hsvScale: no visible global function definition for ‘hsv’
plotConcentric: no visible global function definition for ‘plot’
plotConcentric: no visible global function definition for ‘points’
plotConcentric: no visible global function definition for ‘legend’
plotPoints: no visible global function definition for ‘plot’
plotStress: no visible global function definition for ‘plot’
plotStress: no visible global function definition for ‘polygon’
plotStress: no visible global function definition for ‘points’
Undefined global functions or variables:
  hsv legend plot points polygon
Consider adding
  importFrom("grDevices", "hsv")
  importFrom("graphics", "legend", "plot", "points", "polygon")
to your NAMESPACE file.
File ‘SOD/libs/SOD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘aqp’ ‘lattice’ ‘methods’ ‘munsell’ ‘splancs’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  head.profile.data.frame plot.profile.data.frame
  print.profile.data.frame summary.profile.data.frame
  tail.profile.data.frame
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
'library' or 'require' calls in package code:
  ‘chemometrics’ ‘spatstat’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following apparent S3 methods exported but not registered:
  plot.Spectra plot.ken.sto plot.trans predict.SpectraPoints
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.soma: no visible global function definition for ‘plot’
soma: no visible global function definition for ‘runif’
Undefined global functions or variables:
  plot runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
to your NAMESPACE file.
bm: no visible global function definition for ‘rnorm’
bm: no visible global function definition for ‘ts’
fbm: no visible global function definition for ‘fft’
fbm: no visible global function definition for ‘rnorm’
fbm: no visible global function definition for ‘ts’
gbm: no visible global function definition for ‘rnorm’
gbm: no visible global function definition for ‘ts’
Undefined global functions or variables:
  fft rnorm ts
Consider adding
  importFrom("stats", "fft", "rnorm", "ts")
to your NAMESPACE file.
getAlpha: no visible global function definition for ‘pbinom’
kfweOrd: no visible global function definition for ‘qnbinom’
Undefined global functions or variables:
  pbinom qnbinom
Consider adding
  importFrom("stats", "pbinom", "qnbinom")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from ‘someMTP’ for: ‘show’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard files/directories found at top level:
  ‘README.markdown’ ‘build_package.sh’ ‘upload.sh’
simdata_contaminated : <anonymous>: no visible global function
  definition for ‘rbinom’
simdata_uniform : multivariate_uniform : <anonymous>: no visible global
  function definition for ‘runif’
which_min: no visible global function definition for ‘head’
which_min: no visible global function definition for ‘tail’
Undefined global functions or variables:
  head rbinom runif tail
Consider adding
  importFrom("stats", "rbinom", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
convert_municipality_names: no visible global function definition for
  ‘read.csv’
regression_plot: no visible binding for global variable ‘loess’
regression_plot: no visible global function definition for
  ‘colorRampPalette’
regression_plot: no visible global function definition for
  ‘loess.control’
regression_plot: no visible global function definition for ‘predict’
regression_plot : <anonymous>: no visible global function definition
  for ‘quantile’
regression_plot : <anonymous>: no visible global function definition
  for ‘pnorm’
regression_plot: no visible global function definition for
  ‘flush.console’
regression_plot: no visible global function definition for ‘density’
Undefined global functions or variables:
  colorRampPalette density flush.console loess loess.control pnorm
  predict quantile read.csv
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "density", "loess", "loess.control", "pnorm",
             "predict", "quantile")
  importFrom("utils", "flush.console", "read.csv")
to your NAMESPACE file.
Non-standard files/directories found at top level:
  ‘sandbox’ ‘sos4R-Ex.R’
'library' or 'require' call to ‘rgdal’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  as.data.frame.OmMeasurement as.data.frame.OmObservation
  as.list.OmObservationCollection length.OmObservationCollection
  names.OmMeasurement names.OmObservation names.OmObservationCollection
  plot.SOS plot.SensorML plot.SosObservationOffering
  print.summary.GmlTimePeriod print.summary.OmObservation
  print.summary.OmObservationCollection print.summary.OwsRange
  print.summary.SOS print.summary.SosObservationOffering
  summary.GmlTimePeriod summary.OmObservation
  summary.OmObservationCollection summary.OwsRange summary.SOS
  summary.SosObservationOffering
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/soundecology.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘SciencesPo’
File ‘SoundexBR/libs/SoundexBR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/spaceExt.Rcheck/00install.out’ for details.
Packages in Depends field not imported from:
  ‘glasso’ ‘limSolve’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
glasso.miss: no visible global function definition for ‘cov’
glasso.miss: no visible global function definition for ‘glasso’
glasso.miss: no visible global function definition for ‘Solve’
space.miss: no visible global function definition for ‘Solve’
Undefined global functions or variables:
  Solve cov glasso
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
Rd file 'glasso.miss.Rd':
  \examples lines wider than 100 characters:
     data(finStocksCn)  ##data of finance sector of Chinese Stock Market, from January 4th, 2011 to July 26th, 2011

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Missing link or links in documentation object 'FeatureAxis.Rd':
  ‘bounding.box’

Missing link or links in documentation object 'FeatureProps.Rd':
  ‘bounding.box’

Missing link or links in documentation object 'locperf.Rd':
  ‘bounding.box’

See section 'Cross-references' in the 'Writing R Extensions' manual.
File ‘SpaTimeClus/libs/SpaTimeClus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  print.summary.specificity summary.specificity
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
randomCorrelations: no visible global function definition for ‘cor’
specGlm : <anonymous>: no visible global function definition for ‘coef’
specLm : <anonymous>: no visible global function definition for ‘coef’
Undefined global functions or variables:
  coef cor
Consider adding
  importFrom("stats", "coef", "cor")
to your NAMESPACE file.
File ‘spectral/libs/spectral.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  all.equal.list all.equal.list
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Unknown package ‘antaresViz’ in Rd xrefs
R2.global: no visible global function definition for ‘var’
calculer.var.exp: no visible global function definition for ‘var’
creer.noeud: no visible global function definition for ‘var’
ponderer.classe: no visible global function definition for ‘var’
ponderer.classe: no visible global function definition for ‘cov’
spodt: no visible global function definition for ‘model.frame’
spodt.tree: no visible global function definition for ‘plot.new’
spodt.tree: no visible global function definition for ‘par’
spodt.tree: no visible global function definition for ‘plot.window’
spodt.tree: no visible global function definition for ‘text’
spodt.tree: no visible global function definition for ‘segments’
test.spodt: no visible global function definition for ‘model.frame’
test.spodt: no visible global function definition for ‘hist’
test.spodt: no visible global function definition for ‘abline’
tracer.noeud: no visible global function definition for ‘text’
tracer.noeud: no visible global function definition for ‘segments’
Undefined global functions or variables:
  abline cov hist model.frame par plot.new plot.window segments text
  var
Consider adding
  importFrom("graphics", "abline", "hist", "par", "plot.new",
             "plot.window", "segments", "text")
  importFrom("stats", "cov", "model.frame", "var")
to your NAMESPACE file.
File ‘SPODT/libs/SPODT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Ell.Theta: no visible global function definition for ‘ell.theta’
confid.int.theta: no visible global function definition for ‘qchisq’
confid.int.theta : sim.c: no visible global function definition for
  ‘runif’
confid.int.theta: no visible global function definition for ‘quantile’
dd.est: no visible global function definition for ‘ecdf’
ks.sporm : Simul: no visible global function definition for ‘runif’
ks.stat: no visible global function definition for ‘ecdf’
plotor: no visible global function definition for ‘ecdf’
plotor: no visible global function definition for ‘plot’
test.theta: no visible global function definition for ‘ecdf’
test.theta : sim: no visible global function definition for ‘runif’
Undefined global functions or variables:
  ecdf ell.theta plot qchisq quantile runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "ecdf", "qchisq", "quantile", "runif")
to your NAMESPACE file.
prepare_Rd: H.Binv.Rd:48-50: Dropping empty section \note
prepare_Rd: V.theta.Rd:28-30: Dropping empty section \details
prepare_Rd: V.theta.Rd:43-45: Dropping empty section \note
prepare_Rd: V.theta.Rd:49-51: Dropping empty section \seealso
prepare_Rd: V.theta.Rd:52-53: Dropping empty section \examples
prepare_Rd: confid.int.theta.Rd:62-64: Dropping empty section \note
prepare_Rd: dd.est.Rd:39-41: Dropping empty section \note
prepare_Rd: dd.est.Rd:45-47: Dropping empty section \seealso
prepare_Rd: ell.theta.Rd:60-62: Dropping empty section \note
prepare_Rd: ell.theta.Rd:69-70: Dropping empty section \examples
prepare_Rd: grad.hessinv.Rd:47-49: Dropping empty section \note
prepare_Rd: ks.sporm.Rd:43-45: Dropping empty section \note
prepare_Rd: ks.stat.Rd:39-41: Dropping empty section \note
prepare_Rd: mrle.sporm.Rd:66-68: Dropping empty section \note
prepare_Rd: mrle.sporm.Rd:72-74: Dropping empty section \seealso
prepare_Rd: newton.theta.Rd:47-49: Dropping empty section \note
prepare_Rd: phi.Rd:32-38: Dropping empty section \value
prepare_Rd: phi.Rd:48-50: Dropping empty section \note
prepare_Rd: plotor.Rd:26-32: Dropping empty section \value
prepare_Rd: plotor.Rd:42-44: Dropping empty section \note
prepare_Rd: plotor.Rd:48-50: Dropping empty section \seealso
prepare_Rd: sporm-package.Rd:53-54: Dropping empty section \seealso
prepare_Rd: sporm-package.Rd:55-56: Dropping empty section \examples
prepare_Rd: test.theta.Rd:54-56: Dropping empty section \note
prepare_Rd: elltheta.rd:53-55: Dropping empty section \note
prepare_Rd: elltheta.rd:62-63: Dropping empty section \examples
fetch_NBAPlayerStatistics: no visible global function definition for
  ‘read.table’
Undefined global functions or variables:
  read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  coef.Lifedata.MLE coef.deglmx.MLE logLik.Lifedata.MLE plot.MICsplines
  print.Lifedata.MLE print.deglmx print.summary.Lifedata.MLE sqrt.mat
  summary.Lifedata.MLE
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'SlrArd.Rd':
  \usage lines wider than 90 characters:
     SlrArd(T, X, bias = TRUE, method = c("VB", "VBMacKay", "PX-VB"), control = list(), check.lb=TRUE, a0 = 0, b0 = 0, mu0 = 0, xi0 = 1)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  coef.heckit5rob coef.heckitrob fitted.heckit5rob fitted.heckitrob
  print.heckit5rob print.heckitrob print.summary.heckit5rob
  print.summary.heckitrob residuals.heckit5rob residuals.heckitrob
  summary.heckit5rob summary.heckitrob vcov.heckit5rob vcov.heckitrob
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
map.world: no visible global function definition for ‘par’
map.world: no visible global function definition for ‘plot.new’
map.world: no visible global function definition for ‘plot.window’
map.world: no visible global function definition for ‘lines’
map.world: no visible global function definition for ‘title’
map.world: no visible global function definition for ‘axis’
map.world: no visible global function definition for ‘box’
plot.smooth.sspline: no visible global function definition for
  ‘predict’
plot.smooth.sspline: no visible global function definition for
  ‘filled.contour’
plot.smooth.sspline: no visible binding for global variable
  ‘terrain.colors’
plot.smooth.sspline: no visible global function definition for ‘title’
plot.smooth.sspline: no visible global function definition for ‘axis’
station: no visible binding for global variable ‘WTdiff’
station: no visible global function definition for ‘points’
Undefined global functions or variables:
  WTdiff axis box filled.contour lines par plot.new plot.window points
  predict terrain.colors title
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "axis", "box", "filled.contour", "lines", "par",
             "plot.new", "plot.window", "points", "title")
  importFrom("stats", "predict")
to your NAMESPACE file.
File ‘sspline/libs/sspline.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following hidden files and directories:
  inst/.Renviron.d
  inst/.Rprofile.d
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running ‘texi2dvi’ on ‘StatCharrms.tex’ failed.
LaTeX errors:
! Too many }'s.
l.675 ...toc}{subsection}{Other Endpoints Graphs}}
                                                  
You've closed more groups than you opened.
Such booboos are generally harmless, so keep going.
! Undefined control sequence.
<argument> ...Data}. Wiley\textemdashInterscience 
                                                  . 
l.749 ...nt Data}. Wiley\textemdashInterscience. }
                                                  
! Undefined control sequence.
l.758 	Wiley\textemdashInterscience
                                   .
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
<argument> ...t {Indagationes Mathematicae} \bold 
                                                  {14}:327\textemdash 333.
l.772 ...thematicae} \bold{14}:327\textemdash333.}
                                                  
! Undefin
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
File ‘statcomp/libs/statcomp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  print.corsign
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
actvspred: no visible global function definition for ‘quantile’
actvspred: no visible global function definition for ‘aggregate’
actvspred: no visible global function definition for ‘par’
actvspred: no visible global function definition for ‘plot’
actvspred: no visible global function definition for ‘lines’
auc: no visible global function definition for ‘par’
auc: no visible global function definition for ‘plot’
decile: no visible global function definition for ‘quantile’
dqcontinuous : numoutliers: no visible global function definition for
  ‘quantile’
dqcontinuous : <anonymous>: no visible global function definition for
  ‘sd’
dqcontinuous : <anonymous>: no visible global function definition for
  ‘quantile’
gini: no visible global function definition for ‘par’
gini: no visible global function definition for ‘plot’
gini: no visible global function definition for ‘abline’
iv: no visible global function definition for ‘quantile’
iv: no visible global function definition for ‘aggregate’
ks: no visible global function definition for ‘aggregate’
ks: no visible global function definition for ‘par’
ks: no visible global function definition for ‘plot’
ks: no visible global function definition for ‘lines’
outliers: no visible global function definition for ‘quantile’
outliers: no visible global function definition for ‘na.omit’
pentile: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  abline aggregate lines na.omit par plot quantile sd
Consider adding
  importFrom("graphics", "abline", "lines", "par", "plot")
  importFrom("stats", "aggregate", "na.omit", "quantile", "sd")
to your NAMESPACE file.
inspect: no visible global function definition for ‘par’
inspect: no visible global function definition for ‘abline’
inspect: no visible global function definition for ‘lines’
inspect: no visible global function definition for ‘points’
plotfit: no visible global function definition for ‘dev.off’
plotfit: no visible global function definition for ‘par’
plotfit: no visible global function definition for ‘lines’
plotfit: no visible global function definition for ‘points’
plotfit: no visible global function definition for ‘legend’
plothill: no visible global function definition for ‘par’
plothill: no visible global function definition for ‘abline’
plothill: no visible global function definition for ‘points’
plotmultifit: no visible global function definition for ‘par’
plotmultifit: no visible global function definition for ‘lines’
plotmultifit: no visible global function definition for ‘points’
plotmultifit: no visible global function definition for ‘pexp’
plotmultifit: no visible global function definition for ‘plnorm’
plotmultifit: no visible global function definition for ‘ppois’
plotmultifit: no visible global function definition for ‘legend’
plotols: no visible global function definition for ‘dev.off’
plotols: no visible global function definition for ‘lm’
plotols: no visible global function definition for ‘par’
plotols: no visible global function definition for ‘abline’
plotols: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline dev.off legend lines lm par pexp plnorm points ppois
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("graphics", "abline", "legend", "lines", "par", "points")
  importFrom("stats", "lm", "pexp", "plnorm", "ppois")
to your NAMESPACE file.
File ‘staTools/libs/staTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
getStp: no visible global function definition for ‘lm’
plot.steeptest: no visible global function definition for ‘plot’
plot.steeptest: no visible global function definition for ‘axis’
plot.steeptest: no visible global function definition for ‘box’
plot.steeptest: no visible global function definition for ‘lm’
plot.steeptest: no visible global function definition for ‘abline’
plot.steeptest: no visible global function definition for ‘legend’
plot.steeptest: no visible global function definition for
  ‘as.graphicsAnnot’
steeptest: no visible global function definition for ‘lm’
summary.steeptest: no visible global function definition for ‘var’
summary.steeptest: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  abline as.graphicsAnnot axis box legend lm plot quantile var
Consider adding
  importFrom("grDevices", "as.graphicsAnnot")
  importFrom("graphics", "abline", "axis", "box", "legend", "plot")
  importFrom("stats", "lm", "quantile", "var")
to your NAMESPACE file.
File ‘steepness/libs/steepness.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Stem.Bootstrap: no visible global function definition for ‘runif’
filtering: no visible global function definition for ‘is.ts’
filtering: no visible global function definition for ‘ts’
filtering: no visible global function definition for ‘start’
filtering: no visible global function definition for ‘end’
filtering: no visible global function definition for ‘frequency’
kalman: no visible global function definition for ‘ts’
smoothing: no visible global function definition for ‘is.ts’
smoothing: no visible global function definition for ‘ts’
smoothing: no visible global function definition for ‘start’
smoothing: no visible global function definition for ‘end’
smoothing: no visible global function definition for ‘frequency’
Undefined global functions or variables:
  end frequency is.ts runif start ts
Consider adding
  importFrom("stats", "end", "frequency", "is.ts", "runif", "start",
             "ts")
to your NAMESPACE file.
File ‘stepp/libs/stepp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
d1spectrum: no visible global function definition for ‘fft’
d2spectrum: no visible global function definition for ‘fft’
plot.d1nat: no visible global function definition for ‘plot’
plot.d1nat: no visible global function definition for ‘lines’
plot.d1nat: no visible global function definition for ‘legend’
plot.d1nat: no visible global function definition for ‘title’
plot.d1spec: no visible global function definition for ‘plot’
plot.d1spec: no visible global function definition for ‘lines’
plot.d1spec: no visible global function definition for ‘legend’
plot.d1spec: no visible global function definition for ‘title’
plot.d2spec: no visible global function definition for ‘plot’
plot.d2spec: no visible global function definition for ‘lines’
plot.d2spec: no visible global function definition for ‘legend’
plot.d2spec: no visible global function definition for ‘title’
plot.pvalign: no visible global function definition for ‘plot’
plot.pvalign: no visible global function definition for ‘lines’
plot.pvalign: no visible global function definition for ‘legend’
plot.pvalign: no visible global function definition for ‘title’
print.d1nat: no visible global function definition for ‘plot’
print.d1spec: no visible global function definition for ‘plot’
print.d2spec: no visible global function definition for ‘plot’
print.pvalign: no visible global function definition for ‘plot’
utild1bin: no visible global function definition for ‘median’
utild1bin: no visible global function definition for ‘sd’
utild1clean: no visible global function definition for ‘sd’
utild1filt: no visible global function definition for ‘convolve’
Undefined global functions or variables:
  convolve fft legend lines median plot sd title
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "title")
  importFrom("stats", "convolve", "fft", "median", "sd")
to your NAMESPACE file.
Running examples in ‘Stickbreaker-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sim.data.from.priors.for.mod.selection
> ### Title: Simulate data from priors for doing model selection
> ### Aliases: sim.data.from.priors.for.mod.selection
> 
> ### ** Examples
> 
>  n.muts <- 4
>  n.muts <- length(Khan.data[1,])-1
>  geno.matrix <- Khan.data[,seq(1, n.muts)]
>  fit.matrix <- as.matrix(Khan.data[,(n.muts+1)])
>  outdir <- system.file("extdata",package="Stickbreaker")
>  file.name <- paste("Training_simulated_priors_fit_data_", n.muts, "muts.txt", sep="")
>  outpath <- paste(outdir, file.name, sep="/")
>  sim.data.from.priors.for.mod.selection(n.muts,
+    c(0.05, 0.5),
+    c(0, 0.25),
+    c(4),
+    1,
+    c(0.1, 10),
+    1.1,
+    1,
+    c(2,1),
+    outpath,
+    50,
+    coe.sim.model="identical",
+    coe.dist.par=NA,
+    print.interval=NA)
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Stickbreaker/extdata/Training_simulated_priors_fit_data_5muts.txt': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: sim.data.from.priors.for.mod.selection -> write.table -> file
Execution halted
Found the following apparent S3 methods exported but not registered:
  na.stinterp.default
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
na.stinterp.default: no visible global function definition for ‘time’
na.stinterp.default: no visible global function definition for
  ‘na.omit’
Undefined global functions or variables:
  na.omit time
Consider adding
  importFrom("stats", "na.omit", "time")
to your NAMESPACE file.
File ‘stlplus/libs/stlplus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

These lines will be truncated in the PDF manual.
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
Warning: geocode failed with status OVER_QUERY_LIMIT, location = "georgia"
Quitting from lines 220-233 (Details.Rmd) 
Error: processing vignette ‘Details.Rmd’ failed with diagnostics:
arguments imply differing number of rows: 0, 1
Execution halted
Namespace with empty importFrom: ‘tcltk2’
DetailOpLines: no visible global function definition for
  ‘tkProgressBar’
DetailOpLines: no visible global function definition for
  ‘setTkProgressBar’
MultiTrainWithInventory: no visible global function definition for
  ‘tkProgressBar’
MultiTrainWithInventory: no visible global function definition for
  ‘setTkProgressBar’
SimHistory: no visible global function definition for ‘tkProgressBar’
SimHistory: no visible global function definition for
  ‘setTkProgressBar’
Undefined global functions or variables:
  setTkProgressBar tkProgressBar
File ‘stosim/libs/stosim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  plot.icweib print.icweib
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
HRatio: no visible global function definition for ‘qnorm’
icweib: no visible global function definition for ‘model.frame’
icweib: no visible binding for global variable ‘na.pass’
icweib: no visible global function definition for ‘complete.cases’
icweib: no visible global function definition for ‘model.matrix’
icweib: no visible global function definition for ‘optim’
icweib: no visible global function definition for ‘pchisq’
icweib: no visible global function definition for ‘pnorm’
plot.icweib : getstat: no visible global function definition for
  ‘qnorm’
plot.icweib: no visible global function definition for ‘plot’
plot.icweib: no visible global function definition for ‘lines’
plot.icweib: no visible global function definition for ‘legend’
print.icweib: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  complete.cases legend lines model.frame model.matrix na.pass optim
  pchisq plot pnorm qnorm
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "complete.cases", "model.frame", "model.matrix",
             "na.pass", "optim", "pchisq", "pnorm", "qnorm")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/streamR.Rcheck/00install.out’ for details.
'library' or 'require' call to ‘ROAuth’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
File ‘stremr/libs/stremr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

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

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

These lines will be truncated in the PDF manual.
playSudoku : replot: no visible global function definition for ‘par’
playSudoku : replot: no visible global function definition for ‘plot’
playSudoku : replot: no visible global function definition for
  ‘segments’
playSudoku : replot: no visible global function definition for ‘text’
playSudoku: no visible global function definition for ‘tktoplevel’
playSudoku: no visible global function definition for ‘tkwm.title’
playSudoku: no visible global function definition for ‘tkrplot’
playSudoku: no visible global function definition for ‘tktext’
playSudoku: no visible global function definition for ‘tkscrollbar’
playSudoku : <anonymous>: no visible global function definition for
  ‘tkyview’
playSudoku: no visible global function definition for ‘tkconfigure’
playSudoku : <anonymous>: no visible global function definition for
  ‘tkset’
playSudoku: no visible global function definition for ‘tkpack’
playSudoku: no visible global function definition for ‘tcl’
playSudoku: no visible global function definition for ‘tkcget’
playSudoku : showz: no visible global function definition for
  ‘tkrreplot’
playSudoku : type: no visible global function definition for ‘tkinsert’
playSudoku : type: no visible global function definition for ‘tksee’
playSudoku : kb: no visible global function definition for ‘tkdestroy’
playSudoku: no visible global function definition for
  ‘getGraphicsEvent’
playSudoku: no visible global function definition for ‘tkbind’
playSudoku: no visible global function definition for ‘tkwait.window’
Undefined global functions or variables:
  getGraphicsEvent par plot segments tcl text tkbind tkcget tkconfigure
  tkdestroy tkinsert tkpack tkrplot tkrreplot tkscrollbar tksee tkset
  tktext tktoplevel tkwait.window tkwm.title tkyview
Consider adding
  importFrom("grDevices", "getGraphicsEvent")
  importFrom("graphics", "par", "plot", "segments", "text")
to your NAMESPACE file.
SUE.fitted.values: no visible global function definition for
  ‘model.frame’
SUE.lm: no visible global function definition for ‘model.frame’
SUE.lm: no visible global function definition for ‘lm’
SUE.lm: no visible global function definition for ‘anova’
SUE.plot: no visible global function definition for ‘plot’
SUE.residuals: no visible global function definition for ‘model.frame’
parameters : para2: no visible global function definition for ‘uniroot’
parameters: no visible global function definition for ‘optimize’
parameters: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  anova lm model.frame optimize plot uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "anova", "lm", "model.frame", "optimize",
             "uniroot")
to your NAMESPACE file.
Rd file 'SUE.lm.Rd':
  \examples lines wider than 100 characters:
     ##We analysis the well known stackloss data by using ordinary linear method and the subsampling method. 
     ##proportion of outliers in the data. The subsample size is chosen to be the default size of ns = 11.
     plot(SUE.fitted.values(a2),SUE.residuals(a2),xlab="(b) fitted values",ylab="residuals",ylim=c(-12,12))
     plot(SUE.fitted.values(a3),SUE.residuals(a3),xlab="(c) fitted values",ylab="residuals",ylim=c(-12,12))

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package which this enhances but not available for checking: ‘gputools’
HCLtree: no visible global function definition for ‘hclust’
HCLtree: no visible global function definition for ‘as.dist’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘matplot’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘matlines’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘axis’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘box’
plotProfilesWithinBicluster: no visible global function definition for
  ‘matplot’
plotProfilesWithinBicluster: no visible global function definition for
  ‘title’
plotProfilesWithinBicluster: no visible global function definition for
  ‘axis’
plotProfilesWithinBicluster: no visible global function definition for
  ‘par’
plotProfilesWithinBicluster: no visible global function definition for
  ‘box’
plotProfilesWithinBicluster: no visible global function definition for
  ‘matlines’
plotProfilesWithinBicluster: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  as.dist axis box hclust legend matlines matplot par title
Consider adding
  importFrom("graphics", "axis", "box", "legend", "matlines", "matplot",
             "par", "title")
  importFrom("stats", "as.dist", "hclust")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘boa’ ‘coda’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
superdiag: no visible global function definition for ‘as.mcmc.list’
superdiag: no visible global function definition for ‘as.mcmc’
superdiag: no visible global function definition for ‘runif’
superdiag: no visible global function definition for ‘geweke.diag’
superdiag: no visible global function definition for ‘heidel.diag’
superdiag: no visible global function definition for ‘raftery.diag’
superdiag: no visible global function definition for ‘gelman.diag’
Undefined global functions or variables:
  as.mcmc as.mcmc.list gelman.diag geweke.diag heidel.diag raftery.diag
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: ‘dbarts’
Missing or unexported object: ‘gam::predict.gam’
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.
Found the following significant warnings:
  dists.cc:4239:21: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SuppDists.Rcheck/00install.out’ for details.
File ‘SuppDists/libs/SuppDists.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

plot.survAUC: no visible global function definition for ‘plot’
plot.survAUC: no visible global function definition for ‘lines’
plot.survErr: no visible global function definition for ‘plot’
plot.survErr: no visible global function definition for ‘lines’
schemper: no visible global function definition for ‘predict’
schemper: no visible global function definition for ‘survfit’
schemper: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx lines plot predict survfit
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "approx", "predict")
to your NAMESPACE file.
File ‘survAUC/libs/survAUC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

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

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

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

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

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.tp.survtmle
> ### Title: Plot Results of Cumulative Incidence Estimates
> ### Aliases: plot.tp.survtmle
> 
> ### ** Examples
> 
> library(survtmle)
> set.seed(341796)
> n <- 100
> t_0 <- 10
> W <- data.frame(W1 = runif(n), W2 = rbinom(n, 1, 0.5))
> A <- rbinom(n, 1, 0.5)
> T <- rgeom(n,plogis(-4 + W$W1 * W$W2 - A)) + 1
> C <- rgeom(n, plogis(-6 + W$W1)) + 1
> ftime <- pmin(T, C)
> ftype <- as.numeric(ftime == T)
> suppressWarnings(
+   fit <- survtmle(ftime = ftime, ftype = ftype,
+                   adjustVars = W, glm.ftime = "I(W1*W2) + trt + t",
+                   trt = A, glm.ctime = "W1 + t", method = "hazard",
+                   verbose = TRUE,  t0 = t_0, maxIter = 2)
+ )
> tpfit <- timepoints(fit, times = seq_len(t_0))
> plot(tpfit)
Error in names(x) <- value : 
  'names' attribute [3] must be the same length as the vector [2]
Calls: plot -> plot.tp.survtmle -> colnames<-
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 540-542 (survtmle_intro.Rmd) 
Error: processing vignette ‘survtmle_intro.Rmd’ failed with diagnostics:
‘names’ attribute [3] must be the same length as the vector [2]
Execution halted
fitModel: no visible global function definition for ‘var’
fitModel: no visible global function definition for ‘cov’
svpls: no visible global function definition for ‘pt’
Undefined global functions or variables:
  cov pt var
Consider adding
  importFrom("stats", "cov", "pt", "var")
to your NAMESPACE file.
Calls with DUP:
   .C("myInversion", Senv$diag, Senv$env, Senv$xenv, Senv$N, Senv$Nenv, 
       Senv$Nplus1, DUP = FALSE, PACKAGE = "svcm")
   .C("myTrace", Senv$diag, Senv$env, Senv$xenv, Senv$N, Senv$Nenv, 
       Senv$Nplus1, BBenv$diag, BBenv$env, BBenv$xenv, BBenv$N, 
       BBenv$Nenv, BBenv$Nplus1, ED = ED, DUP = FALSE, PACKAGE = "svcm")
   .C("dsC2env", N, A@x, as.integer(A@i), as.integer(A@p), diagvec = diagvec, 
       env = env, xenv = as.integer(xenv), DUP = FALSE)
DUP is no longer supported and will be ignored.
File ‘svcm/libs/svcm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.jgrRun: no visible global function definition for ‘capture.output’
.macDlgList: no visible global function definition for ‘select.list’
.unixDlgForm: no visible global function definition for ‘as’
.unixDlgMessage: no visible global function definition for ‘alarm’
.winDlgList: no visible global function definition for ‘select.list’
dlgForm.textCLI: no visible global function definition for ‘as’
dlgList.textCLI: no visible global function definition for
  ‘select.list’
dlgMessage.textCLI: no visible global function definition for
  ‘select.list’
dlgSave.textCLI: no visible global function definition for
  ‘select.list’
Undefined global functions or variables:
  alarm as capture.output select.list
Consider adding
  importFrom("methods", "as")
  importFrom("utils", "alarm", "capture.output", "select.list")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
dlgMessage.tcltkGUI: no visible global function definition for ‘alarm’
Undefined global functions or variables:
  alarm
Consider adding
  importFrom("utils", "alarm")
to your NAMESPACE file.
Found the following significant warnings:
  trlan/trlcore.c:983:15: warning: comparison of array 'info->oldcpf' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlcore.c:1642:9: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  trlan/trlcore.c:1642:20: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  trlan/trlaux.c:28:13: warning: comparison of array 'info->log_file' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlaux.c:41:13: warning: comparison of array 'info->log_file' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlaux.c:62:13: warning: comparison of array 'info->cpfile' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlan.c:171:20: warning: comparison of array 'info->oldcpf' equal to a null pointer is always false [-Wtautological-pointer-compare]
  trlan/ztrlcore.c:1418:12: warning: comparison of array 'info->oldcpf' not equal to a null pointer is always true [-Wtautological-pointer-compare]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/svd.Rcheck/00install.out’ for details.
svd3dplot: no visible global function definition for ‘wireframe’
svd3dplot: no visible global function definition for ‘levelplot’
Undefined global functions or variables:
  levelplot wireframe
startHttpServer : <anonymous> : Rjsonp: no visible global function
  definition for ‘localeToCharset’
Undefined global functions or variables:
  localeToCharset
Consider adding
  importFrom("utils", "localeToCharset")
to your NAMESPACE file.
.onAttach : svBrowser: no visible global function definition for
  ‘browseURL’
.onAttach: no visible global function definition for ‘loadhistory’
Undefined global functions or variables:
  browseURL loadhistory
Consider adding
  importFrom("utils", "browseURL", "loadhistory")
to your NAMESPACE file.
File ‘svmadmm/libs/svmadmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

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

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

These lines will be truncated in the PDF manual.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/Makefile.win
  src/SWAT2005/Makefile
  src/SWAT2005/Makefile.win
  src/SWAT2009/Makefile
  src/SWAT2009/Makefile.win
  src/SWAT2012/Makefile
  src/SWAT2012/Makefile.win
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
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').
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/sybilEFBA.Rcheck/00install.out’ for details.
FECorr: no visible global function definition for ‘is’
FECorr: no visible global function definition for ‘write.csv’
FECorr: no visible global function definition for ‘aggregate’
FECorr: no visible global function definition for ‘lm’
FECorr: no visible global function definition for ‘nlm’
eFBA_gene: no visible global function definition for ‘is’
eFBA_gene: no visible global function definition for ‘as’
eFBA_rxn : adjustTol: no visible global function definition for ‘is’
eFBA_rxn: no visible global function definition for ‘is’
eFBA_rxn: no visible global function definition for ‘as’
findFluxGeneExpr: no visible global function definition for ‘as’
findMDCFlux: no visible global function definition for ‘is’
findMDCFlux: no visible global function definition for ‘as’
gene2Rule: no visible global function definition for ‘is’
Undefined global functions or variables:
  aggregate as is lm nlm write.csv
Consider adding
  importFrom("methods", "as", "is")
  importFrom("stats", "aggregate", "lm", "nlm")
  importFrom("utils", "write.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages suggested but not available for checking:
  ‘sylly.de’ ‘sylly.en’ ‘sylly.es’
symbol: no visible global function definition for ‘plot.new’
symbol: no visible global function definition for ‘plot.window’
symbol: no visible global function definition for ‘axis’
symbol: no visible global function definition for ‘box’
symbol: no visible global function definition for ‘title’
symbol: no visible global function definition for ‘rainbow’
symbol: no visible global function definition for ‘hsv’
symbol: no visible global function definition for ‘rect’
symbol: no visible global function definition for ‘polygon’
symbol: no visible global function definition for ‘lines’
symbol: no visible global function definition for ‘text’
Undefined global functions or variables:
  axis box hsv lines plot.new plot.window polygon rainbow rect text
  title
Consider adding
  importFrom("grDevices", "hsv", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "polygon", "rect", "text", "title")
to your NAMESPACE file.
Rd file 'symbol.Rd':
  \usage lines wider than 90 characters:
     symbol(df, type="star", colin=NULL, colout=NULL, colin2=NA, colout2=1, ssize=NULL, labels=0, labelsize=0.6,
            scheme=1, sortby=0, descending=FALSE, coorx=NULL, coory=NULL, lty=1, main=NULL, sub=NULL, xlab=NULL, ylab=NULL,
            add=FALSE, xlim=NULL, ylim=NULL, facew=0.5, faceh=0.5, eyes=0.5, eyed=0.5, mouthw=0.5, mouthc=0.5, brows=0.5,
            browp=0.5, nosel=0.5, nosew=0.5, ears=0.5, pupils=0.5, body=0.5, limb1=0.5, limb2=0.5, limb3=0.5, limb4=0.5, defcol=NA)

These lines will be truncated in the PDF manual.
integrate.polynomial : f: no visible global function definition for
  ‘dmvnorm’
Undefined global functions or variables:
  dmvnorm
Found the following apparent S3 methods exported but not registered:
  [.GenMap [.relationshipMatrix
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Package in Depends field not imported from: ‘fields’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cwt_fw: no visible global function definition for ‘fft’
cwt_iw: no visible global function definition for ‘fft’
est_riskshrink_thresh: no visible global function definition for
  ‘median’
Undefined global functions or variables:
  fft median
Consider adding
  importFrom("stats", "fft", "median")
to your NAMESPACE file.
File ‘SynchWave/libs/SynchWave.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SynergizeR.Rcheck/00install.out’ for details.
Packages in Depends field not imported from:
  ‘RCurl’ ‘RJSONIO’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'available_ranges.Rd':
  \usage lines wider than 90 characters:
       available_ranges(authority = "ensembl", species = "Homo sapiens", domain = "hgnc_symbol")

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

These lines will be truncated in the PDF manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘tcltk’ ‘tkrplot’
  Please remove these calls from your code.
Rd file 'SyNet-package.rd':
  \examples lines wider than 100 characters:
       # Run NAM method on the previously inferred sympatry network                                           

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

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

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

These lines will be truncated in the PDF manual.
Namespaces with empty importFrom:
  ‘Rcpp’ ‘methods’
File ‘synlik/libs/synlik.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
mainNetFunction: no visible global function definition for ‘png’
mainNetFunction: no visible global function definition for ‘plot’
mainNetFunction: no visible global function definition for ‘lines’
mainNetFunction: no visible global function definition for ‘legend’
mainNetFunction: no visible global function definition for ‘dev.off’
plotPR: no visible global function definition for ‘plot’
plotROC: no visible global function definition for ‘plot’
plotROC: no visible global function definition for ‘lines’
simulatedData: no visible global function definition for ‘rpois’
simulatedData : <anonymous>: no visible global function definition for
  ‘rpois’
simulatedData : rlognormpois: no visible global function definition for
  ‘rnorm’
simulatedData : rlognormpois: no visible global function definition for
  ‘rpois’
Undefined global functions or variables:
  dev.off legend lines plot png rnorm rpois
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "rnorm", "rpois")
to your NAMESPACE file.
File ‘synthACS/libs/synthACS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls in package code:
  ‘LowRankQP’ ‘rgenoud’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
fn.V: no visible global function definition for ‘LowRankQP’
gaps.plot: no visible global function definition for ‘abline’
path.plot: no visible global function definition for ‘lines’
path.plot: no visible global function definition for ‘abline’
path.plot: no visible global function definition for ‘legend’
synth: no visible binding for global variable ‘sd’
synth: no visible binding for global variable ‘var’
synth: no visible global function definition for ‘LowRankQP’
Undefined global functions or variables:
  LowRankQP abline legend lines sd var
Consider adding
  importFrom("graphics", "abline", "legend", "lines")
  importFrom("stats", "sd", "var")
to your NAMESPACE file.
Found the following significant warnings:
  lib_FeasibleMatrix.cpp:53:7: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  lib_FeasibleMatrix.cpp:168:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  lib_FeasibleMatrix.cpp:176:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  lib_sample_kcycle.cpp:141:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/systemicrisk.Rcheck/00install.out’ for details.
.checkDimAndTest: no visible global function definition for
  ‘chisq.test’
.checkDimAndTest: no visible global function definition for
  ‘fisher.test’
plotTable1Heatmap: no visible global function definition for ‘par’
plotTable1Heatmap: no visible global function definition for ‘image’
plotTable1Heatmap: no visible global function definition for ‘abline’
plotTable1Heatmap: no visible global function definition for ‘axis’
plotTable1Heatmap: no visible global function definition for ‘text’
plotTable1Heatmap: no visible global function definition for ‘legend’
plotTable1Heatmap: no visible global function definition for ‘box’
Undefined global functions or variables:
  abline axis box chisq.test fisher.test image legend par text
Consider adding
  importFrom("graphics", "abline", "axis", "box", "image", "legend",
             "par", "text")
  importFrom("stats", "chisq.test", "fisher.test")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  rbind.tableList rbind.tableMatrix
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'rbind.tableList':
  ‘rbind.tableList’

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

These lines will be truncated in the PDF manual.
Found the following apparent S3 methods exported but not registered:
  end.TawnyPortfolio start.TawnyPortfolio
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
end.TawnyPortfolio: no visible global function definition for ‘end’
start.TawnyPortfolio: no visible global function definition for ‘start’
Undefined global functions or variables:
  end start
Consider adding
  importFrom("stats", "end", "start")
to your NAMESPACE file.
File ‘tbart/libs/tbart.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
BootTree: no visible global function definition for ‘hclust’
BootTree: no visible global function definition for ‘dist’
BootTree: no visible global function definition for ‘as.dist’
BootTree: no visible global function definition for ‘cor’
BootTree: no visible binding for global variable ‘var’
Pgpd: no visible global function definition for ‘optim’
Pgpd : <anonymous>: no visible global function definition for ‘optim’
Pgpd: no visible global function definition for ‘var’
Pgpd: no visible global function definition for ‘rnorm’
Pgpd: no visible global function definition for ‘quantile’
Pvalue: no visible global function definition for ‘rnorm’
SigTree: no visible global function definition for ‘data’
TreeStat: no visible global function definition for ‘hclust’
TreeStat: no visible global function definition for ‘as.dist’
TreeStat: no visible global function definition for ‘dist’
TreeStat: no visible global function definition for ‘cor’
plot.best: no visible global function definition for ‘hclust’
plot.best: no visible global function definition for ‘as.dist’
plot.best: no visible global function definition for ‘dist’
plot.best: no visible global function definition for ‘cor’
plot.best: no visible global function definition for ‘plot’
treetext: no visible global function definition for ‘par’
treetext: no visible global function definition for ‘text’
Undefined global functions or variables:
  as.dist cor data dist hclust optim par plot quantile rnorm text var
Consider adding
  importFrom("graphics", "par", "plot", "text")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "optim",
             "quantile", "rnorm", "var")
  importFrom("utils", "data")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Loading required package: data.table
No methods found in package ‘RSQLite’ for request: ‘dbGetQuery’ when loading ‘tcpl’
tcpl (v1.2.2) loaded with the following settings:
  TCPL_DB:    /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/tcpl/sql/tcpldb.sqlite
  TCPL_USER:  NA
  TCPL_HOST:  NA
  TCPL_DRVR:  SQLite
Default settings stored in TCPL.conf. See ?tcplConf for more information.

Error: processing vignette ‘tcpl_Overview.Rnw’ failed with diagnostics:
 chunk 4 
Error in rsqlite_send_query(conn@ptr, statement) : 
  attempt to write a readonly database
Execution halted
Found the following apparent S3 methods exported but not registered:
  slice.fun
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'top.fun':
  ‘slice.fun’

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
E.2SI: no visible binding for global variable ‘var’
E.2SI: no visible global function definition for ‘var’
E.BE: no visible global function definition for ‘var’
E.Beta: no visible global function definition for ‘var’
E.PO: no visible global function definition for ‘var’
E.PPS: no visible global function definition for ‘var’
E.SI: no visible global function definition for ‘var’
E.STPPS: no visible global function definition for ‘var’
E.STSI: no visible global function definition for ‘var’
E.STpiPS: no visible global function definition for ‘var’
E.SY: no visible global function definition for ‘var’
E.WR: no visible global function definition for ‘var’
E.piPS: no visible global function definition for ‘var’
GREG.SI: no visible global function definition for ‘var’
S.BE: no visible global function definition for ‘runif’
S.PO: no visible global function definition for ‘runif’
S.PPS: no visible global function definition for ‘runif’
S.SI: no visible global function definition for ‘runif’
S.STPPS: no visible global function definition for ‘runif’
S.WR: no visible global function definition for ‘rbinom’
S.piPS: no visible global function definition for ‘runif’
p.WR: no visible global function definition for ‘dmultinom’
Undefined global functions or variables:
  dmultinom rbinom runif var
Consider adding
  importFrom("stats", "dmultinom", "rbinom", "runif", "var")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  predict.Weights predict.Weights2
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
TeachNet: no visible global function definition for ‘predict’
createWeights1: no visible global function definition for ‘rnorm’
createWeights2: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  predict rnorm
Consider adding
  importFrom("stats", "predict", "rnorm")
to your NAMESPACE file.
aniplotevents: no visible global function definition for ‘plot’
aniplotevents: no visible global function definition for ‘lines’
cbfs: no visible global function definition for ‘rnorm’
cbfs: no visible global function definition for ‘runif’
cbfs_red: no visible global function definition for ‘arima.sim’
cbfs_red: no visible global function definition for ‘runif’
eventCluster: no visible global function definition for ‘princomp’
eventCluster: no visible global function definition for ‘kmeans’
measures: no visible global function definition for ‘sd’
measures: no visible global function definition for ‘var’
measures: no visible global function definition for ‘PP.test’
noiseTests: no visible global function definition for ‘Box.test’
noiseTests: no visible global function definition for ‘PP.test’
noiseTests: no visible global function definition for ‘ar’
plotevents: no visible global function definition for ‘plot’
plotevents: no visible global function definition for ‘lines’
ur.za.fast : roll: no visible global function definition for ‘coef’
ur.za.fast : roll: no visible global function definition for ‘lm’
Undefined global functions or variables:
  Box.test PP.test ar arima.sim coef kmeans lines lm plot princomp
  rnorm runif sd var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "Box.test", "PP.test", "ar", "arima.sim", "coef",
             "kmeans", "lm", "princomp", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  $.tensor ^.tensor as.contravariate.character as.covariate.character
  as.tensor.default as.tensor.tensor is.contravariate.character
  is.contravariate.numeric is.contravariate.tensor
  is.covariate.character is.covariate.numeric is.covariate.tensor
  mean.tensor |.tensor
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Calls with DUP:
   .C(tensoraCmulhelper, dimx = as.integer(c(outerx, inner, para)), 
       as.integer(c(inner, outery, para)), as.integer(c(outerx, 
           outery, para)), as.complex(X[xtidx]), as.complex(Y[ytidx]), 
       erg = complex(outerx * outery * para), NAOK = TRUE, DUP = FALSE)
   .C(tensoramulhelper, dimx = as.integer(c(outerx, inner, para)), 
       as.integer(c(inner, outery, para)), as.integer(c(outerx, 
           outery, para)), as.numeric(X[xtidx]), as.numeric(Y[ytidx]), 
       erg = numeric(outerx * outery * para), NAOK = TRUE, DUP = FALSE)
DUP is no longer supported and will be ignored.
S3 methods shown with full name in documentation object 'mean.tensor':
  ‘mean.tensor’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/tensorBF.Rcheck/00install.out’ for details.
TER.deesc.1.B : A1.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.1.B : A1.f: no visible binding for global variable ‘ID’
TER.deesc.1.B : A2.n.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.1.B : A2.n.f: no visible binding for global variable ‘ID’
TER.deesc.1.B: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.1.B: no visible binding for global variable ‘ID’
TER.deesc.A.B : A1.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : A1.f: no visible binding for global variable ‘ID’
TER.deesc.A.B : A3.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : A3.f: no visible binding for global variable ‘ID’
TER.deesc.A.B : A2.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : A2.f: no visible binding for global variable ‘ID’
TER.deesc.A.B : B1.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : B1.f: no visible binding for global variable ‘ID’
TER.deesc.A.B: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B: no visible binding for global variable ‘ID’
Undefined global functions or variables:
  ID
Found the following apparent S3 methods exported but not registered:
  plot.df_curves plot.dyntermstrc_nss plot.dyntermstrc_param
  plot.dyntermstrc_yields plot.error plot.fwr_curves plot.ir_curve
  plot.s_curves plot.spot_curves plot.spsearch plot.termstrc_cs
  plot.termstrc_nss plot.zeroyields print.couponbonds
  print.dyncouponbonds print.dyntermstrc_nss print.dyntermstrc_yields
  print.summary.dyntermstrc_nss print.summary.dyntermstrc_param
  print.summary.dyntermstrc_yields print.summary.termstrc_cs
  print.summary.termstrc_nss print.termstrc_cs print.termstrc_nss
  print.zeroyields summary.dyntermstrc_nss summary.dyntermstrc_param
  summary.dyntermstrc_yields summary.termstrc_cs summary.termstrc_nss
  summary.zeroyields
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘termstrc/libs/termstrc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File which contains pragma(s) suppressing diagnostics:
  ‘inst/include/testthat/vendor/catch.h’
Found the following apparent S3 methods exported but not registered:
  print.tepAssign print.tepBADA print.tepDICA print.tepGPLS
  print.tepGraphs print.tepPLS print.tepPLSCA print.texpoOutput
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 55-81 (a_start_here.Rmd) 
Error: processing vignette ‘a_start_here.Rmd’ failed with diagnostics:
no stopwords available for 'smart'
Execution halted
phyper_right: no visible global function definition for ‘dhyper’
progression: no visible global function definition for ‘density’
progression: no visible global function definition for ‘plot’
progression: no visible global function definition for ‘points’
progression: no visible global function definition for ‘legend’
progression: no visible global function definition for ‘text’
specificities.distribution.plot: no visible global function definition
  for ‘dhyper’
specificities.distribution.plot: no visible global function definition
  for ‘plot’
specificities.distribution.plot: no visible global function definition
  for ‘Axis’
specificities.distribution.plot: no visible global function definition
  for ‘arrows’
specificities.distribution.plot: no visible global function definition
  for ‘text’
specificities.distribution.plot: no visible global function definition
  for ‘title’
specificities.probabilities.vector: no visible global function
  definition for ‘phyper’
Undefined global functions or variables:
  Axis arrows density dhyper legend phyper plot points text title
Consider adding
  importFrom("graphics", "Axis", "arrows", "legend", "plot", "points",
             "text", "title")
  importFrom("stats", "density", "dhyper", "phyper")
to your NAMESPACE file.
File ‘textreg/libs/textreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package unavailable to check Rd xrefs: ‘dada2’
Calls with DUP:
   .C("zstat_pathway_perm", as.double(g), as.integer(m), as.integer(length(m)), 
       as.double(aff), as.integer(length(aff)), as.double(thresh), 
       as.integer(gsubsetmatrix), as.integer(nrow(gsubsetmatrix)), 
       as.integer(use_sign), as.integer(use_weight), as.integer(strategy), 
       as.integer(nperm), ret_pvalue, DUP = FALSE)
   .C("zstat_perm", as.double(g), as.integer(m), as.integer(length(m)), 
       as.double(aff), as.integer(length(aff)), as.double(thresh), 
       as.integer(gsubsetmatrix), as.integer(nrow(gsubsetmatrix)), 
       as.integer(use_sign), as.integer(use_weight), as.integer(strategy), 
       as.integer(nperm), ret_pvalue, DUP = FALSE)
DUP is no longer supported and will be ignored.
File ‘thgenetics/libs/thgenetics.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
coef_traceplot: no visible global function definition for ‘rainbow’
coef_traceplot: no visible global function definition for ‘plot’
coef_traceplot: no visible global function definition for ‘abline’
coef_traceplot : <anonymous>: no visible global function definition for
  ‘lines’
coef_traceplot: no visible global function definition for ‘text’
ee.GEE.aux : <anonymous>: no visible global function definition for
  ‘combn’
Undefined global functions or variables:
  abline combn lines plot rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "plot", "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
summary.tsls: no visible global function definition for ‘printCoefmat’
threesls: no visible global function definition for ‘cor’
threesls: no visible global function definition for ‘pt’
tsls.formula: no visible global function definition for ‘model.matrix’
tsls.formula: no visible global function definition for
  ‘model.response’
Undefined global functions or variables:
  cor model.matrix model.response printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.matrix", "model.response",
             "printCoefmat", "pt")
to your NAMESPACE file.
.LoadTickDataHK: no visible global function definition for ‘read.csv’
.LoadTickDataSHSZ: no visible global function definition for ‘read.csv’
DrawDown: no visible global function definition for ‘na.omit’
PerformanceReport: no visible global function definition for
  ‘aggregate’
PerformanceReport: no visible global function definition for ‘sd’
Undefined global functions or variables:
  aggregate na.omit read.csv sd
Consider adding
  importFrom("stats", "aggregate", "na.omit", "sd")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
newTiddler: no visible global function definition for ‘new’
twImage: no visible global function definition for ‘new’
twLink: no visible global function definition for ‘new’
twList: no visible global function definition for ‘new’
twTable: no visible global function definition for ‘new’
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package required but not available: ‘fuzzyjoin’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidyinftheo)
  > 
  > test_check("tidyinftheo")
  ── 1. Error: right number of columns given (@test-errors.R#10)  ────────────────
  argument "expr" is missing, with no default
  1: expect_length(tab %>% select(vs) %>% shannon_entropy(), 1) at testthat/test-errors.R:10
  2: quasi_label(enquo(object))
  3: eval_bare(get_expr(quo), get_env(quo))
  4: tab %>% select(vs) %>% shannon_entropy()
  5: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  6: eval(quote(`_fseq`(`_lhs`)), env, env)
  7: eval(quote(`_fseq`(`_lhs`)), env, env)
  8: `_fseq`(`_lhs`)
  9: freduce(value, `_function_list`)
  10: withVisible(function_list[[k]](value))
  11: function_list[[k]](value)
  12: shannon_entropy(.)
  13: reduce_data(.data, !(!enquo(X)), numvars = 1, na.rm = na.rm)
  14: tidyselect::vars_select(names(reduced_tab), !(!(!quos(...))))
  15: vars_select_eval(.vars, quos)
  16: map_lgl(quos, quo_is_helper)
  17: .f(.x[[i]], ...)
  18: extract_expr(quo)
  19: is_call(expr, paren_sym)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 37 SKIPPED: 0 FAILED: 1
  1. Error: right number of columns given (@test-errors.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘tidyxl/libs/tidyxl.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
    Object: ‘xlex.o’

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

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

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

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

These lines will be truncated in the PDF manual.
'library' or 'require' call to ‘shiny’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘ggplot2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
timeline: no visible global function definition for ‘ggplot’
timeline: no visible global function definition for ‘geom_segment’
timeline: no visible global function definition for ‘aes_string’
timeline: no visible global function definition for ‘geom_rect’
timeline: no visible global function definition for ‘geom_text’
timeline: no visible global function definition for ‘theme’
timeline: no visible global function definition for ‘element_blank’
timeline: no visible global function definition for ‘xlab’
timeline: no visible global function definition for ‘ylab’
timeline: no visible global function definition for ‘xlim’
timeline: no visible global function definition for
  ‘scale_y_continuous’
timeline: no visible global function definition for ‘geom_point’
timeline: no visible global function definition for ‘scale_color_grey’
timeline: no visible global function definition for ‘geom_hline’
Undefined global functions or variables:
  aes_string element_blank geom_hline geom_point geom_rect geom_segment
  geom_text ggplot scale_color_grey scale_y_continuous theme xlab xlim
  ylab
Found the following significant warnings:
  tm.c:184:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  tm.c:185:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TimeMachine.Rcheck/00install.out’ for details.
Found the following apparent S3 methods exported but not registered:
  density.tm mean.tm print.tm quantile.tm summary.tm
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
density.tm: no visible global function definition for ‘density’
mu.mle: no visible global function definition for ‘optimize’
pophistory.tm: no visible binding for global variable ‘quantile’
quantile.tm: no visible global function definition for ‘quantile’
sample.pop: no visible global function definition for ‘runif’
summary.tm: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  density optimize quantile runif
Consider adding
  importFrom("stats", "density", "optimize", "quantile", "runif")
to your NAMESPACE file.
File ‘TimeMachine/libs/TimeMachine.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘ExPosition’ ‘InPosition’ ‘TExPosition’ ‘prettyGraphs’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  print.tepBADA.inference.battery print.tepDICA.inference.battery
  print.tinpoAllBoots print.tinpoBoot print.tinpoBootTests
  print.tinpoComponents print.tinpoLOO print.tinpoOmni
  print.tinpoOutput print.tinpoR2
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Non-standard files/directories found at top level:
  ‘DESCRIPTION.orig’ ‘README.rst’
tipom.car: no visible global function definition for ‘abline’
tipom.car: no visible global function definition for ‘axis’
tipom.heat: no visible global function definition for ‘image’
tipom.heat: no visible global function definition for ‘gray’
tipom.lw: no visible global function definition for ‘plot’
tipom.lw: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline axis gray image plot
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "image", "plot")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘boot’ ‘lattice’ ‘splines’ ‘tcltk’
  Please remove these calls from your code.
ls.tree: no visible global function definition for ‘lm’
ls.tree: no visible global function definition for ‘coef’
Undefined global functions or variables:
  coef lm
Consider adding
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
File ‘TKF/libs/TKF.so’:
  Found no call to: ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as.data.frame.survTP
> ### Title: as.data.frame method for a survTP object
> ### Aliases: as.data.frame.survTP
> ### Keywords: manip methods survival
> 
> ### ** Examples
> 
> # Example for the "TPmsm" format
> weiTP <- dgpTP(n=100, corr=1, dist="weibull", dist.par=c(2, 7, 2, 7),
+ model.cens="exponential", cens.par = 6, state2.prob=0.6)
*** invalid %N$ use detected ***
Aborted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/tpr.Rcheck/00install.out’ for details.
Found the following calls to attach():
File ‘track/R/track.attach.R’:
  attach(what = NULL, pos = pos, name = name)
See section ‘Good practice’ in ‘?attach’.
DeadReckoning: no visible global function definition for ‘filter’
DeadReckoning: no visible global function definition for ‘approx’
DeadReckoning: no visible global function definition for ‘lm’
Mapper: no visible global function definition for ‘colorRampPalette’
Mapper: no visible global function definition for ‘terrain.colors’
Mapper: no visible global function definition for ‘points’
Mapper: no visible global function definition for ‘axis’
Standardize: no visible global function definition for ‘lm’
Undefined global functions or variables:
  approx axis colorRampPalette filter lm points terrain.colors
Consider adding
  importFrom("grDevices", "colorRampPalette", "terrain.colors")
  importFrom("graphics", "axis", "points")
  importFrom("stats", "approx", "filter", "lm")
to your NAMESPACE file.
Running ‘trackr-tests.R’ [6s/6s]
Running the tests in ‘tests/trackr-tests.R’ failed.
Complete output:
  > library(trackr)
  Loading required package: histry
  > library(knitr)
  > be = JSONBackend(tempfile())
  > tdb = TrackrDB(backend=be, img_dir = tempdir())
  > defaultTDB(tdb)
  An object of class "TrackrDB"
  Slot "opts":
  An object of class "TrackrOptions"
  Slot "insert_delay":
  [1] 0
  
  Slot "img_dir":
  [1] "/tmp/RtmpH68N9s"
  
  Slot "img_ext":
  [1] "png"
  
  Slot "backend_opts":
  list()
  
  
  Slot "backend":
  Reference class object of class "JSONBackend"
  Field "docs":
  DocList (0x0)
  Field ".file":
  [1] "/tmp/RtmpH68N9s/file28fa31d4cbdb"
  Field "file":
  [1] "/tmp/RtmpH68N9s/file28fa31d4cbdb"
  
