'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.
'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.
binom.ci : bc: no visible global function definition for 'qf'
binom.ci : bc: no visible global function definition for 'qnorm'
cvar: no visible global function definition for 'sd'
eta2: no visible global function definition for 'lm'
eta2: no visible global function definition for 'as.formula'
gg_qqplot: no visible binding for global variable 'qnorm'
gg_qqplot: no visible global function definition for 'quantile'
panel.hist: no visible global function definition for 'par'
panel.hist: no visible global function definition for 'hist'
panel.hist: no visible global function definition for 'rect'
plotcdf2: no visible global function definition for 'colorRampPalette'
plotcdf2 : jet.colors: no visible global function definition for 'gray'
plotcdf2: no visible global function definition for 'persp'
poi.ci: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  as.formula colorRampPalette gray hist lm par persp qchisq qf qnorm
  quantile rect sd
Consider adding
  importFrom("grDevices", "colorRampPalette", "gray")
  importFrom("graphics", "hist", "par", "persp", "rect")
  importFrom("stats", "as.formula", "lm", "qchisq", "qf", "qnorm",
             "quantile", "sd")
to your NAMESPACE file.
Depends: includes the non-default packages:
  'colorspace' 'deldir' 'rgl' 'tcltk' 'tcltk2' 'tkrplot'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'colorspace'
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  'deldir' 'rgl' 'tcltk' 'tcltk2' 'tkrplot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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: '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.
'library' or 'require' calls in package code:
  'Matrix' 'sna'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
S3 methods shown with full name in documentation object 'plot.mat':
  'plot.mat' 'plot.mat.nm'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
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.
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.
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.
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.
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.
scene4d: no visible global function definition for 'rainbow'
write4D.file : <anonymous>: no visible global function definition for
  'col2rgb'
writeWebGL_split : split_triangles: no visible global function
  definition for 'rgb'
Undefined global functions or variables:
  col2rgb rainbow rgb
Consider adding
  importFrom("grDevices", "col2rgb", "rainbow", "rgb")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/BRugs.Rcheck/00install.out' for details.
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.
'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.
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.
C5.0.formula: no visible binding for global variable 'na.pass'
C5.0.formula: no visible global function definition for 'model.extract'
C5.0.formula: no visible global function definition for '.getXlevels'
as.party.C5.0: no visible global function definition for 'model.frame'
as.party.C5.0: no visible global function definition for 'as.formula'
as.party.C5.0: no visible global function definition for 'terms'
as.party.C5.0 : C5.0_fitted: no visible global function definition for
  'model.weights'
model.frame.C5.0: no visible binding for global variable 'na.omit'
plot.C5.0: no visible global function definition for 'plot'
predict.C5.0: no visible binding for global variable 'na.pass'
predict.C5.0: no visible global function definition for
  'delete.response'
predict.C5.0: no visible global function definition for 'model.frame'
Undefined global functions or variables:
  .getXlevels as.formula delete.response model.extract model.frame
  model.weights na.omit na.pass plot terms
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", ".getXlevels", "as.formula", "delete.response",
             "model.extract", "model.frame", "model.weights", "na.omit",
             "na.pass", "terms")
to your NAMESPACE file.
File 'C50/libs/i386/C50.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'getdata.o'
File 'C50/libs/x64/C50.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'getdata.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
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.
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.
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 the system RNG.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
CAM: no visible global function definition for 'object.size'
CAM: no visible global function definition for 'as'
computeScoreMat: no visible global function definition for 'combn'
computeScoreMat: no visible global function definition for 'var'
computeScoreMatParallel: no visible global function definition for
  'var'
selLm: no visible global function definition for 'lm'
selLm: no visible global function definition for 'coef'
train_gam: no visible global function definition for 'formula'
train_lasso: no visible global function definition for 'predict'
train_linear: no visible global function definition for 'lm'
Undefined global functions or variables:
  as coef combn formula lm object.size predict var
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "coef", "formula", "lm", "predict", "var")
  importFrom("utils", "combn", "object.size")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'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.
Error in re-building vignettes:
  ...
Zoom: 4
Fetching 16 missing tiles
====================...complete!
Quitting from lines 114-146 (cartography.Rmd) 
Error: processing vignette 'cartography.Rmd' failed with diagnostics:
task 1 failed - "arg 'X2' has dims=256, 256, 4; but need dims=X, 256, 3"
Execution halted
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.
Found the following Makefile(s) without a final LF:
  inst/doc/Makefile
Some 'make' programs ignore lines not ending in LF.
The following files look like leftovers/mistakes:
  'Causata-vignette.log'
Please remove them from your package.
The following directory looks like a leftover from 'knitr':
  'figure'
Please remove from your package.
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.
bw: no visible global function definition for 'optimize'
Undefined global functions or variables:
  optimize
Consider adding
  importFrom("stats", "optimize")
to your NAMESPACE file.
Unexported objects imported by ':::' calls:
  'copula:::dCdu' 'copula:::fitCopStart'
  See the note in ?`:::` about the use of this operator.
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.
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.
'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.
'library' or 'require' call to 'ggplot2' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
fixed.effect: no visible global function definition for 'glm'
fixed.effect: no visible global function definition for 'qnorm'
fixed.effect.cluster.level: no visible global function definition for
  'aggregate'
fixed.effect.cluster.level: no visible global function definition for
  'formula'
fixed.effect.cluster.level: no visible global function definition for
  'glm'
fixed.effect.cluster.level: no visible global function definition for
  'qnorm'
hayes.power.poisson: no visible global function definition for 'qnorm'
hayes.power.poisson: no visible global function definition for 'pnorm'
power.sim.binomial: no visible global function definition for 'rnorm'
power.sim.binomial: no visible global function definition for 'rbinom'
power.sim.normal: no visible global function definition for 'rnorm'
power.sim.poisson: no visible global function definition for 'rnorm'
power.sim.poisson: no visible global function definition for 'rnbinom'
power.sim.poisson: no visible global function definition for 'rpois'
random.effect: no visible global function definition for 'qt'
random.effect: no visible global function definition for 'coef'
weighted.crossover.cluster.level: no visible global function definition
  for 'aggregate'
weighted.crossover.cluster.level: no visible global function definition
  for 'reshape'
weighted.crossover.cluster.level: no visible global function definition
  for 'lm'
Undefined global functions or variables:
  aggregate coef formula glm lm pnorm qnorm qt rbinom reshape rnbinom
  rnorm rpois
Consider adding
  importFrom("stats", "aggregate", "coef", "formula", "glm", "lm",
             "pnorm", "qnorm", "qt", "rbinom", "reshape", "rnbinom",
             "rnorm", "rpois")
to your NAMESPACE file.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
    pdf   2.2Mb
hclustgeo.uniq: no visible global function definition for 'dist'
plot.hclustgeo: no visible global function definition for 'pdf'
plot.hclustgeo: no visible global function definition for 'par'
plot.hclustgeo: no visible global function definition for 'plot'
plot.hclustgeo: no visible global function definition for 'axis'
plot.hclustgeo: no visible global function definition for 'points'
plot.hclustgeo: no visible global function definition for 'legend'
plot.hclustgeo: no visible global function definition for 'dev.off'
plot.hclustgeo.uniq: no visible global function definition for 'pdf'
plot.hclustgeo.uniq: no visible global function definition for 'par'
plot.hclustgeo.uniq: no visible global function definition for 'plot'
plot.hclustgeo.uniq: no visible global function definition for
  'recordPlot'
plot.hclustgeo.uniq: no visible global function definition for
  'dev.off'
plot.hclustgeo.uniq: no visible global function definition for 'cutree'
summary.hclustgeo.uniq: no visible global function definition for
  'cutree'
Undefined global functions or variables:
  axis cutree dev.off dist legend par pdf plot points recordPlot
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "recordPlot")
  importFrom("graphics", "axis", "legend", "par", "plot", "points")
  importFrom("stats", "cutree", "dist")
to your NAMESPACE file.
E.step: no visible global function definition for 'pnorm'
ObsLogLikelihood: no visible global function definition for 'pnorm'
ObsLogLikelihood: no visible binding for global variable 'D'
clustMD : Zstart: no visible global function definition for 'rnorm'
clustMD: no visible global function definition for 'kmeans'
clustMD: no visible global function definition for 'hclust'
clustMD: no visible global function definition for 'dist'
clustMD: no visible global function definition for 'cutree'
perc.cutoffs: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  D cutree dist hclust kmeans pnorm qnorm rnorm
Consider adding
  importFrom("stats", "D", "cutree", "dist", "hclust", "kmeans", "pnorm",
             "qnorm", "rnorm")
to your NAMESPACE file.
Package suggested but not available for checking: 'moe430a.db'
'library' or 'require' calls in package code:
  'Biobase' 'GO.db' 'annotate' 'kohonen' 'mclust'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Error in re-building vignettes:
  ...

