out of bounds
Calls: plot ... trim.once -> oblique.tree.prune.nodes -> %in% -> match
Execution halted
Running examples in ‘openssl-Ex.R’ failed
The error most likely occurred in:

> ### Name: cert_verify
> ### Title: X509 certificates
> ### Aliases: cert_verify download_ssl_cert ca_bundle
> 
> ### ** Examples
> 
> # Verify the r-project HTTPS cert
> chain <- download_ssl_cert("www.r-project.org", 443)
> print(chain)
[[1]]
[x509 certificate] FG800C3912801741
md5: 1b5cca4b7fb5e85281bd2ee3f083970f
sha1: 24a7bdbb25ebce5d7c18b4ff9a8cf02958522a68

> print(as.list(chain[[1]])$pubkey)
[2048-bit rsa public key]
md5: 53bcd5f63407760ce4e868bf565e37b7
> cert_verify(chain, ca_bundle())
Error in cert_verify_cert(cert[[1]], cert[-1], root) : 
  Certificate validation failed: self signed certificate
Calls: cert_verify -> cert_verify_cert -> .Call
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      2.8Mb
    data   2.4Mb
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    libs  25.3Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(postGIStools)
  Loading required package: sp
  > 
  > test_check("postGIStools")
  
   *** caught segfault ***
  address b0bc4c44, cause 'memory not mapped'
  Error in doWithOneRestart(return(expr), restart) : 
    promise already under evaluation: recursive default argument reference or earlier problems?
Packages which this enhances but not available for checking:
  ‘org.Ag.eg.db’ ‘org.Pt.eg.db’ ‘org.Rn.eg.db’ ‘org.Ss.eg.db’
  ‘org.Bt.eg.db’ ‘org.Ce.eg.db’ ‘org.Cf.eg.db’ ‘org.Dm.eg.db’
  ‘org.Dr.eg.db’ ‘org.EcSakai.eg.db’ ‘org.Gg.eg.db’ ‘org.Mmu.eg.db’
  ‘org.Pf.plasmo.db’ ‘org.Xl.eg.db’
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    contrib   3.7Mb
    doc       3.2Mb
    libs      1.0Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.7Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    include   4.0Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    include   1.5Mb
    lib       3.0Mb
    libs      1.2Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    include   3.7Mb
    lib       5.1Mb
    libs      1.6Mb
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help  10.6Mb
    libs   7.8Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc   9.5Mb
installed size is 46.5Mb
  sub-directories of 1Mb or more:
    exe  46.5Mb
Running examples in ‘RKEEL-Ex.R’ failed
The error most likely occurred in:

> ### Name: Alatasetal_A
> ### Title: Alatasetal_A KEEL Association Rules Algorithm
> ### Aliases: Alatasetal_A R6_Alatasetal_A
> ### Keywords: association rules
> 
> ### ** Examples
> 
> 
> #Load KEEL dataset iris
> dat<-loadKeelDataset("iris")
/home/ripley/R/Lib32/RKEELdata/datasets/> 
> #Create algorithm
> algorithm <- Alatasetal_A(dat)
> 
> #Run algorithm
> algorithm$run()
Executing algorithm...
/tmp/RtmpktaiJG/experiment_2017-01-11_10-08-002656/results/KEELToPMML/TSTAlatasetal_A/result0s0file0.pmml
Error! Error in private$readOutputs(paste0(private$mainPath, "/results/KEELToPMML/TST", : Results were not stored. Execution error.
> 
> #Rules in format arules
> algorithm$rules
NULL
> 
> #Show a number of rules
> algorithm$showRules(2)
Error! Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘inspect’ for signature ‘"NULL"’
> 
> #Return a data.frame with all interest measures of set rules
> algorithm$getInterestMeasures()
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘quality’ for signature ‘"NULL"’
Calls: <Anonymous> -> <Anonymous> -> <Anonymous>
Execution halted
Running examples in ‘Rlibeemd-Ex.R’ failed
The error most likely occurred in:

> ### Name: ceemdan
> ### Title: CEEMDAN decomposition
> ### Aliases: ceemdan
> 
> ### ** Examples
> 
> imfs <- ceemdan(UKgas, threads = 1)
Error reported by gsl_linalg_solve_tridiag: tried to divide by zero
Error reported by gsl_linalg_solve_tridiag: tried to divide by zero
Error reported by gsl_linalg_solve_tridiag: tried to divide by zero
> # trend extraction
> ts.plot(UKgas, imfs[, ncol(imfs)], col = 1:2, 
+         main = "Quarterly UK gas consumption", ylab = "Million therms")
> 
> # CEEMDAN for logarithmic demand, note that increasing ensemble size 
> # will produce smoother results
> imfs <- ceemdan(log(UKgas), ensemble_size = 50, threads = 1)
Error reported by gsl_linalg_solve_tridiag: tried to divide by zero
Error reported by gsl_linalg_solve_tridiag: tried to divide by zero
> plot(ts.union("log(obs)" = log(UKgas), Seasonal = imfs[, 1], 
+      Irregular = rowSums(imfs[, 2:5]), Trend = imfs[, 6]), 
+      main = "Quarterly UK gas consumption")
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Error in plot.window(...) : need finite 'ylim' values
Calls: plot ... plotts -> plot.default -> localWindow -> plot.window
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/Rsomoclu.Rcheck/00install.out’ for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs        4.3Mb
    unitTests   1.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data        1.7Mb
    sequences   2.1Mb
Running examples in ‘seqminer-Ex.R’ failed
The error most likely occurred in:

> ### Name: annotateGene
> ### Title: Annotate a test variant
> ### Aliases: annotateGene
> 
> ### ** Examples
> 
> param <- list(reference = system.file("tabanno/test.fa", package = "seqminer"),
+               geneFile = system.file("tabanno/test.gene.txt", package = "seqminer"))
> param <- makeAnnotationParameter(param)
> print(param)
$reference
[1] "/home/ripley/R/Lib32/seqminer/tabanno/test.fa"

$geneFile
[1] "/home/ripley/R/Lib32/seqminer/tabanno/test.gene.txt"

$geneFileFormat
[1] "refFlat"

$codonFile
[1] "/home/ripley/R/Lib32/seqminer/tabanno/codon.txt"

$priorityFile
[1] "/home/ripley/R/Lib32/seqminer/tabanno/priority.txt"

$upstreamRange
[1] 50

$downstreamRange
[1] 50

$spliceIntoExon
[1] 3

$spliceIntoIntron
[1] 8

$bed
NULL

$genomeScore
NULL

$tabix
NULL

$indexOutput
[1] FALSE

$inputFormat
[1] "vcf"

$checkReference
[1] TRUE

> annotateGene(param, c("1", "1"), c(3, 5) , c("A", "C"), c("G", "C"))
Load reference genome /home/ripley/R/Lib32/seqminer/tabanno/test.fa...
DONE: 1 chromosomes and 74 bases are loaded.
Load codon file /home/ripley/R/Lib32/seqminer/tabanno/codon.txt...
DONE: codon file loaded.
Load priority file /home/ripley/R/Lib32/seqminer/tabanno/priority.txt...
DONE: 25 priority annotation types loaded.
Load gene file /home/ripley/R/Lib32/seqminer/tabanno/test.gene.txt...
DONE: 3 gene loaded from /home/ripley/R/Lib32/seqminer/tabanno/test.gene.txt.

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

Traceback:
 1: .Call("annotateGene", param, chrom, position, ref, alt, PACKAGE = "seqminer")
 2: annotateGene(param, c("1", "1"), c(3, 5), c("A", "C"), c("G",     "C"))
An irrecoverable exception occurred. R is aborting now ...
Running examples in ‘SMCP-Ex.R’ failed
The error most likely occurred in:

> ### Name: SMCP
> ### Title: Smoothed minimax concave penalization (SMCP) method for
> ###   genome-wide association studies.
> ### Aliases: SMCP sp
> ### Keywords: model fitting
> 
> ### ** Examples
> 
> x=matrix(rnorm(100*20),100,20)
> y=rnorm(100)
> fit=SMCP(x,y,0.3,0.3,3)
> #solution path for this data
> s.p=sp(x,y,0.3,10,0.05,3)
Error in SMCP(x, y, alpha, delta * i, gamma) : 
  NA/NaN/Inf in foreign function call (arg 6)
Calls: sp -> SMCP -> .C
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot60ec820352.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot60ec820352.png': No such file or directory
Quitting from lines 20-30 (intro_sparkline.Rmd) 
Error: processing vignette 'intro_sparkline.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running ‘formats.R’ [4s/12s]
Running the tests in ‘tests/formats.R’ failed.
Complete output:
  > ## any sparse matrix format that inherits from dMatrix should work
  > library(sparsesvd)
  > library(Matrix)
  > 
  > M <- rbind(
  +   c(20, 10, 15,  0,  2),
  +   c(10,  5,  8,  1,  0),
  +   c( 0,  1,  2,  6,  3),
  +   c( 1,  0,  0, 10,  5))
  > 
  > res1 <- sparsesvd(as(M, "dgCMatrix")) # standard format (column-compressed)
  
   *** caught segfault ***
  address 4, cause 'memory not mapped'
  
  Traceback:
   1: .Call(svdLAS2_, dim(M), M@i, M@p, M@x, as.integer(rank), as.double(tol *     c(-1, 1)), as.double(kappa))
   2: sparsesvd(as(M, "dgCMatrix"))
  An irrecoverable exception occurred. R is aborting now ...
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    R      4.2Mb
    data   3.5Mb
    doc    4.9Mb
    help   5.0Mb
    libs   1.5Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 108-112 (introducing-stplanr.Rmd) 
Error: processing vignette 'introducing-stplanr.Rmd' failed with diagnostics:
could not find function "read_osm"
Execution halted
Package suggested but not available for checking: ‘h2oEnsemble’
installed size is 32.3Mb
  sub-directories of 1Mb or more:
    libs  31.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.8Mb
Running examples in ‘svd-Ex.R’ failed
The error most likely occurred in:

> ### Name: extmat
> ### Title: External matrices operations.
> ### Aliases: is.extmat extmat.ncol extmat.nrow extmat ematmul
> 
> ### ** Examples
> 
> ## Not run: 
> ##D library(Matrix)
> ##D f <- function(v) as.numeric(A %*% v) # Convert Matrix object back to vector
> ##D tf <- function(v) as.numeric(tA %*% v) # Convert Matrix object back to vector
> ##D 
> ##D e <- new.env()
> ##D assign("A", USCounties, e)
> ##D assign("tA", t(USCounties), e)
> ##D environment(f) <- e
> ##D environment(tf) <- e
> ##D 
> ##D m <-extmat(f, tf, nrow(USCounties), ncol(USCounties))
> ##D system.time(v1 <- propack.svd(m, neig = 10))
> ##D #   user  system elapsed 
> ##D #  0.252   0.007   0.259 
> ##D system.time(v2 <- propack.svd(as.matrix(USCounties), neig = 10))
> ##D #   user  system elapsed 
> ##D #  8.563   0.027   8.590 
> ## End(Not run)
> 
> # The largest eigenvalue and the corresponding eigenvector of a Hilbert matrix
> h <- outer(1:5000, 1:5000, function(i, j) 1 / (i + j - 1))
> v1 <- trlan.eigen(h, neig = 1)
> # Same, but using complex numbers
> v2 <- ztrlan.eigen(h, neig = 1)

 *** caught segfault ***
address 18feffac, cause 'memory not mapped'

Traceback:
 1: .Call("ztrlan_eigen", X, neig, opts, lambda, U)
 2: ztrlan.eigen(h, neig = 1)
An irrecoverable exception occurred. R is aborting now ...
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Running examples in ‘TimeMachine-Ex.R’ failed
The error most likely occurred in:

> ### Name: mu.mle
> ### Title: Maximum-Likelihood Estimation of the Mutation Rate
> ### Aliases: mu.mle
> 
> ### ** Examples
> 
> # Load example dataset
> data(pdm)
> transitions <- full.transitions(pdm$unitary.transitions, pdm$loci)
> pi <- stationary.dist(transitions)
> 
> mu.int <- c(0.1, 10)
> samples <- 10
> 
> # MLE of the mutation rate for a single target population size
> n <- 10
> mle.res <- mu.mle(transitions, pi, pdm$population, n, mu.int, samples)
Error: C stack usage  184836240 is too close to the limit
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    2.7Mb
Running examples in ‘wbsts-Ex.R’ failed
The error most likely occurred in:

> ### Name: tau.fun
> ### Title: Universal thresholds
> ### Aliases: tau.fun
> ### Keywords: threshold
> 
> ### ** Examples
>  
> 
> cps=c(400,470)
> set.seed(101)
> y=sim.pw.ar(N =2000,sd_u = 1,b.slope=c(0.4,-0.6,0.5),br.loc=cps)[[2]]
> #tau.fun(y) is the default value for C_i
> #Binary segmentation
> wbs.lsw(y,M=1)$cp.aft
NULL
> #Wild binary segmentation
> wbs.lsw(y,M=3500)$cp.aft
Error in while (b < 0 | b > e) { : missing value where TRUE/FALSE needed
Calls: wbs.lsw -> uh.wbs
Execution halted
Running examples in ‘XRJulia-Ex.R’ failed
The error most likely occurred in:

> ### Name: JuliaFunction-class
> ### Title: Proxy Objects in R for Julia Functions
> ### Aliases: JuliaFunction JuliaFunction-class
> ###   initialize,JuliaFunction-method
> 
> ### ** Examples
> 
> if(findJulia(test = TRUE)) {
+   set.seed(228)
+   x <- matrix(rnorm(1000),20,5)
+   xm <- juliaSend(x)
+   svdJ <- JuliaFunction("svdfact")
+   sxm <- svdJ(xm)
+   sxm
+ }
sh: no:  not found

Error in .Object$initialize(...) : 
  Unable to start Julia connection on port 1658: all connections are in use
Calls: juliaSend ... <Anonymous> -> new -> initialize -> initialize -> <Anonymous>
Execution halted
Found the following significant warnings:
  Warning: namespace ‘unmarked’ is not available and has been replaced
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/AMModels.Rcheck/00install.out’ for details.
Running examples in ‘anametrix-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: authenticate
> ### Title: authenticate
> ### Aliases: authenticate
> 
> ### ** Examples
> 
> username <- "demo.user@demoanametrix.com"
> password <- "password"
> auth     <- authenticate("https://demo.anametrix.com/api", username, password)
Failed to authenticate with Anametrix API 
Error: Connection timed out after 100001 milliseconds 
Error in xmlTreeParse(resp) : object 'resp' not found
Calls: authenticate -> xmlTreeParse
Execution halted
Running examples in ‘animation-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: vanke1127
> ### Title: Stock prices of Vanke Co., Ltd on 2009/11/27
> ### Aliases: vanke1127
> 
> ### ** Examples
> 
> tab.price = table(vanke1127$price)
> plot(as.numeric(names(tab.price)), as.numeric(tab.price), type = 'h',
+      xlab = 'price', ylab = 'frequency')
> 
> oopt = ani.options(interval = 0.5, loop = FALSE, title = 'Stock price of Vanke')
> 
> ## a series of HTML animations with different time spans
> saveHTML({
+   price.ani(vanke1127$price, vanke1127$time, lwd = 2)
+ }, img.name = 'vanke_a', description = 'Prices changing along with time interval 15 min',
+   htmlfile = "vanke1127_1.html")
HTML file created at: vanke1127_1.html
> 
> saveHTML({
+   price.ani(vanke1127$price, vanke1127$time, span = 30 * 60, lwd = 3)
+ }, img.name = 'vanke_b', description = 'Prices changing along with time interval 30 min',
+   htmlfile = "vanke1127_2.html")
HTML file created at: vanke1127_2.html
> 
> saveHTML({
+   price.ani(vanke1127$price, vanke1127$time, span = 5 * 60, lwd = 2)
+ }, img.name = 'vanke_c', description = 'Prices changing along with time interval 5 min',
+   htmlfile = "vanke1127_3.html")
HTML file created at: vanke1127_3.html
> 
> ## GIF animation
> saveGIF(price.ani(vanke1127$price, vanke1127$time, lwd = 2),
+         movie.name = 'price.gi= 1)
+ 
+ ani.options(oopt)
+ 
+ 
+ 
+ base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
+ base::cat("vanke1127", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
Error: unexpected symbol in:
"base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
base::cat("vanke1127", base::get(".format_ptime", pos = 'CheckExEnv"
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-release-gcc/Work/PKGS/audio.Rcheck/00install.out’ for details.
Running the tests in ‘tests/testthat-biom.R’ failed.
Last 13 lines of output:
  1. Failure: show method output tests (@test-IO.R#69) ---------------------------
  `x1` produced no output
  
  
  2. Failure: show method output tests (@test-IO.R#70) ---------------------------
  `x4` produced no output
  
  
  DONE ===========================================================================
  Error: Test failures
  In addition: Warning message:
  Placing tests in `inst/tests/` is deprecated. Please use `tests/testthat/` instead 
  Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  Creating comparison table...
  Loading required namespace: htmlTable
  Creating HTML table for first 100 rows
  Error in test_check("compareDF") : 
    Assertion failed. One of the following must apply:
   * check_matrix(css.cell): Must be of type 'matrix', not 'data.frame'
   * check_character(css.cell): Must be of type 'character', not
   * 'data.frame'
  Calls: test_check ... htmlTable.data.frame -> htmlTable.default -> assert -> mstop
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/deeplearning.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/DNAprofiles.Rcheck/00install.out’ for details.
Running examples in ‘EcoHydRology-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_usgs_gage
> ### Title: A function to grab daily stream flow measurements from the USGS
> ###   waterdata.usgs.gov server.
> ### Aliases: get_usgs_gage
> 
> ### ** Examples
> 
> 
> flowgage_id="04216500"
> flowgage=get_usgs_gage(flowgage_id)
Error in file(con, "r") : cannot open the connection
Calls: get_usgs_gage -> readLines -> file
Execution halted
Error in re-building vignettes:
  ...
Retrieving result page 1
Retrieving result page 1
Retrieving result page 1
Retrieving result page 2
Retrieving result page 1
Retrieving result page 1
Retrieving result page 1
Retrieving result page 1
Retrieving result page 1
Retrieving result page 1
197 records found. Returning 100
18 records found. Returning 18
Quitting from lines 233-234 (introducing-europepmc.Rmd) 
Error: processing vignette ‘introducing-europepmc.Rmd’ failed with diagnostics:
Not Found (HTTP 404).
Execution halted
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-release-gcc/Work/PKGS/FastRWeb.Rcheck/00install.out’ for details.
Running the tests in ‘tests/run-all.R’ failed.
Last 13 lines of output:
  4: theme(line = element_blank(), strip.background = element_rect(fill = "white", color = "white"), 
         strip.text.x = element_text(), strip.text.y = element_text(), axis.ticks = element_blank(), 
         axis.text.x = element_blank(), axis.text.y = element_blank(), axis.title.x = element_blank(), 
         axis.title.y = element_blank(), line = element_blank(), legend.position = "right", 
         panel.border = element_blank(), plot.margin = unit(c(1, 1, 1, 1), "mm"), panel.margin = unit(2, 
             "mm"))
  
  testthat results ================================================================
  OK: 859 SKIPPED: 0 FAILED: 1
  1. Error: Image (@test-Image.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  5: generate_grViz(x, ...)
  6: do.call(DiagrammeR::create_nodes, create_nodes_call)
  7: DiagrammeR::create_nodes
  8: getExportedValue(pkg, name)
  9: stop(gettextf("'%s' is not an exported object from 'namespace:%s'", name, getNamespaceName(ns)), 
         call. = FALSE, domain = NA)
  
  testthat results ================================================================
  OK: 118 SKIPPED: 0 FAILED: 1
  1. Error: plotting a tree works (@test_plot.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(gesis)
  > 
  > test_check("gesis")
  1. Failure: get_study_groups() works (@test-availability.R#6) ------------------
  nrow(groups) is not strictly more than 0. Difference: 0
  
  
  testthat results ================================================================
  OK: 3 SKIPPED: 0 FAILED: 1
  1. Failure: get_study_groups() works (@test-availability.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘githubinstall-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gh_suggest
> ### Title: Suggest Github Repository from a Incomplete Name
> ### Aliases: gh_suggest
> 
> ### ** Examples
> 
> gh_suggest("AnomalyDetection")
Error in if (all(!inds)) { : missing value where TRUE/FALSE needed
Calls: gh_suggest -> suggest_no_fullname -> lapply -> FUN
Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1.  Error: Install a single package (@test-gh_install_packages.R#9) 
  2.  Error: Install two package (@test-gh_install_packages.R#18) 
  3.  Error: Install: ask yes (@test-gh_install_packages.R#37) 
  4.  Error: no full name: single result (@test-gh_suggest.R#17) 
  5.  Error: no full name: multi result (@test-gh_suggest.R#23) 
  6.  Error: no full name: has title (@test-gh_suggest.R#29) 
  7.  Error: to_candidates: no inds (@test-gh_suggest.R#37) 
  8.  Failure: to_candidates: single result (@test-gh_suggest.R#44) 
  9.  Error: select_repository: single candidate (@test-utils_for_install.R#121) 
  10. Error: select_repository: multi candidates (@test-utils_for_install.R#130) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 214-215 (githubinstall.Rmd) 
Error: processing vignette ‘githubinstall.Rmd’ failed with diagnostics:
missing value where TRUE/FALSE needed
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/HydeNet.Rcheck/00install.out’ for details.
Running examples in ‘icesDatras-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: checkSurveyOK
> ### Title: Check that a survey name is in the database
> ### Aliases: checkSurveyOK
> 
> ### ** Examples
> 
> checkSurveyOK(survey = "ROCKALL")
Warning in download.file(url, destfile = tmp, quiet = TRUE, method = "wget") :
  download had nonzero exit status
Unable to download file so using slower method url().
Try setting an appropriate value via
	options(download.file.method = ...)
see ?download.file for more information.
Warning in scan(con, what = "", sep = "\n", quiet = TRUE) :
  URL 'https://datras.ices.dk/WebServices/DATRASWebService.asmx/getSurveyList': status was 'Couldn't resolve host name'
Error in scan(con, what = "", sep = "\n", quiet = TRUE) : 
  cannot open connection
Calls: checkSurveyOK ... getSurveyList -> checkDatrasWebserviceOK -> readDatras -> scan
Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  cannot open connection
  1: expect_equal(checkDatrasWebserviceOK(), TRUE) at testthat/test-test.R:4
  2: compare(object, expected, ...)
  3: checkDatrasWebserviceOK()
  4: readDatras("https://datras.ices.dk/WebServices/DATRASWebService.asmx/getSurveyList")
  5: scan(con, what = "", sep = "\n", quiet = TRUE)
  
  testthat results ================================================================
  OK: 2 SKIPPED: 0 FAILED: 1
  1. Error: Webservice access is okay (@test-test.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘icesSAG-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: findKey
> ### Title: Find a Key
> ### Aliases: findKey
> 
> ### ** Examples
> 
> findKey("cod-347d", 2015, full = TRUE)
Warning in download.file(url, destfile = tmp, quiet = TRUE, method = "wget") :
  download had nonzero exit status
Unable to download file so using slower method url().
Try setting an appropriate value via 
	options(download.file.method = ...)
see ?download.file for more information.
Warning in scan(con, what = "", sep = "\n", quiet = TRUE) :
  URL 'https://sg.ices.dk/StandardGraphsWebServices.asmx/getSummaryTable?key=-1': status was 'Couldn't resolve host name'
Error in scan(con, what = "", sep = "\n", quiet = TRUE) : 
  cannot open connection
Calls: findKey -> checkSAGWebserviceOK -> readSAG -> scan
Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  cannot open connection
  1: expect_equal(checkSAGWebserviceOK(), TRUE) at testthat/test-test.R:4
  2: compare(object, expected, ...)
  3: checkSAGWebserviceOK()
  4: readSAG("https://sg.ices.dk/StandardGraphsWebServices.asmx/getSummaryTable?key=-1")
  5: scan(con, what = "", sep = "\n", quiet = TRUE)
  
  testthat results ================================================================
  OK: 2 SKIPPED: 0 FAILED: 1
  1. Error: Webservice access is okay (@test-test.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘icesVocab-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: findAphia
> ### Title: Find Aphia Code
> ### Aliases: findAphia
> 
> ### ** Examples
> 
> findAphia("cod")
Warning in download.file(url, destfile = tmp, quiet = TRUE, method = "wget") :
  download had nonzero exit status
Unable to download file so using slower method url().
Try setting an appropriate value via 
	options(download.file.method = ...)
see ?download.file for more information.
Warning in scan(con, what = "", sep = "\n", quiet = TRUE) :
  unable to resolve 'vocab.ices.dk'
Error in scan(con, what = "", sep = "\n", quiet = TRUE) : 
  cannot open the connection
Calls: findAphia -> getCodeList -> readVocab -> scan
Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  cannot open the connection
  1: expect_equal(checkVocabWebserviceOK(), TRUE) at testthat/test-test.R:4
  2: compare(object, expected, ...)
  3: checkVocabWebserviceOK()
  4: readVocab(url = "http://vocab.ices.dk/services/pox/GetCodeDetail/SpecWoRMS/101170")
  5: scan(con, what = "", sep = "\n", quiet = TRUE)
  
  testthat results ================================================================
  OK: 2 SKIPPED: 0 FAILED: 1
  1. Error: Webservice access is okay (@test-test.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(ids)
  > 
  > test_check("ids")
  1. Failure: functional interface (@test-adjective-animal.R#64) -----------------
  all(grepl(re, x)) isn't true.
  
  
  testthat results ================================================================
  OK: 97 SKIPPED: 0 FAILED: 1
  1. Failure: functional interface (@test-adjective-animal.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
   # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/igraph.Rcheck/00install.out’ for details.
Running examples in ‘KODAMA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: knn.double.cv
> ### Title: Cross-Validation with k-Nearest Neighbors algorithm.
> ### Aliases: knn.double.cv
> 
> ### ** Examples
> 
>  data(iris)
>  data=iris[,-5]
>  labels=iris[,5]
>  pp=knn.double.cv(data,labels)
..................
 *** caught segfault ***
address 0xc000001fff, cause 'memory not mapped'
Segmentation fault
Running the tests in ‘tests/run-base.R’ failed.
Last 13 lines of output:
  1. Error: downsample wrapper works with xgboost, we had issue #492 (@test_base_downsample.R#38) 
  2. Failure: generateCalibrationData (@test_base_generateCalibration.R#55) 
  3. Failure: generateCalibrationData (@test_base_generateCalibration.R#57) 
  4. Failure: plotFilterValues (@test_base_generateFilterValuesData.R#72) 
  5. Failure: plotFilterValues (@test_base_generateFilterValuesData.R#74) 
  6. Failure: generateLearningCurve (@test_base_generateLearningCurve.R#46) 
  7. Failure: generateLearningCurve (@test_base_generateLearningCurve.R#48) 
  8. Failure: generatePartialDependenceData (@test_base_generatePartialDependence.R#216) 
  9. Failure: generatePartialDependenceData (@test_base_generatePartialDependence.R#219) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Error: `mapped_plot` not equal to lazyLoadDBfetch(c(36521L, 321L), datafile, compressed, envhook).
  Component "layers": Component 1: Component 3: Component 2: Modes of target, current: function, environment
  Component "layers": Component 1: Component 3: Component 2: target, current do not match when deparsed
  Component "layers": Component 1: Component 7: Component 2: Modes of target, current: function, environment
  Component "layers": Component 1: Component 7: Component 2: target, current do not match when deparsed
  Component "layers": Component 1: Component 9: Component 2: Modes of target, current: function, environment
  Component "layers": Component 1: Component 9: Component 2: target, current do not match when deparsed
  Component "layers": Component 1: Component 12: Modes of target, current: function, environment
  Component "layers": Component 1: Component 12: target, current do not match when deparsed
  Component "layers": Component 2: Component 3: Component 2: Modes of target, current: fun
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  9: `$<-.data.table`(`*tmp*`, "id", value = 1:11)
  10: `$<-.data.frame`(x, name, value)
  11: stop(sprintf(ngettext(N, "replacement has %d row, data has %d", "replacement has %d rows, data has %d"), 
         N, nrows), domain = NA)
  
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 3
  1. Error: output has 17 columns (@test_tableproperties.R#27) 
  2. Error: output has the right column names (@test_tableproperties.R#31) 
  3. Error: output is of class data.frame & data.table (@test_tableproperties.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
Attaching package: ‘BiocGenerics’