  > 
  > rmdfil = system.file("test_docs/knitr_test.Rmd", package = "trackr")
  > knit_and_record(rmdfil)
  
  
  processing file: knitr_test.Rmd
    ordinary text without R code
  
  label: plot
  Error in file(file, ifelse(append, "a", "w")) : 
    cannot open the connection
  Calls: knit_and_record ... replayPlot -> .handleSimpleError -> h -> cat -> file
  In addition: Warning messages:
  1: In dir.create(dirname(name), recursive = TRUE) :
    cannot create dir 'knitr_test_files/figure-html', reason 'No such file or directory'
  2: In file(file, ifelse(append, "a", "w")) :
    cannot open file 'knitr_test.knit.md': Read-only file system
  Execution halted
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TrajDataMining.Rcheck/00install.out’ for details.
File ‘TransferEntropy/libs/TransferEntropy.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/turboEM.Rcheck/00install.out’ for details.
accelerate: no visible global function definition for ‘modifyList’
boxplot.turbosim: no visible global function definition for ‘par’
boxplot.turbosim: no visible global function definition for ‘axis’
boxplot.turbosim: no visible global function definition for ‘mtext’
dataprof.turbosim: no visible global function definition for ‘quantile’
dataprof.turbosim: no visible global function definition for ‘par’
dataprof.turbosim: no visible global function definition for ‘plot’
dataprof.turbosim: no visible global function definition for ‘lines’
dataprof.turbosim: no visible global function definition for ‘segments’
dataprof.turbosim: no visible global function definition for ‘legend’
line.search: no visible global function definition for ‘optimize’
pairs.turbosim: no visible global function definition for ‘par’
pairs.turbosim: no visible global function definition for ‘plot’
pairs.turbosim: no visible global function definition for ‘legend’
pairs.turbosim: no visible global function definition for ‘axis’
pairs.turbosim: no visible global function definition for ‘title’
pairs.turbosim: no visible global function definition for ‘coef’
pairs.turbosim: no visible global function definition for ‘abline’
pairs.turbosim: no visible global function definition for ‘text’
plot.turbo: no visible global function definition for ‘plot’
plot.turbo: no visible global function definition for ‘lines’
plot.turbo: no visible global function definition for ‘legend’
turboSim: no visible binding for global variable ‘par’
turboem: no visible global function definition for ‘modifyList’
Undefined global functions or variables:
  abline axis coef legend lines modifyList mtext optimize par plot
  quantile segments text title
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "mtext",
             "par", "plot", "segments", "text", "title")
  importFrom("stats", "coef", "optimize", "quantile")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
turf: no visible global function definition for ‘read.table’
turf: no visible global function definition for ‘flush.console’
turf.combos: no visible global function definition for ‘combn’
Undefined global functions or variables:
  combn flush.console read.table
Consider adding
  importFrom("utils", "combn", "flush.console", "read.table")
to your NAMESPACE file.
File ‘TUWmodel/libs/TUWmodel.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
dudewicz.unif.test: no visible global function definition for ‘runif’
frosini.unif.test: no visible global function definition for ‘runif’
hegazy.unif.test: no visible global function definition for ‘runif’
kolmogorov.unif.test: no visible global function definition for ‘runif’
kuiper.unif.test: no visible global function definition for ‘runif’
neyman.unif.test: no visible global function definition for ‘runif’
quesenberry.unif.test: no visible global function definition for
  ‘runif’
sarkadi.unif.test: no visible global function definition for ‘runif’
sherman.unif.test: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
cumcount: no visible global function definition for ‘setNames’
uniqtag: no visible global function definition for ‘setNames’
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
File ‘unsystation/libs/unsystation.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Mammen: no visible global function definition for ‘runif’
PR2: no visible global function definition for ‘ar.burg’
PR2: no visible global function definition for ‘pt’
PR2: no visible global function definition for ‘pf’
PR3: no visible global function definition for ‘ar.burg’
PR3: no visible global function definition for ‘pt’
PR3: no visible global function definition for ‘pf’
VAR.FOR: no visible global function definition for ‘qnorm’
VAR.ForeB: no visible global function definition for ‘runif’
VAR.LRtest: no visible global function definition for ‘pchisq’
VAR.LRtest: no visible global function definition for ‘pf’
VAR.PI: no visible global function definition for ‘quantile’
VAR.Waldtest: no visible global function definition for ‘pf’
VAR.irf: no visible global function definition for ‘par’
VAR.irf: no visible global function definition for ‘plot’
VAR.irf: no visible global function definition for ‘abline’
VAR1.sim: no visible global function definition for ‘rnorm’
resamp: no visible global function definition for ‘runif’
Undefined global functions or variables:
  abline ar.burg par pchisq pf plot pt qnorm quantile rnorm runif
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("stats", "ar.burg", "pchisq", "pf", "pt", "qnorm",
             "quantile", "rnorm", "runif")
to your NAMESPACE file.
File ‘VariABEL/libs/VariABEL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard file/directory found at top level:
  ‘Todo’
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/VarReg.Rcheck/00install.out’ for details.
Packages in Depends field not imported from:
  ‘MASS’ ‘strucchange’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
black_scholes: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
burdenPlot: no visible global function definition for ‘density’
burdenPlot: no visible global function definition for ‘axis’
burdenPlot: no visible global function definition for ‘points’
burdenPlot: no visible global function definition for ‘lines’
burdenPlot: no visible global function definition for ‘abline’
burdenPlot: no visible global function definition for ‘text’
burdenPlot: no visible global function definition for ‘sd’
burdenPlot: no visible global function definition for ‘segments’
vbdm: no visible global function definition for ‘var’
vbdm: no visible global function definition for ‘pchisq’
vbdmR : run_discrete_mixture_vanilla: no visible global function
  definition for ‘var’
vbdmR: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  abline axis density lines pchisq points sd segments text var
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "points", "segments",
             "text")
  importFrom("stats", "density", "pchisq", "sd", "var")
to your NAMESPACE file.
File ‘vbdm/libs/vbdm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/vcfR.Rcheck/00install.out’ for details.
cv.vda.le.default: no visible global function definition for ‘predict’
cv.vda.r.default: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
File ‘VDA/libs/VDA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Compare2FDS: no visible global function definition for ‘runif’
Compare2FDS: no visible global function definition for ‘lm’
Compare2FDS: no visible global function definition for ‘model.matrix’
Compare2FDS: no visible global function definition for ‘plot’
Compare2FDS: no visible global function definition for ‘abline’
Compare2FDS: no visible global function definition for ‘lines’
Compare2FDS: no visible global function definition for ‘text’
Compare2Vdg: no visible global function definition for ‘par’
Compare2Vdg: no visible global function definition for ‘plot’
Compare2Vdg: no visible global function definition for ‘lines’
Compare2Vdg: no visible global function definition for ‘legend’
FDSPlot: no visible global function definition for ‘runif’
FDSPlot: no visible global function definition for ‘lm’
FDSPlot: no visible global function definition for ‘model.matrix’
FDSPlot: no visible global function definition for ‘plot’
FDSPlot: no visible global function definition for ‘abline’
Vdgraph: no visible global function definition for ‘par’
Vdgraph: no visible global function definition for ‘plot’
Vdgraph: no visible global function definition for ‘lines’
Vdgraph: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline legend lines lm model.matrix par plot runif text
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "plot",
             "text")
  importFrom("stats", "lm", "model.matrix", "runif")
to your NAMESPACE file.
File ‘Vdgraph/libs/Vdgraph.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Weighted.Box.test: no visible global function definition for ‘acf’
Weighted.Box.test: no visible binding for global variable ‘na.pass’
Weighted.Box.test: no visible global function definition for ‘pgamma’
Weighted.Box.test: no visible global function definition for ‘pchisq’
Weighted.LM.test: no visible global function definition for ‘acf’
Weighted.LM.test: no visible binding for global variable ‘na.pass’
Weighted.LM.test: no visible global function definition for ‘pgamma’
Undefined global functions or variables:
  acf na.pass pchisq pgamma
Consider adding
  importFrom("stats", "acf", "na.pass", "pchisq", "pgamma")
to your NAMESPACE file.
File ‘weightedScores/libs/weightedScores.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
print.palette: no visible global function definition for ‘par’
print.palette: no visible global function definition for ‘image’
print.palette: no visible global function definition for ‘rect’
print.palette: no visible global function definition for ‘rgb’
print.palette: no visible global function definition for ‘text’
wes_palette: no visible global function definition for
  ‘colorRampPalette’
Undefined global functions or variables:
  colorRampPalette image par rect rgb text
Consider adding
  importFrom("grDevices", "colorRampPalette", "rgb")
  importFrom("graphics", "image", "par", "rect", "text")
to your NAMESPACE file.
Package in Depends field not imported from: ‘snpStats’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Z.value: no visible global function definition for ‘sd’
Z.value: no visible global function definition for ‘pnorm’
pairtest: no visible global function definition for ‘is’
pairtest: no visible global function definition for ‘new’
pairtest: no visible global function definition for ‘rbind2’
pairtest: no visible global function definition for ‘p.value’
pairtest: no visible global function definition for ‘single.snp.tests’
scoretest: no visible global function definition for ‘pchisq’
varplot : <anonymous>: no visible global function definition for ‘var’
varplot: no visible global function definition for ‘plot’
varplot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline is new p.value pchisq plot pnorm rbind2 sd single.snp.tests
  var
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("methods", "is", "new", "rbind2")
  importFrom("stats", "pchisq", "pnorm", "sd", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' call to ‘markdown’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Error in re-building vignettes:
  ...
Quitting from lines 34-37 (Running_WhiteStripe.Rmd) 
Error: processing vignette ‘Running_WhiteStripe.Rmd’ failed with diagnostics:
File(s) not found!
Execution halted
Found the following significant warnings:
  t_region.cpp:78:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:115:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:120:7: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/WhopGenome.Rcheck/00install.out’ for details.
dlog.norm: no visible global function definition for ‘rnorm’
fun.load.hals.a: no visible global function definition for ‘sfExport’
fun.load.hals.a: no visible global function definition for ‘sfLibrary’
fun.load.hals.fill: no visible global function definition for
  ‘sfExport’
fun.load.hals.fill: no visible global function definition for
  ‘sfLibrary’
fun.load.widals.a: no visible global function definition for ‘sfExport’
fun.load.widals.a: no visible global function definition for
  ‘sfLibrary’
fun.load.widals.fill: no visible global function definition for
  ‘sfExport’
fun.load.widals.fill: no visible global function definition for
  ‘sfLibrary’
unif.mh: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rnorm runif sfExport sfLibrary
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
File ‘widals/libs/widals.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘fuzzyjoin’
Error in re-building vignettes:
  ...
If you use data from the unvotes package, please cite the following:

Erik Voeten "Data and Analyses of Voting in the UN General Assembly" Routledge Handbook of International Organization, edited by Bob Reinalda (published May 27, 2013)
Quitting from lines 70-78 (united_nations.Rmd) 
Error: processing vignette ‘united_nations.Rmd’ failed with diagnostics:
there is no package called 'fuzzyjoin'
Execution halted
Bundesliga.Mannschaft: no visible global function definition for ‘data’
Bundesliga.Mannschaft: no visible binding for global variable
  ‘Bundesliga’
Bundesliga.Tabelle: no visible global function definition for ‘data’
Bundesliga.Tabelle: no visible binding for global variable ‘Bundesliga’
Bundesliga.XML: no visible global function definition for ‘data’
Bundesliga.XML: no visible binding for global variable ‘Bundesliga’
sens.spec: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘wikibooks/R/Bundesliga.Mannschaft.R’:
  data(Bundesliga)
File ‘wikibooks/R/Bundesliga.Tabelle.R’:
  data(Bundesliga)
File ‘wikibooks/R/Bundesliga.XML.R’:
  data(Bundesliga)
See section ‘Good practice’ in ‘?data’.
wilcox.selection.split: no visible global function definition for
  ‘pnorm’
wilcox.test2: no visible global function definition for ‘wilcox.test’
Undefined global functions or variables:
  pnorm wilcox.test
Consider adding
  importFrom("stats", "pnorm", "wilcox.test")
to your NAMESPACE file.
Cs: no visible global function definition for ‘wilcox.test’
Don: no visible global function definition for ‘points’
Don: no visible global function definition for ‘chisq.test’
Lixn: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  chisq.test pchisq points wilcox.test
Consider adding
  importFrom("graphics", "points")
  importFrom("stats", "chisq.test", "pchisq", "wilcox.test")
to your NAMESPACE file.
plotTrait: no visible global function definition for ‘plot’
plotTrait: no visible global function definition for ‘points’
plotTrait: no visible global function definition for ‘legend’
test.windex: no visible global function definition for ‘hist’
test.windex: no visible global function definition for ‘abline’
test.windex: no visible global function definition for ‘legend’
windex: no visible global function definition for ‘sd’
windex: no visible global function definition for ‘var’
windex: no visible global function definition for ‘dist’
windex: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  abline dist hist legend plot points quantile sd var
Consider adding
  importFrom("graphics", "abline", "hist", "legend", "plot", "points")
  importFrom("stats", "dist", "quantile", "sd", "var")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/windfarmGA.Rcheck/00install.out’ for details.
File ‘wingui/libs/wingui.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
dbayes: no visible global function definition for ‘mahalanobis’
dbayes: no visible global function definition for ‘var’
wmd: no visible global function definition for ‘cor’
wmd: no visible global function definition for ‘var’
Undefined global functions or variables:
  cor mahalanobis var
Consider adding
  importFrom("stats", "cor", "mahalanobis", "var")
to your NAMESPACE file.
fit,Leader: no visible global function definition for ‘lm’
plotfit,Leader: no visible global function definition for ‘par’
plotfit,Leader: no visible global function definition for ‘plot’
Undefined global functions or variables:
  lm par plot
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "lm")
to your NAMESPACE file.
'library' or 'require' call to ‘tm’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
File ‘wordcloud/libs/wordcloud.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘plyr’ ‘reshape2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
wordmatch: no visible global function definition for ‘llply’
wordmatch : <anonymous>: no visible global function definition for
  ‘llply’
wordmatch: no visible global function definition for ‘melt’
wordmatch: no visible global function definition for ‘count’
Undefined global functions or variables:
  count llply melt
pickList : <anonymous>: no visible global function definition for
  ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Running examples in ‘WordR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: addFlexTables
> ### Title: Read Word document with bookmarks and create other Word document
> ###   with rendered tables in place.
> ### Aliases: addFlexTables
> 
> ### ** Examples
> 
> library(ReporteRs)
Loading required package: ReporteRsjars
> ft_mtcars <- vanilla.table(mtcars)
> ft_iris <- vanilla.table(iris)
> FT <- list(ft_mtcars=ft_mtcars,ft_iris=ft_iris)
> addFlexTables(
+   paste(examplePath(),'templates/templateFT.docx',sep = ''),
+   paste(examplePath(),'results/resultFT.docx',sep = ''),
+   FT)
Error in writeDoc.docx(doc, docxOut) : 
  writeDoc: Cannot write to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/WordR/examples/results/resultFT.docx
Calls: addFlexTables -> <Anonymous> -> writeDoc.docx
Execution halted
File ‘wordspace/libs/wordspace.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
simul.wsvm: no visible binding for global variable ‘mixture.example’
wsvm.boost: no visible global function definition for ‘plot’
Undefined global functions or variables:
  mixture.example plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Rd file 'simul.wsvm.Rd':
  \usage lines wider than 90 characters:
         simul.wsvm(set.seeds = 123, obs.num = 1000, mu = c(0,0), cov.mat = 0.2*diag(2), X = NULL, Y = NULL)

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

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

These lines will be truncated in the PDF manual.
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.
Running examples in ‘XGR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ImmunoBase
> ### Title: Immune-disease associated variants, regions and genes from
> ###   ImmunoBase (hg19)
> ### Aliases: ImmunoBase
> ### Keywords: datasets
> 
> ### ** Examples
> 
> ImmunoBase <- xRDataLoader(RData.customised='ImmunoBase')
'ImmunoBase' (from http://galahad.well.ox.ac.uk/bigdata/ImmunoBase.RData) has been loaded into the working environment (at 2018-02-28 18:43:29)
> names(ImmunoBase)
 [1] "AA"  "AS"  "ATD" "CEL" "CRO" "IBD" "IGE" "JIA" "MS"  "NAR" "PBC" "PSC"
[13] "PSO" "RA"  "SJO" "SLE" "SSC" "T1D" "UC"  "VIT"
> str(ImmunoBase$AS)
List of 5
 $ disease       : chr "Ankylosing Spondylitis (AS)"
 $ variants      :Error in FUN(X[[i]], ...) : 
  no slot of name "elementType" for this object of class "GRanges"
Calls: str ... <Anonymous> -> str -> str.default -> sapply -> lapply -> FUN
Execution halted
XHWE: no visible global function definition for ‘read.table’
result: no visible global function definition for ‘pchisq’
result: no visible global function definition for ‘rbinom’
result: no visible global function definition for ‘rmultinom’
Undefined global functions or variables:
  pchisq rbinom read.table rmultinom
Consider adding
  importFrom("stats", "pchisq", "rbinom", "rmultinom")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  +.CellStyle CellBlock.default CellStyle.default
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
.xssfcolor: no visible global function definition for ‘col2rgb’
Undefined global functions or variables:
  col2rgb
Consider adding
  importFrom("grDevices", "col2rgb")
to your NAMESPACE file.
R5.value.default: no visible binding for global variable ‘data.table’
R5.value.default: no visible global function definition for
  ‘as.data.table’
R5.value.parse: no visible binding for global variable ‘data.table’
R5.value.parse: no visible global function definition for
  ‘is.data.table’
R5.value.parse: no visible global function definition for
  ‘as.data.table’
stampme: no visible global function definition for ‘flush.console’
stampmsg: no visible global function definition for ‘flush.console’
write.data.table: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  as.data.table data.table flush.console is.data.table write.table
Consider adding
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE file.
File ‘xml2/libs/xml2.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_WriteConnection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard files/directories found at top level:
  ‘Bug.R’ ‘Bugs.html’ ‘Check’ ‘CodeDetails’ ‘DESCRIPTION.in’ ‘Docs’
  ‘FAQ.html’ ‘FIXME_NOW’ ‘GNUmakefile’ ‘GNUmakefile.admin’
  ‘Makevars.in’ ‘MemoryBug.R’ ‘NAMESPACE.in’ ‘NodeFuns’ ‘Notes’
  ‘QuestionSolutions’ ‘README.windows’ ‘Rsamples’ ‘TAGS’
  ‘Todo-orig.html’ ‘Todo.xml’ ‘VersionInfo’ ‘addFinalizer’ ‘checkLinks’
  ‘dotCalls’ ‘expat’ ‘index.html’ ‘index.html.in’ ‘libxml’
  ‘libxml2.9.R’ ‘scrapingData.xml’ ‘testRemoveFinalizers.R’
  ‘testRemoveFinalizers.c’ ‘xpathPointer.xml’
newXMLDoc: no visible binding for global variable ‘doc’
source: no visible binding for global variable ‘use_file’
xmlFlatListTree : f: no visible binding for global variable ‘nodeNames’
xmlFlatListTree : f: no visible binding for global variable ‘idx’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘nodeSet’
xmlFlatListTree : addNode: no visible binding for global variable
  ‘nodeSet’
xmlFlatListTree : addNode: no visible binding for global variable ‘idx’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘nodeNames’
xmlFlatListTree : addNode: no visible binding for global variable
  ‘nodeNames’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘idx’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘parentCount’
xmlFlatListTree : addNode: no visible binding for global variable
  ‘parentCount’
xmlFlatListTree : <anonymous>: no visible binding for global variable
  ‘e’
xmlFlatTree : <anonymous>: no visible binding for global variable ‘e’
Undefined global functions or variables:
  doc e idx nodeNames nodeSet parentCount use_file
Rd file 'makeClassTemplate.Rd':
  \examples lines wider than 100 characters:
     "<doc><part><name>ABC</name><type>XYZ</type><cost>3.54</cost><status>available</status></part></doc>"

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

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

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

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
xpose.gam: no visible global function definition for ‘step.gam’
Undefined global functions or variables:
  step.gam
Running examples in ‘xpose4-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: xpose.bootgam
> ### Title: Title
> ### Aliases: xpose.bootgam
> 
> ### ** Examples
> 
> 
> ## filter out occasion as a covariate as only one value
> all_covs <- xvardef("covariates",simpraz.xpdb)
> some_covs <- all_covs[!(all_covs %in% "OCC") ] 
> 
> ## here only running n=5 replicates to see that things work
> ##   use something like n=100 for resonable results
> boot_gam_obj <- xpose.bootgam(simpraz.xpdb,5,parnam="KA",covnams=some_covs,seed=1234)

Starting bootstrap (max 5 replicates, seed = 1234).
Bootgam progress:

  |                                                                            
  |==============                                                        |  20%Error in step.gam(bam.start, trace = trace, scope, keep = bam.keep) : 
  could not find function "step.gam"
Calls: xpose.bootgam ... evalVis -> withVisible -> eval -> eval -> xpose.gam
Execution halted
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/XR.Rcheck/00install.out’ for details.
File ‘xseq/libs/xseq.so’:
  Found no call to: ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard file/directory found at top level:
  ‘CONTRIBUTORS’
Found the following apparent S3 methods exported but not registered:
  plot.cca print.F.test.cca print.cca print.summary.cca summary.cca
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘yakmoR/libs/yakmoR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bam_to_reads
> ### Title: Convert BAM files into BED files containing the reads overlaping
> ###   the specified annotations.
> ### Aliases: bam_to_reads
> 
> ### ** Examples
> 
> bamfile <- system.file("extdata", "wt_rep1.bam", package = "yCrypticRNAs")
> data(annotations)
> bam_to_reads(bamfile, annotations)
Error in FUN(X[[i]], ...) : failed to build index
  file: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/yCrypticRNAs/extdata/wt_rep1.bam
Calls: bam_to_reads -> .index_bam
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 48-60 (yCrypticRNAs.Rmd) 
Error: processing vignette ‘yCrypticRNAs.Rmd’ failed with diagnostics:
failed to build index
  file: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/yCrypticRNAs/extdata/wt_rep1.bam
Execution halted
.NS.estimator: no visible global function definition for ‘lm’
.NS.estimator: no visible global function definition for ‘coef’
.NS.estimator: no visible global function definition for ‘na.omit’
.NS.estimator: no visible global function definition for ‘resid’
.NSS.estimator: no visible global function definition for ‘lm’
.NSS.estimator: no visible global function definition for ‘coef’
.NSS.estimator: no visible global function definition for ‘na.omit’
.NSS.estimator: no visible global function definition for ‘resid’
NSrates: no visible global function definition for ‘time’
Nelson.Siegel: no visible global function definition for ‘optimize’
Srates: no visible global function definition for ‘time’
Svensson: no visible global function definition for ‘median’
Svensson: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  coef lm median na.omit optimize resid time
Consider adding
  importFrom("stats", "coef", "lm", "median", "na.omit", "optimize",
             "resid", "time")
to your NAMESPACE file.
Rd file 'ECBYieldCurve.Rd':
  \examples lines wider than 100 characters:
     plot(mat.ECB, ECBYieldCurve[i,], type="o", xlab="Maturities structure in years", ylab="Interest rates values")

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

These lines will be truncated in the PDF manual.
kmeansN: no visible global function definition for ‘kmeans’
kmeansN: no visible global function definition for ‘aggregate’
kmeansN2: no visible global function definition for ‘aggregate’
kmeansN2: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  aggregate kmeans sd
Consider adding
  importFrom("stats", "aggregate", "kmeans", "sd")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘deSolve’ ‘triangle’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: ‘loon’
Deprecated license: CC BY-SA 2.0 + file LICENSE
Package suggested but not available for checking: ‘zdat’
Found the following apparent S3 methods exported but not registered:
  cbind.zoocat
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'merge':
  ‘cbind.zoocat’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
.getPath: no visible global function definition for ‘predict’
ZIClass: no visible binding for global variable ‘na.omit’
ZIClass: no visible global function definition for ‘predict’
analyzeClass: no visible global function definition for ‘plot’
calibrate : findmax: no visible global function definition for ‘lowess’
calibrate: no visible global function definition for ‘lm’
calibrate: no visible global function definition for ‘anova’
calibrate: no visible global function definition for ‘coef’
focusGraph: no visible global function definition for ‘dev.list’
getTrain: no visible global function definition for ‘na.omit’
makeClass : selectVars: no visible global function definition for
  ‘as.formula’
predict.ZIClass: no visible global function definition for ‘predict’
processSampleAll: no visible global function definition for ‘predict’
viewResults: no visible global function definition for ‘par’
viewResults: no visible global function definition for ‘plot’
viewResults: no visible global function definition for ‘points’
viewResults: no visible global function definition for ‘text’
zidbDrawVignette: no visible global function definition for ‘dev.size’
zidbDrawVignette: no visible global function definition for ‘par’
zidbDrawVignette: no visible global function definition for ‘dev.cur’
zidbDrawVignette: no visible global function definition for
  ‘rasterImage’
zidbPlotNew: no visible global function definition for ‘par’
zidbPlotNew: no visible global function definition for ‘plot’
Undefined global functions or variables:
  anova as.formula coef dev.cur dev.list dev.size lm lowess na.omit par
  plot points predict rasterImage text
Consider adding
  importFrom("grDevices", "dev.cur", "dev.list", "dev.size")
  importFrom("graphics", "par", "plot", "points", "rasterImage", "text")
  importFrom("stats", "anova", "as.formula", "coef", "lm", "lowess",
             "na.omit", "predict")
to your NAMESPACE file.
File which contains pragma(s) suppressing diagnostics:
  ‘src/third_party/zstd-1.2.0/lib/dictBuilder/divsufsort.c’
ztable.glm: no visible global function definition for ‘confint’
ztable.glm: no visible global function definition for ‘coef’
ztable.nls: no visible global function definition for ‘formula’
Undefined global functions or variables:
  coef confint formula
Consider adding
  importFrom("stats", "coef", "confint", "formula")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  confint.zyp
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
confint.zyp: no visible global function definition for ‘qnorm’
confint.zyp: no visible global function definition for ‘var’
zyp.sen: no visible global function definition for ‘terms’
zyp.sen: no visible global function definition for ‘median’
zyp.trend.csv: no visible global function definition for ‘read.csv’
zyp.trend.csv: no visible global function definition for ‘write.csv’
zyp.yuepilon: no visible global function definition for ‘acf’
zyp.yuepilon: no visible binding for global variable ‘na.pass’
zyp.yuepilon: no visible global function definition for ‘confint’
zyp.yuepilon: no visible global function definition for ‘lm’
zyp.zhang: no visible global function definition for ‘acf’
zyp.zhang: no visible binding for global variable ‘na.pass’
zyp.zhang: no visible global function definition for ‘confint’
zyp.zhang: no visible global function definition for ‘lm’
Undefined global functions or variables:
  acf confint lm median na.pass qnorm read.csv terms var write.csv
Consider adding
  importFrom("stats", "acf", "confint", "lm", "median", "na.pass",
             "qnorm", "terms", "var")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ACTCD.Rcheck/00install.out’ for details.
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/anapuce.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Anthropometry.Rcheck/00install.out’ for details.
Running examples in ‘ApacheLogProcessor-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: read.multiple.apache.access.log
> ### Title: Reads multiple files of apache web server.
> ### Aliases: read.multiple.apache.access.log
> 
> ### ** Examples
> 
> path <- system.file("examples", package="ApacheLogProcessor")
> path <- paste(path, "/", sep="")
> 
> #read multiple gziped logs with the prefix m_access_log_combined_
> dfLog <- read.multiple.apache.access.log(path, "m_access_log_combined_")
[1] "Starting the log processing. This may take a long time..."
[1] "Processing file  m_access_log_combined_1.log.gz"
[1] "Unziping  m_access_log_combined_1.log.gz"
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/ApacheLogProcessor/examples/m_access_log_combined_1.log': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: read.multiple.apache.access.log -> write -> cat -> file
Execution halted
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/aroma.affymetrix.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ARTP.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [8s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ashr)
  > 
  > test_check("ashr")
  ── 1. Failure: logF error with df=(10,10) gives similar answers to normal error 
  ash.norm.out$result$PosteriorMean not equal to ash.logF.out$result$PosteriorMean.
  1/100 mismatches
  [14] -0.238 - -1.96 == 1.73
  
  ── 2. Failure: new results match old ones  (@test_old_vs_new.R#8)  ─────────────
  get_pm(oldres) not equal to get_pm(z.ash).
  3/100 mismatches (average diff: 1.83)
  [14] -3.21 - -1.525 == -1.68
  [24] -2.97 - -1.096 == -1.87
  [67] -2.77 - -0.825 == -1.94
  
  ── 3. Failure: new results match old ones  (@test_old_vs_new.R#9)  ─────────────
  get_psd(oldres) not equal to get_psd(z.ash).
  3/100 mismatches (average diff: 1.01)
  [14] 0.723 - 1.93 == -1.212
  [24] 0.728 - 1.75 == -1.020
  [67] 0.764 - 1.57 == -0.809
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 82 SKIPPED: 1 FAILED: 3
  1. Failure: logF error with df=(10,10) gives similar answers to normal error (@test_logF.R#21) 
  2. Failure: new results match old ones  (@test_old_vs_new.R#8) 
  3. Failure: new results match old ones  (@test_old_vs_new.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘ASIP-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: arvi
> ### Title: Atmospherically Resistant Vegetation Index
> ### Aliases: arvi
> 
> ### ** Examples
> 
> library (raster)
Loading required package: sp
> library (rgdal)
rgdal: version: 1.2-16, (SVN revision 701)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.2.3, released 2017/11/20
 Path to GDAL shared files: /usr/share/gdal/2.2
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.2-7 
> # Finding the path of the sample satellite image directory.
> # User may define paths directly like "/home/ur_folder" or "C:/ur_folder"
> path <- system.file ("TM_sample", package = "ASIP")
> shapefil <- paste0 (path, "/test.shp")
> arvi (directory = path, crop = "y", ext2crop = shapefil)
OGR data source with driver: ESRI Shapefile 
Source: "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/ASIP/TM_sample/test.shp", layer: "test"
with 1 features
It has 1 fields
Integer64 fields read as strings:  id 
Error in .local(.Object, ...) : Dataset copy failed
Calls: arvi ... <Anonymous> -> new -> initialize -> initialize -> .local
Execution halted
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/assignPOP.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]
  pa.c:247:2: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/audio.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BANFF.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Bayesthresh.Rcheck/00install.out’ for details.
Running examples in ‘biclique-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bi.format
> ### Title: Add number of vertices and edges to the input file
> ### Aliases: bi.format
> 
> ### ** Examples
> 
> bi.format(system.file("extdata", "example2.el", package = "biclique"))
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/biclique/extdata/example2.el': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: bi.format -> cat -> file
Execution halted
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/biclust.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bigpca.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bioimagetools.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BioPhysConnectoR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BlockFeST.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: next may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/boclust.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/cem.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: ggmap
Loading required package: ggplot2
Loading required package: RCurl
Loading required package: bitops
Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=Chicago,%20IL&sensor=false
Warning: geocode failed with status OVER_QUERY_LIMIT, location = "Chicago, IL"
Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=New%20York&sensor=false
Warning: geocode failed with status OVER_QUERY_LIMIT, location = "New York"
Quitting from lines 16-23 (getting-started.Rmd) 
Error: processing vignette ‘getting-started.Rmd’ failed with diagnostics:
undefined columns selected
Execution halted
Found the following significant warnings:
  Note: next may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CHAT.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: possible error in 'log.likelihood(list(latent.space.pos.prop, ': unused argument (edge.list.rows[[dd]]) 
  Note: possible error in 'log.likelihood(list(latent.space.pos.hold, ': unused argument (edge.list.rows[[dd]]) 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CIDnetworks.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CircE.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CircStats.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/climatol.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/clustrd.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/cmm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Combine.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CompetingRisk.Rcheck/00install.out’ for details.
Running examples in ‘Compind-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ci_smaa_constr
> ### Title: Constrained stochastic multi-objective acceptability analysis
> ###   (C-SMAA)
> ### Aliases: ci_smaa_constr
> 
> ### ** Examples
> 
> data(EU_NUTS1)
> 
> # Standard SMAA 
> test <- ci_smaa_constr(EU_NUTS1,c(2,3), rep=200, label = EU_NUTS1[,1])
> source("http://www.phaget4.org/R/myImagePlot.R") 
Warning in file(filename, "r", encoding = encoding) :
  URL 'http://www.phaget4.org/R/myImagePlot.R': status was 'Failure when receiving data from the peer'
Error in file(filename, "r", encoding = encoding) : 
  cannot open the connection to 'http://www.phaget4.org/R/myImagePlot.R'
Calls: source -> file
Execution halted
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CorReg.Rcheck/00install.out’ for details.
Found the following significant warnings:
  bdsmatrix_stub.h:41:5: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  bdsmatrix_stub.h:44:12: warning: return makes integer from pointer without a cast [-Wint-conversion]
  bdsmatrix_stub.h:50:5: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  bdsmatrix_stub.h:53:12: warning: return makes integer from pointer without a cast [-Wint-conversion]
  bdsmatrix_stub.h:97:5: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  bdsmatrix_stub.h:100:12: warning: return from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/coxme.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/cplm.Rcheck/00install.out’ for details.
Running examples in ‘CREAM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CREAM
> ### Title: CREAM is the main function for CORE identification
> ### Aliases: CREAM
> 
> ### ** Examples
> 
> CREAM(system.file("extdata", "A549_Chr21.bed", package = "CREAM"),
+ system.file("extdata", "A549_Chr21_COREs.bed", package = "CREAM"),
+ MinLength = 1000, peakNumMin = 2)
[1] "Please make sure there is no overlap between the input genomic regions. Overlap between the input regions may cause error."
[1] "Identifying window size for each Order"
[1] "Identifying COREs"
[1] "Filtering clusters of low order"
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/CREAM/extdata/A549_Chr21_COREs.bed': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: CREAM -> write.table -> file
Execution halted
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ctsem.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Cyclops.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dartR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  convert_util.cpp:299:20: warning: null destination pointer [-Wformat-overflow=]
  convert_util.cpp:307:20: warning: null destination pointer [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DatABEL.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dbplot)
  Loading required package: dplyr
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  Loading required package: rlang
  
  Attaching package: 'rlang'
  
  The following objects are masked from 'package:testthat':
  
      is_false, is_null, is_true
  
  > library(dplyr)
  > library(ggplot2)
  > 
  > test_check("dbplot")
  ── 1. Failure: Correct binwidth formula is returned  ───────────────────────────
  db_bin(var, binwidth = 10) not equal to rlang::expr(...).
  target, current do not match when deparsed
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 11 SKIPPED: 0 FAILED: 1
  1. Failure: Correct binwidth formula is returned 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/deBInfer.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
  Note: next may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/debug.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
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")
Compiling model
the number of chains is less than 1; sampling not done
Saving compiled model to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/DeLorean/extdata/exact-sizes.rds
Quitting from lines 145-146 (DeLorean.Rmd) 
Error: processing vignette ‘DeLorean.Rmd’ failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/derivmkts.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dhglm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/diffractometry.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/diffusionMap.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/di.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DoE.base.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Dominance.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dvfBm.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
pandoc: Could not fetch https://github.com/paulgovan/eAnalytics/blob/master/inst/images/Dashboard.png?raw=true
HttpExceptionRequest Request {
  host                 = "github.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/paulgovan/eAnalytics/blob/master/inst/images/Dashboard.png"
  queryString          = "?raw=true"
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 ConnectionTimeout
Error: processing vignette ‘eAnalytics.Rmd’ failed with diagnostics:
pandoc document conversion failed with error 67
Execution halted
Running examples in ‘EasyStrata-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: EasyStrata
> ### Title: Function to run EasyStrata (v8.6).
> ### Aliases: EasyStrata
> 
> ### ** Examples
> 
> extDataDir=system.file("extdata", package="EasyStrata")
> ## Example Pipeline:
> ecfPipe=paste(extDataDir,"example_pipeline.ecf",sep="/")
> EasyStrata(ecfPipe)
Warning message:
In file(fileLog, open = "a") :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/EasyStrata/extdata/example_pipeline.ecf.out': Read-only file system
Execution halted
Found the following significant warnings:
  Note: next may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ecospat.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: possible error in 'savePlot(filename = "Clustplot", ': unused argument (restoreConsole = TRUE) 
  Note: possible error in 'savePlot(filename = "MCAplotindclasse", ': unused argument (restoreConsole = TRUE) 
  Note: possible error in 'savePlot(filename = "MCAplotvar", ': unused argument (restoreConsole = TRUE) 
  Note: possible error in 'savePlot(filename = "MCAplotind", ': unused argument (restoreConsole = TRUE) 
  Note: possible error in 'savePlot(filename = "MCAplotquantisup", ': unused argument (restoreConsole = TRUE) 
  Note: possible error in 'savePlot(filename = "Ellipse", ': unused argument (restoreConsole = TRUE) 
  Note: possible error in 'savePlot(filename = "Lisib", ': unused argument (restoreConsole = TRUE) 
  Note: possible error in 'savePlot(filename = "Density", ': unused argument (restoreConsole = TRUE) 
  Note: possible error in 'savePlot(filename = "Densitypop", ': unused argument (restoreConsole = TRUE) 
  Note: possible error in 'savePlot(filename = "barplotgr", ': unused argument (restoreConsole = TRUE) 
  Note: possible error in 'savePlot(filename = paste("barvarclus", ': unused argument (restoreConsole = TRUE) 
  Note: possible error in 'hsv(h = 1, s = 1, v = 1, ': unused argument (1) 
  Note: possible error in 'hsv(h = 1, s = 0.4 + ': unused argument (1) 
  Note: possible error in 'hsv(h = a * i, s = 1, ': unused argument (1) 
  Note: possible error in 'hsv(h = a * m, s = 1, ': unused argument (1) 
  Note: possible error in 'hsv(h = a * m, s = 0.4 + ': unused argument (1) 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/EnQuireR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/EnvStats.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/EpiWeek.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/esmprep.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/eVenn.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: iteration 7 invokes undefined behavior [-Waggressive-loop-optimizations]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/expoRkit.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FACTscorer.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fArma.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FastRWeb.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fifer.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FindIt.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FisherEM.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fpc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/frailtyHL.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(funrar)
  > 
  > test_check("funrar")
  ── 1. Error: 'distinctiveness_dimensions()' outputs good objects (@test-rarity_d
  bad value
  1: expect_true(di_dim %>% vapply(class, c("char")) %>% =="matrix" %>% all()) at testthat/test-rarity_dimensions.R:42
  2: quasi_label(enquo(object), label)
  3: force(quo)
  4: enquo(object)
  
  ── 2. Error: 'distinctiveness_dimensions()' works with sparse matrices (@test-ra
  bad value
  1: expect_true(sparse_di_dim %>% vapply(class, c("char")) %>% =="dgeMatrix" %>% all()) at testthat/test-rarity_dimensions.R:94
  2: quasi_label(enquo(object), label)
  3: force(quo)
  4: enquo(object)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 167 SKIPPED: 0 FAILED: 2
  1. Error: 'distinctiveness_dimensions()' outputs good objects (@test-rarity_dimensions.R#42) 
  2. Error: 'distinctiveness_dimensions()' works with sparse matrices (@test-rarity_dimensions.R#94) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  convert_util.cpp:299:20: warning: null destination pointer [-Wformat-overflow=]
  convert_util.cpp:307:20: warning: null destination pointer [-Wformat-overflow=]
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GenABEL.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GeneFeST.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/geo.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gettingtothebottom.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gfer.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GPGame.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GPseq.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GroupSeq.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hbmem.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: possible error in 'dgpd(x, xi = a, mu = 0, ': unused arguments (xi = a, mu = 0, beta = 1 - a) 
  Note: possible error in 'pgpd(q, xi = a, mu = 0, ': unused arguments (xi = a, mu = 0, beta = 1 - a) 
  Note: possible error in 'qgpd(p, xi = a, mu = 0, ': unused arguments (xi = a, mu = 0, beta = 1 - a) 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/HiDimMaxStable.Rcheck/00install.out’ for details.
Running examples in ‘highcharter-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hchart.survfit
> ### Title: Plot survival curves using Highcharts
> ### Aliases: hchart.survfit
> 
> ### ** Examples
> 
> 
> # Plot Kaplan-Meier curves
> require("survival")
Loading required package: survival

 *** caught segfault ***
address 0x80000001a, cause 'memory not mapped'
Segmentation fault
Error in re-building vignettes:
  ...
Highcharts (www.highcharts.com) is a Highsoft software product which is
not free for commercial and Governmental use

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

trying URL ‘https://code.highcharts.com/mapdata/countries/nz/nz-all.js’
Content type 'application/x-javascript' length 36810 bytes (35 KB)
==================================================
downloaded 35 KB

trying URL ‘https://code.highcharts.com/mapdata/custom/usa-and-canada.js’
Content type 'application/x-javascript' length 134466 bytes (131 KB)
==================================================
downloaded 131 KB

trying URL ‘https://code.highcharts.com/mapdata/countries/us/us-ca-all.js’
Content type 'application/x-javascript' length 40824 bytes (39 KB)
==================================================
downloaded 39 KB

trying URL ‘https://code.highcharts.com/mapdata/countries/us/us-all.js’
Content type 'application/x-javascript' length 66923 bytes (65 KB)
==================================================
downloaded 65 KB

trying URL ‘https://code.highcharts.com/mapdata/countries/us/us-all.js’
Content type 'application/x-javascript' length 66923 bytes (65 KB)
==================================================
downloaded 65 KB

trying URL ‘https://code.highcharts.com/mapdata/countries/fj/fj-all.js’
Content type 'application/x-javascript' length 20412 bytes (19 KB)
==================================================
downloaded 19 KB

Quitting from lines 110-132 (charting-maps.Rmd) 
Error: processing vignette ‘charting-maps.Rmd’ failed with diagnostics:
Please install xml2 package
Execution halted
Found the following significant warnings:
  Note: next may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hmmm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/HMMpa.Rcheck/00install.out’ for details.
Running ‘test-all.R’ [1s/2s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("hrbrthemes")
  Loading required package: hrbrthemes
  ── 1. Error: we can do something (@test-hrbrthemes.R#60)  ──────────────────────
  cannot open the connection
  1: import_roboto_condensed() at testthat/test-hrbrthemes.R:60
  2: suppressWarnings(suppressMessages(extrafont::font_import(rc_font_dir, prompt = FALSE)))
  3: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  4: suppressMessages(extrafont::font_import(rc_font_dir, prompt = FALSE))
  5: withCallingHandlers(expr, message = function(c) invokeRestart("muffleMessage"))
  6: extrafont::font_import(rc_font_dir, prompt = FALSE)
  7: ttf_import(paths, recursive, pattern)
  8: ttf_extract(ttfiles)
  9: gzcopy_exclude(paste(tmpfiles[i], ".afm", sep = ""), paste(outfiles[i], ".afm.gz", 
         sep = ""), delete = TRUE, exclusions = c("^Characters"))
  10: gzfile(dest, "w")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 3 SKIPPED: 0 FAILED: 1
  1. Error: we can do something (@test-hrbrthemes.R#60) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IDTurtle.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/intpoint.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: possible error in 'get.smiles(x, aromatic = T, ': unused arguments (aromatic = T, type = "generic") 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/iqspr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: next may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IRISMustangMetrics.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kmc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lava.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: next may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/liso.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LncPriCNet.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘nsimp’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/localdepth.Rcheck/00install.out’ for details.
Found the following significant warnings:
  global.c:548:5: warning: specified bound 256 equals the size of the destination [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LogConcDEAD.Rcheck/00install.out’ for details.
Found the following significant warnings:
  cvrout.c:286:35: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LogicOpt.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lqmm.Rcheck/00install.out’ for details.
Running examples in ‘MAGNAMWAR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: FormatMCLFastas
> ### Title: Format all raw GenBank fastas to single OrthoMCL compatible
> ###   fasta file
> ### Aliases: FormatMCLFastas
> 
> ### ** Examples
> 
> 
> dir <- system.file('extdata', 'fasta_dir', package='MAGNAMWAR')
> dir <- paste(dir,'/',sep='')
> formatted_file <- FormatMCLFastas(dir)
Warning in file.remove(outfile) :
  cannot remove file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/MAGNAMWAR/extdata/fasta_dir/MCLformatted_all.fasta', reason 'Read-only file system'
Writing out to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/MAGNAMWAR/extdata/fasta_dir/MCLformatted_all.fasta 
Warning in file(description = file.out, open = open) :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/MAGNAMWAR/extdata/fasta_dir/MCLformatted_all.fasta': Read-only file system
Error in file(description = file.out, open = open) : 
  cannot open the connection
Calls: FormatMCLFastas -> <Anonymous> -> file
Execution halted
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MagneticMap.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: possible error in 'writeLines(as.character(yy), ': unused argument (file = outfile) 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/matR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mclcar.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mdhglm.Rcheck/00install.out’ for details.
Running examples in ‘MetaSubtract-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: meta.subtract
> ### Title: Subtracts GWAS results from one or more cohorts from the
> ###   meta-GWAS results
> ### Aliases: meta.subtract
> ### Keywords: Correct meta-GWAS results Leave-one-out
> 
> ### ** Examples
> 
> metafile="meta_results.txt"
> cohortfiles=c("cohort1_results.txt","cohort2_results.txt")
> # Subtract summary statistics of the two cohorts from the meta summary statistics in metafile.
> # Genomic control correction of the imported meta summary statistics will be undone using 
> # lambda.meta. Genomic control will be applied to the corrected meta summary statistics 
> # (gc_meta=TRUE by default) based on a lambda derived from the new meta summary statistics 
> # (calculate_lambda.meta=TRUE by default). The cohorts summary statistics will always be first 
> # corrected for genomic control before subtracting them from the meta summary statistics. By 
> # default, the lambda will be calculated from the data (calculate_lambdas.cohort=TRUE by default).
> m1<-meta.subtract(metafile=metafile, cohortfiles=cohortfiles, lambda.meta=1.046, 
+       dir=system.file("extdata", package="MetaSubtract"))
[1] "Thu Mar  1 16:44:38 2018"
Reading meta_results.txt 
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file 'MetaSubtract.log': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: meta.subtract -> write.table -> file
Execution halted
Warning in utils::download.file(extDB, destfile = localDB, quiet = T) :
  URL https://github.com/cflagg/metScanR/raw/master/data/metScanR_DB.rda: cannot open destfile '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/metScanR/data/metScanR_DB.rda', reason 'Read-only file system'
Warning in utils::download.file(extDB, destfile = localDB, quiet = T) :
  download had nonzero exit status
Warning in utils::download.file(extTermsDB, destfile = localTermsDB, quiet = T) :
  URL https://github.com/cflagg/metScanR/raw/master/data/metScanR_terms.rda: cannot open destfile '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/metScanR/data/metScanR_terms.rda', reason 'Read-only file system'
Warning in utils::download.file(extTermsDB, destfile = localTermsDB, quiet = T) :
  download had nonzero exit status

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

Probably some imports need to be declared in the NAMESPACE file.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mixor.Rcheck/00install.out’ for details.
Running ‘run-base.R’ [311s/402s]
Running the tests in ‘tests/run-base.R’ failed.
Complete output:
  > library(testthat)
  > test_check("mlr", filter = "base")
  Loading required package: mlr
  Loading required package: ParamHelpers
  ── 1. Error: check measure calculations (@test_base_measures.R#637)  ───────────
  object 'mldr_HL' not found
  1: expect_equal(mldr:::mldr_HL(multi.y, multi.p), measureMultilabelHamloss(multi.y, 
         multi.p)) at testthat/test_base_measures.R:637
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: mldr:::mldr_HL
  5: get(name, envir = asNamespace(pkg), inherits = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2652 SKIPPED: 8 FAILED: 1
  1. Error: check measure calculations (@test_base_measures.R#637) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [5s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(Momocs)
  This is Momocs 1.2.2
  
  Attaching package: 'Momocs'
  
  The following object is masked from 'package:stats':
  
      filter
  
  The following object is masked from 'package:base':
  
      table
  
  > 
  > test_check("Momocs")
  ── 1. Error: filter works fine (@test-nse.R#62)  ───────────────────────────────
  bad value
  1: expect_true(x_lite$fac %>% sapply(nlevels) %>% ==1 %>% all) at testthat/test-nse.R:62
  2: quasi_label(enquo(object), label)
  3: force(quo)
  4: enquo(object)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 159 SKIPPED: 1 FAILED: 1
  1. Error: filter works fine (@test-nse.R#62) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MortHump.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mstR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: possible error in 'theme(axis.text.x = element_text(size = 6, ': formal argument "axis.text.x" matched by multiple actual arguments 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/multilevelPSA.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: next may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MultiPhen.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: next may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mvmeta.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: next may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ncappc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ncf.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
  Note: next may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nimble.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/novelist.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/npde.Rcheck/00install.out’ for details.
Compilation used the following non-portable flag(s):
  ‘-Wno-deprecated-declarations’ ‘-Wno-ignored-attributes’
  ‘-Wno-int-in-bool-context’ ‘-Wno-misleading-indentation’
  ‘-Wno-pragmas’ ‘-Wno-unknown-pragmas’ ‘-Wno-unused-function’
  ‘-Wno-unused-local-typedefs’ ‘-Wno-unused-parameter’ ‘-Wvla’
including flag(s) suppressing warnings
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/OpenRepGrid.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [13s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > test_check("openxlsx")
  Loading required package: openxlsx
  ── 1. Error: loadWorkbook from different sources (@test-read_sources.R#49)  ────
  subscript out of bounds
  1: expect_true(all.equal.Workbook(wb_url, wb_file), "Loading from URL vs local not equal") at testthat/test-read_sources.R:49
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: all.equal.Workbook(wb_url, wb_file)
  5: sapply(1:nSheets, function(i) isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]])))
  6: lapply(X = X, FUN = FUN, ...)
  7: FUN(X[[i]], ...)
  8: isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]]))
  9: all.equal(x$colWidths[[i]], y$colWidths[[i]])
  10: all.equal.list(x$colWidths[[i]], y$colWidths[[i]])
  11: attr.all.equal(target, current, ...)
  12: mode(current)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 505 SKIPPED: 2 FAILED: 1
  1. Error: loadWorkbook from different sources (@test-read_sources.R#49) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in .local(x, ...) :
  The following sequence IDs are not in the dataset: 311, 222
Warning in .local(x, ...) :
  The following sequence IDs are not in the dataset: 311, 222
Warning in (if (out_format(c("latex", "sweave", "listings"))) sanitize_fn else paste0)(path,  :
  replaced special characters in figure filename "figs/OutbreakTools-out.width==".8\\textwidth"" -> "figs/OutbreakTools-out.width___.8\\textwidth_"
Warning in (if (out_format(c("latex", "sweave", "listings"))) sanitize_fn else paste0)(path,  :
  dots in figure paths replaced with _ ("figs/OutbreakTools-out_width____8//textwidth_")
Warning: The shape palette can deal with a maximum of 6 discrete values because
more than 6 becomes difficult to discriminate; you have 11. Consider
specifying shapes manually if you must have them.
Warning: Removed 58 rows containing missing values (geom_point).
Warning: `show_guide` has been deprecated. Please use `show.legend` instead.
Warning: `show_guide` has been deprecated. Please use `show.legend` instead.
Warning in download.file(url, destfile = tmp, quiet = !messaging, mode = "wb") :
  cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=51.516439,-0.171146&zoom=14&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false': HTTP status was '403 Forbidden'
Quitting from lines 1022-1023 (OutbreakTools.Rnw) 
Error: processing vignette ‘OutbreakTools.Rnw’ failed with diagnostics:
cannot open URL ‘http://maps.googleapis.com/maps/api/staticmap?center=51.516439,-0.171146&zoom=14&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false’
Execution halted
Found the following significant warnings:
  Note: next may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PAactivPAL.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: next may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/packrat.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [9s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(palm)
  Loading required package: Rcpp
  > 
  > test_check("palm")
  
  ── 1. Failure: Matern fitting (@test-fits.r#55)  ───────────────────────────────
  `par.fit.matern` not equal to c(38.76459565, 0.73561864, 0.05327295).
  2/3 mismatches (average diff: 0.0646)
  [1] 38.892 - 38.765 ==  0.12698
  [2]  0.733 -  0.736 == -0.00229
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 11 SKIPPED: 0 FAILED: 1
  1. Failure: Matern fitting (@test-fits.r#55) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pdolsms.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pendensity.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/penRvine.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phalen.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: possible error in 'try(xtriple, ftriple, ': unused arguments (lfmid, 1, 2) 
  Note: possible error in 'try(xtriple, ftriple, ': unused arguments (rfmid, 2, 3) 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phyreg.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: next may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PhySortR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/picante.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/plsRglm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pmlr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PopGenome.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: next may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PortfolioAnalytics.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/powerCompRisk.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: possible error in 'geneSim(as.character(Sims[[1]][i]), ': unused arguments (ont = "BP", organism = wh_organism) 
  Note: possible error in 'geneSim(as.character(Sims[[1]][i]), ': unused arguments (ont = "MF", organism = wh_organism) 
  Note: possible error in 'geneSim(as.character(Sims[[1]][i]), ': unused arguments (ont = "CC", organism = wh_organism) 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ppiPre.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: possible error in 'psf(data = dataIn1, n.ahead = nextVal)': unused argument (n.ahead = nextVal) 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PredictTestbench.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/processmapR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PROFANCY.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/profileR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/psidR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PsiHat.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PSM.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Quitting from lines 126-132 (Maps_and_Timeseries_Plots.Rmd) 
Error: processing vignette ‘Maps_and_Timeseries_Plots.Rmd’ failed with diagnostics:
cannot open URL ‘http://maps.google.com/maps/api/staticmap?center=47,-118&zoom=7&size=640x640&maptype=roadmap&format=png32&sensor=true’
Execution halted
Running ‘testthat.R’ [4s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pxweb)
  pxweb: R tools for PX-WEB API.
  Copyright (C) 2014 Mans Magnusson, Leo Lahti, Love Hansson
  https://github.com/ropengov/pxweb
  
  New PXWEB API(s):
   - prognos.konj.se
   - data.ssb.no
   - pxweb.asub.ax
   - makstat.stat.gov.mk
   - data.csb.gov.lv
  
  Use update_pxweb_apis() to update the api catalogue.
  > test_check("pxweb")
  ── 1. Failure: pxweb_api_class (@test-pxweb_api_class.R#20)  ───────────────────
  NOT(success)
  
  ── 2. Failure: pxweb_api_class (@test-pxweb_api_class.R#22)  ───────────────────
  "foo.bar" %in% unlist(lapply(api_catalogue(), function(X) X$api)) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 98 SKIPPED: 16 FAILED: 2
  1. Failure: pxweb_api_class (@test-pxweb_api_class.R#20) 
  2. Failure: pxweb_api_class (@test-pxweb_api_class.R#22) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/QoLR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: next may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/QuantTools.Rcheck/00install.out’ for details.
Running examples in ‘R2GUESS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as.ESS.object
> ### Title: Compiles the main input and output files from a previous run of
> ###   'R2GUESS' and creates an ESS object.
> ### Aliases: as.ESS.object
> 
> ### ** Examples
> 
> dataX <- "data-X-C-CODE.txt"
> dataY <- "data-Y-ALL-C-CODE.txt"
> 
> path.input <- system.file("Input", package="R2GUESS")
> path.output <- system.file("Output", package="R2GUESS")
> path.par <- system.file("extdata", package="R2GUESS")
> file.par <- "Par_file_example_Hopx.xml"
> root.file.output <- "Example-GUESS-Y-Hopx"
> label.Y <- c("ADR","Fat","Heart","Kidney")
> my.env <- new.env()
> data(MAP.file,envir=my.env)
> MAP.file <- my.env$MAP.file
> modelY_Hopx <-as.ESS.object(dataY=dataY,dataX=dataX,path.input=path.input,
+     path.output=path.output,root.file.output=root.file.output,label.X=NULL,
+     label.Y=label.Y,path.par=path.par,file.par=file.par,MAP.file=MAP.file)
Warning in gzfile(file, "wb") :
  cannot open compressed file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/R2GUESS/Output/Example-GUESS-Y-Hopx_output_best_visited_models.RData', probable reason 'Read-only file system'
Error in gzfile(file, "wb") : cannot open the connection
Calls: as.ESS.object -> get.best.models -> save -> gzfile
Execution halted
Found the following significant warnings:
  Note: possible error in 'unlist(strsplit(.$removeSpaces(.$ivField)), ': unused argument (fixed = TRUE) 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/R2STATS.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ramidst.Rcheck/00install.out’ for details.
Found the following significant warnings:
  intersection.cc:384:1: warning: ‘%g’ directive writing 12 bytes into a region of size between 0 and 41 [-Wformat-overflow=]
  intersection.cc:384:1: warning: ‘%g’ directive writing 12 bytes into a region of size between 0 and 42 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RCALI.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [28s/46s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rdomains)
  > 
  > test_check("rdomains")
  DMOZ Data saved to the following destination: . 
  ── 1. Error: shallalist cat (@test-shalla-cat.R#5)  ────────────────────────────
  Timeout was reached: Resolving timed out after 10000 milliseconds
  1: get_shalla_data() at testthat/test-shalla-cat.R:5
  2: curl_download("http://www.shallalist.de/Downloads/shallalist.tar.gz", tmp)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2 SKIPPED: 1 FAILED: 1
  1. Error: shallalist cat (@test-shalla-cat.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/refund.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/relax.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RGoogleAnalytics.Rcheck/00install.out’ for details.
Found the following significant warnings:
  atkClasses.c:1050:25: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  atkClasses.c:1058:34: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  atkClasses.c:1397:51: warning: passing argument 2 of ‘object_class->active_descendant_changed’ from incompatible pointer type [-Wincompatible-pointer-types]
  gdkFuncs.c:6000:36: warning: passing argument 2 of ‘gdk_window_get_user_data’ from incompatible pointer type [-Wincompatible-pointer-types]
  gioClasses.c:1948:17: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gioClasses.c:1964:20: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gtkClasses.c:8665:28: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gtkClasses.c:11110:21: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RGtk2.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’,
    ‘R_GlobalContext’
File ‘rJava/libs/rJava.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Note: possible error in 'write(self$rules, file = paste0(fileName, ': unused argument (col.names = NA) 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RKEEL.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: next may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rlda.Rcheck/00install.out’ for details.
Found the following significant warnings:
  newmat5.cpp:525:69: warning: throw will always call terminate() [-Wterminate]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rmixmod.Rcheck/00install.out’ for details.
File ‘Rmixmod/libs/Rmixmod.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rmpi.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RM.weights.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [1s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(RonFHIR)
  > 
  > test_check("RonFHIR")
  ── 1. Error: fhirClient checks only connects to FHIR Servers STU 3 (@test-fhirCl
  Could not connect to endpoint
  1: expect_silent(fhirClient$new("http://test.fhir.org/r3")) at testthat/test-fhirClient.R:8
  2: quasi_capture(enquo(object), evaluate_promise)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: withr::with_output_sink(temp, withCallingHandlers(withVisible(code), warning = handle_warning, 
         message = handle_message))
  5: force(code)
  6: withCallingHandlers(withVisible(code), warning = handle_warning, message = handle_message)
  7: withVisible(code)
  8: eval_bare(get_expr(quo), get_env(quo))
  9: fhirClient$new("http://test.fhir.org/r3")
  10: .subset2(public_bind_env, "initialize")(...)
  11: initialize(self, private, endpoint)
  12: getJSON(paste(endpoint, "metadata", sep = ""))
  13: tryCatch(GET(URLencode(url), accept_json()), error = function(e) {
         stop("Could not connect to endpoint")
     })
  14: tryCatchList(expr, classes, parentenv, handlers)
  15: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  16: value[[3L]](cond)
  17: stop("Could not connect to endpoint")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 77 SKIPPED: 0 FAILED: 1
  1. Error: fhirClient checks only connects to FHIR Servers STU 3 (@test-fhirClient.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rootWishart.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: next may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RSEIS.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: meteofrance
> ### Title: Snow Weather Data in France
> ### Aliases: meteofrance
> 
> ### ** Examples
> 
>  
> 
> library(ggmap)
Loading required package: ggplot2
> data(meteofrance)
> 
> dates <- as.Date(meteofrance$timestamp)
> 
> data=meteofrance[dates==dates[1],]
> 
> 
> 
> map <- get_map(location ="France", zoom = 6)
Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=France&zoom=6&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false
Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=France&sensor=false
Warning: geocode failed with status OVER_QUERY_LIMIT, location = "France"
Error in data.frame(ll.lat = ll[1], ll.lon = ll[2], ur.lat = ur[1], ur.lon = ur[2]) : 
  arguments imply differing number of rows: 0, 1
Calls: get_map -> get_googlemap -> data.frame
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rsunlight.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: next may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RSurvey.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RWildbook.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: possible error in 'saveSession(force = TRUE)': unused argument (force = TRUE) 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rz.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SAENET.Rcheck/00install.out’ for details.
Running examples in ‘satscanMapper-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: satscanMapper
> ### Title: Function to map Results data produced by a SaTScan (TM) cluster
> ###   analysis
> ### Aliases: satscanMapper
> 
> ### ** Examples
> 
> ######
> #
> #  These examples focus on mapping the SaTScan (TM) data after the analysis
> #  has been completed.
> #  See the section on the CreateGeo4SS function for an example of how 
> #  to build a coordinates file (.geo) that matches the satscanMapper 
> #  boundary data.
> #
> ######
> 
> ######
> #
> #  Example # 1 - Mapping existing SaTScan (TM) results - "USStateLung" result files
> #     Make sure SaTScan (TM) results files are still located in the directories
> #     documented in the session saved (.prm) file.
> #
> #     This example maps data for the US States containing circular clusters.
> #
> #   Get location of .prm file and location to write mapping output files
> #
> 
> SSMInstDir <- system.file(package="satscanMapper", "extdata")
> 
> TT =c("Contiguous US States All Lung Cancer Mortality, 2004")
> 
> satscanMapper(resDir=SSMInstDir,                # path to .prm file location for output files. 
+                      prmFile  = "stateLung.prm", 
+                      title    = TT          )
Error in pdf(file = OutputFNpdf, width = vW, height = vH) : 
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/satscanMapper/extdata/stateLung-R01.pdf'
Calls: satscanMapper -> pdf
Execution halted
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sensors4plumes.Rcheck/00install.out’ for details.
Running ‘betabin.R’ [2s/3s]
  Comparing ‘betabin.Rout’ to ‘betabin.Rout.save’ ... OK
  Running ‘discrim.R’ [2s/4s]
  Comparing ‘discrim.Rout’ to ‘discrim.Rout.save’ ... OK
  Running ‘test-all.R’ [6s/7s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > 
  > if(require(testthat) && require(sensR)) {
  +     test_check("sensR")
  + }
  Loading required package: testthat
  Loading required package: sensR
  ── 1. Failure: dod estimates are stable (@test-dod.R#39)  ──────────────────────
  coef(fm) not equal to `coefExpect`.
  2/4 mismatches (average diff: 6.2e-07)
  [1] 0.952 - 0.952 == -9.67e-07
  [2] 0.309 - 0.309 ==  2.72e-07
  
  ── 2. Failure: dod works for extreme data settings (@test-dod.R#47)  ───────────
  `dod(data[1, ], data[2, ])` produced unexpected warnings.
  Expected match: Cannot assess convergence: non-finite gradient
  Actual values:
  * Cannot determine upper confidence bound
  
  ── 3. Failure: dod works for extreme data settings (@test-dod.R#49)  ───────────
  `dod_fit(data[1, ], data[2, ])` did not produce any warnings.
  