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: XML

Attaching package: 'XML'

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

    toHTML

Loading required package: GO.db

Loading required package: moe430a.db
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'moe430a.db'
Loading required package: RankAggreg
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "clValid.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.3/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'clValid.tex' failed

LaTeX errors:
!pdfTeX error: pdflatex.EXE (file ./clValid-022.pdf): PDF inclusion: required p
age does not exist <0>
 ==> Fatal error occurred, no output PDF file produced!
Execution halted
copynumberBootstrap: no visible global function definition for
  'txtProgressBar'
copynumberBootstrap: no visible global function definition for
  'quantile'
copynumberBootstrap: no visible global function definition for
  'setTxtProgressBar'
gethits: no visible global function definition for 'read.table'
normalizeGC: no visible global function definition for 'median'
plotCNOGpro: no visible global function definition for 'par'
plotCNOGpro: no visible global function definition for 'plot'
plotCNOGpro: no visible global function definition for 'rainbow'
plotCNOGpro: no visible global function definition for 'density'
plotCNOGpro: no visible global function definition for 'polygon'
plotCNOGpro: no visible global function definition for 'lines'
plotCNOGpro: no visible global function definition for 'legend'
plotCNOGpro: no visible global function definition for 'boxplot'
sampleChromosome: no visible global function definition for 'median'
sampleChromosome: no visible binding for global variable 'var'
setupEmissionMatrix: no visible global function definition for 'dgeom'
store: no visible global function definition for 'write.table'
Undefined global functions or variables:
  boxplot density dgeom legend lines median par plot polygon quantile
  rainbow read.table setTxtProgressBar txtProgressBar var write.table
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "boxplot", "legend", "lines", "par", "plot",
             "polygon")
  importFrom("stats", "density", "dgeom", "median", "quantile", "var")
  importFrom("utils", "read.table", "setTxtProgressBar",
             "txtProgressBar", "write.table")
to your NAMESPACE file.
CNclusterNcenter: no visible global function definition for 'median'
CNclusterNcenter: no visible binding for global variable 'var'
breakIntoGaps: no visible global function definition for 'runif'
centerprob: no visible global function definition for 'pnorm'
getz: no visible global function definition for 'predict'
smad: no visible global function definition for 'mad'
smedian: no visible global function definition for 'median'
smedian.sample: no visible global function definition for 'median'
smedmad: no visible global function definition for 'median'
smedmad: no visible global function definition for 'mad'
Undefined global functions or variables:
  mad median pnorm predict runif var
Consider adding
  importFrom("stats", "mad", "median", "pnorm", "predict", "runif",
             "var")
to your NAMESPACE file.
coalescentMCMC: no visible global function definition for
  'packageVersion'
coalescentMCMC : getparams: no visible global function definition for
  'nlminb'
sim.coalescent: no visible global function definition for 'plot'
sim.coalescent: no visible global function definition for 'segments'
sim.coalescent: no visible global function definition for 'points'
Undefined global functions or variables:
  nlminb packageVersion plot points segments
Consider adding
  importFrom("graphics", "plot", "points", "segments")
  importFrom("stats", "nlminb")
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
CoClust: no visible binding for global variable 'median'
CoClust: no visible global function definition for 'cor'
fit.margin : ecdfc: no visible global function definition for
  'approxfun'
fit.margin3: no visible global function definition for 'optim'
fit.margin3: no visible global function definition for 'sd'
fit.margin3: no visible global function definition for 'pnorm'
stima_cop: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  approxfun cor median optim pnorm sd
Consider adding
  importFrom("stats", "approxfun", "cor", "median", "optim", "pnorm",
             "sd")
to your NAMESPACE file.
Package which this enhances but not available for checking: 'rkward'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.1Mb
    libs   1.4Mb
Running examples in 'colourlovers-Ex.R' failed
The error most likely occurred in:

> ### Name: clpatterns
> ### Title: Retrieve pattern or patterns
> ### Aliases: clpattern clpatterns print.clpattern print.clpatterns
> 
> ### ** Examples
> 
> e <- function(e) NULL # function for tryCatch to fail in examples
> 
> # get a random pattern
> tryCatch( clpatterns('random'), error = e)
Pattern ID:      2193216 
Title:           <U+6C50> <U+7559> lonely metro 
Created by user: <U+3061><U+3087><U+308F> <U+3082><U+3055> 
Date created:    2012-02-10 02:29:21 
Views:           16 
Votes:           1 
Comments:        1 
Hearts:          0 
Rank:            0 
URL:             http://www.colourlovers.com/pattern/2193216/<U+6C50> <U+7559> lonely_metro 
Image URL:       
Colors:          #FFFEA9, #FFEFA9, #FFE1A9, #FFC4A9, #FFA9C7 

> 
> # plot at a single pattern
> p <- tryCatch( clpattern('1451', fmt='json'), error = e)
> if(!is.null(p)) plot(p)
Warning in download.file(u, tmp, quiet = TRUE, mode = "wb") :
  cannot open URL 'http://colourlovers.com.s3.amazonaws.com/images/patterns/1/1451.png': HTTP status was '503 Service Unavailable'
Error in download.file(u, tmp, quiet = TRUE, mode = "wb") : 
  cannot open URL 'http://colourlovers.com.s3.amazonaws.com/images/patterns/1/1451.png'
Calls: plot -> plot.clpattern -> clpng -> download.file
Execution halted
Hopkins.index: no visible global function definition for 'runif'
MBM.em: no visible global function definition for 'runif'
PAM.cluster: no visible global function definition for 'dist'
calculate.layout: no visible global function definition for 'optim'
min.distance: no visible global function definition for 'dist'
plot.conceptmap: no visible global function definition for 'par'
plot.conceptmap: no visible global function definition for 'plot'
plot.conceptmaps: no visible global function definition for 'plot'
Undefined global functions or variables:
  dist optim par plot runif
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "dist", "optim", "runif")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'lattice' 'rgl'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
CIFplot: no visible global function definition for 'plot'
CIFplot: no visible global function definition for 'gray'
CIFplot: no visible global function definition for 'lines'
iprop: no visible global function definition for 'qnorm'
irates: no visible global function definition for 'qnorm'
irates.ratio: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  gray lines plot qnorm
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "qnorm")
to your NAMESPACE file.
Package suggested but not available for checking: 'mogene10sttranscriptcluster.db'
conf: no visible global function definition for 'read.csv'
conf: no visible global function definition for 'write.csv'
mya.conf_input : <anonymous>: no visible global function definition for
  'sd'
mya.conf_input : <anonymous>: no visible global function definition for
  'qt'
mya.conf_input : <anonymous>: no visible global function definition for
  'pt'
plot.mya: no visible global function definition for 'dt'
plot.mya: no visible global function definition for 'rgb'
write_html.conf_input: no visible global function definition for
  'browseURL'
Undefined global functions or variables:
  browseURL dt pt qt read.csv rgb sd write.csv
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "dt", "pt", "qt", "sd")
  importFrom("utils", "browseURL", "read.csv", "write.csv")
to your NAMESPACE file.
Conjoint: no visible global function definition for 'dev.new'
Conjoint: no visible global function definition for 'barplot'
caFactorialDesign: no visible global function definition for 'cor'
caModel: no visible global function definition for 'as.formula'
caModel: no visible global function definition for 'lm'
caModel: no visible global function definition for 'summary.lm'
caSegmentation: no visible global function definition for 'kmeans'
caUtilities: no visible global function definition for 'as.formula'
caUtilities: no visible global function definition for 'lm'
caUtilities: no visible global function definition for 'summary.lm'
partutilities: no visible global function definition for 'as.formula'
partutilities: no visible global function definition for 'lm'
partutils: no visible global function definition for 'as.formula'
partutils: no visible global function definition for 'lm'
profsimcode: no visible global function definition for 'as.formula'
profsimcode: no visible global function definition for 'lm'
profsimcode: no visible global function definition for 'model.matrix'
totalutilities: no visible global function definition for 'as.formula'
totalutilities: no visible global function definition for 'lm'
totalutilities: no visible global function definition for
  'model.matrix'
utlsplot: no visible global function definition for 'dev.new'
utlsplot: no visible global function definition for 'barplot'
Undefined global functions or variables:
  as.formula barplot cor dev.new kmeans lm model.matrix summary.lm
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "barplot")
  importFrom("stats", "as.formula", "cor", "kmeans", "lm",
             "model.matrix", "summary.lm")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Quitting from lines 219-220 (my-vignette.Rmd) 
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
'is.hole.xypolygon' is not an exported object from 'namespace:spatstat'
Execution halted
convnum: no visible global function definition for 'points'
convnum: no visible global function definition for 'arrows'
convnumsig: no visible global function definition for 'hist'
maxdist: no visible global function definition for 'dist'
plotellipse: no visible global function definition for 'lines'
Undefined global functions or variables:
  arrows dist hist lines points
Consider adding
  importFrom("graphics", "arrows", "hist", "lines", "points")
  importFrom("stats", "dist")
to your NAMESPACE file.
Running 'testthat.R' [185s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  note that this function must be run on the full survey design object immediately after the svydesign() or svrepdesign() call.
  