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

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

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

    IQR, mad, xtabs

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

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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1. Failure: createTable (@test-poplite.R#252) 
  2. Failure: createTable (@test-poplite.R#252) 
  3. Failure: createTable (@test-poplite.R#252) 
  4. Failure: createTable (@test-poplite.R#252) 
  5. Failure: insertStatement (@test-poplite.R#330) 
  6. Failure: insertStatement (@test-poplite.R#350) 
  7. Failure: insertStatement (@test-poplite.R#330) 
  8. Failure: insertStatement (@test-poplite.R#350) 
  9. Failure: insertStatement (@test-poplite.R#330) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: replacing previous import ‘ape::complement’ by ‘Biostrings::complement’ when loading ‘RADami’
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RADami.Rcheck/00install.out’ for details.
Codoc mismatches from documentation object 'c,Medline-method':
\S4method{c}{Medline}
  Code: function(x, ..., recursive = FALSE)
  Docs: function(x, ...)
  Argument names in code not in docs:
    recursive
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API call to R: ‘R_GlobalContext’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  libjson/Source/JSONGlobals.h:43:50: warning: invoking macro json_global_decl argument 3: empty macro arguments are undefined in ISO C++98 [-Wpedantic]
  libjson/Source/JSONGlobals.h:44:49: warning: invoking macro json_global_decl argument 3: empty macro arguments are undefined in ISO C++98 [-Wpedantic]
  JSONValidator.cpp:394:105: warning: invoking macro JSON_ASSERT_SAFE argument 3: empty macro arguments are undefined in ISO C++98 [-Wpedantic]
  JSONValidator.cpp:397:104: warning: invoking macro JSON_ASSERT_SAFE argument 3: empty macro arguments are undefined in ISO C++98 [-Wpedantic]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RJSONIO.Rcheck/00install.out’ for details.
Running the tests in ‘tests/RMongo-Ex.R’ failed.
Last 13 lines of output:
  +   
  +   # print(length(output))
  +   print(as.character(output[1]))
  + 
  +   checkEquals("{ \"_id\" : \"bar\"}", as.character(output[1]))
  +   # checkEquals("bar", as.character(output[1]))
  + }
  > 
  > test.dbInsertDocument()
  Error in .jcall(rmongo.object@javaMongo, "S", "dbInsertDocument", collection,  : 
    com.mongodb.MongoException$Network: Write operation to server /127.0.0.1:27017 failed on database test
  Calls: test.dbInsertDocument ... dbInsertDocument -> dbInsertDocument -> .jcall -> .jcheck -> .Call
  Execution halted
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running the tests in ‘tests/prediction-test.R’ failed.
Last 13 lines of output:
  > stopifnot(predict(nsom, iris[1,1:4])==nsom$clustering[1])
  > stopifnot(identical(predict(nsom), nsom$clustering))
  > 
  > rsom <- trainSOM(dissim.lesmis, type="relational", maxit=10, scaling= "none")
  > stopifnot(identical(predict(rsom, dissim.lesmis), rsom$clustering))
  > stopifnot(predict(rsom, dissim.lesmis[1,])==rsom$clustering[1])
  > stopifnot(identical(predict(rsom), rsom$clustering))
  > 
  > rsom <- trainSOM(dissim.lesmis, type="relational", maxit=10, 
  +                  radius.type="letremy")
  > stopifnot(identical(predict(rsom, dissim.lesmis), rsom$clustering))
  Error: identical(predict(rsom, dissim.lesmis), rsom$clustering) is not TRUE
  Execution halted
Running the tests in ‘tests/tests.R’ failed.
Last 13 lines of output:
  > ## is not available
  > 
  > myurl <- "http://www.biostat.jhsph.edu/MCAPS/data_v0.3/"
  > 
  > ## create a 'remoteDB' object ##
  > db <- new("remoteDB", url= myurl, dir = dir, name= "MCAPS")
  Error in download.file(rpath, versionFile(db, where = "local"), mode = "w",  : 
    cannot open URL 'http://www.biostat.jhsph.edu/MCAPS/data_v0.3/version'
  Calls: new ... initialize -> initialize -> cacheVersionFile -> download.file
  In addition: Warning message:
  In download.file(rpath, versionFile(db, where = "local"), mode = "w",  :
    cannot open URL 'http://www.biostat.jhsph.edu/MCAPS/data_v0.3/version': HTTP status was '404 Not Found'
  Execution halted
Codoc mismatches from documentation object 'c,SessionManifest-method':
\S4method{c}{PkgManifest}
  Code: function(x, ..., recursive = FALSE)
  Docs: function(x, ...)
  Argument names in code not in docs:
    recursive
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  5: getExportedValue(pkg, name)
  6: stop(gettextf("'%s' is not an exported object from 'namespace:%s'", name, getNamespaceName(ns)), 
         call. = FALSE, domain = NA)
  
  testthat results ================================================================
  OK: 132 SKIPPED: 0 FAILED: 4
  1. Error: visualization of empty automat works (@test-automat.R#131) 
  2. Error: visualization without set state works (@test-automat.R#139) 
  3. Error: visualization with implicit state works (@test-automat.R#148) 
  4. Error: visualization works (@test-automat.R#163) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/abcdeFBA.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyPackages 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.
Invalid MIT-MAGIC-COOKIE-1 key
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 key
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
Invalid MIT-MAGIC-COOKIE-1 key
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 key
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 key
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 the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  x[1]: "\"a\"e\"i\"o\"u\"A\"E\"I\"O\"U\"y"
  y[1]: "aeiouAEIOUy"
  
  
  testthat results ================================================================
  OK: 10 SKIPPED: 0 FAILED: 4
  1. Failure: rm_accent is the converted version of a string with all non-ASCII characters removed. (@test-rm_accent.R#30) 
  2. Failure: rm_accent is the converted version of a string with all non-ASCII characters removed. (@test-rm_accent.R#32) 
  3. Failure: rm_accent is the converted version of a string with all non-ASCII characters removed. (@test-rm_accent.R#33) 
  4. Failure: rm_accent is the converted version of a string with all non-ASCII characters removed. (@test-rm_accent.R#34) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    bootstrapping_example   1.2Mb
    libs                    2.9Mb
Error in re-building vignettes:
  ...
  input string 348 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 354 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'acceptance_sampling_manual.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cf>
          K^^[]^^W>o<fc>h^^Zj<93>^(E<94><98><e1>B<a1><85>`^^GfW<b0>q<91><b5><bb>v<e5><da>MW]<b9><95><ae>tӮ<eb><bf><e0><aa>Y<94>B<b2>H^^P^^J
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.19 ...߾<bd>s<e7>N6<9b><c5>O)<a5><94>rmm<cd>0<8c>B<a1> <a5>dX<ee><ed><ed><e1><95>eY<8f>^^^=<da><dd>ݽ}
                                                  <fb><f6><f2><f2><b2>R^^J
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Undefined control sequence.
l.20 ...ZYYY[[^^C2<9f>?^^?<8e>-<87><9f><d9>l<d6>4<cd>l6<fb><e2><c5><
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because ACSN-vignette.Rmd appears to be an R Markdown v2 document.
Quitting from lines 70-71 (ACSN-vignette.Rmd) 
Error: processing vignette 'ACSN-vignette.Rmd' failed with diagnostics:
the table must have a header (column names)
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Error in re-building vignettes:
  ...
  input string 348 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 354 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'AER.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.18 ...<bc>Aι<ee>M<ea>^^X<84>^^PA^^P<e8><ba>.<84>H$^^R<ba><ae>æ^^GA<d0><ed>v<87>t\<a8>
                                                  <ff><f9><f3><e7>l6[<af><d7>e'D<f4><ea>ի<d5><d5>UT^^[<c3>
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.21 ...ޯP<af><d7><d5>`|H@<f8><93>V<bf>^^Q<c8><c9>9<97>S^^[<86><a1><a6>i(<f7>}^^_<fb>/9<cd>x<f6>}
                                                  <9f><88>@`<c6>؟^^?<be><fb><e3><8f>^^?9N<c3>0d<c3>0<9f>g...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Undefined control sequence.
l.24 ...^^?<d7>2^^L^^F۷<d
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘AFM-Ex.R’ failed
The error most likely occurred in:

> ### Name: evaluateVariogramModels
> ### Title: evaluateVariogramModels method to evaluate the basic variogram
> ###   models
> ### Aliases: evaluateVariogramModels
> ###   evaluateVariogramModels,AFMImageVariogramAnalysis-method
> 
> ### ** Examples
> 
> library(AFM)
> 
> data("AFMImageOfRegularPeaks")
> # take an extract of the image to fasten the calculation      
> AFMImage<-extractAFMImage(AFMImageOfRegularPeaks, 40, 40, 32)
[1] "40 40 31 40 71 40 71"
> # e.g. AFMImage@fullfilename<-"/users/ubuntu/AFMImageOfRegularPeaks-extract.txt"
> AFMImage@fullfilename<-paste(tempdir(), "AFMImageOfRegularPeaks-extract.txt", sep="/")
>  
> AFMImageAnalyser<-AFMImageAnalyser(AFMImage)
Warning in data.table(lib = c("AFM", "gstat", "fractaldim", "fftwtools"),  :
  Item 1 is of size 4 but maximum size is 5 (recycled leaving remainder of 1 items)
>  
>  # Variogram analysis 
> sampleFitPercentage<-3.43/100
> variogramAnalysis<-AFMImageVariogramAnalysis(sampleFitPercentage)
> variogramAnalysis@omnidirectionalVariogram<- 
+               AFM::calculateOmnidirectionalVariogram(AFMImage=AFMImage,
+                                                      AFMImageVariogramAnalysis=variogramAnalysis)
[1] "using automatic width of 1"
[1] "calculating omnidirectional variogram using width of 1 ..."
Error in CRS("+init") : no colon in init= string
Calls: <Anonymous> -> CRS
Execution halted
Package required and available but unsuitable version: ‘miscF’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/alphashape3d.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 350 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'amei.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 ...߾<8d><c6>L&<c3>9<ff><ee><bb><ef>^^Xc_~<f9><e5><f5><eb><d7>s<b9>^^\<ba>q<ce><ef>޽<fb><c5>^^W_\<bc>
                                                  xq~~~aa!<9b><cd><ce><ce><ce>b<e4>\.W<af><d7><c7><c7><c7>^^Y...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.20 ...<9b>^^L<c7>0<8f>Z<ad><86><bb><b2><85><88>8<e7>^^@<92><aa><aa><a6>i<a2><b1>X,<fa><be><8f>G<d0><e2><fb>~4|Å\D
                                                  Ƙ<bc><85><b7><d4>j<b5>v<e6><dc>^^Y8;<c5>ի<8d>ȨSp^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.23 <c3>0<96><97><97><af>\<b9>
             <e2><ba>.F+^^T^^J
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.24
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: network
network: Classes for Relational Data
Version 1.13.0 created on 2015-08-31.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
                    Mark S. Handcock, University of California -- Los Angeles
                    David R. Hunter, Penn State University
                    Martina Morris, University of Washington
                    Skye Bender-deMoll, University of Washington
 For citation information, type citation("network").
 Type help("network-package") to get started.


Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/anacor.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/analogueExtra.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/animalTrack.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...

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

    %>%

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

    id

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

    escape, explain

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 56-58 (ANLP_Documentation.Rmd) 
Error: processing vignette 'ANLP_Documentation.Rmd' failed with diagnostics:
java.lang.UnsupportedClassVersionError: weka/core/tokenizers/NGramTokenizer : Unsupported major.minor version 51.0
Execution halted
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘tcltk’ which was already attached by Depends.
  Please remove these calls from your code.
Invalid MIT-MAGIC-COOKIE-1 keyannot : 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’
Undefined global functions or variables:
  flush.console read.table write.table
Consider adding
  importFrom("utils", "flush.console", "read.table", "write.table")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Anthropometry.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘tkrplot’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  Warning: Conversion from REAL(8) to default-kind COMPLEX(4) at (1) might loose precision, consider using the KIND argument
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/appell.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keykristen.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.
Error in re-building vignettes:
  ...
sh: rst2pdf: command not found
Error: processing vignette 'argparse.Rrst' failed with diagnostics:
conversion by rst2pdf failed!
Execution halted
Package suggested but not available for checking: ‘AffymetrixDataTestFiles’
Found the following significant warnings:
  Warning: failed to assign NativeSymbolInfo for lhs since lhs is already defined in the ‘lazyeval’ namespace
  Warning: failed to assign NativeSymbolInfo for rhs since rhs is already defined in the ‘lazyeval’ namespace
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/arulesViz.Rcheck/00install.out’ for details.
Running the tests in ‘tests/run-all.R’ failed.
Last 13 lines of output:
  
  Attaching package: 'llama'
  
  The following object is masked from 'package:BBmisc':
  
      normalize
  
  > test_check("aslib")
  Loading required package: aslib
  Error in .jnew("weka/core/Instances", .jcast(reader, "java/io/Reader")) : 
    java.lang.UnsupportedClassVersionError: weka/core/Instances : Unsupported major.minor version 51.0
  Calls: test_check ... eval -> parseASScenario -> read.arff -> .jnew -> .External
  Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/AtelieR.Rcheck/00install.out’ for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    libs   1.4Mb
Error in re-building vignettes:
  ...
  input string 487 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'bartMachine.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cd>
          o^^[<d5>^^V?uh<92>yJ=<b9><b4>/qG8q<86>V<a4>-JSy<c3>C<aa>^^\!<8b>%^^[^^T<84><c4>^^V<f5>^^O`<c3>6<cb>v^^A6^^H...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 ...T*e<9a><a6>eY<f1>u<92>R<fe><f0><c3>^^O<b6>m^^O^^O^^O<a3><f4><e7><9f>^^?<fe>裏<ae>\<b9>
                                                  <92>L&<e3><f1>x<c0><b8><ab><cf>^^Gݸq<a3>X,nV:55<b5><b3>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.16 ...ȣG<8f><c0><86>eY<9f>}<f6>^^Y$MU <a2>^^O?<fc>0<9d>N^^O^^O^^O<ef>r
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package unavailable to check Rd xrefs: ‘Rmpi’
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  10: .subset2(public_bind_env, "initialize")(...)
  11: runOSCommand(self$script, "number-of-cpus")
  12: suppressWarnings(system2(command = sys.cmd, args = sys.args, stdout = TRUE, stderr = TRUE, 
         wait = TRUE))
  13: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  14: system2(command = sys.cmd, args = sys.args, stdout = TRUE, stderr = TRUE, wait = TRUE)
  
  testthat results ================================================================
  OK: 958 SKIPPED: 6 FAILED: 1
  1. Error: clusterFunctions constructor (@test_ClusterFunctions.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  10.2Mb
Package unavailable to check Rd xrefs: ‘mritc’
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs  17.8Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘rgl’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: ‘R2jags’
Running examples in ‘BCEs0-Ex.R’ failed
The error most likely occurred in:

> ### Name: bces0
> ### Title: Bayesian Cost-Effectiveness models in the presence of structural
> ###   zeros
> ### Aliases: bces0 bces0.default
> ### Keywords: JAGS Markov Chain Monte Carlo Bayesian models for
> ###   cost-effectiveness analysis
> 
> ### ** Examples
> 
> data(acupuncture)
> m <- bces0(data,dist.c="gamma",dist.e="beta",n.iter=1000,n.burnin=500,n.chains=2)
Installing package into ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/BCEs0.Rcheck’
(as ‘lib’ is unspecified)
Error in contrib.url(repos, "source") : 
  trying to use CRAN without setting a mirror
Calls: bces0 -> bces0.default -> install.packages -> contrib.url
Execution halted
Package suggested but not available for checking: ‘beadarrayExampleData’
Running examples in ‘beadarrayFilter-Ex.R’ failed
The error most likely occurred in:

> ### Name: MLM.beadarray
> ### Title: Multi-level Mixed model
> ### Aliases: MLM.beadarray
> ### Keywords: differential expression
> 
> ### ** Examples
> 
> require(beadarrayExampleData)
Loading required package: beadarrayExampleData
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘beadarrayExampleData’
> data(exampleSummaryData)
Warning in data(exampleSummaryData) :
  data set ‘exampleSummaryData’ not found
> exampleSummaryDatalog2 <- channel(exampleSummaryData, "G")[1:40,]
Error in channel(exampleSummaryData, "G") : 
  object 'exampleSummaryData' not found
Execution halted
Package required but not available: ‘rggobi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 356 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'beanplot.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cd>
          k^^S<dd>^^Z^^?<9a><be><a1>w@frn<ef><d5><da>2<a6>^^\<f0><f6><95>+i<a1><f0>.^^DM<c1><e8>Fp<d7>U<f7><ae><dd>	<ae><dc><f6>/<90>׽<a2><88>.<b2>m^^V
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 ...<cd>qb-s<fd>H<ee><e2>w<f3>0o?<92><c6>&jj~<8b>rr<be><e6><s~<e7><f9>8<e7>L^^G<ea><f5>:<9d>\D
                                                  ~<f4>^^@<ba><8b><be>x<bd><8c><be>x<bd><8c><be>x<bd><8c><be>x<bd><8c><be>x<bd>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
l.19 ...<d3>D<ce><ce><ce>N"<91><d0>ZW<ab>U<d3>4<
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 45.4Mb
  sub-directories of 1Mb or more:
    libs  44.4Mb
This data.table install has not detected OpenMP support. It will work but slower in single threaded mode.
Running examples in ‘benchmarkme-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_ram
> ### Title: Get the amount of RAM
> ### Aliases: get_ram
> 
> ### ** Examples
> 
> ## Return (and pretty print) the amount of RAM
> get_ram()
sh: system_profiler: command not found
Error in if (power < 1) { : missing value where TRUE/FALSE needed
Calls: <Anonymous> -> print.bytes
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keybeqi2: 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.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 425 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'betareg-ext.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.17 ...x(^^T<f2>}?^^R<89>^^L,<e7><d3><e2><ff>۴<^^Q<f0>Ȝs<d7>uM<d3>ܩZ<cb>[<fc><f4>}
                                                  ?^^T^^J
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Missing $ inserted.
<inserted text> 
                $
l.18 ...<9a>f<ad>V<b3>,<eb><db>o<bf>=z<f4><e8><c4>ĄeYB^^HM<d3>^^P3p<ce>QF<83><9d>D^^Q]<8c>^
                                                  6<9b><cd>d2B^^H<c7>q^^P<be><98><a6>iY^^V^^Q#...
! Extra }, or forgotten $.
l.18 ...t<ee>ܹF<a3><c1>^^X[XX0M3<91>H^^P<d1><db>o<bf>m<9a><e6><f0><f0>0^^Q<f9><be><af>$A<d9><f7>}
                                                  <df><f7>5<ad>#<ce
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 123.2Mb
  sub-directories of 1Mb or more:
    include  123.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   3.9Mb
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘RODBC’
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Biocomb.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/bios2mds.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/birdring.Rcheck/00install.out’ for details.
BEEM: no visible binding for global variable ‘data’
BEEM: no visible global function definition for ‘txtProgressBar’
BEEM: no visible global function definition for ‘fisher.test’
BEEM: no visible global function definition for ‘setTxtProgressBar’
BIGEE: no visible binding for global variable ‘data’
BIGEE: no visible global function definition for ‘txtProgressBar’
BIGEE: no visible global function definition for ‘sd’
BIGEE: no visible global function definition for ‘setTxtProgressBar’
BISEP : <anonymous>: no visible global function definition for ‘runif’
BISEP : indexing: no visible global function definition for ‘quantile’
BISEP : data: no visible global function definition for ‘read.csv’
expressionPlot: no visible binding for global variable ‘data’
expressionPlot: no visible global function definition for ‘plot’
expressionPlot: no visible global function definition for ‘abline’
waterfallPlot: no visible global function definition for ‘rnorm’
waterfallPlot: no visible global function definition for ‘density’
waterfallPlot: no visible global function definition for ‘layout’
waterfallPlot: no visible global function definition for ‘plot’
waterfallPlot: no visible global function definition for ‘barplot’
waterfallPlot: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline barplot data density fisher.test layout legend plot quantile
  read.csv rnorm runif sd setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "abline", "barplot", "layout", "legend", "plot")
  importFrom("stats", "density", "fisher.test", "quantile", "rnorm",
             "runif", "sd")
  importFrom("utils", "data", "read.csv", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because profiling.Rmd appears to be an R Markdown v2 document.
Quitting from lines 40-46 (profiling.Rmd) 
Error: processing vignette 'profiling.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Package required but not available: ‘fPortfolio’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘gtools’ ‘knitr’ ‘nnet’ ‘parallel’ ‘rJava’ ‘reshape’
  ‘rmarkdown’ ‘shinyjs’
  All declared Imports should be used.
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    libs  29.5Mb
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/blockmodeling.Rcheck/00install.out’ for details.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
Found the following significant warnings:
  Warning: Possible change of value in conversion from INTEGER(8) to INTEGER(4) at (1)
  Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1)
  Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
  Warning: Dummy argument 'ch_mymsg' at (1) was declared INTENT(OUT) but was not set
  Warning: Dummy argument 'da_gpvals' at (1) was declared INTENT(OUT) but was not set
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Blossom.Rcheck/00install.out’ for details.
installed size is 29.1Mb
  sub-directories of 1Mb or more:
    libs  28.9Mb
installed size is 280.4Mb
  sub-directories of 1Mb or more:
    include    2.6Mb
    lib      277.7Mb
installed size is 39.0Mb
  sub-directories of 1Mb or more:
    libs  38.8Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/bootsPLS.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/bpca.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 449 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'BradleyTerry.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.16 ...^Ha<db><f6><f0><f0>0<d8>~<fd><f5><d7>^^[7nܹs'^^\^^Ns<ce>^^_?~<fc>駟޾}
                                                  <fb><fc><f9><f3><c9>d<f2>H^^T{dګ^^Xƥx<fc><91>i^^...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Missing $ inserted.
<inserted text> 
                $
l.16 ...^@+<c6>X<^^^^^WB<cc><ce><ce>~<f1><c5>^^W<e9>t<fa><f9><f3><e7><c1>`^^P<e8>D<ef>څfff^
                                                  <bc>x188X<af><d7>?<fb><ec><b3>t:=>><be><b2><b2><92>J<a5>^^N...
! Extra }, or forgotten $.
l.16 ...^^Hڜs۶^^S<89>D<f7><e3><ec>Hg<be>w<92>锋<d7>!<b4>d<b3><d9><e3><99><c7>ah^^O<ec>z<ca>}
              
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/brainR.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyscene4d: no visible global function definition for ‘rainbow’
write4D.file : <anonymous>: no visible global function definition for
  ‘col2rgb’
writeWebGL_split : split_triangles: no visible global function
  definition for ‘rgb’
Undefined global functions or variables:
  col2rgb rainbow rgb
Consider adding
  importFrom("grDevices", "col2rgb", "rainbow", "rgb")
to your NAMESPACE file.
installed size is 49.5Mb
  sub-directories of 1Mb or more:
    libs  49.2Mb
Running examples in ‘c3net-Ex.R’ failed
The error most likely occurred in:

> ### Name: c3net
> ### Title: All in one function to infer network with C3NET
> ### Aliases: c3net
> ### Keywords: misc
> 
> ### ** Examples
> 
> data(expdata)
> data(truenet)
> 
> net <- c3net(expdata, network=TRUE)
Invalid MIT-MAGIC-COOKIE-1 keyWarning in fun(libname, pkgname) : couldn't connect to display ":0"
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "font".
Calls: c3net ... .tkplot.convert.font -> <Anonymous> -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/CampaR1.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: sp
rgdal: version: 1.2-5, (SVN revision 648)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.1.2, released 2016/10/24
 Path to GDAL shared files: /usr/local/share/gdal
 Loaded PROJ.4 runtime: Rel. 4.9.1, 04 March 2015, [PJ_VERSION: 491]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.2-3 
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 50-54 (DataExtraction.Rmd) 
Error: processing vignette 'DataExtraction.Rmd' failed with diagnostics:
cannot find ExifTool
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/cape.Rcheck/00install.out’ for details.
Running examples in ‘caRpools-Ex.R’ failed
The error most likely occurred in:

> ### Name: carpools.hit.overview
> ### Title: Analysis: Analysis of pooled CRISPR screening data using a
> ###   Wilcoxon Test
> ### Aliases: carpools.hit.overview
> ### Keywords: ~Analysis
> 
> ### ** Examples
> 
> data(caRpools)
> 
> data.wilcox = stat.wilcox(untreated.list = list(CONTROL1, CONTROL2),
+   treated.list = list(TREAT1,TREAT2), namecolumn=1, fullmatchcolumn=2,
+   normalize=TRUE, norm.fun=median, sorting=FALSE, controls="random",
+   control.picks=NULL)
> 
> 
> data.deseq = stat.DESeq(untreated.list = list(CONTROL1, CONTROL2),
+   treated.list = list(TREAT1,TREAT2), namecolumn=1,
+   fullmatchcolumn=2, extractpattern=expression("^(.+?)(_.+)"),
+   sorting=FALSE, filename.deseq = "ANALYSIS-DESeq2-sgRNA.tab",
+   fitType="parametric")
Error in `rownames<-`(`*tmp*`, value = c("CTRL", "CTRL", "TREAT", "TREAT" : 
  duplicate rownames not allowed
Calls: stat.DESeq -> <Anonymous> -> rownames<- -> rownames<-
Execution halted
Error in re-building vignettes:
  ...
Warning in readLines(con) :
  incomplete final line found on 'CaRpools.Rmd'
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because CaRpools.Rmd appears to be an R Markdown v2 document.
Quitting from lines 1875-1881 (CaRpools.Rmd) 
Error: processing vignette 'CaRpools.Rmd' failed with diagnostics:
duplicate rownames not allowed
Execution halted
Package required but not available: ‘OpenCL’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/cati.Rcheck/00install.out’ for details.
Found the following Makefile(s) without a final LF:
  inst/doc/Makefile
Some ‘make’ programs ignore lines not ending in LF.
The following files look like leftovers/mistakes:
  ‘Causata-vignette.log’
Please remove them from your package.
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/cdcsis.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keybw: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  optimize
Consider adding
  importFrom("stats", "optimize")
to your NAMESPACE file.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   9.2Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/cems.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 505 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ChainLadder.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.17 w<ab><b4><b4><90><c1>TQ	\nS
                 ;<e8><d0>7\x<83><df>/<ef><f1><fa>K<df><f5>|<86>p^^H7<c9><f9><90>s^^?<95>&<d0><ef><f7><e1>^^[^^P<fc><ec>^^D&^^Dz<ca>^^Ez<ca>^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 w<ab><b4><b4><90><c1>TQ	\nS;<e8><d0>7\x
                       <83><df>/<ef><f1><fa>K<df><f5>|<86>p^^H7<c9><f9><90>s^^?<95>&<d0><ef><f7><e1>^^[^^P<fc><ec>^^D&^^Dz<ca>^^Ez<ca>^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.17 ...e3^^X<d8>?<e5>b^^Du[.<97>s<b9><9c>mۙLFUU۶<a7><a
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘Rmpi’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ChaosGame.Rcheck/00install.out’ for details.
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=Auckland&zoom=8&size=640x640&scale=2&maptype=hybrid&language=en-EN&sensor=false
Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=Auckland&sensor=false
Quitting from lines 136-154 (cfStation.Rmd) 
Error: processing vignette 'cfStation.Rmd' failed with diagnostics:
GeomRasterAnn was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/clpAPI.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/clues.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘moe430a.db’
Error in re-building vignettes:
  ...

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: XML

Attaching package: ‘XML’

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

    toHTML

Loading required package: GO.db

Loading required package: moe430a.db
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘moe430a.db’
Loading required package: RankAggreg
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'clValid.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file ./clValid-022.pdf): PDF inclusion: required page 
does not exist <0>
 ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! LaTeX Error: Unknown float option `H'.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! LaTeX Error: Unknown float option `H'.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! LaTeX Error: Unknown float option `H'.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! LaTeX Error: Unknown float option `H'.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                     
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/comato.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyHopkins.index: no visible global function definition for ‘runif’
MBM.em: no visible global function definition for ‘runif’
PAM.cluster: no visible global function definition for ‘dist’
calculate.layout: no visible global function definition for ‘optim’
min.distance: no visible global function definition for ‘dist’
plot.conceptmap: no visible global function definition for ‘par’
plot.conceptmap: no visible global function definition for ‘plot’
plot.conceptmaps: no visible global function definition for ‘plot’
Undefined global functions or variables:
  dist optim par plot runif
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "dist", "optim", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: ‘mogene10sttranscriptcluster.db’
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘rgl’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Invalid MIT-MAGIC-COOKIE-1 keyconf: no visible global function definition for ‘read.csv’
conf: no visible global function definition for ‘write.csv’
mya.conf_input : <anonymous>: no visible global function definition for
  ‘sd’
mya.conf_input : <anonymous>: no visible global function definition for
  ‘qt’
mya.conf_input : <anonymous>: no visible global function definition for
  ‘pt’
plot.mya: no visible global function definition for ‘dt’
plot.mya: no visible global function definition for ‘rgb’
write_html.conf_input: no visible global function definition for
  ‘browseURL’
Undefined global functions or variables:
  browseURL dt pt qt read.csv rgb sd write.csv
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "dt", "pt", "qt", "sd")
  importFrom("utils", "browseURL", "read.csv", "write.csv")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/conjoint.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyConjoint: no visible global function definition for ‘dev.new’
Conjoint: no visible global function definition for ‘barplot’
caFactorialDesign: no visible global function definition for ‘cor’
caModel: no visible global function definition for ‘as.formula’
caModel: no visible global function definition for ‘lm’
caModel: no visible global function definition for ‘summary.lm’
caSegmentation: no visible global function definition for ‘kmeans’
caUtilities: no visible global function definition for ‘as.formula’
caUtilities: no visible global function definition for ‘lm’
caUtilities: no visible global function definition for ‘summary.lm’
partutilities: no visible global function definition for ‘as.formula’
partutilities: no visible global function definition for ‘lm’
partutils: no visible global function definition for ‘as.formula’
partutils: no visible global function definition for ‘lm’
profsimcode: no visible global function definition for ‘as.formula’
profsimcode: no visible global function definition for ‘lm’
profsimcode: no visible global function definition for ‘model.matrix’
totalutilities: no visible global function definition for ‘as.formula’
totalutilities: no visible global function definition for ‘lm’
totalutilities: no visible global function definition for
  ‘model.matrix’
utlsplot: no visible global function definition for ‘dev.new’
utlsplot: no visible global function definition for ‘barplot’
Undefined global functions or variables:
  as.formula barplot cor dev.new kmeans lm model.matrix summary.lm
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "barplot")
  importFrom("stats", "as.formula", "cor", "kmeans", "lm",
             "model.matrix", "summary.lm")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ConsRank.Rcheck/00install.out’ for details.
Running examples in ‘ConvergenceConcepts-Ex.R’ failed
The error most likely occurred in:

> ### Name: investigate
> ### Title: Investigate examples and exercises from the paper
> ### Aliases: investigate
> ### Keywords: dplot iplot distribution htest
> 
> ### ** Examples
> 
> investigate()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: investigate ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because CopulaDTA_Vignette.Rmd appears to be an R Markdown v2 document.
Quitting from lines 253-256 (CopulaDTA_Vignette.Rmd) 
Error: processing vignette 'CopulaDTA_Vignette.Rmd' failed with diagnostics:
SSL connect error
Execution halted
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   6.5Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/corehunter.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/corregp.Rcheck/00install.out’ for details.
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    libs  21.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Invalid MIT-MAGIC-COOKIE-1 keyPackage in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘cpa-Ex.R’ failed
The error most likely occurred in:

> ### Name: cpa-package
> ### Title: Confirmatory Path Analysis through the d-sep tests
> ### Aliases: cpa-package
> ### Keywords: package
> 
> ### ** Examples
> 
> x <- cpa()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: cpa ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is 31.0Mb
  sub-directories of 1Mb or more:
    libs  30.8Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/cplexAPI.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 238 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 244 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'cplm.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 ...<cb>^^L<8e><99><98>y<8b>#<8e><a6><98><d8>^^Fl^^By><b2><ac><f1>̹^^_g~<f7>|<dc>s<8f><db>\<d7>
                                                  <85><97><97><da>_<f4>^^D<9a>K-<f1><8e>3<b5><c4>;<ce><d4>^^R<ef>8<d3>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.15 ...}<f6><d9>g<a3><a3><a3>B<88><c5><c5>ť<a5><a5>|>^^?<f9><f2>e|<a4>i^^Zʃ<bd><fd><f0><c3>^^O^^_}
                                                  <f4><91><a6>i׮]<db><c3>tݽS.<97><ab><f2><f4><c1><83>^^G<fb><e8><b3>...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Missing $ in
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   4.1Mb
Error in re-building vignettes:
  ...
  input string 416 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 422 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'crch.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 ...<cc><db><c0>H<bb>^^^<b7><d8>]<f1>^^\^^Y;-E<f9>)c<c9>O<8a><94><8b>9p<ca>^^A<e5><c2>-g<94>\<f3>
                                                  ^^W<e4><9a>?a9gOsC9^^RiFV^^T<81>4bl...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.15 ...^X-&<e2><8d>3&<e2><8d>3&<e2><8d>3&<e2><8d>3&<e2><8d>3&<e2><fd>^^]J)<a5>^^T.N?<d5>Z<f3>}
                                                  <a5><94><d6><fa><ac><96><a7><db><f3><f5><fa><fa><fa><e9>.<b8><93>l?^^L<fe>5|<d3>...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Extra }, or forgotten \endgroup.
l.15 .
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/crimCV.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/crs.Rcheck/00install.out’ for details.
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  15.2Mb
Invalid MIT-MAGIC-COOKIE-1 keygen.xnorm: no visible global function definition for ‘extendrange’
plot.clsd: no visible global function definition for ‘plot’
plot.crs: no visible global function definition for ‘par’
plot.crs: no visible global function definition for ‘plot’
plot.crs: no visible global function definition for ‘topo.colors’
plot.npglpreg: no visible global function definition for ‘par’
plot.npglpreg: no visible global function definition for ‘plot’
plot.npglpreg: no visible global function definition for ‘topo.colors’
printClear: no visible global function definition for ‘flush.console’
printPop: no visible global function definition for ‘flush.console’
printPush: no visible global function definition for ‘flush.console’
Undefined global functions or variables:
  extendrange flush.console par plot topo.colors
Consider adding
  importFrom("grDevices", "extendrange", "topo.colors")
  importFrom("graphics", "par", "plot")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
D.SN: no visible global function definition for ‘dnorm’
D.SN: no visible global function definition for ‘pnorm’
beta2cp: no visible global function definition for ‘pnorm’
cSFM.est: no visible global function definition for ‘predict’
cSFM.est: no visible global function definition for ‘optim’
cSFM.est: no visible global function definition for ‘qnorm’
cSFM.est: no visible global function definition for ‘cor’
case2.b.initial: no visible global function definition for ‘predict’
case2.b.initial: no visible global function definition for ‘var’
case2.gr: no visible global function definition for ‘pnorm’
case2.gr: no visible global function definition for ‘dnorm’
case2.unmll.optim: no visible global function definition for ‘pnorm’
cp2beta: no visible global function definition for ‘qnorm’
data.generator.y.F: no visible global function definition for ‘cov2cor’
data.generator.y.F: no visible global function definition for ‘rnorm’
data.generator.y.F : <anonymous>: no visible global function definition
  for ‘pnorm’
g: no visible global function definition for ‘dnorm’
g: no visible global function definition for ‘pnorm’
predict.cSFM: no visible global function definition for ‘predict’
predict.cSFM : <anonymous>: no visible global function definition for
  ‘qnorm’
predict.cSFM: no visible global function definition for ‘qnorm’
predict.cSFM: no visible global function definition for ‘pnorm’
predict.kpbb: no visible global function definition for ‘predict’
uni.fpca: no visible global function definition for ‘predict’
Undefined global functions or variables:
  cor cov2cor dnorm optim pnorm predict qnorm rnorm var
Consider adding
  importFrom("stats", "cor", "cov2cor", "dnorm", "optim", "pnorm",
             "predict", "qnorm", "rnorm", "var")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ctsem.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
l.19 ...<d1><f3>Sw<e0>^^D,<b9><ed>E^^N0<e3>m!`6^^A<e0><eb>ׯ^^[<86>^^Q<8d>Fs<b9>\<bd>
                                                  ^<b7>,krrR<d7><f5>H$<82><8e>^^X<8d><88>^^J
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Missing $ inserted.
<inserted text> 
                $
l.19 ...<f3>Sw<e0>^^D,<b9><ed>E^^N0<e3>m!`6^^A<e0><eb>ׯ^^[<86>^^Q<8d>Fs<b9>\<bd>^
                                                  <b7>,krrR<d7><f5>H$<82><8e>^^X<8d><88>^^J
! Please use \mathaccent for accents in math mode.
\add@accent ...@spacefactor \spacefactor }\accent 
                                                  #1 #2\egroup \spacefactor ...
l.21 <ec>B<bc>\.g
  