  ── 4. Failure: dod works for extreme data settings (@test-dod.R#61)  ───────────
  `dod(data[1, ], data[2, ])` did not produce any warnings.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 234 SKIPPED: 1 FAILED: 4
  1. Failure: dod estimates are stable (@test-dod.R#39) 
  2. Failure: dod works for extreme data settings (@test-dod.R#47) 
  3. Failure: dod works for extreme data settings (@test-dod.R#49) 
  4. Failure: dod works for extreme data settings (@test-dod.R#61) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Note: next may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SeqFeatR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/shp2graph.Rcheck/00install.out’ for details.
Running examples in ‘sim1000G-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: generateChromosomeRecombinationPositions
> ### Title: Generates a recombination vector arising from one meiotic event.
> ###   The origin of segments is coded as (0 - haplotype1 , 1 - haplotype2 )
> ### Aliases: generateChromosomeRecombinationPositions
> 
> ### ** Examples
> 
> 
> library("sim1000G")
> 
> # generate a recombination events for chromosome 4
> readGeneticMap(4)
 -> Downloading genetic map from: https://github.com/adimitromanolakis/geneticMap-GRCh37/raw/master/genetic_map_GRCh37_chr4.txt.gz 
 -> Saving genetic map to:  /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sim1000G/datasets/genetic_map_GRCh37_chr4.txt.gz 
Warning in download.file(url, destfile = dest_path, quiet = TRUE) :
  URL https://github.com/adimitromanolakis/geneticMap-GRCh37/raw/master/genetic_map_GRCh37_chr4.txt.gz: cannot open destfile '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sim1000G/datasets/genetic_map_GRCh37_chr4.txt.gz', reason 'Read-only file system'
Warning in download.file(url, destfile = dest_path, quiet = TRUE) :
  download had nonzero exit status
Error in readGeneticMapFromFile(fname) : 
  Genetic map file /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sim1000G/datasets/genetic_map_GRCh37_chr4.txt.gz not found
Calls: readGeneticMap -> readGeneticMapFromFile
Execution halted
Error in re-building vignettes:
  ...
Loading required package: hapsim
Loading required package: MASS
Loading required package: stringr
Loading required package: readr
Parsed with column specification:
cols(
  .default = col_character(),
  `#CHROM` = col_integer(),
  POS = col_integer(),
  QUAL = col_integer()
)
See spec(...) for full column specifications.
Warning in gplots::heatmap.2(C, col = rev(heat.colors(100)), Rowv = F, Colv = F,  :
  Discrepancy: Rowv is FALSE, while dendrogram is `both'. Omitting row dendogram.
Warning in gplots::heatmap.2(C, col = rev(heat.colors(100)), Rowv = F, Colv = F,  :
  Discrepancy: Colv is FALSE, while dendrogram is `column'. Omitting column dendogram.
Parsed with column specification:
cols(
  .default = col_character(),
  `#CHROM` = col_integer(),
  POS = col_integer(),
  QUAL = col_integer()
)
See spec(...) for full column specifications.
Warning in download.file(url, destfile = dest_path, quiet = TRUE) :
  URL https://github.com/adimitromanolakis/geneticMap-GRCh37/raw/master/genetic_map_GRCh37_chr4.txt.gz: cannot open destfile '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sim1000G/datasets/genetic_map_GRCh37_chr4.txt.gz', reason 'Read-only file system'
Warning in download.file(url, destfile = dest_path, quiet = TRUE) :
  download had nonzero exit status
Quitting from lines 68-81 (SimulatingFamilyData.Rmd) 
Error: processing vignette ‘SimulatingFamilyData.Rmd’ failed with diagnostics:
Genetic map file /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sim1000G/datasets/genetic_map_GRCh37_chr4.txt.gz not found
Execution halted
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/slickR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SocialMediaLab.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/soundecology.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘r2cytoscape’
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/spaceExt.Rcheck/00install.out’ for details.
Running examples in ‘Stickbreaker-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sim.data.from.priors.for.mod.selection
> ### Title: Simulate data from priors for doing model selection
> ### Aliases: sim.data.from.priors.for.mod.selection
> 
> ### ** Examples
> 
>  n.muts <- 4
>  n.muts <- length(Khan.data[1,])-1
>  geno.matrix <- Khan.data[,seq(1, n.muts)]
>  fit.matrix <- as.matrix(Khan.data[,(n.muts+1)])
>  outdir <- system.file("extdata",package="Stickbreaker")
>  file.name <- paste("Training_simulated_priors_fit_data_", n.muts, "muts.txt", sep="")
>  outpath <- paste(outdir, file.name, sep="/")
>  sim.data.from.priors.for.mod.selection(n.muts,
+    c(0.05, 0.5),
+    c(0, 0.25),
+    c(4),
+    1,
+    c(0.1, 10),
+    1.1,
+    1,
+    c(2,1),
+    outpath,
+    50,
+    coe.sim.model="identical",
+    coe.dist.par=NA,
+    print.interval=NA)
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Stickbreaker/extdata/Training_simulated_priors_fit_data_5muts.txt': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: sim.data.from.priors.for.mod.selection -> write.table -> file
Execution halted
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/streamR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sybilEFBA.Rcheck/00install.out’ for details.
Found the following significant warnings:
  sybilSBML.c:2236:32: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=]
  sybilSBML.c:2247:34: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sybilSBML.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SynergizeR.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: data.table
No methods found in package ‘RSQLite’ for request: ‘dbGetQuery’ when loading ‘tcpl’
tcpl (v1.2.2) loaded with the following settings:
  TCPL_DB:    /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/tcpl/sql/tcpldb.sqlite
  TCPL_USER:  NA
  TCPL_HOST:  NA
  TCPL_DRVR:  SQLite
Default settings stored in TCPL.conf. See ?tcplConf for more information.

Error: processing vignette ‘tcpl_Overview.Rnw’ failed with diagnostics:
 chunk 4 
Error in rsqlite_send_query(conn@ptr, statement) : 
  attempt to write a readonly database
Execution halted
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tensorBF.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidyinftheo)
  > 
  > test_check("tidyinftheo")
  ── 1. Error: right number of columns given (@test-errors.R#10)  ────────────────
  argument "expr" is missing, with no default
  1: expect_length(tab %>% select(vs) %>% shannon_entropy(), 1) at testthat/test-errors.R:10
  2: quasi_label(enquo(object))
  3: eval_bare(get_expr(quo), get_env(quo))
  4: tab %>% select(vs) %>% shannon_entropy()
  5: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  6: eval(quote(`_fseq`(`_lhs`)), env, env)
  7: eval(quote(`_fseq`(`_lhs`)), env, env)
  8: `_fseq`(`_lhs`)
  9: freduce(value, `_function_list`)
  10: withVisible(function_list[[k]](value))
  11: function_list[[k]](value)
  12: shannon_entropy(.)
  13: reduce_data(.data, !(!enquo(X)), numvars = 1, na.rm = na.rm)
  14: tidyselect::vars_select(names(reduced_tab), !(!(!quos(...))))
  15: vars_select_eval(.vars, quos)
  16: map_lgl(quos, quo_is_helper)
  17: .f(.x[[i]], ...)
  18: extract_expr(quo)
  19: is_call(expr, paren_sym)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 37 SKIPPED: 0 FAILED: 1
  1. Error: right number of columns given (@test-errors.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
Package in Depends field not imported from: ‘lgtdl’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ci.plot: no visible global function definition for ‘gaussian’
ci.plot: no visible global function definition for ‘qnorm’
ci.plot: no visible global function definition for ‘plot’
ci.plot: no visible global function definition for ‘lines’
cst.fit.ff: no visible global function definition for ‘pnorm’
cstfit.1: no visible global function definition for ‘var’
gof.test.boots.pf: no visible binding for global variable ‘sd’
gof.test.int.1.ff: no visible global function definition for ‘quantile’
gof.test.int.1.ff: no visible global function definition for ‘var’
gof.test.int.ff: no visible global function definition for ‘pnorm’
gofTest: no visible binding for global variable ‘sd’
plotGof: no visible global function definition for ‘plot’
plotGof : <anonymous>: no visible global function definition for
  ‘lines’
plotGof: no visible global function definition for ‘lines’
sig.test.int.1.ff: no visible global function definition for ‘quantile’
sig.test.int.1.ff: no visible global function definition for ‘var’
sig.test.int.ff: no visible global function definition for ‘pnorm’
test.boots.1: no visible binding for global variable ‘sd’
tpr: no visible global function definition for ‘poisson’
tpr: no visible global function definition for ‘glm.fit’
tpr: no visible global function definition for ‘coef’
tpr: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx coef gaussian glm.fit lines plot pnorm poisson qnorm quantile
  sd var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "approx", "coef", "gaussian", "glm.fit", "pnorm",
             "poisson", "qnorm", "quantile", "sd", "var")
to your NAMESPACE file.
Rd file 'ci.plot.Rd':
  \usage lines wider than 90 characters:
     ci.plot(x, y, se, level = 0.95, ylim = NULL, newplot = TRUE, fun = gaussian()$linkinv, dfun = gaussian()$mu.eta, ...)

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘trackr-tests.R’ [5s/8s]
Running the tests in ‘tests/trackr-tests.R’ failed.
Complete output:
  > library(trackr)
  Loading required package: histry
  > library(knitr)
  > be = JSONBackend(tempfile())
  > tdb = TrackrDB(backend=be, img_dir = tempdir())
  > defaultTDB(tdb)
  An object of class "TrackrDB"
  Slot "opts":
  An object of class "TrackrOptions"
  Slot "insert_delay":
  [1] 0
  
  Slot "img_dir":
  [1] "/tmp/Rtmp8wg5Te"
  
  Slot "img_ext":
  [1] "png"
  
  Slot "backend_opts":
  list()
  
  
  Slot "backend":
  Reference class object of class "JSONBackend"
  Field "docs":
  DocList (0x0)
  Field ".file":
  [1] "/tmp/Rtmp8wg5Te/file19641f85f01c"
  Field "file":
  [1] "/tmp/Rtmp8wg5Te/file19641f85f01c"
  
  > 
  > rmdfil = system.file("test_docs/knitr_test.Rmd", package = "trackr")
  > knit_and_record(rmdfil)
  
  
  processing file: knitr_test.Rmd
    ordinary text without R code
  
  label: plot
  Error in file(file, ifelse(append, "a", "w")) : 
    cannot open the connection
  Calls: knit_and_record ... replayPlot -> .handleSimpleError -> h -> cat -> file
  In addition: Warning messages:
  1: In dir.create(dirname(name), recursive = TRUE) :
    cannot create dir 'knitr_test_files/figure-html', reason 'No such file or directory'
  2: In file(file, ifelse(append, "a", "w")) :
    cannot open file 'knitr_test.knit.md': Read-only file system
  Execution halted
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TrajDataMining.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/turboEM.Rcheck/00install.out’ for details.
Found the following significant warnings:
  convert_util.cpp:299:20: warning: null destination pointer [-Wformat-overflow=]
  convert_util.cpp:307:20: warning: null destination pointer [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/VariABEL.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/VarReg.Rcheck/00install.out’ for details.
Found the following significant warnings:
  EM.c:386:25: warning: ‘sprintf’ writing a terminating nul past the end of the destination [-Wformat-overflow=]
  EM.c:391:25: warning: ‘sprintf’ writing a terminating nul past the end of the destination [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/VBmix.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/vcfR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/windfarmGA.Rcheck/00install.out’ for details.
Running examples in ‘WordR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: addFlexTables
> ### Title: Read Word document with bookmarks and create other Word document
> ###   with rendered tables in place.
> ### Aliases: addFlexTables
> 
> ### ** Examples
> 
> library(ReporteRs)
Loading required package: ReporteRsjars
> ft_mtcars <- vanilla.table(mtcars)
> ft_iris <- vanilla.table(iris)
> FT <- list(ft_mtcars=ft_mtcars,ft_iris=ft_iris)
> addFlexTables(
+   paste(examplePath(),'templates/templateFT.docx',sep = ''),
+   paste(examplePath(),'results/resultFT.docx',sep = ''),
+   FT)
Error in writeDoc.docx(doc, docxOut) : 
  writeDoc: Cannot write to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/WordR/examples/results/resultFT.docx
Calls: addFlexTables -> <Anonymous> -> writeDoc.docx
Execution halted
Running examples in ‘XGR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ImmunoBase
> ### Title: Immune-disease associated variants, regions and genes from
> ###   ImmunoBase (hg19)
> ### Aliases: ImmunoBase
> ### Keywords: datasets
> 
> ### ** Examples
> 
> ImmunoBase <- xRDataLoader(RData.customised='ImmunoBase')
'ImmunoBase' (from http://galahad.well.ox.ac.uk/bigdata/ImmunoBase.RData) has been loaded into the working environment (at 2018-03-01 17:37:13)
> names(ImmunoBase)
 [1] "AA"  "AS"  "ATD" "CEL" "CRO" "IBD" "IGE" "JIA" "MS"  "NAR" "PBC" "PSC"
[13] "PSO" "RA"  "SJO" "SLE" "SSC" "T1D" "UC"  "VIT"
> str(ImmunoBase$AS)
List of 5
 $ disease       : chr "Ankylosing Spondylitis (AS)"
 $ variants      :Error in FUN(X[[i]], ...) : 
  no slot of name "elementType" for this object of class "GRanges"
Calls: str ... <Anonymous> -> str -> str.default -> sapply -> lapply -> FUN
Execution halted
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/XR.Rcheck/00install.out’ for details.
Running examples in ‘yCrypticRNAs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bam_to_reads
> ### Title: Convert BAM files into BED files containing the reads overlaping
> ###   the specified annotations.
> ### Aliases: bam_to_reads
> 
> ### ** Examples
> 
> bamfile <- system.file("extdata", "wt_rep1.bam", package = "yCrypticRNAs")
> data(annotations)
> bam_to_reads(bamfile, annotations)
Error in FUN(X[[i]], ...) : failed to build index
  file: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/yCrypticRNAs/extdata/wt_rep1.bam
Calls: bam_to_reads -> .index_bam
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 48-60 (yCrypticRNAs.Rmd) 
Error: processing vignette ‘yCrypticRNAs.Rmd’ failed with diagnostics:
failed to build index
  file: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/yCrypticRNAs/extdata/wt_rep1.bam
Execution halted
Namespaces in Imports field not imported from:
  ‘httr’ ‘progress’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rARPACK’ ‘sparseLDA’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    R  13.6Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/ACTCD.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
Namespaces in Imports field not imported from:
  ‘plotly’ ‘shinydashboard’
  All declared Imports should be used.
asp: no visible global function definition for ‘as.formula’
asp: no visible global function definition for ‘var’
aspm: no visible binding for global variable ‘X.Declan’
aspm: no visible binding for global variable ‘Z.Jaida’
aspm: no visible binding for global variable ‘group.vec.Handan’
aspm: no visible global function definition for ‘as.formula’
aspm: no visible global function definition for ‘glm’
aspm: no visible global function definition for ‘binomial’
aspm: no visible global function definition for ‘poisson’
Undefined global functions or variables:
  X.Declan Z.Jaida as.formula binomial glm group.vec.Handan poisson var
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "poisson", "var")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘AdaptFit/R/aspm.R’:
  assign("group.vec.Handan", group.vec, pos = 1)
  assign("X.Declan", X, pos = 1)
  assign("Z.Jaida", Z, pos = 1)
Namespace in Imports field not imported from: ‘Benchmarking’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       2.8Mb
    pictures   2.1Mb
Namespace in Imports field not imported from: ‘filehash’
  All declared Imports should be used.
Found the following significant warnings:
  ADM3.c:34:19: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:34:31: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:34:15: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:39:61: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:39:73: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:39:57: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:52:6: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:54:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:54:56: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:55:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:55:42: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:56:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:56:38: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/ADM3.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Namespaces in Imports field not imported from:
  ‘fields’ ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DBI’ ‘assertthat’ ‘tibble’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Biostrings’
Packages unavailable to check Rd xrefs: ‘Biostrings’, ‘Starr’
Missing or unexported object: ‘DiagrammeR::set_global_graph_attrs’
Running ‘testthat.R’ [18s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("ahp")
  Loading required package: ahp
  ── 1. Error: Visualize (@test-Visualize.R#8)  ──────────────────────────────────
  'set_global_graph_attrs' is not an exported object from 'namespace:DiagrammeR'
  1: GetGraph(carAhp) at testthat/test-Visualize.R:8
  2: DiagrammeR::set_global_graph_attrs
  3: getExportedValue(pkg, name)
  4: stop(gettextf("'%s' is not an exported object from 'namespace:%s'", name, getNamespaceName(ns)), 
         call. = FALSE, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 463 SKIPPED: 0 FAILED: 1
  1. Error: Visualize (@test-Visualize.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘rjson’ ‘xml2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Biobase’
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    data  15.6Mb
Found the following significant warnings:
  matrix.c:629:8: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  matrix.c:631:49: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  matrix.c:632:39: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/amei.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘unmarked’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    libs  25.0Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/anapuce.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rgdal’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘caret’
  All declared Imports should be used.
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
Package suggested but not available for checking: ‘rhdf5’
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/Anthropometry.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Packages suggested but not available for checking: ‘Biostrings’ ‘kebabs’
Error in re-building vignettes:
  ...

Attaching package: 'apcluster'

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

    heatmap

Quitting from lines 293-307 (apcluster.Rnw) 
Error: processing vignette 'apcluster.Rnw' failed with diagnostics:
object 'apres1b' not found
Execution halted
Namespace in Imports field not imported from: ‘pls’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
runAPSIM: warning in scan(reports_file[i], "", sep = "", skip =
  length(temp), nline = 1): partial argument match of 'nline' to
  'nlines'
runAPSIM: no visible global function definition for ‘write.table’
runAPSIM: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Running examples in ‘aqp-Ex.R’ failed
The error most likely occurred in:

> ### Name: addBracket
> ### Title: Add Depth Brackets
> ### Aliases: addBracket addDiagnosticBracket
> 
> ### ** Examples
> 
> # sample data
> data(sp1)
> 
> # add color vector
> sp1$soil_color <- with(sp1, munsell2rgb(hue, value, chroma))
> 
> # promote to SoilProfileCollection
> depths(sp1) <- id ~ top + bottom
> 
> # plot profiles
> plot(sp1)
guessing horizon designations are stored in `name`
> 
> # extract top/bottom depths associated with all A horizons
> f <- function(i) {
+   h <- horizons(i)
+   idx <- grep('^A', h$name)
+   c(min(h$top[idx]), max(h$bottom[idx], na.rm=TRUE))
+ }
> 
> # apply function to sp1, result is a list
> a <- profileApply(sp1, f, simplify=FALSE)
> # convert list into matrix
> a <- do.call('rbind', a)
> 
> # plot
> plot(sp1)
guessing horizon designations are stored in `name`
> # annotate with brackets
> # note that plotting order is derived from the call to `plot(sp1)`
> addBracket(a[, 1], a[, 2], col='red')
> 
> # more interesting example using diagnostic horizons
> if(require(soilDB)) {
+   # load some sample data with diagnostic horizons
+   data(loafercreek)
+   
+   # extract first 15 profiles
+   x <- loafercreek[1:15, ]
+   s <- site(x)
+ 
+   # plot
+   par(mar=c(0,0,0,0))
+   plot(x, name='hzname', id.style='top')
+   
+   # add brackets describing the argillic horizon
+   addDiagnosticBracket(x, 'argillic horizon', col='red')
+   # add brackets describing paralithic contact
+   addDiagnosticBracket(x, 'paralithic contact', col='blue')
+ }
Loading required package: soilDB
Error in segments(x.1, top[plot.order], x.2, top[plot.order], lend = 2,  : 
  cannot mix zero-length and non-zero-length coordinates
Calls: addDiagnosticBracket -> addBracket -> segments
Execution halted
Found the following significant warnings:
  am.c:275:9: warning: comparison of array 'readByte' not equal to a null pointer is always true [-Wtautological-pointer-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/aqr.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
Package suggested but not available for checking: ‘affxparser’
Package unavailable to check Rd xrefs: ‘affxparser’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.2Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/ARTP.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Packages suggested but not available for checking: ‘cacheSweave’ ‘weaver’
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Packages suggested but not available for checking: ‘REBayes’ ‘Rmosek’
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/assignPOP.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   9.6Mb
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
File ‘audio/libs/audio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

> ### Name: auk_country
> ### Title: Filter the eBird data by country
> ### Aliases: auk_country
> 
> ### ** Examples
> 
> # country names and ISO2 codes can be mixed
> # not case sensitive
> country <- c("CA", "United States", "mexico")
> system.file("extdata/ebd-sample.txt", package = "auk") %>%
+   auk_ebd() %>%
+   auk_country(country)
Error: 'countrycode_data' is not an exported object from 'namespace:countrycode'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 173-190 (auk.Rmd) 
Error: processing vignette 'auk.Rmd' failed with diagnostics:
'countrycode_data' is not an exported object from 'namespace:countrycode'
Execution halted
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
Package suggested but not available for checking: ‘BiocInstaller’
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.6Mb
installed size is 67.2Mb
  sub-directories of 1Mb or more:
    java  67.2Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   8.9Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    libs   2.8Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package suggested but not available for checking: ‘mzR’
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/BAMBI.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/BANFF.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 103.4Mb
  sub-directories of 1Mb or more:
    libs  102.6Mb
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.8Mb
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  15.3Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is 58.0Mb
  sub-directories of 1Mb or more:
    libs  57.2Mb
Namespace in Imports field not imported from: ‘inline’
  All declared Imports should be used.
installed size is 29.3Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs  24.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R     1.7Mb
    doc   3.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    ex-data   4.7Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/Bayesthresh.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 92.6Mb
  sub-directories of 1Mb or more:
    libs  92.5Mb
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Package suggested but not available for checking: ‘DNAcopy’
Namespace in Imports field not imported from: ‘readxl’
  All declared Imports should be used.
installed size is 53.0Mb
  sub-directories of 1Mb or more:
    libs  51.5Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘chron’ ‘colorspace’ ‘gtable’ ‘htmltools’ ‘htmlwidgets’
  ‘httpuv’ ‘magrittr’ ‘munsell’ ‘plyr’ ‘scales’ ‘stringi’ ‘xtable’
  ‘yaml’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘crochet’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
installed size is 28.8Mb
  sub-directories of 1Mb or more:
    libs  27.7Mb
Error in re-building vignettes:
  ...
Quitting from lines 183-186 (BETS_basic_usage.Rmd) 
Error: processing vignette 'BETS_basic_usage.Rmd' failed with diagnostics:
invalid time series parameters specified
Execution halted
installed size is 144.8Mb
  sub-directories of 1Mb or more:
    include  144.7Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/biclust.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.9Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   5.5Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
installed size is 28.8Mb
  sub-directories of 1Mb or more:
    libs  28.7Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/bigpca.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘lattice’ ‘zoo’
  All declared Imports should be used.
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  15.1Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   7.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   2.3Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/BioPhysConnectoR.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Package suggested but not available for checking: ‘IHW’
Package suggested but not available for checking: ‘RQuantLib’
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RGtk2’ ‘cairoDevice’ ‘ergm’ ‘foreign’ ‘gWidgets’ ‘gWidgetsRGtk2’
  ‘haven’ ‘plot3D’ ‘plot3Drgl’ ‘rgl’ ‘sna’ ‘statnet.common’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘gtools’ ‘knitr’ ‘nnet’ ‘parallel’ ‘rJava’ ‘reshape’
  ‘rmarkdown’ ‘shinyjs’
  All declared Imports should be used.
Missing or unexported object: ‘xgboost::predict’
installed size is 43.5Mb
  sub-directories of 1Mb or more:
    libs  42.3Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/BlockFeST.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
Namespace in Imports field not imported from: ‘plm’
  All declared Imports should be used.
installed size is 32.3Mb
  sub-directories of 1Mb or more:
    libs  32.0Mb
File ‘BMN/libs/BMN.so’:
  Found ‘_ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
    Objects: ‘JunctionTree.o’, ‘pseudoLikelihood.o’
File ‘BMN/libs/BMN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  conditional.least.squares.c:232:20: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  conditional.least.squares.c:233:20: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  conditional.least.squares.c:234:20: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/bnlearn.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ./sampling.h:84:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/BNSP.Rcheck/00install.out’ for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.7Mb
Package suggested but not available for checking: ‘sangerseqR’
Namespaces in Imports field not imported from:
  ‘knitr’ ‘yaml’
  All declared Imports should be used.
installed size is 272.9Mb
  sub-directories of 1Mb or more:
    include    2.9Mb
    lib      269.7Mb
installed size is 48.5Mb
  sub-directories of 1Mb or more:
    libs  48.1Mb
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘tidyr’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
installed size is 29.9Mb
  sub-directories of 1Mb or more:
    libs  29.7Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘profileModel’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R     3.0Mb
    doc   2.3Mb
Running examples in ‘broom-Ex.R’ failed
The error most likely occurred in:

> ### Name: gam_tidiers
> ### Title: Tidying methods for a generalized additive model (gam)
> ### Aliases: gam_tidiers tidy.gam glance.gam
> 
> ### ** Examples
> 
> 
> if (require("gam", quietly = TRUE)) {
+     data(kyphosis)
+     g <- gam(Kyphosis ~ s(Age,4) + Number, family = binomial, data = kyphosis)
+     tidy(g)
+     augment(g)
+     glance(g)
+ }
Loaded gam 1.15

Error in 1:ncol(co) : argument of length 0
Calls: tidy -> tidy.lm -> tidy.summary.lm -> fix_data_frame
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    bin    2.2Mb
    doc    1.1Mb
    libs   2.2Mb
Namespaces in Imports field not imported from:
  ‘rworldxtra’ ‘sp’
  All declared Imports should be used.
Found the following significant warnings:
  helpers.c:365:19: warning: absolute value function 'fabsf' given an argument of type 'double' but has parameter of type 'float' which may cause truncation of value [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/BSquare.Rcheck/00install.out’ for details.
installed size is 32.5Mb
  sub-directories of 1Mb or more:
    libs  31.3Mb
installed size is 56.7Mb
  sub-directories of 1Mb or more:
    libs  56.3Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
Running examples in ‘cablecuttr-Ex.R’ failed
The error most likely occurred in:

> ### Name: can_i_stream
> ### Title: Query CanIStream.It
> ### Aliases: can_i_stream can_i_stream_id can_i_stream_it
> 
> ### ** Examples
> 
> can_i_stream_id("4eb0173df5f8079d29000002", "purchase")
Error: CanIStream.It API request for movie #4eb0173df5f8079d29000002 failed (500)
Server errorCanIStream.It API request for movie #4eb0173df5f8079d29000002 failed (500)
Internal Server ErrorCanIStream.It API request for movie #4eb0173df5f8079d29000002 failed (500)
Server error: (500) Internal Server Error
Execution halted
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
Packages suggested but not available for checking:
  ‘GenomicRanges’ ‘IRanges’ ‘S4Vectors’
Package unavailable to check Rd xrefs: ‘GenomicRanges’
Package suggested but not available for checking: ‘limma’
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R        1.0Mb
    data     1.5Mb
    models   2.4Mb
Package unavailable to check Rd xrefs: ‘limma’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Found the following significant warnings:
  slpcovis.cpp:381:12: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/catlearn.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
estim.regul: warning in matrix(res, nc = length(grid2)): partial
  argument match of 'nc' to 'ncol'
comput: no visible global function definition for ‘cor’
img.estim.regul: no visible global function definition for ‘par’
img.estim.regul: no visible global function definition for ‘image’
img.estim.regul: no visible global function definition for
  ‘heat.colors’
img.estim.regul: no visible global function definition for ‘axis’
img.estim.regul: no visible global function definition for ‘box’
img.matcor: no visible global function definition for ‘par’
img.matcor: no visible global function definition for ‘image’
img.matcor: no visible global function definition for ‘box’
img.matcor: no visible global function definition for ‘abline’
img.matcor: no visible global function definition for ‘layout’
loo: no visible global function definition for ‘cor’
matcor: no visible global function definition for ‘cor’
plt.cc: no visible global function definition for ‘par’
plt.cc: no visible global function definition for ‘layout’
plt.indiv: no visible global function definition for ‘plot’
plt.indiv: no visible global function definition for ‘text’
plt.indiv: no visible global function definition for ‘abline’
plt.var: no visible global function definition for ‘plot’
plt.var: no visible global function definition for ‘points’
plt.var: no visible global function definition for ‘text’
plt.var: no visible global function definition for ‘abline’
plt.var: no visible global function definition for ‘lines’
rcc: no visible global function definition for ‘var’
rcc: no visible global function definition for ‘cov’
Undefined global functions or variables:
  abline axis box cor cov heat.colors image layout lines par plot
  points text var
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "abline", "axis", "box", "image", "layout",
             "lines", "par", "plot", "points", "text")
  importFrom("stats", "cor", "cov", "var")
to your NAMESPACE file.
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
Found the following significant warnings:
  ./MCMC_prob.h:2091:41: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/CCMnet.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘units’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lazyeval’ ‘purrr’ ‘roxygen2’
  All declared Imports should be used.
Running examples in ‘CDECRetrieve-Ex.R’ failed
The error most likely occurred in:

> ### Name: cdec_available
> ### Title: Function returns a dataframe of the available data
> ### Aliases: cdec_available
> 
> ### ** Examples
> 
> # get a list of dataframes available for CCR
> cdec_datasets("ccr")
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: Connection timed out after 10000 milliseconds
Calls: cdec_datasets ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘rgdal’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   5.8Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   9.3Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.1Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/cem.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
get.switch.time: warning in uniroot(f = switch.func, int =
  c(last_boundary, boundary), lower = last_boundary, upper = boundary,
  maxiter = 1000, tol = tol, e): partial argument match of 'int' to
  'interval'
plot.cggd: warning in axis(4, at = b[nrow(b), ], label = paste(cnums),
  cex = 0.8, adj = 0): partial argument match of 'label' to 'labels'
plot.cggd: no visible global function definition for ‘gen.beta’
plotCVcggd: no visible binding for global variable ‘cv’
plotCVcggd: no visible binding for global variable ‘cv.error’
predict.cggd: no visible binding for global variable ‘max.tk’
predict.cggd: no visible global function definition for ‘gen.beta’
Undefined global functions or variables:
  cv cv.error gen.beta max.tk
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Found the following significant warnings:
  costfunctions.c:33:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  costfunctions.c:57:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/changepoint.np.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘datasets’ ‘foreach’
  All declared Imports should be used.
Package suggested but not available for checking: ‘speaq’
Package suggested but not available for checking: ‘multtest’
Namespace in Imports field not imported from: ‘gamlss.dist’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tools’
  All declared Imports should be used.
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘stringr’
  All declared Imports should be used.
Found the following significant warnings:
  Note: possible error in 'log.likelihood(list(latent.space.pos.prop, ': unused argument (edge.list.rows[[dd]]) 
  Note: possible error in 'log.likelihood(list(latent.space.pos.hold, ': unused argument (edge.list.rows[[dd]]) 
See ‘/data/gannet/ripley/R/packages/tests-clang/CIDnetworks.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Namespace in Imports field not imported from: ‘circlize’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/CircE.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Package suggested but not available for checking: ‘ComplexHeatmap’
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/CircStats.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Files which contain pragma(s) suppressing diagnostics:
  ‘src/cld_3/protos/feature_extractor.pb.h’
  ‘src/cld_3/protos/sentence.pb.h’ ‘src/cld_3/protos/task_spec.pb.h’
installed size is 22.0Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/climatol.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Namespaces in Imports field not imported from:
  ‘R6’ ‘infuser’ ‘purrr’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
    pdf   2.2Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/clustrd.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Packages suggested but not available for checking:
  ‘Biobase’ ‘annotate’ ‘GO.db’ ‘moe430a.db’
Package unavailable to check Rd xrefs: ‘Biobase’
Error in re-building vignettes:
  ...
Loading required package: cluster
Read 7 items
Loading required package: Biobase
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘Biobase’
Loading required package: RankAggreg
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'clValid.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file /data/gannet/ripley/R/packages/tests-clang/clVali
d.Rcheck/vign_test/clValid/vignettes/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
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/cmm.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data     3.5Mb
    exdata   5.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   4.1Mb
Namespaces in Imports field not imported from:
  ‘geometry’ ‘parallel’ ‘plot3D’ ‘reshape2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘grid’ ‘gridExtra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/Combine.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Package suggested but not available for checking: ‘rscala’
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘PearsonDS’ ‘VGAM’ ‘actuar’ ‘fExtremes’ ‘rmutil’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/CompetingRisk.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Utility.c:162:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:187:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:211:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:392:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:417:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:442:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/CompRandFld.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘MASS’ ‘geepack’
  All declared Imports should be used.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   6.5Mb
Namespaces in Imports field not imported from:
  ‘Rtsne’ ‘scatterplot3d’
  All declared Imports should be used.
Package suggested but not available for checking: ‘ProData’
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/CorReg.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 28.9Mb
  sub-directories of 1Mb or more:
    libs  28.5Mb
Namespace in Imports field not imported from: ‘xtable’
  All declared Imports should be used.
Package in Depends field not imported from: ‘calibrate’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   5.1Mb
Namespace in Imports field not imported from: ‘maps’
  All declared Imports should be used.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
Namespace in Imports field not imported from: ‘gstat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘misc3d’
  All declared Imports should be used.
Found the following significant warnings:
  ./bdsmatrix_stub.h:44:11: warning: incompatible pointer to integer conversion returning 'int *' from a function with result type 'int'; dereference with * [-Wint-conversion]
  ./bdsmatrix_stub.h:53:11: warning: incompatible pointer to integer conversion returning 'int *' from a function with result type 'int'; dereference with * [-Wint-conversion]
  ./bdsmatrix_stub.h:100:11: warning: incompatible pointer types returning 'double *' from a function with result type 'double **' [-Wincompatible-pointer-types]
See ‘/data/gannet/ripley/R/packages/tests-clang/coxme.Rcheck/00install.out’ for details.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Package suggested but not available for checking: ‘qvalue’
installed size is 38.8Mb
  sub-directories of 1Mb or more:
    libs  38.6Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/cplm.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
QR.cd: no visible global function definition for ‘quantile’
QR.lasso.cd: no visible global function definition for ‘quantile’
cqr.cd: no visible global function definition for ‘quantile’
cqr.lasso.cd: no visible global function definition for ‘quantile’
cqr.lasso.mm: no visible global function definition for ‘quantile’
cqr.mm: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
File ‘cqrReg/libs/cqrReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 11 marked Latin-1 strings
  Note: found 57 marked UTF-8 strings
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Packages suggested but not available for checking:
  ‘clusterProfiler’ ‘org.Hs.eg.db’ ‘AnnotationDbi’ ‘BiocInstaller’
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘r6extended’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘png’
  All declared Imports should be used.
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    libs  22.6Mb
Namespace in Imports field not imported from: ‘httpcode’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘qte’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    shp   7.8Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data  10.9Mb
Note: found 59670 marked Latin-1 strings
  Note: found 16 marked UTF-8 strings
Found the following significant warnings:
  ./ctl.h:38:23: warning: token pasting of ',' and __VA_ARGS__ is a GNU extension [-Wgnu-zero-variadic-macro-arguments]
  ./ctl.h:36:25: warning: token pasting of ',' and __VA_ARGS__ is a GNU extension [-Wgnu-zero-variadic-macro-arguments]
See ‘/data/gannet/ripley/R/packages/tests-clang/ctl.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/ctsem.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 32.0Mb
  sub-directories of 1Mb or more:
    extdata  31.9Mb
Packages unavailable to check Rd xrefs: ‘DNAcopy’, ‘tilingArray’
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   5.1Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/Cyclops.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
.onLoad : <anonymous>: no visible global function definition for
  ‘read.table’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbConnect’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbListTables’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbExistsTable’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbReadTable’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbWriteTable’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbDisconnect’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbRemoveTable’
Undefined global functions or variables:
  dbConnect dbDisconnect dbExistsTable dbListTables dbReadTable
  dbRemoveTable dbWriteTable read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
installed size is 77.0Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  74.9Mb
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
Package suggested but not available for checking: ‘GenomicRanges’
ToDiagrammeRGraph: no visible global function definition for
  ‘set_global_graph_attrs’
Undefined global functions or variables:
  set_global_graph_attrs
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: plot.Node ToDiagrammeRGraph SetNodeStyle SetEdgeStyle
> ###   SetGraphStyle GetDefaultTooltip
> 
> ### ** Examples
> 
> data(acme)
> SetGraphStyle(acme, rankdir = "TB")
> SetEdgeStyle(acme, arrowhead = "vee", color = "blue", 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$leaves, function(node) SetNodeStyle(node, shape = "egg"))
> plot(acme)
Error in set_global_graph_attrs(graph, "layout", "dot", "graph") : 
  could not find function "set_global_graph_attrs"
Calls: plot -> plot.Node -> ToDiagrammeRGraph
Execution halted
Running ‘testthat.R’ [12s/28s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("data.tree")
  Loading required package: data.tree
  ── 1. Error: grViz (@test-draw.R#18)  ──────────────────────────────────────────
  could not find function "set_global_graph_attrs"
  1: ToDiagrammeRGraph(acme, direction = "descend", pruneFun = function(x) x$level < 3) at testthat/test-draw.R:18
  
  ── 2. Error: grViz single attribute (@test-draw.R#29)  ─────────────────────────
  could not find function "set_global_graph_attrs"
  1: ToDiagrammeRGraph(acme) at testthat/test-draw.R:29
  
  ── 3. Error: grViz single attribute names not uniuqe (@test-draw.R#67)  ────────
  could not find function "set_global_graph_attrs"
  1: ToDiagrammeRGraph(mytree) at testthat/test-draw.R:67
  
                            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: 354 SKIPPED: 0 FAILED: 3
  1. Error: grViz (@test-draw.R#18) 
  2. Error: grViz single attribute (@test-draw.R#29) 
  3. Error: grViz single attribute names not uniuqe (@test-draw.R#67) 
  
  Error: testthat unit tests failed
  Execution halted
browse: no visible global function definition for ‘slot’
browse: no visible global function definition for ‘page’
default.options: no visible binding for global variable ‘object.size’
heat.view: no visible global function definition for ‘head’
heat.view: no visible global function definition for ‘tail’
whos: no visible global function definition for ‘slotNames’
whos : <anonymous> : <anonymous>: no visible global function definition
  for ‘slot’
Undefined global functions or variables:
  head object.size page slot slotNames tail
Consider adding
  importFrom("methods", "slot", "slotNames")
  importFrom("utils", "head", "object.size", "page", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dbplot)
  Loading required package: dplyr
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  Loading required package: rlang
  
  Attaching package: 'rlang'
  
  The following objects are masked from 'package:testthat':
  
      is_false, is_null, is_true
  
  > library(dplyr)
  > library(ggplot2)
  > 
  > test_check("dbplot")
  ── 1. Failure: Correct binwidth formula is returned  ───────────────────────────
  db_bin(var, binwidth = 10) not equal to rlang::expr(...).
  target, current do not match when deparsed
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 11 SKIPPED: 0 FAILED: 1
  1. Failure: Correct binwidth formula is returned 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   6.5Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘gridExtra’ ‘latticeExtra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘CDM’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   3.6Mb
Running examples in ‘ddeploy-Ex.R’ failed
The error most likely occurred in:

> ### Name: duke_deploy
> ### Title: Deploy model using REST API
> ### Aliases: duke_deploy
> 
> ### ** Examples
> 
> duke_auth <- list(
+ user_name = "try_it",
+ api_key   = "db1542b66f16aba5768d8a19c27dec4facf9168a",
+ endpoint = "/api/v1.0"
+ )
> example_data <- as.data.frame(cbind(gl(3,50),rnorm(150)));names(example_data) <- c("x","y")
> example_fit  <- lm(y~x,data=example_data)
> duke_deploy(auth_details=duke_auth,model_object=example_fit)
Error: lexical error: invalid char in json text.
                                       <html>  <head><title>502 Bad Ga
                     (right here) ------^
Execution halted
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    libs  23.8Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/deBInfer.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/debug.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
'library' or 'require' call to ‘UScensus2010’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘UScensus2010’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘JavaGD’ ‘OpenStreetMap’ ‘maptools’ ‘rgdal’ ‘scales’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Note: found 83 marked Latin-1 strings
  Note: found 62 marked UTF-8 strings
Bootstrapping.CI: no visible global function definition for ‘quantile’
D.Jost: no visible global function definition for ‘read.table’
D.Jost: no visible global function definition for ‘write.table’
Dv.locis.corrected.calc: no visible global function definition for
  ‘p.adjust’
Gst.Nei: no visible global function definition for ‘read.table’
Gst.Nei: no visible global function definition for ‘write.table’
H.out: no visible global function definition for ‘write.table’
Hardy.calc: no visible global function definition for ‘chisq.test’
critical.ci.values: no visible global function definition for
  ‘quantile’
inputformat: no visible global function definition for ‘read.table’
inputformat: no visible global function definition for ‘write.table’
over.all.pops: no visible global function definition for ‘write.table’
p.value.correcture: no visible global function definition for
  ‘p.adjust’
pair.pops: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  chisq.test p.adjust quantile read.table write.table
Consider adding
  importFrom("stats", "chisq.test", "p.adjust", "quantile")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Packages unavailable to check Rd xrefs: ‘WGCNA’, ‘moduleColor’
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
Found the following significant warnings:
  DEploid/updateHap.cpp:670:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
  DEploid/updateHap.cpp:678:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
  DEploid/updateHap.cpp:681:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
  DEploid/updateHap.cpp:682:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/DEploid.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/derivmkts.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Error in re-building vignettes:
  ...
Quitting from lines 133-140 (DescriptiveStatsObeu.Rmd) 
Error: processing vignette 'DescriptiveStatsObeu.Rmd' failed with diagnostics:
Required package curl not found. Please run: install.packages('curl')
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.7Mb
    help   1.3Mb
    libs   1.3Mb
Packages suggested but not available for checking: ‘gurobi’ ‘Rcplex’
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    libs  18.4Mb
installed size is 46.4Mb
  sub-directories of 1Mb or more:
    libs  45.9Mb
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  17.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
Namespace in Imports field not imported from: ‘mgcv’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/dhglm.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Namespace in Imports field not imported from: ‘gplots’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/diffractometry.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/diffusionMap.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/di.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    include  19.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   3.3Mb
Error in re-building vignettes:
  ...
Loading required package: doBy
Loading required package: Matrix
Warning in if (class(object) %in% c("matrix", "Matrix")) { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(object) %in% c("matrix", "Matrix")) { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(object) %in% c("matrix", "Matrix")) { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(object) %in% c("matrix", "Matrix")) { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(object) %in% c("matrix", "Matrix")) { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(object) %in% c("matrix", "Matrix")) { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(object) %in% c("matrix", "Matrix")) { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(object) %in% c("matrix", "Matrix")) { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(object) %in% c("matrix", "Matrix")) { :
  the condition has length > 1 and only the first element will be used

Error: processing vignette 'LSmeans.Rnw' failed with diagnostics:
 chunk 47 
Error in VV %*% kk : non-conformable arguments
Execution halted
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   5.8Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/Dominance.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘tidyverse’
  All declared Imports should be used.
installed size is 29.0Mb
  sub-directories of 1Mb or more:
    libs  26.9Mb
Namespaces in Imports field not imported from:
  ‘bit64’ ‘rstudioapi’ ‘tidyverse’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   3.5Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘drc’ ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘readr’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
drtmle: TMLE with doubly robust inference
Version: 1.0.2
Loading required package: nnls
Super Learner
Version: 2.0-22
Package created on 2017-07-18

Loading required package: nloptr
Loading required package: quadprog
Loading required package: gam
Loading required package: splines
Loading required package: foreach
Loaded gam 1.15

Error : 'predict.gam' is not an exported object from 'namespace:gam'
Error : 'predict.gam' is not an exported object from 'namespace:gam'
Error : 'predict.gam' is not an exported object from 'namespace:gam'
Error : 'predict.gam' is not an exported object from 'namespace:gam'
Error : 'predict.gam' is not an exported object from 'namespace:gam'
Error : 'predict.gam' is not an exported object from 'namespace:gam'
Error : 'predict.gam' is not an exported object from 'namespace:gam'
Error : 'predict.gam' is not an exported object from 'namespace:gam'
Error : 'predict.gam' is not an exported object from 'namespace:gam'
Error : 'predict.gam' is not an exported object from 'namespace:gam'
Quitting from lines 492-499 (using_drtmle.Rmd) 
Error: processing vignette 'using_drtmle.Rmd' failed with diagnostics:
matrix D in quadratic function is not positive definite!
Execution halted
Namespace in Imports field not imported from: ‘shapefiles’
  All declared Imports should be used.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   7.4Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/dvfBm.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
perturbFBM: warning in circFBM(n, H, plot = FALSE): partial argument
  match of 'plot' to 'plotfBm'
circFBM: no visible global function definition for ‘fft’
circFBM: no visible global function definition for ‘rnorm’
circFBM: no visible global function definition for ‘par’
circFBM: no visible global function definition for ‘plot’
dvFBM: no visible global function definition for ‘filter’
dvFBM: no visible global function definition for ‘quantile’
dvFBM: no visible global function definition for ‘lm’
dvFBM: no visible global function definition for ‘plot’
dvFBM: no visible global function definition for ‘abline’
filt: no visible global function definition for ‘wavDaubechies’
perturbFBM: no visible global function definition for ‘rnorm’
perturbFBM: no visible global function definition for ‘rbinom’
perturbFBM: no visible global function definition for ‘par’
perturbFBM: no visible global function definition for ‘segments’
perturbFBM: no visible global function definition for ‘points’
Undefined global functions or variables:
  abline fft filter lm par plot points quantile rbinom rnorm segments
  wavDaubechies
Consider adding
  importFrom("graphics", "abline", "par", "plot", "points", "segments")
  importFrom("stats", "fft", "filter", "lm", "quantile", "rbinom",
             "rnorm")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘xml2’
  All declared Imports should be used.
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.2Mb
    libs  16.9Mb
Namespaces in Imports field not imported from:
  ‘maptools’ ‘tools’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘reshape2’ ‘scales’ ‘xtable’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘base64enc’ ‘knitr’ ‘markdown’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    hac    4.0Mb
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/ecospat.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Namespaces in Imports field not imported from:
  ‘dae’ ‘dplyr’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
    doc    1.2Mb
installed size is 45.4Mb
  sub-directories of 1Mb or more:
    libs  45.0Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data  11.5Mb
Namespaces in Imports field not imported from:
  ‘FNN’ ‘ggmap’ ‘simFrame’
  All declared Imports should be used.
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  16.4Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    xsd   5.4Mb
'library' or 'require' calls to packages already attached by Depends:
  ‘clusterSim’ ‘earth’
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘clusterSim’ ‘earth’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: ‘ggtree’
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.5Mb
Error in re-building vignettes:
  ...
Quitting from lines 46-54 (phylomoji.Rmd) 
Error: processing vignette 'phylomoji.Rmd' failed with diagnostics:
there is no package called 'ggtree'
Execution halted
Note: found 23639 marked Latin-1 strings
Found the following significant warnings:
  Note: possible error in 'savePlot(filename = "Clustplot", ': unused argument (restoreConsole = TRUE) 
  Note: possible error in 'savePlot(filename = "MCAplotindclasse", ': unused argument (restoreConsole = TRUE) 
  Note: possible error in 'savePlot(filename = "MCAplotvar", ': unused argument (restoreConsole = TRUE) 
  Note: possible error in 'savePlot(filename = "MCAplotind", ': unused argument (restoreConsole = TRUE) 
  Note: possible error in 'savePlot(filename = "MCAplotquantisup", ': unused argument (restoreConsole = TRUE) 
  Note: possible error in 'savePlot(filename = "Ellipse", ': unused argument (restoreConsole = TRUE) 
  Note: possible error in 'savePlot(filename = "Lisib", ': unused argument (restoreConsole = TRUE) 
  Note: possible error in 'savePlot(filename = "Density", ': unused argument (restoreConsole = TRUE) 
  Note: possible error in 'savePlot(filename = "Densitypop", ': unused argument (restoreConsole = TRUE) 
  Note: possible error in 'savePlot(filename = "barplotgr", ': unused argument (restoreConsole = TRUE) 
  Note: possible error in 'savePlot(filename = paste("barvarclus", ': unused argument (restoreConsole = TRUE) 
  Note: possible error in 'hsv(h = 1, s = 1, v = 1, ': unused argument (1) 
  Note: possible error in 'hsv(h = 1, s = 0.4 + ': unused argument (1) 
  Note: possible error in 'hsv(h = a * i, s = 1, ': unused argument (1) 
  Note: possible error in 'hsv(h = a * m, s = 1, ': unused argument (1) 
  Note: possible error in 'hsv(h = a * m, s = 0.4 + ': unused argument (1) 
See ‘/data/gannet/ripley/R/packages/tests-clang/EnQuireR.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    Sweave   6.0Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/EnvStats.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    doc    3.3Mb
    help   3.4Mb
Found the following significant warnings:
  input2.c:767:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/epanet2toolkit.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘colorspace’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘llogistic’ ‘logitnorm’
  All declared Imports should be used.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘readr’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/EpiWeek.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Namespace in Imports field not imported from: ‘signal’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘searcher’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/esmprep.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    libs  25.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Namespace in Imports field not imported from: ‘EnvStats’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/eVenn.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
Namespaces in Imports field not imported from:
  ‘curl’ ‘openxlsx’ ‘stringr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘polynom’
  All declared Imports should be used.
print.cdf : numform: warning in formatC(x, dig = digits): partial
  argument match of 'dig' to 'digits'
print.cdf: warning in get("x", env = environment(x)): partial argument
  match of 'env' to 'envir'
print.cdf: warning in get("y", env = environment(x)): partial argument
  match of 'env' to 'envir'
print.ogive : numform: warning in formatC(x, dig = digits): partial
  argument match of 'dig' to 'digits'
print.ogive: warning in get("x", env = environment(x)): partial
  argument match of 'env' to 'envir'
print.ogive: warning in get("y", env = environment(x)): partial
  argument match of 'env' to 'envir'
quantile.expert: warning in formatC(paste(100 * probs, "%", sep = ""),
  format = "fg", wid = 1, digits = dig): partial argument match of
  'wid' to 'width'
MS: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: iteration 7 invokes undefined behavior [-Waggressive-loop-optimizations]
See ‘/data/gannet/ripley/R/packages/tests-clang/expoRkit.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  ‘Biobase’ ‘edgeR’ ‘GEOquery’ ‘limma’ ‘pathClass’
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Namespace in Imports field not imported from: ‘refund’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘forcats’ ‘formula.tools’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/FACTscorer.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/fArma.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  15.6Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.1Mb
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  17.2Mb
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/data/gannet/ripley/R/packages/tests-clang/FastRWeb.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘whisker’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.6Mb
installed size is 53.7Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  50.6Mb
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    libs  22.3Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   7.2Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Found the following significant warnings:
  ff.cpp:256:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ff.cpp:256:54: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/data/gannet/ripley/R/packages/tests-clang/ff.Rcheck/00install.out’ for details.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Namespace in Imports field not imported from: ‘desc’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/fifer.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Namespace in Imports field not imported from: ‘rappdirs’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/FindIt.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/FisherEM.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R   6.4Mb
Namespaces in Imports field not imported from:
  ‘stats’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
Running examples in ‘forega-Ex.R’ failed
The error most likely occurred in:

> ### Name: ForecastArima
> ### Title: Floating-Point Genetic Algorithms with Statistical Forecast
> ###   Based Inheritance Operator
> ### Aliases: ForecastArima
> ### Keywords: methods
> 
> ### ** Examples
> 
> 
> # Required package forega
> require("forega")
> 
> set.seed(12345)
> 
> # This function has the global minimum at x_1 = pi and x_2 = exp(1)
> f <- function (x){
+ 	return( (x[1]-pi)^2 + (x[2]-2.71828)^2 )
+ }
> 
> # Performing a floating-point genetic algorithm search with forecast probability of 0.10
> res <- forecasting_ga(evalFunc=f, chsize=2, minv=rep(-10.0,2),
+                       maxv=rep(10.0,2), crossprob=0.80, mutationprob=0.01, 
+                       popsize=100, maxiter=1000, MinimumForecastLength=20, 
+                       ForecastFunction=ForecastArima, elitism=2, forecastprob=0.01)
Error in forecasting_ga(evalFunc = f, chsize = 2, minv = rep(-10, 2),  : 
  Evaluation error: only replacement of elements is allowed.
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/fpc.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Namespaces in Imports field not imported from:
  ‘base’ ‘pbapply’ ‘stringr’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/frailtyHL.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Running examples in ‘FREddyPro-Ex.R’ failed
The error most likely occurred in:

> ### Name: buildTimestamp
> ### Title: Build a timestamp
> ### Aliases: buildTimestamp
> 
> ### ** Examples
> 
> ## Load the data
> data(fluxes)
> 
> ## Clean fluxes
> fluxes=cleanFluxes(fluxes,sdCor=TRUE,sdTimes=3,timesList=3,distCor=TRUE,
+                    thresholdList=list(H=c(-100,1000),LE=c(-100,1000)))	
> 
> ## Remove some line as an example
> fluxes=fluxes[-c(832,833,834,835,840,953),]
> 
> ## Create timestamp from date and time
> fluxes=createTimestamp(fluxes)
> 
> ## Now fill the gap timestmaps with NA's
> fluxes=fillTimestamp(fluxes,flux=TRUE)
[1] Discontinuity in 3 instances
[1] 2014-06-14 03:30:00 UTC 2014-06-14 06:00:00 UTC 2014-06-16 14:30:00 UTC
Error in FUN(X[[i]], ...) : subscript out of bounds
Calls: fillTimestamp ... shift_time -> [[ -> [[.POSIXlt -> .POSIXlt -> lapply
Execution halted
Found the following significant warnings:
  psplines.c:975:16: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  psplines.c:1087:15: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/freeknotsplines.Rcheck/00install.out’ for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   5.7Mb
Package which this enhances but not available for checking: ‘dggrids’
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    1.6Mb
Package suggested but not available for checking: ‘RTCGA.rnaseq’
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   9.1Mb
Namespaces in Imports field not imported from:
  ‘R.utils’ ‘grDevices’ ‘graphics’ ‘matrixStats’ ‘stats’
  All declared Imports should be used.
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    libs  18.0Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(funrar)
  > 
  > test_check("funrar")
  ── 1. Error: 'distinctiveness_dimensions()' outputs good objects (@test-rarity_d
  bad value
  1: expect_true(di_dim %>% vapply(class, c("char")) %>% =="matrix" %>% all()) at testthat/test-rarity_dimensions.R:42
  2: quasi_label(enquo(object), label)
  3: force(quo)
  4: enquo(object)
  
  ── 2. Error: 'distinctiveness_dimensions()' works with sparse matrices (@test-ra
  bad value
  1: expect_true(sparse_di_dim %>% vapply(class, c("char")) %>% =="dgeMatrix" %>% all()) at testthat/test-rarity_dimensions.R:94
  2: quasi_label(enquo(object), label)
  3: force(quo)
  4: enquo(object)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 167 SKIPPED: 0 FAILED: 2
  1. Error: 'distinctiveness_dimensions()' outputs good objects (@test-rarity_dimensions.R#42) 
  2. Error: 'distinctiveness_dimensions()' works with sparse matrices (@test-rarity_dimensions.R#94) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
fuzzyBHexact: warning in round(pvals, d = dp): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(pprev, d = dp): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(p.minus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(p.plus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(a.minus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(a.plus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(new.p.minus, d = 4): partial argument
  match of 'd' to 'digits'
fuzzyBHexact: warning in round(new.p.plus, d = 4): partial argument
  match of 'd' to 'digits'
fuzzyBHexact: warning in round(pvals, d = 4): partial argument match of
  'd' to 'digits'
fuzzyBHexact: warning in round(pprev, d = 4): partial argument match of
  'd' to 'digits'
fuzzyBHexact: warning in round(tau, d = 4): partial argument match of
  'd' to 'digits'
probRejTies: no visible binding for global variable ‘nn’
Undefined global functions or variables:
  nn
Package suggested but not available for checking: ‘WGCNA’
Package suggested but not available for checking: ‘ArrayBin’
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘maptools’ ‘rgeos’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘DAAGbio’
Running examples in ‘GAMens-Ex.R’ failed
The error most likely occurred in:

> ### Name: GAMens
> ### Title: Applies the GAMbag, GAMrsm or GAMens ensemble classifier to a
> ###   data set
> ### Aliases: GAMens
> ### Keywords: models classif
> 
> ### ** Examples
> 
> 
> ## Load data (mlbench library should be loaded)
> library(mlbench)
> data(Ionosphere)
> 
> ## Train a GAMens ensemble,
> ## estimated using 4 nonparametric terms and 2 linear terms
> Ionosphere.GAMens <- GAMens(Class~s(V3,4)+s(V4,4)+s(V5,3)+s(V6,5)+V7+V8,
+ Ionosphere ,3 , autoform=FALSE, iter=10 )
Error in predict.gam(gam_model, oob_data, type = "response") : 
  could not find function "predict.gam"
Calls: GAMens
Execution halted
Namespaces in Imports field not imported from:
  ‘MASS’ ‘gamlss’
  All declared Imports should be used.
finterp.data.frame: no visible global function definition for
  ‘as.formula’
finterp.data.frame: no visible global function definition for ‘terms’
finterp.data.frame: no visible global function definition for
  ‘model.matrix’
finterp.data.frame: no visible global function definition for
  ‘model.frame’
finterp.default: no visible global function definition for ‘terms’
finterp.default: no visible global function definition for
  ‘model.matrix’
finterp.default: no visible global function definition for
  ‘model.frame’
gamlss.nl: no visible global function definition for ‘nlm’
nl: no visible global function definition for ‘is’
nlgamlss: no visible global function definition for ‘NO’
nlgamlss: no visible global function definition for ‘as.gamlss.family’
nlgamlss: no visible global function definition for ‘nlm’
nlgamlss: no visible global function definition for ‘cov2cor’
summary.nlgamlss: no visible global function definition for ‘coef’
summary.nlgamlss: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  NO as.formula as.gamlss.family coef cov2cor is model.frame
  model.matrix nlm pnorm terms
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "as.formula", "coef", "cov2cor", "model.frame",
             "model.matrix", "nlm", "pnorm", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   8.4Mb
installed size is 63.1Mb
  sub-directories of 1Mb or more:
    libs  62.7Mb
installed size is 77.0Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     73.7Mb
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  16.3Mb
Found the following significant warnings:
  cGetHCS.c:9:33: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  cIdentical.c:9:34: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/gdmp.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘rootSolve’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/GenABEL.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   4.8Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/GeneFeST.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    exdata   5.1Mb
Packages suggested but not available for checking:
  ‘KEGG.db’ ‘reactome.db’ ‘AnnotationDbi’
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.6Mb
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    data  26.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R         3.5Mb
    extdata   1.4Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   8.9Mb
Namespace in Imports field not imported from: ‘velociraptr’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/geo.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘shinydashboard’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/gettingtothebottom.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/gfer.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Namespace in Imports field not imported from: ‘plotly’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Namespaces in Imports field not imported from:
  ‘GGEBiplotGUI’ ‘gge’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colorspace’ ‘grid’ ‘rstan’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘lazyeval’ ‘readr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘XML’ ‘mapproj’ ‘moonBook’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘NHANES’ ‘gridExtra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gcookbook’ ‘ggthemes’ ‘moonBook’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘randomForest’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   2.1Mb
Namespaces in Imports field not imported from:
  ‘DBI’ ‘GGally’ ‘RColorBrewer’ ‘Rcpp’ ‘assertthat’ ‘backports’
  ‘colorspace’ ‘colourpicker’ ‘evaluate’ ‘futile.options’ ‘gdtools’
  ‘gtable’ ‘htmltools’ ‘htmlwidgets’ ‘httpuv’ ‘labeling’ ‘lambda.r’
  ‘lazyeval’ ‘magrittr’ ‘miniUI’ ‘munsell’ ‘plyr’ ‘reshape’ ‘rprojroot’
  ‘scales’ ‘stringi’ ‘stringr’ ‘svglite’ ‘tibble’ ‘xtable’ ‘yaml’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Quitting from lines 332-362 (ggrepel.Rmd) 
Error: processing vignette 'ggrepel.Rmd' failed with diagnostics:
there is no package called 'gridExtra'
Execution halted
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Namespace in Imports field not imported from: ‘mockery’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is 29.3Mb
  sub-directories of 1Mb or more:
    libs  29.0Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is 51.1Mb
  sub-directories of 1Mb or more:
    libs  50.2Mb
installed size is 47.2Mb
  sub-directories of 1Mb or more:
    libs  46.0Mb
Package suggested but not available for checking: ‘cplexAPI’
Package suggested but not available for checking: ‘mutoss’
Found the following significant warnings:
  Evaluation.cpp:173:9: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to true [-Wtautological-undefined-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/gnmf.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘car’ ‘wordcloud’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/GPGame.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/GPseq.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    R  19.3Mb
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Sxslt’
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
Namespaces in Imports field not imported from:
  ‘methods’ ‘raster’ ‘rgeos’ ‘sp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘deldir’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘BiasedUrn’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/GroupSeq.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
Package suggested but not available for checking: ‘impute’
Namespace in Imports field not imported from: ‘rrcov’
  All declared Imports should be used.
Package suggested but not available for checking: ‘interval’
installed size is 126.4Mb
  sub-directories of 1Mb or more:
    java  124.6Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
Found the following significant warnings:
  SNPHWEX.cpp:50:31: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  SNPHWEX.cpp:51:65: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/data/gannet/ripley/R/packages/tests-clang/HardyWeinberg.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ./City.h:82:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  City.cpp:93:26: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  City.cpp:94:26: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  City.cpp:95:26: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  City.cpp:96:26: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  MurmurHash3.cpp:87:8: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  MurmurHash3.cpp:89:8: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  MurmurHash3.cpp:267:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  MurmurHash3.cpp:268:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ./Spooky.h:285:36: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/data/gannet/ripley/R/packages/tests-clang/hashFunction.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ../inst/include/hashmap/sparsepp/spp.h:2342:21: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ../inst/include/hashmap/sparsepp/spp.h:2365:22: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/data/gannet/ripley/R/packages/tests-clang/hashmap.Rcheck/00install.out’ for details.
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    libs  18.2Mb
Namespace in Imports field not imported from: ‘hms’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/hbmem.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  20.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Package suggested but not available for checking: ‘synbreed’
Packages suggested but not available for checking:
  ‘marray’ ‘affy’ ‘Biobase’ ‘limma’
Namespace in Imports field not imported from: ‘ratelimitr’
  All declared Imports should be used.
Found the following significant warnings:
  Note: possible error in 'dgpd(x, xi = a, mu = 0, ': unused arguments (xi = a, mu = 0, beta = 1 - a) 
  Note: possible error in 'pgpd(q, xi = a, mu = 0, ': unused arguments (xi = a, mu = 0, beta = 1 - a) 
  Note: possible error in 'qgpd(p, xi = a, mu = 0, ': unused arguments (xi = a, mu = 0, beta = 1 - a) 
See ‘/data/gannet/ripley/R/packages/tests-clang/HiDimMaxStable.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Package suggested but not available for checking: ‘XMLRPC’
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    doc          13.7Mb
    htmlwidgets   1.9Mb
Error in re-building vignettes:
  ...
Highcharts (www.highcharts.com) is a Highsoft software product which is
not free for commercial and Governmental use

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

trying URL 'https://code.highcharts.com/mapdata/countries/nz/nz-all.js'
Content type 'application/x-javascript' length 36810 bytes (35 KB)
==================================================
downloaded 35 KB

trying URL 'https://code.highcharts.com/mapdata/custom/usa-and-canada.js'
Content type 'application/x-javascript' length 134466 bytes (131 KB)
==================================================
downloaded 131 KB

trying URL 'https://code.highcharts.com/mapdata/countries/us/us-ca-all.js'
Content type 'application/x-javascript' length 40824 bytes (39 KB)
==================================================
downloaded 39 KB

trying URL 'https://code.highcharts.com/mapdata/countries/us/us-all.js'
Content type 'application/x-javascript' length 66923 bytes (65 KB)
==================================================
downloaded 65 KB

trying URL 'https://code.highcharts.com/mapdata/countries/us/us-all.js'
Content type 'application/x-javascript' length 66923 bytes (65 KB)
==================================================
downloaded 65 KB

trying URL 'https://code.highcharts.com/mapdata/countries/fj/fj-all.js'
Content type 'application/x-javascript' length 20412 bytes (19 KB)
==================================================
downloaded 19 KB