  preparing your full survey design to work with R convey package functions
  
  note that this function must be run on the full survey design object immediately after the svydesign() or svrepdesign() call.
  
  preparing your full survey design to work with R convey package functions
  
  note that this function must be run on the full survey design object immediately after the svydesign() or svrepdesign() call.
  
  Error: 'order_quant' must be a integer values in [0, 100]
  testthat results ================================================================
  OK: 251 SKIPPED: 0 FAILED: 0
  Execution halted
maCooperative: no visible global function definition for 'points'
maCooperative: no visible global function definition for 'legend'
maPessimistic: no visible global function definition for 'combn'
maRules: no visible global function definition for 'capture.output'
mstCooperative: no visible global function definition for 'points'
mstCooperative: no visible global function definition for 'legend'
mstOptimistic: no visible global function definition for 'combn'
mstPessimistic: no visible global function definition for 'combn'
mstRules: no visible global function definition for 'capture.output'
plotCoreSet: no visible global function definition for 'points'
plotCoreSet: no visible global function definition for 'polygon'
plotImputationSet: no visible global function definition for 'par'
plotImputationSet: no visible global function definition for 'plot'
plotImputationSet: no visible global function definition for 'box'
plotImputationSet: no visible global function definition for 'polygon'
plotImputationSet: no visible global function definition for 'text'
shapleyValue: no visible global function definition for 'combn'
Undefined global functions or variables:
  box capture.output combn legend par plot points polygon text
Consider adding
  importFrom("graphics", "box", "legend", "par", "plot", "points",
             "polygon", "text")
  importFrom("utils", "capture.output", "combn")
to your NAMESPACE file.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   6.5Mb
density_conditional: no visible global function definition for 'ppois'
density_joint: no visible global function definition for 'ppois'
dgam: no visible global function definition for 'dgamma'
dpolicy_loss: no visible global function definition for 'ppois'
dztp: no visible global function definition for 'dpois'
epolicy_loss: no visible global function definition for 'integrate'
mle_joint: no visible global function definition for 'optim'
mle_marginal: no visible global function definition for 'glm'
mle_marginal: no visible global function definition for 'Gamma'
mle_marginal: no visible global function definition for 'vcov'
mle_marginal: no visible global function definition for 'poisson'
mle_marginal: no visible global function definition for 'coef'
mle_marginal: no visible global function definition for 'ppois'
mle_marginal: no visible global function definition for 'optim'
pgam: no visible global function definition for 'pgamma'
ppolicy_loss: no visible global function definition for 'integrate'
pztp: no visible global function definition for 'ppois'
qpolicy_loss: no visible global function definition for 'uniroot'
rgam: no visible global function definition for 'rgamma'
vuongtest: no visible global function definition for 'sd'
ztp.glm: no visible global function definition for 'coef'
ztp.glm: no visible global function definition for 'glm'
ztp.glm: no visible binding for global variable 'poisson'
ztp.glm: no visible global function definition for 'optim'
Undefined global functions or variables:
  Gamma coef dgamma dpois glm integrate optim pgamma poisson ppois
  rgamma sd uniroot vcov
Consider adding
  importFrom("stats", "Gamma", "coef", "dgamma", "dpois", "glm",
             "integrate", "optim", "pgamma", "poisson", "ppois",
             "rgamma", "sd", "uniroot", "vcov")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/CorrectOverloadedPeaks.Rcheck/00install.out' for details.
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.
correlogram: no visible global function definition for 'par'
correlogram: no visible global function definition for 'plot'
correlogram: no visible global function definition for 'points'
correlogram: no visible global function definition for 'textxy'
correlogram: no visible global function definition for 'arrows'
correlogram: no visible global function definition for 'circle'
fit_angles: no visible global function definition for 'runif'
fit_angles: no visible global function definition for 'nlminb'
linangplot: no visible global function definition for 'cor'
linangplot: no visible global function definition for 'rad2degree'
linangplot: no visible global function definition for 'ginv'
linangplot: no visible global function definition for 'par'
linangplot: no visible global function definition for 'plot'
linangplot: no visible global function definition for 'calibrate'
linangplot: no visible global function definition for 'var'
pfa: no visible global function definition for 'cor'
Undefined global functions or variables:
  arrows calibrate circle cor ginv nlminb par plot points rad2degree
  runif textxy var
Consider adding
  importFrom("graphics", "arrows", "par", "plot", "points")
  importFrom("stats", "cor", "nlminb", "runif", "var")
to your NAMESPACE file.
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(testthat)
  > test_check("corset")
  Loading required package: corset
  1. Failure: Corset - class gts/hts  (@test-bezier.R#142) -----------------------
  `cx` not equal to structure(...).
  Component "bts": Mean relative difference: 0.8147274
  Component "histy": Mean relative difference: 0.1075422
  
  
  testthat results ================================================================
  OK: 23 SKIPPED: 3 FAILED: 1
  1. Failure: Corset - class gts/hts  (@test-bezier.R#142) 
  