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package which this enhances but not available for checking: ‘pbdMPI’
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/cudaBayesreg.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/curvHDR.Rcheck/00install.out’ for details.
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    libs  19.8Mb
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 341 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 350 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'DAKS.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 ...<8e><ad>^^_<b6><9c>X<ae><de>A<8c>fgf<e7><cd><fb><cc>{o޼<fd><c4><f7>}<ba><be>^^T<fa><d8>^^S<b8>\^^Z
                                                  <b3>7<ca>4fo<94>i<cc><de>(Ә<bd>Q<a6>1{<a3>L<ff>l<f6>LӔ...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...|~gg端<be><c2><d0><f9>|<de>4<cd>l6<ab>:d^^X<c6>ӧO<f1><ee><cf>><fb>lgg<e7><e1>Ç<b9>\N
                                                  ^^H^^A<96>VVV<a4><94>h<a0><94>^^RB,//<f3>PD<f4>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 ...?<fe><f9><e7><f9><f9><f9>p8<bc><b2><b2><f2><dd>w<df>^^Y<86><a1><eb>z.<97><db><dc><dc><fc><fe><fb><ef>s<b9>^^\^^F\F
                                                  /DCDB^^W^^J
The control sequence at the end of the top 
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  1: GenerateReport(iris, output_file = file_name, output_dir = dir_name, quiet = TRUE) at testthat/test-generate-report.r:8
  2: render(input = report_dir, output_file = output_file, output_dir = output_dir, intermediates_dir = output_dir, 
         params = list(data = input_data, fun_options = list()), ...)
  3: pandoc_available(required_pandoc, error = TRUE)
  4: stop(paste(msg, collapse = " "), call. = FALSE)
  
  testthat results ================================================================
  OK: 34 SKIPPED: 0 FAILED: 1
  1. Error: test if report is generated (@test-generate-report.r#8) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshotd0b5ddd2219.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotd0b5ddd2219.png': No such file or directory
Quitting from lines 512-515 (data.tree.Rmd) 
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/DBKGrad.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  21.6Mb
Invalid MIT-MAGIC-COOKIE-1 keyThere are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘debug.Recall’ ‘debug.eval’ ‘debug.eval.guts’ ‘debug.fun.name’
  ‘evaluator’ ‘find.debug.HQ’ ‘mvb.sys.on.exit’ ‘stepping’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/demography.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
The following objects are masked from 'package:seriation':

    bluered, greenred

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

    lowess

Loading required package: pkgmaker
Loading required package: registry

Attaching package: 'pkgmaker'

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

    isNamespaceLoaded

Loading required package: rngtools
# NOTE - CRAN check detected: limiting maximum number of cores [2/16]
NMF - BioConductor layer [OK] | Shared memory capabilities [OK] | Cores 2/2 | CRAN check
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 856-858 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.8Mb
    help   1.3Mb
    libs   1.1Mb
Package suggested but not available for checking: ‘dclone’
Invalid MIT-MAGIC-COOKIE-1 keyPackage in Depends field not imported from: ‘dplR’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.get’ ‘InteractiveDetrending’ ‘RemoveTrend’
Running examples in ‘detrendeR-Ex.R’ failed
The error most likely occurred in:

> ### Name: detrendeR-package
> ### Title: detrendeR - A Graphical User Interface to process and visualize
> ###   tree-ring data using R
> ### Aliases: detrendeR-package detrendeR
> ### Keywords: package
> 
> ### ** Examples
> 
> detrender()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: detrender ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
installed size is 37.3Mb
  sub-directories of 1Mb or more:
    libs  37.1Mb
Package required but not available: ‘ALL’

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

> ### Name: dgmb-package
> ### Title: Simulating Data for PLS Mode B Structural Models
> ### Aliases: dgmb-package dgmb
> ### Keywords: package
> 
> ### ** Examples
> 
> dgmbGui()
 --------------------------------------------------
| Simulating Data for PLS Mode B Structural Models |
| Version: 1.2                                     |
| Depends: abind, tcltk, MASS                      |
| Licence: GPL >= 2                                |
| System Requirements: tktable, BWidget            |
 --------------------------------------------------
Invalid MIT-MAGIC-COOKIE-1 keyWarning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Invalid MIT-MAGIC-COOKIE-1 keyWarning in tclRequire("Tktable") : Tcl package 'Tktable' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: dgmbGui ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/DiceView.Rcheck/00install.out’ for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/directPA.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/DirichletReg.Rcheck/00install.out’ for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/DiversityOccupancy.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘glmnet’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘glmnet’ ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘DivMelt-Ex.R’ failed
The error most likely occurred in:

> ### Name: DivMelt_gui
> ### Title: User Interface for the Diversity Assay Analysis Tool
> ### Aliases: DivMelt_gui
> ### Keywords: interface
> 
> ### ** Examples
> 
> ##
> library (DivMelt)
> DivMelt_gui()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: DivMelt_gui ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
Zibs.pairwise.pr.locus: no visible global function definition for
  ‘combn’
dist.pair.cdf : r.scalar: no visible global function definition for
  ‘uniroot’
dist.pair.cdf: no visible global function definition for ‘head’
dist.pair.cdf: no visible global function definition for ‘tail’
est.freqs: no visible global function definition for ‘setNames’
write.genepop: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  combn head setNames tail uniroot write.table
Consider adding
  importFrom("stats", "setNames", "uniroot")
  importFrom("utils", "combn", "head", "tail", "write.table")
to your NAMESPACE file.
.ccd.1.41: no visible global function definition for ‘rnorm’
.ccd.1.41: no visible global function definition for ‘formula’
.ccd.1.41: no visible global function definition for ‘coef’
.ccd.1.41: no visible global function definition for ‘runif’
.ccd.1.41 : <anonymous>: no visible global function definition for
  ‘as.formula’
.gen.des.old.way: no visible global function definition for ‘runif’
Dopt.augment: no visible global function definition for ‘rnorm’
Dopt.augment: no visible global function definition for ‘as.formula’
Dopt.augment: no visible global function definition for ‘model.matrix’
Dopt.design: no visible global function definition for ‘as.formula’
Dopt.design: no visible global function definition for ‘model.matrix’
Scalc: no visible global function definition for ‘dist’
bbd.design: no visible global function definition for ‘model.matrix’
ccd.augment: no visible global function definition for ‘as.formula’
ccd.augment: no visible global function definition for ‘model.matrix’
ccd.augment: no visible global function definition for ‘model.frame’
ccd.augment: no visible binding for global variable ‘na.pass’
generators.from.design: no visible global function definition for
  ‘formula’
generators.from.design : <anonymous>: no visible global function
  definition for ‘as.formula’
lhs.design: no visible global function definition for ‘cor’
rsm.design: no visible global function definition for ‘as.formula’
rsmformula: no visible global function definition for ‘formula’
Undefined global functions or variables:
  as.formula coef cor dist formula model.frame model.matrix na.pass
  rnorm runif
Consider adding
  importFrom("stats", "as.formula", "coef", "cor", "dist", "formula",
             "model.frame", "model.matrix", "na.pass", "rnorm", "runif")
to your NAMESPACE file.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  2: domino.runCommand(loginCommand, domino.OK, "Login failed", theinput)
  3: domino.runCommandFromDefaultPath(commandAndArgs, successCallback, failureMessage, 
         stdInput)
  4: domino.handleCommandNotFound(failureMessage)
  5: stop(paste("Couldn't find domino client in the PATH or in default locations.\n  Add domino client directory path to PATH environment variable.\n  If you don't have domino client installed follow instructions on 'http://help.dominodatalab.com/client'.\n  If you use R-Studio Domino on GNU/Linux through a desktop launcher, add domino path to the .desktop file.\n\n  If you need more help, email support@dominodatalab.com or visit http://help.dominodatalab.com/troubleshooting\n\n  - ", 
         failureMessage), call. = FALSE)
  
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: The login command works (@test-login.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘doMPI’
Package unavailable to check Rd xrefs: ‘doMPI’
Running examples in ‘dpa-Ex.R’ failed
The error most likely occurred in:

> ### Name: dpa-package
> ### Title: Dynamic Path Approach for Analyzing time-dependent simulation
> ###   data
> ### Aliases: dpa-package dpa
> 
> ### ** Examples
> 
> #Start the GUI with:
> dpa.start()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: dpa.start ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Package suggested but not available for checking: ‘dtplyr’
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
Missing or unexported object: ‘RSQLite::rsqliteVersion’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/dprep.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 341 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 352 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'DSL.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.18 ...<ce><fc><fc><bc><e3>8X^^W<c6>X<bb><dd>^^F<fd><9a><a6><e1>E<ac>:^^O8<e7><e3><e9><de>><a1>^^_\^^G
                                                  <8e><ee>^^?<dc>q^^F<c7>1<c8>3^^L^^C<cc><c1>O<a9>3<fb>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.23 <fa><e8><de>e)<e9><8d><c6>_[<f7><86>^^]<97><e4><9d>^^@0<ad><bd><d7>}7<f2><fe><8c>p<b6>e\<d3>
                                        4<d3><e9><b4>i<9a>H<c0>^^A8<92><f9><f9>y<d3>4www<9f>>}<fa><f9>矟<d1>^^D.-<e7>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
\GenericError  ...                                
                                                    #4  \errhelp \@err@     ...
l.25 ...^^X^^R^^@<c6>&<9b>ͦ<d3><e9>l<d6>L<a7><e3><a6>Yo6<9f><ee><ec><<e7>|<ab>Ri
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because DT.Rmd appears to be an R Markdown v2 document.
Quitting from lines 23-25 (DT.Rmd) 
Error: processing vignette 'DT.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
  input string 371 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 387 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'dtw.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.15 ...4?<fa><e8><a3>w<de>y<87><88>T^^?)<e5><ec><ec>,<98><8f><c7><e3>[[[<bf><fc><f2>˗_~)<84>x>^^C<ed>^
                                                  <e8><c1><83>^^G<fb>Z<ee>޽[<af><d7>{<9a>$<<e4><d9>	{<dd><c9><e1>^...
! Please use \mathaccent for accents in math mode.
\add@accent ...@spacefactor \spacefactor }\accent 
                                                  #1 #2\egroup \spacefactor ...
l.15 ...<bf><93>^^?<a1><f6><b1> z><93>^^O<b4><fb><c1><88><cb>KW<9c><bd><93><8a><96><a3>^^P<84><87>^^P²<ac>\.<f7>
                                                  <e8>ѣ^^O><f8> <97>˽<fa>꫻<bb><bb><b3><b3><b3>g<b7><f4><bb>...
! You can't use `\spacefactor' in math mode.
\add@accen
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls to packages already attached by Depends:
  ‘ggm’ ‘tcltk’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘ggm’ ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘dynamicGraph-Ex.R’ failed
The error most likely occurred in:

> ### Name: DynamicGraph
> ### Title: DEPRECATED: Simple interface to dynamicGraph
> ### Aliases: DynamicGraph
> ### Keywords: dplot hplot iplot dynamic graphs methods multivariate
> 
> ### ** Examples
> 
> require(tcltk); require(dynamicGraph)
> 
> # Example 1:
> 
> W <- dg(as(new("dg.simple.graph", vertex.names = 1:5), "dg.graph"),
+         control = dg.control(title = "Very simple"))
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: dg ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/dynamichazard.Rcheck/00install.out’ for details.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs     2.1Mb
    models   4.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/edrGraphicalTools.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/eegkit.Rcheck/00install.out’ for details.
installed size is 40.7Mb
  sub-directories of 1Mb or more:
    libs  40.4Mb
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 421 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'elrm.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.20 ...V^^AZ^^[<e1>dF^^L{^^C<94>ұ<b1><b1>`0<88><a4>^^[<86>Q<ab>հj<92><c9>d<ae>\<b9>
                                                  ^^B^^@mm<da>^^^<bb>r<a2>f樺ǈ;<cd>4<a7>s...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.25 <c1><8e>N<92>$<d4>:<8c>^^A<d8>^^X<8e><e3>J<a5>R<8b>^^[ ^^G><bd>c,^^Y<9d>B<f5><a9>}
                                             !<d0>^^Y<f8><ec>	<97>𥪪<f5>z<9d><b5><cb>^^Y<d1>X>d<87><8f>u{t!...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Undefined control sequence.
l.45 x<9c><ed>\<cf>
          k^^[<d7>^^V>Q쪢<89
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘hgu133plus2.db’
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  16.7Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    xsd   5.4Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
sh: +RTS: command not found
Quitting from lines 315-317 (creating-EML.Rmd) 
Error: processing vignette 'creating-EML.Rmd' failed with diagnostics:
pandoc document conversion failed with error 127
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/emma.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'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.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 119-144 (emojifont.Rmd) 
Error: processing vignette 'emojifont.Rmd' failed with diagnostics:
StatTreeHorizontal was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyPackages in Depends field not imported from:
  ‘FactoMineR’ ‘MASS’ ‘Rcmdr’ ‘SensoMineR’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Error in re-building vignettes:
  ...
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.15 ...<e5><81>h	ԂXqI<a9><c9><c0>H^^H<b5>N<93>K<c6>C<99><e0>^^D_i<aa>:<d3>&<96><df><e2><d7>9<dc><e7>/}
                                                  <c4>v,Gg!<c6>wν<ba><e7><9e><df>=<f7>|\ydkk<8b>N.<8d>...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Undefined control sequence.
l.15 ...<99><e0>^^D_i<aa>:<d3>&<96><df><e2><d7
Calls: buildVignettes -> texi2pdf -> texi2dvi
In addition: Warning messages:
1: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 390 is invalid in this locale
2: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 391 is invalid in this locale
3: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 405 is invalid in this locale
4: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 406 is invalid in this locale
5: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 412 is invalid in this locale
Execution halted
Running examples in ‘erpR-Ex.R’ failed
The error most likely occurred in:

> ### Name: erp.infl
> ### Title: inspect the influence of a subject on the average (single
> ###   electrode).
> ### Aliases: erp.infl
> 
> ### ** Examples
> 
> 
> data(ERPsets)
> 
> erp.infl(base="Exp1_word_subj", numbers=1:20, electrode="OZ", 
+ startmsec=-200, endmsec=1500, erplist=ERPsets)
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: erp.infl ... handshake -> fun -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ETAS.Rcheck/00install.out’ for details.
Package unavailable to check Rd xrefs: ‘RODBC’
Package required but not available: ‘forensim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because eurostat_tutorial.Rmd appears to be an R Markdown v2 document.
Loading required package: xml2
trying URL 'http://ec.europa.eu/eurostat/estat-navtree-portlet-prod/BulkDownloadListing?sort=1&file=data%2Ftsdtr210.tsv.gz'
Content type 'application/octet-stream;charset=UTF-8' length 4136 bytes
==================================================
downloaded 4136 bytes

Table tsdtr210 cached at /tmp/RtmpmVGUrL/eurostat/tsdtr210_num_code_TF.rds
Quitting from lines 129-131 (eurostat_tutorial.Rmd) 
Error: processing vignette 'eurostat_tutorial.Rmd' failed with diagnostics:
Timeout was reached
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Evomorph.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: survival
Loading required package: TH.data
Loading required package: MASS

Attaching package: 'TH.data'

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

    geyser

Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 437 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 438 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'evtree.tex' failed.
LaTeX errors:
! TeX capacity exceeded, sorry [text input levels=15].
\@filef@und ->evtree.tpt 
                         
l.16 ...BO=<b5><e4><d0><de>r<88><ce>m)<88>B<f1><a1><a5>X^^Em^^E)^^NYX-&<c4>M<bd>x-<8c><9e>\[
                                                  <d3><dd>纛<84>H<ef><f0><a9><e7><ed>S^^\<fd><b0>c'<ca><d3><f7> vg...
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 356 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'exams.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 ...^^^{<ec><bd><e7>Rȭ<f4>蛡<85>P^^]bL^^L6^^L<ac>^^W<e1><d6>-^^Y<b4>Y\U
                                                  <e2><8f>ǻU<ed><8d><f3>K<fa>^^O_<f5><fe><ad>^^Sےc'<91><ab>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 ...<a5>RQJY<96>5`'A^^P<ec><ef><ef><97><cb><e5>z<bd>n<9a>&<fa>!<a2><ad><ad><ad><d9><d9>Y4^^[<b0><b7><b8>\q
                                                  <e6>|Ypb<8e>a<ba>D"<81><89>'<a2>z<bd><de><ed>v<cf>1<df>^^W+...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Please use \mathaccent for accents in math mode.
\add@accent ...@sp
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    exiftool  10.2Mb
Package suggested but not available for checking: ‘golubEsets’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: kernlab
Quitting from lines 23-26 (advanced-vignette.Rmd) 
Error: processing vignette 'advanced-vignette.Rmd' failed with diagnostics:
there is no package called 'golubEsets'
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/FAiR.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘OpenML’
Running the tests in ‘tests/run-all.R’ failed.
Last 13 lines of output:
  Loading required package: farff
  1. Error: quick test with small arffs (@test_quick.R#6) ------------------------
  java.lang.UnsupportedClassVersionweka/core/Instances : Unsupported major.minor version 51.0
  1: compareRWeka(INST_ARFF_DIR, "iris.arff", data.reader = dreader) at testthat/test_quick.R:6
  2: RWeka::read.arff(path2) at /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/farff.Rcheck/tests/testthat/helper.R:17
  3: .jnew("weka/core/Instances", .jcast(reader, "java/io/Reader"))
  
  testthat results ================================================================
  OK: 8 SKIPPED: 0 FAILED: 1
  1. Error: quick test with small arffs (@test_quick.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/fastcox.Rcheck/00install.out’ for details.
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  14.6Mb
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls in package code:
  ‘akima’ ‘spatial’ ‘tcltk’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.7Mb
Running examples in ‘FCMapper-Ex.R’ failed
The error most likely occurred in:

> ### Name: graph.fcm
> ### Title: Fuzzy cognitive map graph
> ### Aliases: graph.fcm
> 
> ### ** Examples
> 
> 
> matrix = matrix(nrow=7,ncol=7)
> matrix[1,] = c(0,-0.5,0,0,1,0,1)
> matrix[2,] = c(1,0,1,0.2,0,0,0.6)
> matrix[3,] = c(0,1,0,0,0,0,0)
> matrix[4,] = c(0.6,0,0,1,0,0,0.1)
> matrix[5,] = c(0,0.5,0,0,1,0,-0.6) 
> matrix[6,] = c(0,0,-1,0,0,0,0)
> matrix[7,] = c(0,0,0,-0.5,0,0,1)
> concept.names = c("A","B","C","D","E","F","G")
> 
> results = nochanges.scenario(matrix,iter=25,concept.names)
> 
> graph.fcm(matrix,concept.sizes=results$Equilibrium_value,concept.names)
Invalid MIT-MAGIC-COOKIE-1 keyWarning in fun(libname, pkgname) : couldn't connect to display ":0"
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "font".
Calls: graph.fcm ... .tkplot.convert.font -> <Anonymous> -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is 36.6Mb
  sub-directories of 1Mb or more:
    libs  35.9Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/fdaPDE.Rcheck/00install.out’ for details.
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    libs  19.8Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   6.4Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/fds.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyread.hmd: 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 significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/feature.Rcheck/00install.out’ for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘tcltk’ 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: ‘tools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘tools:::fetchRdDB’
  See the note in ?`:::` about the use of this operator.
Invalid MIT-MAGIC-COOKIE-1 keyparseHelp: no visible global function definition for ‘help’
parseHelp: no visible global function definition for ‘unzip’
Undefined global functions or variables:
  help unzip
Consider adding
  importFrom("utils", "help", "unzip")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/FieldSim.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyfieldsim: no visible global function definition for ‘rnorm’
midpoint: no visible global function definition for ‘rnorm’
setAtlas_under: no visible global function definition for ‘runif’
setCovf_under : Ibeta: no visible global function definition for
  ‘pbeta’
visualize: no visible global function definition for ‘colorRampPalette’
Undefined global functions or variables:
  colorRampPalette pbeta rnorm runif
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "pbeta", "rnorm", "runif")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 83-87 (fiftystater.Rmd) 
Error: processing vignette 'fiftystater.Rmd' failed with diagnostics:
ScaleColorPlane was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because Best_Prectices.Rmd appears to be an R Markdown v2 document.
Quitting from lines 2-23 (Best_Prectices.Rmd) 
Error: processing vignette 'Best_Prectices.Rmd' failed with diagnostics:
could not find function "doc_date"
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘tkrplot’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘methods’ ‘tkrplot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘fisheyeR-Ex.R’ failed
The error most likely occurred in:

> ### Name: POIcoords<-
> ### Title: Update POI slots
> ### Aliases: POIcoords<-
> 
> ### ** Examples
> 
>    ## IRIS Example
>    data(iris)
>    
>    # distance of each element to each dimension max and min
>    matrizSim = cbind(
+                1 - (max(iris[,1]) - iris[,1]) / (max(max(iris[,1]) - iris[,1])),
+                1 - (max(iris[,2]) - iris[,2]) / (max(max(iris[,2]) - iris[,2])),
+                1 - (max(iris[,3]) - iris[,3]) / (max(max(iris[,3]) - iris[,3])),
+                1 - (max(iris[,4]) - iris[,4]) / (max(max(iris[,4]) - iris[,4])),
+ 
+                1 - (min(iris[,1]) - iris[,1]) / (min(min(iris[,1]) - iris[,1])),
+                1 - (min(iris[,2]) - iris[,2]) / (min(min(iris[,2]) - iris[,2])),
+                1 - (min(iris[,3]) - iris[,3]) / (min(min(iris[,3]) - iris[,3])),
+                1 - (min(iris[,4]) - iris[,4]) / (min(min(iris[,4]) - iris[,4])))
> 
>    # exaggerate diffs
>    matrizSim  = matrizSim^3 
>    
>    # Create POI plot
>    irisPOI = POICreate('POI')
>    irisPOI@matrizSim <- matrizSim
>    irisPOI@wordsInQuery <- c('high.Sepal.Length', 'high.Sepal.Width', 'high.Petal.Length', 'high.Petal.Width',
+                              'low.Sepal.Length', 'low.Sepal.Width', 'low.Petal.Length', 'low.Petal.Width')
>    POIcoords(irisPOI) <- POICalc(irisPOI ,length(irisPOI@wordsInQuery))
>    irisPOI@docs <- cbind(matrix(seq(1:nrow(irisPOI@objeto))),matrix(seq(1:nrow(irisPOI@objeto))))
>    irisPOI@colores <- c(rep(2,50),rep(3,50),rep(4,50))
>    try(rm('POI.env'), silent = T)
Warning in rm("POI.env") : object 'POI.env' not found
>    plotPOI(irisPOI)
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: plotPOI ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/fit4NM.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because fitbitScraper-examples.Rmd appears to be an R Markdown v2 document.
Quitting from lines 29-40 (fitbitScraper-examples.Rmd) 
Error: processing vignette 'fitbitScraper-examples.Rmd' failed with diagnostics:
Value for option cookie (10022) must be length-1 string
Execution halted
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
     estimating mean dists
     estimating probs of migration
     estimating median dists
     creating output DONE!
  DONE!
  bird likely dod not move, exiting without result
  testthat results ================================================================
  OK: 27 SKIPPED: 0 FAILED: 2
  1. Error: map_flightr_ggmap_works (@test_data_result_summary_and_plotting.R#36) 
  2. Error: plot_util_distr_works (@test_data_result_summary_and_plotting.R#57) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/foodweb.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘rgl’ which was already attached by Depends.
  Please remove these calls from your code.
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: only replacement of elements is allowed
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/forestFloor.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ForImp.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyForImp: no visible global function definition for ‘head’
ForImp: no visible global function definition for ‘tail’
ForImp: no visible global function definition for ‘dist’
medianimp: no visible global function definition for ‘quantile’
rancatmat: no visible global function definition for ‘runif’
transfmatcat: no visible global function definition for ‘qnorm’
transfmatcat: no visible global function definition for ‘sd’
Undefined global functions or variables:
  dist head qnorm quantile runif sd tail
Consider adding
  importFrom("stats", "dist", "qnorm", "quantile", "runif", "sd")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because formattable-data-frame.Rmd appears to be an R Markdown v2 document.
Quitting from lines 168-169 (formattable-data-frame.Rmd) 
Error: processing vignette 'formattable-data-frame.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
  input string 346 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 356 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Formula.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
l.22 p<81>'<f6>^^\<f3>`<cc><e9><e7><c0>^^Sa<ee>yB<b0><81><c4>q<9c><fe>7<f2><e7><8a>9/<db><de><fc><b4>\<f1>
                                           <fd>ޫ<9d><c6>E<80><82><f4>^^V<e7>^^\<b8>^^G^^Y0<c6>hG^^W<87><cc>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Missing $ inserted.
<inserted text> 
                $
l.23 ...G<9e>3<97><cb><cd><cc><cc><d4>j5<ac><93>B<a1><b0><b0><b0>P(^^T^^R<89><84>a^^X<aa><aa>nmm)<8a><e2>y^
                                                  <a5>Ra<8c>U*^^U^^\<c3>i<b7><db><c8>|2<c6><f0><ab>^^P<e2>...
! Undefined control sequence.
l.23 ...Ra<8c>U*^^U^^\<c3>i<b7><db><c8>|2<c6><f0><ab>^^P<e2>ѣG<b3><b3><b3>B<88>X,<96><c
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘Rsymphony’

Packages suggested but not available for checking:
  ‘Rsocp’ ‘Rnlminb2’ ‘Rdonlp2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
  Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/frailtypack.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/frontiles.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyROCscore: no visible global function definition for ‘par’
ROCscore: no visible global function definition for ‘axis’
ROCscore: no visible global function definition for ‘mtext’
ROCscore: no visible global function definition for ‘legend’
alphafrontier.2d: no visible global function definition for ‘par’
alphafrontier.2d: no visible global function definition for ‘polygon’
alphafrontier.2d: no visible global function definition for ‘lines’
alphafrontier.2d: no visible global function definition for ‘points’
alphafrontier.3d: no visible global function definition for ‘layout’
alphafrontier.3d: no visible global function definition for ‘barplot’
alphafrontier.3d: no visible global function definition for ‘axis’
alphafrontier.3d: no visible global function definition for ‘lines’
alphafrontier.3d: no visible global function definition for ‘na.omit’
ordermfrontier.2d: no visible global function definition for ‘par’
ordermfrontier.2d: no visible global function definition for ‘polygon’
ordermfrontier.2d: no visible global function definition for ‘lines’
ordermfrontier.2d: no visible global function definition for ‘points’
ordermscore.boot: no visible global function definition for ‘sd’
Undefined global functions or variables:
  axis barplot layout legend lines mtext na.omit par points polygon sd
Consider adding
  importFrom("graphics", "axis", "barplot", "layout", "legend", "lines",
             "mtext", "par", "points", "polygon")
  importFrom("stats", "na.omit", "sd")
to your NAMESPACE file.
Running examples in ‘FSelector-Ex.R’ failed
The error most likely occurred in:

> ### Name: as.simple.formula
> ### Title: Converting to formulas
> ### Aliases: as.simple.formula
> 
> ### ** Examples
> 
>   data(iris)
>   result <- cfs(Species ~ ., iris)
Error in .jnew("weka/core/Attribute", attname[i], .jcast(levels, "java/util/List")) : 
  java.lang.UnsupportedClassVersionError: weka/core/Attribute : Unsupported major.minor version 51.0
Calls: cfs ... read_model_frame_into_Weka -> read_data_into_Weka -> .jnew -> .External
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/fso.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ftsa.Rcheck/00install.out’ for details.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
Package required but not available: ‘breastCancerVDX’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package unavailable to check Rd xrefs: ‘cffdrs’
Error in re-building vignettes:
  ...
  input string 191 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 192 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 200 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'CNY.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.31 ...<f9><f3><a7>\.;q*<e0><88><ed><ed><ed><d0> <ac>~<d0><e6>+W<88><ca><e5>2J<fb>Μ^^@σ<83><83>0<89><f1>x\T
                                                  <c3>^^Q^^Y<e2>~^^H<ed><de>^^U`<8c><f5><f7><f7><e3><93>s<ce>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.34 ΘeY<b9>\N
            <84>x<a2>B^^DX^^@E?T<ed>^^P<91>E<a3>ю<8e><8e>|>/<8a>GD<94><cb>尙<c3><dd>z^^E<f6>^^P+x<^^^I<92>$I<d2>4M<92>$UU^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.36 <8c>C@^^OP^^D\<b2>
                 <c0><fd>\<a6>A<bb>X<ee><a0><cd>7x<8d><a1><f2><d9>ù<87>	<99><9e><9e>~<f4><e8>^^QB<8d><ab>W<af>^^B^^Tt^<f2><a2>]^^Nq<d2>^^@<d4>#O<ab>^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you h
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘gamlss.demo-Ex.R’ failed
The error most likely occurred in:

> ### Name: demoDist
> ### Title: Interface for demonstrating the gamlss.family distributions
> ### Aliases: demoDist
> ### Keywords: distribution regression
> 
> ### ** Examples
> 
> ## do not run 
> demoDist()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: demoDist ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Package which this enhances but not available for checking: ‘doMPI’
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    data    3.7Mb
    doc     2.9Mb
    tests   2.7Mb
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 354 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'jss.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.18 <92><a1>><df><ef><af>NJ^^C^^C~<d2><e7>^^[^^Zhl|<fb><f6><ed><e6><a3>ٶ}
                                       <f3><e6>M۶gffZ<b6>ll<86><bd><f6><80>^^V<dc>;^^W<f2><e9>k<f5>X<ea>w<9f><fc><e5><ef>֦...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Undefined control sequence.
l.18 ...`<8c>QJ3<99>L^^?^^?<ff><e0><e0> ^^@PJ^^S<89>D:<9d>ƨ<ea><ec>ٳ<8b><8b><8b>W<ae>\<99>
                                                  <9e><9e><be>r<e5><ca><de>'<b7><b7>@<e3><87>a<cb>^^^b<96><e6>]fff^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Missing $ inserted.
<inserted text> 
        
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    1.0Mb
    libs   8.7Mb
installed size is 45.7Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     42.9Mb
Package suggested but not available for checking: ‘paleofire’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/gdimap.Rcheck/00install.out’ for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.4Mb
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because tutorial.Rmd appears to be an R Markdown v2 document.
Quitting from lines 102-103 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
timedelay.lm: no visible global function definition for ‘lm’
timedelay.lm: no visible global function definition for ‘AIC’
timedelay.lm: no visible global function definition for ‘pdf’
timedelay.lm: no visible global function definition for ‘x11’
timedelay.lm: no visible global function definition for ‘rainbow’
timedelay.lm: no visible global function definition for ‘title’
timedelay.lm: no visible global function definition for ‘lines’
timedelay.lm: no visible global function definition for ‘predict’
timedelay.lm: no visible global function definition for ‘points’
timedelay.lm: no visible global function definition for ‘legend’
timedelay.lm: no visible global function definition for ‘dev.off’
timedelay.univariate.lm: no visible global function definition for ‘lm’
timedelay.univariate.lm: no visible global function definition for
  ‘AIC’
ts.bspline: no visible global function definition for ‘lm’
ts.bspline: no visible global function definition for ‘predict’
Undefined global functions or variables:
  AIC dev.off legend lines lm pdf points predict rainbow title x11
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "rainbow", "x11")
  importFrom("graphics", "legend", "lines", "points", "title")
  importFrom("stats", "AIC", "lm", "predict")
to your NAMESPACE file.
Packages suggested but not available for checking: ‘KEGG.db’ ‘reactome.db’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/gensphere.Rcheck/00install.out’ for details.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/geoelectrics.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyimage.glm.krige.bayes: no visible global function definition for
  ‘heat.colors’
Undefined global functions or variables:
  heat.colors
Consider adding
  importFrom("grDevices", "heat.colors")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 key.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.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/GeoXp.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘stable’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 102-115 (examples-from-paper.Rmd) 
Error: processing vignette 'examples-from-paper.Rmd' failed with diagnostics:
StatEdges was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/GGEBiplotGUI.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
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 ‘GGEBiplotGUI-Ex.R’ failed
The error most likely occurred in:

> ### Name: GGEBiplot
> ### Title: GGEBiplotGUI: Interactive GGE Biplots in R
> ### Aliases: GGEBiplot
> 
> ### ** Examples
> 
> data(Ontario)
> GGEBiplot(Data = Ontario)
Invalid MIT-MAGIC-COOKIE-1 keyWarning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: GGEBiplot ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Running examples in ‘ggiraphExtra-Ex.R’ failed
The error most likely occurred in:

> ### Name: ggAncova
> ### Title: Make an interactive plot for an ANCOVA model
> ### Aliases: ggAncova ggAncova.default ggAncova.formula ggAncova.lm
> 
> ### ** Examples
> 
> require(moonBook)
Loading required package: moonBook
> require(ggplot2)
Loading required package: ggplot2
> require(ggiraph)
Loading required package: ggiraph
> ggAncova(radial,aes(age,NTAV,color=sex),interactive=TRUE)
Error: GeomInteractivePoint was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  > library(testthat)
  > library(ggiraphExtra)
  > 
  > test_check("ggiraphExtra")
  Loading required package: ggplot2
  Loading required package: ggiraph
  Loading required package: plyr
  Error: GeomInteractivePoint was built with an incompatible version of ggproto.
  Please reinstall the package that provides this extension.
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra
Quitting from lines 28-33 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
GeomInteractivePoint was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because an_introduction.Rmd appears to be an R Markdown v2 document.
Loading required package: ggplot2
Fontconfig warning: line 146: blank doesn't take any effect anymore. please remove it from your fonts.conf
Fontconfig warning: line 146: blank doesn't take any effect anymore. please remove it from your fonts.conf
Fontconfig warning: line 146: blank doesn't take any effect anymore. please remove it from your fonts.conf
Fontconfig warning: line 146: blank doesn't take any effect anymore. please remove it from your fonts.conf
Fontconfig warning: line 146: blank doesn't take any effect anymore. please remove it from your fonts.conf
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshotfc0629dcd35c.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotfc0629dcd35c.png': No such file or directory
Quitting from lines 13-27 (an_introduction.Rmd) 
Error: processing vignette 'an_introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because using_ggmcmc.Rmd appears to be an R Markdown v2 document.
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: tidyr
Loading required package: ggplot2
Registering fonts with R
Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Quitting from lines 142-143 (using_ggmcmc.Rmd) 
Error: processing vignette 'using_ggmcmc.Rmd' failed with diagnostics:
polygon edge not found
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Packages suggested but not available for checking:
  ‘BSgenome.Hsapiens.UCSC.hg18.masked’
  ‘BSgenome.Hsapiens.UCSC.hg19.masked’
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Running the tests in ‘tests/bym.R’ failed.
Last 13 lines of output:
  + 
  + kentucky = mergeBugsData(kentucky, kSummary)
  + 
  + if(require('sp', quietly=TRUE)) {
  +   pdf("spplotBym.pdf",height=4,width=8)
  +   print(spplot(kentucky, "FittedRateCounty.mean"))
  +   dev.off()
  + }
  + 
  + }
  Error in R2OpenBUGS::bugs(forBugs$ragged, inits = int2, model.file = "bym.txt",  : 
    Cannot find the OpenBUGS program
  Execution halted
installed size is 37.4Mb
  sub-directories of 1Mb or more:
    libs  36.7Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/gmatrix.Rcheck/00install.out’ for details.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  'help.start()' for an HTML browser interface to help.
  Type 'q()' to quit R.
  