Quitting from lines 110-132 (charting-maps.Rmd) 
Error: processing vignette 'charting-maps.Rmd' failed with diagnostics:
Please install xml2 package
Execution halted
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    highlight   1.1Mb
    libs        7.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   4.1Mb
Package suggested but not available for checking: ‘trackr’
Namespace in Imports field not imported from: ‘lmtest’
  All declared Imports should be used.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/hmmm.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/HMMpa.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
print.summary.hotspots: warning in sort(x$data, dec = TRUE): partial
  argument match of 'dec' to 'decreasing'
print.summary.hotspots: warning in sort(x$disprop$positive, dec =
  TRUE): partial argument match of 'dec' to 'decreasing'
print.summary.hotspots: warning in sort(x$disprop$negative, dec =
  TRUE): partial argument match of 'dec' to 'decreasing'
Lchs: no visible global function definition for ‘plot’
Lchs: no visible global function definition for ‘points’
disprop: no visible global function definition for ‘median’
hotspots: no visible global function definition for ‘median’
hotspots: no visible global function definition for ‘qnorm’
hotspots: no visible global function definition for ‘qt’
plot.hotspots: no visible global function definition for ‘par’
summary.hotspots: no visible global function definition for ‘median’
Undefined global functions or variables:
  median par plot points qnorm qt
Consider adding
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "median", "qnorm", "qt")
to your NAMESPACE file.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R     1.9Mb
    doc   2.5Mb
Found the following significant warnings:
  language.c:41:5: warning: flexible array initialization is a GNU extension [-Wgnu-flexible-array-initializer]
See ‘/data/gannet/ripley/R/packages/tests-clang/htmltidy.Rcheck/00install.out’ for details.
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    data  12.8Mb
    doc    1.3Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    dict   1.3Mb
    libs   4.6Mb
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
hyper.plot2d: warning in magmap(sigmas, lo = sigscale[1], hi =
  sigscale[2], flip = TRUE, type = "num"): partial argument match of
  'lo' to 'locut'
hyper.plot2d: warning in magmap(sigmas, lo = sigscale[1], hi =
  sigscale[2], flip = TRUE, type = "num"): partial argument match of
  'hi' to 'hicut'
hyper.plot2d: warning in magmap(seq(sigscale[1], sigscale[2], len =
  100), lo = sigscale[1], hi = sigscale[2], flip = TRUE, type = "num"):
  partial argument match of 'lo' to 'locut'
hyper.plot2d: warning in magmap(seq(sigscale[1], sigscale[2], len =
  100), lo = sigscale[1], hi = sigscale[2], flip = TRUE, type = "num"):
  partial argument match of 'hi' to 'hicut'
hyper.plot3d: warning in magmap(sigmas, lo = sigscale[1], hi =
  sigscale[2], flip = TRUE, type = "num"): partial argument match of
  'lo' to 'locut'
hyper.plot3d: warning in magmap(sigmas, lo = sigscale[1], hi =
  sigscale[2], flip = TRUE, type = "num"): partial argument match of
  'hi' to 'hicut'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   3.9Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘ggplot2’ ‘pander’
  All declared Imports should be used.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   5.2Mb
Found the following significant warnings:
  IBDsim.c:27:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:39:20: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:54:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:61:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/IBDsim.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   1.3Mb
    doc    2.2Mb
    libs   1.3Mb
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
Running examples in ‘icesSAG-Ex.R’ failed
The error most likely occurred in:

> ### Name: getSAGGraphs
> ### Title: Get Summary Graphs of Stock Assessment Output
> ### Aliases: getSAGGraphs
> 
> ### ** Examples
> 
> assessmentKey <- findAssessmentKey("cod", 2015)
GETing ... http://sg.ices.dk/StandardGraphsWebServices.asmx/getListStocks?year=2015
> graphs <- getSAGGraphs(assessmentKey[1])
> plot(graphs)
Error in UseMethod("as.raster") : 
  no applicable method for 'as.raster' applied to an object of class "c('ices_standardgraph_list', 'list')"
Calls: plot ... plot.ices_standardgraph_list -> <Anonymous> -> rasterGrob -> as.raster
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      2.1Mb
installed size is 39.8Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs  35.4Mb
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  24.1Mb
Package suggested but not available for checking: ‘PROcess’
Package unavailable to check Rd xrefs: ‘PROcess’
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/IDTurtle.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  src/foreign-pajek-parser.y:449:41: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  src/foreign-pajek-parser.y:453:44: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  src/foreign-pajek-parser.y:464:41: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  src/foreign-pajek-parser.y:468:44: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  ./vector.pmt:1971:19: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  ./vector.pmt:1971:19: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/igraph.Rcheck/00install.out’ for details.
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  15.8Mb
apparently using $(BLAS_LIBS) without following $(FLIBS) in ‘src/Makevars’
  apparently using $(BLAS_LIBS) without following $(FLIBS) in ‘src/Makevars.in’
installed size is 39.6Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       4.9Mb
    extdata   1.0Mb
    include   2.8Mb
    libs     28.9Mb
Namespace in Imports field not imported from: ‘jpeg’
  All declared Imports should be used.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R  10.8Mb
Namespace in Imports field not imported from: ‘mediation’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘count_compare’
Namespaces in Imports field not imported from:
  ‘lme4’ ‘reshape2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘rgeos’
  All declared Imports should be used.
Package unavailable to check Rd xrefs: ‘minfi’
installed size is 26.2Mb
  sub-directories of 1Mb or more:
    libs  26.0Mb
.nndsvd.internal: no visible global function definition for ‘runif’
nmf.mnnals: no visible global function definition for ‘runif’
nmf.opt.k: no visible global function definition for ‘flush.console’
nmf.opt.k: no visible global function definition for ‘points’
nmf.opt.k: no visible global function definition for ‘lines’
nmf.opt.k: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  flush.console lines mtext points runif
Consider adding
  importFrom("graphics", "lines", "mtext", "points")
  importFrom("stats", "runif")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/intpoint.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.4Mb
Found the following significant warnings:
  Note: possible error in 'get.smiles(x, aromatic = T, ': unused arguments (aromatic = T, type = "generic") 
See ‘/data/gannet/ripley/R/packages/tests-clang/iqspr.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   6.8Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘gridExtra’ ‘rBayesianOptimization’
  All declared Imports should be used.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/IRISMustangMetrics.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Package suggested but not available for checking: ‘PMA’
Namespaces in Imports field not imported from:
  ‘colorRamps’ ‘virtualspecies’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘animation’ ‘dplyr’ ‘ndtv’ ‘statnet’ ‘xergm’
  All declared Imports should be used.
Running examples in ‘itunesr-Ex.R’ failed
The error most likely occurred in:

> ### Name: getReviews
> ### Title: Extract Reviews from iTunes App Store
> ### Aliases: getReviews
> 
> ### ** Examples
> 
> getReviews(742044692,'in',1)
Error in open.connection(x, "rb") : HTTP error 502.
Calls: getReviews ... read_xml.character -> read_xml.connection -> open -> open.connection
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(itunesr)
  > 
  > test_check("itunesr")
  ── 1. Error: The output dataframe Type is  (@test-fun.R#6)  ────────────────────
  HTTP error 502.
  1: expect_equal(class(getReviews(370901726, "gb", 1)), "data.frame") at testthat/test-fun.R:6
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: getReviews(370901726, "gb", 1)
  5: xml2::read_xml(xml_url)
  6: read_xml.character(xml_url)
  7: read_xml.connection(con, encoding = encoding, ..., as_html = as_html, base_url = x, 
         options = options)
  8: open(x, "rb")
  9: open.connection(x, "rb")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: The output dataframe Type is  (@test-fun.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘fAssets’ ‘timeDate’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   6.6Mb
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘GGally’ ‘GPArotation’ ‘PMCMR’ ‘R6’ ‘afex’ ‘car’
  ‘emmeans’ ‘ggridges’ ‘lavaan’ ‘multcomp’ ‘mvnormtest’ ‘psych’ ‘vcd’
  ‘vcdExtra’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.7Mb
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    include   1.2Mb
    libs      4.4Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
Namespace in Imports field not imported from: ‘mclust’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stinepack’
  All declared Imports should be used.
Missing or unexported objects:
  ‘MVN::hzTest’ ‘MVN::mardiaTest’ ‘MVN::uniNorm’
Namespaces in Imports field not imported from:
  ‘EQL’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lme4’ ‘metafor’ ‘nlme’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Package suggested but not available for checking: ‘org.Hs.eg.db’
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/kmc.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Package in Depends field not imported from: ‘cluster’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   3.3Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    java   6.0Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R   7.6Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘tibble’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.7Mb
Namespace in Imports field not imported from: ‘RUnit’
  All declared Imports should be used.
kztp: warning in rowMeans(kztp, dim = 2): partial argument match of
  'dim' to 'dims'
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   8.3Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
Found the following significant warnings:
  W_gamma_Cpp.cpp:14:39: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/LambertW.Rcheck/00install.out’ for details.
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs          14.0Mb
    testdata       1.8Mb
    vignettedata   2.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/lava.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    geojson  11.9Mb
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘htmlwidgets’ ‘shiny’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets   4.5Mb
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘scales’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
Package suggested but not available for checking: ‘EBImage’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘memoise’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   8.1Mb
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/liso.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    doc        1.5Mb
    libs      21.9Mb
    testdata   1.5Mb
lmec: warning in qr.Q(qrZ, compl = TRUE): partial argument match of
  'compl' to 'complete'
lmec: warning in qr.Q(qra, compl = TRUE): partial argument match of
  'compl' to 'complete'
lmec: no visible global function definition for ‘lm’
lmec: no visible global function definition for ‘pnorm’
lmec: no visible global function definition for ‘dnorm’
lmec : vtrnorm2: no visible global function definition for ‘runif’
lmec : vtrnorm2: no visible global function definition for ‘qnorm’
lmec : vtrnorm2: no visible global function definition for ‘pnorm’
lmec: no visible global function definition for ‘rnorm’
lmec: no visible global function definition for ‘ar’
Undefined global functions or variables:
  ar dnorm lm pnorm qnorm rnorm runif
Consider adding
  importFrom("stats", "ar", "dnorm", "lm", "pnorm", "qnorm", "rnorm",
             "runif")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘boot’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mnormt’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/LncPriCNet.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Warning: ‘nsimp’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-clang/localdepth.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘distr’
  All declared Imports should be used.
Package in Depends field not imported from: ‘logcondens’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  lsdall.c:2078:21: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2200:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2209:12: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2219:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2225:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/logspline.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘RDRToolbox’
Namespaces in Imports field not imported from:
  ‘NLRoot’ ‘ade4’ ‘glmnet’ ‘lars’ ‘lattice’ ‘logmult’ ‘pdist’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/lqmm.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Note: found 143 marked Latin-1 strings
  Note: found 833 marked UTF-8 strings
Error in re-building vignettes:
  ...
Loading required package: Matrix
Loading required package: sglOptim
Loading required package: foreach
Loading required package: doParallel
Loading required package: iterators
Loading required package: parallel
pandoc: Could not determine mime type for `https://raw.github.com/vincent-dk/lsgl/master/fig1.png'
CallStack (from HasCallStack):
  error, called at src/Text/Pandoc/SelfContained.hs:156:35 in pandoc-1.19.2.1-HmHZrsGgUrp4c4IkMOs9Vr:Text.Pandoc.SelfContained
Error: processing vignette 'README.Rmd' failed with diagnostics:
pandoc document conversion failed with error 1
Execution halted
installed size is 47.9Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  46.1Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘lavaan’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tcltk2’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.3Mb
Namespaces in Imports field not imported from:
  ‘e1071’ ‘utils’
  All declared Imports should be used.
Running examples in ‘m4fe-Ex.R’ failed
The error most likely occurred in:

> ### Name: currentStocks
> ### Title: Current Stock Info (Yahoo Finance API)
> ### Aliases: currentStocks
> 
> ### ** Examples
> 
> currentStocks()
Warning in file(file, "rt") :
  URL 'http://download.finance.yahoo.com/d/quotes.csv?s=GOOGL&f=abb2b3poydr1qc1cc6k2p2d1d2t1c8c3m5m6m7m8m3m4ghk1ll1t8w1w4p1mm2g1g3g4g5g6t7t6i5l2l3v1v7s6kjj5k4j6k5wvj1j3f6nn4ss1xs2ee7e8e9b4j4p5p6rr2r5r6r7s7': status was 'Couldn't resolve host name'
Error in file(file, "rt") : 
  cannot open the connection to 'http://finance.yahoo.com/d/quotes.csv?s=GOOGL&f=abb2b3poydr1qc1cc6k2p2d1d2t1c8c3m5m6m7m8m3m4ghk1ll1t8w1w4p1mm2g1g3g4g5g6t7t6i5l2l3v1v7s6kjj5k4j6k5wvj1j3f6nn4ss1xs2ee7e8e9b4j4p5p6rr2r5r6r7s7'
Calls: currentStocks -> read.csv -> read.table -> file
Execution halted
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    TS_files     5.9Mb
    base_files   6.3Mb
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    libs  24.3Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘cmprsk’ ‘colorspace’ ‘etm’ ‘fracdiff’ ‘gtable’ ‘munsell’
  ‘numDeriv’ ‘plyr’ ‘quadprog’ ‘scales’ ‘timeDate’ ‘tseries’ ‘zoo’
  All declared Imports should be used.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs   4.6Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/MagneticMap.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/ManifoldOptim.Rcheck/00install.out’ for details.
installed size is 32.7Mb
  sub-directories of 1Mb or more:
    mapdata  32.6Mb
Found the following significant warnings:
  perspective.c:12:23: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/mapproj.Rcheck/00install.out’ for details.
Found the following significant warnings:
  mapclip.c:321:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/maps.Rcheck/00install.out’ for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   6.7Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   8.2Mb
Package suggested but not available for checking: ‘ASGSCA’
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Found the following significant warnings:
  Note: possible error in 'writeLines(as.character(yy), ': unused argument (file = outfile) 
See ‘/data/gannet/ripley/R/packages/tests-clang/matR.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
File ‘maxent/libs/maxent.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘kangar00’
Package unavailable to check Rd xrefs: ‘kangar00’
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  10.4Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/mclcar.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   2.7Mb
installed size is 35.9Mb
  sub-directories of 1Mb or more:
    libs  34.8Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
Namespaces in Imports field not imported from:
  ‘parallelMap’ ‘reshape2’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/mdhglm.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   3.9Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   8.0Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘ggplot2’ ‘lavaan’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘RGtk2’ ‘RNifti’ ‘cairoDevice’ ‘gtools’ ‘jsonlite’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘RColorBrewer’ ‘RODBC’ ‘dplyr’ ‘formattable’ ‘ggplot2’
  ‘ggthemes’ ‘magrittr’ ‘mem’ ‘openxlsx’ ‘plotly’ ‘readxl’ ‘shinyBS’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stringi’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘shinyBS’ ‘shinycssloaders’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.4Mb
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.3Mb
Packages suggested but not available for checking:
  ‘GEOquery’ ‘affy’ ‘hgu133plus2.db’ ‘doSMP’ ‘impute’
Packages suggested but not available for checking:
  ‘HTSFilter’ ‘DESeq’ ‘DESeq2’
Error in re-building vignettes:
  ...

Error: processing vignette 'metaRNASeq.Rnw' failed with diagnostics:
 chunk 2 (label = loadparameters) 
Error in library(DESeq2) : there is no package called ‘DESeq2’
Execution halted
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/MetaSubtract.Rcheck/MetaSubtract/extdata’, resetting
Found the following significant warnings:
  binomial-twostage.cpp:78:4: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  binomial-twostage.cpp:280:4: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/mets.Rcheck/00install.out’ for details.
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  16.2Mb
    misc   1.1Mb
File ‘mFilter/R/zzz.R’:
  .onLoad calls:
    writeLines(strwrap(txt, indent = 4, exdent = 4))

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

.onLoad: warning in packageDescription("mFilter", lib = mylib): partial
  argument match of 'lib' to 'lib.loc'
bkfilter: warning in ts(x.cycle, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
bkfilter: warning in ts(x.trend, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
bkfilter: warning in ts(x, star = tsp.x[1], frequency = tsp.x[3]):
  partial argument match of 'star' to 'start'
bwfilter: warning in ts(x.cycle, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
bwfilter: warning in ts(x.trend, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
bwfilter: warning in ts(x, star = tsp.x[1], frequency = tsp.x[3]):
  partial argument match of 'star' to 'start'
cffilter: warning in ts(x.cycle, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
cffilter: warning in ts(x.trend, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
cffilter: warning in ts(x, star = tsp.x[1], frequency = tsp.x[3]):
  partial argument match of 'star' to 'start'
hpfilter: warning in ts(x.cycle, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
hpfilter: warning in ts(x.trend, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
hpfilter: warning in ts(x, star = tsp.x[1], frequency = tsp.x[3]):
  partial argument match of 'star' to 'start'
Package suggested but not available for checking: ‘structSSI’
Running examples in ‘micompr-Ex.R’ failed
The error most likely occurred in:

> ### Name: assumptions.cmpoutput
> ### Title: Get assumptions for parametric tests performed on output
> ###   comparisons
> ### Aliases: assumptions.cmpoutput
> 
> ### ** Examples
> 
> 
> # Create a cmpoutput object from the provided datasets
> cmp <- cmpoutput("All", 0.9, pphpc_ok$data[["All"]], pphpc_ok$obs_lvls)
> 
> # Get the assumptions for the parametric tests performed in cmp
> acmp <- assumptions(cmp)
sROC 0.1-2 loaded
Error: 'roystonTest' is not an exported object from 'namespace:MVN'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 341-342 (paper.Rnw) 
Error: processing vignette 'paper.Rnw' failed with diagnostics:
'roystonTest' is not an exported object from 'namespace:MVN'
Execution halted
Namespaces in Imports field not imported from:
  ‘DiceDesign’ ‘MaxPro’ ‘doSNOW’ ‘jpeg’
  All declared Imports should be used.
cdf.pval: no visible global function definition for ‘median’
cdf.pval: no visible binding for global variable ‘ecdf’
find_hits: no visible global function definition for ‘na.omit’
mad.scores: no visible global function definition for ‘as.formula’
mad.scores: no visible binding for global variable ‘median’
mad.scores: no visible binding for global variable ‘mad’
rm.outliers: no visible global function definition for ‘as.formula’
rm.outliers: no visible binding for global variable ‘median’
rm.outliers: no visible binding for global variable ‘mad’
Undefined global functions or variables:
  as.formula ecdf mad median na.omit
Consider adding
  importFrom("stats", "as.formula", "ecdf", "mad", "median", "na.omit")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘cluster’ ‘dendextend’ ‘npmv’ ‘utils’
  All declared Imports should be used.
Found the following significant warnings:
  ggum_derivs.cpp:299:47: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  ggum_derivs.cpp:299:51: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  ggum_derivs.cpp:301:49: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  ggum_derivs.cpp:301:53: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  ggum_derivs.cpp:306:50: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  ggum_derivs.cpp:306:54: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  ggum_derivs.cpp:1800:58: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  ggum_derivs.cpp:1800:62: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  ggum_derivs.cpp:1841:58: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  ggum_derivs.cpp:1841:62: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/mirt.Rcheck/00install.out’ for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   5.4Mb
Found the following significant warnings:
  simcensor.cpp:91:16: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:91:41: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:95:17: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/missDeaths.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   4.0Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/mixor.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Namespace in Imports field not imported from: ‘rjags’
  All declared Imports should be used.
Packages unavailable to check Rd xrefs: ‘genefilter’, ‘limma’
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘foreach’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘iterators’ ‘parallel’
  All declared Imports should be used.
Package suggested but not available for checking: ‘GeneSelector’
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
Packages suggested but not available for checking:
  ‘minfi’ ‘GEOquery’ ‘BiocStyle’
Error in re-building vignettes:
  ...
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called ‘BiocStyle’
Execution halted
Running ‘run-base.R’ [400s/425s]
  Running ‘run-classif.R’
  Running ‘run-cluster.R’
  Running ‘run-featsel.R’
  Running ‘run-learners-classif.R’
  Running ‘run-learners-classiflabelswitch.R’
  Running ‘run-learners-cluster.R’
  Running ‘run-learners-general.R’
  Running ‘run-learners-multilabel.R’
  Running ‘run-learners-regr.R’
  Running ‘run-learners-surv.R’
  Running ‘run-multilabel.R’
  Running ‘run-parallel.R’
  Running ‘run-regr.R’
  Running ‘run-stack.R’
  Running ‘run-surv.R’
  Running ‘run-tune.R’
Running the tests in ‘tests/run-base.R’ failed.
Complete output:
  > library(testthat)
  > test_check("mlr", filter = "base")
  Loading required package: mlr
  Loading required package: ParamHelpers
  OMP: Warning #96: Cannot form a team with 6 threads, using 2 instead.
  OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  ── 1. Error: check measure calculations (@test_base_measures.R#637)  ───────────
  object 'mldr_HL' not found
  1: expect_equal(mldr:::mldr_HL(multi.y, multi.p), measureMultilabelHamloss(multi.y, 
         multi.p)) at testthat/test_base_measures.R:637
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: mldr:::mldr_HL
  5: get(name, envir = asNamespace(pkg), inherits = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2652 SKIPPED: 8 FAILED: 1
  1. Error: check measure calculations (@test_base_measures.R#637) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: ‘plotrix’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sads’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘fields’ ‘iterpc’
  All declared Imports should be used.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.7Mb
    libs   2.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    2.3Mb
Running ‘testthat.R’ [8s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(Momocs)
  This is Momocs 1.2.2
  
  Attaching package: 'Momocs'
  
  The following object is masked from 'package:stats':
  
      filter
  
  The following object is masked from 'package:base':
  
      table
  
  > 
  > test_check("Momocs")
  ── 1. Error: filter works fine (@test-nse.R#62)  ───────────────────────────────
  bad value
  1: expect_true(x_lite$fac %>% sapply(nlevels) %>% ==1 %>% all) at testthat/test-nse.R:62
  2: quasi_label(enquo(object), label)
  3: force(quo)
  4: enquo(object)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 159 SKIPPED: 1 FAILED: 1
  1. Error: filter works fine (@test-nse.R#62) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   7.7Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/MortHump.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘caret’ ‘ggformula’ ‘knitr’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   2.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.7Mb
export.summary.mpm: warning in complex(real = x$Rows[, FdimsR[1]], imag
  = x$Rows[, FdimsR[2]]): partial argument match of 'imag' to
  'imaginary'
export.summary.mpm: warning in complex(real = x$Columns[, FdimsC[1]],
  imag = x$Columns[, FdimsC[2]]): partial argument match of 'imag' to
  'imaginary'
.onAttach: no visible global function definition for
  ‘packageDescription’
export.summary.mpm: no visible global function definition for
  ‘write.table’
mpm: no visible binding for global variable ‘median’
plot.mpm: no visible global function definition for ‘rainbow’
plot.mpm: no visible global function definition for ‘quantile’
plot.mpm: no visible global function definition for ‘par’
plot.mpm: no visible global function definition for ‘points’
plot.mpm: no visible global function definition for ‘smoothScatter’
plot.mpm: no visible global function definition for ‘colorRampPalette’
plot.mpm: no visible global function definition for ‘symbols’
plot.mpm: no visible global function definition for ‘text’
plot.mpm: no visible global function definition for ‘lines’
plot.mpm: no visible global function definition for ‘box’
Undefined global functions or variables:
  box colorRampPalette lines median packageDescription par points
  quantile rainbow smoothScatter symbols text write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "rainbow")
  importFrom("graphics", "box", "lines", "par", "points",
             "smoothScatter", "symbols", "text")
  importFrom("stats", "median", "quantile")
  importFrom("utils", "packageDescription", "write.table")
to your NAMESPACE file.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    libs  14.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   2.5Mb
Package unavailable to check Rd xrefs: ‘Biostrings’
Namespaces in Imports field not imported from:
  ‘MASS’ ‘moments’ ‘mvtnorm’
  All declared Imports should be used.
installed size is 45.0Mb
  sub-directories of 1Mb or more:
    libs  44.6Mb
Error in re-building vignettes:
  ...
pandoc: Could not determine mime type for `https://raw.github.com/vincent-dk/msgl/master/fig1.png'
CallStack (from HasCallStack):
  error, called at src/Text/Pandoc/SelfContained.hs:156:35 in pandoc-1.19.2.1-HmHZrsGgUrp4c4IkMOs9Vr:Text.Pandoc.SelfContained
Error: processing vignette 'README.Rmd' failed with diagnostics:
pandoc document conversion failed with error 1
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/mstR.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Namespaces in Imports field not imported from:
  ‘hms’ ‘methods’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Found the following significant warnings:
  Note: possible error in 'theme(axis.text.x = element_text(size = 6, ': formal argument "axis.text.x" matched by multiple actual arguments 
See ‘/data/gannet/ripley/R/packages/tests-clang/multilevelPSA.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 72.2Mb
  sub-directories of 1Mb or more:
    libs  72.0Mb
Package unavailable to check Rd xrefs: ‘ComplexHeatmap’
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/MultiPhen.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Namespaces in Imports field not imported from:
  ‘boot’ ‘ggplot2’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/mvmeta.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    java  13.8Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
Namespace in Imports field not imported from: ‘purrrlyr’
  All declared Imports should be used.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/ncappc.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/ncf.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   3.8Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘fields’ ‘mvtnorm’
  All declared Imports should be used.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   6.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   5.9Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Namespaces in Imports field not imported from:
  ‘mgcv’ ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘devtools’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
Namespaces in Imports field not imported from:
  ‘htmlTable’ ‘lme4’ ‘stringi’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/nimble.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    CppCode        1.0Mb
    R              5.8Mb
    classic-bugs   1.6Mb
    include        5.8Mb
    tests          1.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
Namespaces in Imports field not imported from:
  ‘dparser’ ‘inline’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.3Mb
Packages suggested but not available for checking: ‘RcppOctave’ ‘Biobase’
Package unavailable to check Rd xrefs: ‘Biobase’
Unknown package ‘RcppOctave’ in Rd xrefs
Error in .requirePackage(package) : 
    unable to find required package 'Biobase'
  Calls: <Anonymous> ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 385-398 (NMF-vignette.Rnw) 
Error: processing vignette 'NMF-vignette.Rnw' failed with diagnostics:
unable to find required package 'Biobase'
Execution halted
Namespaces in Imports field not imported from:
  ‘geosphere’ ‘lwgeom’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘XML’ ‘choroplethr’ ‘choroplethrMaps’ ‘data.table’
  ‘forcats’ ‘hurricaneexposure’ ‘plyr’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/novelist.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  utilities.c:175:32: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/npcp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/npde.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘mclust’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Namespace in Imports field not imported from: ‘rts’
  All declared Imports should be used.
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs  14.2Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   8.1Mb
Note: found 13172 marked Latin-1 strings
installed size is 39.0Mb
  sub-directories of 1Mb or more:
    extdata  38.9Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   8.7Mb
File ‘nws/R/zzz.R’:
  .onLoad calls:
    require(methods)

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

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

Found the following assignments to the global environment:
File ‘nws/R/workerLoop.R’:
  assign("SleighName", displayName, globalenv())
  assign("SleighNws", nws, globalenv())
  assign("SleighUserNws", userNws, globalenv())
  assign("SleighRank", rank, globalenv())
  assign("SleighWorkerCount", workerCount, globalenv())
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   2.2Mb
installed size is 97.9Mb
  sub-directories of 1Mb or more:
    libs  97.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Namespaces in Imports field not imported from:
  ‘randomForest’ ‘ranger’
  All declared Imports should be used.
installed size is 147.2Mb
  sub-directories of 1Mb or more:
    R         2.3Mb
    libs    137.4Mb
    models    4.7Mb
apparently using $(LAPACK_LIBS) without following $(BLAS_LIBS) in ‘src/Makevars’
  apparently using $(BLAS_LIBS) without following $(FLIBS) in ‘src/Makevars’
  apparently using $(LAPACK_LIBS) without following $(BLAS_LIBS) in ‘src/Makevars.in’
  apparently using $(BLAS_LIBS) without following $(FLIBS) in ‘src/Makevars.in’
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    java     1.2Mb
    models   6.0Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/OpenRepGrid.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Running ‘testthat.R’ [18s/24s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > test_check("openxlsx")
  Loading required package: openxlsx
  ── 1. Error: loadWorkbook from different sources (@test-read_sources.R#49)  ────
  subscript out of bounds
  1: expect_true(all.equal.Workbook(wb_url, wb_file), "Loading from URL vs local not equal") at testthat/test-read_sources.R:49
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: all.equal.Workbook(wb_url, wb_file)
  5: sapply(1:nSheets, function(i) isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]])))
  6: lapply(X = X, FUN = FUN, ...)
  7: FUN(X[[i]], ...)
  8: isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]]))
  9: all.equal(x$colWidths[[i]], y$colWidths[[i]])
  10: all.equal.list(x$colWidths[[i]], y$colWidths[[i]])
  11: attr.all.equal(target, current, ...)
  12: mode(current)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 505 SKIPPED: 2 FAILED: 1
  1. Error: loadWorkbook from different sources (@test-read_sources.R#49) 
  
  Error: testthat unit tests failed
  Execution halted
Packages suggested but not available for checking:
  ‘Biobase’ ‘annotate’ ‘GO.db’ ‘org.At.tair.db’
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      3.2Mb
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of 'nr' to 'nrow'
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of 'nc' to 'ncol'
bgmm: no visible global function definition for ‘ecdf’
bgmm : SplineGMM: no visible global function definition for
  ‘constrOptim’
blr: no visible global function definition for ‘ecdf’
blr: no visible global function definition for ‘constrOptim’
blr: no visible global function definition for ‘lm’
parentcdf : combinations: no visible global function definition for
  ‘combn’
parentcdf : solver: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  combn constrOptim ecdf lm uniroot
Consider adding
  importFrom("stats", "constrOptim", "ecdf", "lm", "uniroot")
  importFrom("utils", "combn")
to your NAMESPACE file.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Packages suggested but not available for checking: ‘IsoGene’ ‘Biobase’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    nifti   3.8Mb
Found the following significant warnings:
  ccaRevolution.c:31:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:44:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:97:23: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:98:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:110:23: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:111:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/osc.Rcheck/00install.out’ for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   5.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
Package suggested but not available for checking: ‘Rcplex’
Namespace in Imports field not imported from: ‘quantreg’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   2.1Mb
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/PAactivPAL.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Package which this enhances but not available for checking: ‘BiocInstaller’
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/packrat.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
[,ClassW: warning in switch(EXP = i, u1 = {: partial argument match of
  'EXP' to 'EXPR'
[,ClassW: warning in return(x@u1): partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in }, u2 = {: partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in return(x@u2): partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in }, w1 = {: partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in return(x@w1): partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in }): partial argument match of 'EXP' to 'EXPR'
[<-,ClassW: warning in switch(EXP = i, u1 = {: partial argument match
  of 'EXP' to 'EXPR'
[<-,ClassW: warning in x@u1 <- value: partial argument match of 'EXP'
  to 'EXPR'
[<-,ClassW: warning in }, u2 = {: partial argument match of 'EXP' to
  'EXPR'
[<-,ClassW: warning in x@u2 <- value: partial argument match of 'EXP'
  to 'EXPR'
[<-,ClassW: warning in }, w1 = {: partial argument match of 'EXP' to
  'EXPR'
[<-,ClassW: warning in x@w1 <- value: partial argument match of 'EXP'
  to 'EXPR'
[<-,ClassW: warning in }): partial argument match of 'EXP' to 'EXPR'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data        1.6Mb
    localdata   3.1Mb
Running examples in ‘patentsview-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_fields
> ### Title: Get list of retrievable fields
> ### Aliases: get_fields
> 
> ### ** Examples
> 
> # Get all assignee-level fields for the patents endpoint:
> fields <- get_fields(endpoint = "patents", groups = "assignees")
> 
> #...Then pass to search_pv:
> search_pv(
+   query = '{"_gte":{"patent_date":"2007-01-04"}}',
+   fields = fields
+ )
$data
#### A list with a single data frame (with list column(s) inside) on a patent level:

List of 1
 $ patents:'data.frame':	25 obs. of  1 variable:
  ..$ assignees:List of 25

$query_results
#### Distinct entity counts across all downloadable pages of output:

total_patent_count = 100,000
> 
> # Get all patent and assignee-level fields for the patents endpoint:
> fields <- get_fields(endpoint = "patents", groups = c("assignees", "patents"))
> 
> #...Then pass to search_pv:
> search_pv(
+   query = '{"_gte":{"patent_date":"2007-01-04"}}',
+   fields = fields
+ )
Error: Query execution failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
Namespace in Imports field not imported from: ‘ade4’
  All declared Imports should be used.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    lib   9.5Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc        1.3Mb
    examples   1.7Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pander’
  All declared Imports should be used.
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   2.1Mb
    libs   6.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
Namespace in Imports field not imported from: ‘fda’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/pdolsms.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Namespaces in Imports field not imported from:
  ‘car’ ‘sandwich’
  All declared Imports should be used.
Found the following significant warnings:
  spectrum.c:707:14: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:715:20: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1606:41: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1654:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1654:63: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/Peaks.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘globaltest’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Error in re-building vignettes:
  ...
Loading required package: survival
Welcome to penalized. For extended examples, see vignette("penalized").

Error: processing vignette 'penalized.Rnw' failed with diagnostics:
 chunk 31 (label = globaltest) 
Error in library(globaltest) : there is no package called ‘globaltest’
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/pendensity.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/penRvine.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘devtools’ ‘ggplot2’ ‘haven’ ‘tidyverse’
  All declared Imports should be used.
Running examples in ‘PerformanceAnalytics-Ex.R’ failed
The error most likely occurred in:

> ### Name: Omega
> ### Title: calculate Omega for a return series
> ### Aliases: Omega
> 
> ### ** Examples
> 
> data(edhec)
>     Omega(edhec)
               Convertible Arbitrage CTA Global Distressed Securities
Omega (L = 0%)              2.602138   1.936841              3.230443
               Emerging Markets Equity Market Neutral Event Driven
Omega (L = 0%)         1.765435              6.213714     2.999655
               Fixed Income Arbitrage Global Macro Long/Short Equity
Omega (L = 0%)               2.585943     3.516616          2.438064
               Merger Arbitrage Relative Value Short Selling Funds of Funds
Omega (L = 0%)         4.595886       3.815368      1.228785       2.460153
>     Omega(edhec[,13],method="interp",output="point")
Error: 'Ecdf.default' is not an exported object from 'namespace:Hmisc'
Execution halted
Namespace in Imports field not imported from: ‘goft’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      4.4Mb
    data   3.1Mb
Namespaces in Imports field not imported from:
  ‘Rgraphviz’ ‘cluster’ ‘graph’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/phalen.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
color.bar: no visible global function definition for ‘axis’
color.bar: no visible global function definition for ‘rect’
load.data: no visible global function definition for ‘read.csv’
load.geneset: no visible global function definition for ‘read.csv’
phantom.report.optk: no visible global function definition for
  ‘write.table’
plot.pareto.front: no visible global function definition for ‘points’
plot.pareto.front: no visible global function definition for ‘lines’
plot.pareto.front: no visible global function definition for ‘legend’
plot.pareto.front: no visible global function definition for ‘title’
plot.phantom: no visible global function definition for ‘par’
plot.phantom: no visible global function definition for ‘layout’
plot.phantom: no visible global function definition for ‘points’
plot.phantom: no visible global function definition for ‘lines’
plot.phantom: no visible global function definition for ‘title’
Undefined global functions or variables:
  axis layout legend lines par points read.csv rect title write.table
Consider adding
  importFrom("graphics", "axis", "layout", "legend", "lines", "par",
             "points", "rect", "title")
  importFrom("utils", "read.csv", "write.table")
to your NAMESPACE file.
Package suggested but not available for checking: ‘BiocParallel’
Found the following significant warnings:
  LJMA_arms.c:297:11: warning: comparison of array 'env->p' equal to a null pointer is always false [-Wtautological-pointer-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/PhaseType.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘RankProd’
Package unavailable to check Rd xrefs: ‘RankProd’
Found the following significant warnings:
  phreeqcpp/cvode.cpp:3783:8: warning: explicitly assigning value of variable of type 'realtype' (aka 'double') to itself [-Wself-assign]
  phreeqcpp/model.cpp:3047:7: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  phreeqcpp/model.cpp:3048:7: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:142:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:155:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:167:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:179:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:193:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:205:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/transport.cpp:630:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/phreeqc.Rcheck/00install.out’ for details.
installed size is 42.0Mb
  sub-directories of 1Mb or more:
    libs  41.3Mb
Namespaces in Imports field not imported from:
  ‘gplots’ ‘phytools’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Found the following significant warnings:
  Note: possible error in 'try(xtriple, ftriple, ': unused arguments (lfmid, 1, 2) 
  Note: possible error in 'try(xtriple, ftriple, ': unused arguments (rfmid, 2, 3) 
See ‘/data/gannet/ripley/R/packages/tests-clang/phyreg.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/PhySortR.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/picante.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.4Mb
Package suggested but not available for checking: ‘ReportingTools’
Package suggested but not available for checking: ‘BiocStyle’
installed size is 30.4Mb
  sub-directories of 1Mb or more:
    libs  30.3Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘RColorBrewer’ ‘arm’ ‘epiDisplay’ ‘foreign’ ‘gbm’
  ‘grid’ ‘lattice’ ‘latticeExtra’ ‘lme4’ ‘nnet’ ‘parallel’ ‘splines’
  ‘survey’ ‘twang’ ‘xtable’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘hexbin’ ‘quantreg’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘stats’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/plsRglm.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: possible error in 'add_edges_from_table(p, ': unused argument (ndf_mapping = "name_without_space") 
See ‘/data/gannet/ripley/R/packages/tests-clang/pmap.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
create_pmap_graph: possible error in add_edges_from_table(p, table =
  edges %>% select(-amount), from_col = "from", to_col = "to",
  ndf_mapping = "name_without_space"): unused argument (ndf_mapping =
  "name_without_space")
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/pmlr.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘digest’ ‘htmltools’ ‘knitr’ ‘lazyWeave’ ‘lubridate’ ‘rJava’
  All declared Imports should be used.
Running examples in ‘pointblank-Ex.R’ failed
The error most likely occurred in:

> ### Name: col_exists
> ### Title: Verify that one or more columns exist
> ### Aliases: col_exists
> 
> ### ** Examples
> 
> # Validate that column `a` exists in
> # the `small_table` CSV file; do this
> # by creating an agent, focussing on
> # that table, creating a `col_exists()`
> # step, and then interrogating the table
> agent <-
+   create_agent() %>%
+   focus_on(
+     file_name = 
+       system.file(
+         "extdata", "small_table.csv",
+         package = "pointblank"),
+     col_types = "TDicidlc") %>%
+   col_exists(column = a) %>%
+   interrogate()
Error: `UQ()` can only be used within a quasiquoted argument
Execution halted
Found the following significant warnings:
  heftall.c:1389:2: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  lsdall.c:2077:21: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  lspecall.c:505:12: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  lspecall.c:999:21: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  lspecall.c:1078:18: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2199:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2208:12: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2218:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2224:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/polspline.Rcheck/00install.out’ for details.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      6.4Mb
    data   2.5Mb
Found the following significant warnings:
  whopgenome/rdnapp_MAF.h:243:12: warning: explicitly assigning value of variable of type 'unsigned int' to itself [-Wself-assign]
  whopgenome/whoptbi_info.cpp:115:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  whopgenome/whoptbi_info.cpp:120:7: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  whopgenome/whoptbi_region.cpp:78:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/PopGenome.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Package suggested but not available for checking: ‘lfa’
Package suggested but not available for checking: ‘VariantAnnotation’
Error in re-building vignettes:
  ...
Loading required package: dplyr

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: DBI

Attaching package: ‘poplite’

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

    select

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

    filter

Error in makeSchemaFromData(dna, "dna") : 
  ERROR: The names of the supplied data.frame need to be modified for the database see correct.df.names
Starting clinical
Starting samples
Starting dna
Warning: call dbDisconnect() when finished working with a connection
Error in filter_.Database(.data, .dots = compat_as_lazy_dots(...)) : 
  ERROR: Cannot uniquely map columns to table, try using: tableX.columnY
Starting gender
Starting clinical
Starting samples
Starting dna

Error: processing vignette 'poplite.Rnw' failed with diagnostics:
 chunk 15 
Error in library(VariantAnnotation) : 
  there is no package called ‘VariantAnnotation’
Execution halted
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/PortfolioAnalytics.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
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 ‘/data/gannet/ripley/R/packages/tests-clang/powell.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/powerCompRisk.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  ppcctest_pearson3.c:19:66: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/ppcc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ./shared.h:56:9: warning: result of comparison of constant 2147483648 with expression of type 'int' is always false [-Wtautological-constant-out-of-range-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/praznik.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘PerfMeas’
Found the following significant warnings:
  sum.c:221:11: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  sum.c:221:22: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  sum.c:227:52: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  sum.c:227:60: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/PreciseSums.Rcheck/00install.out’ for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.6Mb
Found the following significant warnings:
  Note: possible error in 'psf(data = dataIn1, n.ahead = nextVal)': unused argument (n.ahead = nextVal) 
See ‘/data/gannet/ripley/R/packages/tests-clang/PredictTestbench.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘graphics’ ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘methods’ ‘utils’
  All declared Imports should be used.
Packages suggested but not available for checking: ‘gurobi’ ‘lpsymphony’
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    libs  19.8Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/processmapR.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
process_map: no visible global function definition for
  ‘set_global_graph_attrs’
Undefined global functions or variables:
  set_global_graph_attrs
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/PROFANCY.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/profileR.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Package suggested but not available for checking: ‘qtbase’
Namespaces in Imports field not imported from:
  ‘distcrete’ ‘incidence’
  All declared Imports should be used.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
Packages suggested but not available for checking: ‘ALDEx2’ ‘limma’
Files which contain pragma(s) suppressing diagnostics:
  ‘src/geobuf.pb.h’ ‘src/rexp.pb.h’
Packages suggested but not available for checking:
  ‘Biostrings’ ‘GOSemSim’ ‘org.Hs.eg.db’
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.1Mb
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘forecast’ ‘knitr’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/psidR.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/PSM.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     1.6Mb
    doc   2.4Mb
Found the following significant warnings:
  pinpolyhedronA.cc:594:7: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  pinpolyhedronA.cc:1766:5: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/ptinpoly.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    dict   5.1Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc        4.6Mb
    examples   2.3Mb
Namespaces in Imports field not imported from:
  ‘bookdown’ ‘descr’ ‘gee’ ‘lme4’ ‘nlme’ ‘nnet’ ‘ordinal’ ‘pander’
  ‘papeR’ ‘rmdformats’ ‘visreg’
  All declared Imports should be used.
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    libs  25.5Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
Compilation used the following non-portable flag(s):
  ‘-Werror=format-security’ ‘-Wp,-D_FORTIFY_SOURCE=2’
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/QoLR.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
Found the following significant warnings:
  upwindorderedv4.c:542:54: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  upwindorderedv4.c:542:72: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/QPot.Rcheck/00install.out’ for details.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  11.8Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.8Mb
    doc       2.9Mb
    libs      1.4Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs  12.7Mb
Namespace in Imports field not imported from: ‘digest’
  All declared Imports should be used.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/QuantTools.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   4.9Mb
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘gridExtra’ ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lmerTest’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    Output   2.2Mb
    bin      2.9Mb
Found the following significant warnings:
  Note: possible error in 'unlist(strsplit(.$removeSpaces(.$ivField)), ': unused argument (fixed = TRUE) 
See ‘/data/gannet/ripley/R/packages/tests-clang/R2STATS.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Namespaces in Imports field not imported from:
  ‘AlgDesign’ ‘psych’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    extdata   1.4Mb
Package suggested but not available for checking: ‘KEGGgraph’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   3.7Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Packages unavailable to check Rd xrefs: ‘Biobase’, ‘CGHbase’
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    htmlwidgets   6.4Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/ramidst.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Package suggested but not available for checking: ‘Heatplus’
Package unavailable to check Rd xrefs: ‘Heatplus’
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs   4.0Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘dtplyr’
  All declared Imports should be used.
Package unavailable to check Rd xrefs: ‘WGCNA’
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs   2.1Mb
Running examples in ‘RAtmosphere-Ex.R’ failed
The error most likely occurred in:

> ### Encoding: UTF-8
> 
> ### Name: suncalc
> ### Title: Sunrise and Sunset calculations
> ### Aliases: suncalc
> ### Keywords: sun sunset sunrise
> 
> ### ** Examples
> 
> t<-Sys.time()+seq(-3600*12,3600*12,,by=600)
> t0=as.POSIXlt(Sys.time(),tz='UTC')
> plot(t,90-SZA(t,Lat=0,Lon=0),main='SZA',xlab='Time',ylab='El [°deg]')
> sun=suncalc(t0[['yday']],UTC=TRUE)
Error in FUN(X[[i]], ...) : subscript out of bounds
Calls: suncalc -> [[ -> [[.POSIXlt -> .POSIXlt -> lapply
Execution halted
installed size is 29.0Mb
  sub-directories of 1Mb or more:
    libs  27.6Mb
Namespace in Imports field not imported from: ‘lme4’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Loading required package: RCurl
Loading required package: bitops
Loading required package: RJSONIO

Error: processing vignette 'rbiouml.Rnw' failed with diagnostics:
 chunk 5 
Error in queryJSON("/web/table/createTable", params = c(de = path, columns = toJSON(columns),  : 
  Invalid query: parameter 'data' has an invalid value
Execution halted
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    blp    7.1Mb
    libs   7.0Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    cont  23.3Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
Package suggested but not available for checking: ‘ROpenOffice’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   2.7Mb
    po    2.2Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    include   5.2Mb
    libs      1.4Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Found the following warnings:
  ../inst/include/blaze/math/smp/openmp/Functions.h:98:1: warning: control may reach end of non-void function [-Wreturn-type]
See ‘/data/gannet/ripley/R/packages/tests-clang/RcppBlaze.Rcheck/00install.out’ for details.
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    include  25.5Mb
    libs      1.8Mb
installed size is 32.1Mb
  sub-directories of 1Mb or more:
    include   7.9Mb
    libs     23.5Mb
Error in re-building vignettes:
  ...
Latexmk: This is Latexmk, John Collins, 17 Jan. 2018, version: 4.55.
Loading required package: RcppGSL
installed size is 52.4Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib      38.9Mb
    libs     11.3Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    include   7.0Mb
    libs      2.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Found the following significant warnings:
  ../inst/include/tthread/tinythread.h:632:9: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ../inst/include/tbb/tbb_stddef.h:463:32: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ../inst/include/tbb/atomic.h:436:19: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ../inst/include/tbb/atomic.h:437:28: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ../inst/include/tbb/tick_count.h:42:9: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ../inst/include/tbb/tick_count.h:43:30: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ../inst/include/tbb/tick_count.h:75:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ../inst/include/tbb/tick_count.h:102:5: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ../inst/include/tbb/tick_count.h:82:32: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ../inst/include/tbb/tick_count.h:116:35: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ../inst/include/tbb/tick_count.h:116:72: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ../inst/include/tbb/tick_count.h:116:108: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ../inst/include/tbb/tick_count.h:127:25: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ../inst/include/tbb/enumerable_thread_specific.h:118:86: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ../inst/include/tbb/internal/_concurrent_unordered_impl.h:1523:90: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ../inst/include/tbb/internal/_flow_graph_tagged_buffer_impl.h:77:78: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/data/gannet/ripley/R/packages/tests-clang/RcppParallel.Rcheck/00install.out’ for details.
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    include   8.9Mb
    libs     14.0Mb
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    include   6.4Mb
    libs      4.0Mb
installed size is 153.4Mb
  sub-directories of 1Mb or more:
    include    4.6Mb
    lib      112.7Mb
    libs      35.9Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Found the following significant warnings:
  cwb/cqp/corpmanag.c:1832:12: warning: comparison of function 'split_subcorpus_name' equal to a null pointer is always false [-Wtautological-pointer-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/rcqp.Rcheck/00install.out’ for details.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘smcure’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rcompression’
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Subdirectory ‘src’ contains:
  CLRApi.hpp CLRFactory.hpp CLRObjectRef.hpp Common.hpp OS.hpp
  RValue.hpp TcpClient.hpp
These are unlikely file names for src files.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   8.6Mb
Found the following apparent object files/libraries:
  inst/obj/cube.obj inst/obj/cube_badmtl.obj
Object files/libraries should not be included in a source package.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Note: found 1 marked Latin-1 string
  Note: found 1 marked UTF-8 string
  Note: found 7 strings marked as "bytes"
xy: warning in assign(xname, X, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
xy: warning in assign(yname, y, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
bestmods: no visible global function definition for ‘abline’
bestmods: no visible global function definition for ‘axis’
bestmods: no visible global function definition for ‘lines’
cic: no visible global function definition for ‘lsfit’
cic: no visible global function definition for ‘var’
cvic: no visible global function definition for ‘lsfit’
cvic: no visible global function definition for ‘lm’
eic: no visible global function definition for ‘lsfit’
eic: no visible global function definition for ‘lm’
ic.min: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘var’
xy: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline axis lines lm lsfit rnorm var
Consider adding
  importFrom("graphics", "abline", "axis", "lines")
  importFrom("stats", "lm", "lsfit", "rnorm", "var")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘reams/R/xy.R’:
  assign(xname, X, env = .GlobalEnv)
  assign(yname, y, env = .GlobalEnv)
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.8Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.8Mb
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   4.5Mb
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  15.4Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/refund.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Namespaces in Imports field not imported from:
  ‘R6’ ‘nnet’ ‘purrr’
  All declared Imports should be used.
Packages suggested but not available for checking: ‘interval’ ‘Icens’
Package unavailable to check Rd xrefs: ‘interval’
Package which this enhances but not available for checking: ‘Rcplex’
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/relax.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    libs  20.8Mb
Namespaces in Imports field not imported from:
  ‘compiler’ ‘data.table’
  All declared Imports should be used.
Found the following significant warnings:
  gar.c:356:29: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  gar.c:356:80: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/repeated.Rcheck/00install.out’ for details.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    java   5.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘methods’
  All declared Imports should be used.
installed size is 56.5Mb
  sub-directories of 1Mb or more:
    libs  55.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    java   5.3Mb
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.6Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    doc     3.9Mb
    fonts   1.5Mb
    libs    2.6Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/RGoogleAnalytics.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Packages suggested but not available for checking:
  ‘hyperdraw’ ‘hypergraph’ ‘pmg’ ‘SVGAnnotation’
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extra   9.4Mb
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    R      3.6Mb
    help  10.5Mb
    libs   8.1Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc   9.8Mb
Found the following significant warnings:
  filterhr.c:21:11: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  filterhr.c:21:53: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  filterhr.c:21:95: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/RHRV.Rcheck/00install.out’ for details.
Found the following significant warnings:
  computePvals.c:488:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/ridge.Rcheck/00install.out’ for details.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-clang/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’,
    ‘R_GlobalContext’
File ‘rJava/libs/rJava.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘crul’
  All declared Imports should be used.
Found the following significant warnings:
  libjson/Source/JSONGlobals.h:43:50: warning: empty macro arguments are a C99 feature [-Wc99-extensions]
  libjson/Source/JSONGlobals.h:44:49: warning: empty macro arguments are a C99 feature [-Wc99-extensions]
  libjson/Source/JSONSharedString.h:180:47: warning: field 'len' will be initialized after field '_str' [-Wreorder]
  libjson/Source/JSONSharedString.h:182:66: warning: field 'len' will be initialized after field '_str' [-Wreorder]
  JSONStream.cpp:8:130: warning: field 'state' will be initialized after field 'call' [-Wreorder]
  JSONStream.cpp:8:157: warning: field 'err_call' will be initialized after field 'buffer' [-Wreorder]
  JSONStream.cpp:12:64: warning: field 'state' will be initialized after field 'call' [-Wreorder]
  JSONStream.cpp:12:100: warning: field 'err_call' will be initialized after field 'buffer' [-Wreorder]
  JSONValidator.cpp:394:105: warning: empty macro arguments are a C99 feature [-Wc99-extensions]
  JSONValidator.cpp:397:104: warning: empty macro arguments are a C99 feature [-Wc99-extensions]
  internalJSONNode.cpp:78:117: warning: field '_name_encoded' will be initialized after field '_name' [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-clang/RJSONIO.Rcheck/00install.out’ for details.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    datasets   8.6Mb
installed size is 45.1Mb
  sub-directories of 1Mb or more:
    exe  45.0Mb
Found the following significant warnings:
  Note: possible error in 'write(self$rules, file = paste0(fileName, ': unused argument (col.names = NA) 
See ‘/data/gannet/ripley/R/packages/tests-clang/RKEEL.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘arules’ ‘pmml’ ‘rJava’
  All declared Imports should be used.
Packages suggested but not available for checking:
  ‘Biobase’ ‘genefilter’ ‘golubEsets’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/Rlda.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    libs  18.2Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    rmd   6.1Mb
.onLoad: warning in dir(dll.path, pattern = this.ext, full = FALSE):
  partial argument match of 'full' to 'full.names'
diagnos.envel: warning in apply(jumpDistRes, MARG = 2, FUN = quantile,
  probs = perc[1], na.rm = TRUE): partial argument match of 'MARG' to
  'MARGIN'
diagnos.envel: warning in apply(jumpDistRes, MARG = 2, FUN = quantile,
  probs = perc[2], na.rm = TRUE): partial argument match of 'MARG' to
  'MARGIN'
diagnos.envel: no visible global function definition for ‘quantile’
diagnos.envel: no visible global function definition for ‘qnorm’
diagnos.envel: no visible binding for global variable ‘quantile’
hrplot: no visible global function definition for ‘plot’
hrplot: no visible global function definition for ‘lines’
hrplot: no visible global function definition for ‘abline’
hrplot: no visible global function definition for ‘text’
sim.chain: no visible global function definition for ‘rnorm’
simRandWalk: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline lines plot qnorm quantile rnorm text
Consider adding
  importFrom("graphics", "abline", "lines", "plot", "text")
  importFrom("stats", "qnorm", "quantile", "rnorm")
to your NAMESPACE file.
File ‘RMC/libs/RMC.so’:
  Found ‘_ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
    Objects: ‘RMC.o’, ‘predict.o’
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘ap.o’
File ‘RMC/libs/RMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   5.4Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/Rmpi.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/RM.weights.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Packages suggested but not available for checking: ‘topGO’ ‘DESeq’
Packages unavailable to check Rd xrefs: ‘DESeq’, ‘topGO’
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/progress/include/RProgress.h:172:13: warning: variable length arrays are a C99 feature [-Wvla-extension]
  /data/gannet/ripley/R/test-clang/progress/include/RProgress.h:220:16: warning: variable length arrays are a C99 feature [-Wvla-extension]
See ‘/data/gannet/ripley/R/packages/tests-clang/rncl.Rcheck/00install.out’ for details.
installed size is 25.2Mb
  sub-directories of 1Mb or more:
    libs  25.0Mb
Packages suggested but not available for checking: ‘rrdf’ ‘Sxslt’
installed size is 97.6Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     95.5Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R   9.7Mb
Found the following significant warnings:
  ./hammock.h:369:15: warning: assigning field to itself [-Wself-assign-field]
See ‘/data/gannet/ripley/R/packages/tests-clang/robfilter.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘SSOAP’
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs  20.8Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
o.rocc: warning in factor(pr, level = c(0, 1)): partial argument match
  of 'level' to 'levels'
p.rocc: warning in factor(pr, level = c(0, 1)): partial argument match
  of 'level' to 'levels'
o.rocc: no visible global function definition for ‘prediction’
o.rocc: no visible global function definition for ‘performance’
o.rocc: no visible global function definition for ‘binom.test’
tr.rocc: no visible global function definition for ‘prediction’
tr.rocc: no visible global function definition for ‘performance’
Undefined global functions or variables:
  binom.test performance prediction
Consider adding
  importFrom("stats", "binom.test")
to your NAMESPACE file.
Package which this enhances but not available for checking: ‘ROI.plugin.cplex’
Namespace in Imports field not imported from: ‘matrixcalc’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/rootWishart.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    libs  24.6Mb
Package suggested but not available for checking: ‘RobLox’
Package unavailable to check Rd xrefs: ‘RobLox’
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.3Mb
    libs   5.2Mb
Namespaces in Imports field not imported from:
  ‘httpuv’ ‘utils’
  All declared Imports should be used.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Package suggested but not available for checking: ‘seqLogo’
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      3.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.3Mb
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   7.3Mb
Namespace in Imports field not imported from: ‘vegan’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
Package suggested but not available for checking: ‘scrypt’

Package which this enhances but not available for checking: ‘BiocInstaller’
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/RSEIS.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Namespaces in Imports field not imported from:
  ‘binman’ ‘httr’
  All declared Imports should be used.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-clang/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘ctc’

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.
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
Namespace in Imports field not imported from: ‘gdalUtils’
  All declared Imports should be used.
installed size is 51.1Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  49.6Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
Namespace in Imports field not imported from: ‘pkgconfig’
  All declared Imports should be used.
Found the following significant warnings:
  100:30: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/data/gannet/ripley/R/packages/tests-clang/rstanarm.Rcheck/00install.out’ for details.
installed size is 156.9Mb
  sub-directories of 1Mb or more:
    R       1.4Mb
    doc     2.4Mb
    libs  152.5Mb
installed size is 293.7Mb
  sub-directories of 1Mb or more:
    libs  291.1Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/rsunlight.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘mc2d’
  All declared Imports should be used.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/RSurvey.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    Lib  11.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘stats’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       1.5Mb
    projects   2.7Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘rmarkdown’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   1.9Mb
Namespace in Imports field not imported from: ‘RGtk2’
  All declared Imports should be used.
installed size is 42.1Mb
  sub-directories of 1Mb or more:
    libs  41.4Mb
rvideopoker: warning in rp.radiogroup(mypanel, var =
  state$penny.nickel.quarter.dollar, initval = 1, values = c(1, 5, 25,
  100), title = "Bet (in Cents)", action = setbet): partial argument
  match of 'var' to 'variable'
rvideopoker: warning in rp.slider(mypanel, var = state$no.of.credits,
  from = 1, to = 5, initval = 1, title = "How many Credits?",
  resolution = 1, action = creditset, showvalue = TRUE): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC1, action = card1check, title = "Keep Card 1?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC2, action = card2check, title = "Keep Card 2?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC3, action = card3check, title = "Keep Card 3?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC4, action = card4check, title = "Keep Card 4?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC5, action = card5check, title = "Keep Card 5?"): partial
  argument match of 'var' to 'variable'
rvideopoker : plotFrame: no visible global function definition for
  ‘par’
rvideopoker : showBack: no visible global function definition for
  ‘title’
rvideopoker : showCardsInitially: no visible global function definition
  for ‘title’
Undefined global functions or variables:
  par title
Consider adding
  importFrom("graphics", "par", "title")
to your NAMESPACE file.
Package suggested but not available for checking: ‘gpuR’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    include   5.4Mb
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
    test  19.6Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java  10.6Mb
Found the following significant warnings:
  qwiener.c:60:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  qwiener.c:69:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/RWiener.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/RWildbook.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Running examples in ‘rwunderground-Ex.R’ failed
The error most likely occurred in:

> ### Name: set_location
> ### Title: Specifies location of request
> ### Aliases: set_location
> 
> ### ** Examples
> 
> set_location(zip_code = "90210")
[1] "90210"
> set_location(territory = "Hawaii", city = "Honolulu")
Error: 'countrycode_data' is not an exported object from 'namespace:countrycode'
Execution halted
Found the following significant warnings:
  nchg.c:555:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/RxCEcolInf.Rcheck/00install.out’ for details.
Found the following significant warnings:
  call_dvode.c:746:18: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  sum.c:221:11: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  sum.c:221:22: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  sum.c:227:45: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  sum.c:227:53: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/RxODE.Rcheck/00install.out’ for details.
Found the following significant warnings:
  yacas/src/obmalloc.cpp:584:23: warning: result of comparison of constant 384307168202282325 with expression of type 'unsigned int' is always false [-Wtautological-constant-out-of-range-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/Ryacas.Rcheck/00install.out’ for details.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs    7.5Mb
    yacas   1.5Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
Found the following significant warnings:
  Note: possible error in 'saveSession(force = TRUE)': unused argument (force = TRUE) 
See ‘/data/gannet/ripley/R/packages/tests-clang/Rz.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    sample_data   3.1Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Namespace in Imports field not imported from: ‘spanel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘subplex’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/SAENET.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  dists.cc:4239:21: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/SafeBayes.Rcheck/00install.out’ for details.
Running examples in ‘SAGA-Ex.R’ failed
The error most likely occurred in:

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

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

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


AICc weights were used to select the minimum number of models whose weights sum 
to greater than 95% this model set includes 12 model(s)
> plot(results)
Error in if (maxval < 0) maxval <- 0 : 
  missing value where TRUE/FALSE needed
Calls: plot -> plot.genarch
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 267-270 (model-averaged-analysis.Rmd) 
Error: processing vignette 'model-averaged-analysis.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
Execution halted
Packages suggested but not available for checking:
  ‘GO.db’ ‘GOstats’ ‘mixer’ ‘org.Sc.sgd.db’
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Namespace in Imports field not imported from: ‘pvclust’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘cowplot’ ‘ggplot2’ ‘ggridges’ ‘ggstance’ ‘jmvcore’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.7Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘testthat’
  All declared Imports should be used.
Package suggested but not available for checking: ‘oligoClasses’
Namespace in Imports field not imported from: ‘gbm’
  All declared Imports should be used.
Found the following significant warnings:
  pointinpolygon.c:60:7: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  slope.aspect.c:128:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  slope.aspect.c:128:33: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  vincenty.geodesics.c:50:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  vincenty.geodesics.c:126:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/SDMTools.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    data   1.1Mb
    doc    1.2Mb
Found the following significant warnings:
  BinNegative.cpp:108:5: warning: assigning field to itself [-Wself-assign-field]
See ‘/data/gannet/ripley/R/packages/tests-clang/Segmentor3IsBack.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘cluster’ ‘factoextra’ ‘tidyr’
  All declared Imports should be used.
predict.SEL: warning in splineDesign(newdata, knots = knts, ord =
  object$nord, deriv = rep(deriv, length(newdata)), outer.ok = TRUE):
  partial argument match of 'deriv' to 'derivs'
getbinPost: no visible binding for global variable ‘dbeta’
getbinPost: no visible binding for global variable ‘pbeta’
getbinPost : fu: no visible global function definition for ‘dbinom’
getbinPost : fu: no visible global function definition for ‘predict’
getbinPost: no visible global function definition for ‘integrate’
getbinPost: no visible global function definition for ‘splinefun’
int.funct: no visible global function definition for ‘integrate’
int.funct2: no visible global function definition for ‘integrate’
min.abs: no visible global function definition for ‘uniroot’
plot.SEL: no visible global function definition for ‘plot’
print.SEL: no visible global function definition for ‘integrate’
print.summary.SEL : foo1: no visible global function definition for
  ‘predict’
print.summary.SEL : foo2: no visible global function definition for
  ‘predict’
print.summary.SEL: no visible global function definition for
  ‘integrate’
quantSEL: no visible global function definition for ‘predict’
quantSEL: no visible global function definition for ‘splinefun’
rvSEL: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dbeta dbinom integrate pbeta plot predict runif splinefun uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dbeta", "dbinom", "integrate", "pbeta", "predict",
             "runif", "splinefun", "uniroot")
to your NAMESPACE file.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/sensors4plumes.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘XML’ ‘mgcv’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lexicon’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘compiler’
  All declared Imports should be used.
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    doc    6.0Mb
    libs  13.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
Found the following significant warnings:
  vcf.c:253:15: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/seqminer.Rcheck/00install.out’ for details.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  17.2Mb
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.
Packages suggested but not available for checking:
  ‘SummarizedExperiment’ ‘MAST’ ‘DESeq2’
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    doc     10.1Mb
    libs     4.7Mb
    sqlite   1.5Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    www   9.7Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘htmlwidgets’ ‘jsonlite’ ‘viridis’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘data.table’ ‘gridExtra’ ‘knitr’ ‘latticeExtra’ ‘msm’ ‘plotly’
  ‘xtable’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘KGode’ ‘XML’ ‘ggplot2’ ‘gridExtra’ ‘mvtnorm’ ‘reshape2’ ‘shinyjs’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘shinyBS’ ‘shinythemes’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    www   6.5Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    semantic   5.7Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/shp2graph.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘viridis’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘grid’
  All declared Imports should be used.
Running examples in ‘simmer.plot-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot.trajectory
> ### Title: Plot Method for 'trajectory' Objects
> ### Aliases: plot.trajectory
> 
> ### ** Examples
> 
> x <- trajectory() %>%
+   seize("res", 1) %>%
+   timeout(1) %>%
+   release("res", 1) %>%
+   rollback(3)
> 
> plot(x)
`()` INFO: created a new selection of 1 node
`()` INFO: there is an active selection of 1 node
`()` INFO: cleared an existing selection of 1 node
Error: 'set_global_graph_attrs' is not an exported object from 'namespace:DiagrammeR'
Execution halted
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  11.8Mb
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'
Namespace in Imports field not imported from: ‘metafor’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pracma’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   4.4Mb
Namespace in Imports field not imported from: ‘mcmc’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.0Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/slickR.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Note: found 15 marked Latin-1 strings
  Note: found 2 marked UTF-8 strings
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   8.1Mb
Found the following significant warnings:
  MCP_efficient.c:114:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  MCP_efficient.c:134:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  MCP_efficient.c:154:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/SMCP.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘compiler’ ‘lmtest’
  All declared Imports should be used.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   6.2Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘nlme’ ‘survival’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/sm.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  /usr/include/python2.7/unicodeobject.h:534:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/unicodeobject.h:553:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/unicodeobject.h:575:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/unicodeobject.h:593:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/stringobject.h:173:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/stringobject.h:174:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/stringobject.h:175:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/data/gannet/ripley/R/packages/tests-clang/SnakeCharmR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ./snappy-stubs-internal.h:95:51: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/data/gannet/ripley/R/packages/tests-clang/snappier.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/SocialMediaLab.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/soundecology.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Namespaces in Imports field not imported from:
  ‘gtools’ ‘hashmap’ ‘reshape2’
  All declared Imports should be used.
Packages suggested but not available for checking:
  ‘r2cytoscape’ ‘BiocStyle’ ‘Biobase’ ‘graphite’ ‘hgu95av2.db’ ‘ALL’
  ‘org.Hs.eg.db’
Packages unavailable to check Rd xrefs: ‘ALL’, ‘simPATHy’, ‘graphite’
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, sd, var, xtabs

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

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

Identifing all possible orderings..
Total run time: 2.16 secs
Identifing all possible orderings..
Total run time: 2.14 secs
Quitting from lines 386-388 (SourceSet.Rmd) 
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
there is no package called 'ALL'
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/spaceExt.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘rstudioapi’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘fastdigest’ ‘httr’
  All declared Imports should be used.
installed size is 36.2Mb
  sub-directories of 1Mb or more:
    libs  34.4Mb
Namespace in Imports field not imported from: ‘foreach’
  All declared Imports should be used.
Package suggested but not available for checking: ‘RCy3’
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘SpatialEpi’ ‘dplyr’ ‘dygraphs’ ‘ggplot2’
  ‘htmlwidgets’ ‘knitr’ ‘leaflet’ ‘mapproj’ ‘maptools’ ‘rgdal’ ‘rgeos’
  ‘rmarkdown’ ‘shinyjs’ ‘spdep’ ‘xts’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘moments’ ‘poweRlaw’
  All declared Imports should be used.
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    R      4.9Mb
    doc    4.7Mb
    help   4.9Mb
    libs   1.8Mb
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  25.5Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data     2.6Mb
    shapes   3.2Mb
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nr' to 'nrow'
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nc' to 'ncol'
spe: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘maptools’
  All declared Imports should be used.
Note: found 8 marked Latin-1 strings
  Note: found 83 marked UTF-8 strings
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   7.8Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs  12.0Mb
Namespaces in Imports field not imported from:
  ‘BayesX’ ‘BayesXsrc’ ‘automap’ ‘plyr’ ‘rgdal’ ‘splines’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘viridisLite’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shinyFiles’
  All declared Imports should be used.
stkde: no visible global function definition for ‘npudensbw’
stkde: no visible global function definition for ‘npudens’
stkde: no visible global function definition for ‘quantile’
stkde: no visible global function definition for ‘heat.colors’
stkde: no visible global function definition for ‘par’
stkde: no visible global function definition for ‘image’
stkde: no visible global function definition for ‘contour’
stkde.base: no visible global function definition for ‘npudensbw’
stkde.base: no visible global function definition for ‘npudens’
stkde.sig: no visible global function definition for ‘SpatialPoints’
stkde.sig: no visible global function definition for ‘spsample’
stkde.sig: no visible global function definition for ‘bbox’
stkde.sig: no visible global function definition for ‘quantile’
stkde.sig: no visible global function definition for ‘heat.colors’
stkde.sig: no visible global function definition for ‘par’
stkde.sig: no visible global function definition for ‘image’
stkde.sig: no visible global function definition for ‘contour’
Undefined global functions or variables:
  SpatialPoints bbox contour heat.colors image npudens npudensbw par
  quantile spsample
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "contour", "image", "par")
  importFrom("stats", "quantile")
to your NAMESPACE file.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    include   9.1Mb
    lib       1.5Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   4.9Mb
Namespace in Imports field not imported from: ‘MCMCpack’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'StatCharrms.tex' failed.
LaTeX errors:
! Too many }'s.
l.675 ...toc}{subsection}{Other Endpoints Graphs}}
                                                  
You've closed more groups than you opened.
Such booboos are generally harmless, so keep going.
! Undefined control sequence.
<argument> ...Data}. Wiley\textemdashInterscience 
                                                  . 
l.749 ...nt Data}. Wiley\textemdashInterscience. }
                                                  
! Undefined control sequence.
l.758 	Wiley\textemdashInterscience
                                   .
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
<argument> ...t {Indagationes Mathematicae} \bold 
                                                  {14}:327\textemdash 333.
l.772 ...thematicae} \bold{14}:327\textemdash333.}
                                                  
! Undefined contr
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘stringr’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
Namespaces in Imports field not imported from:
  ‘lattice’ ‘xtable’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘tm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘huge’ ‘scales’ ‘shinyjs’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R          2.0Mb
    datasets   2.6Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
Packages suggested but not available for checking: ‘limma’ ‘samr’
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.7Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/streamR.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Running ‘testthat.R’ [8s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(subprocess)
  > 
  > # See for more details:
  > # https://github.com/hadley/testthat/issues/144
  > # https://github.com/hadley/testthat/issues/86
  > # https://github.com/luckyrandom/cmaker/commit/b85813ac2b7aef69932eca8fbb4fa0ec225e0af0
  > #
  > # When R CMD check runs tests, it sets R_TESTS. When the tests
  > # themeselves run R CMD xxxx, as is the case with the tests in
  > # devtools, having R_TESTS set causes errors because it confuses
  > # the R subprocesses. Unsetting it here avoids those problems.
  > #
  > # We need this because we spawn child R processes and they get very
  > # confused if this variable (R_TESTS) is present in their environment.
  > Sys.setenv("R_TESTS" = "")
  > 
  > test_check("subprocess")
  ── 1. Error: child process is terminated in Linux (@test-termination.R#85)  ────
  is_process_handle(handle) is not TRUE
  1: expect_true(wait_until_appears(child_id)) at testthat/test-termination.R:85
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: wait_until_appears(child_id)
  5: process_wait(handle, TIMEOUT_IMMEDIATE) at /data/gannet/ripley/R/packages/tests-clang/subprocess.Rcheck/tests/testthat/helper-processes.R:58
  6: stopifnot(is_process_handle(handle))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 71 SKIPPED: 2 FAILED: 1
  1. Error: child process is terminated in Linux (@test-termination.R#85) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: ‘fields’
  All declared Imports should be used.
Packages suggested but not available for checking:
  ‘dbarts’ ‘genefilter’ ‘sva’
Found the following significant warnings:
  dists.cc:4239:21: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/SuppDists.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.3Mb
    help   1.0Mb
    libs   1.5Mb
installed size is 69.6Mb
  sub-directories of 1Mb or more:
    libs  68.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.6Mb
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
Package unavailable to check Rd xrefs: ‘survJamda’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Running examples in ‘survtmle-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot.tp.survtmle
> ### Title: Plot Results of Cumulative Incidence Estimates
> ### Aliases: plot.tp.survtmle
> 
> ### ** Examples
> 
> library(survtmle)
> set.seed(341796)
> n <- 100
> t_0 <- 10
> W <- data.frame(W1 = runif(n), W2 = rbinom(n, 1, 0.5))
> A <- rbinom(n, 1, 0.5)
> T <- rgeom(n,plogis(-4 + W$W1 * W$W2 - A)) + 1
> C <- rgeom(n, plogis(-6 + W$W1)) + 1
> ftime <- pmin(T, C)
> ftype <- as.numeric(ftime == T)
> suppressWarnings(
+   fit <- survtmle(ftime = ftime, ftype = ftype,
+                   adjustVars = W, glm.ftime = "I(W1*W2) + trt + t",
+                   trt = A, glm.ctime = "W1 + t", method = "hazard",
+                   verbose = TRUE,  t0 = t_0, maxIter = 2)
+ )
> tpfit <- timepoints(fit, times = seq_len(t_0))
> plot(tpfit)
Error in names(x) <- value : 
  'names' attribute [3] must be the same length as the vector [2]
Calls: plot -> plot.tp.survtmle -> colnames<-
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 540-542 (survtmle_intro.Rmd) 
Error: processing vignette 'survtmle_intro.Rmd' failed with diagnostics:
'names' attribute [3] must be the same length as the vector [2]
Execution halted
Found the following significant warnings:
  trlan/trlcore.c:983:15: warning: comparison of array 'info->oldcpf' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlcore.c:1642:9: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  trlan/trlcore.c:1642:20: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  trlan/trlaux.c:28:13: warning: comparison of array 'info->log_file' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlaux.c:41:13: warning: comparison of array 'info->log_file' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlaux.c:62:13: warning: comparison of array 'info->cpfile' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlan.c:171:20: warning: comparison of array 'info->oldcpf' equal to a null pointer is always false [-Wtautological-pointer-compare]
  trlan/ztrlcore.c:1418:12: warning: comparison of array 'info->oldcpf' not equal to a null pointer is always true [-Wtautological-pointer-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/svd.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: GNU Extension: Different type kinds at (1)
  Warning: GNU Extension: initialization of common block variable ‘iset’ in DATA statement at (1)
  Warning: GNU Extension: Variable ‘iset’ at (1) is in COMMON but only in BLOCK DATA initialization is allowed
  Warning: GNU Extension: Missing comma at (1)
  Warning: CHARACTER expression will be truncated in assignment (10/13) at (1) [-Wcharacter-truncation]
  Warning: ‘pst_kg’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘burn_frlb’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘hi_ovr’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘harveff’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘frac_harvk’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘cnop’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘lai_init’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘orig_tnylda’ is used uninitialized in this function [-Wuninitialized]
  Warning: CHARACTER expression will be truncated in assignment (1/3) at (1) [-Wcharacter-truncation]
  Warning: ‘fr_curb’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-clang/SWATmodel.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘lazyeval’ ‘lubridate’ ‘tidyr’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/sybilEFBA.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/SynergizeR.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   3.6Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘lazyeval’ ‘rlang’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘PerformanceAnalytics’
  All declared Imports should be used.
Packages suggested but not available for checking:
  ‘limma’ ‘edgeR’ ‘DESeq2’ ‘S4Vectors’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    tklibs   4.9Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    sql   8.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.9Mb
installed size is 36.7Mb
  sub-directories of 1Mb or more:
    libs  35.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    apps   2.6Mb
    libs   1.5Mb
Namespaces in Imports field not imported from:
  ‘data.table’ ‘datasets’ ‘stats’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
Namespaces in Imports field not imported from:
  ‘nlme’ ‘tidyr’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/tensorBF.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Namespace in Imports field not imported from: ‘rprojroot’
  All declared Imports should be used.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.6Mb
    libs   5.3Mb
Namespace in Imports field not imported from: ‘irlba’
  All declared Imports should be used.
Note: found 10051 marked UTF-8 strings
  Note: found 10523 strings marked as "bytes"
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   8.5Mb
Error in re-building vignettes:
  ...
Quitting from lines 55-81 (a_start_here.Rmd) 
Error: processing vignette 'a_start_here.Rmd' failed with diagnostics:
no stopwords available for 'smart'
Execution halted
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    rda    3.8Mb
Namespaces in Imports field not imported from:
  ‘tibble’ ‘tidyverse’
  All declared Imports should be used.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidyinftheo)
  > 
  > test_check("tidyinftheo")
  ── 1. Error: right number of columns given (@test-errors.R#10)  ────────────────
  argument "expr" is missing, with no default
  1: expect_length(tab %>% select(vs) %>% shannon_entropy(), 1) at testthat/test-errors.R:10
  2: quasi_label(enquo(object))
  3: eval_bare(get_expr(quo), get_env(quo))
  4: tab %>% select(vs) %>% shannon_entropy()
  5: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  6: eval(quote(`_fseq`(`_lhs`)), env, env)
  7: eval(quote(`_fseq`(`_lhs`)), env, env)
  8: `_fseq`(`_lhs`)
  9: freduce(value, `_function_list`)
  10: withVisible(function_list[[k]](value))
  11: function_list[[k]](value)
  12: shannon_entropy(.)
  13: reduce_data(.data, !(!enquo(X)), numvars = 1, na.rm = na.rm)
  14: tidyselect::vars_select(names(reduced_tab), !(!(!quos(...))))
  15: vars_select_eval(.vars, quos)
  16: map_lgl(quos, quo_is_helper)
  17: .f(.x[[i]], ...)
  18: extract_expr(quo)
  19: is_call(expr, paren_sym)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 37 SKIPPED: 0 FAILED: 1
  1. Error: right number of columns given (@test-errors.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘broom’ ‘curl’ ‘devtools’ ‘rvest’ ‘timeSeries’ ‘tseries’ ‘zoo’
  All declared Imports should be used.
Packages suggested but not available for checking: ‘ggtree’ ‘treeio’
Namespaces in Imports field not imported from:
  ‘dbplyr’ ‘reprex’ ‘rlang’
  All declared Imports should be used.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
Found the following significant warnings:
  tm.c:184:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  tm.c:185:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/TimeMachine.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘forecast’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc         3.7Mb
    rmarkdown   1.3Mb
Namespaces in Imports field not imported from:
  ‘broom’ ‘tibble’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.3Mb
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    examples  14.0Mb
    include    3.0Mb
installed size is 24.2Mb
  sub-directories of 1Mb or more:
    libs  24.0Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘jmvcore’
  All declared Imports should be used.
Note: found 42 marked Latin-1 strings
  Note: found 360 marked UTF-8 strings
File ‘tpr/libs/tpr.so’:
  Found ‘_ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’
File ‘tpr/libs/tpr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.7Mb
Namespace in Imports field not imported from: ‘neuralnet’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/TrajDataMining.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘magrittr’ ‘rgeos’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    example   4.1Mb
installed size is 37.5Mb
  sub-directories of 1Mb or more:
    libs  37.0Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Found the following significant warnings:
  ./tsBSS.h:10:22: warning: 'varExx_k' has C-linkage specified, but returns user-defined type 'arma::mat' (aka 'Mat<double>') which is incompatible with C [-Wreturn-type-c-linkage]
See ‘/data/gannet/ripley/R/packages/tests-clang/tsBSS.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘gsDesign’
  All declared Imports should be used.
covTranspose11: warning in glasso(sc, 2 * rhoc/n, wi.init = gc$wi,
  w.init = gc$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
covTranspose11: warning in glasso(sr, 2 * rhor/p, wi.init = gr$wi,
  w.init = gr$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
.help.ESS: no visible global function definition for ‘index.search’
TransSphere : ttin: no visible global function definition for ‘t.test’
TransSphere: no visible global function definition for ‘sd’
TransSphere: no visible global function definition for ‘quantile’
TransSphere: no visible global function definition for ‘pt’
Undefined global functions or variables:
  index.search pt quantile sd t.test
Consider adding
  importFrom("stats", "pt", "quantile", "sd", "t.test")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/turboEM.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 28.9Mb
  sub-directories of 1Mb or more:
    doc         4.1Mb
    dummydata   1.4Mb
    libs       22.3Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    1.6Mb
    libs   2.7Mb
Namespace in Imports field not imported from: ‘mcmcplots’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    data  26.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    extdata   6.2Mb
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/VarReg.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/vcfR.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘maptools’ ‘rgeos’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
H: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = H, func.arg = list(func.arg), boot.arg)):
  partial argument match of 'arg' to 'args'
M.homog: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = M.homog, func.arg = list(func.arg),
  boot.arg)): partial argument match of 'arg' to 'args'
Rel.homog: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = Rel.homog, func.arg = list(func.arg),
  boot.arg)): partial argument match of 'arg' to 'args'
bootstrap: warning in do.call(what = func, arg = list(boots[, , i])):
  partial argument match of 'arg' to 'args'
bootstrap: warning in do.call(what = func, arg = c(abundances =
  list(boots[, , i]), func.arg)): partial argument match of 'arg' to
  'args'
d: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = d, func.arg = list(func.arg), boot.arg)):
  partial argument match of 'arg' to 'args'
sim.groups: warning in do.call(what = bootstrap, arg = c(abundances =
  list(rbind(scores[i, ], scores[j, ])), func = similarity, func.arg =
  list(func.arg), boot.arg)): partial argument match of 'arg' to 'args'
sim.table: warning in do.call(what = bootstrap, arg = c(abundances =
  list(rbind(scores[i, ], scores[j, ])), func = similarity, func.arg =
  list(func.arg), boot.arg)): partial argument match of 'arg' to 'args'
similarity: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = similarity, func.arg = list(func.arg),
  boot.arg)): partial argument match of 'arg' to 'args'
turnover: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = turnover, func.arg = list(func.arg),
  boot.arg)): partial argument match of 'arg' to 'args'
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    libs  26.4Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      3.4Mb
    doc    1.2Mb
    help   2.7Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc           4.8Mb
    htmlwidgets   3.7Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    extdata  10.8Mb
Namespaces in Imports field not imported from:
  ‘iterators’ ‘knitr’ ‘purrr’ ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘XML’ ‘checkmate’ ‘gstat’ ‘intervals’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lubridate’ ‘tibble’
  All declared Imports should be used.
installed size is 52.7Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  50.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘ENMeval’ ‘RColorBrewer’ ‘dismo’ ‘dplyr’ ‘leaflet.extras’
  ‘maptools’ ‘raster’ ‘rgdal’ ‘rgeos’ ‘shinyjs’ ‘shinythemes’ ‘spThin’
  ‘spocc’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘WRS2’ ‘ggplot2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘proxy’ ‘signal’
  All declared Imports should be used.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    doc  12.1Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    client   9.6Mb
    doc      1.0Mb
Namespace in Imports field not imported from: ‘fauxpas’
  All declared Imports should be used.
Package suggested but not available for checking: ‘AnnotationDbi’
Found the following significant warnings:
  t_region.cpp:78:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:115:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:120:7: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/WhopGenome.Rcheck/00install.out’ for details.
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
Package suggested but not available for checking: ‘genefilter’
Error in re-building vignettes:
  ...
If you use data from the unvotes package, please cite the following:

Erik Voeten "Data and Analyses of Voting in the UN General Assembly" Routledge Handbook of International Organization, edited by Bob Reinalda (published May 27, 2013)
Quitting from lines 70-78 (united_nations.Rmd) 
Error: processing vignette 'united_nations.Rmd' failed with diagnostics:
there is no package called 'fuzzyjoin'
Execution halted
Namespaces in Imports field not imported from:
  ‘drc’ ‘imputeTestbench’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/windfarmGA.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Namespace in Imports field not imported from: ‘RandomFields’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.7Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.2Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    data  11.4Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    data  14.1Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    bin   5.4Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    java  19.0Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    java   9.8Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    exampleData   1.6Mb
    examples      4.6Mb
Running examples in ‘xpose4-Ex.R’ failed
The error most likely occurred in:

> ### Name: xpose.bootgam
> ### Title: Title
> ### Aliases: xpose.bootgam
> 
> ### ** Examples
> 
> 
> ## filter out occasion as a covariate as only one value
> all_covs <- xvardef("covariates",simpraz.xpdb)
> some_covs <- all_covs[!(all_covs %in% "OCC") ] 
> 
> ## here only running n=5 replicates to see that things work
> ##   use something like n=100 for resonable results
> boot_gam_obj <- xpose.bootgam(simpraz.xpdb,5,parnam="KA",covnams=some_covs,seed=1234)

Starting bootstrap (max 5 replicates, seed = 1234).
Bootgam progress:

  |                                                                            
  |==============                                                        |  20%Error in step.gam(bam.start, trace = trace, scope, keep = bam.keep) : 
  could not find function "step.gam"
Calls: xpose.bootgam ... evalVis -> withVisible -> eval -> eval -> xpose.gam
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/XR.Rcheck/00install.out’ for details.
Further information on the location(s) of code generating the ‘Notes’
can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Namespaces in Imports field not imported from:
  ‘Amelia’ ‘MatchIt’ ‘WhatIf’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘lubridate’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/ACTCD.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
asp: no visible global function definition for ‘as.formula’
asp: no visible global function definition for ‘var’
aspm: no visible binding for global variable ‘X.Declan’
aspm: no visible binding for global variable ‘Z.Jaida’
aspm: no visible binding for global variable ‘group.vec.Handan’
aspm: no visible global function definition for ‘as.formula’
aspm: no visible global function definition for ‘glm’
aspm: no visible global function definition for ‘binomial’
aspm: no visible global function definition for ‘poisson’
Undefined global functions or variables:
  X.Declan Z.Jaida as.formula binomial glm group.vec.Handan poisson var
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "poisson", "var")
to your NAMESPACE file.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       2.8Mb
    pictures   2.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Running ‘testthat.R’ [18s/44s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("ahp")
  Loading required package: ahp
  ── 1. Error: Visualize (@test-Visualize.R#8)  ──────────────────────────────────
  'set_global_graph_attrs' is not an exported object from 'namespace:DiagrammeR'
  1: GetGraph(carAhp) at testthat/test-Visualize.R:8
  2: DiagrammeR::set_global_graph_attrs at /data/gannet/ripley/R/packages/tests-devel/ahp/R/visualize.R:86
  3: getExportedValue(pkg, name)
  4: stop(gettextf("'%s' is not an exported object from 'namespace:%s'", name, getNamespaceName(ns)), 
         call. = FALSE, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 463 SKIPPED: 0 FAILED: 1
  1. Error: Visualize (@test-Visualize.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    libs  24.0Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/anapuce.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/Anthropometry.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Error in re-building vignettes:
  ...




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

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





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

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





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

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





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

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





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

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





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

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





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

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





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

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





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

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





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

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





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

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





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

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





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

            Enter rownumber of taxon (other inputs will return 'NA'):
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/ARTP.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/assignPOP.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See ‘/data/gannet/ripley/R/packages/tests-devel/audio.Rcheck/00install.out’ for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    libs   3.7Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/BANFF.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 156.7Mb
  sub-directories of 1Mb or more:
    libs  155.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.3Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  17.5Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
installed size is 53.5Mb
  sub-directories of 1Mb or more:
    libs  52.7Mb
installed size is 34.4Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs  29.6Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/Bayesthresh.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 98.0Mb
  sub-directories of 1Mb or more:
    libs  97.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 48.9Mb
  sub-directories of 1Mb or more:
    libs  47.4Mb
installed size is 28.8Mb
  sub-directories of 1Mb or more:
    libs  27.8Mb
Error in re-building vignettes:
  ...
Quitting from lines 151-152 (BETS_basic_usage.Rmd) 
Error: processing vignette 'BETS_basic_usage.Rmd' failed with diagnostics:
Connetcion fail!
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/biclust.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.3Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   6.0Mb
installed size is 30.3Mb
  sub-directories of 1Mb or more:
    libs  30.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
bigglm.RODBC: no visible global function definition for ‘odbcQuery’
bigglm.RODBC : chunk: no visible global function definition for
  ‘odbcQuery’
bigglm.RODBC : chunk: no visible global function definition for
  ‘sqlGetResults’
bigglm,ANY-DBIConnection: no visible global function definition for
  ‘dbSendQuery’
bigglm,ANY-DBIConnection: no visible global function definition for
  ‘dbClearResult’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘dbClearResult’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘dbSendQuery’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘fetch’
Undefined global functions or variables:
  dbClearResult dbSendQuery fetch odbcQuery sqlGetResults
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/bigpca.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   5.7Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   3.1Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/BioPhysConnectoR.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
blighty: no visible global function definition for ‘par’
blighty: no visible global function definition for ‘polygon’
blighty: no visible global function definition for ‘points’
blighty: no visible global function definition for ‘box’
blighty: no visible global function definition for ‘axis’
blighty: no visible global function definition for ‘abline’
map.scale: no visible global function definition for ‘locator’
map.scale: no visible global function definition for ‘segments’
map.scale: no visible global function definition for ‘text’
north.pointer: no visible global function definition for ‘locator’
north.pointer: no visible global function definition for ‘text’
north.pointer: no visible global function definition for ‘arrows’
north.pointer: no visible global function definition for ‘segments’
sqlimits: no visible global function definition for ‘frame’
sqlimits: no visible global function definition for ‘par’
Undefined global functions or variables:
  abline arrows axis box frame locator par points polygon segments text
Consider adding
  importFrom("graphics", "abline", "arrows", "axis", "box", "frame",
             "locator", "par", "points", "polygon", "segments", "text")
to your NAMESPACE file.
installed size is 52.3Mb
  sub-directories of 1Mb or more:
    libs  51.2Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/BlockFeST.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
installed size is 33.3Mb
  sub-directories of 1Mb or more:
    libs  33.0Mb
installed size is 417.5Mb
  sub-directories of 1Mb or more:
    include    2.9Mb
    lib      414.3Mb
installed size is 80.1Mb
  sub-directories of 1Mb or more:
    libs  79.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    libs  30.3Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    bin    2.5Mb
    doc    1.1Mb
    libs   2.4Mb
installed size is 37.7Mb
  sub-directories of 1Mb or more:
    libs  36.4Mb
installed size is 88.4Mb
  sub-directories of 1Mb or more:
    libs  88.0Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    libs  17.7Mb
Running examples in ‘cablecuttr-Ex.R’ failed
The error most likely occurred in:

> ### Name: can_i_stream
> ### Title: Query CanIStream.It
> ### Aliases: can_i_stream can_i_stream_id can_i_stream_it
> 
> ### ** Examples
> 
> can_i_stream_id("4eb0173df5f8079d29000002", "purchase")
Error in as.POSIXlt.character(x, tz, ...) : 
  character string is not in a standard unambiguous format
Calls: can_i_stream_id ... as.POSIXct.default -> as.POSIXct -> as.POSIXlt -> as.POSIXlt.character
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    libs  17.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   2.7Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   5.8Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.3Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.4Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/cem.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: possible error in 'log.likelihood(list(latent.space.pos.prop, ': unused argument (edge.list.rows[[dd]]) 
  Note: possible error in 'log.likelihood(list(latent.space.pos.hold, ': unused argument (edge.list.rows[[dd]]) 
See ‘/data/gannet/ripley/R/packages/tests-devel/CIDnetworks.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/CircE.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/CircStats.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    libs  21.7Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/climatol.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/clustrd.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Error in re-building vignettes:
  ...
Loading required package: cluster
Read 7 items
Loading required package: Biobase
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘Biobase’
Loading required package: RankAggreg
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'clValid.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file /data/gannet/ripley/R/packages/tests-devel/clVali
d.Rcheck/vign_test/clValid/vignettes/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
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/cmm.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   5.9Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/Combine.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/CompetingRisk.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/CorReg.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 30.4Mb
  sub-directories of 1Mb or more:
    libs  30.0Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   6.4Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Found the following significant warnings:
  bdsmatrix_stub.h:41:5: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  bdsmatrix_stub.h:44:12: warning: return makes integer from pointer without a cast [-Wint-conversion]
  bdsmatrix_stub.h:50:5: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  bdsmatrix_stub.h:53:12: warning: return makes integer from pointer without a cast [-Wint-conversion]
  bdsmatrix_stub.h:97:5: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  bdsmatrix_stub.h:100:12: warning: return from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/data/gannet/ripley/R/packages/tests-devel/coxme.Rcheck/00install.out’ for details.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
installed size is 37.3Mb
  sub-directories of 1Mb or more:
    libs  37.0Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/cplm.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    libs  21.7Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/ctsem.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   6.1Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/Cyclops.Rcheck/00install.out’ for details.
Found the following significant warnings:
  convert_util.cpp:299:20: warning: null destination pointer [-Wformat-overflow=]
  convert_util.cpp:307:20: warning: null destination pointer [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/DatABEL.Rcheck/00install.out’ for details.
installed size is 54.7Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  52.7Mb
ToDiagrammeRGraph: no visible global function definition for
  ‘set_global_graph_attrs’
  (/data/gannet/ripley/R/packages/tests-devel/data.tree/R/node_plot.R:155)
Undefined global functions or variables:
  set_global_graph_attrs
Running ‘testthat.R’ [12s/30s]
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)  ──────────────────────────────────────────
  could not find function "set_global_graph_attrs"
  1: ToDiagrammeRGraph(acme, direction = "descend", pruneFun = function(x) x$level < 3) at testthat/test-draw.R:18
  
  ── 2. Error: grViz single attribute (@test-draw.R#29)  ─────────────────────────
  could not find function "set_global_graph_attrs"
  1: ToDiagrammeRGraph(acme) at testthat/test-draw.R:29
  
  ── 3. Error: grViz single attribute names not uniuqe (@test-draw.R#67)  ────────
  could not find function "set_global_graph_attrs"
  1: ToDiagrammeRGraph(mytree) at testthat/test-draw.R:67
  
                            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: 354 SKIPPED: 0 FAILED: 3
  1. Error: grViz (@test-draw.R#18) 
  2. Error: grViz single attribute (@test-draw.R#29) 
  3. Error: grViz single attribute names not uniuqe (@test-draw.R#67) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   7.7Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   4.9Mb
installed size is 24.1Mb
  sub-directories of 1Mb or more:
    libs  24.0Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/deBInfer.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/debug.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/derivmkts.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.7Mb
    help   1.3Mb
    libs   1.7Mb
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
installed size is 43.5Mb
  sub-directories of 1Mb or more:
    libs  43.0Mb
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  25.0Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/dhglm.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R             2.9Mb
    htmlwidgets   3.1Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/diffractometry.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/diffusionMap.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/di.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Found the following significant warnings:
  dcm2niix/nii_dicom.cpp:617:5: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 24 [-Wformat-truncation=]
See ‘/data/gannet/ripley/R/packages/tests-devel/divest.Rcheck/00install.out’ for details.
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    include  19.7Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   4.6Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   6.0Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/Dominance.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 32.9Mb
  sub-directories of 1Mb or more:
    libs  30.8Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs  11.9Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/dvfBm.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.2Mb
    libs  19.6Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/ecospat.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 42.7Mb
  sub-directories of 1Mb or more:
    libs  42.4Mb
installed size is 29.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  27.5Mb
Found the following significant warnings:
  Note: possible error in 'savePlot(filename = "Clustplot", ': unused argument (restoreConsole = TRUE) 
  Note: possible error in 'savePlot(filename = "MCAplotindclasse", ': unused argument (restoreConsole = TRUE) 
  Note: possible error in 'savePlot(filename = "MCAplotvar", ': unused argument (restoreConsole = TRUE) 
  Note: possible error in 'savePlot(filename = "MCAplotind", ': unused argument (restoreConsole = TRUE) 
  Note: possible error in 'savePlot(filename = "MCAplotquantisup", ': unused argument (restoreConsole = TRUE) 
  Note: possible error in 'savePlot(filename = "Ellipse", ': unused argument (restoreConsole = TRUE) 
  Note: possible error in 'savePlot(filename = "Lisib", ': unused argument (restoreConsole = TRUE) 
  Note: possible error in 'savePlot(filename = "Density", ': unused argument (restoreConsole = TRUE) 
  Note: possible error in 'savePlot(filename = "Densitypop", ': unused argument (restoreConsole = TRUE) 
  Note: possible error in 'savePlot(filename = "barplotgr", ': unused argument (restoreConsole = TRUE) 
  Note: possible error in 'savePlot(filename = paste("barvarclus", ': unused argument (restoreConsole = TRUE) 
  Note: possible error in 'hsv(h = 1, s = 1, v = 1, ': unused argument (1) 
  Note: possible error in 'hsv(h = 1, s = 0.4 + ': unused argument (1) 
  Note: possible error in 'hsv(h = a * i, s = 1, ': unused argument (1) 
  Note: possible error in 'hsv(h = a * m, s = 1, ': unused argument (1) 
  Note: possible error in 'hsv(h = a * m, s = 0.4 + ': unused argument (1) 
See ‘/data/gannet/ripley/R/packages/tests-devel/EnQuireR.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/EnvStats.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/EpiWeek.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/esmprep.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    libs  25.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/eVenn.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Warning: iteration 7 invokes undefined behavior [-Waggressive-loop-optimizations]
See ‘/data/gannet/ripley/R/packages/tests-devel/expoRkit.Rcheck/00install.out’ for details.
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    libs  20.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/FACTscorer.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/fArma.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  15.7Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.6Mb
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/data/gannet/ripley/R/packages/tests-devel/FastRWeb.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.8Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is 50.7Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  47.6Mb
installed size is 23.6Mb
  sub-directories of 1Mb or more:
    libs  23.3Mb
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs  11.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/fifer.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/FindIt.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/FisherEM.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/fpc.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/frailtyHL.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    1.6Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  12.8Mb
installed size is 59.3Mb
  sub-directories of 1Mb or more:
    libs  58.9Mb
installed size is 80.8Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     77.5Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  17.7Mb
Found the following significant warnings:
  convert_util.cpp:299:20: warning: null destination pointer [-Wformat-overflow=]
  convert_util.cpp:307:20: warning: null destination pointer [-Wformat-overflow=]
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/GenABEL.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   5.4Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/GeneFeST.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   4.2Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  13.2Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/geo.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
.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:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/gettingtothebottom.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/gfer.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    1.2Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   2.7Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
installed size is 29.1Mb
  sub-directories of 1Mb or more:
    libs  28.7Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
installed size is 51.9Mb
  sub-directories of 1Mb or more:
    libs  51.0Mb
installed size is 46.1Mb
  sub-directories of 1Mb or more:
    libs  44.9Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/GPGame.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/GPseq.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   4.3Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/GroupSeq.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    libs  18.3Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
normalweight: no visible binding for global variable ‘NW_above’
normalweight: no visible binding for global variable ‘NW_below’
obese: no visible global function definition for ‘data’
obese: no visible binding for global variable ‘OB_above’
obese: no visible binding for global variable ‘OB_below’
overweight: no visible global function definition for ‘data’
overweight: no visible binding for global variable ‘OW_above’
overweight: no visible binding for global variable ‘OW_below’
Undefined global functions or variables:
  NW_above NW_below OB_above OB_below OW_above OW_below data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/hbmem.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
print.tsum: warning in print.default(x$resid, digits = digits, na = "",
  print.gap = 2): partial argument match of 'na' to 'na.print'
print.tsum: no visible global function definition for ‘quantile’
print.tsum: no visible global function definition for ‘printCoefmat’
print.tsum: no visible global function definition for ‘symnum’
tlm: no visible global function definition for ‘formula’
tlm: no visible binding for global variable ‘na.fail’
tlm: no visible global function definition for ‘model.matrix’
tlm: no visible global function definition for ‘model.extract’
tlm: no visible binding for global variable ‘response’
tlm: no visible global function definition for ‘lm.fit’
tlm: no visible global function definition for ‘coef’
tlm: no visible global function definition for ‘resid’
tlm: no visible global function definition for ‘Gamma’
tlm: no visible binding for global variable ‘dofse’
tlm: no visible binding for global variable ‘logLik’
tscore: no visible global function definition for ‘model.extract’
tscore: no visible binding for global variable ‘response’
tscore : <anonymous>: no visible global function definition for
  ‘model.matrix’
tscore: no visible global function definition for ‘resid’
tscore: no visible global function definition for ‘pchisq’
tscore: no visible global function definition for ‘printCoefmat’
tsum: no visible global function definition for ‘pnorm’
tsum: no visible global function definition for ‘pt’
tsum: no visible global function definition for ‘residuals’
Undefined global functions or variables:
  Gamma coef dofse formula lm.fit logLik model.extract model.matrix
  na.fail pchisq pnorm printCoefmat pt quantile resid residuals
  response symnum
Consider adding
  importFrom("stats", "Gamma", "coef", "formula", "lm.fit", "logLik",
             "model.extract", "model.matrix", "na.fail", "pchisq",
             "pnorm", "printCoefmat", "pt", "quantile", "resid",
             "residuals", "symnum")
to your NAMESPACE file.
Found the following significant warnings:
  Note: possible error in 'dgpd(x, xi = a, mu = 0, ': unused arguments (xi = a, mu = 0, beta = 1 - a) 
  Note: possible error in 'pgpd(q, xi = a, mu = 0, ': unused arguments (xi = a, mu = 0, beta = 1 - a) 
  Note: possible error in 'qgpd(p, xi = a, mu = 0, ': unused arguments (xi = a, mu = 0, beta = 1 - a) 
See ‘/data/gannet/ripley/R/packages/tests-devel/HiDimMaxStable.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    highlight   1.1Mb
    libs        6.8Mb
PlotOptPower: no visible global function definition for ‘bmp’
PlotOptPower: no visible global function definition for
  ‘filled.contour’
PlotOptPower: no visible global function definition for ‘title’
PlotOptPower: no visible global function definition for ‘grey.colors’
PlotOptPower: no visible global function definition for ‘axis’
PlotOptPower: no visible global function definition for ‘polygon’
PlotOptPower: no visible global function definition for ‘legend’
PlotOptPower: no visible global function definition for ‘mtext’
PlotOptPower: no visible global function definition for ‘dev.off’
PlotOptPower: no visible global function definition for
  ‘terrain.colors’
ShowOptDesign: no visible global function definition for ‘head’
diffVariantError: no visible global function definition for ‘pbinom’
predictPoolNCP: no visible global function definition for ‘data’
probDetEqual3: no visible global function definition for ‘dbinom’
probDetEqual3: no visible global function definition for ‘pbinom’
Undefined global functions or variables:
  axis bmp data dbinom dev.off filled.contour grey.colors head legend
  mtext pbinom polygon terrain.colors title
Consider adding
  importFrom("grDevices", "bmp", "dev.off", "grey.colors",
             "terrain.colors")
  importFrom("graphics", "axis", "filled.contour", "legend", "mtext",
             "polygon", "title")
  importFrom("stats", "dbinom", "pbinom")
  importFrom("utils", "data", "head")
to your NAMESPACE file.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   4.3Mb
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/hmmm.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/HMMpa.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    dict   1.3Mb
    libs   5.3Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   8.4Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   1.3Mb
    doc    2.2Mb
    libs   1.1Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      2.3Mb
installed size is 41.5Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs  37.0Mb
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  25.7Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/IDTurtle.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  17.4Mb
installed size is 43.1Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       4.9Mb
    extdata   1.0Mb
    include   2.8Mb
    libs     32.4Mb
Interpol: no visible global function definition for ‘splinefun’
Undefined global functions or variables:
  splinefun
Consider adding
  importFrom("stats", "splinefun")
to your NAMESPACE file.
installed size is 27.1Mb
  sub-directories of 1Mb or more:
    libs  26.9Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/intpoint.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.9Mb
Found the following significant warnings:
  Note: possible error in 'get.smiles(x, aromatic = T, ': unused arguments (aromatic = T, type = "generic") 
See ‘/data/gannet/ripley/R/packages/tests-devel/iqspr.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/IRISMustangMetrics.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   8.3Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   4.9Mb
installed size is 21.9Mb
  sub-directories of 1Mb or more:
    libs  21.4Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    include   1.2Mb
    libs      4.6Mb
comp.npci: no visible global function definition for ‘qnorm’
epband.fun: no visible global function definition for ‘data’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.90’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.95’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.99’
hall.wellner.fun: no visible global function definition for ‘data’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.90’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.95’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.99’
lrt.confints: no visible global function definition for ‘qchisq’
rothman.fun: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  critical.value.hall.90 critical.value.hall.95 critical.value.hall.99
  critical.value.nair.90 critical.value.nair.95 critical.value.nair.99
  data qchisq qnorm
Consider adding
  importFrom("stats", "qchisq", "qnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/kmc.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   3.8Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   4.1Mb
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    libs          15.0Mb
    testdata       1.8Mb
    vignettedata   2.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/lava.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs     24.0Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   7.9Mb
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/liso.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/LncPriCNet.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Warning: ‘nsimp’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-devel/localdepth.Rcheck/00install.out’ for details.
Found the following significant warnings:
  cvrout.c:286:35: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/LogicOpt.Rcheck/00install.out’ for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      1.3Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/lqmm.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 45.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  43.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   4.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   2.1Mb
installed size is 26.2Mb
  sub-directories of 1Mb or more:
    libs  25.9Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs   6.1Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/MagneticMap.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   1.7Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   8.5Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   9.2Mb
plot.mathgraph: no visible global function definition for ‘plot’
plot.mathgraph: no visible global function definition for ‘box’
plot.mathgraph: no visible global function definition for ‘segments’
plot.mathgraph: no visible global function definition for ‘arrows’
plot.mathgraph: no visible global function definition for ‘text’
Undefined global functions or variables:
  arrows box plot segments text
Consider adding
  importFrom("graphics", "arrows", "box", "plot", "segments", "text")
to your NAMESPACE file.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Found the following significant warnings:
  Note: possible error in 'writeLines(as.character(yy), ': unused argument (file = outfile) 
See ‘/data/gannet/ripley/R/packages/tests-devel/matR.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  17.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/mclcar.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    libs  25.8Mb
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/mdhglm.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    extdata   3.9Mb
    libs      1.4Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   9.2Mb
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   5.7Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/MetaSubtract.Rcheck/MetaSubtract/extdata’, resetting
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  18.2Mb
    misc   1.1Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   6.8Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/mixor.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
listGenoToTable: no visible binding for global variable ‘dummy’
Undefined global functions or variables:
  dummy
Running ‘run-base.R’ [402s/465s]
  Running ‘run-classif.R’
  Running ‘run-cluster.R’
  Running ‘run-featsel.R’
  Running ‘run-learners-classif.R’
  Running ‘run-learners-classiflabelswitch.R’
  Running ‘run-learners-cluster.R’
  Running ‘run-learners-general.R’
  Running ‘run-learners-multilabel.R’
  Running ‘run-learners-regr.R’
  Running ‘run-learners-surv.R’
  Running ‘run-multilabel.R’
  Running ‘run-parallel.R’
  Running ‘run-regr.R’
  Running ‘run-stack.R’
  Running ‘run-surv.R’
  Running ‘run-tune.R’
Running the tests in ‘tests/run-base.R’ failed.
Complete output:
  > library(testthat)
  > test_check("mlr", filter = "base")
  Loading required package: mlr
  Loading required package: ParamHelpers
  ── 1. Error: check measure calculations (@test_base_measures.R#637)  ───────────
  object 'mldr_HL' not found
  1: expect_equal(mldr:::mldr_HL(multi.y, multi.p), measureMultilabelHamloss(multi.y, 
         multi.p)) at testthat/test_base_measures.R:637
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: mldr:::mldr_HL
  5: get(name, envir = asNamespace(pkg), inherits = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2652 SKIPPED: 8 FAILED: 1
  1. Error: check measure calculations (@test_base_measures.R#637) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.7Mb
    libs   3.5Mb
Running ‘testthat.R’ [9s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(Momocs)
  This is Momocs 1.2.2
  
  Attaching package: 'Momocs'
  
  The following object is masked from 'package:stats':
  
      filter
  
  The following object is masked from 'package:base':
  
      table
  
  > 
  > test_check("Momocs")
  ── 1. Error: filter works fine (@test-nse.R#62)  ───────────────────────────────
  bad value
  1: expect_true(x_lite$fac %>% sapply(nlevels) %>% ==1 %>% all) at testthat/test-nse.R:62
  2: quasi_label(enquo(object), label)
  3: force(quo)
  4: enquo(object)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 159 SKIPPED: 1 FAILED: 1
  1. Error: filter works fine (@test-nse.R#62) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs  18.3Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  10.8Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/MortHump.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   4.4Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 42.1Mb
  sub-directories of 1Mb or more:
    libs  41.7Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/mstR.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Found the following significant warnings:
  Note: possible error in 'theme(axis.text.x = element_text(size = 6, ': formal argument "axis.text.x" matched by multiple actual arguments 
See ‘/data/gannet/ripley/R/packages/tests-devel/multilevelPSA.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 67.4Mb
  sub-directories of 1Mb or more:
    libs  67.2Mb
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/MultiPhen.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/mvmeta.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/ncappc.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/ncf.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.1Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   7.4Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   7.8Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/nimble.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    R              5.8Mb
    classic-bugs   1.6Mb
    include        5.8Mb
    tests          1.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.1Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/novelist.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/npde.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs  15.4Mb
File ‘nws/R/zzz.R’:
  .onLoad calls:
    require(methods)

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

blendOptions: warning in assign(names[i], new[[i]], env = options):
  partial argument match of 'env' to 'envir'
docall: warning in get(as.character(fun), env = .GlobalEnv, mode =
  "function"): partial argument match of 'env' to 'envir'
logMsg: no visible global function definition for ‘flush.console’
nwsPkgInfo: no visible global function definition for
  ‘packageDescription’
initialize,nwsServer: no visible global function definition for
  ‘make.socket’
initialize,nwsServer: no visible global function definition for
  ‘close.socket’
Undefined global functions or variables:
  close.socket flush.console make.socket packageDescription
Consider adding
  importFrom("utils", "close.socket", "flush.console", "make.socket",
             "packageDescription")
to your NAMESPACE file.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   2.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is 91.3Mb
  sub-directories of 1Mb or more:
    libs  90.8Mb
mapvar: no visible global function definition for ‘data’
mapvar: no visible binding for global variable ‘state.fips’
mapvar: no visible global function definition for ‘rgb’
mapvar: no visible global function definition for ‘rect’
mapvar: no visible global function definition for ‘text’
rowScrape: no visible global function definition for ‘tail’
rowScrape: no visible global function definition for ‘head’
scrapeTable: no visible binding for global variable ‘tail’
Undefined global functions or variables:
  data head rect rgb state.fips tail text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "rect", "text")
  importFrom("utils", "data", "head", "tail")
to your NAMESPACE file.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is 154.2Mb
  sub-directories of 1Mb or more:
    R         2.3Mb
    libs    144.4Mb
    models    4.7Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/OpenRepGrid.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Running ‘testthat.R’ [18s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > test_check("openxlsx")
  Loading required package: openxlsx
  ── 1. Error: loadWorkbook from different sources (@test-read_sources.R#49)  ────
  subscript out of bounds
  1: expect_true(all.equal.Workbook(wb_url, wb_file), "Loading from URL vs local not equal") at testthat/test-read_sources.R:49
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: all.equal.Workbook(wb_url, wb_file)
  5: sapply(1:nSheets, function(i) isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]])))
  6: lapply(X = X, FUN = FUN, ...)
  7: FUN(X[[i]], ...)
  8: isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]]))
  9: all.equal(x$colWidths[[i]], y$colWidths[[i]])
  10: all.equal.list(x$colWidths[[i]], y$colWidths[[i]])
  11: attr.all.equal(target, current, ...)
  12: mode(current)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 505 SKIPPED: 2 FAILED: 1
  1. Error: loadWorkbook from different sources (@test-read_sources.R#49) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      5.6Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   3.3Mb
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/PAactivPAL.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  pads_circle_pack.cpp:233:6: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=]
See ‘/data/gannet/ripley/R/packages/tests-devel/packcircles.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/packrat.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    lib  12.3Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc        1.3Mb
    examples   1.7Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   2.1Mb
    libs   6.5Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/pdolsms.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/pendensity.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/penRvine.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/phalen.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 35.5Mb
  sub-directories of 1Mb or more:
    libs  34.8Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Found the following significant warnings:
  Note: possible error in 'try(xtriple, ftriple, ': unused arguments (lfmid, 1, 2) 
  Note: possible error in 'try(xtriple, ftriple, ': unused arguments (rfmid, 2, 3) 
See ‘/data/gannet/ripley/R/packages/tests-devel/phyreg.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/PhySortR.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/picante.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 27.7Mb
  sub-directories of 1Mb or more:
    libs  27.6Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/plsRglm.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: possible error in 'add_edges_from_table(p, ': unused argument (ndf_mapping = "name_without_space") at create_pmap_graph.R:110 
See ‘/data/gannet/ripley/R/packages/tests-devel/pmap.Rcheck/00install.out’ for details.
create_pmap_graph: possible error in add_edges_from_table(p, table =
  edges %>% select(-amount), from_col = "from", to_col = "to",
  ndf_mapping = "name_without_space"): unused argument (ndf_mapping =
  "name_without_space")
  (/data/gannet/ripley/R/packages/tests-devel/pmap/R/create_pmap_graph.R:110-116)
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/pmlr.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/PopGenome.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/PortfolioAnalytics.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/powerCompRisk.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   7.0Mb
Found the following significant warnings:
  Note: possible error in 'psf(data = dataIn1, n.ahead = nextVal)': unused argument (n.ahead = nextVal) 
See ‘/data/gannet/ripley/R/packages/tests-devel/PredictTestbench.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/processmapR.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/PROFANCY.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/profileR.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    libs  22.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   2.8Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   3.3Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.4Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/psidR.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/PSM.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 25.7Mb
  sub-directories of 1Mb or more:
    libs  25.2Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/QoLR.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 67.0Mb
  sub-directories of 1Mb or more:
    libs   56.6Mb
    local   9.4Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.8Mb
    doc       2.9Mb
    libs      1.2Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs  15.4Mb
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/QuantTools.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   6.4Mb
Found the following significant warnings:
  Note: possible error in 'unlist(strsplit(.$removeSpaces(.$ivField)), ': unused argument (fixed = TRUE) 
See ‘/data/gannet/ripley/R/packages/tests-devel/R2STATS.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    app   4.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   3.8Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/ramidst.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs   4.7Mb
.disableThreads: no visible global function definition for
  ‘stopCluster’
.enableThreads: no visible global function definition for ‘detectCores’
.enableThreads: no visible global function definition for
  ‘makePSOCKcluster’
.enableThreads: no visible global function definition for
  ‘clusterExport’
.enableThreads: no visible global function definition for ‘clusterCall’
.forwardSelection: no visible binding for global variable ‘var’
.forwardSelection: no visible global function definition for ‘glm’
.forwardSelection: no visible global function definition for ‘formula’
.forwardSelection: no visible global function definition for ‘binomial’
.forwardSelection: no visible global function definition for ‘lm’
.forwardSelection: no visible global function definition for ‘predict’
.predict.internal: no visible global function definition for ‘predict’
randomGLM: no visible binding for global variable ‘cor’
randomGLM: no visible binding for global variable ‘sd’
randomGLM: no visible global function definition for ‘var’
thinRandomGLM: no visible global function definition for ‘glm’
thinRandomGLM: no visible global function definition for ‘binomial’
thinRandomGLM: no visible global function definition for ‘lm’
Undefined global functions or variables:
  binomial clusterCall clusterExport cor detectCores formula glm lm
  makePSOCKcluster predict sd stopCluster var
Consider adding
  importFrom("stats", "binomial", "cor", "formula", "glm", "lm",
             "predict", "sd", "var")
to your NAMESPACE file.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs   3.3Mb
installed size is 30.6Mb
  sub-directories of 1Mb or more:
    libs  29.2Mb
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    blp    7.1Mb
    libs   9.1Mb
Found the following significant warnings:
  intersection.cc:384:1: warning: ‘%g’ directive writing 12 bytes into a region of size between 0 and 41 [-Wformat-overflow=]
  intersection.cc:384:1: warning: ‘%g’ directive writing 12 bytes into a region of size between 0 and 42 [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/RCALI.Rcheck/00install.out’ for details.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    include   5.2Mb
    libs      1.9Mb
installed size is 28.0Mb
  sub-directories of 1Mb or more:
    include  25.5Mb
    libs      2.4Mb
installed size is 32.5Mb
  sub-directories of 1Mb or more:
    include   7.9Mb
    libs     24.0Mb
installed size is 81.1Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib      62.4Mb
    libs     16.5Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    include   7.0Mb
    libs      3.3Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib       3.1Mb
installed size is 57.4Mb
  sub-directories of 1Mb or more:
    include   8.9Mb
    libs     48.3Mb
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    include   6.4Mb
    libs      3.9Mb
installed size is 170.4Mb
  sub-directories of 1Mb or more:
    include    4.6Mb
    lib      129.4Mb
    libs      36.1Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  10.9Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
xy: warning in assign(xname, X, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
xy: warning in assign(yname, y, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
bestmods: no visible global function definition for ‘abline’
bestmods: no visible global function definition for ‘axis’
bestmods: no visible global function definition for ‘lines’
cic: no visible global function definition for ‘lsfit’
cic: no visible global function definition for ‘var’
cvic: no visible global function definition for ‘lsfit’
cvic: no visible global function definition for ‘lm’
eic: no visible global function definition for ‘lsfit’
eic: no visible global function definition for ‘lm’
ic.min: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘var’
xy: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline axis lines lm lsfit rnorm var
Consider adding
  importFrom("graphics", "abline", "axis", "lines")
  importFrom("stats", "lm", "lsfit", "rnorm", "var")
to your NAMESPACE file.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   4.6Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   6.0Mb
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  15.3Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/refund.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/relax.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 23.5Mb
  sub-directories of 1Mb or more:
    libs  22.4Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
installed size is 81.6Mb
  sub-directories of 1Mb or more:
    libs  80.6Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      2.4Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/RGoogleAnalytics.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Packages suggested but not available for checking:
  ‘hyperdraw’ ‘hypergraph’ ‘pmg’
Found the following significant warnings:
  atkClasses.c:1050:25: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  atkClasses.c:1058:34: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  atkClasses.c:1397:51: warning: passing argument 2 of ‘object_class->active_descendant_changed’ from incompatible pointer type [-Wincompatible-pointer-types]
  gdkFuncs.c:6000:36: warning: passing argument 2 of ‘gdk_window_get_user_data’ from incompatible pointer type [-Wincompatible-pointer-types]
  gioClasses.c:1948:17: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gioClasses.c:1964:20: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gtkClasses.c:8665:28: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gtkClasses.c:11110:21: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/data/gannet/ripley/R/packages/tests-devel/RGtk2.Rcheck/00install.out’ for details.
installed size is 26.7Mb
  sub-directories of 1Mb or more:
    R      3.6Mb
    help  10.5Mb
    libs  10.8Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-devel/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’,
    ‘R_GlobalContext’
File ‘rJava/libs/rJava.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Note: possible error in 'write(self$rules, file = paste0(fileName, ': unused argument (col.names = NA) 
See ‘/data/gannet/ripley/R/packages/tests-devel/RKEEL.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/Rlda.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    rmd   6.1Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   5.7Mb
Found the following significant warnings:
  newmat5.cpp:525:69: warning: throw will always call terminate() [-Wterminate]
See ‘/data/gannet/ripley/R/packages/tests-devel/Rmixmod.Rcheck/00install.out’ for details.
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/Rmpi.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/RM.weights.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 21.5Mb
  sub-directories of 1Mb or more:
    libs  21.3Mb
installed size is 97.8Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     95.7Mb
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  20.4Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/rootWishart.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    libs  20.9Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.3Mb
    libs   6.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      4.8Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  11.0Mb
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/RSEIS.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-devel/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is 50.9Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  49.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   2.8Mb
installed size is 152.4Mb
  sub-directories of 1Mb or more:
    R       1.4Mb
    doc     2.4Mb
    libs  148.0Mb
installed size is 252.1Mb
  sub-directories of 1Mb or more:
    libs  249.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/rsunlight.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/RSurvey.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
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
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       2.9Mb
    projects   2.7Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
installed size is 44.9Mb
  sub-directories of 1Mb or more:
    libs  44.2Mb
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
    test  19.6Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/RWildbook.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs    8.0Mb
    yacas   1.5Mb
Found the following significant warnings:
  Note: possible error in 'saveSession(force = TRUE)': unused argument (force = TRUE) 
See ‘/data/gannet/ripley/R/packages/tests-devel/Rz.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/SAENET.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
prime.factor: no visible global function definition for ‘data’
prime.factor: no visible binding for global variable ‘primlist’
Undefined global functions or variables:
  data primlist
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   2.1Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/sensors4plumes.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 23.2Mb
  sub-directories of 1Mb or more:
    doc    6.0Mb
    libs  16.4Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    doc     10.1Mb
    libs     6.1Mb
    sqlite   1.5Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/shp2graph.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  11.7Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   6.9Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.4Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/slickR.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   6.5Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/sm.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/SocialMediaLab.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/soundecology.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
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, sd, var, xtabs