  Error: testthat unit tests failed
  Execution halted
cosinor.lm: no visible binding for global variable 'na.omit'
cosinor.lm: no visible global function definition for 'terms'
cosinor.lm: no visible global function definition for 'as.formula'
cosinor.lm: no visible global function definition for 'lm'
cosinor_analyzer: no visible binding for global variable 'vitamind'
cosinor_analyzer : <anonymous>: no visible global function definition
  for 'as.formula'
ggplot.cosinor.lm: no visible global function definition for 'predict'
predict.cosinor.lm: no visible global function definition for 'fitted'
predict.cosinor.lm: no visible global function definition for 'predict'
simulate_cosinor: no visible global function definition for 'runif'
simulate_cosinor: no visible global function definition for 'rbinom'
simulate_cosinor: no visible global function definition for 'rnorm'
summary.cosinor.lm: no visible global function definition for 'vcov'
summary.cosinor.lm: no visible global function definition for 'qnorm'
summary.cosinor.lm: no visible global function definition for 'pnorm'
test_cosinor: no visible global function definition for 'pchisq'
test_cosinor: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  as.formula fitted lm na.omit pchisq pnorm predict qnorm rbinom rnorm
  runif terms vcov vitamind
Consider adding
  importFrom("stats", "as.formula", "fitted", "lm", "na.omit", "pchisq",
             "pnorm", "predict", "qnorm", "rbinom", "rnorm", "runif",
             "terms", "vcov")
to your NAMESPACE file.
CosmoPhotoZestimator: no visible global function definition for
  'predict'
computeCombPCA: no visible global function definition for 'prcomp'
computeDiagPhotoZ: no visible global function definition for 'sd'
computeDiagPhotoZ: no visible global function definition for 'median'
computeDiagPhotoZ: no visible global function definition for 'mad'
glmPredictPhotoZ: no visible global function definition for 'predict'
glmTrainPhotoZ: no visible global function definition for 'glm'
glmTrainPhotoZ: no visible global function definition for 'Gamma'
glmTrainPhotoZ: no visible global function definition for
  'inverse.gaussian'
plotDiagPhotoZ: no visible global function definition for 'median'
plotDiagPhotoZ: no visible global function definition for 'mad'
Undefined global functions or variables:
  Gamma glm inverse.gaussian mad median prcomp predict sd
Consider adding
  importFrom("stats", "Gamma", "glm", "inverse.gaussian", "mad",
             "median", "prcomp", "predict", "sd")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'Rglpk' 'glmnet' 'parallel' 'quadprog'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
calcz02: no visible global function definition for 'coxph'
calcz02: no visible global function definition for 'residuals'
covTest: no visible global function definition for 'Surv'
covTest: no visible global function definition for 'predict'
covTest: no visible global function definition for 'update'
covTest: no visible global function definition for 'lsfit'
covTest: no visible global function definition for 'pexp'
covTest: no visible global function definition for 'pf'
lars.en: no visible binding for global variable 'var'
predict.lars.en: no visible global function definition for 'predict'
Undefined global functions or variables:
  Surv coxph lsfit pexp pf predict residuals update var
Consider adding
  importFrom("stats", "lsfit", "pexp", "pf", "predict", "residuals",
             "update", "var")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'rms' 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
phcpe: no visible global function definition for 'model.matrix'
phcpe: no visible global function definition for 'sd'
phcpe2: no visible global function definition for 'sd'
Undefined global functions or variables:
  model.matrix sd
Consider adding
  importFrom("stats", "model.matrix", "sd")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/cplexAPI.Rcheck/00install.out' for details.
CPMCGLM: no visible binding for global variable 'binomial'
CPMCGLM: no visible binding for global variable 'gaussian'
CPMCGLM: no visible binding for global variable 'poisson'
CPMCGLM: no visible global function definition for 'update'
CPMCGLM: no visible global function definition for 'model.response'
CPMCGLM: no visible global function definition for 'model.frame'
CPMCGLM: no visible global function definition for 'is.empty.model'
CPMCGLM: no visible global function definition for 'model.matrix'
CPMCGLM: no visible binding for global variable 'contrasts'
CPMCGLM: no visible global function definition for 'pchisq'
CPMCGLM: no visible global function definition for 'glm'
CPMCGLM: no visible global function definition for 'pnorm'
CPMCGLM: no visible global function definition for 'rnorm'
CPMCGLM: no visible global function definition for 'sd'
CPMCGLM: no visible global function definition for 'rbinom'
CPMCGLM: no visible global function definition for 'rpois'
test.liquet: no visible global function definition for 'glm'
test.liquet: no visible global function definition for 'var'
test.score: no visible global function definition for 'glm'
test.score: no visible global function definition for 'var'
tmultboot: no visible global function definition for 'glm'
tmultboot: no visible global function definition for 'var'
Undefined global functions or variables:
  binomial contrasts gaussian glm is.empty.model model.frame
  model.matrix model.response pchisq pnorm poisson rbinom rnorm rpois
  sd update var
Consider adding
  importFrom("stats", "binomial", "contrasts", "gaussian", "glm",
             "is.empty.model", "model.frame", "model.matrix",
             "model.response", "pchisq", "pnorm", "poisson", "rbinom",
             "rnorm", "rpois", "sd", "update", "var")
to your NAMESPACE file.
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.
'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' 'chron'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
collateDaily: no visible global function definition for 'read.table'
collateDaily: no visible global function definition for 'write.table'
collateHourly: no visible global function definition for 'read.table'
collateHourly: no visible global function definition for 'write.table'
downloadCRN: no visible global function definition for 'download.file'