  > library('testthat')
  > 
  > test_check('Gmisc')
  Loading required package: Gmisc
  Loading required package: Rcpp
  Loading required package: htmlTable
  Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  testthat results ================================================================
  OK: 116 SKIPPED: 0 FAILED: 0
  Execution halted
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  14.8Mb
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
Error in re-building vignettes:
  ...
  input string 205 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 206 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 214 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'googleVis.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 <ed><c1>E<98>e҃<a7>z<ea>ѣ<82>x^^V<(xt^^?<80><88><ee>\E
                                  <8a>B^^[<88>^^Y<e2><L'a"A:'^^AM<b2><c9>V<fb><98>&Vs<b0><f9>^^\^^^^^\...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 ...<97><cb>=x<f0>`vv<f6>ڵk<87>^^O^^_<be>x<f1><a2>i<9a><8f>^^_?<f6>}<ff>ʕ+^^W.\<98>
                                                  <9d><9d><d5>4mmmM<92><a4><b9><b9><b9>;w<ee>D^^^<d5>n<b6>[<d3>4...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.20 ^^@^^X<86>^^A^^@<c5>b<b1><eb> {<ba><9f><84><90>r<b9>L<bb>\<b3>
                                  <d9>$<84><8c><8f><8f>˲L^^Hy<f9><f2><a5><e7>y<93><93><93><8d>F^^C^^@<c2>0ܖ<a4>q^^O
The control sequence at the end of the top line
of your error message was nev
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/GPC.Rcheck/00install.out’ for details.
installed size is 41.9Mb
  sub-directories of 1Mb or more:
    libs  40.0Mb
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1. Error: gpuMatrix Integer Matrix multiplication (@test_gpuMatrix_algebra.R#318) 
  2. Error: gpuMatrix Single Precision Matrix Cholesky Decomposition (@test_gpuMatrix_chol.R#25) 
  3. Error: vclMatrix permute (@test_order.R#21) 
  4. Error: Switching GPU vclMatrix Single Precision Column Sums (@test_switch_gpu_vclMatrix_row_col.R#36) 
  5. Error: Switching GPU vclMatrix Single Precision Row Sums (@test_switch_gpu_vclMatrix_row_col.R#82) 
  6. Error: Switching GPU vclMatrix Single Precision Column Means (@test_switch_gpu_vclMatrix_row_col.R#127) 
  7. Error: Switching GPU vclMatrix Single Precision Row Means (@test_switch_gpu_vclMatrix_row_col.R#173) 
  8. Error: Switching GPU vclMatrix Single Precision Block Column Sums (@test_switch_gpu_vclMatrix_row_col.R#376) 
  9. Error: Switching GPU vclMatrix Single Precision Block Row Sums (@test_switch_gpu_vclMatrix_row_col.R#424) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/gputools.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/GrammR.Rcheck/00install.out’ for details.
Errors in running code in vignettes:
when running code in ‘GRAN-Overview.Rnw’
  ...
Building 0 packages
starting migrateToFinalRepo 2017-01-12 07:20:28
Built 0 packages

  When sourcing ‘GRAN-Overview.R’:
Error: dims [product 0] do not match the length of object [1]
No traceback available 
> proc.time()
   user  system elapsed 
  2.426   0.863   5.051
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Running the tests in ‘tests/demo-graphics.R’ failed.
Last 13 lines of output:
  +           at = mean(par("usr")[1:2]), cex=0.7, font=3)
  + }
  > 
  > demo11 <- function() {
  +     par(bg="cornsilk")
  +     coplot(lat ~ long | depth, data = quakes, pch = 21, bg = "green3")
  + }
  > 
  > plotdiff(expression(demo1()), "demo-1")
  Error in system2("compare", c("-metric AE", paste0(label, c("-graphics.png",  : 
    error in running command
  Calls: plotdiff -> plotcompare -> system2
  Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/GroupSeq.Rcheck/00install.out’ for details.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/grt.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘gdalUtils’
Errors in running code in vignettes:
when running code in ‘gWidgets.Rnw’
  ...

Loading required package: gWidgetstcltk
Error : .onAttach failed in attachNamespace() for 'gWidgetstcltk', details:
  call: structure(.External(.C_dotTcl, ...), class = "tclObj")
  error: [tcl] invalid command name "option".


  When sourcing ‘gWidgets.R’:
Error: [tcl] invalid command name "toplevel".
Execution halted
Error in re-building vignettes:
  ...
Loading required package: gWidgetstcltk
Loading required package: tcltk
Invalid MIT-MAGIC-COOKIE-1 keyWarning in fun(libname, pkgname) : couldn't connect to display ":0"
Loading required package: digest
Error : .onAttach failed in attachNamespace() for 'gWidgetstcltk', details:
  call: structure(.External(.C_dotTcl, ...), class = "tclObj")
  error: [tcl] invalid command name "option".

Loading required package: gWidgetstcltk
Error : .onAttach failed in attachNamespace() for 'gWidgetstcltk', details:
  call: structure(.External(.C_dotTcl, ...), class = "tclObj")
  error: [tcl] invalid command name "option".

Loading required package: gWidgetstcltk
Error : .onAttach failed in attachNamespace() for 'gWidgetstcltk', details:
  call: structure(.External(.C_dotTcl, ...), class = "tclObj")
  error: [tcl] invalid command name "option".


Error: processing vignette 'gWidgets.Rnw' failed with diagnostics:
 chunk 3 
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".

Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/gWidgetsRGtk2.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/gWidgetstcltk.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/h5.Rcheck/00install.out’ for details.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Invalid MIT-MAGIC-COOKIE-1 keyPackage 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.
Error in re-building vignettes:
  ...
The following object is masked from 'package:stats':

    filter

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

    layout

Loading required package: viridis

---------------------
Welcome to heatmaply version 0.6.0
Type ?heatmaply for the main documentation.
The github page is: https://github.com/talgalili/heatmaply/

Suggestions and bug-reports can be submitted at: https://github.com/talgalili/heatmaply/issues
Or contact: <tal.galili@gmail.com>

	To suppress this message use:  suppressPackageStartupMessages(library(heatmaply))
---------------------

Quitting from lines 83-85 (heatmaply.Rmd) 
Error: processing vignette 'heatmaply.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/hgam.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyPackages in Depends field not imported from:
  ‘grplasso’ ‘lattice’ ‘rgl’ ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/HierO.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because replicating-highcharts-demos.Rmd appears to be an R Markdown v2 document.
Quitting from lines 58-81 (replicating-highcharts-demos.Rmd) 
Error: processing vignette 'replicating-highcharts-demos.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls in package code:
  ‘MASS’ ‘cubature’ ‘mvtnorm’ ‘numDeriv’ ‘quantmod’ ‘robustbase’
  ‘sandwich’ ‘timeDate’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    highlight   1.0Mb
    libs        7.8Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/highriskzone.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/HiPLARM.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/hiPOD.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyPlotOptPower: 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.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/hoardeR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/homals.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/HomoPolymer.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Found the following significant warnings:
  Warning: multiple methods tables found for ‘colMeans’
  Warning: multiple methods tables found for ‘colSums’
  Warning: multiple methods tables found for ‘rowMeans’
  Warning: multiple methods tables found for ‘rowSums’
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/humarray.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/HUM.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyCalculate3D: no visible global function definition for ‘persp’
CalculateHUM_Ex: no visible global function definition for ‘combn’
CalculateHUM_Plot: no visible global function definition for ‘plot’
CalculateHUM_Plot: no visible global function definition for ‘polygon’
CalculateHUM_Plot: no visible global function definition for ‘text’
CalculateHUM_Plot: no visible global function definition for ‘points’
CalculateHUM_Plot: no visible global function definition for ‘lines’
Undefined global functions or variables:
  combn lines persp plot points polygon text
Consider adding
  importFrom("graphics", "lines", "persp", "plot", "points", "polygon",
             "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    dict   1.3Mb
    doc    1.1Mb
    libs   4.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
trying URL 'https://arxiv.org/e-print/1406.4806v1'
Content type 'unknown' length 29273 bytes (28 KB)
==================================================
downloaded 28 KB

Quitting from lines 162-165 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/hypervolume.Rcheck/00install.out’ for details.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   5.6Mb
Package required but not available: ‘RODBC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/iBUGS.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘tcltk’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.1Mb
    libs   7.8Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/iClick.Rcheck/00install.out’ for details.
Running examples in ‘iClick-Ex.R’ failed
The error most likely occurred in:

> ### Name: iClick.ARIMA
> ### Title: iClick GUI for ARIMA
> ### Aliases: iClick.ARIMA
> 
> ### ** Examples
> 
> 
> ##External data
> #data("returnsDaily24")
> #y=returnsDaily24[,c(1,5)]
> 
> ## Simulation data
> dat=rnorm(100,5,1)
> y=ts(dat, start = c(1970, 1), frequency = 12)
> 
> iClick.ARIMA(y)
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: iClick.ARIMA ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Error in re-building vignettes:
  ...
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 350 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ICS.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cf>
          O^^S<df>^^V?ԇ<bc><89><a4>ÄMCRhnbta<a0>d6Ƙ<94>^^Ekw<fe>]<eb><c2>tk\<c1><bf>Ѕ1q<c9>ưe^^VT^^S^^S<88>^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...^S<df>^^V?ԇ<bc><89><a4>ÄMCRhnbta<a0>d6Ƙ<94>^^Ekw<fe>]<eb><c2>tk\<c1>
                                                  <bf>Ѕ1q<c9>ưe^^VT^^S^^S<88>^^S<a7><8d>A...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 <c3>^^PB\<be>
            |<f9>Ǐ^^_<86>a<80>H!D&<93>A7|^^Z<86>a<9a>&c<8c>1<b6><b9><b9>9::jYV&<93>i<e3>z^^O<e0>իWM-+++{{{<bd>X<eb>d^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.20 cB<88><ef><9e>^^W<c4><e3>Q<c6>^^L<c7><f9>O2^^Yk^^
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because US-Engineering-Weather-Map.Rmd appears to be an R Markdown v2 document.
Error in (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  : 
  there is no package called 'states2k'
Quitting from lines 24-109 (US-Engineering-Weather-Map.Rmd) 
Error: processing vignette 'US-Engineering-Weather-Map.Rmd' failed with diagnostics:
object 'states2k_map' not found
Execution halted
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ifa.Rcheck/00install.out’ for details.
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    help   1.2Mb
    libs  14.2Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ilc.Rcheck/00install.out’ for details.
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       3.4Mb
    include   2.6Mb
    libs     13.2Mb
Packages suggested but not available for checking: ‘rsprng’ ‘Rmpi’
Missing link or links in documentation object 'ask.user.yn.question.Rd':
  ‘winDialog’

Missing link or links in documentation object 'check.for.updates.R.Rd':
  ‘winDialog’

Missing link or links in documentation object 'installr.Rd':
  ‘winDialog’

Missing link or links in documentation object 'os.manage.Rd':
  ‘winDialog’

Missing link or links in documentation object 'updateR.Rd':
  ‘winDialog’

See section 'Cross-references' in the 'Writing R Extensions' manual.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Running examples in ‘iqspr-Ex.R’ failed
The error most likely occurred in:

> ### Name: QSPRpred-class
> ### Title: QSPRpredictor class
> ### Aliases: QSPRpred QSPRpred-class
> 
> ### ** Examples
> 
> data(qspr.data)
> smis <- paste(qspr.data[,1])
> ty <- qspr.data[,c(2,5)]
> trainidx <- sample(1:nrow(qspr.data), 5000)
> testidx <- (1:nrow(qspr.data))[-trainidx][1:100]
> 
> data(qsprpred_EG_5k) 
> ## same as run => qsprpred_EG_5k <- 
> 
> #-----arguments
> #smis: SMILES string set (character vector) for training
> #y: property sets (matrix) for training  
> #v_ymin: minimum value of target properties
> #v_ymax: maximum value of target properties
> #v_descriptor: function transforming SMILES strings to feature matrix 
> #v_fpnames: character vectors indicating finger print used in the descriptor
> #w0: matrix representing prior mean of coeffients in linear regression model
> #V0_inv: matrix representing the prior variance of coeffients in linear regression model
> #a0: numeric value representing the location parameter in gamma prior 
> #b0: numeric value representing the shape parameter in gamma prior 
> #------
> 
> predictions <- qsprpred_EG_5k$qspr_predx(smis[testidx])  

get fingerprint graph from SMILES strings          
Error in .jcall("org/openscience/cdk/DefaultChemObjectBuilder", "Lorg/openscience/cdk/interfaces/IChemObjectBuilder;",  : 
  RcallMethod: cannot determine object class
Calls: <Anonymous> ... get.smiles.parser -> .get.chem.object.builder -> .jcall -> .External
Execution halted
Namespaces in Imports field not imported from:
  ‘coda’ ‘lattice’
  All declared Imports should be used.
Running examples in ‘IRATER-Ex.R’ failed
The error most likely occurred in:

> ### Name: clean.admb
> ### Title: delete IRATE (ADMB) run files
> ### Aliases: clean.admb clean.IRATE
> 
> ### ** Examples
> 
> example.setup <- IRATE.examples()
> new.setup <- new.setup.path <- example.setup[1] # select old IRATE setup to reparameterize
> print(new.setup) # print setup name to be run
[1] "HoenigNonMixing"
> old.setup.path <- system.file(paste0("IRATE.examples/",new.setup,".dat"), package = "IRATER")
> 
> system(paste("mkdir -p ",new.setup.path)) # create run folder for new setup
> system(paste("cp",old.setup.path, new.setup.path)) # copy old setup in new run folder
> setwd(new.setup.path)
> 
> run.IRATE(new.setup) # compile and run setup
sh: admb: command not found
Error in R2admb::compile_admb(setup.file, safe = safe, re = re, verbose = verbose,  : 
  base admb command failed: run setup_admb(), or check ADMB installation
Calls: run.IRATE -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
  input string 443 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 451 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 452 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 460 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'isocir.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 ...<b6>m<cb><f6><81>^^?<c9>?<e5><cc>B^^H<<c4><ef><f0>؞p<b9><cb>~<a6>i~<f3><cd>7<bf><fc><f2><8b>i<9a><86>a\<bf>
                                                  ~]<d7>u<<b7>m<bb>P(<88>^^V<b2>٬a^^X<d8><df><f4><f4><f4>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 ...<fd><f6><db><fe><9b>xud^^Lݼy<b3>'a<d6>u]Q^^T<f9><a7>a^^X?<fd><f4><93><a2>(<f1>x\^^H
                                                  <f1><e5><97>_^<bb>vm~~~gg<e7><d7>_^^?<9d><9d><9d>5^^L...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 ...<e6>y<fe><fc>y2<99><f4></<99>L<86><a3>^^E^^L,<95>J<9f>^^?<fe><b9><e3>8<99>L<e6>,<c8><eb>^^W\p
                                                  <dd>^^[<90><d7><cf>8<96><e5>4MS<d7>u<c6><d8><c2><c2><c2><d8><d
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
l.19 ...	]<d7>^^AJ^^R<89>D<b3>ٔ<f3><ef><ef><ef>g<b3><d9>J<a5><92><cd>f^^AP8<e7><e5><b2>_(d\^^W
                                                  <97>})<f6>^^@<ca>)D<84>^^_<be><bf><f3><d3>O<8d>7ޘ<e6><fc>2...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Extra }, or forgotten \endgroup.
l.24 <9e>^^P<91>g}}
             ^^]<d8>^^_^^A<8d><88>^^TEY^^<ae><d5>j<e8>^^Z<db><dc><dc>l6<9b>2<b7>B
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or
Calls: buildVignettes -> texi2pdf -> texi2dvi
In addition: Warning messages:
1: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 424 is invalid in this locale
2: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 425 is invalid in this locale
3: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 433 is invalid in this locale
4: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 434 is invalid in this locale
5: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 442 is invalid in this locale
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   4.8Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.1Mb
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
         ".shp$"))), method = "local", what = "sp", stringsAsFactors = TRUE, encoding = "cp932")
  9: read_json(as.location(x), method, parse, what, ...)
  10: file_to_sp(x, ...)
  11: match.arg(fileext, c("shp", "kml", "url", "geojson"))
  12: stop(gettextf("'arg' should be one of %s", paste(dQuote(choices), collapse = ", ")), 
         domain = NA)
  
  testthat results ================================================================
  OK: 9 SKIPPED: 0 FAILED: 1
  1. Error: Collect administration offices data (@test-spdf_jpn.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  16.1Mb
Invalid MIT-MAGIC-COOKIE-1 keyStartKappa: no visible global function definition for ‘read.csv’
StartKappa: no visible global function definition for ‘na.omit’
StartKappa: no visible global function definition for ‘write.csv2’
Undefined global functions or variables:
  na.omit read.csv write.csv2
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "read.csv", "write.csv2")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Kernelheaping.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 238 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 244 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'kernlab.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cd>
          k^^[G^^[^^?<ec>dc'U<a5>^^N-.u<ba><b2><bb>E<b8><88>e<a3>V^^P<b0>!<dd>^^F<ab><84>^ғo=<e4><a4><d0>C^^O=<e5>VBo<f9>^^C^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.17 ...<f7>}^^Lb<9a>f<9c>5<9f><b8>~<fd>zL<f2><d6><d6><d6>^^XcCCC+++^^_|<f0><c1><fa><fa>z6<9b>}
                                                  <f0><e0><c1><e8><e8><a8><e7>yO<9e><<f1><<8f><88><d2><e9><f4><da><da><da>ŋ^^W...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Extra }, or forgotten \endgroup.
l.17 ...O<9e><<f1><<8f><88><d2><e9><f4><da><da
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/KernSmoothIRT.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/kml3d.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/kml.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/kmlShape.Rcheck/00install.out’ for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   3.4Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ks.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 100 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'kst.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.17 b<84><bd><a5>?^^T<9a>[<c1><bf><a0>^^?Ls^<85><e2>^^_Ћ^^E<a5>$<87>6v<91>\B
                                               <a6><ea><90>[q<d9>M<e8>E^^R<bf><87>^^O>&<ab><8d>k<a2>&<b5><fb>9<88>;...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
l.22 ^^YIN<ac><a5>^^[\<8a>
                 sY<cc>Q<d7>'<db>a^^P^^Dggg<c9>d^^R<8a>M$^^R<f9>|<9e>u^^N<e3>D<8e><87><8d><9c>ե+_)U,^^Vi<94>^^VB5<98>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.22 ...<88>H<b7>L<a5>^^T<8b>^^A/m<8d><d0><ed>v<85>^^P<be><ef><f3>O^^W<8b>E6㩘<99>',<9a><ca>\<de>
     
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Errors in running code in vignettes:
when running code in ‘variablekey.Rnw’
  ...
Warning in file(outfile, "w") :
  cannot open file 'plots/t-Roptions.R': No such file or directory

  When tangling ‘variablekey.Rnw’:
Error: cannot open the connection
Execution halted
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    doc            1.0Mb
    libs          10.3Mb
    testdata       1.9Mb
    vignettedata   2.0Mb
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    dataset   1.4Mb
    include  11.7Mb
    libs      4.0Mb
Error in re-building vignettes:
  ...
  input string 428 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 433 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'an_introduction_to_lifecontingencies_package.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\Ol
           [E^^Z<ff><b0><9b><8d>_q<de><f3><90>n0i^^S<9b><d1>^^VXj^^RKO<da>C^^Q<b8>R}^^B<a9> V9<ad><c4>	<e5>Ω7đ^^^<b8>p<b4>8TB...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
l.15 ...<93><b6><f1><f8><bd><ba><c9>k<da><d8>{<f8>mF&<ff><9c><b4>	M<b2><fe>)zz^^?f<e6><cd><f7><e6><9b><ef><fb>}ߌ<f3>\<ab>
                                                  բ<a3>߳<ee><c0><fe><a2>+<de>aFW<bc>Ì<ae>x<87>^^Y]<f1>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...+<de>aFW<bc>Ì<ae>x<87>^^
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package which this enhances but not available for checking: ‘reactR’
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    doc        1.8Mb
    libs      18.6Mb
    testdata   1.5Mb
Error in re-building vignettes:
  ...
  input string 785 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'lmer.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\Mh
           ^^TK^^P<ae><97>(q$<ee>؈!.L6^^L/($oYX^^Hx^^H<eb>!<a0>'o<de><<eb>ٓ^^A/<a2>O<f0>]ċ^^G<f5>^^]<84><e7>A...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.16 ...F<a0><ba>v<ed>Zggg<ad>V{<fd><fa>5^^Q9<8e>388866<a6><94><8a><e3>^^X<fd>^^]<c7><c1><83><ae>^
                                                  <bd><9a>J<a5>l<db>v^^\^^G<9f>J<a9><87>^^O^^_<c6>q|...
! Extra }, or forgotten $.
l.17 Ԓ<da>[}
          <b8>ӄ<f6><a0><9c>0^^L<89>(<9b><cd><e2>^^A<98><ce>0^^L<85>^^BOm<b9>\^^^^^Z^^Z<8a><a2><88><a7>?<9b><cd>"@a<ce>0<8e>eYP{<a1>P<c0>O<<c8><e3>...
I've deleted a group-closing 
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/LMERConvenienceFunctions.Rcheck/00install.out’ for details.
Running examples in ‘localsolver-Ex.R’ failed
The error most likely occurred in:

> ### Name: add.output.expr
> ### Title: Add expression to output of ls.problem.
> ### Aliases: add.output.expr
> 
> ### ** Examples
> 
> model.text.lsp <- lsp.model.example('extdata/knapsack.txt')
> lsp <- ls.problem(model.text.lsp)
sh: localsolver: command not found
Error: has.localsolver(ls.path) is not TRUE
Execution halted
Error in re-building vignettes:
  ...
Warning in readLines(con) :
  incomplete final line found on 'localsolver.Rmd'
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because localsolver.Rmd appears to be an R Markdown v2 document.
sh: localsolver: command not found
Quitting from lines 66-68 (localsolver.Rmd) 
Error: processing vignette 'localsolver.Rmd' failed with diagnostics:
has.localsolver(ls.path) is not TRUE
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/logcondens.mode.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyNamespace 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:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/logcondens.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 442 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'logcondens.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.16 ...[<f8><f8>㏻~8<9d>NC^^\<cb>d2<ba><ae>^^SB><fd><f4>ӑ<91>^^Q!D&<93><f9>ꫯ<de>}
                                                  <f7><dd>vڙ<9d><9d><b5>,˲,<ce><f9><d7>_^^?=11^^Aa...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Missing $ inserted.
<inserted text> 
                $
l.23 ...<aa>mۚ<a6>I<bb>b<8c><fd><fa><eb><af><c8>e<99><aa><aa><c2>-If<c6>X4^^Z-<97>ˊ<a2>p<ce>UU<a5><94>z<bd>^
                                                  7<c9>^^O<91><a3><92><f3><f0><95><c1><be><bb><a7><bf><8c><e8>^^@^<a1>PP^...
! You can't use `\spacefactor' in math mode.
\@ ->\spacefactor 
                  \@m 
l.24 ...<aa><aa>
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/longitudinalData.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/LOST.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyTOS2D: no visible global function definition for ‘medpolish’
countTextures: no visible global function definition for ‘medpolish’
plot.imageQT: no visible global function definition for ‘segments’
simTexture: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  medpolish rnorm segments
Consider adding
  importFrom("graphics", "segments")
  importFrom("stats", "medpolish", "rnorm")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Maeswrap.Rcheck/00install.out’ for details.
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    doc    6.9Mb
    libs  15.0Mb
objc[22618]: Class GNotificationCenterDelegate is implemented in both /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/magick.Rcheck/magick/libs/magick.so and /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/Rlib/3.3/rsvg/libs/rsvg.so. One of the two will be used. Which one is undefined.
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
Error in re-building vignettes:
  ...
Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Warning in arrange_impl(.data, dots) :
  '.Random.seed' is not an integer vector but of type 'NULL', so ignored
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshotcc924daff2c.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotcc924daff2c.png': No such file or directory
Quitting from lines 95-96 (manhattanly.Rmd) 
Error: processing vignette 'manhattanly.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshotab586b24be3a.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotab586b24be3a.png': No such file or directory
Quitting from lines 63-70 (manipulateWidgets.Rmd) 
Error: processing vignette 'manipulateWidgets.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘MARSS’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘MARSS:::is.diagonal’
  See the note in ?`:::` about the use of this operator.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.4Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   4.3Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  11.5Mb
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs  18.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   4.7Mb
Error in re-building vignettes:
  ...
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 350 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mefa.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.18 <f0>F<b6>9<dc> <9d>N˗<b9>\N
                  <b6>?<<af><9c><a5>)^^EZ<f4>^^X<d2><e9>t*<95><9a><99><99><91>k<d2>u]<ae><fb><97>_~<f9><f0><c3>^^O
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 Ðmt]<c7><ca>._<be>\<ab>
                 <d5>^^Xc<8c><b1><a9><a9><a9>t:
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.21 ...^^L^^Yc<ba><ae><e3>^^Fs^^R<b3>w-g'S^^SӒN<a7>Og^^]OBG\^^O
                                                  <ba><ca><d9><c9>t^^Z<b8>^^G<82><a7>w<e9>ҥH$R<a9>T<e2><f1><f8>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.27 ...]<e6>^^D<cf><d9>lvhh<c8>u]<c8><c4>u<dd>۷o<ef><ec><ec><c4>b<b1>L&S<af><d7>^^]<c7><e9><ef><ef><c
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyworkspace_management : tellme: no visible global function definition
  for ‘file.edit’
workspace_management: no visible global function definition for
  ‘object.size’
Undefined global functions or variables:
  file.edit object.size
Consider adding
  importFrom("utils", "file.edit", "object.size")
to your NAMESPACE file.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/MergeGUI.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.6Mb
Package required and available but unsuitable version: ‘EBImage’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘hgu133plus2.db’ ‘hgu133a.db’ ‘hgu95av2.db’
Packages suggested but not available for checking: ‘hgu133plus2.db’ ‘doSMP’
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/MetSizeR.Rcheck/00install.out’ for details.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/MFHD.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/MicroStrategyR.Rcheck/00install.out’ for details.
Running examples in ‘miniGUI-Ex.R’ failed
The error most likely occurred in:

> ### Name: makeWidgetCmd
> ### Title: R functions to build a GUI window
> ### Aliases: makeWidgetCmd
> ### Keywords: utilities misc
> 
> ### ** Examples
> 
>   require(tcltk)
>   ##
>   ##  a simple example
>   ## 
>   g <- function(a=1,b=rnorm) {cat("--g--");paste("g(a,b)=",a+b(a))}
>   h <- function(a=1,b=3,c=3) {cat("--h--");paste("h(a,b,c)=",a+b+c)}
>   ## create functions
>   gg <- makeWidgetCmd("Hay it is g !!",g,GRAB=FALSE)
>   hh <- makeWidgetCmd("Hay h here !!",h,GRAB=FALSE)
>   ## calling them
>   gg()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: gg ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Running examples in ‘misc3d-Ex.R’ failed
The error most likely occurred in:

> ### Name: slices3d
> ### Title: Interactive Image Slices of 3D or 4D Volume Data
> ### Aliases: slices3d
> ### Keywords: hplot
> 
> ### ** Examples
> 
>   #Example 1: View of a mixture of three tri-variate normal densities
>   nmix3 <- function(x, y, z, m, s) {
+       0.4 * dnorm(x, m, s) * dnorm(y, m, s) * dnorm(z, m, s) +
+       0.3 * dnorm(x, -m, s) * dnorm(y, -m, s) * dnorm(z, -m, s) +
+       0.3 * dnorm(x, m, s) * dnorm(y, -1.5 * m, s) * dnorm(z, m, s)
+   }
>   x<-seq(-2, 2, len=40)
>   g<-expand.grid(x = x, y = x, z = x)
>   v<-array(nmix3(g$x,g$y,g$z, .5,.5), c(40,40,40))
>   slices3d(vol1=v, main="View of a mixture of three tri-variate normals", col1=heat.colors(256))
Loading required package: tkrplot
Loading required package: tcltk
Invalid MIT-MAGIC-COOKIE-1 keyWarning in fun(libname, pkgname) : couldn't connect to display ":0"
Invalid MIT-MAGIC-COOKIE-1 keyWarning: loading Rplot failed
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: slices3d ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Package required but not available: ‘BRugs’

Package suggested but not available for checking: ‘mixAK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/mlDNA.Rcheck/00install.out’ for details.
Running examples in ‘mlr-Ex.R’ failed
The error most likely occurred in:

> ### Name: plotFilterValues
> ### Title: Plot filter values using ggplot2.
> ### Aliases: plotFilterValues
> 
> ### ** Examples
> 
> fv = generateFilterValuesData(iris.task, method = "chi.squared")
Error in .jnew("weka/core/Attribute", attname[i], .jcast(levels, "java/util/List")) : 
  java.lang.UnsupportedClassVersionError: weka/core/Attribute : Unsupported major.minor version 51.0
Calls: generateFilterValuesData ... read_model_frame_into_Weka -> read_data_into_Weka -> .jnew -> .External
Execution halted
Running the tests in ‘tests/run-base.R’ failed.
Last 13 lines of output:
  1. Error: NoFeaturesModel works with FilterWrapper (@test_base_NoFeaturesModel.R#30) 
  2. Error: clustering performance (@test_base_clustering.R#16) 
  3. Error: clustering performance with missing clusters (@test_base_clustering.R#28) 
  4. Error: clustering resample (@test_base_clustering.R#42) 
  5. Error: clustering benchmark (@test_base_clustering.R#55) 
  6. Error: clustering tune (@test_base_clustering.R#72) 
  7. Error: downsample wrapper works with xgboost, we had issue #492 (@test_base_downsample.R#38) 
  8. Error: filterFeatures (@test_base_filterFeatures.R#9) 
  9. Error: plotFilterValues (@test_base_filterFeatures.R#53) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
  input string 341 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 350 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'modTempEff.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 ...2^^F<e2><f5>2^^F<e2><f5>2<9e>m񤔏<bd>TJ<f1><cd>t:<dd>V<ad><c3><e3><96>eI)q<ff><e0>S<b9>\<ce>
                                                  ^^?<93><ab>^^U<8b>E^^?5<a5>^^T^^Z<f1>w<e3><b1>x...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 ...<a5>¯l^^S<d2><ff><e0><c1>^^V<b8>p<f0><92><db><d9><da>ڪxxR<b3><a8>ӹ<e7><dd><c9>	~^^RQ<b9>\<fe>
                                                  <ec><b3><cf><c0>7"<92>R~<f7><dd>w<df>|<f3><cd>G^^_}t<fd><fa>u<d3>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.18 <84>L<a7>Ӧi<82><a5>^^_~<f8><e1><b5>k<d7>r<b9><9c>a^^XB^^H"<ca>f<b3>^^W.\^^X
                                             ^^Y^^Y<d1>4
The control sequence at the end of the top line
of your error message w
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/monogeneaGM.Rcheck/00install.out’ for details.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   6.6Mb
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 872 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'moult.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cd>
          o<db>F^^V^^?<96>[<cb>,^^RSD<82><ae><e2>]F^^J
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
l.18 ...<cd><cd>o<be><f9><a6><c7><d4><fd>s<a6><d5><d5><d5>Z<ad>vD<83>^^G^^O^^^<9c><df><e8>c<fe>(<de>^^[\^^Z
                                                  r<f1><c6><ef>ܹs<ac>^^N<b7>o߾|<f9>r.<97>^^[^^_...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Extra }, or forgotten \endgroup.
l.18 ..._<8f>F<a3><cb><cb>ˏ^^^=<92>eY^^P<84><c3><da>3Ʈ_<bf><9e><cd>f<af>_<bf><8e>[۶u]WUu}
                                                  }<bd>\.<a7>R)4VUUQ<94>
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
Found the following significant warnings:
  Warning: Pointer at (1) in pointer assignment might outlive the pointer target
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/mra.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘org.Mm.eg.db’
installed size is 30.3Mb
  sub-directories of 1Mb or more:
    libs  30.0Mb
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  
  4. check_translations() works (@test.R#73) - running msgfmt on file15e43321a3176 failed
  
  5. check_translations() works (@test.R#73) - running msgfmt on file15e4355a553ac failed
  
  Failed -------------------------------------------------------------------------
  1. Failure: check_for_gettext() works (@test.R#4) ------------------------------
  check_for_gettext() isn't true.
  