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

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

Identifing all possible orderings..
Total run time: 2.83 secs
Identifing all possible orderings..
Total run time: 2.03 secs
Quitting from lines 386-388 (SourceSet.Rmd) 
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
there is no package called 'ALL'
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/spaceExt.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 36.4Mb
  sub-directories of 1Mb or more:
    libs  34.6Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    R      4.9Mb
    doc    4.7Mb
    help   4.9Mb
    libs   2.2Mb
installed size is 29.8Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  27.7Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   9.2Mb
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs  13.2Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    include   9.1Mb
    lib       1.7Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      2.8Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R          2.2Mb
    datasets   2.6Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.4Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/streamR.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.0Mb
Running ‘testthat.R’ [8s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(subprocess)
  > 
  > # See for more details:
  > # https://github.com/hadley/testthat/issues/144
  > # https://github.com/hadley/testthat/issues/86
  > # https://github.com/luckyrandom/cmaker/commit/b85813ac2b7aef69932eca8fbb4fa0ec225e0af0
  > #
  > # When R CMD check runs tests, it sets R_TESTS. When the tests
  > # themeselves run R CMD xxxx, as is the case with the tests in
  > # devtools, having R_TESTS set causes errors because it confuses
  > # the R subprocesses. Unsetting it here avoids those problems.
  > #
  > # We need this because we spawn child R processes and they get very
  > # confused if this variable (R_TESTS) is present in their environment.
  > Sys.setenv("R_TESTS" = "")
  > 
  > test_check("subprocess")
  ── 1. Error: child process is terminated in Linux (@test-termination.R#85)  ────
  is_process_handle(handle) is not TRUE
  1: expect_true(wait_until_appears(child_id)) at testthat/test-termination.R:85
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: wait_until_appears(child_id)
  5: process_wait(handle, TIMEOUT_IMMEDIATE) at /data/gannet/ripley/R/packages/tests-devel/subprocess.Rcheck/tests/testthat/helper-processes.R:58
  6: stopifnot(is_process_handle(handle))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 71 SKIPPED: 2 FAILED: 1
  1. Error: child process is terminated in Linux (@test-termination.R#85) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.3Mb
    help   1.0Mb
    libs   1.7Mb
installed size is 61.4Mb
  sub-directories of 1Mb or more:
    libs  60.5Mb
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: GNU Extension: Different type kinds at (1)
  Warning: GNU Extension: initialization of common block variable ‘iset’ in DATA statement at (1)
  Warning: GNU Extension: Variable ‘iset’ at (1) is in COMMON but only in BLOCK DATA initialization is allowed
  Warning: GNU Extension: Missing comma at (1)
  Warning: CHARACTER expression will be truncated in assignment (10/13) at (1) [-Wcharacter-truncation]
  Warning: ‘pst_kg’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘burn_frlb’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘hi_ovr’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘harveff’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘frac_harvk’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘cnop’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘lai_init’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘orig_tnylda’ is used uninitialized in this function [-Wuninitialized]
  Warning: CHARACTER expression will be truncated in assignment (1/3) at (1) [-Wcharacter-truncation]
  Warning: ‘fr_curb’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-devel/SWATmodel.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/sybilEFBA.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
Found the following significant warnings:
  sybilSBML.c:2236:32: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=]
  sybilSBML.c:2247:34: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/sybilSBML.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/SynergizeR.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   5.5Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.9Mb
    libs   1.1Mb
installed size is 32.9Mb
  sub-directories of 1Mb or more:
    libs  31.5Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    apps   2.6Mb
    libs   2.0Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/tensorBF.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.6Mb
    libs   6.6Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    examples  13.3Mb
    include    3.0Mb
installed size is 25.7Mb
  sub-directories of 1Mb or more:
    libs  25.5Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/TrajDataMining.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 36.6Mb
  sub-directories of 1Mb or more:
    libs  36.1Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/turboEM.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    doc         4.1Mb
    dummydata   1.4Mb
    libs       20.7Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    1.6Mb
    libs   4.0Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
Found the following significant warnings:
  convert_util.cpp:299:20: warning: null destination pointer [-Wformat-overflow=]
  convert_util.cpp:307:20: warning: null destination pointer [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/VariABEL.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/VarReg.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
Found the following significant warnings:
  EM.c:386:25: warning: ‘sprintf’ writing a terminating nul past the end of the destination [-Wformat-overflow=]
  EM.c:391:25: warning: ‘sprintf’ writing a terminating nul past the end of the destination [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/VBmix.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/vcfR.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R      3.4Mb
    doc    1.2Mb
    help   2.7Mb
installed size is 50.7Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  48.2Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Bundesliga.Mannschaft: no visible global function definition for ‘data’
Bundesliga.Mannschaft: no visible binding for global variable
  ‘Bundesliga’
Bundesliga.Tabelle: no visible global function definition for ‘data’
Bundesliga.Tabelle: no visible binding for global variable ‘Bundesliga’
Bundesliga.XML: no visible global function definition for ‘data’
Bundesliga.XML: no visible binding for global variable ‘Bundesliga’
sens.spec: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/windfarmGA.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    exampleData   1.6Mb
    examples      4.6Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/XR.Rcheck/00install.out’ for details.
Further information on the locations of the code referred to in the
Notes can can be obtained by re-running with environnment variable
R_KEEP_PKG_SOURCE set to ‘yes’.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   2.7Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Packages in Depends field not imported from:
  'Rglpk' 'corrplot' 'lattice' 'rgl'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
multiplot: no visible global function definition for 'rainbow'
multiplot: no visible global function definition for 'plot'
multiplot: no visible global function definition for 'text'
multiplot: no visible global function definition for 'lines'
multiplot: no visible global function definition for 'par'
plot.abf2: no visible global function definition for 'plot'
plot.abf2: no visible global function definition for 'abline'
plot.abf2: no visible global function definition for 'text'
plot.abf2split: no visible global function definition for 'plot'
Undefined global functions or variables:
  abline lines par plot rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "par", "plot", "text")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/AbsFilterGSEA.Rcheck/00install.out' for details.
fillCSVData: no visible global function definition for 'read.table'
fillData: no visible global function definition for 'edit'
plotGraphs: no visible global function definition for 'par'
plotGraphs: no visible global function definition for 'plot'
plotGraphs: no visible global function definition for 'lines'
plotGraphs: no visible global function definition for 'legend'
plotGraphs: no visible global function definition for 'dev.new'
Undefined global functions or variables:
  dev.new edit legend lines par plot read.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "legend", "lines", "par", "plot")
  importFrom("utils", "edit", "read.table")
to your NAMESPACE file.
print.funlinWLS: no visible global function definition for 'pchisq'
print.linML: no visible global function definition for 'pchisq'
print.loglinML: no visible global function definition for 'pchisq'
print.satMarML: no visible global function definition for 'pchisq'
print.satMcarWLS: no visible global function definition for 'pchisq'
summary.funlinWLS: no visible global function definition for 'pchisq'
summary.linML: no visible global function definition for 'pchisq'
summary.loglinML: no visible global function definition for 'pchisq'
summary.satMarML: no visible global function definition for 'pchisq'
summary.satMcarWLS: no visible global function definition for 'pchisq'
summary.waldTest: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
Package in Depends field not imported from: 'MASS'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
acm: no visible global function definition for 'read.table'
clusters: no visible global function definition for 'write.matrix'
clusters: no visible global function definition for 'dev.new'
clusters: no visible global function definition for 'par'
clusters: no visible global function definition for 'hist'
clusters: no visible global function definition for 'legend'
clusters: no visible global function definition for 'pdf'
clusters: no visible global function definition for 'dev.off'
erra: no visible global function definition for 'read.table'
erra: no visible global function definition for 'pbeta'
Undefined global functions or variables:
  dev.new dev.off hist legend par pbeta pdf read.table write.matrix
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf")
  importFrom("graphics", "hist", "legend", "par")
  importFrom("stats", "pbeta")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'library' or 'require' call to 'mvtnorm' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Aggregate: no visible global function definition for 'aggregate'
Aggregate: no visible binding for global variable 'tail'
Aggregate: no visible binding for global variable 'var'
cocktailEnsemble: no visible global function definition for 'glm'
cocktailEnsemble: no visible global function definition for 'binomial'
cocktailEnsemble: no visible global function definition for 'step'
cocktailEnsemble: no visible binding for global variable 'na.omit'
imputeMissings : <anonymous>: no visible global function definition for
  'median'
predict.cocktailEnsemble: no visible global function definition for
  'predict'
Undefined global functions or variables:
  aggregate binomial glm median na.omit predict step tail var
Consider adding
  importFrom("stats", "aggregate", "binomial", "glm", "median",
             "na.omit", "predict", "step", "var")
  importFrom("utils", "tail")
to your NAMESPACE file.
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    R  13.6Mb
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/ACTCD.Rcheck/00install.out' for details.
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'SemiPar' 'nlme'
  Please remove these calls from your code.
asp: no visible global function definition for 'as.formula'
asp: no visible global function definition for 'var'
aspm: no visible binding for global variable 'X.Declan'
aspm: no visible binding for global variable 'Z.Jaida'
aspm: no visible binding for global variable 'group.vec.Handan'
aspm: no visible global function definition for 'as.formula'
aspm: no visible global function definition for 'glm'
aspm: no visible global function definition for 'binomial'
aspm: no visible global function definition for 'poisson'
Undefined global functions or variables:
  X.Declan Z.Jaida as.formula binomial glm group.vec.Handan poisson var
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "poisson", "var")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'MASS' 'Matrix'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'Rcpp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Depends: includes the non-default packages:
  'Matrix' 'coda' 'mvtnorm' 'MCMCpack' 'spatstat' 'parallel'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' calls to packages already attached by Depends:
  'MCMCpack' 'Matrix' 'coda' 'mvtnorm' 'parallel' 'spatstat'
  Please remove these calls from your code.
Package in Depends field not imported from: 'lattice'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
critical.values: no visible global function definition for 'rnorm'
critical.values: no visible global function definition for 'quantile'
mandel.test: no visible global function definition for 'qf'
mtukey.test : p.test: no visible global function definition for 'qf'
mtukey.test: no visible binding for global variable 'quantile'
mtukey.test: no visible global function definition for 'rnorm'
tukey.test: no visible global function definition for 'qf'
Undefined global functions or variables:
  qf quantile rnorm
Consider adding
  importFrom("stats", "qf", "quantile", "rnorm")
to your NAMESPACE file.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       2.7Mb
    pictures   2.1Mb
ADM3: no visible global function definition for 'read.table'
ADM3: no visible global function definition for 'write.table'
dLRs: no visible global function definition for 'IQR'
dLRs: no visible global function definition for 'na.omit'
dLRs: no visible global function definition for 'qnorm'
plotADM3: no visible global function definition for 'plot'
plotADM3: no visible global function definition for 'abline'
plotADM3: no visible global function definition for 'segments'
Undefined global functions or variables:
  IQR abline na.omit plot qnorm read.table segments write.table
Consider adding
  importFrom("graphics", "abline", "plot", "segments")
  importFrom("stats", "IQR", "na.omit", "qnorm")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
bayescan: no visible global function definition for 'shortPathName'
Undefined global functions or variables:
  shortPathName
Consider adding
  importFrom("utils", "shortPathName")
to your NAMESPACE file.
aftgee: no visible global function definition for 'model.extract'
aftgee: no visible global function definition for 'model.matrix'
aftgee: no visible global function definition for 'lm'
aftgee: no visible global function definition for 'vcov'
aftgee.fit: no visible global function definition for 'lm'
aftgee.fit: no visible global function definition for 'rexp'
aftgee.fit: no visible global function definition for 'var'
aftsrr: no visible global function definition for 'model.extract'
aftsrr: no visible global function definition for 'model.matrix'
aftsrr.fit: no visible global function definition for 'lm'
aftsrr.fit: no visible global function definition for 'rexp'
aftsrr.fit: no visible global function definition for 'var'
getSmoothSuv: no visible global function definition for 'pnorm'
print.summary.aftgee: no visible global function definition for
  'printCoefmat'
print.summary.aftsrr: no visible global function definition for
  'printCoefmat'
solveGehan: no visible global function definition for 'nlm'
summary.aftgee: no visible global function definition for 'pnorm'
summary.aftsrr: no visible global function definition for 'pnorm'
viEmp: no visible global function definition for 'rexp'
viEmp: no visible global function definition for 'rnorm'
viEmp: no visible global function definition for 'var'
zlFun: no visible global function definition for 'lm'
Undefined global functions or variables:
  lm model.extract model.matrix nlm pnorm printCoefmat rexp rnorm var
  vcov
Consider adding
  importFrom("stats", "lm", "model.extract", "model.matrix", "nlm",
             "pnorm", "printCoefmat", "rexp", "rnorm", "var", "vcov")
to your NAMESPACE file.
closure_total_fair: no visible global function definition for 'is'
closure_transitive: no visible global function definition for 'is'
de_transitive: no visible global function definition for 'is'
get_equivalence_classes: no visible global function definition for 'is'
get_incomparable_pairs: no visible global function definition for 'is'
get_independent_sets: no visible global function definition for 'is'
is_reflexive: no visible global function definition for 'is'
is_total: no visible global function definition for 'is'
is_transitive: no visible global function definition for 'is'
pareto2_estimate_mle: no visible global function definition for
  'uniroot'
pareto2_test_f: no visible global function definition for 'qf'
pareto2_test_f: no visible global function definition for 'pf'
plot.citfun: no visible global function definition for 'plot'
plot.citfun: no visible global function definition for 'par'
plot.citfun: no visible global function definition for 'segments'
plot.citfun: no visible global function definition for 'points'
plot_producer: no visible global function definition for 'plot'
plot_producer: no visible global function definition for 'par'
plot_producer: no visible global function definition for 'segments'
plot_producer: no visible global function definition for 'points'
rpareto2: no visible global function definition for 'runif'
Undefined global functions or variables:
  is par pf plot points qf runif segments uniroot
Consider adding
  importFrom("graphics", "par", "plot", "points", "segments")
  importFrom("methods", "is")
  importFrom("stats", "pf", "qf", "runif", "uniroot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
IIR: no visible global function definition for 'qnorm'
TIR: no visible global function definition for 'qnorm'
agreement: no visible global function definition for 'var'
agreement: no visible global function definition for 'pchisq'
agreement: no visible global function definition for 'dnorm'
agreement: no visible global function definition for 'qnorm'
html.report: no visible global function definition for 'plot'
plot.report: no visible global function definition for 'plot'
plot.report: no visible global function definition for 'axis'
plot.report: no visible global function definition for 'points'
unified.agreement: no visible global function definition for 'lm'
unified.agreement: no visible global function definition for 'qnorm'
unified.agreement: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  axis dnorm lm pchisq plot pnorm points qnorm var
Consider adding
  importFrom("graphics", "axis", "plot", "points")
  importFrom("stats", "dnorm", "lm", "pchisq", "pnorm", "qnorm", "var")
to your NAMESPACE file.
Namespace with empty importFrom: 'survival'
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'survival'
A package should be listed in only one of these fields.
backfit.cox.interaction: no visible global function definition for
  'coxph'
backfit.lm.interaction: no visible global function definition for 'lm'
backfit.logistic.interaction: no visible global function definition for
  'glm'
backfit.logistic.main: no visible global function definition for 'glm'
cox.interaction: no visible global function definition for 'coxph'
cv.cox.interaction: no visible global function definition for 'coxph'
cv.cox.main: no visible global function definition for 'coxph'
cv.lm.interaction: no visible global function definition for 'lm'
cv.lm.main: no visible global function definition for 'lm'
cv.logistic.interaction: no visible global function definition for
  'glm'
cv.logistic.main: no visible global function definition for 'glm'
lm.interaction: no visible global function definition for 'lm'
logistic.interaction: no visible global function definition for 'glm'
logistic.main: no visible global function definition for 'glm'
Undefined global functions or variables:
  coxph glm lm
Consider adding
  importFrom("stats", "glm", "lm")
to your NAMESPACE file.
dke.fun.default: no visible global function definition for 'hist'
kef: no visible global function definition for 'dbinom'
kef: no visible global function definition for 'dgamma'
kef: no visible global function definition for 'dlnorm'
plot.dke.fun: no visible global function definition for 'hist'
plot.dke.fun: no visible global function definition for 'lines'
plot.hcvc.fun1d: no visible global function definition for
  'plot.default'
plot.hcvd.fun1d: no visible global function definition for
  'plot.default'
plot.kern.fun1d: no visible global function definition for
  'plot.default'
plot.kpmfe.fun1d: no visible global function definition for
  'plot.default'
plot.reg.fun1d: no visible global function definition for
  'plot.default'
simp_int: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx dbinom dgamma dlnorm hist lines plot.default
Consider adding
  importFrom("graphics", "hist", "lines", "plot.default")
  importFrom("stats", "approx", "dbinom", "dgamma", "dlnorm")
to your NAMESPACE file.
'library' or 'require' call to 'stats' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
akmeans: no visible global function definition for 'kmeans'
Undefined global functions or variables:
  kmeans
Consider adding
  importFrom("stats", "kmeans")
to your NAMESPACE file.
adpbar: no visible global function definition for 'optim'
alabama: no visible global function definition for 'optim'
auglag: no visible global function definition for 'modifyList'
auglag1: no visible global function definition for 'optim'
auglag1: no visible global function definition for 'nlminb'
auglag2: no visible global function definition for 'optim'
auglag2: no visible global function definition for 'nlminb'
auglag3: no visible global function definition for 'optim'
auglag3: no visible global function definition for 'nlminb'
augpen: no visible global function definition for 'optim'
constrOptim.nl: no visible global function definition for 'modifyList'
Undefined global functions or variables:
  modifyList nlminb optim
Consider adding
  importFrom("stats", "nlminb", "optim")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
eval.blockdesign: no visible global function definition for
  'model.matrix'
eval.design: no visible global function definition for 'model.matrix'
expand.formula: no visible global function definition for 'as.formula'
model.matrix.formula: no visible global function definition for
  'model.matrix.default'
model.matrix.terms: no visible global function definition for
  'model.matrix.default'
optBlock : set.factors: no visible global function definition for 'C'
optBlock : remove.nesting: no visible global function definition for
  'as.formula'
optBlock: no visible global function definition for 'formula'
optBlock: no visible global function definition for 'model.matrix'
optFederov: no visible global function definition for 'formula'
optFederov: no visible global function definition for 'model.matrix'
optMonteCarlo : RandomLevels: no visible global function definition for
  'runif'
optMonteCarlo : RandomMixture: no visible global function definition
  for 'rexp'
optMonteCarlo : expand: no visible global function definition for
  'model.matrix'
optMonteCarlo: no visible global function definition for 'as.formula'
Undefined global functions or variables:
  C as.formula formula model.matrix model.matrix.default rexp runif
Consider adding
  importFrom("stats", "C", "as.formula", "formula", "model.matrix",
             "model.matrix.default", "rexp", "runif")
to your NAMESPACE file.
hierarchical: no visible global function definition for 'terms'
hierarchical: no visible global function definition for 'loglin'
hierarchical: no visible global function definition for 'dmultinom'
markov: no visible global function definition for 'download.file'
metropolis: no visible global function definition for 'runif'
mpolyListToMat : <anonymous>: no visible global function definition for
  'runif'
polyOptim: no visible global function definition for 'deriv'
print.hierarchical: no visible binding for global variable 'sd'
spectral : summarize: no visible global function definition for 'sd'
subsets : <anonymous>: no visible global function definition for
  'combn'
Undefined global functions or variables:
  combn deriv dmultinom download.file loglin runif sd terms
Consider adding
  importFrom("stats", "deriv", "dmultinom", "loglin", "runif", "sd",
             "terms")
  importFrom("utils", "combn", "download.file")
to your NAMESPACE file.
gascuel: no visible global function definition for 'optim'
Undefined global functions or variables:
  optim
Consider adding
  importFrom("stats", "optim")
to your NAMESPACE file.
allanVarSelect: no visible global function definition for 'read.csv'
fitvbiglm: no visible global function definition for 'read.csv'
fitvbiglm: no visible global function definition for 'update'
getbestchunksize: no visible global function definition for 'read.csv'
getbestchunksize: no visible global function definition for
  'object.size'
predictvbiglm: no visible global function definition for 'read.csv'
predictvbiglm: no visible global function definition for 'predict'
predictvbiglm: no visible global function definition for
  'weighted.mean'
readinbigdata : <anonymous>: no visible global function definition for
  'read.csv'
Undefined global functions or variables:
  object.size predict read.csv update weighted.mean
Consider adding
  importFrom("stats", "predict", "update", "weighted.mean")
  importFrom("utils", "object.size", "read.csv")
to your NAMESPACE file.
amCSV.amCluster: no visible global function definition for 'write.csv'
amCSV.amPairwise: no visible global function definition for 'write.csv'
amCSV.amUnique: no visible global function definition for 'write.csv'
amCluster: no visible global function definition for 'hclust'
amCluster: no visible global function definition for 'as.dist'
amHTML.amCluster: no visible global function definition for 'browseURL'
amHTML.amPairwise: no visible global function definition for
  'browseURL'
amHTML.amUnique: no visible global function definition for 'browseURL'
amUniqueProfile: no visible global function definition for 'layout'
amUniqueProfile: no visible global function definition for 'par'
amUniqueProfile: no visible global function definition for
  'plot.default'
amUniqueProfile: no visible global function definition for 'points'
amUniqueProfile: no visible global function definition for 'lines'
amUniqueProfile: no visible global function definition for 'arrows'
amUniqueProfile: no visible global function definition for 'text'
amUniqueProfile: no visible global function definition for 'legend'
Undefined global functions or variables:
  arrows as.dist browseURL hclust layout legend lines par plot.default
  points text write.csv
Consider adding
  importFrom("graphics", "arrows", "layout", "legend", "lines", "par",
             "plot.default", "points", "text")
  importFrom("stats", "as.dist", "hclust")
  importFrom("utils", "browseURL", "write.csv")
to your NAMESPACE file.
batch.possSpells.fnc: no visible binding for global variable 'words'
possSpells.fnc: no visible binding for global variable 'len.phons'
possSpells.fnc: no visible binding for global variable 'phon1'
possSpells.fnc: no visible binding for global variable 'len.total'
possSpells.fnc: no visible binding for global variable 'poss.spells'
Undefined global functions or variables:
  len.phons len.total phon1 poss.spells words
Package in Depends field not imported from: 'car'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' calls which should be '::':
  'car:::bcPower' 'car:::bootCase' 'car:::deltaMethod'
  'car:::infIndexPlot' 'car:::invResPlot' 'car:::invTranEstimate'
  'car:::invTranPlot' 'car:::marginalModelPlot' 'car:::outlierTest'
  'car:::powerTransform' 'car:::residualPlot' 'car:::residualPlots'
  'car:::testTransform'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'car:::residCurvTest' 'car:::tukeyNonaddTest'
  See the note in ?`:::` about the use of this operator.
alr4Web: no visible global function definition for 'browseURL'
print.summary.lm: no visible binding for global variable 'quantile'
print.summary.lm: no visible global function definition for 'quantile'
print.summary.lm: no visible global function definition for
  'printCoefmat'
print.summary.lm: no visible global function definition for 'naprint'
print.summary.lm: no visible global function definition for 'pf'
print.summary.lm: no visible global function definition for 'symnum'
Undefined global functions or variables:
  browseURL naprint pf printCoefmat quantile symnum
Consider adding
  importFrom("stats", "naprint", "pf", "printCoefmat", "quantile",
             "symnum")
  importFrom("utils", "browseURL")
to your NAMESPACE file.
'library' or 'require' call to 'Biobase' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
EXP.step: no visible global function definition for 'rgamma'
EXP.step: no visible global function definition for 'rnorm'
MAX.step: no visible global function definition for 'uniroot'
Norm.GMedian: no visible binding for global variable 'median'
RNASeq.Data.Gene: no visible binding for global variable 'quantile'
decom.initial: no visible global function definition for 'kmeans'
decom.initial: no visible global function definition for 'quantile'
decom.initial: no visible global function definition for 'var'
dispersion.nb.QL: no visible binding for global variable 'quantile'
est.mu.nb.mle: no visible global function definition for 'runif'
est.v.nb.QL: no visible global function definition for 'runif'
pdf2grid: no visible global function definition for 'dnorm'
pdf2grid: no visible global function definition for 'dgamma'
prior.grid: no visible global function definition for 'sd'
prior.grid: no visible global function definition for 'dnorm'
test.AMAP: no visible global function definition for 'rgamma'
test.AMAP: no visible global function definition for 'rnorm'
test.AMAP: no visible global function definition for 'quantile'
Undefined global functions or variables:
  dgamma dnorm kmeans median quantile rgamma rnorm runif sd uniroot var
Consider adding
  importFrom("stats", "dgamma", "dnorm", "kmeans", "median", "quantile",
             "rgamma", "rnorm", "runif", "sd", "uniroot", "var")
to your NAMESPACE file.
Checking should be performed on sources prepared by 'R CMD build'.
amltest: no visible global function definition for 'var'
amltest: no visible global function definition for 'optim'
amltest: no visible global function definition for 'lm'
cleanclust: no visible global function definition for 'cor'
cleanclust: no visible global function definition for 'hclust'
cleanclust: no visible global function definition for 'as.dist'
cleanclust: no visible global function definition for 'cutree'
Undefined global functions or variables:
  as.dist cor cutree hclust lm optim var
Consider adding
  importFrom("stats", "as.dist", "cor", "cutree", "hclust", "lm",
             "optim", "var")
to your NAMESPACE file.
AMOEBA : Classi: no visible global function definition for 'sd'
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
random.init.MLPneuron: no visible global function definition for
  'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Analyz.loadSteps,Analyz: no visible global function definition for
  'read.csv'
Undefined global functions or variables:
  read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/anapuce.Rcheck/00install.out' for details.
Packages in Depends field not imported from:
  'discretization' 'foreign' 'functional' 'stringr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
aode: no visible global function definition for 'Compose'
mdl: no visible global function definition for 'cutPoints'
setVar: no visible global function definition for 'Compose'
Undefined global functions or variables:
  Compose cutPoints
andrews: no visible global function definition for 'plot.new'
andrews: no visible global function definition for 'plot.window'
andrews: no visible global function definition for 'title'
andrews: no visible global function definition for 'axis'
andrews: no visible global function definition for 'box'
andrews: no visible global function definition for 'lines'
andrews: no visible global function definition for 'rainbow'
andrews: no visible global function definition for 'hsv'
selectand: no visible global function definition for 'lines'
Undefined global functions or variables:
  axis box hsv lines plot.new plot.window rainbow title
Consider adding
  importFrom("grDevices", "hsv", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "title")
to your NAMESPACE file.
plot,ANFIS: no visible binding for global variable 'X'
plotMF,ANFIS : <anonymous>: no visible global function definition for
  'lines'
plotMFs,ANFIS: no visible global function definition for 'par'
Undefined global functions or variables:
  X lines par
Consider adding
  importFrom("graphics", "lines", "par")
to your NAMESPACE file.
'library' or 'require' call to 'tcltk' which was already attached by Depends.
  Please remove these calls from your code.
annot : annotlist: no visible global function definition for
  'read.table'
annot : annotlist: no visible global function definition for
  'write.table'
annot: no visible global function definition for 'flush.console'
annot: no visible global function definition for 'read.table'
annot: no visible global function definition for 'choose.dir'
Undefined global functions or variables:
  choose.dir flush.console read.table write.table
Consider adding
  importFrom("utils", "choose.dir", "flush.console", "read.table",
             "write.table")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from 'anoint' for: 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
installed size is 35.3Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/Anthropometry.Rcheck/00install.out' for details.
Running examples in 'antiword-Ex.R' failed
The error most likely occurred in:

> ### Name: antiword
> ### Title: Antiword
> ### Aliases: antiword
> 
> ### ** Examples
> 
> text <- antiword("https://jeroen.github.io/files/UDHR-english.doc")
trying URL 'https://jeroen.github.io/files/UDHR-english.doc'
Warning in utils::download.file(file, tmp, mode = "wb") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in utils::download.file(file, tmp, mode = "wb") : 
  cannot open URL 'https://jeroen.github.io/files/UDHR-english.doc'
Calls: antiword -> <Anonymous>
Execution halted
aw_map: no visible global function definition for 'browseURL'
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
'library' or 'require' call to 'boot' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
varbin: no visible global function definition for 'boot'
Undefined global functions or variables:
  boot
'library' or 'require' call to 'boot' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'boot' 'lme4' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' call to 'tkrplot' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
TSPM: no visible global function definition for 'glm'
TSPM: no visible binding for global variable 'poisson'
TSPM: no visible global function definition for 'hatvalues'
TSPM: no visible global function definition for 'residuals'
TSPM: no visible global function definition for 'deviance'
TSPM: no visible global function definition for 'qchisq'
TSPM: no visible global function definition for 'qf'
TSPM: no visible global function definition for 'pf'
TSPM: no visible global function definition for 'pchisq'
TSPM: no visible global function definition for 'p.adjust'
norm.inttable: no visible global function definition for 'median'
norm.inttable : <anonymous>: no visible global function definition for
  'quantile'
saint_permF: no visible global function definition for 'read.table'
saint_permF: no visible global function definition for 'write.table'
saint_permF: no visible global function definition for 'write.csv2'
tspm_apms: no visible global function definition for 'read.table'
varFilter : <anonymous>: no visible global function definition for
  'median'
varFilter: no visible global function definition for 'median'
varFilter: no visible global function definition for 'quantile'
Undefined global functions or variables:
  deviance glm hatvalues median p.adjust pchisq pf poisson qchisq qf
  quantile read.table residuals write.csv2 write.table
Consider adding
  importFrom("stats", "deviance", "glm", "hatvalues", "median",
             "p.adjust", "pchisq", "pf", "poisson", "qchisq", "qf",
             "quantile", "residuals")
  importFrom("utils", "read.table", "write.csv2", "write.table")
to your NAMESPACE file.
apple: no visible global function definition for 'ginv'
apple: no visible global function definition for 'runif'
deri: no visible global function definition for 'ginv'
logit: no visible global function definition for 'qlogis'
plot.apple: no visible global function definition for 'matplot'
plot.apple: no visible global function definition for 'lines'
y.app: no visible global function definition for 'ginv'
Undefined global functions or variables:
  ginv lines matplot qlogis runif
Consider adding
  importFrom("graphics", "lines", "matplot")
  importFrom("stats", "qlogis", "runif")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'ellipse' 'lattice'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
bookTheme: no visible global function definition for 'trellis.par.set'
easyBoundaryFunc: no visible global function definition for 'runif'
getPackages: no visible global function definition for
  'install.packages'
permuteRelief: no visible binding for global variable 'sd'
quadBoundaryFunc: no visible global function definition for 'runif'
transparentTheme: no visible global function definition for 'rgb'
transparentTheme: no visible global function definition for
  'trellis.par.set'
upperp: no visible global function definition for 'ellipse'
upperp: no visible global function definition for 'panel.xyplot'
upperp: no visible global function definition for 'trellis.par.get'
Undefined global functions or variables:
  ellipse install.packages panel.xyplot rgb runif sd trellis.par.get
  trellis.par.set
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "runif", "sd")
  importFrom("utils", "install.packages")
to your NAMESPACE file.
Package in Depends field not imported from: 'emulator'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Afun: no visible global function definition for 'corr.matrix'
betahat.app.H: no visible global function definition for 'quad.form'
betahat.app.H: no visible global function definition for
  'quad.form.inv'
cdash.fun: no visible global function definition for 'quad.3form'
cdash.fun: no visible global function definition for 'quad.form'
generate.toy.observations : delta: no visible global function
  definition for 'rmvnorm'
generate.toy.observations : delta: no visible global function
  definition for 'corr.matrix'
object: no visible global function definition for 'quad.form'
opt.1: no visible global function definition for 'optim'
opt.gt.1: no visible global function definition for 'optim'
subsets.fun : select: no visible global function definition for
  'rbinom'
Undefined global functions or variables:
  corr.matrix optim quad.3form quad.form quad.form.inv rbinom rmvnorm
Consider adding
  importFrom("stats", "optim", "rbinom")
to your NAMESPACE file.
runAPSIM: warning in scan(reports_file[i], "", sep = "", skip =
  length(temp), nline = 1): partial argument match of 'nline' to
  'nlines'
runAPSIM: no visible global function definition for 'write.table'
runAPSIM: no visible global function definition for 'read.table'
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
kristen.colors: no visible global function definition for
  'colorRampPalette'
kristen.colors: no visible global function definition for 'grey'
plot3d.points: no visible global function definition for 'heat.colors'
plot3d.points: no visible global function definition for 'plot'
ragged.image: no visible global function definition for 'heat.colors'
ragged.image: no visible global function definition for 'image'
scatterplot.density: no visible global function definition for 'grey'
scatterplot.density: no visible global function definition for 'image'
scatterplot.density: no visible global function definition for 'abline'
scatterplot.density: no visible global function definition for 'lm'
scatterplot.density: no visible global function definition for 'legend'
vertical.image.legend: no visible global function definition for 'par'
vertical.image.legend: no visible global function definition for
  'image'
vertical.image.legend: no visible global function definition for 'axis'
vertical.image.legend: no visible global function definition for 'box'
Undefined global functions or variables:
  abline axis box colorRampPalette grey heat.colors image legend lm par
  plot
Consider adding
  importFrom("grDevices", "colorRampPalette", "grey", "heat.colors")
  importFrom("graphics", "abline", "axis", "box", "image", "legend",
             "par", "plot")
  importFrom("stats", "lm")
to your NAMESPACE file.
Running examples in 'aqp-Ex.R' failed
The error most likely occurred in:

> ### Name: addBracket
> ### Title: Add Depth Brackets
> ### Aliases: addBracket addDiagnosticBracket
> 
> ### ** Examples
> 
> # sample data
> data(sp1)
> 
> # add color vector
> sp1$soil_color <- with(sp1, munsell2rgb(hue, value, chroma))
> 
> # promote to SoilProfileCollection
> depths(sp1) <- id ~ top + bottom
> 
> # plot profiles
> plot(sp1)
guessing horizon designations are stored in `name`
> 
> # extract top/bottom depths associated with all A horizons
> f <- function(i) {
+   h <- horizons(i)
+   idx <- grep('^A', h$name)
+   c(min(h$top[idx]), max(h$bottom[idx], na.rm=TRUE))
+ }
> 
> # apply function to sp1, result is a list
> a <- profileApply(sp1, f, simplify=FALSE)
> # convert list into matrix
> a <- do.call('rbind', a)
> 
> # plot
> plot(sp1)
guessing horizon designations are stored in `name`
> # annotate with brackets
> # note that plotting order is derived from the call to `plot(sp1)`
> addBracket(a[, 1], a[, 2], col='red')
> 
> # more interesting example using diagnostic horizons
> if(require(soilDB)) {
+   # load some sample data with diagnostic horizons
+   data(loafercreek)
+   
+   # extract first 15 profiles
+   x <- loafercreek[1:15, ]
+   s <- site(x)
+ 
+   # plot
+   par(mar=c(0,0,0,0))
+   plot(x, name='hzname', id.style='top')
+   
+   # add brackets describing the argillic horizon
+   addDiagnosticBracket(x, 'argillic horizon', col='red')
+   # add brackets describing paralithic contact
+   addDiagnosticBracket(x, 'paralithic contact', col='blue')
+ }
Loading required package: soilDB
Error in segments(x.1, top[plot.order], x.2, top[plot.order], lend = 2,  : 
  cannot mix zero-length and non-zero-length coordinates
Calls: addDiagnosticBracket -> addBracket -> segments
Execution halted
aqDayOfWeekStat: no visible global function definition for 'index'
aqDropHour: no visible global function definition for 'index'
aqFilterOHLCSD: no visible binding for global variable 'sd'
aqHourIndex: no visible global function definition for 'index'
aqHourlyStat: no visible global function definition for 'index'
aqLoadOHLC: no visible global function definition for 'read.csv'
aqLoadSeriesField: no visible global function definition for 'read.csv'
aqLoadXtsFromCsv: no visible global function definition for 'read.csv2'
aqLoadYahooEOD: no visible global function definition for 'read.csv'
aqSaveXtsToCsv: no visible global function definition for 'write.csv2'
aqStoreSeriesField: no visible global function definition for 'index'
aqStoreSeriesField: no visible global function definition for
  'capture.output'
aqStoreSeriesField: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  capture.output index read.csv read.csv2 sd write.csv2 write.table
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "capture.output", "read.csv", "read.csv2",
             "write.csv2", "write.table")
to your NAMESPACE file.
AR1seg_func: no visible global function definition for 'median'
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'MASS' 'TSP'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
ardec: no visible global function definition for 'filter'
ardec.lm: no visible global function definition for 'ar'
ardec.lm: no visible global function definition for 'lm'
Undefined global functions or variables:
  ar filter lm
Consider adding
  importFrom("stats", "ar", "filter", "lm")
to your NAMESPACE file.
arfimaOLS: no visible global function definition for 'lm'
arfimaPrep: no visible global function definition for 'aggregate'
arfimaPrep: no visible global function definition for 'arima'
arfimaPrep: no visible global function definition for 'lm'
arfimaPrep: no visible global function definition for 'residuals'
Undefined global functions or variables:
  aggregate arima lm residuals
Consider adding
  importFrom("stats", "aggregate", "arima", "lm", "residuals")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/aroma.affymetrix.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R             2.3Mb
    help          1.1Mb
    testScripts   1.1Mb
Packages suggested but not available for checking:
  'sfit' 'expectile' 'HaarSeg' 'mpcbs'
binarize.array: no visible binding for global variable 'sd'
mskmeans: no visible global function definition for 'kmeans'
Undefined global functions or variables:
  kmeans sd
Consider adding
  importFrom("stats", "kmeans", "sd")
to your NAMESPACE file.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.5Mb
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/ARTP.Rcheck/00install.out' for details.
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    bin   12.0Mb
    misc   2.1Mb
Package suggested but not available for checking: 'cacheSweave'
Warning: no function found corresponding to methods exports from 'ascii' for: 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
'library' or 'require' calls in package code:
  'cacheSweave' 'weaver'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'utils:::RtangleSetup'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'survival:::survmean' 'utils:::.SweaveValidFilenameRegexp'
  'utils:::RtangleFinish' 'utils:::RtangleRuncode'
  'utils:::SweaveParseOptions'
  See the note in ?`:::` about the use of this operator.
Unavailable namespace imported from by a ':::' call: 'cacheSweave'
  See the note in ?`:::` about the use of this operator.
S3 methods shown with full name in documentation object 'cbind.ascii':
  'cbind.ascii'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Packages suggested but not available for checking: 'REBayes' 'Rmosek'
'library' or 'require' calls to packages already attached by Depends:
  'Hmisc' 'splancs'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'Hmisc' 'shapefiles' 'splancs'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ASP.Score: no visible global function definition for 'pnorm'
Graphs.Bayesian: no visible global function definition for 'dev.new'
colorhex: no visible global function definition for 'gray'
colorhex: no visible global function definition for 'rgb'
Undefined global functions or variables:
  dev.new gray pnorm rgb
Consider adding
  importFrom("grDevices", "dev.new", "gray", "rgb")
  importFrom("stats", "pnorm")
to your NAMESPACE file.
Package which this enhances but not available for checking: 'asreml'
':::' call which should be '::': 'assertive.base:::print_and_capture'
  See the note in ?`:::` about the use of this operator.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/assignPOP.Rcheck/00install.out' for details.
Running examples in 'assist-Ex.R' failed
The error most likely occurred in:

> ### Name: anova.ssr
> ### Title: Testing a Non-parametric Function Fitted via Smoothing Splines
> ### Aliases: anova.ssr
> ### Keywords: file
> 
> ### ** Examples
> 
> data(acid)
> 
> # fit a partial thin-plate spline
> temp <- ssr(ph~t1+x1+x2, rk=tp(t1), data=acid, spar="m")
At line 1992 of file rkpk1.f
Fortran runtime error: Index '2' of dimension 1 of array 'jpvt' above upper bound of 1
Package in Depends field not imported from: 'mvtnorm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CALPHA: no visible global function definition for 'dbinom'
CALPHA: no visible global function definition for 'pchisq'
CAST: no visible global function definition for 'fisher.test'
CAST: no visible global function definition for 'chisq.test'
CMC: no visible global function definition for 'pf'
MULTI: no visible global function definition for 'complete.cases'
RVT1: no visible global function definition for 'pchisq'
RVT2: no visible global function definition for 'pchisq'
RWAS: no visible global function definition for 'pnorm'
SKAT: no visible global function definition for 'dbeta'
SKAT: no visible global function definition for 'pchisq'
TTEST: no visible global function definition for 'complete.cases'
TTEST: no visible global function definition for 'pf'
WST: no visible global function definition for 'mvfft'
WST: no visible global function definition for 'pnorm'
my_cmc_method: no visible global function definition for
  'complete.cases'
my_getUV: no visible global function definition for 'complete.cases'
my_orwss_method: no visible global function definition for 'sd'
my_rarecov_method: no visible global function definition for
  'chisq.test'
my_rbt_method: no visible global function definition for 'ppois'
my_score_method: no visible global function definition for 'pchisq'
my_ssu_method: no visible global function definition for 'pchisq'
my_ssuw_method: no visible global function definition for 'pchisq'
my_sum_method: no visible global function definition for 'pchisq'
my_uminp_method: no visible global function definition for 'pchisq'
my_uminp_method: no visible global function definition for 'pmvnorm'
Undefined global functions or variables:
  chisq.test complete.cases dbeta dbinom fisher.test mvfft pchisq pf
  pmvnorm pnorm ppois sd
Consider adding
  importFrom("stats", "chisq.test", "complete.cases", "dbeta", "dbinom",
             "fisher.test", "mvfft", "pchisq", "pf", "pnorm", "ppois",
             "sd")
to your NAMESPACE file.
beamDiskOverlap: no visible global function definition for 'integrate'
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
fm_unred: no visible global function definition for 'spline'
galage: no visible global function definition for 'integrate'
lumdist: no visible global function definition for 'integrate'
Undefined global functions or variables:
  integrate spline
Consider adding
  importFrom("stats", "integrate", "spline")
to your NAMESPACE file.
VPC.graph : findQuantile: no visible global function definition for
  'quantile'
VPC.graph : findQuantileCI : <anonymous>: no visible global function
  definition for 'quantile'
asVPC.binW: no visible global function definition for 'median'
asVPC.binW : <anonymous>: no visible global function definition for
  'quantile'
asVPC.binW: no visible global function definition for 'quantile'
asVPC.distanceW: no visible global function definition for 'median'
asVPC.distanceW : <anonymous>: no visible global function definition
  for 'quantile'
asVPC.distanceW: no visible global function definition for 'quantile'
makeCOVbin: no visible global function definition for 'quantile'
makeCOVbin: no visible global function definition for 'median'
read_Simdata: no visible global function definition for 'read.table'
Undefined global functions or variables:
  median quantile read.table
Consider adding
  importFrom("stats", "median", "quantile")
  importFrom("utils", "read.table")
to your NAMESPACE file.
asymp.test.default: no visible global function definition for 'var'
asymp.test.default: no visible global function definition for 'pnorm'
asymp.test.default: no visible global function definition for 'qnorm'
asymp.test.formula: no visible global function definition for 'terms'
seDMean.default: no visible global function definition for 'var'
seDMeanG.default: no visible global function definition for 'var'
seDVar.default: no visible global function definition for 'var'
seMean.default: no visible global function definition for 'var'
seRMean.default: no visible global function definition for 'var'
seRVar.default: no visible global function definition for 'var'
seVar.default: no visible global function definition for 'var'
Undefined global functions or variables:
  pnorm qnorm terms var
Consider adding
  importFrom("stats", "pnorm", "qnorm", "terms", "var")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'cairoDevice' 'gWidgetsRGtk2' 'partitions' 'proto'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
get.est.ATT: no visible global function definition for 'tail'
get.est.MT: no visible global function definition for 'tail'
get.est.simple: no visible global function definition for 'tail'
newton.r: no visible global function definition for 'tail'
plot.ATE: no visible global function definition for 'par'
plot.ATE: no visible global function definition for 'plot'
plot.ATE: no visible global function definition for 'axis'
plot.ATE: no visible global function definition for 'abline'
plot.ATE: no visible global function definition for 'lines'
plot.ATE: no visible global function definition for 'legend'
plot.ATE: no visible global function definition for 'points'
print.summary.ATE: no visible global function definition for
  'printCoefmat'
summary.ATE: no visible global function definition for 'qnorm'
summary.ATE: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  abline axis legend lines par plot pnorm points printCoefmat qnorm
  tail
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "plot", "points")
  importFrom("stats", "pnorm", "printCoefmat", "qnorm")
  importFrom("utils", "tail")
to your NAMESPACE file.
atmcmc : rmvtnorm: no visible global function definition for 'rnorm'
atmcmc: no visible global function definition for 'rnorm'
atmcmc: no visible global function definition for 'runif'
atmcmc: no visible global function definition for 'par'
atmcmc: no visible global function definition for 'lm'
atmcmc: no visible global function definition for 'lines'
atmcmc: no visible global function definition for 'var'
atmcmc: no visible global function definition for 'cov'
atmcmc: no visible global function definition for 'quantile'
atmcmc: no visible global function definition for 'sd'
plotmcmc: no visible global function definition for 'pdf'
plotmcmc: no visible global function definition for 'par'
plotmcmc: no visible global function definition for 'dev.new'
plotmcmc: no visible global function definition for 'png'
plotmcmc: no visible global function definition for 'hist'
plotmcmc: no visible global function definition for 'dev.off'
plotmcmc: no visible global function definition for 'plot'
plotmcmc: no visible global function definition for 'lines'
Undefined global functions or variables:
  cov dev.new dev.off hist lines lm par pdf plot png quantile rnorm
  runif sd var
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf", "png")
  importFrom("graphics", "hist", "lines", "par", "plot")
  importFrom("stats", "cov", "lm", "quantile", "rnorm", "runif", "sd",
             "var")
to your NAMESPACE file.
LHSdesign: no visible global function definition for 'qnorm'
LHSdesign: no visible global function definition for 'qunif'
LHSdesign: no visible global function definition for 'qt'
MCdesign: no visible global function definition for 'rnorm'
MCdesign: no visible global function definition for 'runif'
MCdesign: no visible global function definition for 'rt'
Undefined global functions or variables:
  qnorm qt qunif rnorm rt runif
Consider adding
  importFrom("stats", "qnorm", "qt", "qunif", "rnorm", "rt", "runif")
to your NAMESPACE file.
PlotAtm.lin : scale_image: no visible global function definition for
  'heat.colors'
PlotAtm.lin : scale_image: no visible global function definition for
  'par'
PlotAtm.lin : scale_image: no visible global function definition for
  'sd'
PlotAtm.lin : scale_image: no visible global function definition for
  'approx'
PlotAtm.lin : scale_image: no visible global function definition for
  'image'
PlotAtm.lin : scale_image: no visible global function definition for
  'axis'
PlotAtm.lin : scale_image: no visible global function definition for
  'mtext'
PlotAtm.lin: no visible global function definition for 'arrows'
PlotAtm.lin: no visible global function definition for 'text'
PlotAtm.lin: no visible global function definition for 'polygon'
sky.colors: no visible global function definition for 'rgb'
Undefined global functions or variables:
  approx arrows axis heat.colors image mtext par polygon rgb sd text
Consider adding
  importFrom("grDevices", "heat.colors", "rgb")
  importFrom("graphics", "arrows", "axis", "image", "mtext", "par",
             "polygon", "text")
  importFrom("stats", "approx", "sd")
to your NAMESPACE file.
attribrisk: no visible global function definition for 'terms'
attribrisk: no visible global function definition for '.getXlevels'
attribrisk: no visible global function definition for 'model.response'
attribrisk: no visible global function definition for 'model.weights'
attribrisk: no visible global function definition for 'model.offset'
attribrisk: no visible global function definition for 'model.matrix'
attribrisk: no visible global function definition for 'model.frame'
attribrisk.fit: no visible global function definition for 'glm.fit'
attribrisk.fit: no visible global function definition for 'binomial'
attribrisk.fit: no visible global function definition for 'glm.control'
attribrisk.fit: no visible global function definition for 'coef'
attribrisk.fit: no visible global function definition for
  'coefficients'
attribrisk_boot: no visible global function definition for 'var'
print.attribrisk: no visible global function definition for 'qnorm'
summary.attribrisk: no visible global function definition for 'hasArg'
summary.attribrisk: no visible global function definition for 'var'
Undefined global functions or variables:
  .getXlevels binomial coef coefficients glm.control glm.fit hasArg
  model.frame model.matrix model.offset model.response model.weights
  qnorm terms var
Consider adding
  importFrom("methods", "hasArg")
  importFrom("stats", ".getXlevels", "binomial", "coef", "coefficients",
             "glm.control", "glm.fit", "model.frame", "model.matrix",
             "model.offset", "model.response", "model.weights", "qnorm",
             "terms", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
plot.AUC: no visible global function definition for 'plot'
plot.AUC: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines plot
Consider adding
  importFrom("graphics", "lines", "plot")
to your NAMESPACE file.
AUCRFcv: no visible global function definition for 'predict'
plot.AUCRF: no visible global function definition for 'par'
plot.AUCRF: no visible global function definition for 'dotchart'
plot.AUCRF: no visible global function definition for 'title'
plot.AUCRF: no visible global function definition for 'text'
Undefined global functions or variables:
  dotchart par predict text title
Consider adding
  importFrom("graphics", "dotchart", "par", "text", "title")
  importFrom("stats", "predict")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'RJSONIO' 'hexbin' 'plotrix'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
audioHist: no visible global function definition for 'hist'
audioHist: no visible global function definition for 'rescale'
audioHist: no visible global function definition for 'toJSON'
audioScatter: no visible binding for global variable 'formula'
audioScatter: no visible global function definition for 'hexbinplot'
audioScatter: no visible global function definition for 'cor'
audioScatter: no visible global function definition for 'toJSON'
audioSplom: no visible global function definition for 'hexplom'
audioSplom: no visible binding for global variable 'BTY'
audioSplom: no visible binding for global variable 'panel.hexboxplot'
audioSplom: no visible global function definition for 'combn'
audioSplom : <anonymous>: no visible global function definition for
  'cor'
audioSplom : <anonymous>: no visible global function definition for
  'toJSON'
audiolyzRcheck: no visible global function definition for
  'download.file'
audiolyzRcheck: no visible global function definition for 'unzip'
matricize: no visible global function definition for 'hexbin'
panel.audiolyzR: no visible global function definition for
  'panel.hexbinplot'
Undefined global functions or variables:
  BTY combn cor download.file formula hexbin hexbinplot hexplom hist
  panel.hexbinplot panel.hexboxplot rescale toJSON unzip
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "cor", "formula")
  importFrom("utils", "combn", "download.file", "unzip")
to your NAMESPACE file.
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.5/audio.Rcheck/00install.out' for details.
simulateD: no visible global function definition for 'rgamma'
simulateT: no visible global function definition for 'runif'
simulateT: no visible global function definition for 'rbeta'
simulateT: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  rbeta rbinom rgamma runif
Consider adding
  importFrom("stats", "rbeta", "rbinom", "rgamma", "runif")
to your NAMESPACE file.
Missing or unexported object: 'countrycode::countrycode_data'
Running examples in 'auk-Ex.R' failed
The error most likely occurred in:

> ### Name: auk_country
> ### Title: Filter the eBird data by country
> ### Aliases: auk_country
> 
> ### ** Examples
> 
> # country names and ISO2 codes can be mixed
> # not case sensitive
> country <- c("CA", "United States", "mexico")
> system.file("extdata/ebd-sample.txt", package = "auk") %>%
+   auk_ebd() %>%
+   auk_country(country)
Error: 'countrycode_data' is not an exported object from 'namespace:countrycode'
Execution halted
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  9: auk_country(., country)
  10: auk_country.auk_ebd(., country)
  11: tolower(countrycode::countrycode_data$iso2c)
  12: countrycode::countrycode_data
  13: getExportedValue(pkg, name)
  14: stop(gettextf("'%s' is not an exported object from 'namespace:%s'", name, getNamespaceName(ns)), 
         call. = FALSE, domain = NA)
  
  == testthat results  ===========================================================
  OK: 197 SKIPPED: 13 FAILED: 2
  1. Error: auk_ebd prints method (@test_auk-ebd.r#66) 
  2. Error: auk_country (@test_filters.r#36) 
  
  Error: testthat unit tests failed
  Execution halted
Package which this enhances but not available for checking: 'rPython'
'library' or 'require' calls in package code:
  'ggplot2' 'gpclib' 'maptools'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
gLog.ep: no visible global function definition for 'quantile'
gedestp: no visible global function definition for 'na.omit'
gedestp: no visible global function definition for 'optim'
gets.mean: no visible global function definition for 'start'
gets.mean: no visible global function definition for 'end'
gets.mean: no visible global function definition for 'window'
gets.mean: no visible global function definition for 'pt'
gets.mean: no visible global function definition for 'Box.test'
gets.mean: no visible global function definition for 'pchisq'
gets.vol: no visible global function definition for 'start'
gets.vol: no visible global function definition for 'end'
gets.vol: no visible global function definition for 'window'
gets.vol: no visible global function definition for 'pt'
gets.vol: no visible global function definition for 'Box.test'
gets.vol: no visible global function definition for 'pchisq'
jb.test: no visible global function definition for 'pchisq'
skewness.test: no visible global function definition for 'pchisq'
sm: no visible global function definition for 'start'
sm: no visible global function definition for 'end'
sm: no visible global function definition for 'window'
sm: no visible global function definition for 'pt'
sm: no visible global function definition for 'pchisq'
sm: no visible global function definition for 'Box.test'
Undefined global functions or variables:
  Box.test end na.omit optim pchisq pt quantile start window
Consider adding
  importFrom("stats", "Box.test", "end", "na.omit", "optim", "pchisq",
             "pt", "quantile", "start", "window")
to your NAMESPACE file.
installed size is 67.3Mb
  sub-directories of 1Mb or more:
    java  67.2Mb
best: no visible global function definition for 'optim'
randomboards: no visible global function definition for 'runif'
randomprobs: no visible global function definition for 'runif'
Undefined global functions or variables:
  optim runif
Consider adding
  importFrom("stats", "optim", "runif")
to your NAMESPACE file.
File 'aylmer/libs/i386/aylmer.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'aylmer.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'aylmer.o'
File 'aylmer/libs/x64/aylmer.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'aylmer.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'aylmer.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
CRexp_set: no visible global function definition for 'runif'
b6e6rl: no visible global function definition for 'runif'
derand_RL: no visible global function definition for 'runif'
derandexp_RL: no visible global function definition for 'runif'
nahvyb_expt: no visible global function definition for 'runif'
roulete: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
.generateTransform: no visible global function definition for 'sd'
.generateUnitHyperCube: no visible global function definition for
  'runif'
.makeBoundedSingleStep: no visible global function definition for
  'runif'
.makeBoundedStep: no visible global function definition for 'runif'
.makeStep: no visible global function definition for 'runif'
.staircaseSampling: no visible global function definition for 'runif'
GaussianPrior: no visible global function definition for 'qnorm'
LogNormalPrior: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  qnorm runif sd
Consider adding
  importFrom("stats", "qnorm", "runif", "sd")
to your NAMESPACE file.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   8.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/BACA.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'sybilSBML'
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.8Mb
BACprior.CV: no visible global function definition for 'na.fail'
BACprior.CV: no visible global function definition for 'plot'
BACprior.CV: no visible global function definition for 'abline'
BACprior.boot: no visible global function definition for 'na.fail'
BACprior.boot: no visible global function definition for 'plot'
BACprior.boot: no visible global function definition for 'abline'
BACprior.lm: no visible global function definition for 'na.fail'
BACprior.lm: no visible global function definition for 'coef'
BACprior.lm: no visible global function definition for 'vcov'
Undefined global functions or variables:
  abline coef na.fail plot vcov
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("stats", "coef", "na.fail", "vcov")
to your NAMESPACE file.
'library' or 'require' call to 'mvtnorm' which was already attached by Depends.
  Please remove these calls from your code.
bagging: no visible global function definition for 'predict'
samme: no visible global function definition for 'predict'
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
Package suggested but not available for checking: 'mzR'
best_binomial_bandit : f: no visible global function definition for
  'dbeta'
best_binomial_bandit : f: no visible global function definition for
  'pbeta'
best_binomial_bandit: no visible global function definition for
  'integrate'
best_poisson_bandit : f: no visible global function definition for
  'dgamma'
best_poisson_bandit : f: no visible global function definition for
  'pgamma'
best_poisson_bandit: no visible global function definition for
  'integrate'
deseasonalized_trend: no visible global function definition for
  'predict'
distribution_estimate: no visible global function definition for
  'quantile'
distribution_estimate: no visible global function definition for
  'qbeta'
significance_analysis: no visible global function definition for
  'prop.test'
sim_post: no visible global function definition for 'rbeta'
summarize_metrics: no visible global function definition for 'median'
summarize_metrics: no visible global function definition for
  'prop.test'
Undefined global functions or variables:
  dbeta dgamma integrate median pbeta pgamma predict prop.test qbeta
  quantile rbeta
Consider adding
  importFrom("stats", "dbeta", "dgamma", "integrate", "median", "pbeta",
             "pgamma", "predict", "prop.test", "qbeta", "quantile",
             "rbeta")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/BANFF.Rcheck/00install.out' for details.
installed size is 33.7Mb
  sub-directories of 1Mb or more:
    libs  33.0Mb
extractAffybatch: 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').
'library' or 'require' calls to packages already attached by Depends:
  'grid' 'lattice'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'grid' 'lattice'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
barcode: no visible global function definition for 'unit'
barcode: no visible global function definition for 'grid.newpage'
barcode: no visible global function definition for 'grid.text'
barcode: no visible global function definition for 'gpar'
barcode: no visible global function definition for 'pushViewport'
barcode: no visible global function definition for 'viewport'
barcode: no visible global function definition for 'convertHeight'
barcode: no visible global function definition for 'convertWidth'
barcode: no visible global function definition for 'grid.rect'
barcode: no visible global function definition for 'popViewport'
barcode.panel: no visible global function definition for 'unit'
barcode.panel: no visible global function definition for 'hist'
barcode.panel: no visible global function definition for 'pushViewport'
barcode.panel: no visible global function definition for 'viewport'
barcode.panel: no visible global function definition for 'grid.xaxis'
barcode.panel: no visible global function definition for 'gpar'
barcode.panel: no visible global function definition for 'grid.text'
barcode.panel: no visible global function definition for 'popViewport'
barcode.panel: no visible global function definition for
  'grid.segments'
barcode.panel: no visible global function definition for 'grid.points'
Undefined global functions or variables:
  convertHeight convertWidth gpar grid.newpage grid.points grid.rect
  grid.segments grid.text grid.xaxis hist popViewport pushViewport unit
  viewport
Consider adding
  importFrom("graphics", "hist")
to your NAMESPACE file.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.8Mb
    libs   1.9Mb
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == testthat results  ===========================================================
  OK: 104 SKIPPED: 0 FAILED: 70
  1. Failure: encode and decode on random strings (@test_base32.R#10) 
  2. Failure: encode and decode on random strings (@test_base32.R#10) 
  3. Failure: encode and decode on random strings (@test_base32.R#10) 
  4. Failure: encode and decode on random strings (@test_base32.R#10) 
  5. Failure: encode and decode on random strings (@test_base32.R#10) 
  6. Failure: encode and decode on random strings (@test_base32.R#10) 
  7. Failure: encode and decode on random strings (@test_base32.R#10) 
  8. Failure: encode and decode on random strings (@test_base32.R#10) 
  9. Failure: encode and decode on random strings (@test_base32.R#10) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == testthat results  ===========================================================
  OK: 104 SKIPPED: 0 FAILED: 70
  1. Failure: encode and decode on random strings (@test_base32.R#10) 
  2. Failure: encode and decode on random strings (@test_base32.R#10) 
  3. Failure: encode and decode on random strings (@test_base32.R#10) 
  4. Failure: encode and decode on random strings (@test_base32.R#10) 
  5. Failure: encode and decode on random strings (@test_base32.R#10) 
  6. Failure: encode and decode on random strings (@test_base32.R#10) 
  7. Failure: encode and decode on random strings (@test_base32.R#10) 
  8. Failure: encode and decode on random strings (@test_base32.R#10) 
  9. Failure: encode and decode on random strings (@test_base32.R#10) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(baseballDBR)
  > 
  > test_check("baseballDBR")
  -- 1. Failure: (unknown) (@test-check_urls.R#25)  ------------------------------
  urlExists("http://www.fangraphs.com/guts.aspx?type=cn") isn't true.
  