getUrlsCRN: no visible global function definition for 'getURL'
writeDataset: no visible global function definition for 'read.table'
writeDataset: no visible global function definition for 'write.table'
Undefined global functions or variables:
  download.file getURL read.table write.table
Consider adding
  importFrom("utils", "download.file", "read.table", "write.table")
to your NAMESPACE file.
gen.xnorm: no visible global function definition for 'extendrange'
plot.clsd: no visible global function definition for 'plot'
plot.crs: no visible global function definition for 'par'
plot.crs: no visible global function definition for 'plot'
plot.crs: no visible global function definition for 'topo.colors'
plot.npglpreg: no visible global function definition for 'par'
plot.npglpreg: no visible global function definition for 'plot'
plot.npglpreg: no visible global function definition for 'topo.colors'
printClear: no visible global function definition for 'flush.console'
printPop: no visible global function definition for 'flush.console'
printPush: no visible global function definition for 'flush.console'
Undefined global functions or variables:
  extendrange flush.console par plot topo.colors
Consider adding
  importFrom("grDevices", "extendrange", "topo.colors")
  importFrom("graphics", "par", "plot")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
'library' or 'require' call to 'parallel' 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:
  'car' 'ellipse' 'rJPSGCS'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    shp   7.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
File 'Cubist/libs/i386/Cubist.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'getdata.o'
File 'Cubist/libs/x64/Cubist.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'getdata.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/cudaBayesreg.Rcheck/00install.out' for details.
Cut: no visible global function definition for 'cor'
MissSimulation: no visible global function definition for 'rbinom'
cutoff: no visible global function definition for 'cor'
Undefined global functions or variables:
  cor rbinom
Consider adding
  importFrom("stats", "cor", "rbinom")
to your NAMESPACE file.
ci.cvAUC: no visible global function definition for 'qnorm'
ci.pooled.cvAUC: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  qnorm
Consider adding
  importFrom("stats", "qnorm")
to your NAMESPACE file.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'lattice' 'robustbase'
A package should be listed in only one of these fields.
create_clustering_problem: no visible global function definition for
  'rnorm'
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
compareModels: no visible binding for global variable 'fgl'
compareModels: no visible global function definition for 'rlm'
compareModels: no visible global function definition for 'lm'
compareModels: no visible global function definition for 'predict'
compareModels: no visible global function definition for 'resid'
plotSampDist: no visible global function definition for 'par'
plotSampDist: no visible global function definition for 'density'
plotSampDist: no visible global function definition for 'plot'
plotSampDist: no visible global function definition for 'lines'
plotSampDist: no visible global function definition for 'legend'
plotSampDist: no visible global function definition for 'qqnorm'
plotSampDist: no visible global function definition for 'points'
plotSampDist: no visible global function definition for 'mtext'
simulateSampDist: no visible binding for global variable 'rnorm'
Undefined global functions or variables:
  density fgl legend lines lm mtext par plot points predict qqnorm
  resid rlm rnorm
Consider adding
  importFrom("graphics", "legend", "lines", "mtext", "par", "plot",
             "points")
  importFrom("stats", "density", "lm", "predict", "qqnorm", "resid",
             "rnorm")
to your NAMESPACE file.
DAMOCLES_ML: no visible global function definition for 'flush.console'
DAMOCLES_bootstrap: no visible global function definition for
  'cophenetic'
DAMOCLES_bootstrap: no visible global function definition for 'sd'
DAMOCLES_bootstrap: no visible global function definition for
  'quantile'
DAMOCLES_sim: no visible global function definition for 'na.omit'
DAMOCLES_sim: no visible global function definition for 'runif'
DAMOCLES_sim: no visible global function definition for 'lines'
DAMOCLES_sim: no visible global function definition for 'rnorm'
DAMOCLES_sim: no visible global function definition for 'dexp'
DAMOCLES_sim: no visible global function definition for 'dist'
DAMOCLES_simplex: no visible global function definition for
  'flush.console'
Undefined global functions or variables:
  cophenetic dexp dist flush.console lines na.omit quantile rnorm runif
  sd
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "cophenetic", "dexp", "dist", "na.omit",
             "quantile", "rnorm", "runif", "sd")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Package unavailable to check Rd xrefs: 'gputools'
get_temporary_file_name: no visible global function definition for
  'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
datadict.profile: no visible global function definition for
  'txtProgressBar'
datadict.profile: no visible global function definition for
  'setTxtProgressBar'
datadict_profile: no visible global function definition for
  'txtProgressBar'
datadict_profile: no visible global function definition for
  'setTxtProgressBar'
heatmap.quality: no visible global function definition for
  'colorRampPalette'
heatmap.quality: no visible global function definition for 'heatmap'
heatmap_quality: no visible global function definition for
  'colorRampPalette'
heatmap_quality: no visible global function definition for 'heatmap'
is.oneOf: no visible global function definition for 'read.csv'
is_one_of: no visible global function definition for 'read.csv'
pkg.version: no visible global function definition for 'citation'
pkg_version: no visible global function definition for 'citation'
ruleCoverage: no visible global function definition for 'dotchart'
ruleCoverage: no visible global function definition for 'abline'
rule_coverage: no visible global function definition for 'dotchart'
rule_coverage: no visible global function definition for 'abline'