  
  DONE ===========================================================================
  Error: Test failures
  Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/msir.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/MSQC.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/msr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/mtk.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘MASS’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Invalid MIT-MAGIC-COOKIE-1 keyDesigner.sobol: no visible global function definition for ‘runif’
basicMonteCarlo: no visible global function definition for ‘runif’
lhs003: no visible global function definition for ‘runif’
plmm.mtk : GenereXplmm: no visible binding for global variable ‘poly’
plmm.mtk : calc.plm: no visible global function definition for ‘lm.fit’
plmm.mtk: no visible global function definition for ‘var’
plmm.mtk: no visible global function definition for ‘lm’
plmm.mtk: no visible global function definition for ‘formula’
plmm.mtk: no visible global function definition for ‘update’
plmm.mtk: no visible global function definition for ‘stepAIC’
plot.plmm: no visible global function definition for ‘par’
plot.plmm: no visible global function definition for ‘barplot’
plot.plmm: no visible global function definition for ‘segments’
plot.plmm: no visible global function definition for ‘abline’
plot.plmm: no visible global function definition for ‘title’
plot.plmm: no visible global function definition for ‘legend’
plot.regressionSI: no visible global function definition for ‘par’
plot.regressionSI: no visible global function definition for ‘title’
plot.regressionSI: no visible global function definition for ‘abline’
plot,mtkProcess: no visible global function definition for ‘dev.new’
Undefined global functions or variables:
  abline barplot dev.new formula legend lm lm.fit par poly runif
  segments stepAIC title update var
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "barplot", "legend", "par",
             "segments", "title")
  importFrom("stats", "formula", "lm", "lm.fit", "poly", "runif",
             "update", "var")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 keyNote: found 2 marked UTF-8 strings
Invalid MIT-MAGIC-COOKIE-1 keyNamespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Package suggested but not available for checking: ‘pgirmess’
Error in re-building vignettes:
  ...
  input string 414 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'multgee.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 "M\<cd>
         U[<a1>Ffa<89>^^]<ea><86>^^?!<a8>ˮ<ba>E<dd><f1>^^WT<ed><be>^^R<92>%<a4>f<c1><a2>^^Y<a9>1^^QT<89>^^Xն<d2>^^T<df><ca>Gc<dc>`L<89>O<...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 ^^D^^B<cd>fSI|<f2>H^^?<<97>J<a5>X,<86>i<eb><f5><ba><ea>LD<b9>\n
                                      ||<9c>1<96><cd>fc<b1>^^X<b0><d0><d9>^!<a2><bd>8=<85>:<f5><b0><a6>}<e7>3wO<ff><df><e0><84>lx<cb>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.17 ...<cd>fc<b1>^^X<b0><d0><d9>^!<a2><bd>8=<85>:<f5><b0><a6>}
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    examples   1.8Mb
    libs       2.7Mb
Package suggested but not available for checking: ‘multigraph’
Package unavailable to check Rd xrefs: ‘multigraph’
Error in re-building vignettes:
  ...
Quitting from lines 218-223 (TwoModeNetworks.Rnw) 
Error: processing vignette 'TwoModeNetworks.Rnw' failed with diagnostics:
there is no package called 'multigraph'
Execution halted
Error in re-building vignettes:
  ...
  input string 305 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 306 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 307 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Ch-Errata.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.34 ...<a5>OK<9f><96>>-}Z<fa><b4><f4>i<e9><d3>ҧ<a5>OK<9f><96>>-}Z<fa><b4><f4>i<e9><d3>ҧ<a5>OK<9f><96>>-}
                                                  Z<fa><b4><f4>i<e9><d3>ҧ<a5>OK<9f><96>>-}Z<fa><b4><f4>i<e9><d3>ҧ...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Extra }, or forgotten \endgroup.
l.34 ...<a5>OK<9f><96>>-}Z<fa><b4><f4>i<e9><d3>ҧ<a5>OK<9f><96>>-}Z<fa><b4><f4>i<e9><d3>ҧ<a5>OK<9f><96>>-}
                                                  Z<fa><b4><f4>i<e9><d3>ҧ<a5>OK<9f><96>>-}Z<fa><b4><f4>i<e9><d3>ҧ...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the 
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyconceptIndicesSkm: no visible global function definition for
  ‘txtProgressBar’
conceptIndicesSkm: no visible global function definition for
  ‘setTxtProgressBar’
conceptVectorsSkm: no visible global function definition for
  ‘txtProgressBar’
conceptVectorsSkm: no visible global function definition for
  ‘setTxtProgressBar’
mvcmb: no visible global function definition for ‘runif’
mvcmb: no visible global function definition for ‘str’
mvcsph: no visible global function definition for ‘pdf’
mvcsph: no visible global function definition for ‘heatmap’
mvcsph: no visible global function definition for ‘dev.off’
mvcsph: no visible global function definition for ‘hclust’
mvcsph: no visible global function definition for ‘dist’
mvcsph: no visible global function definition for ‘str’
Undefined global functions or variables:
  dev.off dist hclust heatmap pdf runif setTxtProgressBar str
  txtProgressBar
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("stats", "dist", "hclust", "heatmap", "runif")
  importFrom("utils", "setTxtProgressBar", "str", "txtProgressBar")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 keyplot.matchedwake: no visible global function definition for
  ‘filled.contour’
plot.matchedwake: no visible binding for global variable ‘gray.colors’
plot.matchedwake: no visible global function definition for ‘axis’
plot.matchedwake: no visible global function definition for ‘rect’
slideWakeMatch: no visible binding for global variable ‘lm’
slideWakeMatch: no visible global function definition for ‘as.formula’
slideWakeMatch: no visible global function definition for ‘summary.glm’
Undefined global functions or variables:
  as.formula axis filled.contour gray.colors lm rect summary.glm
Consider adding
  importFrom("grDevices", "gray.colors")
  importFrom("graphics", "axis", "filled.contour", "rect")
  importFrom("stats", "as.formula", "lm", "summary.glm")
to your NAMESPACE file.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/nat.nblast.Rcheck/00install.out’ for details.
Running examples in ‘nat.nblast-Ex.R’ failed
The error most likely occurred in:

> ### Name: nblast
> ### Title: Calculate similarity score for neuron morphologies
> ### Aliases: nblast
> 
> ### ** Examples
> 
> # load sample Kenyon cell data from nat package
> data(kcs20, package='nat')
> # search one neuron against all neurons
> scores=nblast(kcs20[['GadMARCM-F000142_seg002']], kcs20)
> # scores from best to worst, top hit is of course same neuron
> sort(scores, decreasing = TRUE)
GadMARCM-F000142_seg002 ChaMARCM-F000586_seg002 GadMARCM-F000423_seg001 
              4043.1766               1914.8224               1772.8506 
GadMARCM-F000442_seg002 FruMARCM-M000115_seg001 FruMARCM-F000085_seg001 
              1007.4565                853.8108                713.2106 
FruMARCM-F001929_seg001 FruMARCM-F001494_seg002 GadMARCM-F000050_seg001 
               604.4071                481.4737                480.4146 
GadMARCM-F000071_seg001 FruMARCM-M001339_seg001 FruMARCM-F000188_seg001 
               448.1516                433.9340                404.0470 
GadMARCM-F000476_seg001 FruMARCM-F000270_seg001 FruMARCM-F000706_seg001 
               313.2021                254.7516                204.2116 
FruMARCM-M000842_seg002 FruMARCM-M001051_seg002 FruMARCM-M001205_seg002 
               196.4543                140.8164               -251.4999 
GadMARCM-F000122_seg001 FruMARCM-F001115_seg002 
              -262.2352               -520.2581 
> hist(scores, breaks=25, col='grey')
> abline(v=1500, col='red')
> 
> # plot query neuron
> open3d()
null 
   1 
> # plot top 3 hits (including self match with thicker lines)
> plot3d(kcs20[which(sort(scores, decreasing = TRUE)>1500)], lwd=c(3,1,1))
Error in xyz.coords(x, y, z, xlab = xlabel, ylab = ylabel, zlab = zlabel,  : 
  'x' is a list, but does not have components 'x', 'y'  and 'z'
Calls: plot3d -> plot3d.default -> xyz.coords
Execution halted
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because NBLAST-Clustering.Rmd appears to be an R Markdown v2 document.
Invalid MIT-MAGIC-COOKIE-1 keyQuitting from lines 56-59 (NBLAST-Clustering.Rmd) 
Error: processing vignette 'NBLAST-Clustering.Rmd' failed with diagnostics:
'x' is a list, but does not have components 'x', 'y'  and 'z'
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/nat.templatebrains.Rcheck/00install.out’ for details.
Errors in running code in vignettes:
when running code in ‘test-vignette.ipynbmeta’
  ...

  When tangling ‘test-vignette.ipynbmeta’:
Error: Either IPython 3+ or Jupyter has to be installed, but neither could be called.
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'test-vignette.ipynbmeta' failed with diagnostics:
Either IPython 3+ or Jupyter has to be installed, but neither could be called.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/NeatMap.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keydata.reduction: no visible global function definition for ‘prcomp’
data.reduction: no visible global function definition for ‘hclust’
data.reduction: no visible global function definition for ‘as.dist’
data.reduction: no visible global function definition for ‘cor’
data.reduction: no visible global function definition for ‘dist’
heatmap1: no visible global function definition for ‘sd’
lineplot: no visible global function definition for ‘sd’
normalize: no visible global function definition for ‘sd’
profileplot3d : ColorFunction: no visible global function definition
  for ‘rgb’
profileplot3d : ColorFunction: no visible global function definition
  for ‘colorRamp’
profileplot3d: no visible global function definition for ‘sd’
profileplot3d: no visible global function definition for ‘gray’
Undefined global functions or variables:
  as.dist colorRamp cor dist gray hclust prcomp rgb sd
Consider adding
  importFrom("grDevices", "colorRamp", "gray", "rgb")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "prcomp", "sd")
to your NAMESPACE file.
Package suggested but not available for checking: ‘KEGG.db’
Running examples in ‘netClass-Ex.R’ failed
The error most likely occurred in:

> ### Name: cv.aep
> ### Title: Cross validation for aepSVM (aepSVM)
> ### Aliases: cv.aep
> ### Keywords: aep
> 
> ### ** Examples
> 
> library(netClass)
> data(expr)
> data(ad.matrix)
> x <- expr$genes
> y <- expr$y
> 
>  library(KEGG.db)
Error in library(KEGG.db) : there is no package called ‘KEGG.db’
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.7Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   5.0Mb
Running examples in ‘network-Ex.R’ failed
The error most likely occurred in:

> ### Name: read.paj
> ### Title: Read a Pajek Project or Network File and Convert to an R
> ###   'Network' Object
> ### Aliases: read.paj read.paj.simplify switchArcDirection
> ###   readAndVectorizeLine
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> require(network)
> 
> par(mfrow=c(2,2))
> 
> test.net.1 <- read.paj("http://vlado.fmf.uni-lj.si/pub/networks/data/GD/gd98/A98.net")
Warning in file(file, "rt") :
  cannot open URL 'http://vlado.fmf.uni-lj.si/pub/networks/data/GD/gd98/A98.net': HTTP status was '0 (null)'
Error in file(file, "rt") : cannot open the connection
Calls: read.paj -> file
Execution halted
Running the tests in ‘tests/read.paj_tests.R’ failed.
Last 13 lines of output:
  > 
  > 
  > 
  > # this file has character encoding issues
  > scotland<-tempfile('scotland',fileext='.zip')
  > download.file('http://vlado.fmf.uni-lj.si/pub/networks/data/esna/scotland.zip',scotland)
  trying URL 'http://vlado.fmf.uni-lj.si/pub/networks/data/esna/scotland.zip'
  Error in download.file("http://vlado.fmf.uni-lj.si/pub/networks/data/esna/scotland.zip",  : 
    cannot open URL 'http://vlado.fmf.uni-lj.si/pub/networks/data/esna/scotland.zip'
  In addition: Warning message:
  In download.file("http://vlado.fmf.uni-lj.si/pub/networks/data/esna/scotland.zip",  :
    cannot open URL 'http://vlado.fmf.uni-lj.si/pub/networks/data/esna/scotland.zip': HTTP status was '0 (null)'
  Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/neuroim.Rcheck/00install.out’ for details.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    CppCode        3.5Mb
    R              2.4Mb
    classic-bugs   1.5Mb
    include        3.7Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.2Mb
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because trees_with_root_edge.Rmd appears to be an R Markdown v2 document.
Error: processing vignette 'vignette_get_nltt_values.Rmd' failed with diagnostics:
(converted from warning) It seems you should call rmarkdown::render() instead of knitr::knit2html() because vignette_get_nltt_values.Rmd appears to be an R Markdown v2 document.
Execution halted
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/nmcdr.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘RcppOctave’ ‘doMPI’
Running examples in ‘NoiseFiltersR-Ex.R’ failed
The error most likely occurred in:

> ### Name: EF
> ### Title: Ensemble Filter
> ### Aliases: EF EF.default EF.formula
> 
> ### ** Examples
> 
> data(iris)
> # We fix a seed since there exists a random partition for the ensemble
> set.seed(1)
> out <- EF(Species~., data = iris, consensus = FALSE)
Error in .jnew("weka/core/Attribute", attname[i], .jcast(levels, "java/util/List")) : 
  java.lang.UnsupportedClassVersionError: weka/core/Attribute : Unsupported major.minor version 51.0
Calls: EF ... read_model_frame_into_Weka -> read_data_into_Weka -> .jnew -> .External
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 190-198 (NoiseFiltersR.Rnw) 
Error: processing vignette 'NoiseFiltersR.Rnw' failed with diagnostics:
java.lang.UnsupportedClassVersionError: weka/core/Attribute : Unsupported major.minor version 51.0
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/nonlinearTseries.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/norm2.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/NPCirc.Rcheck/00install.out’ for details.
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    libs  23.3Mb
Running examples in ‘oasis-Ex.R’ failed
The error most likely occurred in:

> ### Name: voxel_selection
> ### Title: Voxel Selection Procedure
> ### Aliases: voxel_selection
> 
> ### ** Examples
> 
> library(neurobase)
Loading required package: oro.nifti
oro.nifti 0.7.2
> library(fslr)
> library(oasis)
> niis = tempfile(fileext = ".nii.gz")
> if (require(httr)) {
+    url = paste0("https://dl.dropbox.com/u/2785709/brainder",
+    "/software/flair/templates/GG-853-FLAIR-2.0mm.nii.gz")
+    req <- httr::GET(url,
+    httr::write_disk(path = niis))
+ 
+  flair <- readnii(niis)
+  if (have.fsl()) {
+    brain_mask = fslbet(niis) > 0
+  } else {
+    ind = list(c(10L, 81L), c(12L, 101L), c(3L, 78L))
+    all.ind = lapply(ind, function(x) seq(x[1], x[2]))
+    brain_mask = niftiarr(flair, 0)
+    eg = expand.grid(all.ind)
+    eg = as.matrix(eg)
+    brain_mask[eg] = 1
+  }
+  voxel_selection_mask <- voxel_selection(flair,
+    brain_mask, cutoff = .85)
+ }
Loading required package: httr
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  SSL connect error
Calls: <Anonymous> ... request_fetch -> request_fetch.write_disk -> <Anonymous> -> .Call
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/OceanView.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    help   2.1Mb
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/oc.Rcheck/00install.out’ for details.
installed size is 98.0Mb
  sub-directories of 1Mb or more:
    libs  97.7Mb
MLparameters: no visible global function definition for ‘optim’
comp.freq: no visible global function definition for ‘x11’
comp.freq: no visible global function definition for ‘par’
comp.freq: no visible global function definition for ‘plot’
Undefined global functions or variables:
  optim par plot x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "par", "plot")
  importFrom("stats", "optim")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
  input string 348 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 359 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'OneTwoSamples.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.16 ...^^G0X<b9>To<98><e5>R<bd>a<96>K<f5><86>Y.<d5>^^[f<b9>To<98><e5>o<af><9e>^^PB^^H<d1><fd>^
                                                  J)<84><98><9b><9b><8b>~<ed>.|૪<db>]<a5><bb><97>R<a9>$:^^R...
! Undefined control sequence.
l.16 ...A<a0><9e><89>h@^^Z<9e>^^]s<c2>J^^C<b5>U<b7>\:<86>a<96>><cc>Y*<95><ce>f^^\/"<b9>\<ee>
                                                  y<80><bf><e0><e0>^^\<b8><df>SR*<95><a4><94>o<be><f9><e6><f8><f8>x<b3><d9>L...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.20 ...a<9a><e6><d6>֖<aa><8e>q^^_Ѝs<ce>^^XS<9b><84> ^^H0^^W<f8><9a><c9>d<80>|h"<a5>\YY
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because ontologySimilarity-GO-example.Rmd appears to be an R Markdown v2 document.
Quitting from lines 46-49 (ontologySimilarity-GO-example.Rmd) 
Error: processing vignette 'ontologySimilarity-GO-example.Rmd' failed with diagnostics:
could not find function "intersection_with_descendants"
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/OpenCL.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘mlr’

Package suggested but not available for checking: ‘farff’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 120.8Mb
  sub-directories of 1Mb or more:
    libs    113.0Mb
    models    4.4Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/OpenRepGrid.Rcheck/00install.out’ for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   2.6Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/optBiomarker.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyavg2Lower: no visible global function definition for ‘optimize’
classificationError.data.frame: no visible binding for global variable
  ‘na.omit’
classificationError.data.frame: no visible global function definition
  for ‘terms’
classificationError.data.frame: no visible binding for global variable
  ‘predict’
classpredict.lda: no visible global function definition for ‘predict’
simData: no visible global function definition for ‘rnorm’
simData: no visible global function definition for ‘runif’
simData: no visible global function definition for ‘var’
tnormAvg: no visible global function definition for ‘dnorm’
tnormAvg: no visible global function definition for ‘pnorm’
yapprox: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx dnorm na.omit optimize pnorm predict rnorm runif terms var
Consider adding
  importFrom("stats", "approx", "dnorm", "na.omit", "optimize", "pnorm",
             "predict", "rnorm", "runif", "terms", "var")
to your NAMESPACE file.
Package suggested but not available for checking: ‘org.At.tair.db’
Error in re-building vignettes:
  ...
sh: rst2pdf: command not found
Error: processing vignette 'optparse.Rrst' failed with diagnostics:
conversion by rst2pdf failed!
Execution halted
Package required but not available: ‘ROracle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Attaching package: ‘BiocGenerics’

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

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

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

    IQR, mad, xtabs

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

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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘IsoGene’
Invalid MIT-MAGIC-COOKIE-1 keygenRidge: no visible global function definition for ‘plogis’
ordGene: no visible global function definition for ‘anova’
ordGene: no visible global function definition for ‘lm’
ordSelect: no visible binding for global variable ‘sd’
ordSmooth: no visible binding for global variable ‘sd’
plot.ordPen: no visible global function definition for ‘grey’
plot.ordPen: no visible global function definition for ‘devAskNewPage’
plot.ordPen: no visible global function definition for ‘plot’
plot.ordPen: no visible global function definition for ‘lines’
predict.ordPen: no visible global function definition for ‘plogis’
Undefined global functions or variables:
  anova devAskNewPage grey lines lm plogis plot sd
Consider adding
  importFrom("grDevices", "devAskNewPage", "grey")
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "anova", "lm", "plogis", "sd")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
  input string 411 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 412 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 420 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'dicom.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\Al
           ^^SG^^W~<b1><89><cc>V<c2><de>^^Q^^T<b6><a1>&<d6>J^^P<a4>D!<c2>B*H<91>s<f0>9<b7><dc>z<e6>^^D<87><f6>^^BG<ae>\9r<ab>P%<84>^^O<95>"...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...<de>^^Q^^T<b6><a1>&<d6>J^^P<a4>D!<c2>B*H<91>s<f0>9<b7><dc>z<e6>^^D<87><f6>^^BG<ae>\9
                                                  r<ab>P%<84>^^O<95>".(>`YTj<a4>^^U<b6><eb>?-<b4>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 ...<83>/<be><f8>b^^O<8b>^^\<f0><d8><eb>61l^^W@y.<97>K<a5>R<d9>l<f6>ȑ#sss<b9>\nzz
                                                  :^^H<d9>B<88>d2^^Y<bc>Q<e5>+<df><f7><a3>Ѩi<9a>B^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you 
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 420 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'nifti.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cd>
          k^^S[^^[^^?L<95>:P'9Ko1M^^X<90><ca>U<92>\^^FD^^DI^^W<85><ba>r#<fe>]<b9>r<a3>K<b7>ݸ^^U<bb>^^UA^^L...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 x<9c><ed>\<cd>k^^S[^^[^^?L<95>:P'9Ko1M^^X<90><ca>U<92>\^^F
                                           D^^DI^^W<85><ba>r#<fe>]<b9>r<a3>K<b7>ݸ^^U<bb>^^UA^^L...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...!^^Dc^^L<f7>s<b9><dc><ce><ce>N<a5>Ry<fb><f6>-c^^L<8f>8<e7><9c><f3><e1><e1>aιl"[	!\<d7>
                                                  
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 !<96><96><96><aa><d5><ea><eb>ׯ?|<f8>^^@<af>ptW<b9>\<ae>
   
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘osi-Ex.R’ failed
The error most likely occurred in:

> ### Name: extract_id
> ### Title: Extract components from OSI metadata
> ### Aliases: extract_id extract_keywords extract_name extract_superseded
> ###   extractors
> 
> ### ** Examples
> 
> 
> #Get the names of all licenses
> all_license_metadata <- license_list()
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Peer certificate cannot be authenticated with given CA certificates
Calls: license_list ... request_fetch -> request_fetch.write_memory -> <Anonymous> -> .Call
Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 8
  1. Error: All licenses can be retrieved (@test_connectors.R#6) 
  2. Error: Keyword retrieval works (@test_connectors.R#14) 
  3. Error: ID retrieval works (@test_connectors.R#22) 
  4. Error: Content retrieval works (@test_connectors.R#29) 
  5. Error: licenses IDs can be retrieved (@test_extractors.R#4) 
  6. Error: licenses names can be retrieved (@test_extractors.R#11) 
  7. Error: licenses superseded states can be retrieved (@test_extractors.R#18) 
  8. Error: licenses keywords can be retrieved (@test_extractors.R#25) 
  
  Error: testthat unit tests failed
  Execution halted
Packages suggested but not available for checking:
  ‘genealogicalSorting’ ‘phybase’ ‘Rmpi’
Running the tests in ‘tests/regtest-party.R’ failed.
Last 13 lines of output:
  > fit <- rpart(Kyphosis ~ Age + Number + Start, data = kyphosis)
  > pfit <- as.party(fit)
  > all(predict(pfit, newdata = kyphosis, type = "node") == fit$where)
  [1] TRUE
  > 
  > ## J48: iris data
  > library("RWeka")
  > data("iris", package = "datasets")
  > itree <- J48(Species ~ ., data = iris)
  Error in .jnew("weka/core/Attribute", attname[i], .jcast(levels, "java/util/List")) : 
    java.lang.UnsupportedClassVersionError: weka/core/Attribute : Unsupported major.minor version 51.0
  Calls: J48 ... read_model_frame_into_Weka -> read_data_into_Weka -> .jnew -> .External
  Execution halted
Errors in running code in vignettes:
when running code in ‘constparty.Rnw’
  ...
       8 0.5408163 0.4591837
       9 0.0729927 0.9270073

> library("RWeka")

> (j48 <- J48(Survived ~ ., data = ttnc))

  When sourcing ‘constparty.R’:
Error: java.lang.UnsupportedClassVersionError: weka/core/Attribute : Unsupported major.minor version 51.0
Execution halted
Error in re-building vignettes:
  ...
Loading required package: grid

Error: processing vignette 'constparty.Rnw' failed with diagnostics:
 chunk 10 (label = J48) 
Error in .jnew("weka/core/Attribute", attname[i], .jcast(levels, "java/util/List")) : 
  java.lang.UnsupportedClassVersionError: weka/core/Attribute : Unsupported major.minor version 51.0
Execution halted
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 419 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'party.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.18 !8<e7>hV*<95>p]<ad>V?<ff><fc><f3><f9><f9><f9>R<a9><84>^^A<a5>^^X<ed>v<fb><f2><e5><cb>B^^H!D<b9>\<fe>
                                                <f2><cb>/?<f9><e4><93>J<a5>r<e3><c6>
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.19 ...^Uc,^^H^^B<c3>0<a0><<e7><e6><e6>*<95><ca><f8><f8><f8>G^^_}<d4>^^Oϧ|<ef><8d>}<f6><d9>g}
                                                  6<c5><fb>^^SB<f8><be><df>n<b7><a1>֛<cd>f*<95><8a><e3>xcc<a3><db>...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Missing $ inserted.
<inserted text> 
                
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘hu6800.db’ ‘golubEsets’

Depends: includes the non-default packages:
  ‘svmpath’ ‘kernlab’ ‘affy’ ‘Biobase’ ‘ROCR’ ‘igraph’ ‘lpSolve’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Errors in running code in vignettes:
when running code in ‘pathClass.rnw’
  ...

    union

Loading required package: lpSolve

> library(golubEsets)

  When sourcing ‘pathClass.R’:
Error: there is no package called ‘golubEsets’
Execution halted
Error in re-building vignettes:
  ...

    lowess

Loading required package: igraph

Attaching package: ‘igraph’

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

    normalize, union

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

    decompose, spectrum

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

    union

Loading required package: lpSolve

Error: processing vignette 'pathClass.rnw' failed with diagnostics:
 chunk 2 (label = loadALLpackage) 
Error in library(golubEsets) : there is no package called ‘golubEsets’
Execution halted
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘rootSolve’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘kinship2’ ‘tcltk’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘rootSolve’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 keyCall with DUP:
   .C("powerR", as.integer(numOffspring), as.integer(numParents), 
       as.integer(numFamilies), as.integer(additionalOffspringPhenos), 
       as.integer(ascertainment), as.integer(modelGen), as.integer(modelTest), 
       as.double(afreqMarker), as.double(penAA), as.double(penAB), 
       as.double(penBB), as.double(heritability), as.double(contsAscertainmentLower), 
       as.double(contsAscertainmentUpper), as.double(pDiseaseAlleleGivenMarkerAllele), 
       as.double(afreqDSL), as.double(qnorm(1 - alpha/2)), as.double(offset), 
       as.integer(numSim), as.integer(ITERATION_KILLER), result, 
       DUP = FALSE)
DUP is no longer supported and will be ignored.
Packages required but not available: ‘pbdMPI’ ‘pbdSLAP’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘pbdPROF’
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pbdMPI.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pbdPROF.Rcheck/00install.out’ for details.
Packages which this enhances but not available for checking:
  ‘pbdMPI’ ‘pbdCS’
Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘pbdRPC’
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 key.win.appendLog: no visible binding for global variable ‘lines’
plotMC : panel: no visible global function definition for ‘points’
plotMC: no visible global function definition for ‘pairs’
plotMC: no visible global function definition for ‘mtext’
plotMC: no visible global function definition for ‘axis’
plotMC: no visible global function definition for ‘par’
readADpaths: no visible global function definition for ‘read.table’
readRep: no visible global function definition for ‘read.table’
saveADpaths: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  axis lines mtext pairs par points read.table write.table
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "pairs", "par",
             "points")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
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  6.3Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.3Mb
Running examples in ‘PBSmodelling-Ex.R’ failed
The error most likely occurred in:

> ### Name: PBSoptions-class
> ### Title: S4: Project Options Class
> ### Aliases: PBSoptions-class print,PBSoptions-method
> ###   show,PBSoptions-method
> ### Keywords: classes methods
> 
> ### ** Examples
> 
> local(envir=.PBSmodEnv,expr={
+   #initialize an option manager with a single logical option
+   .mypkg <- new( "PBSoptions", filename="my_pkg.txt", 
+     initial.options=list( sillyhatday=FALSE ) )
+ 
+   #retrieving an option
+   silly <- getOptions( .mypkg, "sillyhatday" )
+   cat( "today is", ifelse( silly, "silly hat day!", "monday" ), "\n" )
+ 
+   #set an option
+   setOptions( .mypkg, sillyhatday = TRUE, photos = "/shares/silly_hat_photos" )
+ 
+   #create a GUI which works with options
+   createWin( c( 
+     "check name=optionsillyhatday text=\"silly hat day\"",
+     "entry name=optionphotos width=22 mode=character label=\"photos directory\"",
+     "button func=doAction text=save action=saveOptionsGUI(.mypkg)" ), astext = TRUE )
+ 
+   #update GUI values based on values stored in .mypkg's options
+   loadOptionsGUI( .mypkg )
+   print(getOptions( .mypkg ))
+ })
today is monday 
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "tk_setPalette".
Calls: local ... eval -> eval -> createWin -> tcl -> .Tcl.objv -> structure
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pca3d.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pcaL1.Rcheck/00install.out’ for details.
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    data   2.1Mb
    libs   6.5Mb
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 399 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 400 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 408 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'pcse.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 ...<cb>^^RB^^X<86><c1>^^X#<a2><a5><a5><a5><8f>^^_?r<ce>s<b9>^^\<e7>|ee<e5><fa><f5><eb><8c>1\<cd>
                                                  f<b3><85>BA<8e><8a>1v<ef>޽^^NC?<e8>E<96><97><97><8f>o0?...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 ...<ba><ae>^^GA^^@<ad><a8><e5>gu<af>^^^O<e0><d4>4<ad>M7EQ<a4>n^^X^^AΣ<a5>\ZXW
                                                  <9a><a6><95><cb>eιi<9a><ae><eb>b<b8><8e><e3>^^DA<c0>9<c7>^^B^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 ...b<b8><8e><e3>^^DA<c0>9<c7>^^B^^VB^^@<ae><ae><eb>B7<c3>0<e2><f1>8<b6>^^G<d7>uGFF\<d7>
                                                  E?݌<f9><ac><c0><f9><8d>0j^^O<e0>^^D~<a8>5u<98>^^\...
The control sequence at the end of
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Invalid MIT-MAGIC-COOKIE-1 keyNamespaces in Imports field not imported from:
  ‘car’ ‘sandwich’
  All declared Imports should be used.
Packages suggested but not available for checking: ‘georob’ ‘spsurvey’
Packages unavailable to check Rd xrefs: ‘spsurvey’, ‘georob’
Running examples in ‘pedometrics-Ex.R’ failed
The error most likely occurred in:

> ### Name: vgmICP
> ### Title: Initial covariance parameters (ICP)
> ### Aliases: vgmICP
> 
> ### ** Examples
> 
> data(meuse, package = "sp")
> icp <- vgmICP(z = log(meuse$copper), coords = meuse[, 1:2])
Invalid MIT-MAGIC-COOKIE-1 keyWarning in fun(libname, pkgname) : couldn't connect to display ":0"
Error: Package(s) needed for this function to work but notinstalled: georob
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/permGPU.Rcheck/00install.out’ for details.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

infoImage: no visible global function definition for ‘quantile’
markPoisson: no visible global function definition for ‘runif’
markPoisson: no visible global function definition for ‘flush.console’
phantom : model: missing arguments not allowed in calls to ‘c’
readData: no visible global function definition for ‘read.table’
readData: no visible global function definition for ‘read.image’
readSifData: no visible global function definition for ‘flush.console’
viewData: no visible global function definition for ‘gray’
viewData: no visible global function definition for ‘dev.cur’
viewData: no visible global function definition for ‘dev.set’
viewData: no visible global function definition for ‘X11’
viewData: no visible global function definition for ‘par’
viewData: no visible global function definition for ‘image’
viewData: no visible global function definition for ‘title’
writeData: no visible global function definition for ‘write.table’
writeData: no visible global function definition for ‘make.image’
writeData: no visible global function definition for ‘write.image’
Undefined global functions or variables:
  X11 dev.cur dev.set flush.console gray image make.image par quantile
  read.image read.table runif title write.image write.table
Consider adding
  importFrom("grDevices", "X11", "dev.cur", "dev.set", "gray")
  importFrom("graphics", "image", "par", "title")
  importFrom("stats", "quantile", "runif")
  importFrom("utils", "flush.console", "read.table", "write.table")
to your NAMESPACE file.
installed size is 46.1Mb
  sub-directories of 1Mb or more:
    libs  45.4Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pi0.Rcheck/00install.out’ for details.
Package required but not available: ‘rggobi’

Depends: includes the non-default packages:
  ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’ ‘lattice’ ‘rggobi’ ‘ggplot2’
  ‘proto’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 28.0Mb
  sub-directories of 1Mb or more:
    libs  27.9Mb
Package required and available but unsuitable version: ‘SummarizedExperiment’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/playwith.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/plot3Drgl.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘GSIF’ ‘gdalUtils’
Errors in running code in vignettes:
when running code in ‘jss1079.Rnw’
  ...
+ }
Loading required package: GSIF
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘GSIF’
Installing package into ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/plotKML.Rcheck’
(as ‘lib’ is unspecified)

  When sourcing ‘jss1079.R’:
Error: trying to use CRAN without setting a mirror
Execution halted
Error in re-building vignettes:
  ...
Loading required package: gstat
Loading required package: raster
Loading required package: sp
Loading required package: plotKML
plotKML version 0.5-6 (2016-05-02)
URL: http://plotkml.r-forge.r-project.org/
Loading required package: GSIF
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘GSIF’
Installing package into ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/plotKML.Rcheck’
(as ‘lib’ is unspecified)

Error: processing vignette 'jss1079.Rnw' failed with diagnostics:
 chunk 1 
Error in contrib.url(repos, "source") : 
  trying to use CRAN without setting a mirror
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/plsRcox.Rcheck/00install.out’ for details.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
         return(val)
     }, finally = options(warn = oldWarn))
  3: tryCatchList(expr, classes, parentenv, handlers)
  4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  5: value[[3L]](cond)
  6: private$errorHandler(req, res, e)
  
  testthat results ================================================================
  OK: 220 SKIPPED: 0 FAILED: 1
  1. Error: Includes work (@test-include.R#28) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   2.1Mb
Packages required but not available: ‘pbdMPI’ ‘pbdBASE’ ‘pbdDMAT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in treedata(phy, dat) :
  The following tips were not found in 'data' and were dropped from 'phy':
	olivacea
Warning in treedata(phy, dat) :
  The following tips were not found in 'data' and were dropped from 'phy':
	olivacea
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda

Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pmg.Rcheck/00install.out’ for details.
Package required but not available: ‘rcqp’

Package suggested but not available for checking: ‘polmineR.sampleCorpus’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
File ‘PottsUtils/libs/PottsUtils.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘sw.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  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 ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/powell.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 356 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'd_jss_paper.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.15 ...R,<89><ad>qI^J<a6>^^NT^^B<81>^^U6^^P<ac><f8><a5>^^O<c5>}n!<d4>^^O}
                                                  (<ec>e~h<fb>TJMa/3dx<b0>U^^O<83>b<b5>H^^Q...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Missing $ inserted.
<inserted text> 
                $
l.15 ...<ec><e8>ڎ<e4>V<8a>~^^Xsu<ee>9<e7><9e><ef>~<df><f9><fe><9d><ef>v^^Y<86>^^A<ed><cb><f7><bd><80><e6><a2>C^
                                                  +<a3>C^+<a3>C^+<a3><cd>ɳ5d^^VJ)<e7><bc>!S^^...
! Extra }, or forgotten $.
l.15 ...<93>MXp<c3>`B<9e>^^?[<eb>1v<ff><f8><e7><a5>^^?W6^^?q<f9>'<d7>T<d7>i<d8><d4>7<bf>]<88><ad>}
                  
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyfnfam: no visible global function definition for ‘qnorm’
fx: no visible global function definition for ‘qnorm’
normplot : <local> : replot: no visible global function definition for
  ‘qnorm’
normplot : <local> : replot: no visible global function definition for
  ‘pnorm’
normplot : <local> : replot: no visible global function definition for
  ‘plot’
normplot : <local> : replot: no visible global function definition for
  ‘dnorm’
normplot : <local> : replot: no visible global function definition for
  ‘points’
normplot : <local> : replot: no visible global function definition for
  ‘lines’
normplot : <local> : regen: no visible global function definition for
  ‘rnorm’
normplot : <local> : regen: no visible global function definition for
  ‘rexp’
nsibs: no visible global function definition for ‘qnorm’
ntdt: no visible global function definition for ‘uniroot’
plotDom: no visible global function definition for ‘plot’
plotNsibs: no visible global function definition for ‘plot’
plotNtdt: no visible global function definition for ‘plot’
plotNtdt: no visible global function definition for ‘lines’
plotNtdt: no visible global function definition for ‘legend’
ptdt: no visible global function definition for ‘optimize’
ptdt: no visible global function definition for ‘uniroot’
ptdt: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dnorm legend lines optimize plot pnorm points qnorm rexp rnorm
  uniroot
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points")
  importFrom("stats", "dnorm", "optimize", "pnorm", "qnorm", "rexp",
             "rnorm", "uniroot")
to your NAMESPACE file.
Packages which this enhances but not available for checking:
  ‘KEGG.db’ ‘org.Sc.sgd.db’ ‘org.Ag.eg.db’ ‘org.Pt.eg.db’
  ‘org.Rn.eg.db’ ‘org.Ss.eg.db’ ‘org.At.tair.db’ ‘org.Bt.eg.db’
  ‘org.Ce.eg.db’ ‘org.Cf.eg.db’ ‘org.Dm.eg.db’ ‘org.Dr.eg.db’
  ‘org.EcK12.eg.db’ ‘org.EcSakai.eg.db’ ‘org.Gg.eg.db’ ‘org.Mm.eg.db’
  ‘org.Mmu.eg.db’ ‘org.Pf.plasmo.db’ ‘org.Xl.eg.db’
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rosm’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/prim.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because PRISMA.Rmd appears to be an R Markdown v2 document.
Quitting from lines 31-43 (PRISMA.Rmd) 
Error: processing vignette 'PRISMA.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    extdata  10.9Mb
    libs      1.2Mb
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/PropClust.Rcheck/00install.out’ for details.
LastFirstDiscreteSparse: Error while checking: evaluation nested too
  deeply: infinite recursion / options(expressions=)?
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'countreg.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 <c4><eb>g^^Z<88><d7><cf>4^^P<af><9f>i <de>^^Q^^RB^^H!<8e>ޗR<aa><eb>B<a1><80>1RJ\<e0>
                                                o<b5>Z
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
l.18 \K
       ?<d3><f0><e7><9f>^^?~<fa><d1><d8><e5>R<ca>J<a5><b2><b3><b3><b3><b8><b8><b8><b8><b8><c8>9^^?<f8><f0><a1>m۷n<dd>::<9e>s^<ad>V766^^J
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Missing $ inserted.
<inserted text> 
                $
l.18 ...<f0><e7><9f>^^?~<fa><d1><d8><e5>R<ca>J<a5><b2><b3><b3><b3><b8><b8><b8><b8><b8><c8>9^^?<f8><f0><a1>m۷n<dd>::<9e>s^
         
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Error in re-building vignettes:
  ...
  input string 401 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 409 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 410 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 418 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'raschmix.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.19 <82>`ss3<97>˹<ae><9b>L&^^Q<85>^^PQ<b9>\<9e>
                            <99><99><b1>,+<9d>N<c3><ee><a3>?^^H<82><bd><bd>=vhRJ<c4>.<9e><e7><e5>r<b9>C<93><f3><f8>X,<86><c9>^^]ǉ^^N;rN...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.23 ...<b3><a8>nC!_<d7><ed><e8><be>͹<89><f7>V<e8><8c>`<ee>l<f5><b0><9b><c3>^^Z<a5><94><c2>"<a0>͡&<f6><ab>8g<e5>\<e6>
                                                  <d4>\<9e><9a><ae><fa>ꝑ<ae>y<9d><b3><8d>߃<a2>///<c7><e3>qM<d3>\...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.23 ...C!_<d7><ed><e8><be>͹<89><f7>V<e8><8c>`<ee>l<f5><b0><9b><c3>^^Z<a5><94><c2>"<a0>͡&<f6><ab>8g<e5>\<e6><d4>\<9e>
                                                  <9a><ae><fa>ꝑ<ae>y<9d><b3><8d>߃<a2>//
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc        3.5Mb
    examples   2.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/qpcR.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyMHbi2: no visible global function definition for ‘runif’
QRLMM: no visible binding for global variable ‘D’
QRLMM: no visible global function definition for ‘par’
QRLMM: no visible global function definition for ‘plot.ts’
QRLMM: no visible global function definition for ‘abline’
QRLMM: no visible global function definition for ‘qnorm’
QRLMM: no visible global function definition for ‘plot’
QRLMM: no visible global function definition for ‘axis’
QRLMM: no visible global function definition for ‘polygon’
QRLMM: no visible global function definition for ‘lines’
QRLMM: no visible global function definition for ‘smooth.spline’
QRLMM: no visible global function definition for ‘title’
QSAEM_COM_7: no visible global function definition for ‘pnorm’
grid_example: no visible global function definition for ‘par’
grid_example: no visible global function definition for ‘smooth.spline’
grid_example: no visible global function definition for ‘plot’
grid_example: no visible global function definition for ‘axis’
grid_example: no visible global function definition for ‘polygon’
grid_example: no visible global function definition for ‘lines’
grid_example: no visible global function definition for ‘abline’
grid_example: no visible global function definition for ‘title’
rALD: no visible global function definition for ‘runif’
Undefined global functions or variables:
  D abline axis lines par plot plot.ts pnorm polygon qnorm runif
  smooth.spline title
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "par", "plot",
             "polygon", "title")
  importFrom("stats", "D", "plot.ts", "pnorm", "qnorm", "runif",
             "smooth.spline")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/qrmtools.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyNamespace in Imports field not imported from: ‘xts’
  All declared Imports should be used.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/qtbase.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/qtlc.Rcheck/00install.out’ for details.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    contrib   3.7Mb
    doc       2.9Mb
    libs      1.1Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    2.5Mb
    libs   4.9Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/QuantifQuantile.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 430 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 438 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'quantspec.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.21 ...[L=^^X^^L^^F<83>A<8e>Pض],^^V5M<b3>,<8b>]X0#<a5><c4>Z^^PQ<b9>\<b6>
                                                  ,+^^R<89>X<96><c5>^^A<8e>6<e9>E?{^^\e<e9>N^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.21 ...A<8e>6<e9>E?{^^\e<e9>N^^Nu^^V<8c><b0>,<8b><88>fff<d2><e9><b4>^^[c<a8>`<db>v<b9>\<8e>
                                                  D"<8c>Ir!VUU<80>
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.25 <a7>ޭ^^@<89>^^H<be>ҹ<b0>^^G<ca><e5>rSSS<b9>\<8e>
                               <88><e0>^^VY<96>utt4<<^^\^^L^^F<a5><94>^<af>^^W^^F4/^^G<e4>!<f7><80>r0<ef>>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.25 ...
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   3.6Mb
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because Release.Rmd appears to be an R Markdown v2 document.
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because Use_case.Rmd appears to be an R Markdown v2 document.
Warning: Removed 16 rows containing missing values (geom_point).
Warning: Removed 16 rows containing missing values (geom_point).
Quitting from lines 141-142 (Use_case.Rmd) 
Error: processing vignette 'Use_case.Rmd' failed with diagnostics:
the table must have a header (column names)
Execution halted
FancyPies: no visible global function definition for ‘rainbow’
FancyPies: no visible global function definition for ‘plot’
FancyPies: no visible global function definition for ‘polygon’
Hist2GE: no visible global function definition for ‘dist’
Pies2GE: no visible global function definition for ‘rainbow’
Plots2GE: no visible global function definition for ‘aggregate’
Plots2GE: no visible global function definition for ‘x11’
Plots2GE: no visible global function definition for ‘title’
Plots2GE: no visible global function definition for ‘png’
Plots2GE: no visible global function definition for ‘dev.off’
PolyLines2GE: no visible global function definition for ‘rainbow’
Shapes2GE: no visible global function definition for ‘rainbow’
Undefined global functions or variables:
  aggregate dev.off dist plot png polygon rainbow title x11
Consider adding
  importFrom("grDevices", "dev.off", "png", "rainbow", "x11")
  importFrom("graphics", "plot", "polygon", "title")
  importFrom("stats", "aggregate", "dist")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/R2GUESS.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 231 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 232 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 240 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'R2OpenBUGS.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\AL
           ^^[W^^S^^^^^L^^FL<8c><97><a7>^^R0N^^V̪nCq<8d><cb>V<88> ^^Q~UT<ad><9a>*<f4><92>S<a2><f6>ƥ<97><f6><94>^^^<a3>ޫ^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Extra }, or forgotten \endgroup.
l.18 ...Tf<92><95><d4>/<aa>^^@e<e1>p^^X9<ee><ec><ec><8c>D"<99>L<a6><b1><b1><f1><e5><97>_<ce>f<b3>O<9e><<d1>u}}
                                                  }<bd><b9><b9><b9><bf><bf>?<9f><cf>744,,,tww<af><ad><ad>577^...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Extra }, or forgotten \endgroup.
l.18 ...f<92><95><d4>/<aa>^^@e<e1>p^^X9<ee><ec><ec><8c>D"<99>L<a6><b1><b1><f1><e5><97>_<ce>f<b3>O<9e><<d1>u}}}
                                                  <bd><b9><b9><b9><bf><bf>?<9f><cf>744,,,tww<af><ad><ad>577^^...
I've deleted a 
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
'library' or 'require' calls in package code:
  ‘RDCOMClient’ ‘rcom’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/R2STATS.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 231 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 232 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 240 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'R2WinBUGS.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.17 ...^L^^L<e8><ba>N^^Hq8^^\8<ad><c7><e3>Y\\,^^V<8b><9d><9d><9d>o<bf><fd><b6>In^^O\<cb>
                                                  <b3>^^H<e3>o<^^^<a7><ba>gf^^H<f6>G,f<fe>]^^S...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 ...<da>ڪiZOO<8f><a6>i<cb><cb><cb>^^V<8b>^^E^^@*<95>Jgg<a7><a2>(<8f>^^^=r:<9d><b9>\<ae>
                                                  V<ab><f5><f5><f5><cd><ce><ce><f6><f7><f7><ff><f6><db>o<ad><ad><ad>^^W/^^^D...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 <9d>?^^?^^^<eb>\N
                <a7>szz^^Z7^^A<ed>jqq<91><e7>yUU<91><b3>|><8f>\<86><c3>a<97>˅@^^\[^^X<86>!<84><9c>9s&<95>J<c5>b1Q^^T^^A<e0>...
The control sequence at the end of the top line
of your error message was neve
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/R330.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘rgl’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘lattice’ ‘leaps’ ‘rgl’ ‘s20x’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RadOnc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rainbow.Rcheck/00install.out’ for details.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    htmlwidgets   6.3Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RAppArmor.Rcheck/00install.out’ for details.
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.7Mb
    libs   9.7Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rase.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘rggobi’ ‘RODBC’
Invalid MIT-MAGIC-COOKIE-1 key
(R:2730): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
Invalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keydatgen: no visible global function definition for ‘rnorm’
optimization.IC: no visible global function definition for ‘optim’
outlier.replace: no visible global function definition for ‘qnorm’
pargen: no visible global function definition for ‘runif’
rav: no visible global function definition for ‘optim’
rav2file: no visible global function definition for ‘write.table’
standardized: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  optim qnorm rnorm runif sd write.table
Consider adding
  importFrom("stats", "optim", "qnorm", "rnorm", "runif", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RBerkeley.Rcheck/00install.out’ for details.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    blp    5.9Mb
    libs   4.2Mb
Package required and available but unsuitable version: ‘mlr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rCBA.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rcdk.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because RClone_qmsevpops.Rmd appears to be an R Markdown v2 document.
Quitting from lines 336-337 (RClone_qmsevpops.Rmd) 
Error: processing vignette 'RClone_qmsevpops.Rmd' failed with diagnostics:
the table must have a header (column names)
Execution halted
Invalid MIT-MAGIC-COOKIE-1 key.onAttach: no visible global function definition for ‘palette’
.onAttach: no visible global function definition for ‘dev.off’
helpAboutBCA: no visible global function definition for ‘help’
Undefined global functions or variables:
  dev.off help palette
Consider adding
  importFrom("grDevices", "dev.off", "palette")
  importFrom("utils", "help")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 keyenterTableMHTest : onOK: no visible global function definition for
  ‘na.omit’
startStop: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls to packages already attached by Depends:
  ‘depthTools’ ‘tcltk’
  Please remove these calls from your code.
Invalid MIT-MAGIC-COOKIE-1 keycomputeMBD : OnOutput: no visible global function definition for
  ‘tkbutton’
computeMBD: no visible global function definition for ‘tkbutton’
computeMBD : OnPlot: no visible global function definition for
  ‘tkcanvas’
computeMBD : OnPlot: no visible global function definition for
  ‘tkbutton’
computeTmean: no visible global function definition for ‘tkcanvas’
computeTmean: no visible global function definition for ‘tkbutton’
computeTmean : onOK: no visible global function definition for ‘par’
plotCentralCurves: no visible global function definition for ‘tkcanvas’
plotCentralCurves: no visible global function definition for ‘tkbutton’
plotCentralCurves : onOK: no visible global function definition for
  ‘par’
Undefined global functions or variables:
  par tkbutton tkcanvas
Consider adding
  importFrom("graphics", "par")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘FrF2.catlg128’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Invalid MIT-MAGIC-COOKIE-1 keyPackages in Depends field not imported from:
  ‘Rcmdr’ ‘multcomp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘tseries’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘MASS’ ‘Rcmdr’ ‘TeachingDemos’ ‘abind’ ‘forecast’ ‘tseries’ ‘xts’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls in package code:
  ‘abind’ ‘e1071’ ‘qcc’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Invalid MIT-MAGIC-COOKIE-1 keyPackages in Depends field not imported from:
  ‘ENmisc’ ‘Hmisc’ ‘Rcmdr’ ‘vcd’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 keyPackages in Depends field not imported from:
  ‘orloca’ ‘orloca.es’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 keyRcmdr.new.loca.p: no visible binding for global variable ‘top’
Rcmdr.new.loca.p: no visible binding for global variable ‘buttonsFrame’
Rcmdr.orloca.norm: no visible binding for global variable ‘top’
Rcmdr.orloca.norm : onOK: no visible binding for global variable
  ‘normaVariable’
Rcmdr.orloca.norm: no visible binding for global variable ‘normaFrame’
Rcmdr.orloca.norm: no visible binding for global variable
  ‘buttonsFrame’
Rcmdr.rloca.p: no visible binding for global variable ‘top’
Rcmdr.rloca.p: no visible binding for global variable ‘buttonsFrame’
Rcmdr.zsum: no visible binding for global variable ‘top’
Rcmdr.zsum: no visible binding for global variable ‘buttonsFrame’
Rcmdr.zsummin: no visible binding for global variable ‘top’
Rcmdr.zsummin : onOK: no visible binding for global variable
  ‘algorithmVariable’
Rcmdr.zsummin : onOK: no visible binding for global variable ‘.sol’
Rcmdr.zsummin: no visible binding for global variable ‘algorithmFrame’
Rcmdr.zsummin: no visible binding for global variable ‘buttonsFrame’
Undefined global functions or variables:
  .sol algorithmFrame algorithmVariable buttonsFrame normaFrame
  normaVariable top
Invalid MIT-MAGIC-COOKIE-1 keyBOXWP: no visible binding for global variable ‘top’
BOXWP: no visible binding for global variable ‘buttonsFrame’
HIST: no visible binding for global variable ‘top’
HIST: no visible binding for global variable ‘buttonsFrame’
QQN: no visible binding for global variable ‘top’
QQN: no visible binding for global variable ‘buttonsFrame’
Undefined global functions or variables:
  buttonsFrame top
Invalid MIT-MAGIC-COOKIE-1 keyfncLRpROC: no visible global function definition for ‘palette’
fncLRpROC : onOK : convert: no visible global function definition for
  ‘col2rgb’
fncLRpROC : onOK : convert: no visible global function definition for
  ‘rgb’
fncPairedpROC: no visible global function definition for ‘palette’
fncPairedpROC : onOK : convert: no visible global function definition
  for ‘col2rgb’
fncPairedpROC : onOK : convert: no visible global function definition
  for ‘rgb’
fncUnpairedpROC: no visible global function definition for ‘palette’
fncUnpairedpROC : onOK : convert: no visible global function definition
  for ‘col2rgb’
fncUnpairedpROC : onOK : convert: no visible global function definition
  for ‘rgb’
fncvpROC: no visible global function definition for ‘palette’
fncvpROC : onOK : convert: no visible global function definition for
  ‘col2rgb’
fncvpROC : onOK : convert: no visible global function definition for
  ‘rgb’
Undefined global functions or variables:
  col2rgb palette rgb
Consider adding
  importFrom("grDevices", "col2rgb", "palette", "rgb")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 keySampleSizes: no visible global function definition for ‘xtabs’
SampleSizes: no visible global function definition for ‘weighted.mean’
SampleSizes: no visible global function definition for ‘reshape’
stage1Sample.fn: no visible global function definition for ‘runif’
stage2Sample.fn: no visible global function definition for ‘runif’
strata.options : onOK: no visible global function definition for
  ‘packageDescription’
Undefined global functions or variables:
  packageDescription reshape runif weighted.mean xtabs
Consider adding
  importFrom("stats", "reshape", "runif", "weighted.mean", "xtabs")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 keyPackages in Depends field not imported from:
  ‘Rcmdr’ ‘seeg’ ‘sgeostat’ ‘spatstat’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘SLC’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘SLC’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘car’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RColorBrewer’ ‘Rcmdr’ ‘car’ ‘colorspace’ ‘vcd’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 keyRcmdr.steeptestDij : onOK: no visible binding for global variable
  ‘replications’
Rcmdr.steeptestPij : onOK: no visible binding for global variable
  ‘replications’
Undefined global functions or variables:
  replications
Consider adding
  importFrom("stats", "replications")
to your NAMESPACE file.
Packages suggested but not available for checking: ‘ROpenOffice’ ‘RODBC’
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
    po    2.0Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rcplex.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RcppAPT.Rcheck/00install.out’ for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    include   4.6Mb
    libs      1.5Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    include   4.4Mb
    libs     22.5Mb
Error in re-building vignettes:
  ...
  input string 420 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 428 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 429 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 437 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RcppEigen-Introduction.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 ...^?^^_Q<bd>^^Y<ec>^^^<c1><d2><d2><d2><ce><ce>N<af><b0>u<88><b3>킞<b1><87><b0><b1><b1><b1><b1><b1><81>ǹ\<8e>
                                                  ^^^۶<fd><f0><e1><c3>gϞ<9d><b4><b8>ue^^O<e1><9a><dd><d3>tv...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.20 ...<8e><8d><8d>!1<84>^^P<96>e<db><d2>܅<ee><e1><83>^^EAh-^^U<82>@<a5>HQ^^TT^^L\<83>
                                                  <be><9b>.C<b6>eY<c6>^^E<84>^^PUUQ<a9><e8><ab><d1>4<ad>V<ab>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.20 ...^^W^^@Lӌ<c7><e3><8f>^^^=<9a><9a><9a><a2><95>_|4jc<ab><c4><f6><80><bd>^^N_<c1>yl`<b9>\<ee>
                                                  <c4><dc>w^^N]^^De<f9>|<de><e7><f3>i<9a>^^V<
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 34.3Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib      21.4Mb
    libs     11.0Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RcppOctave.Rcheck/00install.out’ for details.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    include   6.2Mb
    libs      3.1Mb
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 382 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Rcpp-introduction.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.16 ...<d1><d7>P<f1>x^^\<b6><84>s<ee><f3><f9><88>(^^Z<8d><c2>0^^L6<bd>SνS<ae>ZN9y=<f6>^
                                                  6<9b>=<9e>y^^\^^DкO|t<ca><f7><de>A5<e7><fe><91><cd>f...
! Extra }, or forgotten $.
l.16 ...y^^\^^DкO|t<ca><f7><de>A5<e7><fe><91><cd>f9<e7>/<bc><f0>B(^^Tr^^\gjjj`}
                                                  <b8>^^?^^L<b9><f7>^^X^^P<80>1ƾ<ff><fe><fb>7<de>x<83>...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Please use \mathaccent for accents in math mode.
\add@accent ...@spacefactor \spacefactor }\accent 
                                         
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 88.2Mb
  sub-directories of 1Mb or more:
    include   4.1Mb
    lib      52.5Mb
    libs     31.4Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RcppTOML.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rcqp.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rcrypt.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RDieHarder.Rcheck/00install.out’ for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Package required but not available: ‘Rmosek’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Missing link or links in documentation object 'ClassGroups.Rd':
  ‘[rebus.unicode]{UnicodeProperty}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
Error in re-building vignettes:
  ...
Warning in readLines(con) :
  incomplete final line found on 'recexcavAAR-vignette-1.Rmd'
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because recexcavAAR-vignette-1.Rmd appears to be an R Markdown v2 document.
Loading recexcavAAR
Loading required package: kriging

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 46-61 (recexcavAAR-vignette-1.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-1.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages suggested but not available for checking: ‘RODBC’ ‘RODBCext’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   3.8Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs  11.4Mb
Invalid MIT-MAGIC-COOKIE-1 keycook.outliers: no visible global function definition for ‘lm’
cook.outliers: no visible global function definition for
  ‘cooks.distance’
nonparRI: no visible global function definition for ‘quantile’
plot.interval: no visible global function definition for ‘par’
plot.interval: no visible global function definition for ‘plot.new’
plot.interval: no visible global function definition for ‘plot.window’
plot.interval: no visible global function definition for ‘segments’
plot.interval: no visible global function definition for ‘axis’
plot.interval: no visible global function definition for ‘title’
plot.interval: no visible global function definition for ‘legend’
plot.interval: no visible global function definition for ‘box’
plot.interval: no visible global function definition for ‘text’
robust: no visible global function definition for ‘qt’
singleRefLimit: no visible global function definition for ‘qnorm’
singleRefLimit: no visible global function definition for
  ‘shapiro.test’
singleRefLimit: no visible global function definition for ‘ks.test’
Undefined global functions or variables:
  axis box cooks.distance ks.test legend lm par plot.new plot.window
  qnorm qt quantile segments shapiro.test text title
Consider adding
  importFrom("graphics", "axis", "box", "legend", "par", "plot.new",
             "plot.window", "segments", "text", "title")
  importFrom("stats", "cooks.distance", "ks.test", "lm", "qnorm", "qt",
             "quantile", "shapiro.test")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
  input string 84 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 85 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 93 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'registry.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>[Ok^^S<dd>^^W>o<fa><ab><b5>Pf<bc> <b1>(i<ea>l*^^H5<a5> <a5>P<c6>EvBw<ee>\<fb>
                                                 1<c4>m<bf><82>[wfe<b1><b8><b0><9b><f8>'Be ^^]<82>]^^H^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...<a2>J<a5>2??<af><94><9a><9e><9e><f6>}?<97><cb><d5>j5۶]<d7><c5>x!^^D^^C^^X^^Qv<b9>\<ce>
                                                  <e5>r<f8>Y<ad>V-<cb><c2><e4><fc>^^W7<c3>0<b4>,<ab><95>+0^^@...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 ...<c7>h<b1>2O<8c><ba>u<eb>X[)^^E<ac>Ǌ<b8>ID<bb><bb><bb><90>^^V<88>ª<b0><b1>@,<cb><d0>h4\<d7>
                                                  <85>E
The control sequence at the end of the top line
of your error message was
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘tkrplot’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1. Error: can't see environment of caller (@test-env.R#5) 
  2. Error: reprex doesn't write into environment of caller (@test-env.R#11) 
  3. Error: I understand exactly what I'm putting in reprex env (@test-env.R#22) 
  4. Error: reprex: clipboard input works (@test-input.R#12) 
  5. Error: reprex: expression input works (@test-input.R#17) 
  6. Error: reprex: character input works (@test-input.R#23) 
  7. Error: reprex: file input works (@test-input.R#31) 
  8. Error: reprex: file input in a subdirectory works (@test-input.R#40) 
  9. Error: Circular use is detected before render (@test-input.R#47) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/reshapeGUI.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/restlos.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyGUI_template : onHelp: no visible global function definition for ‘help’
Undefined global functions or variables:
  help
Consider adding
  importFrom("utils", "help")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/retistruct.Rcheck/00install.out’ for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is 102.7Mb
  sub-directories of 1Mb or more:
    libs      100.2Mb
    pictures    1.3Mb
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rggobi.Rcheck/00install.out’ for details.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc     2.0Mb
    fonts   1.5Mb
    libs    6.0Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rgnuplot.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key
(R:76308): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘gWidgetsRGtk2’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘RGtk2’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘RGtk2Extras-Ex.R’ failed
The error most likely occurred in:

> ### Name: gtkDfEdit
> ### Title: gtkDfEdit
> ### Aliases: gtkDfEdit [.gtkDfEdit [<-.gtkDfEdit RGtk2DfEdit
> 
> ### ** Examples
> 
>   win <- gtkWindowNew()

(R:2383): GLib-GObject-WARNING **: invalid (NULL) pointer instance

(R:2383): GLib-GObject-CRITICAL **: g_signal_connect_data: assertion `G_TYPE_CHECK_INSTANCE (instance)' failed

(R:2383): Gtk-WARNING **: Screen for GtkWindow not set; you must always set
a screen for a GtkWindow before using the window

(R:2383): Gdk-CRITICAL **: gdk_screen_get_default_colormap: assertion `GDK_IS_SCREEN (screen)' failed

(R:2383): Gdk-CRITICAL **: gdk_colormap_get_visual: assertion `GDK_IS_COLORMAP (colormap)' failed

(R:2383): Gdk-CRITICAL **: gdk_screen_get_default_colormap: assertion `GDK_IS_SCREEN (screen)' failed

(R:2383): Gdk-CRITICAL **: gdk_screen_get_root_window: assertion `GDK_IS_SCREEN (screen)' failed

(R:2383): Gdk-CRITICAL **: gdk_screen_get_root_window: assertion `GDK_IS_SCREEN (screen)' failed

(R:2383): Gdk-CRITICAL **: gdk_window_new: assertion `GDK_IS_WINDOW (parent)' failed

 *** caught segfault ***
address 0x18, cause 'memory not mapped'

Traceback:
 1: .Call(name, ..., PACKAGE = PACKAGE)
 2: .RGtkCall("S_gtk_widget_show_all", object, PACKAGE = "RGtk2")
 3: gtkWidgetShowAll(w)
 4: gtkWindowNew()
An irrecoverable exception occurred. R is aborting now ...
installed size is 29.1Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    help  10.9Mb
    libs  14.7Mb
Invalid MIT-MAGIC-COOKIE-1 key.install_system_dependencies : <anonymous>: no visible global function
  definition for ‘unzip’
.install_system_dependencies : install_system_dep: no visible global
  function definition for ‘menu’
.install_system_dependencies : install_system_dep: no visible global
  function definition for ‘download.file’
as.GParamSpec: no visible global function definition for ‘new’
Undefined global functions or variables:
  download.file menu new unzip
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "download.file", "menu", "unzip")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because intro_rhandsontable.Rmd appears to be an R Markdown v2 document.
Quitting from lines 34-47 (intro_rhandsontable.Rmd) 
Error: processing vignette 'intro_rhandsontable.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rhpc.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls in package code:
  ‘doMC’ ‘doSNOW’ ‘e1071’ ‘fftw’ ‘foreach’ ‘jpeg’ ‘png’ ‘rggobi’
  ‘tkrplot’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘parallel’ ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 keyrite : loadHistory: no visible global function definition for
  ‘savehistory’
rite : saveGist: no visible global function definition for ‘browseURL’
rite : uploadToRPubs : processEntry: no visible global function
  definition for ‘browseURL’
rite : runCode: no visible global function definition for ‘savehistory’
rite : runCode: no visible global function definition for ‘loadhistory’
rite : knittxt: no visible global function definition for ‘Sweave’
rite : knittxt: no visible global function definition for ‘browseURL’
rite : addHighlighting : addHighlight: no visible global function
  definition for ‘packageDescription’
rite : addHighlighting : addHighlight: no visible global function
  definition for ‘na.omit’
rite : about : <anonymous>: no visible global function definition for
  ‘browseURL’
rite : <anonymous>: no visible global function definition for
  ‘capture.output’
rite : <anonymous>: no visible global function definition for
  ‘update.packages’
rite : <anonymous>: no visible global function definition for ‘help’
rite : f1: no visible global function definition for ‘help’
rite : f1: no visible global function definition for ‘help.search’
rite : commandCompletion: no visible global function definition for
  ‘apropos’
rite : findreplace : <anonymous>: no visible global function definition
  for ‘browseURL’
Undefined global functions or variables:
  Sweave apropos browseURL capture.output help help.search loadhistory
  na.omit packageDescription savehistory update.packages
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "Sweave", "apropos", "browseURL", "capture.output",
             "help", "help.search", "loadhistory", "packageDescription",
             "savehistory", "update.packages")
to your NAMESPACE file.
Note: information on .o files is not available
File ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API call to R: ‘R_GlobalContext’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package required and available but unsuitable version: ‘plumber’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RKEELjars.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘RKEELjars’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rLiDAR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rLindo.Rcheck/00install.out’ for details.
Mallows: no visible global function definition for ‘runif’
Mallows: no visible global function definition for ‘x11’
Mallows: no visible global function definition for ‘plot’
Mallows: no visible global function definition for ‘dev.off’
UpdateLambda: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  dev.off plot runif uniroot x11
Consider adding
  importFrom("grDevices", "dev.off", "x11")
  importFrom("graphics", "plot")
  importFrom("stats", "runif", "uniroot")
to your NAMESPACE file.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RMark.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rmgarch.Rcheck/00install.out’ for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
Running examples in ‘RMongo-Ex.R’ failed
The error most likely occurred in:

> ### Name: dbAggregate-methods
> ### Title: Performing a MongoDB aggregate query
> ### Aliases: dbAggregate dbAggregate-methods
> ###   dbAggregate,RMongo,character,character-method
> 
> ### ** Examples
> 
>   mongo <- mongoDbConnect("test")
>   # insert two records
>   dbInsertDocument(mongo, "test_data", '{"foo": "bar", "size": 5 }')
Error in .jcall(rmongo.object@javaMongo, "S", "dbInsertDocument", collection,  : 
  com.mongodb.MongoException$Network: Write operation to server /127.0.0.1:27017 failed on database test
Calls: dbInsertDocument -> dbInsertDocument -> .jcall -> .jcheck -> .Call
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rmosek.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rmpi.Rcheck/00install.out’ for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RnavGraph.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key.isPath: no visible global function definition for ‘tail’
.isPath: no visible global function definition for ‘head’
navGraph : <anonymous>: no visible global function definition for
  ‘tail’
navGraph : <anonymous>: no visible global function definition for ‘sd’
navGraph: no visible global function definition for ‘colors’
ng_image_array_gray : <anonymous>: no visible global function
  definition for ‘grey’
scagGraph: no visible global function definition for ‘quantile’
closeViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.off’
initializeViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.new’
initializeViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.cur’
plot,NG_graph-ANY: no visible global function definition for ‘box’
plot,NG_graph-ANY: no visible global function definition for ‘axis’
plot,NG_graph-ANY: no visible global function definition for ‘points’
plot,NG_graph-ANY: no visible global function definition for ‘text’
plot,NG_graph-ANY: no visible global function definition for ‘segments’
updateViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.set’
Undefined global functions or variables:
  axis box colors dev.cur dev.new dev.off dev.set grey head points
  quantile sd segments tail text
Consider adding
  importFrom("grDevices", "colors", "dev.cur", "dev.new", "dev.off",
             "dev.set", "grey")
  importFrom("graphics", "axis", "box", "points", "segments", "text")
  importFrom("stats", "quantile", "sd")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Running examples in ‘RnavGraph-Ex.R’ failed
The error most likely occurred in:

> ### Name: ng_get_color
> ### Title: Extract point coloring from an active navGraph session for a
> ###   particular data set.
> ### Aliases: ng_get_color
> 
> ### ** Examples
> 
> ## Define a NG_data object
> ng.iris <- ng_data(name = "IrisData", data = iris[,1:4])
> 
> ## start a navGraph session
> nav <- navGraph(ng.iris)
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: navGraph ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Errors in running code in vignettes:
when running code in ‘RnavGraph.Rnw’
  ...
> sel <- sample(x = 1:11000, size = 600)

> p.digits <- digits[, sel]

> ng.i.digits <- ng_image_array_gray("USPS Handwritten Digits", 
+     p.digits, 16, 16, invert = TRUE, img_in_row = FALSE)

  When sourcing ‘RnavGraph.R’:
Error: [tcl] invalid command name "image".
Execution halted
Error in re-building vignettes:
  ...
    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Invalid MIT-MAGIC-COOKIE-1 keyWarning in rgl.init(initValue, onlyNULL) :
  RGL: unable to open X11 display
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE

RnavGraph Version 0.1.8
Please read the package vignette. Use vignette("RnavGraph").


Invalid MIT-MAGIC-COOKIE-1 keyWarning in tclRequire("Img") : Tcl package 'Img' not found
Can not load the tk Img extension. Hence you can not use the 'ng_image_files' R function. Read the package vignette on how to set up tcl/tk.
Loading required package: grid

Error: processing vignette 'RnavGraph.Rnw' failed with diagnostics:
 chunk 57 
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "image".

Execution halted
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    libs  23.1Mb
installed size is 83.5Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     81.4Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R   9.9Mb
Error in re-building vignettes:
  ...
  input string 547 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 548 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 556 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RobPer_vignette.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cd>
          k^^[G^^[^^?,<bf><ae><ba>`K^^Y^^B<89>P<ea>j<bb>PhIP<9d><ee>%<84>^^V<e5><a0>R<e8>!<b7><fc>^^C<a5><e4>_p<8f>9<94>B.=<b6>Đ<d2>^^F...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 ...^z^^ZrՒ^^@N8<c1><ff>r<b2>m{'<88><8e><c0>9Ȕ֥<de>?<c1><8d>~<f3><cd>7s<b9>\^^T
                                                  EP<98><87>=萃<b3><bf><dd>CD<83>B<ab>՚<9e><9e><c6>'^^QE...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.20 <e3><d6>n<b7><d1>^^E^^?<a5>-^^C^^U^^D<c1><cc>̌<ef><fb><b9>\^^N
                                      <f5><ad>V<cd>,˂<89>c<9e>(<97><cb>e!^^D<8f>hY<96>뺨L<9c>p^^_g<cf><f7>}^^...
The control sequence at the end of the top line
of your error message was never \def'ed. I
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RockFab.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RODBC.Rcheck/00install.out’ for details.
Package required but not available: ‘RODBC’

Package suggested but not available for checking: ‘RODBC’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ROracle.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘rcanvec’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rotations.Rcheck/00install.out’ for details.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.7Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rothermel.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keybestFM: no visible global function definition for ‘data’
gaRoth: no visible global function definition for ‘data’
ros: no visible global function definition for ‘na.omit’
rosunc: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  data na.omit rnorm
Consider adding
  importFrom("stats", "na.omit", "rnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rpanel.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rpdb.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keycell.density.default: no visible binding for global variable
  ‘universalConstants’
conect.pdb: no visible binding for global variable ‘elements’
masses.default: no visible binding for global variable ‘elements’
toSymbols.character: no visible binding for global variable ‘elements’
toSymbols.integer: no visible binding for global variable ‘elements’
visualize.coords: no visible binding for global variable ‘elements’
visualize.coords: no visible binding for global variable ‘rgb’
Undefined global functions or variables:
  elements rgb universalConstants
Consider adding
  importFrom("grDevices", "rgb")
to your NAMESPACE file.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rpoppler.Rcheck/00install.out’ for details.
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    libs  17.7Mb
Error in re-building vignettes:
  ...
  input string 348 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 354 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RProtoBuf-paper.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.23 ...<a2>i^^ZVn3*<80><b0>^^X<89>^^H8<e5>ryqq<b1>^^W<d3><d2>_PV<af><d7>MӔۃ\<c9>
                                                  [<bd>^<cf>f<b3><9f>}<f6><99>i<9a><b0><ae><a0>,<93><c9>lmm<c9>w<a4>iZ...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.24 ...<af><d7>q^^T^^Yc<d3><d3><d3>D<e4><fb>>^^Q<c1>^^?<f4><de><e5>^^[<a4>r<b6><a9><d6>Q<9a><f6>"<8b>e}
                                                  X<ce>|><8f><bc><f8><d0>V^^Nc^^L6
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Extra }, or forgotten \endgroup.
l.25 ^^AW&<93>	^^G<96>
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
'library' or 'require' calls to packages already attached by Depends:
  ‘RSAGA’ ‘shapefiles’
  Please remove these calls from your code.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RQuantLib.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RSAP.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_random’, possibly from ‘random’ (C)
  Found ‘_srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rsgcc.Rcheck/00install.out’ for details.
installed size is 21.5Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  19.6Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rsml.Rcheck/00install.out’ for details.
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
installed size is 47.0Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  45.6Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is 52.8Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  50.5Mb
installed size is 237.6Mb
  sub-directories of 1Mb or more:
    libs  235.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rsymphony.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rugarch.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   1.9Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RunuranGUI.Rcheck/00install.out’ for details.
installed size is 30.7Mb
  sub-directories of 1Mb or more:
    libs  30.1Mb
Missing or unexported object: ‘xml2::xml_find_first’
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘pixmap’ which was already attached by Depends.
  Please remove these calls from your code.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyrvideopoker: 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.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RVowpalWabbit.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RVPedigree.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RWeka.Rcheck/00install.out’ for details.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs    8.3Mb
    yacas   1.3Mb
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘vcd’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘foreign’ ‘ggplot2’ ‘grid’ ‘psych’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘foreign:::adQuote’
  See the note in ?`:::` about the use of this operator.
Invalid MIT-MAGIC-COOKIE-1 keycalc.hist.breaks: no visible global function definition for
  ‘nclass.Sturges’
calc.hist.breaks: no visible global function definition for ‘nclass.FD’
calc.hist.breaks: no visible global function definition for
  ‘nclass.scott’
check.class: no visible global function definition for ‘as.formula’
gtkColorSelectionForPlotGetColor: no visible global function definition
  for ‘rgb’
gtkColorSelectionWidgetNew: no visible global function definition for
  ‘colors’
gtkFileChooserDialogFilteredActivate: no visible binding for global
  variable ‘theme_grey’
localize: no visible global function definition for ‘localeToCharset’
summary.CrossTable : twoDimTable: no visible global function definition
  for ‘addmargins’
summary.CrossTable: no visible global function definition for
  ‘assocstats’
write.spss: no visible global function definition for ‘write.table’
write.stata: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  addmargins as.formula assocstats colors localeToCharset nclass.FD
  nclass.Sturges nclass.scott rgb theme_grey write.table
Consider adding
  importFrom("grDevices", "colors", "nclass.FD", "nclass.Sturges",
             "nclass.scott", "rgb")
  importFrom("stats", "addmargins", "as.formula")
  importFrom("utils", "localeToCharset", "write.table")
to your NAMESPACE file.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
Package suggested but not available for checking: ‘org.Sc.sgd.db’
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 356 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'sandwich-OOP.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.18 ...<bb>[<cf>^^VZ^^X!=<cf><cb>d2<f8><8e>TND<b5>Z<ed><83>^^O><c0> @u<ea><b2>@<ce>y<96><d7>\<bd>
                                                  ^^Q<d0>^^BT<f8><97>K<a1>P^^@q^^?Q^<f3>ػ<88>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.19 ...<ee>`0 "<c4>^^L3^^R<dc>[^^Ha<db>v.<97>øa^^X<8e><c3>E<9d><e6>y<9d>_^^?<ed>^
                                                  <bf><fe><ae>a\<95>RJ)<85><82><94>Ҷ<ed>b<b1>H<a1>^^N<8a>a^...
! Undefined control sequence.
l.19 ...^^L3^^R<dc>[^^Ha<db>v.<97>øa^^X<8e><c3>E<9d><e6>y<9d>_^^?<ed>^<bf><fe><ae>a\<95>
                                     
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
    opponent.vote, turnout, winner, winner.bmi, winner.height,
    winner.party, winner.vote

The following objects are masked from stature (pos = 5):

    election, opponent, opponent.height, opponent.party,
    opponent.vote, turnout, winner, winner.bmi, winner.height,
    winner.party, winner.vote

The following objects are masked from stature (pos = 6):

    election, opponent, opponent.height, opponent.party,
    opponent.vote, turnout, winner, winner.bmi, winner.height,
    winner.party, winner.vote

The following object is masked from package:SciencesPo:

    turnout

.data was converted to a dataframe
Warning: New theme missing the following elements: axis.line.x, axis.line.y, panel.grid.major, panel.grid.minor
Quitting from lines 1090-1091 (SciencesPo.Rmd) 
Error: processing vignette 'SciencesPo.Rmd' failed with diagnostics:
invalid 'times' argument
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   2.4Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/SDD.Rcheck/00install.out’ for details.
Found the following executable file:
  inst/external/env/bio14.bil
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/semiArtificial.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 439 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 447 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 448 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 456 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'semPLS-intro.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 ...<f4><af>i<9a>^^X<a2><94>m<db>['<8c>^^N<e9><85><de><eb><fd>ư<b0><b0><c0>^^X<b3>,<eb><e4>ɓW<ae>\1
                                                  M<f3><fe><fd><fb>W<af>^^^UB<98><a6><f9><f8><f1><e3><c9><c9>I<a5>T<bd>^<bf>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 ^^E^^\^^R<c2>^^[<fe>.,,<80>^^Y<a5><d4><e5>˗<a5><94>+++<b6>m^^S\<95>
                                           RB<88><f9><f9><f9>~<ad><a7><cf>ҋK<c4><d2>><cd><ff><8e><d9><db>o^^ZڽA<a6>=<a9>^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.21 <82>?s<b9><94>m<bb><8d><c6><fb><9c>^^_<e5><fc>^^?^^WS<c3>0<94>R<8e><e3><cc><ce>΢^^Ec<b1>\<f2>
                                             E<a4><94><89>Db}}}bb<a2><d9>l&^^R<89>f<b3>)<84><a8>T
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   8.8Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is 127.4Mb
  sub-directories of 1Mb or more:
    doc     3.9Mb
    libs  122.6Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/sgPLS.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/shapes.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/shinyRGL.Rcheck/00install.out’ for details.
randomDAG: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  rbinom
Consider adding
  importFrom("stats", "rbinom")
to your NAMESPACE file.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   3.3Mb
Error in re-building vignettes:
  ...
  input string 420 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 421 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 429 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'smacof.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.22 ...<97><d7><de>׽<9d><f4><82><b1>~<c5><d3>u^^]R<f9><fd>~EQ8<e7>D<f4><f8><f1><e3><d5><d5>Uo3UU!9^^Q}
                                                  <f1><c5>^^W^^X<d3><c6><c6><c6><ec><ec><ec><f2><f2><f2>^^O?<fc><b0><ba><ba>...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Extra }, or forgotten \endgroup.
l.22 ...<f5><d5>W<90>jii	<ed>!<c0><e3>Ǐ^^[<8d><c6><ed>۷!6^^Q<ed><ef><ef>omm<a9><aa><ba><b4><b4><d4><fb>h}
                                                  o0 <ca>d2<9a><a6>a<82>^^F<84>7)<de>^^E`D-Ì<be>...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/smint.Rcheck/00install.out’ for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   4.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/smoothtail.Rcheck/00install.out’ for details.
Running examples in ‘soilphysics-Ex.R’ failed
The error most likely occurred in:

> ### Name: fitsoilwater
> ### Title: Interactive Estimation of van Genuchten's (1980) Model
> ###   Parameters
> ### Aliases: fitsoilwater
> 
> ### ** Examples
> 
> # Liu et al. (2011)
> h <- c(0.001, 50.65, 293.77, 790.14, 992.74, 5065, 10130, 15195)
> w <- c(0.5650, 0.4013, 0.2502, 0.2324, 0.2307, 0.1926, 0.1812, 0.1730)
> fitsoilwater(w, h)
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: fitsoilwater ... handshake -> fun -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Running examples in ‘SPACECAP-Ex.R’ failed
The error most likely occurred in:

> ### Name: SPACECAP
> ### Title: Fits spatially-explicit capture recapture models
> ### Aliases: SPACECAP
> 
> ### ** Examples
> 
> SPACECAP()
Invalid MIT-MAGIC-COOKIE-1 keyError in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: SPACECAP ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Error in re-building vignettes:
  ...

    RFoptions

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

    atan2

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

    abs, acosh, asin, asinh, atan, atan2, atanh, cos, cosh, exp,
    expm1, floor, gamma, lgamma, log, log1p, log2, logb, max, min,
    round, sin, sinh, sqrt, tan, tanh, trunc

Loading required package: grid

Attaching package: 'grid'

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

    gpar

Quitting from lines 352-356 (ii-modules.Rmd) 
Error: processing vignette 'ii-modules.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    libs  24.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshotc2412bdcf402.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotc2412bdcf402.png': No such file or directory
Quitting from lines 20-30 (intro_sparkline.Rmd) 
Error: processing vignette 'intro_sparkline.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/sparr.Rcheck/00install.out’ for details.
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/spatgraphs.Rcheck/00install.out’ for details.
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    data   3.4Mb
    doc    4.6Mb
    help   5.1Mb
    libs   1.6Mb
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  15.2Mb
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
  Warning: 'lgamma' declared at (1) is also the name of an intrinsic.  It can only be called via an explicit interface or if declared EXTERNAL.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/SPECIES.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘rgdal’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/sphereplot.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyPackage 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.
Error in re-building vignettes:
  ...
  input string 415 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 429 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'UsingSpikeSlabGAM.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<c1>
          k^^[W^^S<9f>H5<89><88>><ad>^^_	qm<b3><de><f5><83>^^^<fa><d5><c8>^^B^^]J^^N<a9>|0^^T<f7><90>[(<f4>\^^D<fd>z<ed><b5><87><9e>K}O...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...<ad>^^_	qm<b3><de><f5><83>^^^<fa><d5><c8>^^B^^]J^^N<a9>|0^^T<f7><90>[(<f4>\^^D
                                                  <fd>z<ed><b5><87><9e>K}O/<ba><f9><d0>@<bd>^^D;<82><86><84>,]<ab>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.15 ...^D^^V<ad>^^WU<95><a9><fd><bc>k<c5>]<b7>X<fa>^^N?4<ec><e7>ږ<94>ڎ<e5>j^^Nb<f5><f6
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/sprint.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘RPostgreSQL’
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘tcltk’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages which this enhances but not available for checking:
  ‘RPostgreSQL’ ‘RODBC’
Running examples in ‘SRRS-Ex.R’ failed
The error most likely occurred in:

> ### Name: SRRS-package
> ### Title: The Stepwise Response Refinement Screener (SRRS)
> ### Aliases: SRRS-package
> 
> ### ** Examples
> 
> SRRS()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: SRRS ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    include   8.4Mb
    lib       1.1Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/StatDA.Rcheck/00install.out’ for details.
Running examples in ‘stepwise-Ex.R’ failed
The error most likely occurred in:

> ### Name: maxchi
> ### Title: Stepwise detection of recombination breakpoints using MaxChi
> ### Aliases: maxchi
> ### Keywords: htest
> 
> ### ** Examples
>  demo(maxchi) 


	demo(maxchi)
	---- ~~~~~~

> inputFile<- system.file("extdata", "simulinfile.txt", package = "stepwise")

> breaks<-c(531,616,810)

> WinHalfWidth<-30

> permReps<-10

> a<-maxchi(inputFile, breaks, WinHalfWidth, permReps)
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'gridExtra'

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

    combine

Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=georgia&zoom=5&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false
Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=georgia&sensor=false
Quitting from lines 220-233 (Details.Rmd) 
Error: processing vignette 'Details.Rmd' failed with diagnostics:
GeomRasterAnn was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyDetailOpLines: 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
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  Number of test functions: 18 
  Number of errors: 1 
  Number of failures: 0 
  
   
  1 Test Suite : 
  stremr unit testing - 18 test functions, 1 error, 0 failures
  ERROR in test.speedglm.allestimators10Kdata: Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
  Error: 
  
  unit testing failed (#test failures: 0, #R errors: 1)
  
  Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 7
  1. Error: basic (@test-strip.R#11) 
  2. Error: big (@test-strip.R#18) 
  3. Error: libre (@test-strip.R#25) 
  4. Error: abiword (@test-strip.R#35) 
  5. Error: Japanese (cp932) (@test-strip.R#45) 
  6. Error: Chinese and Korean (@test-strip.R#55) 
  7. Error: Europe (@test-strip.R#65) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘subspaceMOA-Ex.R’ failed
The error most likely occurred in:

> ### Name: DSC_HDDStream
> ### Title: Density-based Projected Clustering over High-Dimensional Data
> ### Aliases: DSC_HDDStream
> 
> ### ** Examples
> 
> dsc <- DSC_HDDStream()
Error in rJava::.jcall("SubspaceClustererBuilder", returnSig = "Lmoa/clusterers/hddstream/HDDStream;",  : 
  RcallMethod: cannot determine object class
Calls: DSC_HDDStream -> <Anonymous> -> .External
Execution halted
Package required but not available: ‘d3r’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   1.2Mb
Package suggested but not available for checking: ‘RTCGA.clinical’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Quitting from lines 55-64 (Informative_Survival_Plots.Rmd) 
Error: processing vignette 'Informative_Survival_Plots.Rmd' failed with diagnostics:
there is no package called 'RTCGA.clinical'
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keydlgMessage.tcltkGUI: no visible global function definition for ‘alarm’
Undefined global functions or variables:
  alarm
Consider adding
  importFrom("utils", "alarm")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 keyprocessSocket: no visible global function definition for ‘URLdecode’
Undefined global functions or variables:
  URLdecode
Consider adding
  importFrom("utils", "URLdecode")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1)
  Warning: 'erfc' declared at (1) is also the name of an intrinsic.  It can only be called via an explicit interface or if declared EXTERNAL.
  Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
  Warning: CHARACTER expression will be truncated in assignment (10/13) at (1)
  apply.f:86:0: warning: ‘pst_kg’ is used uninitialized in this function [-Wuninitialized]
  burnop.f:29:0: warning: ‘burn_frlb’ is used uninitialized in this function [-Wuninitialized]
  harvestop.f:166:0: warning: ‘hi_ovr’ is used uninitialized in this function [-Wuninitialized]
  harvestop.f:195:0: warning: ‘harveff’ is used uninitialized in this function [-Wuninitialized]
  harvgrainop.f:168:0: warning: ‘harveff’ is used uninitialized in this function [-Wuninitialized]
  harvkillop.f:175:0: warning: ‘frac_harvk’ is used uninitialized in this function [-Wuninitialized]
  plantop.f:87:0: warning: ‘lai_init’ is used uninitialized in this function [-Wuninitialized]
  rewind_init.f:171:0: warning: ‘orig_tnylda’ is used uninitialized in this function [-Wuninitialized]
  Warning: CHARACTER expression will be truncated in assignment (1/3) at (1)
  sweep.f:56:0: warning: ‘fr_curb’ is used uninitialized in this function [-Wuninitialized]
  rewind_init.f:172:0: warning: ‘orig_tnylda’ is used uninitialized in this function [-Wuninitialized]
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/SWATmodel.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘cplexAPI’ ‘clpAPI’
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/sybilSBML.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/symbolicDA.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 426 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'symmoments.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\Ol
           ^^S<cb>^^Y<ff>b;^^?^^\<c0><bb>+^^^<90><86>8<b1><b6><e5>E<b4><c1><a1><b2>z^^H^^R5<95>,UBꡕ,<bd>'<ae>O^^QG<de>^^A<e5>^^]...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 <e9>j^^Op<b9>\<82>
               <94><ac><aa><a2><de><d7>^^?<fc>à<89>f<b3><db><d0>y<88><eb><d2>-f=<99><d1>M]<dd>9<bd><b3><a7><fb><f0><f6><f7><f1>o<be><f2>5A<e0><86><a1><8a>zg<b7><95>.=<f7><e7><bf><fe><fb>?<e9><cd>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.16 ...<9e><be>x<f1><a2>,<cb>^^V<8b><85><e7><
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls to packages already attached by Depends:
  ‘tcltk’ ‘tkrplot’
  Please remove these calls from your code.
Package suggested but not available for checking: ‘GISTools’
Running examples in ‘tbart-Ex.R’ failed
The error most likely occurred in:

> ### Name: allocate
> ### Title: Teitz-Bart algorithm applied to Spatial* and Spatial*DataFrame
> ###   objects
> ### Aliases: allocate
> 
> ### ** Examples
> 
> data(meuse)
> coordinates(meuse) <- ~x+y
> allocate(meuse,p=5)
  [1]   9   9   9   9   9   9   9   9   9   9   9   9   9   9   9   9   9  23
 [19]  23  23  23  23  23   9   9   9  23  23  23   9  23  23  23  23  23  23
 [37]  23  23  23  23  23 132 132 132 132 132 132 132 132 132 132 132 132 132
 [55] 132 132 132 132 132 132 132 113 113 113 113 113 113 113 113  77  77  77
 [73]  77  77  77  77  77  77  77  77  77 113 113   9 113 113  77  77  77  77
 [91]  77  77  77  77  77  77  77  77  77  77  77 113 113 113 113 132 113 113
[109] 113 113 113 113 113 113 113 113 113 113 132 132 132 132 132 132 132 132
[127] 132 132   9  23 113 132  23 132 113 113 113  77  77  77  77  77  77  77
[145]  77  77  77  77  77  77  77  77  77  77 113
> 
> 
> 
> require(RColorBrewer)
Loading required package: RColorBrewer
> require(GISTools)
Loading required package: GISTools
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘GISTools’
> data(georgia)
Warning in data(georgia) : data set ‘georgia’ not found
> allocations.list <- allocate(georgia2,p=5)
Error in allocate(georgia2, p = 5) : object 'georgia2' not found
Execution halted
installed size is 35.8Mb
  sub-directories of 1Mb or more:
    libs  34.6Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/TDMR.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyaniplotevents: 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.
Running examples in ‘TELP-Ex.R’ failed
The error most likely occurred in:

> ### Name: telp
> ### Title: The Base Function of This Package The Free Evocation of Words
> ###   Technique
> ### Aliases: telp
> ### Keywords: function
> 
> ### ** Examples
> 
> telp()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: telp ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/termstrc.Rcheck/00install.out’ for details.
installed size is 37.8Mb
  sub-directories of 1Mb or more:
    libs       6.7Mb
    tessdata  31.0Mb
Error in re-building vignettes:
  ...
  input string 398 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'texreg.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cd>
          k^^[<d7>^^V?<95><f2><d1>!A<d2>}-AQQ,.^^D<c3>Kp^^D^^C<85>^^Z<8a>C0Y4P^^J
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.18 RJ<a5><94>^^P^^BS<e7><f3>y)<a5><e3>8B^^H<c3>0<94>R/^
                                 <bc>8s<e6><cc>ݻw<85><82>^^P<c2>4M)<e5><ec>쬮<eb><85>B<81><88><a4><94>RJ<d3>4<85>^^PJ<a9><d5><d5><d5>...
! Please use \mathaccent for accents in math mode.
\add@accent ...@spacefactor \spacefactor }\accent 
                                                  #1 #2\egroup \spacefactor ...
l.21 ...<8b>MMM^^]dÃa<ce>a<db>VG<86><c3>1<a7><94>ҶmP	<e4><c2>/3-^^X<8c>y<
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.5Mb
    libs   6.0Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/textTinyR.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
first():       dplyr, xts
intersect():   lubridate, base
lag():         dplyr, stats
last():        dplyr, xts
setdiff():     lubridate, base
union():       lubridate, base

Attaching package: 'tidyquant'

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

    as_tibble

Getting data...

Warning in fun_transform(eval(parse(text = x)), OHLC = FALSE, ...) :
  missing values removed from data
Getting data...

Warning in value[[3L]](cond) :
  Error at stock symbol FLIR during call to quantmod::getSymbols.
Quitting from lines 626-630 (tidyquant.Rmd) 
Error: processing vignette 'tidyquant.Rmd' failed with diagnostics:
`data` must be a tibble or data.frame.
Execution halted
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because Tigger-Vignette.Rmd appears to be an R Markdown v2 document.
Loading required package: ggplot2

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

sh: sysctl: command not found
Quitting from lines 111-116 (Tigger-Vignette.Rmd) 
Error: processing vignette 'Tigger-Vignette.Rmd' failed with diagnostics:
error in running command
Execution halted
drawGraph: no visible global function definition for ‘eqmcc’
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 eqmcc 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.
Running the tests in ‘tests/simple.R’ failed.
Last 13 lines of output:
  'help.start()' for an HTML browser interface to help.
  Type 'q()' to quit R.
  