  == testthat results  ===========================================================
  OK: 2 SKIPPED: 0 FAILED: 1
  1. Failure: (unknown) (@test-check_urls.R#25) 
  
  Error: testthat unit tests failed
  Execution halted
Packages which this enhances but not available for checking:
  'doMC' 'rPython'
'library' or 'require' call to 'hwriter' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to 'parallel' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
':::' call which should be '::': 'parallel:::detectCores'
  See the note in ?`:::` about the use of this operator.
asyncRunCommands: no visible global function definition for 'runif'
mergeCsv: no visible global function definition for 'read.csv'
mergeCsv: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  read.csv runif write.csv
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
Running examples in 'batchtools-Ex.R' failed
The error most likely occurred in:

> ### Name: addExperiments
> ### Title: Add Experiments to the Registry
> ### Aliases: addExperiments
> 
> ### ** Examples
> 
> tmp = makeExperimentRegistry(file.dir = NA, make.default = FALSE)
No configuration file found
Created registry in 'D:/temp/Rtmp40KyDe/registry10b03373687c' using cluster functions 'Interactive'
> 
> # add first problem
> fun = function(job, data, n, mean, sd, ...) rnorm(n, mean = mean, sd = sd)
> addProblem("rnorm", fun = fun, reg = tmp)
Adding problem 'rnorm'
> 
> # add second problem
> fun = function(job, data, n, lambda, ...) rexp(n, rate = lambda)
> addProblem("rexp", fun = fun, reg = tmp)
Adding problem 'rexp'
> 
> # add first algorithm
> fun = function(instance, method, ...) if (method == "mean") mean(instance) else median(instance)
> addAlgorithm("average", fun = fun, reg = tmp)
Adding algorithm 'average'
> 
> # add second algorithm
> fun = function(instance, ...) sd(instance)
> addAlgorithm("deviation", fun = fun, reg = tmp)
Adding algorithm 'deviation'
> 
> # define problem and algorithm designs
> prob.designs = algo.designs = list()
> prob.designs$rnorm = CJ(n = 100, mean = -1:1, sd = 1:5)
> prob.designs$rexp = data.table(n = 100, lambda = 1:5)
> algo.designs$average = data.table(method = c("mean", "median"))
> algo.designs$deviation = data.table()
> 
> # add experiments and submit
> addExperiments(prob.designs, algo.designs, reg = tmp)
Adding 30 experiments ('rnorm'[15] x 'average'[2] x repls[1]) ...
Error in length(ans$indices) : type must be LANGSXP at this point
Calls: addExperiments ... merge -> merge.data.table -> [ -> [.data.table -> length
Execution halted
Running 'testthat.R' [23s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  -- 37. Error: hooks (@test_hooks.R#12)  ----------------------------------------
  type must be LANGSXP at this point
  1: makeJobCollection(1, reg = reg) at testthat/test_hooks.R:12
  2: makeJobCollection.Registry(1, reg = reg)
  3: createCollection(mergedJobs(reg, convertIds(reg, ids), c("job.id", "job.name", "job.pars")), 
         resources, reg)
  4: setkeyv(jobs, "job.id")
  5: is.data.table(x)
  6: mergedJobs(reg, convertIds(reg, ids), c("job.id", "job.name", "job.pars"))
  7: reg$defs[reg$status[ids, nomatch = 0L, on = "job.id"], cols, on = "def.id", nomatch = 0L, 
         with = missing(cols)]
  8: `[.data.table`(reg$defs, reg$status[ids, nomatch = 0L, on = "job.id"], cols, on = "def.id", 
         nomatch = 0L, with = missing(cols))
  9: length(ans$indices)
Package suggested but not available for checking: 'doMC'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/BayClone2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/bayesCL.Rcheck/00install.out' for details.
FECRT: no visible global function definition for 'pdf'
FECRT: no visible global function definition for 'hist'
FECRT: no visible global function definition for 'abline'
FECRT: no visible global function definition for 'dev.off'
FECRT.analysis: no visible global function definition for 'pdf'
FECRT.analysis: no visible global function definition for 'hist'
FECRT.analysis: no visible global function definition for 'abline'
FECRT.analysis: no visible global function definition for 'dev.off'
fecrt: no visible global function definition for 'pdf'
fecrt: no visible global function definition for 'hist'
fecrt: no visible global function definition for 'abline'
fecrt: no visible global function definition for 'dev.off'
fecrt.analysis: no visible global function definition for 'pdf'
fecrt.analysis: no visible global function definition for 'hist'
fecrt.analysis: no visible global function definition for 'abline'
fecrt.analysis: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  abline dev.off hist pdf
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "hist")
to your NAMESPACE file.
BMAnimalTrack: no visible global function definition for 'nlm'
BMAnimalTrack: no visible global function definition for 'qnorm'
dataSim: no visible global function definition for 'rnorm'
rBBridge: no visible global function definition for 'rnorm'
rBMotion: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  nlm qnorm rnorm
Consider adding
  importFrom("stats", "nlm", "qnorm", "rnorm")
to your NAMESPACE file.
BayesianbetaregEst: no visible global function definition for 'runif'
BayesianbetaregEst: no visible global function definition for 'as.ts'
BayesianbetaregEst: no visible global function definition for 'dev.new'
BayesianbetaregEst: no visible global function definition for 'ts.plot'
BayesianbetaregEst: no visible binding for global variable 'sd'
BayesianbetaregEst: no visible global function definition for
  'quantile'
betaresiduals : lt: no visible global function definition for 'dbeta'
diagnostics: no visible global function definition for 'plot'
diagnostics: no visible global function definition for 'abline'
diagnostics: no visible global function definition for 'qqnorm'
diagnostics: no visible global function definition for 'qqline'
dpostb: no visible global function definition for 'dbeta'
dpostg: no visible global function definition for 'dbeta'
plotresiduals: no visible global function definition for 'plot'
print.summary.Bayesianbetareg: no visible global function definition
  for 'printCoefmat'
summary.Bayesianbetareg: no visible global function definition for
  'coef'
Undefined global functions or variables:
  abline as.ts coef dbeta dev.new plot printCoefmat qqline qqnorm
  quantile runif sd ts.plot
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "plot")
  importFrom("stats", "as.ts", "coef", "dbeta", "printCoefmat", "qqline",
             "qqnorm", "quantile", "runif", "sd", "ts.plot")
to your NAMESPACE file.
NeedsCompilation field should likely be 'yes'
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   4.1Mb
noninform_prior : a : f1: no visible global function definition for
  'pbeta'
noninform_prior : a : f1: no visible global function definition for
  'dbeta'
noninform_prior : a: no visible global function definition for
  'integrate'
noninform_prior: no visible global function definition for 'rbeta'
noninform_prior: no visible global function definition for 'optim'
postNullFun : b : f1: no visible global function definition for 'pbeta'
postNullFun : b : f1: no visible global function definition for 'dbeta'
postNullFun : b: no visible global function definition for 'integrate'
prior_prob : a : f1: no visible global function definition for 'pbeta'
prior_prob : a : f1: no visible global function definition for 'dbeta'
prior_prob : a: no visible global function definition for 'integrate'
Undefined global functions or variables:
  dbeta integrate optim pbeta rbeta
Consider adding
  importFrom("stats", "dbeta", "integrate", "optim", "pbeta", "rbeta")
to your NAMESPACE file.
MHratioPopPref: no visible global function definition for 'runif'
MratioPopMult: no visible global function definition for 'dunif'
MratioPopMult: no visible global function definition for 'runif'
bayesPref: no visible global function definition for 'runif'
calcP: no visible global function definition for 'dunif'
calcP: no visible global function definition for 'dmultinom'
calcdic: no visible global function definition for 'median'
calcdic: no visible binding for global variable 'median'
calcdic: no visible global function definition for 'dmultinom'
calcdicExtern: no visible global function definition for 'median'
calcdicExtern: no visible global function definition for 'dmultinom'
calcdicExtern: no visible binding for global variable 'median'
credibleIntervals: no visible global function definition for 'quantile'
prefPlot: no visible global function definition for 'postscript'
prefPlot: no visible global function definition for 'plot'
prefPlot: no visible global function definition for 'lines'
prefPlot: no visible global function definition for 'density'
prefPlot: no visible global function definition for 'median'
prefPlot: no visible global function definition for 'legend'
prefPlot: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  density dev.off dmultinom dunif legend lines median plot postscript
  quantile runif
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "density", "dmultinom", "dunif", "median",
             "quantile", "runif")
to your NAMESPACE file.
BayesFH: no visible global function definition for 'rnorm'
BayesFH: no visible global function definition for 'rgamma'
BayesSAE: no visible global function definition for 'runif'
BayesSAE: no visible global function definition for 'as.formula'
BayesSAE: no visible global function definition for 'terms'
BayesSAE: no visible global function definition for 'delete.response'
BayesSAE: no visible global function definition for 'model.response'
BayesSAE: no visible global function definition for 'model.matrix'
BayesSAE: no visible global function definition for 'coef'
BayesSAE: no visible global function definition for 'lm'
BayesSFH: no visible global function definition for 'rnorm'
BayesSFH: no visible global function definition for 'runif'
BayesSFH: no visible global function definition for 'rgamma'
BayesSYC: no visible global function definition for 'rnorm'
BayesSYC: no visible global function definition for 'runif'
BayesSYC: no visible global function definition for 'rgamma'
BayesUFH: no visible global function definition for 'rnorm'
BayesUFH: no visible global function definition for 'rgamma'
BayesUYC: no visible global function definition for 'rnorm'
BayesUYC: no visible global function definition for 'rgamma'
BayesYC: no visible global function definition for 'rnorm'
BayesYC: no visible global function definition for 'rgamma'
model.compare: no visible global function definition for 'dnorm'
print.summary.BayesSAE: no visible global function definition for
  'printCoefmat'
replication: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  as.formula coef delete.response dnorm lm model.matrix model.response
  printCoefmat rgamma rnorm runif terms
Consider adding
  importFrom("stats", "as.formula", "coef", "delete.response", "dnorm",
             "lm", "model.matrix", "model.response", "printCoefmat",
             "rgamma", "rnorm", "runif", "terms")
to your NAMESPACE file.
Found the following Makefile(s) without a final LF:
  src/Makevars
Some 'make' programs ignore lines not ending in LF.
File 'BayesSAE/libs/i386/BayesSAE.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'HBsae.o'
File 'BayesSAE/libs/x64/BayesSAE.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'HBsae.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
mlike.alt.g.AR: no visible global function definition for 'integrate'
mlike.alt.gtheta.AR: no visible global function definition for 'dbeta'
mlike.null.AR: no visible global function definition for 'dbeta'
multilevel.Gibbs.AR: no visible global function definition for
  'txtProgressBar'
multilevel.Gibbs.AR : pbFun: no visible global function definition for
  'setTxtProgressBar'
trendtest.Gibbs.AR: no visible global function definition for
  'txtProgressBar'
trendtest.Gibbs.AR : pbFun: no visible global function definition for
  'setTxtProgressBar'
trendtest.Gibbs.AR: no visible global function definition for 'dcauchy'
trendtest.Gibbs.AR: no visible global function definition for 'pcauchy'
trendtest.MC.AR: no visible global function definition for
  'txtProgressBar'
trendtest.MC.AR : pbFun: no visible global function definition for
  'setTxtProgressBar'
trendtest.nullMargLikeAR: no visible global function definition for
  'integrate'
ttest.Gibbs.AR: no visible global function definition for
  'txtProgressBar'
ttest.Gibbs.AR : pbFun: no visible global function definition for
  'setTxtProgressBar'
ttest.Gibbs.AR: no visible global function definition for 'dcauchy'
ttest.Gibbs.AR: no visible global function definition for 'pcauchy'
ttest.MCGQ.AR: no visible global function definition for 'integrate'
Undefined global functions or variables:
  dbeta dcauchy integrate pcauchy setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "dbeta", "dcauchy", "integrate", "pcauchy")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'MASS' 'combinat' 'gplots' 'mnormt'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bayes.regress: no visible binding for global variable 'var'
bayesregressB1S1: no visible global function definition for 'rgamma'
bayesregressB1S2: no visible global function definition for 'rgamma'
bayesregressB2S1: no visible global function definition for 'rgamma'
bayesregressB2S2: no visible global function definition for 'rgamma'
bayesregressB3S1: no visible global function definition for 'rWishart'
bayesregressB3S1: no visible global function definition for 'rgamma'
bayesregressB3S2: no visible global function definition for 'rWishart'
bayesregressB3S2: no visible global function definition for 'rgamma'
Undefined global functions or variables:
  rWishart rgamma var
Consider adding
  importFrom("stats", "rWishart", "rgamma", "var")
to your NAMESPACE file.
Depends: includes the non-default packages:
  'lme4' 'MASS' 'VGAM' 'mvtnorm' 'matrixcalc' 'coda'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/Bayesthresh.Rcheck/00install.out' for details.
Packages in Depends field not imported from:
  'MASS' 'VGAM' 'coda' 'lme4' 'matrixcalc' 'mvtnorm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
validate: no visible binding for global variable 'qnorm'
validate: no visible global function definition for 'pchisq'
validate: no visible global function definition for 'qnorm'
validate: no visible global function definition for 'plot'
validate: no visible global function definition for 'axis'
validate: no visible global function definition for 'points'
validate: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline axis pchisq plot points qnorm
Consider adding
  importFrom("graphics", "abline", "axis", "plot", "points")
  importFrom("stats", "pchisq", "qnorm")
to your NAMESPACE file.
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    libs  23.8Mb
Unexported object imported by a ':::' call: 'boa:::boa.getparms'
  See the note in ?`:::` about the use of this operator.
File 'BayHap/libs/i386/BayHap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'mcmc.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'mcmc.o'
File 'BayHap/libs/x64/BayHap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'mcmc.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'mcmc.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'library' or 'require' call to 'coda' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
'library' or 'require' call to 'mvnmle' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
BilogData: no visible global function definition for 'write.table'
CohensD.rawData: no visible global function definition for 'var'
EtaSq: no visible global function definition for 'summary.aov'
HedgesG.rawData: no visible global function definition for 'var'
LittleMCAR: no visible global function definition for 'mlest'
LittleMCAR: no visible global function definition for 'pchisq'
PseudoR2: no visible global function definition for 'predict'
Undefined global functions or variables:
  mlest pchisq predict summary.aov var write.table
Consider adding
  importFrom("stats", "pchisq", "predict", "summary.aov", "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'fields' 'poibin' 'rjags'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
BMR.plot: no visible global function definition for 'heat.colors'
BMR.plot: no visible global function definition for 'image.plot'
BMR.plot: no visible global function definition for 'title'
BMR.plot: no visible global function definition for 'mtext'
BMR.plot: no visible global function definition for 'par'
baysic.data: no visible global function definition for 'layout'
baysic.data: no visible global function definition for 'barplot'
baysic.data: no visible global function definition for 'rainbow'
baysic.fit: no visible global function definition for 'jags.model'
baysic.fit: no visible global function definition for 'update'
baysic.fit: no visible global function definition for 'coda.samples'
baysic.test: no visible global function definition for 'ppois'
baysic.test : <anonymous>: no visible global function definition for
  'ppoibin'
baysic.test: no visible global function definition for 'pbinom'
fuzzy.FDR.approx: no visible global function definition for 'p.adjust'
fuzzy.FDR.approx: no visible global function definition for 'runif'
Undefined global functions or variables:
  barplot coda.samples heat.colors image.plot jags.model layout mtext
  p.adjust par pbinom ppoibin ppois rainbow runif title update
Consider adding
  importFrom("grDevices", "heat.colors", "rainbow")
  importFrom("graphics", "barplot", "layout", "mtext", "par", "title")
  importFrom("stats", "p.adjust", "pbinom", "ppois", "runif", "update")
to your NAMESPACE file.
BAYSTAR: no visible global function definition for 'median'
BAYSTAR: no visible global function definition for 'ar'
BAYSTAR: no visible global function definition for 'quantile'
BAYSTAR: no visible global function definition for 'dev.new'
BAYSTAR: no visible global function definition for 'ts.plot'
BAYSTAR: no visible global function definition for 'title'
BAYSTAR: no visible global function definition for 'par'
BAYSTAR: no visible global function definition for 'plot.ts'
BAYSTAR: no visible global function definition for 'lines'
BAYSTAR: no visible global function definition for 'acf'
TAR.lagd: no visible global function definition for 'runif'
TAR.sigma: no visible global function definition for 'rgamma'
TAR.simu: no visible global function definition for 'rnorm'
TAR.summary: no visible global function definition for 'quantile'
TAR.summary: no visible global function definition for 'sd'
TAR.thres: no visible global function definition for 'rnorm'
TAR.thres: no visible global function definition for 'runif'
Undefined global functions or variables:
  acf ar dev.new lines median par plot.ts quantile rgamma rnorm runif
  sd title ts.plot
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "lines", "par", "title")
  importFrom("stats", "acf", "ar", "median", "plot.ts", "quantile",
             "rgamma", "rnorm", "runif", "sd", "ts.plot")
to your NAMESPACE file.
Package in Depends field not imported from: 'splines'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
LaplaceMetropolis_admkr: no visible binding for global variable
  'median'
LaplaceMetropolis_admkr: no visible global function definition for
  'mad'
LaplaceMetropolis_gaussian: no visible binding for global variable
  'median'
LaplaceMetropolis_gaussian: no visible global function definition for
  'mad'
cost_admkr: no visible global function definition for 'sd'
cov_chol: no visible global function definition for 'qchisq'
cov_chol_admkr: no visible global function definition for 'qchisq'
gibbs_admkr_erro: no visible global function definition for 'rnorm'
gibbs_admkr_erro: no visible global function definition for 'runif'
gibbs_admkr_nw: no visible global function definition for 'qnorm'
gibbs_admkr_nw: no visible global function definition for 'rnorm'
gibbs_admkr_nw: no visible global function definition for 'runif'
loglikelihood_admkr: no visible global function definition for 'sd'
margin_like_admkr: no visible global function definition for 'sd'
np_gibbs: no visible global function definition for 'qnorm'
np_gibbs: no visible global function definition for 'rnorm'
np_gibbs: no visible global function definition for 'runif'
np_gibbs: no visible global function definition for 'rgamma'
Undefined global functions or variables:
  mad median qchisq qnorm rgamma rnorm runif sd
Consider adding
  importFrom("stats", "mad", "median", "qchisq", "qnorm", "rgamma",
             "rnorm", "runif", "sd")
to your NAMESPACE file.
bbmm.contour: no visible global function definition for 'na.omit'
bbmm.contour: no visible global function definition for 'optimize'
bbmm.contour: no visible global function definition for 'contour'
bbmm.contour: no visible global function definition for 'points'
bbmm.contour: no visible global function definition for 'lines'
brownian.bridge: no visible global function definition for 'sd'
brownian.motion.variance: no visible global function definition for
  'optimize'
Undefined global functions or variables:
  contour lines na.omit optimize points sd
Consider adding
  importFrom("graphics", "contour", "lines", "points")
  importFrom("stats", "na.omit", "optimize", "sd")
to your NAMESPACE file.
bbo: no visible global function definition for 'runif'
bbo: no visible global function definition for 'tail'
plot.bbo: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot runif tail
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
  importFrom("utils", "tail")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'HI' 'lme4' 'locfit' 'secr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
BBRecap: no visible global function definition for 'optimize'
BBRecap: no visible global function definition for 'arms'
BBRecap: no visible global function definition for 'median'
BBRecap : HPD.interval: no visible global function definition for
  'density'
BBRecap : HPD.interval: no visible global function definition for
  'quantile'
BBRecap.custom.part: no visible global function definition for
  'optimize'
LBRecap: no visible global function definition for 'findbars'
LBRecap: no visible global function definition for 'as.formula'
LBRecap: no visible global function definition for 'glm'
LBRecap: no visible global function definition for 'binomial'
LBRecap: no visible global function definition for 'glmer'
LBRecap: no visible global function definition for 'logLik'
LBRecap: no visible global function definition for 'coef'
LBRecap: no visible global function definition for 'na.omit'
LBRecap: no visible global function definition for 'fixef'
LBRecap: no visible global function definition for 'ranef'
LBRecap: no visible global function definition for 'qnorm'
LBRecap: no visible global function definition for 'plot'
LBRecap: no visible global function definition for 'points'
LBRecap: no visible global function definition for 'axis'
LBRecap: no visible global function definition for 'abline'
LBRecap.custom.part: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  abline arms as.formula axis binomial coef density findbars fixef glm
  glmer logLik median na.omit optimize plot points qnorm quantile ranef
Consider adding
  importFrom("graphics", "abline", "axis", "plot", "points")
  importFrom("stats", "as.formula", "binomial", "coef", "density", "glm",
             "logLik", "median", "na.omit", "optimize", "qnorm",
             "quantile")
to your NAMESPACE file.
'library' or 'require' call to 'rgl' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
pairs.bce : panel.cor: no visible global function definition for 'text'
pairs.bce : panel.cor: no visible global function definition for 'cor'
pairs.bce : panel.hist: no visible global function definition for 'par'
pairs.bce : panel.hist: no visible global function definition for
  'hist'
pairs.bce : panel.hist: no visible global function definition for
  'rect'
pairs.bce: no visible global function definition for 'pairs'
panel.cor: no visible global function definition for 'par'
panel.cor: no visible global function definition for 'cor'
panel.cor: no visible global function definition for 'strwidth'
panel.cor: no visible global function definition for 'text'
rdirichlet2: no visible global function definition for 'rgamma'
summary.bce: no visible global function definition for 'cov'
summary.bce: no visible binding for global variable 'sd'
summary.bce: no visible binding for global variable 'quantile'
Undefined global functions or variables:
  cor cov hist pairs par quantile rect rgamma sd strwidth text
Consider adding
  importFrom("graphics", "hist", "pairs", "par", "rect", "strwidth",
             "text")
  importFrom("stats", "cor", "cov", "quantile", "rgamma", "sd")
to your NAMESPACE file.
Packages suggested but not available for checking: 'bcmaps.rdata' 'doMC'
check.summary: no visible global function definition for 'sd'
risk.summary: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  sd write.csv
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
plot.cvsvd: no visible binding for global variable 'sd'
plot.cvsvd: no visible global function definition for 'plot'
plot.cvsvd: no visible global function definition for 'lines'
plot.cvsvd: no visible global function definition for 'segments'
plot.cvsvd: no visible global function definition for 'points'
print.cvsvd: no visible binding for global variable 'sd'
summary.cvsvd: no visible binding for global variable 'sd'
Undefined global functions or variables:
  lines plot points sd segments
Consider adding
  importFrom("graphics", "lines", "plot", "points", "segments")
  importFrom("stats", "sd")
to your NAMESPACE file.
mise: no visible global function definition for 'integrate'
density,BrVitale : density.vitale : <anonymous>: no visible global
  function definition for 'dbeta'
density,Chen99Kernel : <anonymous>: no visible global function
  definition for 'dbeta'
density,HirukawaJLNKernel : <anonymous>: no visible global function
  definition for 'dbeta'
density,MicroBetaChen99Kernel : <anonymous>: no visible global function
  definition for 'dbeta'
density,Vitale : <anonymous>: no visible global function definition for
  'dbeta'
distribution,BernsteinPolynomials : <anonymous>: no visible global
  function definition for 'integrate'
distribution,KernelDensity : <anonymous>: no visible global function
  definition for 'integrate'
print,BoundedDensity: no visible global function definition for 'str'
print,KernelDensity: no visible global function definition for 'str'
rsample,BoundedDensity: no visible global function definition for
  'runif'
setNormalizationConst,MacroBetaChen99Kernel: no visible global function
  definition for 'integrate'
setNormalizationConst,MacroBetaHirukawaTSKernel: no visible global
  function definition for 'integrate'
setNormalizationConstant,MacroBetaHirukawaJLNKernel: no visible global
  function definition for 'integrate'
setNormalizationConstants,MicroBetaChen99Kernel :
  density.kernelFunction: no visible global function definition for
  'dbeta'
setNormalizationConstants,MicroBetaChen99Kernel : <anonymous>: no
  visible global function definition for 'integrate'
show,BoundedDensity: no visible global function definition for 'str'
show,KernelDensity: no visible global function definition for 'str'
Undefined global functions or variables:
  dbeta integrate runif str
Consider adding
  importFrom("stats", "dbeta", "integrate", "runif")
  importFrom("utils", "str")
to your NAMESPACE file.
BDtest: no visible global function definition for 'binom.test'
CIlnpv: no visible global function definition for 'qnorm'
CIlnpvak: no visible global function definition for 'qnorm'
CIlppv: no visible global function definition for 'qnorm'
CIlppvak: no visible global function definition for 'qnorm'
CIpvBI: no visible global function definition for 'rbeta'
CIpvBI: no visible global function definition for 'quantile'
CIpvBI: no visible global function definition for 'median'
CIpvBII: no visible global function definition for 'rbeta'
CIpvBII: no visible global function definition for 'quantile'
CIpvBII: no visible global function definition for 'median'
nNPV: no visible global function definition for 'qnorm'
nPPV: no visible global function definition for 'qnorm'
plotnPV: no visible global function definition for 'na.omit'
plotnPV: no visible global function definition for 'lines'
plotnPV2 : defplot: no visible global function definition for 'plot'
plotnPV2 : defplot: no visible global function definition for 'lines'
plotnPV2: no visible global function definition for 'par'
plotnPV2: no visible global function definition for 'layout'
simPV: no visible global function definition for 'rbinom'
simPV: no visible global function definition for 'quantile'
Undefined global functions or variables:
  binom.test layout lines median na.omit par plot qnorm quantile rbeta
  rbinom
Consider adding
  importFrom("graphics", "layout", "lines", "par", "plot")
  importFrom("stats", "binom.test", "median", "na.omit", "qnorm",
             "quantile", "rbeta", "rbinom")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'RColorBrewer' 'beadarray'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
beadtypeFilter: no visible global function definition for 'na.omit'
beadtypeFilter: no visible global function definition for 'exprs'
beadtypeFilter: no visible global function definition for 'se.exprs'
beadtypeFilter: no visible global function definition for 'beadNum'
beadtypeFilter: no visible global function definition for 'fData'
emCDF: no visible global function definition for 'brewer.pal'
emCDF: no visible global function definition for 'plot'
emCDF: no visible global function definition for 'ecdf'
emCDF: no visible global function definition for 'legend'
emCDF: no visible global function definition for 'lines'
emCDF: no visible global function definition for 'text'
emCDF: no visible global function definition for 'reshape'
iccFun : <anonymous>: no visible global function definition for
  'quantile'
varianceplot: no visible global function definition for 'reshape'
varianceplot: no visible global function definition for 'plot'
varianceplot: no visible global function definition for 'points'
varianceplot: no visible global function definition for 'legend'
Undefined global functions or variables:
  beadNum brewer.pal ecdf exprs fData legend lines na.omit plot points
  quantile reshape se.exprs text
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points", "text")
  importFrom("stats", "ecdf", "na.omit", "quantile", "reshape")
to your NAMESPACE file.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/math/special_functions/detail/bernoulli_details.hpp:72:36: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/math/special_functions/detail/bernoulli_details.hpp:96:9: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.5/beanz.Rcheck/00install.out' for details.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
beep: no visible global function definition for 'download.file'
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
'library' or 'require' call to 'multcomp' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
beqi2: no visible global function definition for 'na.omit'
beqi2: no visible global function definition for 'browseURL'
readAMBI: no visible global function definition for 'read.csv'
readBEQI: no visible global function definition for 'read.csv'
readERF: no visible global function definition for 'read.csv'
readTWN: no visible global function definition for 'read.csv'
read_ITI_FIBI: no visible global function definition for 'read.csv'
Undefined global functions or variables:
  browseURL na.omit read.csv
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "browseURL", "read.csv")
to your NAMESPACE file.
'library' or 'require' call to 'MASS' which was already attached by Depends.
  Please remove these calls from your code.
ber: no visible global function definition for 'model.matrix'
ber: no visible global function definition for 'as.formula'
ber_bg: no visible global function definition for 'model.matrix'
ber_bg: no visible global function definition for 'as.formula'
combat_np: no visible global function definition for 'as.formula'
combat_np: no visible global function definition for 'model.matrix'
combat_p: no visible global function definition for 'as.formula'
combat_p: no visible global function definition for 'model.matrix'
combat_p: no visible binding for global variable 'var'
combat_p: no visible global function definition for 'par'
combat_p: no visible global function definition for 'density'
combat_p: no visible global function definition for 'plot'
combat_p: no visible global function definition for 'lines'
combat_p: no visible global function definition for 'dnorm'
combat_p: no visible global function definition for 'qqnorm'
combat_p: no visible global function definition for 'qqline'
combat_p: no visible global function definition for 'rgamma'
combat_p: no visible global function definition for 'qqplot'
combat_p: no visible global function definition for 'title'
mean_centering: no visible global function definition for
  'model.matrix'
standardization: no visible global function definition for
  'model.matrix'
Undefined global functions or variables:
  as.formula density dnorm lines model.matrix par plot qqline qqnorm
  qqplot rgamma title var
Consider adding
  importFrom("graphics", "lines", "par", "plot", "title")
  importFrom("stats", "as.formula", "density", "dnorm", "model.matrix",
             "qqline", "qqnorm", "qqplot", "rgamma", "var")
to your NAMESPACE file.
Package in Depends field not imported from: 'Rmpfr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bI: no visible global function definition for 'is'
bI: no visible global function definition for 'mpfr'
bI: no visible binding for global variable 'slot'
bI: no visible global function definition for 'as'
Undefined global functions or variables:
  as is mpfr slot
Consider adding
  importFrom("methods", "as", "is", "slot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
betafam: no visible global function definition for 'pnorm'
betafam: no visible global function definition for 'pchisq'
betafam: no visible global function definition for 'lm'
betafam: no visible global function definition for 'coefficients'
betafam: no visible global function definition for 'glm.fit'
betafam: no visible global function definition for 'gaussian'
betafam: no visible global function definition for 'glmnet'
Undefined global functions or variables:
  coefficients gaussian glm.fit glmnet lm pchisq pnorm
Consider adding
  importFrom("stats", "coefficients", "gaussian", "glm.fit", "lm",
             "pchisq", "pnorm")
to your NAMESPACE file.
'library' or 'require' call to 'vegan' which was already attached by Depends.
  Please remove these calls from your code.
S3 methods shown with full name in documentation object 'cca.pertables':
  'cca.pertables'

S3 methods shown with full name in documentation object 'rda.pertables':
  'rda.pertables'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
betas.lm: no visible binding for global variable 'sd'
betas.lm: no visible global function definition for 'sd'
my.wtd.var: no visible global function definition for 'var'
Undefined global functions or variables:
  sd var
Consider adding
  importFrom("stats", "sd", "var")
to your NAMESPACE file.
bezierArcLength: no visible global function definition for 'sd'
bezierArcLength: no visible global function definition for 'lm'
bezierCurveFit: no visible global function definition for 'nls'
bezierCurveFit: no visible global function definition for 'nls.control'
bezierCurveFit: no visible global function definition for 'lm'
bezierCurveFit: no visible global function definition for 'na.omit'
pointsOnBezier: no visible global function definition for 'optim'
Undefined global functions or variables:
  lm na.omit nls nls.control optim sd
Consider adding
  importFrom("stats", "lm", "na.omit", "nls", "nls.control", "optim",
             "sd")
to your NAMESPACE file.
binommh.default : log_lik: no visible global function definition for
  'dbinom'
binommh.default: no visible global function definition for 'dbinom'
binommh.default: no visible global function definition for 'runif'
binommh.formula: no visible global function definition for
  'model.frame'
binommh.formula: no visible global function definition for
  'model.matrix'
binommh.formula: no visible global function definition for
  'model.response'
expmh.default : log_lik: no visible global function definition for
  'dexp'
expmh.default: no visible global function definition for 'dexp'
expmh.default: no visible global function definition for 'runif'
expmh.formula: no visible global function definition for 'model.frame'
expmh.formula: no visible global function definition for 'model.matrix'
expmh.formula: no visible global function definition for
  'model.response'
poissmh.default : log_lik: no visible global function definition for
  'dpois'
poissmh.default: no visible global function definition for 'dpois'
poissmh.default: no visible global function definition for 'runif'
poissmh.formula: no visible global function definition for
  'model.frame'
poissmh.formula: no visible global function definition for
  'model.matrix'
poissmh.formula: no visible global function definition for
  'model.response'
Undefined global functions or variables:
  dbinom dexp dpois model.frame model.matrix model.response runif
Consider adding
  importFrom("stats", "dbinom", "dexp", "dpois", "model.frame",
             "model.matrix", "model.response", "runif")
to your NAMESPACE file.
block.gibbs: no visible global function definition for 'rmultinom'
rdirichlet: no visible global function definition for 'rgamma'
Undefined global functions or variables:
  rgamma rmultinom
Consider adding
  importFrom("stats", "rgamma", "rmultinom")
to your NAMESPACE file.
global: no visible global function definition for 'par'
global: no visible global function definition for 'runif'
global: no visible global function definition for 'cov'
mymcmc: no visible global function definition for 'par'
mymcmc: no visible global function definition for 'rnorm'
mymcmc: no visible global function definition for 'runif'
mymcmc: no visible global function definition for 'cov'
mymcmc: no visible global function definition for 'lines'
plkhci: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  cov lines par qchisq rnorm runif
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "cov", "qchisq", "rnorm", "runif")
to your NAMESPACE file.
installed size is 142.9Mb
  sub-directories of 1Mb or more:
    include  141.9Mb
Package in Depends field not imported from: 'betareg'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bias: no visible global function definition for 'predict'
bias: no visible global function definition for 'pnorm'
bias: no visible global function definition for 'model.matrix'
Undefined global functions or variables:
  model.matrix pnorm predict
Consider adding
  importFrom("stats", "model.matrix", "pnorm", "predict")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/biclust.Rcheck/00install.out' for details.
BiDimRegression: no visible global function definition for 'lm'
BiDimRegression: no visible global function definition for 'pf'
print.BiDimRegression: no visible global function definition for
  'printCoefmat'
print.summary.BiDimRegression: no visible global function definition
  for 'printCoefmat'
Undefined global functions or variables:
  lm pf printCoefmat
Consider adding
  importFrom("stats", "lm", "pf", "printCoefmat")
to your NAMESPACE file.
'library' or 'require' call to 'mvtnorm' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'Rcpp' 'mvtnorm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File 'bifactorial/libs/i386/bifactorial.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'misc.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'krit.o', 'pv.o'
File 'bifactorial/libs/x64/bifactorial.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'misc.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'krit.o', 'pv.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/interprocess/detail/win32_api.hpp:145:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/interprocess/detail/win32_api.hpp:153:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/interprocess/detail/win32_api.hpp:178:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/interprocess/detail/win32_api.hpp:180:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/3.5/bigalgebra.Rcheck/00install.out' for details.
anon_matrix: no visible global function definition for
  'filebacked.big.matrix'
anon_matrix: no visible global function definition for 'capture.output'
finalize_anon_matrix: no visible global function definition for
  'capture.output'
Undefined global functions or variables:
  capture.output filebacked.big.matrix
Consider adding
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/interprocess/detail/win32_api.hpp:145:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/interprocess/detail/win32_api.hpp:153:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/interprocess/detail/win32_api.hpp:178:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/interprocess/detail/win32_api.hpp:180:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/3.5/biganalytics.Rcheck/00install.out' for details.
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/interprocess/detail/win32_api.hpp:145:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/interprocess/detail/win32_api.hpp:153:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/interprocess/detail/win32_api.hpp:178:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/interprocess/detail/win32_api.hpp:180:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/3.5/bigFastlm.Rcheck/00install.out' for details.
Packages in Depends field not imported from:
  'DBI' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bigglm.RODBC: no visible global function definition for 'odbcQuery'
bigglm.RODBC : chunk: no visible global function definition for
  'odbcQuery'
bigglm.RODBC : chunk: no visible global function definition for
  'sqlGetResults'
bigglm,ANY-DBIConnection: no visible global function definition for
  'dbSendQuery'
bigglm,ANY-DBIConnection: no visible global function definition for
  'dbClearResult'
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for 'dbClearResult'
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for 'dbSendQuery'
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for 'fetch'
Undefined global functions or variables:
  dbClearResult dbSendQuery fetch odbcQuery sqlGetResults
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/interprocess/detail/win32_api.hpp:145:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/interprocess/detail/win32_api.hpp:153:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/interprocess/detail/win32_api.hpp:178:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/interprocess/detail/win32_api.hpp:180:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/3.5/bigmemory.Rcheck/00install.out' for details.
Package which this enhances but not available for checking: 'synchronicity'
Package unavailable to check Rd xrefs: 'synchronicity'
quickModel: no visible global function definition for 'tail'
quickSource: no visible global function definition for 'write.table'
Undefined global functions or variables:
  tail write.table
Consider adding
  importFrom("utils", "tail", "write.table")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/bigpca.Rcheck/00install.out' for details.
bigRR: no visible global function definition for 'gaussian'
bigRR.default: no visible global function definition for 'gaussian'
bigRR.formula: no visible global function definition for 'gaussian'
bigRR.formula: no visible global function definition for 'as.formula'
bigRR.formula: no visible global function definition for 'model.frame'
bigRR.formula: no visible global function definition for 'model.matrix'
bigRR.formula: no visible global function definition for
  'model.response'
bigRR_update: no visible global function definition for 'gaussian'
hugeRR: no visible global function definition for 'gaussian'
hugeRR_update: no visible global function definition for 'gaussian'
plot.bigRR: no visible global function definition for 'par'
plot.bigRR: no visible global function definition for 'plot'
plot.bigRR: no visible global function definition for 'rgb'
Undefined global functions or variables:
  as.formula gaussian model.frame model.matrix model.response par plot
  rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "par", "plot")
  importFrom("stats", "as.formula", "gaussian", "model.frame",
             "model.matrix", "model.response")
to your NAMESPACE file.
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/interprocess/detail/win32_api.hpp:145:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/interprocess/detail/win32_api.hpp:153:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/interprocess/detail/win32_api.hpp:178:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/interprocess/detail/win32_api.hpp:180:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/3.5/bigtabulate.Rcheck/00install.out' for details.
Packages in Depends field not imported from:
  'gbm' 'glmnet' 'randomForest' 'tree'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
LDCAEst: no visible global function definition for 'glmnet'
cv.LDCA: no visible global function definition for 'cv.glmnet'
predict.LDCA: no visible global function definition for 'predict'
predict.cv.LDCA: no visible global function definition for 'predict'
predict.tsp.gbm: no visible global function definition for 'predict'
predict.tsp.randomForest: no visible global function definition for
  'predict'
predict.tsp.tree: no visible global function definition for 'predict'
tsp.gbm: no visible global function definition for 'gbm.fit'
tsp.randomForest: no visible global function definition for
  'randomForest'
tsp.tree: no visible global function definition for 'tree.control'
tsp.tree: no visible global function definition for 'tree'
Undefined global functions or variables:
  cv.glmnet gbm.fit glmnet predict randomForest tree tree.control
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   3.1Mb
Running 'testthat.R' [34s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == testthat results  ===========================================================
  OK: 133 SKIPPED: 1 FAILED: 10
  1.  Failure: dl_bikedata dc (@test-download-data.R#58) 
  2.  Failure: dl_bikedata dc (@test-download-data.R#58) 
  3.  Failure: dl_bikedata dc (@test-download-data.R#58) 
  4.  Failure: dl_bikedata dc (@test-download-data.R#58) 
  5.  Failure: dl_bikedata dc (@test-download-data.R#58) 
  6.  Failure: dl_bikedata dc (@test-download-data.R#58) 
  7.  Failure: dl_bikedata dc (@test-download-data.R#58) 
  8.  Failure: dl_bikedata dc (@test-download-data.R#58) 
  9.  Failure: dl_bikedata dc (@test-download-data.R#58) 
  10. Failure: dl_bikedata dc (@test-download-data.R#58) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [35s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == testthat results  ===========================================================
  OK: 133 SKIPPED: 1 FAILED: 10
  1.  Failure: dl_bikedata dc (@test-download-data.R#58) 
  2.  Failure: dl_bikedata dc (@test-download-data.R#58) 
  3.  Failure: dl_bikedata dc (@test-download-data.R#58) 
  4.  Failure: dl_bikedata dc (@test-download-data.R#58) 
  5.  Failure: dl_bikedata dc (@test-download-data.R#58) 
  6.  Failure: dl_bikedata dc (@test-download-data.R#58) 
  7.  Failure: dl_bikedata dc (@test-download-data.R#58) 
  8.  Failure: dl_bikedata dc (@test-download-data.R#58) 
  9.  Failure: dl_bikedata dc (@test-download-data.R#58) 
  10. Failure: dl_bikedata dc (@test-download-data.R#58) 
  
  Error: testthat unit tests failed
  Execution halted
plot,bild-missing: no visible global function definition for
  'dev.interactive'
plot,bild-missing: no visible global function definition for
  'devAskNewPage'
plot,bild-missing: no visible global function definition for
  'extendrange'
Undefined global functions or variables:
  dev.interactive devAskNewPage extendrange
Consider adding
  importFrom("grDevices", "dev.interactive", "devAskNewPage",
             "extendrange")
to your NAMESPACE file.
chisq.sim.factory : chisq.sim.func: no visible global function
  definition for 'chisq.test'
rmultnom: no visible global function definition for 'runif'
Undefined global functions or variables:
  chisq.test runif
Consider adding
  importFrom("stats", "chisq.test", "runif")
to your NAMESPACE file.
commonprob2sigma: no visible global function definition for 'approxfun'
rmvbin: no visible global function definition for 'qnorm'
simul.commonprob: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  approxfun qnorm
Consider adding
  importFrom("stats", "approxfun", "qnorm")
to your NAMESPACE file.
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
             stop("Function ", name, " not found in environment ", environmentName(env), 
                 ".", call. = FALSE)
         mock(name = name, env = env, new = eval(new_values[[qual_name]], eval_env, eval_env))
     })
  4: FUN(X[[i]], ...)
  5: stop("Can't mock functions in base packages (", pkg_name, ")", call. = FALSE)
  
  == testthat results  ===========================================================
  OK: 26 SKIPPED: 0 FAILED: 3
  1. Error: canDownloadFiles (@test-download_files.R#9) 
  2. Error: canReturnEmptyDFWhenEmptyDownloadFiles (@test-download_files.R#27) 
  3. Error: canProcessYaml (@test-process_yaml.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Mtoquant: no visible global function definition for 'qnorm'
NHS: no visible global function definition for 'qnorm'
NHS : WilsonScore: no visible global function definition for 'qnorm'
binMto.formula: no visible global function definition for 'model.frame'
plot.binMto: no visible global function definition for 'plot.new'
plot.binMto: no visible global function definition for 'par'
plot.binMto: no visible global function definition for 'strwidth'
plot.binMto: no visible global function definition for 'axis'
plot.binMto: no visible global function definition for 'box'
plot.binMto: no visible global function definition for 'segments'
plot.binMto: no visible global function definition for 'points'
plot.binMto: no visible global function definition for 'abline'
simPowerI: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  abline axis box model.frame par plot.new points qnorm rbinom segments
  strwidth
Consider adding
  importFrom("graphics", "abline", "axis", "box", "par", "plot.new",
             "points", "segments", "strwidth")
  importFrom("stats", "model.frame", "qnorm", "rbinom")
to your NAMESPACE file.
Package required but not available: 'mzR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
bin_ps: no visible global function definition for 'runif'
bin_ps: no visible global function definition for 'dbinom'
draw_i: no visible global function definition for 'runif'
Undefined global functions or variables:
  dbinom runif
Consider adding
  importFrom("stats", "dbinom", "runif")
to your NAMESPACE file.
IndivdRUMIndMH: no visible global function definition for
  'flush.console'
dRUMAuxMix: no visible global function definition for 'flush.console'
dRUMHAM: no visible global function definition for 'flush.console'
dRUMIndMH: no visible global function definition for 'flush.console'
print.binomlogit: no visible global function definition for 'is'
summary.binomlogit: no visible global function definition for 'is'
Undefined global functions or variables:
  flush.console is
Consider adding
  importFrom("methods", "is")
  importFrom("utils", "flush.console")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' calls in package code:
  'ggplot2' 'lattice' 'polynom' 'tcltk'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
bins.quantiles: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   1.9Mb
'library' or 'require' calls to packages already attached by Depends:
  'ape' 'cladoRcpp' 'phylobase' 'rexpokit'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'ape' 'cladoRcpp' 'methods' 'phylobase' 'rexpokit'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' calls which should be '::':
  'ape:::floating.pie.asp' 'cladoRcpp:::areas_list_to_states_list_old'
  See the note in ?`:::` about the use of this operator.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/bioimagetools.Rcheck/00install.out' for details.
Running examples in 'BioInstaller-Ex.R' failed
The error most likely occurred in:

> ### Name: install.bioinfo
> ### Title: Download and install biology software or database
> ### Aliases: install.bioinfo
> 
> ### ** Examples
> 
> db <- sprintf('%s/.BioInstaller', tempdir())
> set.biosoftwares.db(db)
> install.bioinfo('bwa', show.all.versions = TRUE)
INFO [2018-02-24 10:08:11] Fetching bwa versions....
Error in function (type, msg, asError = TRUE)  : 
  error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
Calls: install.bioinfo ... github2versions -> getURL -> curlPerform -> <Anonymous> -> fun
Execution halted
Running 'testthat.R' [27s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  trying URL 'ftp://ftp.sjtu.edu.cn/pub/CPAN/clpa//index.html'
  ...
  downloaded 3574 bytes
  
  == testthat results  ===========================================================
  OK: 59 SKIPPED: 0 FAILED: 6
  1. Error: install.github (@test_install.R#10) 
  2. Error: install.bioinfo (@test_install.R#57) 
  3. Error: initial (@test_install_uilts.R#39) 
  4. Error: dependence (@test_install_uilts.R#88) 
  5. Error: git.download (@test_install_uilts.R#102) 
  6. Error: download.file.custom (@test_utils.R#104) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 46-70 (BioInstaller.Rmd) 
Error: processing vignette 'BioInstaller.Rmd' failed with diagnostics:
error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
Execution halted
Missing or unexported object: 'gam::step.gam'
'library' or 'require' call to 'MGRASTer' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.onAttach: no visible global function definition for 'packageVersion'
biom.matrix: no visible global function definition for 'packageVersion'
Undefined global functions or variables:
  packageVersion
Consider adding
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/BioPhysConnectoR.Rcheck/00install.out' for details.
extractPDB : atom.select : sel.txt2nums: no visible global function
  definition for 'na.omit'
extractPDB : read.pdb: no visible global function definition for
  'na.omit'
mat.read: no visible global function definition for 'read.table'
mat.write: no visible global function definition for 'write.table'
scpcp: no visible global function definition for 'pgamma'
sim : sim.func: no visible global function definition for 'write.table'
simc: no visible global function definition for 'write.table'
simc : simc.func: no visible global function definition for
  'write.table'
sims: no visible global function definition for 'write.table'
sims : sims.func: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  na.omit pgamma read.table write.table
Consider adding
  importFrom("stats", "na.omit", "pgamma")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
binom.ci : bc: no visible global function definition for 'qf'
binom.ci : bc: no visible global function definition for 'qnorm'
cvar: no visible global function definition for 'sd'
eta2: no visible global function definition for 'lm'
eta2: no visible global function definition for 'as.formula'
gg_qqplot: no visible binding for global variable 'qnorm'
gg_qqplot: no visible global function definition for 'quantile'
panel.hist: no visible global function definition for 'par'
panel.hist: no visible global function definition for 'hist'
panel.hist: no visible global function definition for 'rect'
plotcdf2: no visible global function definition for 'colorRampPalette'
plotcdf2 : jet.colors: no visible global function definition for 'gray'
plotcdf2: no visible global function definition for 'persp'
poi.ci: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  as.formula colorRampPalette gray hist lm par persp qchisq qf qnorm
  quantile rect sd
Consider adding
  importFrom("grDevices", "colorRampPalette", "gray")
  importFrom("graphics", "hist", "par", "persp", "rect")
  importFrom("stats", "as.formula", "lm", "qchisq", "qf", "qnorm",
             "quantile", "sd")
to your NAMESPACE file.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.5Mb
Depends: includes the non-default packages:
  'colorspace' 'deldir' 'rgl' 'tcltk' 'tcltk2' 'tkrplot'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'colorspace'
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  'deldir' 'rgl' 'tcltk' 'tcltk2' 'tkrplot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plot.BIPOD: no visible global function definition for 'par'
plot.BIPOD: no visible global function definition for 'matplot'
plot.BIPOD: no visible global function definition for 'abline'
plot.BIPOD: no visible global function definition for 'plot'
plot.BIPOD: no visible global function definition for 'density'
plot.BIPOD: no visible global function definition for 'curve'
plot.BIPOD: no visible global function definition for 'dlnorm'
plot.BIPOD: no visible global function definition for 'dnorm'
plot.BIPOD: no visible global function definition for 'acf'
plot.BIPOD: no visible global function definition for 'pairs'
plot.BIPOD : standfun: no visible global function definition for 'sd'
plot.BIPOD: no visible global function definition for 'sd'
plot.BIPOD: no visible global function definition for 'points'
plot.BIPOD: no visible global function definition for 'tail'
plot.BIPOD: no visible global function definition for 'matlines'
plot.BIPOD: no visible binding for global variable 'quantile'
plot.BIPOD: no visible global function definition for 'lines'
Undefined global functions or variables:
  abline acf curve density dlnorm dnorm lines matlines matplot pairs
  par plot points quantile sd tail
Consider adding
  importFrom("graphics", "abline", "curve", "lines", "matlines",
             "matplot", "pairs", "par", "plot", "points")
  importFrom("stats", "acf", "density", "dlnorm", "dnorm", "quantile",
             "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
aveslope: no visible global function definition for 'pbeta'
bisoreg : <anonymous>: no visible global function definition for
  'pbeta'
bisoreg: no visible global function definition for 'rgamma'
bisoreg: no visible global function definition for 'rbeta'
bisoreg: no visible global function definition for 'rnorm'
bisoreg: no visible global function definition for 'rbinom'
bisoreg: no visible global function definition for 'dnorm'
bisoreg: no visible global function definition for 'var'
fitted.biso : <anonymous>: no visible global function definition for
  'median'
get.W : <anonymous>: no visible global function definition for 'pbeta'
loess.wrapper : theta.fit: no visible global function definition for
  'loess'
loess.wrapper : theta.predict: no visible global function definition
  for 'predict'
loess.wrapper: no visible global function definition for 'loess'
nd2004 : initfun: no visible global function definition for 'rnorm'
nd2004 : initfun: no visible global function definition for 'rgamma'
plot.biso: no visible global function definition for 'plot'
plot.biso : <anonymous>: no visible global function definition for
  'quantile'
plot.biso: no visible global function definition for 'polygon'
plot.biso: no visible global function definition for 'gray'
plot.biso: no visible global function definition for 'points'
plot.biso : <anonymous>: no visible global function definition for
  'median'
plot.biso: no visible global function definition for 'lines'
summary.biso: no visible binding for global variable 'fivenum'
Undefined global functions or variables:
  dnorm fivenum gray lines loess median pbeta plot points polygon
  predict quantile rbeta rbinom rgamma rnorm var
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "lines", "plot", "points", "polygon")
  importFrom("stats", "dnorm", "fivenum", "loess", "median", "pbeta",
             "predict", "quantile", "rbeta", "rbinom", "rgamma", "rnorm",
             "var")
to your NAMESPACE file.
bivarcalcn: no visible global function definition for 'qnorm'
bivarcalcn: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
biwt.cor: no visible global function definition for 'covMcd'
biwt.cor: no visible binding for global variable 'mad'
biwt.est: no visible global function definition for 'covMcd'
biwt.est: no visible global function definition for 'mahalanobis'
chi.int: no visible global function definition for 'pchisq'
chi.int.p: no visible global function definition for 'dchisq'
chi.int2: no visible global function definition for 'pchisq'
chi.int2.p: no visible global function definition for 'dchisq'
rejpt.bw: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  covMcd dchisq mad mahalanobis pchisq
Consider adding
  importFrom("stats", "dchisq", "mad", "mahalanobis", "pchisq")
to your NAMESPACE file.
Package suggested but not available for checking: 'RQuantLib'
install_blat: no visible global function definition for 'download.file'
install_blat: no visible global function definition for 'unzip'
Undefined global functions or variables:
  download.file unzip
Consider adding
  importFrom("utils", "download.file", "unzip")
to your NAMESPACE file.
blighty: no visible global function definition for 'par'
blighty: no visible global function definition for 'polygon'
blighty: no visible global function definition for 'points'
blighty: no visible global function definition for 'box'
blighty: no visible global function definition for 'axis'
blighty: no visible global function definition for 'abline'
map.scale: no visible global function definition for 'locator'
map.scale: no visible global function definition for 'segments'
map.scale: no visible global function definition for 'text'
north.pointer: no visible global function definition for 'locator'
north.pointer: no visible global function definition for 'text'
north.pointer: no visible global function definition for 'arrows'
north.pointer: no visible global function definition for 'segments'
sqlimits: no visible global function definition for 'frame'
sqlimits: no visible global function definition for 'par'
Undefined global functions or variables:
  abline arrows axis box frame locator par points polygon segments text
Consider adding
  importFrom("graphics", "abline", "arrows", "axis", "box", "frame",
             "locator", "par", "points", "polygon", "segments", "text")
to your NAMESPACE file.
Package suggested but not available for checking: 'bigrf'
Missing or unexported object: 'xgboost::predict'
bglmer: no visible global function definition for 'packageVersion'
getBglmerDevianceFunctionBody: no visible global function definition
  for 'packageVersion'
getParInfo : <anonymous>: no visible global function definition for
  'sd'
makeRefitDevFun: no visible global function definition for
  'packageVersion'
mkBglmerDevfun: no visible global function definition for
  'packageVersion'
namedList: no visible global function definition for 'setNames'
refit.bmerMod: no visible global function definition for
  'packageVersion'
refit.bmerMod: no visible global function definition for 'model.frame'
refit.bmerMod: no visible global function definition for 'family'
refit.bmerMod: no visible global function definition for 'getCall'
Undefined global functions or variables:
  family getCall model.frame packageVersion sd setNames
Consider adding
  importFrom("stats", "family", "getCall", "model.frame", "sd",
             "setNames")
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/BlockFeST.Rcheck/00install.out' for details.
blockMessage : <anonymous>: no visible global function definition for
  'head'
blockMessage: no visible global function definition for 'head'
blockMessage: no visible global function definition for 'tail'
Undefined global functions or variables:
  head tail
Consider adding
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'plot.mat':
  'plot.mat' 'plot.mat.nm'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
blockmodelskmeans: no visible global function definition for 'dist'
matrixplot: no visible global function definition for 'image'
matrixplot: no visible global function definition for 'hsv'
matrixplot: no visible global function definition for 'axis'
Undefined global functions or variables:
  axis dist hsv image
Consider adding
  importFrom("grDevices", "hsv")
  importFrom("graphics", "axis", "image")
  importFrom("stats", "dist")
to your NAMESPACE file.
plotblockrand: no visible global function definition for 'pdf'
plotblockrand: no visible global function definition for 'dev.off'
plotblockrand: no visible global function definition for 'par'
plotblockrand: no visible global function definition for 'plot.new'
plotblockrand: no visible global function definition for 'strheight'
plotblockrand: no visible global function definition for 'strwidth'
plotblockrand: no visible global function definition for 'text'
plotblockrand: no visible global function definition for 'lines'
Undefined global functions or variables:
  dev.off lines par pdf plot.new strheight strwidth text
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "plot.new", "strheight",
             "strwidth", "text")
to your NAMESPACE file.
BLR: no visible global function definition for 'weighted.mean'
BLR: no visible global function definition for 'var'
BLR: no visible global function definition for 'model.matrix'
BLR: no visible global function definition for 'rnorm'
BLR: no visible global function definition for 'rchisq'
BLR: no visible global function definition for 'rgamma'
BLR: no visible global function definition for 'dnorm'
dLambda: no visible global function definition for 'dgamma'
dScaledInvChisq: no visible global function definition for 'dchisq'
metropLambda: no visible global function definition for 'rgamma'
metropLambda: no visible global function definition for 'dexp'
metropLambda: no visible global function definition for 'dbeta'
metropLambda: no visible global function definition for 'dgamma'
metropLambda: no visible global function definition for 'runif'
Undefined global functions or variables:
  dbeta dchisq dexp dgamma dnorm model.matrix rchisq rgamma rnorm runif
  var weighted.mean
Consider adding
  importFrom("stats", "dbeta", "dchisq", "dexp", "dgamma", "dnorm",
             "model.matrix", "rchisq", "rgamma", "rnorm", "runif", "var",
             "weighted.mean")
to your NAMESPACE file.
Package in Depends field not imported from: 'drc'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bmd: no visible global function definition for 'qnorm'
bmd: no visible global function definition for 'predict'
bmd: no visible global function definition for 'LL.2'
bmd: no visible global function definition for 'LN.2'
bmd: no visible global function definition for 'W1.2'
bmd: no visible global function definition for 'W2.2'
bmd: no visible global function definition for 'LL.5'
bmd: no visible global function definition for 'LN.4'
bmd: no visible global function definition for 'W1.4'
bmd: no visible global function definition for 'W2.4'
bmd: no visible global function definition for 'FPL.4'
bmd: no visible global function definition for 'maED'
bmd: no visible global function definition for 'ED'
Undefined global functions or variables:
  ED FPL.4 LL.2 LL.5 LN.2 LN.4 W1.2 W1.4 W2.2 W2.4 maED predict qnorm
Consider adding
  importFrom("stats", "predict", "qnorm")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'Amelia' 'MASS' 'lavaan' 'sem' 'snowfall'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' calls to packages already attached by Depends:
  'coda' 'functional' 'plyr'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'coda' 'functional' 'plyr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
HDistNoSize: no visible global function definition for 'density'
HDistSize: no visible global function definition for 'density'
bmkconverge: no visible global function definition for 'Compose'
bmksensitive: no visible global function definition for 'Compose'
bmksummary: no visible global function definition for 'Compose'
bmksummary: no visible global function definition for 'Curry'
bmksummary: no visible binding for global variable 'quantile'
bmksummary : std.error: no visible global function definition for 'var'
bmksummary: no visible global function definition for 'mcmc'
bmksummary: no visible global function definition for 'mcmc.list'
bmksummary: no visible global function definition for 'median'
bmksummary: no visible global function definition for 'effectiveSize'
bmksummary: no visible global function definition for 'gelman.diag'
Undefined global functions or variables:
  Compose Curry density effectiveSize gelman.diag mcmc mcmc.list median
  quantile var
Consider adding
  importFrom("stats", "density", "median", "quantile", "var")
to your NAMESPACE file.
bmmix : LL.y: no visible global function definition for 'dmultinom'
bmmix : LL.x : <anonymous>: no visible global function definition for
  'dmultinom'
bmmix : LPrior.alpha: no visible global function definition for 'dexp'
bmmix : alpha.move: no visible global function definition for 'rnorm'
bmmix : alpha.move: no visible global function definition for 'runif'
bmmix : phi.move: no visible global function definition for 'rnorm'
bmmix : phi.move: no visible global function definition for 'runif'
bmmix: no visible global function definition for 'read.table'
Undefined global functions or variables:
  dexp dmultinom read.table rnorm runif
Consider adding
  importFrom("stats", "dexp", "dmultinom", "rnorm", "runif")
  importFrom("utils", "read.table")
to your NAMESPACE file.
GibbsIteration: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  rbinom
Consider adding
  importFrom("stats", "rbinom")
to your NAMESPACE file.
File 'BMN/libs/i386/BMN.dll':
  Found '_ZSt4cout', possibly from 'std::cout' (C++)
    Objects: 'JunctionTree.o', 'pseudoLikelihood.o'
File 'BMN/libs/x64/BMN.dll':
  Found '_ZSt4cout', possibly from 'std::cout' (C++)
    Objects: 'JunctionTree.o', 'pseudoLikelihood.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
make_topology: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
bnlr: no visible global function definition for 'dnorm'
bnlr: no visible global function definition for 'runif'
chainsum : <anonymous>: no visible global function definition for
  'quantile'
infocrit: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm quantile runif
Consider adding
  importFrom("stats", "dnorm", "quantile", "runif")
to your NAMESPACE file.
clusterplots: no visible global function definition for 'par'
clusterplots: no visible global function definition for 'rainbow'
clusterplots: no visible global function definition for 'plot'
clusterplots: no visible global function definition for 'axis'
clusterplots: no visible global function definition for 'lines'
diagplots: no visible global function definition for 'par'
diagplots: no visible global function definition for 'plot'
diagplots: no visible global function definition for 'hist'
tseriesca: no visible global function definition for 'rgamma'
tseriesca: no visible global function definition for 'runif'
tseriesca: no visible global function definition for 'dbeta'
tseriesca: no visible global function definition for 'dgamma'
tseriescm: no visible global function definition for 'rgamma'
tseriescm: no visible global function definition for 'runif'
tseriescm: no visible global function definition for 'dbeta'
tseriescm: no visible global function definition for 'dgamma'
tseriescq: no visible global function definition for 'rgamma'
tseriescq: no visible global function definition for 'runif'
tseriescq: no visible global function definition for 'dbeta'
tseriescq: no visible global function definition for 'dgamma'
Undefined global functions or variables:
  axis dbeta dgamma hist lines par plot rainbow rgamma runif
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "hist", "lines", "par", "plot")
  importFrom("stats", "dbeta", "dgamma", "rgamma", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Note: next may be used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/boclust.Rcheck/00install.out' for details.
BOGest: no visible global function definition for 'read.table'
BOGstat: no visible global function definition for 'phyper'
BOGstat: no visible global function definition for 'wilcox.test'
BOGstat: no visible global function definition for 'p.adjust'
gseaplot: no visible global function definition for 'par'
gseaplot: no visible global function definition for 'plot'
gseaplot: no visible global function definition for 'points'
gseaplot: no visible global function definition for 'axis'
gseaplot: no visible global function definition for 'segments'
hgplot: no visible global function definition for 'par'
hgplot: no visible global function definition for 'barplot'
Undefined global functions or variables:
  axis barplot p.adjust par phyper plot points read.table segments
  wilcox.test
Consider adding
  importFrom("graphics", "axis", "barplot", "par", "plot", "points",
             "segments")
  importFrom("stats", "p.adjust", "phyper", "wilcox.test")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/BonEV.Rcheck/00install.out' for details.
print.boolprob: no visible global function definition for 'plot'
print.boolprof: no visible global function definition for 'plot'
start_msg: no visible global function definition for
  'packageDescription'
Undefined global functions or variables:
  packageDescription plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
Found the following non-portable file paths:
  Boom/inst/include/Models/Hierarchical/PosteriorSamplers/HierarchicalGaussianRegressionAsisSampler.hpp
  Boom/inst/include/Models/PointProcess/PosteriorSamplers/HomogeneousPoissonProcessPosteriorSampler.hpp
  Boom/inst/include/Models/PointProcess/PosteriorSamplers/MarkovModulatedPoissonProcessPosteriorSampler.hpp