scoreSum: no visible global function definition for 'plot'
score_sum: no visible global function definition for 'plot'
shortSummary: no visible global function definition for 'sd'
short_summary: no visible global function definition for 'sd'
Undefined global functions or variables:
  abline citation colorRampPalette dotchart heatmap plot read.csv sd
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "abline", "dotchart", "plot")
  importFrom("stats", "heatmap", "sd")
  importFrom("utils", "citation", "read.csv", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file.
Package suggested but not available for checking: 'Rhipe'
Package in Depends field not imported from: 'DBI'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.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.
Missing or unexported object: 'readr::col_numeric'
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').
Depends: includes the non-default packages:
  'xtable' 'akima' 'R.oo' 'R.methodsS3' 'matlab' 'lattice' 'locfit'
  'grid'
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:
  'R.methodsS3' 'R.oo' 'akima' 'graphics' 'grid' 'lattice' 'locfit'
  'matlab' 'xtable'
  Please remove these calls from your code.
'library' or 'require' call to 'R.matlab' 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:
  'R.methodsS3' 'R.oo' 'akima' 'grid' 'lattice' 'locfit' 'matlab'
  'xtable'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
DAT : DATrun : calch: no visible global function definition for
  'preplot'
DAT : DATrun: no visible global function definition for 'rot90'
DAT : DATrun: no visible global function definition for 'median'
DAT : DATrun: no visible global function definition for 'locfit.robust'
DAT : DATrun: no visible global function definition for 'preplot'
DAT : DATrun: no visible global function definition for 'dev.new'
DAT : DATrun: no visible global function definition for 'image'
DAT : DATrun: no visible global function definition for 'palette'
DAT : DATrun: no visible global function definition for
  'colorRampPalette'
DAT : DATrun: no visible global function definition for 'text'
DAT : DATrun: no visible global function definition for 'dev.set'
DAT : DATrun: no visible global function definition for 'locator'
DAT : DATrun: no visible global function definition for 'graphics.off'
DAT : DATrun: no visible global function definition for 'pdf'
DAT : DATrun: no visible global function definition for 'layout'
DAT : DATrun: no visible global function definition for 'par'
DAT : DATrun: no visible global function definition for 'plot'
DAT : DATrun: no visible global function definition for 'frame'
DAT : DATrun: no visible global function definition for 'lines'
DAT : DATrun: no visible global function definition for 'dev.off'
DAT : DATrun: no visible global function definition for 'writeMat'
DAT: no visible binding for global variable 'DAT.simData'
Undefined global functions or variables:
  DAT.simData colorRampPalette dev.new dev.off dev.set frame
  graphics.off image layout lines locator locfit.robust median palette
  par pdf plot preplot rot90 text writeMat
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.new", "dev.off",
             "dev.set", "graphics.off", "palette", "pdf")
  importFrom("graphics", "frame", "image", "layout", "lines", "locator",
             "par", "plot", "text")
  importFrom("stats", "median", "preplot")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'RMySQL' 'gWidgets'
  Please remove these calls from your code.
.CA.fast2: no visible global function definition for 'lsfit'
.T2.fast: no visible global function definition for 'txtProgressBar'
.T2.fast: no visible global function definition for 'setTxtProgressBar'
.dcemri.bayes: no visible global function definition for 'median'
.dcemri.bayes: no visible global function definition for 'sd'
.dcemri.map : posterior: no visible global function definition for
  'dnorm'
.dcemri.map : posterior: no visible global function definition for
  'dgamma'
.dcemri.map : posterior: no visible global function definition for
  'dbeta'
.dcemri.map.single: no visible global function definition for 'optim'
.dcemri.spline: no visible binding for global variable 'median'
.dcemri.spline: no visible global function definition for 'median'
.dcemri.spline.single: no visible binding for global variable
  'quantile'
.dcemri.spline.single: no visible binding for global variable 'median'
.dcemri.spline.single: no visible global function definition for
  'median'
.ftm: no visible global function definition for 'fft'
.ftm: no visible global function definition for 'matplot'
.ftm: no visible global function definition for 'legend'
compartmentalModel : <anonymous>: no visible global function definition
  for 'approx'
convFFT: no visible global function definition for 'fft'
extractAIF : c.start: no visible global function definition for 'sd'
extractAIF : c.start: no visible global function definition for 'cor'
Undefined global functions or variables:
  approx cor dbeta dgamma dnorm fft legend lsfit matplot median optim
  quantile sd setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "legend", "matplot")
  importFrom("stats", "approx", "cor", "dbeta", "dgamma", "dnorm", "fft",
             "lsfit", "median", "optim", "quantile", "sd")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
DrawAlphas: no visible global function definition for 'rmultinom'
DrawClasses: no visible global function definition for 'runif'
GetGammaNames: no visible global function definition for 'combn'
GetLambdaNamesForItem: no visible global function definition for
  'combn'
SampleParameterEstimates: no visible global function definition for
  'rnorm'
plot,attribute.class-missing: no visible binding for global variable
  'attr.number'
plot,attribute.class-missing: no visible binding for global variable
  'mean.attr'
plot,attribute.profile.class-missing: no visible binding for global
  variable 'attr.profile.number'
plot,attribute.profile.class-missing: no visible binding for global
  variable 'mean.attr.profile'
summary,attribute.class: no visible binding for global variable 'value'
summary,attribute.profile.class: no visible binding for global variable
  'max.class'
Undefined global functions or variables:
  attr.number attr.profile.number combn max.class mean.attr