  > 
  > ## run in the R session temp.dir. which gets cleaned
  > setwd(tempdir())                        
  > 
  > ## process html -- should work everywhere
  > file.copy(system.file("examples", "simpleHtml.Rmd", package="tint"), "simpleHtml.Rmd")
  [1] TRUE
  > rmarkdown::render("simpleHtml.Rmd")
  Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  Execution halted
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘boot’ ‘lattice’ ‘splines’ ‘tcltk’
  Please remove these calls from your code.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/tkrgl.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyPackages 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.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key.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.
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    examples  12.1Mb
    include    2.9Mb
Running examples in ‘tm.plugin.dc-Ex.R’ failed
The error most likely occurred in:

> ### Name: tm_map.DCorpus
> ### Title: Transformations on Distributed Corpora
> ### Aliases: tm_map.DCorpus
> 
> ### ** Examples
> 
> data("crude")
> tm_map(as.DCorpus(crude), content_transformer(tolower))
Warning in file(con, "w") :
  cannot open file '/var/folders/8q/c881c7rn7_x34vj58f4ywhvm0000h3/T//Rtmpb0djBE/DSL-20160505-034420-gjoxfxyrqb/chunk-15dc814df4a7b': No such file or directory
Error in file(con, "w") : cannot open the connection
Calls: tm_map ... DS_write_lines -> <Anonymous> -> <Anonymous> -> file
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/tolerance.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'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.
Error in re-building vignettes:
  ...
Warning in readLines(con) :
  incomplete final line found on 'TourDetrackeR.Rmd'
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because TourDetrackeR.Rmd appears to be an R Markdown v2 document.
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: ggplot2

Attaching package: 'trackeR'

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

    append

Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=57.157231,-2.104296&zoom=13&size=640x640&scale=2&maptype=terrain&sensor=false
Quitting from lines 96-97 (TourDetrackeR.Rmd) 
Error: processing vignette 'TourDetrackeR.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘OpenStreetMap’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'TraMineR-state-sequence.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 xí\Ï
          k^^[×^^V>^^]÷áêEñÅ}&ÏA28´`#»^^Hº(¸rÀÝtÿnJ¡Yµ.^^J
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.18 ...l4^^ZDBJùÝwßÝ¿^^?_^^H.¼-eMNNîXVrr2pÝ×^
                                                  O$îæa^^Táú©óo³{ë^^RÑ^^[B...
! Please use \mathaccent for accents in math mode.
\add@accent ...@spacefactor \spacefactor }\accent 
                                                  #1 #2\egroup \spacefactor ...
l.23 ^^G^^G^^GRÊ7oÎÌÌ^^XqæÌz½n^^X^^F|ù\.w
                                      
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/TSclust.Rcheck/00install.out’ for details.
Packages which this enhances but not available for checking:
  ‘TSPostgreSQL’ ‘TSodbc’
Packages suggested but not available for checking: ‘TSodbc’ ‘RODBC’
Packages unavailable to check Rd xrefs: ‘TSodbc’, ‘RODBC’
Errors in running code in vignettes:
when running code in ‘Guide.Stex’
  ...
INFO: Contacting web service with query: http://ec.europa.eu/eurostat/SDMX/diss-web/rest/datastructure/ESTAT/DSD_ei_nama_q/1.0
Jan 12, 2017 7:55:47 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: http://ec.europa.eu/eurostat/SDMX/diss-web/rest/data/ESTAT,ei_nama_q,1.0/Q.MIO-EUR.NSA.CP.NA-P72.IT
Jan 12, 2017 7:55:47 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient getData
INFO: The sdmx call returned messages in the footer:
 Message [code=400, severity=Error, url=null, text=[Error caused by the caller due to incorrect or semantically invalid arguments]]

  When sourcing ‘Guide.R’:
Error: ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.util.SdmxException: The query: ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT did not match any time series on the provider.
Execution halted
when running code in ‘GuideAppendix.Stex’
  ...

> options(continue = "  ")

> user <- Sys.getenv("MYSQL_USER")

> setup <- RMySQL::dbConnect(RMySQL::MySQL(), dbname = "test")

  When sourcing ‘GuideAppendix.R’:
Error: Failed to connect to database: Error: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)
Execution halted
Package unavailable to check Rd xrefs: ‘TSPostgreSQL’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/TSdist.Rcheck/00install.out’ for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.3Mb
Running examples in ‘uplift-Ex.R’ failed
The error most likely occurred in:

> ### Name: checkBalance
> ### Title: Standardized Differences for Stratified Comparisons
> ### Aliases: checkBalance
> ### Keywords: uplift xBalance
> 
> ### ** Examples
> 
> library(uplift)
> 
> set.seed(12345)
> dd <- sim_pte(n = 1000, p = 20, rho = 0, sigma =  sqrt(2), beta.den = 4)
> dd$treat <- ifelse(dd$treat == 1, 1, 0) 
> 
> checkBalance(treat ~ X1 + X2 + X3 + X4 + X5 + X6 , data = dd)
     strata  unstrat                                                              
     stat    treat=0  treat=1 adj.diff adj.diff.null.sd std.diff     z            
vars                                                                              
X1          0.01152  -0.00596 -0.01748         0.06006  -0.01840 -0.29103         
X2          0.03160  -0.02812 -0.05972         0.06236  -0.06057 -0.95778         
X3          0.01145  -0.02242 -0.03387         0.06355  -0.03370 -0.53303         
X4          0.01533  -0.03551 -0.05083         0.06370  -0.05046 -0.79801         
X5          -0.06440 0.02370  0.08810          0.06153  0.09060  1.43175          
X6          0.02237  -0.02177 -0.04414         0.06308  -0.04425 -0.69980         
---Overall Test---
        chisquare df p.value
unstrat      4.54  6   0.604
---
Signif. codes:  0 ‘***’ 0.001 ‘** ’ 0.01 ‘*  ’ 0.05 ‘.  ’ 0.1 ‘   ’ 1 
Error in ncol(DT) : object 'DT' not found
Calls: <Anonymous> ... withOptions -> tryCatch -> do.call -> <Anonymous> -> ncol
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/uroot.Rcheck/00install.out’ for details.
Package unavailable to check Rd xrefs: ‘rgdal’
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
         list(call = mc, handlers = handlers, levels = levels(mf[[1L]]), terms = attr(mf, 
             "terms"))), class = classes)
  5: RWeka_build_classifier(mf, control, name, handlers, options, init)
  6: read_model_frame_into_Weka(mf)
  7: read_data_into_Weka(mf, 1L)
  8: .jnew("weka/core/Attribute", attname[i], .jcast(levels, "java/util/List"))
  
  testthat results ================================================================
  OK: 1068 SKIPPED: 20 FAILED: 1
  1. Error: test train/prediction base learner methods (@test_base_learner.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 428 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 429 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 437 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vars.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 ?<f1><8b><96><eb><96>;<d9>l6^^V<8b>uM<<c3>0n޼<99>N<a7>1\Y
                                 <96><f1><a6><96><fb><9a><a6><a5>R)<88>^^Z<8f><c7><f9>D^^D<83><c1>D"<a1><eb><ba>,˲,뺎6<f8><9a>J<a5>^^N...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 <bd>MMM<e1><9a>c^^?^^?<ff><ee>ݻ^^O^^_><9c><9b><9b><8b><c7>㌱<d9><d9>Y<bc><e8>$^^L\<cc>
                                                <84>H<d7><f5><d3><c7><dd>!<ba>,<9e><ae><eb>D<f4><e1><87>^^_z<9e>G<c7><fa><a1>cB...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.21 0<c6>X<b5>ZE\<e6>
             <a7>.<98>L<c7>[H~n<c7><e3>q<90><b6><a5>^^_<f4><cf>?<fd>!<de>)<8c><b8><88><a6><a5><8b>^^\n<e3>^^X^^Xc<b0>^^G|<c7>^^X^^[<94><f3><f3><f3>t<ec>	^...
The control sequence at the end o
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   2.8Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   3.5Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/VDA.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keycv.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.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/VecStatGraphs3D.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyDrawDensity3D: no visible global function definition for ‘colorRamp’
DrawDensity3D: no visible global function definition for ‘rgb’
ReadFromFile3D: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  colorRamp read.table rgb
Consider adding
  importFrom("grDevices", "colorRamp", "rgb")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Running examples in ‘VecStatGraphs3D-Ex.R’ failed
The error most likely occurred in:

> ### Name: DrawModuleAndAngleDistribution3D
> ### Title: Graphic representation of Module and Angle Distribution.
> ### Aliases: DrawModuleAndAngleDistribution3D
> ### Keywords: graphics
> 
> ### ** Examples
> 
>    FileName<-system.file("data/XYZcoor.txt", package="VecStatGraphs3D")
>    dat<-LoadData3D(FileName, Type=1)
>    DrawModuleAndAngleDistribution3D(dat, plane="XY");
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: DrawModuleAndAngleDistribution3D ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/vegan3d.Rcheck/00install.out’ for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.2Mb
    help   2.6Mb
Error in re-building vignettes:
  ...
  input string 373 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'categoricalVGAM.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.24 ...<d5>j<95><9f>e<db>v<a9>T^^Z^^]^^]<c5><ef><b9>^^P<81>=ʳ]H<e9><a2>^^^<d2>_<a6><89>`L^
                                                  <8e>B<d4>b^^X^^@^^NII^^Fv2<f2>"3r...
! Please use \mathaccent for accents in math mode.
\add@accent ...@spacefactor \spacefactor }\accent 
                                                  #1 #2\egroup \spacefactor ...
l.30 ...<93><ee><d0>Nx^^?^^^<f3>Y|<c0>cE1<ca><fb>J9<a0>C<98><ae>ŧ`<c8><e3>"<91>^^H<ca>\t<e2>
                                                  <e7><bc>;<e8><dd>z<bd>>??<8f>^^O^^B<89>^^H^^Xv<fc>...
! Missing { inserted.
<to be read again> 
                   \edef 
l.30 ...<93><ee><d0>Nx^^?^^^<f3>Y|<c0>cE1<ca>
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘VisuClust-Ex.R’ failed
The error most likely occurred in:

> ### Name: FuzzyPlot
> ### Title: Displays a Fuzzy Plot
> ### Aliases: FuzzyPlot
> 
> ### ** Examples
> 
> 
> library(cluster)
> library(MASS)
> 
> # The example data
> data("MilchSmall")
> 
> M <- scale(MilchSmall[3:6])
> D <- dist(M)
> S <- sammon(D)
Initial stress        : 0.00738
stress after  10 iters: 0.00227, magic = 0.500
stress after  20 iters: 0.00204, magic = 0.500
stress after  30 iters: 0.00203, magic = 0.500
> F <- fanny(D, 6)
> 
> FuzzyPlot(S$points, F$membership, labels=MilchSmall[,2], 
+ 	clusterColors=c("red", "green", "magenta", "yellow", "blue", "black"))
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: FuzzyPlot ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/wand.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/WMCapacity.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 53-54 (Automat.Rmd) 
Error: processing vignette 'Automat.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/wnominate.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because wordcloud.Rmd appears to be an R Markdown v2 document.
Quitting from lines 37-39 (wordcloud.Rmd) 
Error: processing vignette 'wordcloud.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Warning in initDict() :
  cannot find WordNet 'dict' directory: please set the environment variable WNHOME to its parent

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

Probably some imports need to be declared in the NAMESPACE file.
Error in re-building vignettes:
  ...
  input string 432 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'WRS2.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.19 ...VB<e0>+W^^L<ce>O?<fd>^^T^^X[^^&"<ec>^^G"<82>p<e5>rYJ	<81><98>x&<b9>\<ce>
                                                  <f3><bc>d2	A<85>^^PA^^P<94>J%<f4><80>^^[<ef>g<a5>T...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.23 <95>l<f1><81><93>T*<85>ꥮ<eb>^^T<b9>^^]<88>sv<df><f7><85>^^P<cb><cb>˨^^Qan<9c><d7>an\2
                                                <8b><a6>s<b6>m+<a5><82>  "]<d7><f9><e4><bd><d1>h^^Pѩ<ca><ea>)<fa><b0>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.29 èV<ab><8b><8b><8b>tb<
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/x12GUI.Rcheck/00install.out’ for details.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    java        4.6Mb
    unitTests   1.1Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/YplantQMC.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/YuGene.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: D:/temp/Rtmpe86CQi/R.INSTALL3ef42d22ef4/ACEt/man/ACEt-package.Rd:1: All text must be in a section
See 'd:/Rcompile/CRANpkg/local/3.3/ACEt.Rcheck/00install.out' for details.
prepare_Rd: ACEt-package.Rd:1: All text must be in a section
Running examples in 'ActuDistns-Ex.R' failed
The error most likely occurred in:

> ### Name: dgumbeld
> ### Title: Gumbel pdf
> ### Aliases: dgumbeld
> ### Keywords: Gumbel distribution
> 
> ### ** Examples
> x=runif(10,min=0,max=1)
> y=dgumbeld(x)
Error in dgumbel(x, mu = mu, sigma = sigma) : 
  unused arguments (mu = mu, sigma = sigma)
Calls: dgumbeld -> ifelse -> dgumbel
Execution halted
Found the following significant warnings:
  Warning: namespace 'unmarked' is not available and has been replaced
See 'd:/Rcompile/CRANpkg/local/3.3/AMModels.Rcheck/00install.out' for details.
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    bin   12.0Mb
    misc   2.1Mb
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/3.3/audio.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/BayClone2.Rcheck/00install.out' for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
installed size is 125.9Mb
  sub-directories of 1Mb or more:
    include  125.0Mb
Error in re-building vignettes:
  ...
Loading required package: diptest
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "Vignette.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.2/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.2/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'Vignette.tex' failed

BibTeX errors:
I couldn't open database file Vignette.bib.bib
---line 50 of file Vignette.aux
 : \bibdata{Vignette.bib
 :                      }
I'm skipping whatever remains of this command
I found no database files---while reading file Vignette.aux
Execution halted
Running the tests in 'tests/testthat-biom.R' failed.
Last 13 lines of output:
  1. Failure: show method output tests (@test-IO.R#69) ---------------------------
  `x1` produced no output
  
  
  2. Failure: show method output tests (@test-IO.R#70) ---------------------------
  `x4` produced no output
  
  
  DONE ===========================================================================
  Error: Test failures
  In addition: Warning message:
  Placing tests in `inst/tests/` is deprecated. Please use `tests/testthat/` instead 
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: BiSEp
Loading required package: mclust
Package 'mclust' version 5.2.1
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: GOSemSim

GOSemSim v2.0.2  For help: https://guangchuangyu.github.io/GOSemSim

If you use GOSemSim in published research, please cite:
Guangchuang Yu, Fei Li, Yide Qin, Xiaochen Bo, Yibo Wu, Shengqi Wang. GOSemSim: an R package for measuring semantic similarity among GO terms and gene products Bioinformatics 2010, 26(7):976-978

'select()' returned many:1 mapping between keys and columns

Error: processing vignette 'BiSEp.Snw' failed with diagnostics:
 chunk 16 (label = packages) 
Error in mgeneSim(unG5, ont = "MF", organism = "human") : 
  unused arguments (ont = "MF", organism = "human")
Execution halted
installed size is 72.4Mb
  sub-directories of 1Mb or more:
    include   2.7Mb
    lib      69.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/BRugs.Rcheck/00install.out' for details.
Package required but not available: 'OpenCL'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
The following files look like leftovers/mistakes:
  'Causata-vignette.log'
Please remove them from your package.
The following directory looks like a leftover from 'knitr':
  'figure'
Please remove from your package.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/classifierplots.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: XML

Attaching package: 'XML'

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

    toHTML

Loading required package: GO.db

Loading required package: moe430a.db
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'moe430a.db'
Loading required package: RankAggreg
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "clValid.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.2/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.2/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'clValid.tex' failed

LaTeX errors:
!pdfTeX error: pdflatex.EXE (file ./clValid-022.pdf): PDF inclusion: required p
age does not exist <0>
 ==> Fatal error occurred, no output PDF file produced!
Execution halted
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  Creating comparison table...
  Loading required namespace: htmlTable
  Creating HTML table for first 100 rows
  Error in test_check("compareDF") : 
    Assertion failed. One of the following must apply:
   * check_matrix(css.cell): Must be of type 'matrix', not 'data.frame'
   * check_character(css.cell): Must be of type 'character', not
   * 'data.frame'
  Calls: test_check ... htmlTable.data.frame -> htmlTable.default -> assert -> mstop
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/Conigrave.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
  font family not found in Windows font database
Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call.graphics(L_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call.graphics(L_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call.graphics(L_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call.graphics(L_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Quitting from lines 775-800 (CopulaDTA_Vignette.Rmd) 
Error: processing vignette 'CopulaDTA_Vignette.Rmd' failed with diagnostics:
formal argument "axis.title.y" matched by multiple actual arguments
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/cplexAPI.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/cudaBayesreg.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/deeplearning.Rcheck/00install.out' for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.8Mb
    help   1.2Mb
    libs   1.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/Difdtl.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/DNAprofiles.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: running command 'domino help' had status 127
See 'd:/Rcompile/CRANpkg/local/3.3/domino.Rcheck/00install.out' for details.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  2: domino.runCommand(loginCommand, domino.OK, "Login failed", theinput)
  3: domino.runCommandFromDefaultPath(commandAndArgs, successCallback, failureMessage, 
         stdInput)
  4: domino.handleCommandNotFound(failureMessage)
  5: stop(paste("Couldn't find domino client in the PATH or in default locations.\n  Add domino client directory path to PATH environment variable.\n  If you don't have domino client installed follow instructions on 'http://help.dominodatalab.com/client'.\n  If you use R-Studio Domino on GNU/Linux through a desktop launcher, add domino path to the .desktop file.\n\n  If you need more help, email support@dominodatalab.com or visit http://help.dominodatalab.com/troubleshooting\n\n  - ", 
         failureMessage), call. = FALSE)
  
  testthat results ================================================================
  OK: 1 SKIPPED: 0 FAILED: 1
  1. Error: The login command works (@test-login.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Running the tests in 'tests/doRUnit.R' failed.
Last 13 lines of output:
  
  
  Executing test function test.registerDoRNG  ...  done successfully.
  
  ------------------- UNIT TEST SUMMARY ---------------------
  
  Error in .local(x, ...) : Functions: 2 | Errors: 1 | Failures: 0 
  ERROR in runit.dorng.R::test.dorng: Error in mpi.comm.spawn(slave = rscript, slavearg = args, nslaves = count,  : 
    Other MPI error, error stack:
  MPI_Comm_spawn(cmd="D:/RCompile/recent/R-33~1.2/bin/Rscript", argv=0x000000000673F0D0, maxprocs=2, MPI_INFO_NULL, root=0, MPI_COMM_SELF, intercomm=0x00000000071B1398, errors=0x000000000A6CCBD8) failed
  Function not implemented
  Calls: <Anonymous> -> <Anonymous> -> .local -> utest -> utest -> .local
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/ECharts2Shiny.Rcheck/00install.out' for details.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    xsd   5.5Mb
Running examples in 'etl-Ex.R' failed
The error most likely occurred in:

> ### Name: smart_download
> ### Title: Download only those files that don't already exist
> ### Aliases: smart_download
> 
> ### ** Examples
> 
> cars <- etl("mtcars")
Not a valid src. Creating a src_sqlite for you at:
D:\temp\RtmpIjWurR\file3e601de17da6.sqlite3
> urls <- c("http://www.google.com", "http://www.nytimes.com")
> smart_download(cars, src = urls)
trying URL 'http://www.google.com'
Content type 'text/html; charset=ISO-8859-1' length unknown
.........
downloaded 10181 bytes

trying URL 'http://www.nytimes.com'
Error in download.file(url, method = method, ...) : 
  cannot open URL 'http://www.nytimes.com'
Calls: smart_download -> mapply -> <Anonymous>
Execution halted
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
             download.file(url, ...)
         }
     })(dots[[1L]][[2L]], dots[[2L]][[2L]])
  9: suppressWarnings(download.file(url, method = method, ...))
  10: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  11: download.file(url, method = method, ...)
  
  testthat results ================================================================
  OK: 22 SKIPPED: 0 FAILED: 1
  1. Error: smart_download works (@test-etl.R#103) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/ExomeDepth.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/FastRWeb.Rcheck/00install.out' for details.
Running examples in 'fheatmap-Ex.R' failed
The error most likely occurred in:

> ### Name:  Column Annotations 
> ### Title: Annotations of columns in "fheatmap_data"
> ### Aliases: ' annotation_col '
> ### Keywords: annotation_col
> 
> ### ** Examples
> 
> data(annotation_col)
> fheatmap(fheatmap_data,annotation_col=annotation_col)
Error in theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),  : 
  formal argument "plot.margin" matched by multiple actual arguments
Calls: fheatmap -> draw_tree -> theme_blank -> theme
Execution halted
fieldsim: no visible global function definition for 'rnorm'
midpoint: no visible global function definition for 'rnorm'
setAtlas_under: no visible global function definition for 'runif'
setCovf_under : Ibeta: no visible global function definition for
  'pbeta'
visualize: no visible global function definition for 'colorRampPalette'
Undefined global functions or variables:
  colorRampPalette pbeta rnorm runif
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "pbeta", "rnorm", "runif")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/gamsel.Rcheck/00install.out' for details.
Running examples in 'gapfill-Ex.R' failed
The error most likely occurred in:

> ### Name: Image
> ### Title: Image Panels
> ### Aliases: Image
> 
> ### ** Examples
> 
> Image(ndvi)
Error in theme(line = element_blank(), strip.background = element_rect(fill = "white",  : 
  formal argument "line" matched by multiple actual arguments
Calls: Image -> theme
Execution halted
Running the tests in 'tests/run-all.R' failed.
Last 13 lines of output:
  4: theme(line = element_blank(), strip.background = element_rect(fill = "white", color = "white"), 
         strip.text.x = element_text(), strip.text.y = element_text(), axis.ticks = element_blank(), 
         axis.text.x = element_blank(), axis.text.y = element_blank(), axis.title.x = element_blank(), 
         axis.title.y = element_blank(), line = element_blank(), legend.position = "right", 
         panel.border = element_blank(), plot.margin = unit(c(1, 1, 1, 1), "mm"), panel.margin = unit(2, 
             "mm"))
  
  testthat results ================================================================
  OK: 859 SKIPPED: 0 FAILED: 1
  1. Error: Image (@test-Image.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    data    3.7Mb
    doc     2.9Mb
    tests   2.5Mb
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  5: generate_grViz(x, ...)
  6: do.call(DiagrammeR::create_nodes, create_nodes_call)
  7: DiagrammeR::create_nodes
  8: getExportedValue(pkg, name)
  9: stop(gettextf("'%s' is not an exported object from 'namespace:%s'", name, getNamespaceName(ns)), 
         call. = FALSE, domain = NA)
  
  testthat results ================================================================
  OK: 118 SKIPPED: 0 FAILED: 1
  1. Error: plotting a tree works (@test_plot.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(gesis)
  > 
  > test_check("gesis")
  1. Failure: get_study_groups() works (@test-availability.R#6) ------------------
  nrow(groups) is not strictly more than 0. Difference: 0
  
  
  testthat results ================================================================
  OK: 3 SKIPPED: 0 FAILED: 1
  1. Failure: get_study_groups() works (@test-availability.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/gmum.r.Rcheck/00install.out' for details.
Warning: no function found corresponding to methods exports from 'gpclib' for: 'coerce', '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.
read.polyfile: no visible global function definition for 'as'
write.polyfile: no visible global function definition for 'is'
write.polyfile: no visible global function definition for 'as'
[,gpc.poly: no visible global function definition for 'new'
append.poly,gpc.poly-gpc.poly: no visible global function definition
  for 'new'
coerce,data.frame-gpc.poly: no visible global function definition for
  'as'
coerce,list-gpc.poly: no visible global function definition for 'as'
coerce,matrix-gpc.poly: no visible global function definition for 'new'
coerce,numeric-gpc.poly: no visible global function definition for
  'new'
coerce,numeric-gpc.poly.nohole: no visible global function definition
  for 'new'
intersect,gpc.poly-gpc.poly: no visible global function definition for
  'as'
intersect,gpc.poly-gpc.poly: no visible global function definition for
  'new'
setdiff,gpc.poly-gpc.poly: no visible global function definition for
  'as'
setdiff,gpc.poly-gpc.poly: no visible global function definition for
  'new'
tristrip,gpc.poly: no visible global function definition for 'as'
union,gpc.poly-gpc.poly: no visible global function definition for 'as'
union,gpc.poly-gpc.poly: no visible global function definition for
  'new'
Undefined global functions or variables:
  as is new
Consider adding
  importFrom("methods", "as", "is", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running the tests in 'tests/bug1.R' failed.
Last 13 lines of output:
  'help.start()' for an HTML browser interface to help.
  Type 'q()' to quit R.
  
  > suppressMessages(library(gpclib))
  > to_numeric <- selectMethod(coerce, c("gpc.poly", "numeric"))
  > load("bug1_data.RData")
  > plot(p)  ## loads a polygon, looks fine
  > plot(as(vec, "gpc.poly"))  ## looks fine
  > clip <- to_numeric(p); str(clip)
   num [1:17] 1 7 0 570545 7890092 ...
  > 
  > ## Crashes R 2.14 and 2.15 (32-bit) on Windows
  > vec <- .Call("Rgpc_polygon_clip", vec, clip, 3, PACKAGE="gpclib")
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/gpuR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/gputools.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
Loading required package: survival
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "ashg2012.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.2/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.2/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'ashg2012.tex' failed

LaTeX errors:
! LaTeX Error: File `D:/RCompile/recent/R-33\unhbox\voidb@x \penalty \@M \ {}1.
2/share/texmf/tex/latex/Sweave.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
Execution halted
installed size is 63.5Mb
  sub-directories of 1Mb or more:
    java  62.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Calculate3D: no visible global function definition for 'persp'
CalculateHUM_Ex: no visible global function definition for 'combn'
CalculateHUM_Plot: no visible global function definition for 'plot'
CalculateHUM_Plot: no visible global function definition for 'polygon'
CalculateHUM_Plot: no visible global function definition for 'text'
CalculateHUM_Plot: no visible global function definition for 'points'
CalculateHUM_Plot: no visible global function definition for 'lines'
Undefined global functions or variables:
  combn lines persp plot points polygon text
Consider adding
  importFrom("graphics", "lines", "persp", "plot", "points", "polygon",
             "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/HydeNet.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.2Mb
    libs   1.0Mb
NB: this package is only installed for sub-architecture 'x64'
Running examples in 'icesSAG-Ex.R' failed
The error most likely occurred in:

> ### Name: getStandardAssessmentGraps
> ### Title: Get graphs of stock assessment output
> ### Aliases: getFishMortality getFishingMortalityGraph
> ###   getFishingMortalityHistoricalPerformance getLandingsGraph
> ###   getRecruitmentGraph getRecruitmentHistoricalPerformance
> ###   getSSBHistoricalPerformance getSpawningStockBiomassGraph
> ###   getStandardAssessmentGraps getYSSB getstock_recruitment
> 
> ### ** Examples
> 
> keys <- findKey("had", 2015)
> landings_img <- getLandingsGraph(keys[1])
Warning in download.file(fileurl, tmp, mode = "wb", quiet = TRUE) :
  cannot open URL 'http://sg.ices.dk/StandardGraphsWebServices/Download/LandingsGraph8065_1_r5sm5pawnywagvcwugvm34tr2017-01-12_11_46_30.png': HTTP status was '404 Not Found'
Error in download.file(fileurl, tmp, mode = "wb", quiet = TRUE) : 
  cannot open URL 'http://sg.ices.dk/StandardGraphsWebServices/Download/LandingsGraph8065_1_r5sm5pawnywagvcwugvm34tr2017-01-12_11_46_30.png'
Calls: getLandingsGraph -> lapply -> FUN -> download.file
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/igraphinshiny.Rcheck/00install.out' for details.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    help   1.2Mb
    libs  13.4Mb
Running examples in 'inarmix-Ex.R' failed
The error most likely occurred in:

> ### Name: diagnose
> ### Title: Diagnostics for the model fit.
> ### Aliases: diagnose
> ### Keywords: print
> 
> ### ** Examples
> 
> XX <- cbind(rep(1,9),c(0:8)/4)
> colnames(XX) <- c("const","time")
> coefs <- rbind(c(-.2,0),c(1.2,.3))
> alpha <- c(.2,.2)
> scale <- c(2,2)
> mix.prop <- c(.8,.2)
> 
> testdat <- GenerateMixData(200,coefs,alpha,scale,mix.prop,XX)
> testfit <- inarmix(y~time,nclasses=2,id=subject,data=testdat,maxiter=3)
Iteration:  1 
Iteration:  2 
Iteration:  3 
[1] 4.753414e-224
[1] 4.753414e-224
Error in solve.default(hh$dermat, hh$sqmat) : 
  system is computationally singular: reciprocal condition number = 4.75341e-224
Calls: inarmix -> tcrossprod -> solve -> solve -> solve.default
Execution halted
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    geojson  12.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      3.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/medSTC.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
Running the tests in 'tests/run-base.R' failed.
Last 13 lines of output:
  1. Error: downsample wrapper works with xgboost, we had issue #492 (@test_base_downsample.R#38) 
  2. Failure: generateCalibrationData (@test_base_generateCalibration.R#55) 
  3. Failure: generateCalibrationData (@test_base_generateCalibration.R#57) 
  4. Failure: plotFilterValues (@test_base_generateFilterValuesData.R#72) 
  5. Failure: plotFilterValues (@test_base_generateFilterValuesData.R#74) 
  6. Failure: generateLearningCurve (@test_base_generateLearningCurve.R#46) 
  7. Failure: generateLearningCurve (@test_base_generateLearningCurve.R#48) 
  8. Failure: generatePartialDependenceData (@test_base_generatePartialDependence.R#216) 
  9. Failure: generatePartialDependenceData (@test_base_generatePartialDependence.R#219) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  mmap.c:223:48: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  mmap.c:226:46: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.3/mmap.Rcheck/00install.out' for details.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Error: `mapped_plot` not equal to lazyLoadDBfetch(c(36521L, 321L), datafile, compressed, envhook).
  Component "layers": Component 1: Component 3: Component 2: Modes of target, current: function, environment
  Component "layers": Component 1: Component 3: Component 2: target, current do not match when deparsed
  Component "layers": Component 1: Component 7: Component 2: Modes of target, current: function, environment
  Component "layers": Component 1: Component 7: Component 2: target, current do not match when deparsed
  Component "layers": Component 1: Component 9: Component 2: Modes of target, current: function, environment
  Component "layers": Component 1: Component 9: Component 2: target, current do not match when deparsed
  Component "layers": Component 1: Component 12: Modes of target, current: function, environment
  Component "layers": Component 1: Component 12: target, current do not match when deparsed
  Component "layers": Component 2: Component 3: Component 2: Modes of target, current: fun
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/mwaved.Rcheck/00install.out' for details.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    CppCode   1.8Mb
    R         2.4Mb
    include   3.6Mb
    libs      1.5Mb
Error in re-building vignettes:
  ...
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "nonrandom.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.2/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.2/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'nonrandom.tex' failed

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

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

Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    help   2.1Mb
    libs   1.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/OpenCL.Rcheck/00install.out' for details.
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs     5.0Mb
    models   4.5Mb
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  9: `$<-.data.table`(`*tmp*`, "id", value = 1:11)
  10: `$<-.data.frame`(x, name, value)
  11: stop(sprintf(ngettext(N, "replacement has %d row, data has %d", "replacement has %d rows, data has %d"), 
         N, nrows), domain = NA)
  
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 3
  1. Error: output has 17 columns (@test_tableproperties.R#27) 
  2. Error: output has the right column names (@test_tableproperties.R#31) 
  3. Error: output is of class data.frame & data.table (@test_tableproperties.R#36) 
  
  Error: testthat unit tests failed
  Execution halted