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section 'Package structure' in the 'Writing R Extensions' manual.
installed size is 72.3Mb
  sub-directories of 1Mb or more:
    include   2.9Mb
    lib      69.0Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
boostBackend: no visible global function definition for 'model.frame'
findFormulaIn: no visible global function definition for 'as.formula'
kFoldCV: no visible binding for global variable 'par'
predictResponseFromWeightedAverage: no visible global function
  definition for 'weighted.mean'
print.boostr: no visible global function definition for 'str'
Undefined global functions or variables:
  as.formula model.frame par str weighted.mean
Consider adding
  importFrom("graphics", "par")
  importFrom("stats", "as.formula", "model.frame", "weighted.mean")
  importFrom("utils", "str")
to your NAMESPACE file.
'library' or 'require' call to 'lpSolveAPI' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'genetics' 'lpSolveAPI'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
alleleEnrichment: no visible binding for global variable 'na.omit'
alleleEnrichment: no visible binding for global variable 'na.pass'
alleleEnrichment: no visible global function definition for
  'write.table'
alleleEnrichment.data.alleles: no visible binding for global variable
  'na.omit'
alleleEnrichment.data.alleles: no visible binding for global variable
  'na.pass'
alleleEnrichment.data.alleles : <anonymous>: no visible global function
  definition for 'allele.count'
alleleEnrichment.data.alleles: no visible global function definition
  for 'runif'
alleleEnrichment.data.pheno: no visible global function definition for
  'read.table'
alleleEnrichment.lp: no visible global function definition for
  'make.lp'
alleleEnrichment.lp : <anonymous>: no visible global function
  definition for 'set.column'
alleleEnrichment.lp : <anonymous>: no visible global function
  definition for 'set.type'
alleleEnrichment.lp: no visible global function definition for
  'set.objfn'
alleleEnrichment.lp: no visible global function definition for
  'set.constr.type'
alleleEnrichment.lp: no visible global function definition for
  'set.rhs'
alleleEnrichment.lp: no visible global function definition for
  'lp.control'
alleleEnrichment.lp: no visible global function definition for
  'get.variables'
getGenotypes : <anonymous>: no visible global function definition for
  'genotype'
getRefAlleles: no visible global function definition for 'read.table'
getSnpWeights: no visible global function definition for 'read.table'
readMapfile: no visible global function definition for 'read.table'
Undefined global functions or variables:
  allele.count genotype get.variables lp.control make.lp na.omit
  na.pass read.table runif set.column set.constr.type set.objfn set.rhs
  set.type write.table
Consider adding
  importFrom("stats", "na.omit", "na.pass", "runif")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
specdens: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
boot.stepAIC: no visible global function definition for 'update'
boot.stepAIC: no visible binding for global variable 'coef'
boot.stepAIC : <anonymous>: no visible global function definition for
  'anova'
boot.stepAIC: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  anova coef pnorm update
Consider adding
  importFrom("stats", "anova", "coef", "pnorm", "update")
to your NAMESPACE file.
bootSVD: no visible global function definition for 'object.size'
bootSVD : <anonymous> : <anonymous>: no visible global function
  definition for 'quantile'
bootSVD_LD: no visible global function definition for 'txtProgressBar'
bootSVD_LD: no visible global function definition for
  'setTxtProgressBar'
genQ: no visible global function definition for 'rnorm'
getHDpercentiles : <anonymous>: no visible global function definition
  for 'quantile'
getMomentsAndMomentCI: no visible binding for global variable 'var'
os: no visible global function definition for 'object.size'
simEEG: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  object.size quantile rnorm setTxtProgressBar txtProgressBar var
Consider adding
  importFrom("stats", "quantile", "rnorm", "var")
  importFrom("utils", "object.size", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file.
boottol: no visible global function definition for 'setNames'
boottol : shift: no visible global function definition for 'tail'
boottol : shift: no visible global function definition for 'head'
boottol: no visible global function definition for 'na.omit'
vastol: no visible global function definition for 'setNames'
vastol: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  head na.omit setNames tail
Consider adding
  importFrom("stats", "na.omit", "setNames")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
boxplotdou.formula: no visible global function definition for
  'model.frame'
bxpdou: no visible global function definition for 'rainbow'
bxpdou.abox: no visible global function definition for 'rect'
bxpdou.abox: no visible global function definition for 'segments'
bxpdou.abox: no visible global function definition for 'points'
bxpdou.boxplot.stat: no visible global function definition for
  'boxplot'
bxpdou.sheer.color: no visible global function definition for
  'adjustcolor'
bxpdou.stats: no visible global function definition for 'formula'
do.call.with.par: no visible global function definition for
  'modifyList'
only.graphic.pars: no visible global function definition for 'par'
Undefined global functions or variables:
  adjustcolor boxplot formula model.frame modifyList par points rainbow
  rect segments
Consider adding
  importFrom("grDevices", "adjustcolor", "rainbow")
  importFrom("graphics", "boxplot", "par", "points", "rect", "segments")
  importFrom("stats", "formula", "model.frame")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
bPeaksAnalysis: no visible global function definition for 'write.table'
dataReading: no visible global function definition for 'read.table'
dataSmoothing: no visible global function definition for 'filter'
peakDetection: no visible global function definition for 'quantile'
peakDetection: no visible global function definition for 'pdf'
peakDetection: no visible global function definition for 'par'
peakDetection: no visible global function definition for 'plot'
peakDetection: no visible global function definition for 'text'
peakDetection: no visible global function definition for 'abline'
peakDetection: no visible global function definition for 'points'
peakDetection: no visible global function definition for 'dev.off'
peakDetection: no visible global function definition for 'write.table'
peakDrawing: no visible global function definition for 'par'
peakDrawing: no visible global function definition for 'plot'
peakDrawing: no visible global function definition for 'abline'
peakLocation: no visible global function definition for 'read.table'
peakLocation: no visible global function definition for 'pdf'
peakLocation: no visible global function definition for 'barplot'
peakLocation: no visible global function definition for 'dev.off'
peakLocation: no visible global function definition for 'write.table'
Undefined global functions or variables:
  abline barplot dev.off filter par pdf plot points quantile read.table
  text write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "barplot", "par", "plot", "points",
             "text")
  importFrom("stats", "filter", "quantile")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
M0: no visible global function definition for 'fft'
M1: no visible global function definition for 'fft'
bpk: no visible binding for global variable 'dnorm'
bpkde: no visible binding for global variable 'dnorm'
bpkde: no visible binding for global variable 'bw.SJ'
bpkde: no visible global function definition for 'rnorm'
bpkde: no visible global function definition for 'fft'
bpkde: no visible global function definition for 'optimize'
contour.discretize.kernel: no visible global function definition for
  'contour.default'
contour.mvkde: no visible global function definition for
  'contour.default'
image.discretize.kernel: no visible global function definition for
  'image.default'
image.discretize.kernel: no visible global function definition for
  'gray'
image.mvkde: no visible global function definition for 'image.default'
image.mvkde: no visible global function definition for 'gray'
image.mvlinbin: no visible global function definition for 'image'
image.mvlinbin: no visible global function definition for 'gray'
plot.discretize.kernel: no visible global function definition for
  'mtext'
plot.discretize.kernel: no visible global function definition for 'par'
plot.mvkde: no visible global function definition for 'mtext'
plot.mvkde: no visible global function definition for 'par'
plot.mvlinbin: no visible global function definition for 'plot'
plot.mvlinbin: no visible global function definition for 'mtext'
plot.mvlinbin: no visible global function definition for 'par'
Undefined global functions or variables:
  bw.SJ contour.default dnorm fft gray image image.default mtext
  optimize par plot rnorm
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "contour.default", "image", "image.default",
             "mtext", "par", "plot")
  importFrom("stats", "bw.SJ", "dnorm", "fft", "optimize", "rnorm")
to your NAMESPACE file.
Package in Depends field not imported from: 'waveslim'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

const.cor.list: no visible global function definition for
  'wave.correlation'
const.var.list: no visible global function definition for
  'wave.variance'
fitting: no visible global function definition for 'hist'
fitting: no visible global function definition for 'nlm'
fitting: no visible global function definition for 'write.table'
p.value.compute: no visible global function definition for 'pnorm'
p.value.compute: no visible global function definition for 'pt'
random.attack: no visible global function definition for 'runif'
read.convert_1_2: no visible global function definition for
  'read.table'
read.cor.txt: no visible global function definition for 'read.table'
read.var.txt: no visible global function definition for 'read.table'
save.cor.txt: no visible global function definition for 'write.table'
save.var.txt: no visible global function definition for 'write.table'
sim.equadist: no visible global function definition for 'write.table'
small.world: no visible global function definition for 'dist'
small.world: no visible global function definition for 'write.table'
wave.trans: no visible global function definition for 'dwt'
wave.trans: no visible global function definition for 'modwt'
wave.trans: no visible global function definition for 'brick.wall'
Undefined global functions or variables:
  brick.wall dist dwt hist modwt nlm pnorm pt read.table runif
  wave.correlation wave.variance write.table
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "dist", "nlm", "pnorm", "pt", "runif")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
File 'brainwaver/libs/i386/brainwaver.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'connexity_small_world.o'
File 'brainwaver/libs/x64/brainwaver.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'connexity_small_world.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
apply.breaks: no visible binding for global variable 'median'
break.clust: no visible global function definition for 'plot'
break.clust: no visible global function definition for 'median'
breakage.plot: no visible binding for global variable 'median'
breakage.plot: no visible global function definition for 'plot'
breakage.plot: no visible global function definition for 'abline'
breakage.plot: no visible global function definition for 'lm'
find.bottom: no visible global function definition for 'filter'
fit.breakage: no visible global function definition for 'optim'
fit.breakage: no visible global function definition for 'plot'
fit.breakage: no visible global function definition for 'points'
fit.sensitivity.plot: no visible global function definition for
  'contour'
fit.sensitivity.plot: no visible global function definition for
  'points'
fit.sensitivity.plot: no visible global function definition for 'text'
Undefined global functions or variables:
  abline contour filter lm median optim plot points text
Consider adding
  importFrom("graphics", "abline", "contour", "plot", "points", "text")
  importFrom("stats", "filter", "lm", "median", "optim")
to your NAMESPACE file.
Running 'test-all.R' [20s]
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
  > #test_check("breathtestcore", filter = "plot_breathtestfit")
  > test_check("breathtestcore")
  Loading required package: breathtestcore
  -- 1. Failure: read_iris_csv returns with funny identification cleans up (@test_
  iconv(f$study) not equal to "GE-flüssig".
  1/1 mismatches
  x[1]: "GE-flÃ¼ssig"
  y[1]: "GE-flüssig"
  
  == testthat results  ===========================================================
  OK: 351 SKIPPED: 4 FAILED: 1
  1. Failure: read_iris_csv returns with funny identification cleans up (@test_read_iris_csv.R#51) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R     2.9Mb
    doc   2.3Mb
plot,ANY-brob: no visible global function definition for 'plot.default'
plot,ANY-glub: no visible global function definition for 'plot.default'
plot,brob-ANY: no visible global function definition for 'plot.default'
plot,brob-missing: no visible global function definition for
  'plot.default'
plot,glub-ANY: no visible global function definition for 'plot.default'
plot,glub-missing: no visible global function definition for
  'plot.default'
Undefined global functions or variables:
  plot.default
Consider adding
  importFrom("graphics", "plot.default")
to your NAMESPACE file.
Running examples in 'broom-Ex.R' failed
The error most likely occurred in:

> ### Name: gam_tidiers
> ### Title: Tidying methods for a generalized additive model (gam)
> ### Aliases: gam_tidiers tidy.gam glance.gam
> 
> ### ** Examples
> 
> 
> if (require("gam", quietly = TRUE)) {
+     data(kyphosis)
+     g <- gam(Kyphosis ~ s(Age,4) + Number, family = binomial, data = kyphosis)
+     tidy(g)
+     augment(g)
+     glance(g)
+ }
Loaded gam 1.15

Error in 1:ncol(co) : argument of length 0
Calls: tidy -> tidy.lm -> tidy.summary.lm -> fix_data_frame
Execution halted
Running 'test-all.R' [22s]
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
         attr(value, "row.names") <- row.names
         attr(value, "class") <- "data.frame"
         value
     })(null.deviance = 83.2344746889857, `NA` = NULL, check.names = TRUE, fix.empty.names = TRUE, 
         stringsAsFactors = TRUE)
  8: stop(gettextf("arguments imply differing number of rows: %s", paste(unique(nrows), 
         collapse = ", ")), domain = NA)
  
  == testthat results  ===========================================================
  OK: 680 SKIPPED: 12 FAILED: 2
  1. Error: tidy works on gam models (@test-gam.R#6) 
  2. Error: glance works on gam models (@test-gam.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
Foreign function calls to a different package:
  .C("CharArray", ..., PACKAGE = "libOpenBUGS")
  .C("CmdInterpreter", ..., PACKAGE = "libOpenBUGS")
  .C("Integer", ..., PACKAGE = "libOpenBUGS")
  .C("RealArray", ..., PACKAGE = "libOpenBUGS")
  .C("SetTempDir", ..., PACKAGE = "libOpenBUGS")
  .C("SetWorkingDir", ..., PACKAGE = "libOpenBUGS")
Undeclared package in foreign function calls:
   'libOpenBUGS'
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/Brundle.Rcheck/00install.out' for details.
BOOTSimpsonD : BSimpson: no visible global function definition for
  'estSimpsonf'
BOOTSimpsonR : BSimpson: no visible global function definition for
  'estSimpsonf'
CIGLM: no visible global function definition for 'confint'
CIGLM: no visible global function definition for 'univariate_calpha'
CIGLM: no visible global function definition for 'adjusted_calpha'
CInp.default : <anonymous>: no visible global function definition for
  'quantile'
CInp.default: no visible binding for global variable 'median'
R2Bugsdat1w: no visible global function definition for 'model.frame'
R2Bugsdat1w: no visible global function definition for 'model.matrix'
R2Bugsdat1w.data.frame: no visible global function definition for
  'as.formula'
R2Bugsdat1w.data.frame: no visible global function definition for
  'model.frame'
R2Bugsdat1w.data.frame: no visible global function definition for
  'model.matrix'
SCSnp.default: no visible binding for global variable 'median'
modelparm.gamlss: no visible binding for global variable 'coef'
modelparm.gamlss: no visible binding for global variable 'vcov'
modelparm.geeglm: no visible binding for global variable 'coef'
modelparm.geeglm: no visible binding for global variable 'vcov'
simplesimint: no visible global function definition for 'cov2cor'
summary.simplesimint: no visible global function definition for
  'cov2cor'
Undefined global functions or variables:
  adjusted_calpha as.formula coef confint cov2cor estSimpsonf median
  model.frame model.matrix quantile univariate_calpha vcov
Consider adding
  importFrom("stats", "as.formula", "coef", "confint", "cov2cor",
             "median", "model.frame", "model.matrix", "quantile", "vcov")
to your NAMESPACE file.
BSGS.Sample: no visible global function definition for 'rgamma'
BSGS.Simple: no visible global function definition for 'rgamma'
CompWiseGibbs: no visible global function definition for 'runif'
CompWiseGibbs: no visible global function definition for 'rnorm'
CompWiseGibbsSMP: no visible global function definition for 'rbinom'
CompWiseGibbsSMP: no visible global function definition for 'runif'
CompWiseGibbsSMP: no visible global function definition for 'rnorm'
CompWiseGibbsSimple: no visible global function definition for 'runif'
CompWiseGibbsSimple: no visible global function definition for 'rnorm'
CompWiseGibbsSimple: no visible global function definition for 'rgamma'
GroupMH: no visible global function definition for 'runif'
GroupZ.MH: no visible global function definition for 'runif'
Undefined global functions or variables:
  rbinom rgamma rnorm runif
Consider adding
  importFrom("stats", "rbinom", "rgamma", "rnorm", "runif")
to your NAMESPACE file.
bs.design: no visible global function definition for 'spline.des'
bshazard.default: no visible global function definition for
  'model.frame'
bshazard.default: no visible global function definition for
  'model.matrix'
bshazard.default: no visible global function definition for
  'model.response'
bshazard_fit: no visible global function definition for 'aggregate'
bspois: no visible global function definition for 'dpois'
bspois: no visible global function definition for 'var'
bspois: no visible global function definition for 'qnorm'
lines.bshazard: no visible global function definition for 'lines'
plot.bshazard: no visible global function definition for 'plot'
plot.bshazard: no visible global function definition for 'lines'
print.bshazard: no visible global function definition for 'aggregate'
Undefined global functions or variables:
  aggregate dpois lines model.frame model.matrix model.response plot
  qnorm spline.des var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "aggregate", "dpois", "model.frame",
             "model.matrix", "model.response", "qnorm", "var")
to your NAMESPACE file.
plot.bspec: no visible global function definition for 'par'
plot.bspec: no visible global function definition for 'plot'
plot.bspec: no visible global function definition for 'matlines'
plot.bspec: no visible global function definition for 'points'
plot.bspec: no visible global function definition for 'axis'
plot.bspec: no visible global function definition for 'mtext'
plot.bspec: no visible global function definition for 'axTicks'
plot.bspec: no visible global function definition for 'box'
plot.bspecACF: no visible global function definition for 'plot'
plot.bspecACF: no visible global function definition for 'abline'
plot.bspecACF: no visible global function definition for 'matlines'
Undefined global functions or variables:
  abline axTicks axis box matlines mtext par plot points
Consider adding
  importFrom("graphics", "abline", "axTicks", "axis", "box", "matlines",
             "mtext", "par", "plot", "points")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'VGAM' 'quadprog' 'quantreg'
  Please remove these calls from your code.
dqreg: no visible binding for global variable 'median'
dqreg: no visible global function definition for 'median'
log_pdf : q0: no visible global function definition for 'qnorm'
log_pdf : d0: no visible global function definition for 'dnorm'
log_pdf : q0: no visible global function definition for 'qt'
log_pdf : d0: no visible global function definition for 'dt'
log_pdf : q0: no visible global function definition for 'qweibull'
log_pdf : d0: no visible global function definition for 'dweibull'
log_pdf : q0: no visible global function definition for 'qgamma'
log_pdf : d0: no visible global function definition for 'dgamma'
make.B: no visible global function definition for 'qnorm'
make.B: no visible global function definition for 'qweibull'
make.B: no visible global function definition for 'qgamma'
qr_plot: no visible global function definition for 'gray'
qr_plot: no visible binding for global variable 'quantile'
qr_plot: no visible global function definition for 'polygon'
qr_plot: no visible global function definition for 'lines'
qreg: no visible global function definition for 'sd'
qreg: no visible global function definition for 'lm'
qreg: no visible global function definition for 'var'
qreg_spline: no visible global function definition for 'rnorm'
qreg_spline: no visible global function definition for 'var'
qreg_spline: no visible binding for global variable 'quantile'
rootfind: no visible global function definition for 'runif'
Undefined global functions or variables:
  dgamma dnorm dt dweibull gray lines lm median polygon qgamma qnorm qt
  quantile qweibull rnorm runif sd var
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "lines", "polygon")
  importFrom("stats", "dgamma", "dnorm", "dt", "dweibull", "lm",
             "median", "qgamma", "qnorm", "qt", "quantile", "qweibull",
             "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
The following directory looks like a leftover from 'knitr':
  'figure'
Please remove from your package.
alpha.proxy: no visible global function definition for 'filled.contour'
alpha.proxy: no visible global function definition for 'axis'
alpha.proxy: no visible global function definition for 'contour'
factor.model.stat: no visible global function definition for 'quantile'
factor.model.stat: no visible global function definition for 'lsfit'
partial.rainbow: no visible binding for global variable 'rainbow'
var.shrink.eqcor: no visible global function definition for 'var'
var.shrink.eqcor: no visible global function definition for 'quantile'
var.shrink.eqcor: no visible global function definition for 'cov2cor'
Undefined global functions or variables:
  axis contour cov2cor filled.contour lsfit quantile rainbow var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "contour", "filled.contour")
  importFrom("stats", "cov2cor", "lsfit", "quantile", "var")
to your NAMESPACE file.
plot.bursts: no visible global function definition for 'plot'
plot.bursts: no visible global function definition for 'axis'
plot.bursts: no visible global function definition for 'arrows'
Undefined global functions or variables:
  arrows axis plot
Consider adding
  importFrom("graphics", "arrows", "axis", "plot")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'haplo.stats' 'msm'
  Please remove these calls from your code.
fitBVS: no visible global function definition for 'qnorm'
fitBVS: no visible global function definition for 'model.matrix'
fitBVS: no visible global function definition for 'as.formula'
fitBVS: no visible global function definition for 'glm'
fitBVS: no visible global function definition for 'deviance'
fitBVS: no visible global function definition for 'pnorm'
plotBVS: no visible global function definition for 'par'
plotBVS: no visible global function definition for 'image'
plotBVS: no visible global function definition for 'axis'
sampleBVS: no visible global function definition for 'qnorm'
sampleBVS: no visible global function definition for 'pnorm'
sampleBVS: no visible global function definition for 'runif'
summaryBVS: no visible global function definition for 'qnorm'
summaryBVS : inc.prob: no visible global function definition for
  'pnorm'
summaryBVS: no visible global function definition for 'pnorm'
summaryBVS: no visible global function definition for 'model.matrix'
Undefined global functions or variables:
  as.formula axis deviance glm image model.matrix par pnorm qnorm runif
Consider adding
  importFrom("graphics", "axis", "image", "par")
  importFrom("stats", "as.formula", "deviance", "glm", "model.matrix",
             "pnorm", "qnorm", "runif")
to your NAMESPACE file.
makemim: no visible global function definition for 'cor'
sigtestMTC: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  cor p.adjust
Consider adding
  importFrom("stats", "cor", "p.adjust")
to your NAMESPACE file.
Running examples in 'cablecuttr-Ex.R' failed
The error most likely occurred in:

> ### Name: can_i_stream
> ### Title: Query CanIStream.It
> ### Aliases: can_i_stream can_i_stream_id can_i_stream_it
> 
> ### ** Examples
> 
> can_i_stream_id("4eb0173df5f8079d29000002", "purchase")
Error in as.POSIXlt.character(x, tz, ...) : 
  character string is not in a standard unambiguous format
Calls: can_i_stream_id ... as.POSIXct.default -> as.POSIXct -> as.POSIXlt -> as.POSIXlt.character
Execution halted
cabootcrs: no visible global function definition for 'read.table'
cabootcrs: no visible global function definition for 'rmultinom'
cabootcrs: no visible global function definition for 'rpois'
plotca : plotonepic: no visible global function definition for 'qchisq'
plotca : plotonepic: no visible global function definition for
  'dev.new'
plotca : plotonepic: no visible global function definition for 'plot'
plotca : plotonepic: no visible global function definition for 'points'
plotca : plotonepic: no visible global function definition for 'abline'
plotca : plotonepic: no visible global function definition for 'legend'
plotca : plotonepic: no visible global function definition for 'title'
plotca : plotonepic: no visible global function definition for 'lines'
plotca : plotonepic: no visible global function definition for 'text'
plotca: no visible global function definition for 'colours'
plotca: no visible global function definition for 'rainbow'
plotca: no visible global function definition for 'read.table'
Undefined global functions or variables:
  abline colours dev.new legend lines plot points qchisq rainbow
  read.table rmultinom rpois text title
Consider adding
  importFrom("grDevices", "colours", "dev.new", "rainbow")
  importFrom("graphics", "abline", "legend", "lines", "plot", "points",
             "text", "title")
  importFrom("stats", "qchisq", "rmultinom", "rpois")
  importFrom("utils", "read.table")
to your NAMESPACE file.
bcMer: no visible global function definition for 'family'
biasCorrectionBernoulli: no visible global function definition for
  'qlogis'
biasCorrectionBernoulli : <anonymous>: no visible global function
  definition for 'qlogis'
biasCorrectionGaussian: no visible global function definition for
  'model.matrix'
cAIC: no visible global function definition for 'family'
conditionalBootstrap: no visible global function definition for
  'simulate'
conditionalBootstrap : <anonymous>: no visible global function
  definition for 'predict'
conditionalBootstrap: no visible global function definition for 'sigma'
deleteZeroComponents: no visible global function definition for 'lm'
deleteZeroComponents: no visible global function definition for
  'formula'
deleteZeroComponents: no visible global function definition for
  'model.frame'
deleteZeroComponents: no visible global function definition for 'terms'
deleteZeroComponents: no visible global function definition for
  'reformulate'
getcondLL: no visible global function definition for 'family'
getcondLL: no visible global function definition for 'dbinom'
getcondLL: no visible global function definition for 'dpois'
getcondLL: no visible global function definition for 'dnorm'
getcondLL: no visible global function definition for 'sigma'
Undefined global functions or variables:
  dbinom dnorm dpois family formula lm model.frame model.matrix predict
  qlogis reformulate sigma simulate terms
Consider adding
  importFrom("stats", "dbinom", "dnorm", "dpois", "family", "formula",
             "lm", "model.frame", "model.matrix", "predict", "qlogis",
             "reformulate", "sigma", "simulate", "terms")
to your NAMESPACE file.
Package which this enhances but not available for checking: 'FastRWeb'
makemar : predictions: no visible global function definition for
  'rbinom'
mice.impute.rfcat : <anonymous>: no visible global function definition
  for 'predict'
mice.impute.rfcont: no visible global function definition for 'predict'
mice.impute.rfcont: no visible global function definition for 'rnorm'
simdata: no visible global function definition for 'rbinom'
simdata: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  predict rbinom rnorm
Consider adding
  importFrom("stats", "predict", "rbinom", "rnorm")
to your NAMESPACE file.
calibrate: no visible global function definition for 'lines'
calibrate: no visible global function definition for 'text'
canocor: no visible global function definition for 'cor'
circle: no visible global function definition for 'points'
dlines: no visible global function definition for 'lines'
origin: no visible global function definition for 'par'
origin: no visible global function definition for 'lines'
rda: no visible global function definition for 'cor'
rda: no visible global function definition for 'princomp'
rda: no visible global function definition for 'var'
textxy: no visible global function definition for 'text'
Undefined global functions or variables:
  cor lines par points princomp text var
Consider adding
  importFrom("graphics", "lines", "par", "points", "text")
  importFrom("stats", "cor", "princomp", "var")
to your NAMESPACE file.
EK.eqn10.supp: no visible global function definition for 'integrate'
MH: no visible global function definition for 'rmvnorm'
MH: no visible global function definition for 'runif'
computer.model: no visible global function definition for 'rmvnorm'
create.new.toy.datasets: no visible global function definition for
  'rnorm'
model.inadequacy: no visible global function definition for 'rmvnorm'
prob.psi1: no visible global function definition for 'dmvnorm'
prob.psi2: no visible global function definition for 'dmvnorm'
prob.theta: no visible global function definition for 'dmvnorm'
sample.theta: no visible global function definition for 'rmvnorm'
stage1: no visible global function definition for 'optim'
stage2: no visible global function definition for 'optim'
stage3: no visible global function definition for 'optim'
Undefined global functions or variables:
  dmvnorm integrate optim rmvnorm rnorm runif
Consider adding
  importFrom("stats", "integrate", "optim", "rnorm", "runif")
to your NAMESPACE file.
File 'camel/libs/i386/camel.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'SFGen.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'SFGen.o'
File 'camel/libs/x64/camel.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'SFGen.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'SFGen.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
CAM: no visible global function definition for 'object.size'
CAM: no visible global function definition for 'as'
computeScoreMat: no visible global function definition for 'combn'
computeScoreMat: no visible global function definition for 'var'
computeScoreMatParallel: no visible global function definition for
  'var'
selLm: no visible global function definition for 'lm'
selLm: no visible global function definition for 'coef'
train_gam: no visible global function definition for 'formula'
train_lasso: no visible global function definition for 'predict'
train_linear: no visible global function definition for 'lm'
Undefined global functions or variables:
  as coef combn formula lm object.size predict var
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "coef", "formula", "lm", "predict", "var")
  importFrom("utils", "combn", "object.size")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
bootstrapCapwire: no visible global function definition for 'quantile'
drawCapRatesBeta : <anonymous>: no visible global function definition
  for 'rbeta'
drawCapRatesExp : <anonymous>: no visible global function definition
  for 'rexp'
drawCapRatesGamma : <anonymous>: no visible global function definition
  for 'rgamma'
drawCapRatesGeom : <anonymous>: no visible global function definition
  for 'rgeom'
drawCapRatesUnif : <anonymous>: no visible global function definition
  for 'runif'
partitionCountData : find.3.way.partitions: no visible global function
  definition for 'dmultinom'
Undefined global functions or variables:
  dmultinom quantile rbeta rexp rgamma rgeom runif
Consider adding
  importFrom("stats", "dmultinom", "quantile", "rbeta", "rexp", "rgamma",
             "rgeom", "runif")
to your NAMESPACE file.
Sub.pair: no visible global function definition for 'qnorm'
as.record: no visible global function definition for 'capture.output'
estN: no visible global function definition for 'sd'
estN: no visible global function definition for 'qnorm'
estN.bootstrap: no visible global function definition for 'runif'
Undefined global functions or variables:
  capture.output qnorm runif sd
Consider adding
  importFrom("stats", "qnorm", "runif", "sd")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
abundance: no visible global function definition for 'D'
Undefined global functions or variables:
  D
Consider adding
  importFrom("stats", "D")
to your NAMESPACE file.
barplotEQR: no visible global function definition for 'barplot'
barplotEQR: no visible global function definition for 'abline'
barplotEQR: no visible global function definition for 'par'
barplotEQR: no visible global function definition for 'text'
Undefined global functions or variables:
  abline barplot par text
Consider adding
  importFrom("graphics", "abline", "barplot", "par", "text")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'MASS' 'RSQLite' 'grid' 'sm'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package required but not available: 'OpenCL'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
MDR.high.forward1: no visible global function definition for 'combn'
MDR.sing.mod1: no visible global function definition for 'combn'
MDR.sing.mod1: no visible global function definition for
  'complete.cases'
MDR.sing.mod1: no visible global function definition for 'lm'
MDR.sing.mod1: no visible global function definition for 'aov'
MDR.sing.mod1: no visible global function definition for 'anova'
MDR.stage.forward1: no visible global function definition for 'combn'
MDR.stage.forward1: no visible global function definition for
  'complete.cases'
MDR.stage.forward1: no visible global function definition for 'lm'
MDR.stage.forward1: no visible global function definition for 'resid'
MDR.stage.forward1: no visible global function definition for 'pf'
MDR_forward1: no visible global function definition for
  'complete.cases'
MDR_forward1: no visible global function definition for 'lm'
MDR_forward1: no visible global function definition for 'aov'
low.anova: no visible global function definition for 'complete.cases'
low.anova: no visible global function definition for 'lm'
sing.mod1: no visible global function definition for 'combn'
sing.mod1: no visible global function definition for 'complete.cases'
sing.mod1: no visible global function definition for 'lm'
sing.mod1: no visible global function definition for 'pf'
Undefined global functions or variables:
  anova aov combn complete.cases lm pf resid
Consider adding
  importFrom("stats", "anova", "aov", "complete.cases", "lm", "pf",
             "resid")
  importFrom("utils", "combn")
to your NAMESPACE file.
colAUC: no visible global function definition for 'plot'
colAUC: no visible global function definition for 'title'
colAUC: no visible global function definition for 'abline'
colAUC: no visible global function definition for 'legend'
colAUC: no visible global function definition for 'lines'
read.ENVI: no visible global function definition for 'read.table'
read.gif: no visible global function definition for 'download.file'
read.gif: no visible global function definition for 'rgb'
runmad: no visible global function definition for 'runmed'
runmad: no visible binding for global variable 'mad'
runquantile: no visible binding for global variable 'quantile'
runsd: no visible binding for global variable 'sd'
sample.split: no visible global function definition for 'runif'
write.gif: no visible global function definition for 'gray'
write.gif: no visible global function definition for 'colorRampPalette'
write.gif: no visible global function definition for 'col2rgb'
Undefined global functions or variables:
  abline col2rgb colorRampPalette download.file gray legend lines mad
  plot quantile read.table rgb runif runmed sd title
Consider adding
  importFrom("grDevices", "col2rgb", "colorRampPalette", "gray", "rgb")
  importFrom("graphics", "abline", "legend", "lines", "plot", "title")
  importFrom("stats", "mad", "quantile", "runif", "runmed", "sd")
  importFrom("utils", "download.file", "read.table")
to your NAMESPACE file.
mi.inference: no visible binding for global variable 'var'
mi.inference: no visible global function definition for 'qt'
mi.inference: no visible global function definition for 'pt'
Undefined global functions or variables:
  pt qt var
Consider adding
  importFrom("stats", "pt", "qt", "var")
to your NAMESPACE file.
ctab: no visible global function definition for 'xtabs'
mob.eqmain: no visible global function definition for 'model.matrix'
mob.qi: no visible global function definition for 'C'
mob.qi: no visible binding for global variable 'contr.treatment'
mob.rc1: no visible global function definition for 'C'
mob.rc1: no visible binding for global variable 'contr.treatment'
mob.rc1: no visible global function definition for 'model.matrix'
mob.symint: no visible global function definition for 'model.matrix'
print.ctab: no visible global function definition for 'ftable'
Undefined global functions or variables:
  C contr.treatment ftable model.matrix xtabs
Consider adding
  importFrom("stats", "C", "contr.treatment", "ftable", "model.matrix",
             "xtabs")
to your NAMESPACE file.
binParamPosteriorSampling: no visible global function definition for
  'rbeta'
bindagMonteCarloCausalEffect: no visible global function definition for
  'runif'
getBinDAGModelData: no visible global function definition for 'runif'
logitDist: no visible global function definition for 'runif'
logitDist: no visible global function definition for 'rnorm'
simulateWitnessModel: no visible global function definition for 'runif'
summary.covsearch: no visible global function definition for 'quantile'
summary.iv: no visible global function definition for 'quantile'
summary.wpp: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile rbeta rnorm runif
Consider adding
  importFrom("stats", "quantile", "rbeta", "rnorm", "runif")
to your NAMESPACE file.
BinaryCut: no visible global function definition for 'quantile'
CleanNaFromContinuousFunction: no visible global function definition
  for 'median'
CleanNaFromContinuousFunction: no visible global function definition
  for 'na.omit'
GetMetadata.Connect: no visible global function definition for
  'dbGetQuery'
GetRawData.Connect: no visible global function definition for
  'dbGetQuery'
Linearity: no visible global function definition for 'median'
PredictivePowerCv: no visible global function definition for 'sd'
ReadCausataCsv: no visible global function definition for 'read.csv'
ToPmml.GlmnetModelDefinition: no visible global function definition for
  'coef'
ToPmml.GlmnetModelDefinition: no visible global function definition for
  'terms.formula'
ValidateModel: no visible global function definition for 'predict'
predict.GlmnetModelDefinition: no visible global function definition
  for 'model.matrix'
predict.GlmnetModelDefinition: no visible binding for global variable
  'contrasts'
predict.GlmnetModelDefinition: no visible global function definition
  for 'predict'
Undefined global functions or variables:
  coef contrasts dbGetQuery median model.matrix na.omit predict
  quantile read.csv sd terms.formula
Consider adding
  importFrom("stats", "coef", "contrasts", "median", "model.matrix",
             "na.omit", "predict", "quantile", "sd", "terms.formula")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
estim.regul: warning in matrix(res, nc = length(grid2)): partial
  argument match of 'nc' to 'ncol'
comput: no visible global function definition for 'cor'
img.estim.regul: no visible global function definition for 'par'
img.estim.regul: no visible global function definition for 'image'
img.estim.regul: no visible global function definition for
  'heat.colors'
img.estim.regul: no visible global function definition for 'axis'
img.estim.regul: no visible global function definition for 'box'
img.matcor: no visible global function definition for 'par'
img.matcor: no visible global function definition for 'image'
img.matcor: no visible global function definition for 'box'
img.matcor: no visible global function definition for 'abline'
img.matcor: no visible global function definition for 'layout'
loo: no visible global function definition for 'cor'
matcor: no visible global function definition for 'cor'
plt.cc: no visible global function definition for 'par'
plt.cc: no visible global function definition for 'layout'
plt.indiv: no visible global function definition for 'plot'
plt.indiv: no visible global function definition for 'text'
plt.indiv: no visible global function definition for 'abline'
plt.var: no visible global function definition for 'plot'
plt.var: no visible global function definition for 'points'
plt.var: no visible global function definition for 'text'
plt.var: no visible global function definition for 'abline'
plt.var: no visible global function definition for 'lines'
rcc: no visible global function definition for 'var'
rcc: no visible global function definition for 'cov'
Undefined global functions or variables:
  abline axis box cor cov heat.colors image layout lines par plot
  points text var
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "abline", "axis", "box", "image", "layout",
             "lines", "par", "plot", "points", "text")
  importFrom("stats", "cor", "cov", "var")
to your NAMESPACE file.
ccd.sequential: no visible global function definition for 'qchisq'
dominate.random.sample: no visible global function definition for
  'runif'
draw.circle: no visible global function definition for 'polygon'
juggle2: no visible global function definition for 'rbinom'
plot.cccd: no visible global function definition for 'gray'
plot.cccd: no visible global function definition for 'plot'
plot.cccd: no visible global function definition for 'points'
plot.cccdClassifier: no visible global function definition for 'points'
plot.cccdClassifier: no visible global function definition for 'plot'
plot.ccd: no visible global function definition for 'plot'
Undefined global functions or variables:
  gray plot points polygon qchisq rbinom runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "plot", "points", "polygon")
  importFrom("stats", "qchisq", "rbinom", "runif")
to your NAMESPACE file.
VD: no visible binding for global variable 'var'
stratcc : <anonymous>: no visible global function definition for
  'hclust'
stratcc : <anonymous>: no visible global function definition for
  'cutree'
Undefined global functions or variables:
  cutree hclust var
Consider adding
  importFrom("stats", "cutree", "hclust", "var")
to your NAMESPACE file.
ccda.main: no visible global function definition for 'hclust'
ccda.main: no visible global function definition for 'dist'
ccda.main: no visible global function definition for 'cutree'
ccda.main: no visible global function definition for 'quantile'
percentage: no visible global function definition for 'predict'
plotccda.cluster: no visible global function definition for 'par'
plotccda.cluster: no visible global function definition for 'plot'
plotccda.q95: no visible global function definition for 'par'
plotccda.q95: no visible global function definition for 'plot'
plotccda.q95: no visible global function definition for 'density'
plotccda.q95: no visible global function definition for 'abline'
plotccda.q95: no visible global function definition for 'legend'
plotccda.q95: no visible global function definition for 'strwidth'
plotccda.q95: no visible global function definition for 'strheight'
plotccda.results: no visible global function definition for 'par'
plotccda.results: no visible global function definition for 'plot'
plotccda.results: no visible global function definition for 'axis'
plotccda.results: no visible global function definition for 'lines'
plotccda.results: no visible global function definition for 'legend'
plotccda.results: no visible global function definition for 'strwidth'
plotccda.results: no visible global function definition for 'strheight'
Undefined global functions or variables:
  abline axis cutree density dist hclust legend lines par plot predict
  quantile strheight strwidth
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "plot", "strheight", "strwidth")
  importFrom("stats", "cutree", "density", "dist", "hclust", "predict",
             "quantile")
to your NAMESPACE file.
dcc.est: no visible global function definition for 'cov'
dcc.estimation1: no visible global function definition for 'optim'
dcc.estimation2: no visible global function definition for
  'constrOptim'
dlc: no visible global function definition for 'cov'
eccc.estimation: no visible global function definition for 'optim'
hh.test : uni.garch : uni.garch.est : garch.ll: no visible global
  function definition for 'dnorm'
hh.test : uni.garch : uni.garch.est: no visible global function
  definition for 'optim'
hh.test: no visible global function definition for 'lm'
hh.test: no visible global function definition for 'pchisq'
jb.test: no visible global function definition for 'pchisq'
ljung.box.test: no visible global function definition for 'pchisq'
nt.test : uni.garch : uni.garch.est : garch.ll: no visible global
  function definition for 'dnorm'
nt.test : uni.garch : uni.garch.est: no visible global function
  definition for 'optim'
nt.test: no visible global function definition for 'lm'
nt.test: no visible global function definition for 'pchisq'
rob.kr: no visible global function definition for 'quantile'
rob.sk: no visible global function definition for 'quantile'
Undefined global functions or variables:
  constrOptim cov dnorm lm optim pchisq quantile
Consider adding
  importFrom("stats", "constrOptim", "cov", "dnorm", "lm", "optim",
             "pchisq", "quantile")
to your NAMESPACE file.
cor.by.class: no visible global function definition for 'cor'
create.CCM: no visible global function definition for 'cor'
create.CCM: no visible binding for global variable 'cor'
plot.CCM: no visible global function definition for 'boxplot'
Undefined global functions or variables:
  boxplot cor
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "cor")
to your NAMESPACE file.
p.Roy: no visible global function definition for 'pf'
p.asym: no visible global function definition for 'pf'
p.perm: no visible global function definition for 'cancor'
plt.asym: no visible global function definition for 'qf'
plt.asym: no visible global function definition for 'plot'
plt.asym: no visible global function definition for 'df'
plt.asym: no visible global function definition for 'abline'
plt.perm: no visible global function definition for 'hist'
plt.perm: no visible global function definition for 'mtext'
plt.perm: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline cancor df hist mtext pf plot qf
Consider adding
  importFrom("graphics", "abline", "hist", "mtext", "plot")
  importFrom("stats", "cancor", "df", "pf", "qf")
to your NAMESPACE file.
'library' or 'require' call to 'bitops' which was already attached by Depends.
  Please remove these calls from your code.
bw: no visible global function definition for 'optimize'
Undefined global functions or variables:
  optimize
Consider adding
  importFrom("stats", "optimize")
to your NAMESPACE file.
CDFt: no visible global function definition for 'ecdf'
CDFt: no visible global function definition for 'quantile'
CDFt: no visible global function definition for 'approx'
KolmogorovSmirnov: no visible global function definition for 'ecdf'
KolmogorovSmirnov: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx ecdf quantile
Consider adding
  importFrom("stats", "approx", "ecdf", "quantile")
to your NAMESPACE file.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.2Mb
plot.CellularAutomaton: no visible global function definition for
  'image'
Undefined global functions or variables:
  image
Consider adding
  importFrom("graphics", "image")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'gplots' 'minpack.lm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
erf: no visible global function definition for 'pnorm'
fitVolDist: no visible global function definition for 'nls.lm'
fitVolDist: no visible global function definition for 'nls.lm.control'
fitVolDist: no visible global function definition for 'optim'
fitVolDist: no visible global function definition for 'relist'
print.fitVolDist: no visible global function definition for 'coef'
print.fitVolDist: no visible global function definition for 'deviance'
print.fitVolDist: no visible global function definition for 'pt'
print.fitVolDist: no visible global function definition for
  'printCoefmat'
resFunChiSq: no visible global function definition for 'relist'
volEq7: no visible global function definition for 'integrate'
Undefined global functions or variables:
  coef deviance integrate nls.lm nls.lm.control optim pnorm
  printCoefmat pt relist
Consider adding
  importFrom("stats", "coef", "deviance", "integrate", "optim", "pnorm",
             "printCoefmat", "pt")
  importFrom("utils", "relist")
to your NAMESPACE file.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.0Mb
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/cem.Rcheck/00install.out' for details.
cenNID: no visible global function definition for 'sd'
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Unexported objects imported by ':::' calls:
  'copula:::dCdu' 'copula:::fitCopStart'
  See the note in ?`:::` about the use of this operator.
MomNIT: no visible global function definition for 'dnorm'
MomNIT: no visible global function definition for 'pnorm'
cdfNI: no visible global function definition for 'pnorm'
cdfNI: no visible global function definition for 'pt'
em.cens: no visible global function definition for 'lm'
em.cens: no visible global function definition for 'coefficients'
em.cens : ft: no visible global function definition for 'dt'
em.cens : ft: no visible global function definition for 'pt'
em.cens: no visible global function definition for 'optimize'
em.cens: no visible global function definition for 'dnorm'
em.cens: no visible global function definition for 'pnorm'
em.cens: no visible global function definition for 'sd'
Undefined global functions or variables:
  coefficients dnorm dt lm optimize pnorm pt sd
Consider adding
  importFrom("stats", "coefficients", "dnorm", "dt", "lm", "optimize",
             "pnorm", "pt", "sd")
to your NAMESPACE file.
CM: no visible global function definition for 'sd'
Erf: no visible global function definition for 'pnorm'
Erfc: no visible global function definition for 'pnorm'
boot.Cenarma: no visible global function definition for 'coef'
boot.Cenarma: no visible global function definition for 'arima.sim'
cenarma: no visible global function definition for 'arima'
cenarma: no visible global function definition for 'coef'
cenarma: no visible global function definition for 'ARMAacf'
cenarma: no visible global function definition for 'var'
plot.cents: no visible global function definition for 'plot'
plot.cents: no visible global function definition for 'segments'
plot.cents: no visible global function definition for 'rgb'
plot.cents: no visible global function definition for 'points'
rcarma: no visible global function definition for 'arima.sim'
rcarma: no visible global function definition for 'quantile'
scenNID: no visible global function definition for 'sd'
se.Cenarma: no visible global function definition for 'coef'
se.Cenarma: no visible global function definition for 'sd'
Undefined global functions or variables:
  ARMAacf arima arima.sim coef plot pnorm points quantile rgb sd
  segments var
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "plot", "points", "segments")
  importFrom("stats", "ARMAacf", "arima", "arima.sim", "coef", "pnorm",
             "quantile", "sd", "var")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'igraph' 'snow'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
select_lambda: no visible global function definition for 'median'
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
cf_estimate_quantiles: no visible global function definition for
  'qnorm'
Undefined global functions or variables:
  qnorm
Consider adding
  importFrom("stats", "qnorm")
to your NAMESPACE file.
Found the following hidden files and directories:
  .project
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
get.switch.time: warning in uniroot(f = switch.func, int =
  c(last_boundary, boundary), lower = last_boundary, upper = boundary,
  maxiter = 1000, tol = tol, e): partial argument match of 'int' to
  'interval'
plot.cggd: warning in axis(4, at = b[nrow(b), ], label = paste(cnums),
  cex = 0.8, adj = 0): partial argument match of 'label' to 'labels'
plot.cggd: no visible global function definition for 'gen.beta'
plotCVcggd: no visible binding for global variable 'cv'
plotCVcggd: no visible binding for global variable 'cv.error'
predict.cggd: no visible binding for global variable 'max.tk'
predict.cggd: no visible global function definition for 'gen.beta'
Undefined global functions or variables:
  cv cv.error gen.beta max.tk
S3 methods shown with full name in documentation object 'plot.cggd':
  'plot.cggd'

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.
CGH.fused.lasso.one.fast: no visible global function definition for
  'lowess'
L2L1ExpandFit: no visible global function definition for
  'L2L1PathExtract'
consensusFDR: no visible global function definition for 'pbinom'
my.mad: no visible global function definition for 'median'
output.cghFLasso: no visible global function definition for
  'write.table'
plot.CGH.FL.All: no visible global function definition for 'plot'
plot.CGH.FL.All: no visible global function definition for 'segments'
plot.CGH.FL.All: no visible global function definition for 'text'
plot.CGH.FL.Consensus: no visible global function definition for
  'rainbow'
plot.CGH.FL.Consensus: no visible global function definition for 'plot'
plot.CGH.FL.Consensus: no visible global function definition for
  'segments'
plot.CGH.FL.Consensus: no visible global function definition for 'gray'
plot.CGH.FL.Consensus: no visible global function definition for 'text'
plot.CGH.FL.Single: no visible global function definition for 'plot'
plot.CGH.FL.Single: no visible global function definition for 'gray'
plot.CGH.FL.Single: no visible global function definition for
  'segments'
plot.CGH.FL.Single: no visible global function definition for 'text'
plot.cghFLasso: no visible global function definition for 'plot'
plot.cghFLasso: no visible global function definition for 'gray'
plot.cghFLasso: no visible global function definition for 'abline'
plot.cghFLasso: no visible global function definition for 'points'
segment.score: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  L2L1PathExtract abline gray lowess median pbinom plot pnorm points
  rainbow segments text write.table
Consider adding
  importFrom("grDevices", "gray", "rainbow")
  importFrom("graphics", "abline", "plot", "points", "segments", "text")
  importFrom("stats", "lowess", "median", "pbinom", "pnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'plot.cghFLasso':
  'plot.cghFLasso'

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

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.
sw.plot : <anonymous>: no visible global function definition for
  'median'
sw.plot : <anonymous>: no visible global function definition for 'mad'
sw.plot : my.line: no visible global function definition for 'lines'
sw.plot : island.line: no visible global function definition for
  'lines'
sw.plot: no visible global function definition for 'plot'
sw.plot: no visible global function definition for 'rug'
sw.plot: no visible global function definition for 'axis'
sw.plot: no visible global function definition for 'mtext'
sw.plot: no visible global function definition for 'abline'
sw.plot: no visible global function definition for 'points'
sw.rob : <anonymous>: no visible global function definition for
  'median'
sw.rob : <anonymous>: no visible global function definition for 'mad'
sw.threshold : <anonymous>: no visible global function definition for
  'median'
sw.threshold : <anonymous>: no visible global function definition for
  'mad'
Undefined global functions or variables:
  abline axis lines mad median mtext plot points rug
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "mtext", "plot",
             "points", "rug")
  importFrom("stats", "mad", "median")
to your NAMESPACE file.
CGPEst: no visible global function definition for 'dist'
CGPEst : PSI: no visible global function definition for 'dist'
CGPEst : Stand_PSI: no visible global function definition for 'dist'
CGPEst : Fop: no visible global function definition for 'optim'
CGPEst: no visible global function definition for 'optim'
plotCGP: no visible global function definition for 'plot'
Undefined global functions or variables:
  dist optim plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dist", "optim")
to your NAMESPACE file.
Hartree2Joule: no visible binding for global variable
  'universalConstants'
Hertz2Joule: no visible binding for global variable
  'universalConstants'
Joule2Hartree: no visible binding for global variable
  'universalConstants'
Joule2Hertz: no visible binding for global variable
  'universalConstants'
Joule2Kelvin: no visible binding for global variable
  'universalConstants'
Joule2centimeterMinusOne: no visible binding for global variable
  'universalConstants'
Joule2electronVolt: no visible binding for global variable
  'universalConstants'
Joule2kiloCaloriePerMole: no visible binding for global variable
  'universalConstants'
Joule2kiloJoulePerMole: no visible binding for global variable
  'universalConstants'
KMC: no visible global function definition for 'runif'
Kelvin2Joule: no visible binding for global variable
  'universalConstants'
LandauZener: no visible binding for global variable
  'universalConstants'
LandauZenerProbability: no visible binding for global variable
  'universalConstants'
Marcus: no visible binding for global variable 'universalConstants'
MarcusLevichJortner: no visible binding for global variable
  'universalConstants'
centimeterMinusOne2Joule: no visible binding for global variable
  'universalConstants'
electronVolt2Joule: no visible binding for global variable
  'universalConstants'
kiloCaloriePerMole2Joule: no visible binding for global variable
  'universalConstants'
kiloJoulePerMole2Joule: no visible binding for global variable
  'universalConstants'
Undefined global functions or variables:
  runif universalConstants
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Note: next may be used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/CHAT.Rcheck/00install.out' for details.
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.
'library' or 'require' call to 'RCurl' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'RCurl' 'bitops' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
createDataset: no visible global function definition for 'read.csv'
createInventory: no visible global function definition for 'read.csv'
downloadMaster: no visible global function definition for
  'getURLContent'
downloadMaster: no visible global function definition for 'read.csv'
downloadMaster: no visible global function definition for 'write.csv'
getMissingScrape: no visible global function definition for 'read.csv'
readLocalMaster: no visible global function definition for 'read.csv'
readMonthlyCsv: no visible global function definition for 'read.csv'
scrapeToCsv: no visible global function definition for 'download.file'
writeData: no visible global function definition for 'write.csv'
writeGhcn: no visible global function definition for 'write.table'
writeInventory: no visible global function definition for 'write.table'
writeMonthlyStations: no visible global function definition for
  'read.csv'
writeMonthlyStations: no visible global function definition for
  'write.csv'
Undefined global functions or variables:
  download.file getURLContent read.csv write.csv write.table
Consider adding
  importFrom("utils", "download.file", "read.csv", "write.csv",
             "write.table")
to your NAMESPACE file.
Running 'test-all.R' [25s]
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
  checkpoint: Part of the Reproducible R Toolkit from Microsoft
  https://mran.microsoft.com/documents/rro/reproducibility/
  -- 1. Failure: is.404 (@test-0-is-404.R#11)  -----------------------------------
  is.404("http://mran.microsoft.com/snapshot") isn't false.
  
  -- 2. Failure: is.404 (@test-0-is-404.R#14)  -----------------------------------
  is.404("http://mran.microsoft.com/snapshot/2015-05-01") isn't false.
  
  == testthat results  ===========================================================
  OK: 60 SKIPPED: 7 FAILED: 2
  1. Failure: is.404 (@test-0-is-404.R#11) 
  2. Failure: is.404 (@test-0-is-404.R#14) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   2.5Mb
cp.scree: no visible global function definition for 'plot'
dcm.design: no visible global function definition for 'flush.console'
dcm.design: no visible global function definition for 'model.matrix'
dcm.design.cand: no visible global function definition for
  'flush.console'
dcm.design.cand: no visible global function definition for
  'model.matrix'
dcm.design.sort: no visible global function definition for 'runif'
get.file: no visible global function definition for 'read.table'
pw.eval: no visible global function definition for 'sd'
tradeoff.des: no visible global function definition for 'flush.console'
tradeoff.des: no visible global function definition for 'sd'
write.tab: no visible global function definition for 'write.table'
Undefined global functions or variables:
  flush.console model.matrix plot read.table runif sd write.table
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "model.matrix", "runif", "sd")
  importFrom("utils", "flush.console", "read.table", "write.table")
to your NAMESPACE file.
choicemodelr : drawDelta: no visible global function definition for
  'rnorm'
choicemodelr : mnlRwMetropOnce: no visible global function definition
  for 'rnorm'
choicemodelr : mnlRwMetropOnce: no visible global function definition
  for 'runif'
choicemodelr : rmultireg: no visible global function definition for
  'rnorm'
choicemodelr : rwishart: no visible global function definition for
  'rchisq'
choicemodelr : rwishart: no visible global function definition for
  'rnorm'
choicemodelr : fsh: no visible global function definition for
  'flush.console'
choicemodelr: no visible global function definition for 'matplot'
choicemodelr: no visible global function definition for 'write.table'
Undefined global functions or variables:
  flush.console matplot rchisq rnorm runif write.table
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "rchisq", "rnorm", "runif")
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE file.
Qh.times.dhyper: no visible global function definition for 'var'
Qh.times.dhyper: no visible global function definition for 'pnorm'
Qh.times.dhyper: no visible global function definition for 'dhyper'
TDiM: no visible global function definition for 'sd'
choplump.default: no visible global function definition for
  'flush.console'
choplump.formula: no visible global function definition for 'terms'
cm.compact: no visible global function definition for 'dhyper'
Undefined global functions or variables:
  dhyper flush.console pnorm sd terms var
Consider adding
  importFrom("stats", "dhyper", "pnorm", "sd", "terms", "var")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
parse_counts: 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.
combineToSingleMatrix: no visible global function definition for
  'read.table'
combineToSingleMatrix: no visible global function definition for
  'write.table'
compareCIM: no visible global function definition for 'sd'
correctData: no visible global function definition for 'wd'
correctData: no visible global function definition for 'threshold'
correctData: no visible binding for global variable 'madmad'
correctData: no visible global function definition for 'wr'
Undefined global functions or variables:
  madmad read.table sd threshold wd wr write.table
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Found the following significant warnings:
  Note: possible error in 'log.likelihood(list(latent.space.pos.prop, ': unused argument (edge.list.rows[[dd]]) 
  Note: possible error in 'log.likelihood(list(latent.space.pos.hold, ': unused argument (edge.list.rows[[dd]]) 
See 'd:/Rcompile/CRANpkg/local/3.5/CIDnetworks.Rcheck/00install.out' for details.
cin: no visible global function definition for 'pnorm'
gammaHRF: no visible global function definition for 'dgamma'
intertest: no visible global function definition for 'pnorm'
truncSum: no visible global function definition for 'spline'
Undefined global functions or variables:
  dgamma pnorm spline
Consider adding
  importFrom("stats", "dgamma", "pnorm", "spline")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/CircE.Rcheck/00install.out' for details.
CircE.Plot: no visible global function definition for 'dev.new'
CircE.Plot: no visible global function definition for 'par'
CircE.Plot: no visible global function definition for 'plot'
CircE.Plot: no visible global function definition for 'axis'
CircE.Plot: no visible global function definition for 'title'
CircE.Plot: no visible global function definition for 'text'
CircE.Plot: no visible global function definition for 'points'
CircE.Plot: no visible global function definition for 'abline'
CircE.Plot: no visible global function definition for 'segments'
Undefined global functions or variables:
  abline axis dev.new par plot points segments text title
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axis", "par", "plot", "points",
             "segments", "text", "title")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/CircStats.Rcheck/00install.out' for details.
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'boot'
  Please remove these calls from your code.
cit.assignBcmst: no visible binding for global variable 'citbcmst'
cit.assignBcmst : <anonymous>: no visible global function definition
  for 'median'
cit.assignBcmst: no visible global function definition for 'prcomp'
cit.assignBcmst: no visible global function definition for 'par'
cit.assignBcmst: no visible global function definition for 'lines'
cit.assignBcmst: no visible global function definition for 'legend'
cit.centroids : <anonymous>: no visible global function definition for
  'median'
cit.centroids : <anonymous>: no visible global function definition for
  'var'
cit.dist: no visible global function definition for 'dist'
cit.dist: no visible global function definition for 'as.dist'
cit.dist: no visible global function definition for 'cor'
cit.distToCentroids: no visible global function definition for
  'quantile'
cit.distToCentroids : <anonymous>: no visible global function
  definition for 'median'
cit.distToCentroids : <anonymous>: no visible global function
  definition for 'mad'
Undefined global functions or variables:
  as.dist citbcmst cor dist legend lines mad median par prcomp quantile
  var
Consider adding
  importFrom("graphics", "legend", "lines", "par")
  importFrom("stats", "as.dist", "cor", "dist", "mad", "median",
             "prcomp", "quantile", "var")
to your NAMESPACE file.
cit.assignCcmst: no visible binding for global variable 'citccmst'
cit.assignCcmst : <anonymous>: no visible global function definition
  for 'median'
cit.assignCcmst : median.na: no visible global function definition for
  'median'
cit.assignCcmst: no visible global function definition for 'prcomp'
cit.assignCcmst: no visible global function definition for 'par'
cit.assignCcmst: no visible global function definition for 'lines'
cit.assignCcmst: no visible global function definition for 'legend'
cit.centroids : <anonymous>: no visible global function definition for
  'median'
cit.centroids : <anonymous>: no visible global function definition for
  'var'
cit.dist: no visible global function definition for 'dist'
cit.dist: no visible global function definition for 'as.dist'
cit.dist: no visible global function definition for 'cor'
cit.distToCentroids: no visible global function definition for
  'quantile'
cit.distToCentroids : <anonymous>: no visible global function
  definition for 'median'
cit.distToCentroids : <anonymous>: no visible global function
  definition for 'mad'
Undefined global functions or variables:
  as.dist citccmst cor dist legend lines mad median par prcomp quantile
  var
Consider adding
  importFrom("graphics", "legend", "lines", "par")
  importFrom("stats", "as.dist", "cor", "dist", "mad", "median",
             "prcomp", "quantile", "var")
to your NAMESPACE file.
CityPlot: no visible global function definition for 'read.table'
CityPlot: no visible global function definition for 'tail'
CityPlot: no visible global function definition for 'pdf'
CityPlot: no visible global function definition for 'split.screen'
CityPlot: no visible global function definition for 'screen'
CityPlot: no visible global function definition for 'par'
CityPlot: no visible global function definition for 'plot'
CityPlot: no visible global function definition for 'rect'
CityPlot: no visible global function definition for 'text'
CityPlot: no visible global function definition for 'lines'
CityPlot: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  dev.off lines par pdf plot read.table rect screen split.screen tail
  text
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "plot", "rect", "screen",
             "split.screen", "text")
  importFrom("utils", "read.table", "tail")
to your NAMESPACE file.
areas_list_to_states_list_old: no visible global function definition
  for 'combn'
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
'library' or 'require' call to 'rggobi' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
generate_data : <anonymous>: no visible global function definition for
  'runif'
knnf: no visible global function definition for 'terms'
rescaler.default: no visible global function definition for 'sd'
rescaler.default: no visible global function definition for 'median'
rescaler.default: no visible global function definition for 'mad'
simvar.numeric: no visible global function definition for 'runif'
Undefined global functions or variables:
  mad median runif sd terms
Consider adding
  importFrom("stats", "mad", "median", "runif", "sd", "terms")
to your NAMESPACE file.
classify.bug: no visible global function definition for
  'txtProgressBar'
classify.bug: no visible global function definition for
  'setTxtProgressBar'
plot.scores: no visible binding for global variable 'quantile'
plot.scores: no visible global function definition for 'runif'
plot.scores: no visible binding for global variable 'median'
scores.gpcm.bug: no visible global function definition for
  'txtProgressBar'
scores.gpcm.bug: no visible global function definition for
  'setTxtProgressBar'
across.reps,classification: no visible global function definition for
  'sd'
Undefined global functions or variables:
  median quantile runif sd setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "median", "quantile", "runif", "sd")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
.boxRadial: no visible global function definition for 'predict'
.radialSVM: no visible global function definition for 'predict'
cfPredict: no visible global function definition for 'predict'
getPerm5Num: no visible global function definition for 'median'
getPerm5Num: no visible global function definition for 'quantile'
ggClassPred: no visible global function definition for 'ftable'
ggEnsHist: no visible global function definition for 'sd'
ggPermHist: no visible global function definition for 'sd'
Undefined global functions or variables:
  ftable median predict quantile sd
Consider adding
  importFrom("stats", "ftable", "median", "predict", "quantile", "sd")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/cld3.Rcheck/00install.out' for details.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/climatol.Rcheck/00install.out' for details.
climdexInput.csv : get.and.check.data: no visible global function
  definition for 'read.csv'
get.prec.var.quantiles: no visible global function definition for
  'quantile'
growing.season.length : <anonymous>: no visible global function
  definition for 'head'
Undefined global functions or variables:
  head quantile read.csv
Consider adding
  importFrom("stats", "quantile")
  importFrom("utils", "head", "read.csv")
to your NAMESPACE file.
clime: no visible global function definition for 'cov'
cv.clime: no visible global function definition for 'cov'
cv.clime: no visible binding for global variable 'sd'
Undefined global functions or variables:
  cov sd
Consider adding
  importFrom("stats", "cov", "sd")
to your NAMESPACE file.
gxe.cc: no visible global function definition for 'qnorm'
gxe.coh: no visible global function definition for 'qnorm'
utility.cc: no visible global function definition for 'qnorm'
utility.coh: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  qnorm
Consider adding
  importFrom("stats", "qnorm")
to your NAMESPACE file.
cv.clogitL1 : <anonymous>: no visible global function definition for
  'var'
plot.clogitL1: no visible global function definition for 'matplot'
plot.clogitL1: no visible global function definition for 'legend'
plot.clogitL1: no visible global function definition for 'text'
plot.cv.clogitL1: no visible global function definition for 'matplot'
plot.cv.clogitL1: no visible global function definition for 'matlines'
plot.cv.clogitL1: no visible global function definition for 'points'
plot.cv.clogitL1: no visible global function definition for 'axis'
plot.cv.clogitL1: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline axis legend matlines matplot points text var
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "matlines",
             "matplot", "points", "text")
  importFrom("stats", "var")
to your NAMESPACE file.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
socp: 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' call to 'ggplot2' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
IGP.clusterRepro: no visible global function definition for 'cor'
permuteCol: no visible global function definition for 'runif'
Undefined global functions or variables:
  cor runif
Consider adding
  importFrom("stats", "cor", "runif")
to your NAMESPACE file.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
    pdf   2.2Mb
hopkins: no visible global function definition for 'runif'
hopkins: no visible global function definition for 'dist'
Undefined global functions or variables:
  dist runif
Consider adding
  importFrom("stats", "dist", "runif")
to your NAMESPACE file.
clustomit: no visible binding for global variable 'weighted.mean'
sim_unif : multivariate_unif: no visible global function definition for
  'runif'
Undefined global functions or variables:
  runif weighted.mean
Consider adding
  importFrom("stats", "runif", "weighted.mean")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/clustrd.Rcheck/00install.out' for details.
braycurtis: no visible global function definition for 'as.dist'
czekanowski: no visible global function definition for 'as.dist'
findComplementaryIndices: no visible global function definition for
  'na.omit'
genSimilarityProfile: no visible global function definition for 'dist'
simprof: no visible global function definition for 'dist'
simprof: no visible global function definition for 'hclust'
simprof.plot : <local> : colorizer: no visible global function
  definition for 'is.leaf'
simprof.plot: no visible global function definition for 'rainbow'
simprof.plot: no visible global function definition for 'dendrapply'
simprof.plot: no visible global function definition for 'as.dendrogram'
Undefined global functions or variables:
  as.dendrogram as.dist dendrapply dist hclust is.leaf na.omit rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("stats", "as.dendrogram", "as.dist", "dendrapply", "dist",
             "hclust", "is.leaf", "na.omit")
to your NAMESPACE file.