  mean.attr.profile rmultinom rnorm runif value
Consider adding
  importFrom("stats", "rmultinom", "rnorm", "runif")
  importFrom("utils", "combn")
to your NAMESPACE file.
'library' or 'require' call to 'irr' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to 'rgl' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.make3dScatterPlotDialog: no visible global function definition for
  'install.packages'
.makePackageDataDialog: no visible global function definition for
  'data'
.makeVignetteDialog: no visible global function definition for
  'vignette'
.onLoad: no visible global function definition for 'winMenuAdd'
.onLoad: no visible binding for global variable 'winMenuAddItem'
.onLoad: no visible binding for global variable 'jgr.addMenuItem'
.onLoad : gui.addSeperator: no visible global function definition for
  'jgr.addMenuSeparator'
applyModel: no visible global function definition for 'predict'
predict.kmeans : <anonymous>: no visible global function definition for
  'dist'
Undefined global functions or variables:
  data dist install.packages jgr.addMenuItem jgr.addMenuSeparator
  predict vignette winMenuAdd winMenuAddItem
Consider adding
  importFrom("stats", "dist", "predict")
  importFrom("utils", "data", "install.packages", "vignette",
             "winMenuAdd", "winMenuAddItem")
to your NAMESPACE file.
Package in Depends field not imported from: 'Deducer'
  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:
  'Deducer' 'psych' 'GPArotation' 'mvnormtest' 'irr' 'klaR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' call to 'klaR' which was already attached by Depends.
  Please remove these calls from your code.
.makeICCDialog: no visible global function definition for 'J'
.makeICCDialog: no visible global function definition for 'new'
.makeICCDialog: no visible global function definition for '.jnull'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'new'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'J'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'toJava'
.makeNewLDADialog: no visible global function definition for 'new'
.makeNewLDADialog: no visible global function definition for 'J'
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for 'new'
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for 'toJava'
.makeNewLDADialog: no visible global function definition for 'toJava'
.makeNewReliabilityDialog: no visible global function definition for
  'new'
.makeNewReliabilityDialog: no visible global function definition for
  'toJava'
.onLoad: no visible global function definition for '.jnull'
.onLoad: no visible global function definition for 'winMenuAdd'
.onLoad: no visible global function definition for 'winMenuAddItem'
.onLoad: no visible global function definition for 'jgr.getMenuNames'
.onLoad: no visible global function definition for 'jgr.insertMenu'
.onLoad: no visible global function definition for 'jgr.addMenu'
.onLoad: no visible global function definition for 'jgr.addMenuItem'
Undefined global functions or variables:
  .jnull J jgr.addMenu jgr.addMenuItem jgr.getMenuNames jgr.insertMenu
  new toJava winMenuAdd winMenuAddItem
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "winMenuAdd", "winMenuAddItem")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Depends: includes the non-default packages:
  'JavaGD' 'Deducer' 'sp' 'maptools' 'OpenStreetMap' 'scales' 'rgdal'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'UScensus2010'
A package should be listed in only one of these fields.
'library' or 'require' call to 'UScensus2010' 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:
  '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.
.makeQuickWordcloud: no visible global function definition for 'J'
.makeQuickWordcloud: no visible global function definition for 'new'
.makeQuickWordcloud: no visible global function definition for '.jnull'
.makeTextPlot: no visible global function definition for 'J'
.makeTextPlot: no visible global function definition for 'new'
.makeTextPlot: no visible global function definition for '.jnull'
.onLoad: no visible global function definition for '.jpackage'
.onLoad: no visible global function definition for '.jnew'
.onLoad: no visible global function definition for 'J'
make.color.scale: no visible global function definition for 'rgb'
Undefined global functions or variables:
  .jnew .jnull .jpackage J new rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
DEMIPathway: no visible global function definition for 'dhyper'
DEMIPathway: no visible global function definition for 'p.adjust'
calcHypergeoExon: no visible global function definition for 'dhyper'
calcHypergeoProb: no visible global function definition for 'dhyper'
demi: no visible global function definition for 'write.table'
demi.t.test: no visible global function definition for 't.test'
demi.wilcox.test: no visible global function definition for
  'wilcox.test'
demi.wilcox.test.fast: no visible global function definition for
  'wilcox.test'
demiequal: no visible global function definition for 'wilcox.test'
wprob: no visible global function definition for 'combn'
diffexp,DEMIDiff: no visible global function definition for 'median'
diffexp,DEMIDiff: no visible global function definition for 'p.adjust'
loadAnnotation,DEMIExperiment-environment: no visible global function
  definition for 'data'
loadBlat,DEMIExperiment-environment: no visible global function
  definition for 'data'
loadCytoband,DEMIExperiment-environment: no visible global function
  definition for 'data'
loadPathway,DEMIExperiment-environment: no visible global function
  definition for 'data'
Undefined global functions or variables:
  combn data dhyper median p.adjust t.test wilcox.test write.table
Consider adding
  importFrom("stats", "dhyper", "median", "p.adjust", "t.test",
             "wilcox.test")
  importFrom("utils", "combn", "data", "write.table")
to your NAMESPACE file.
color_clusters: no visible binding for global variable 'rainbow'
color_clusters: no visible global function definition for
  'as.dendrogram'
color_clusters : descendTree: no visible global function definition for
  'dendrapply'
colour_clusters: no visible binding for global variable 'rainbow'
colour_clusters: no visible global function definition for
  'as.dendrogram'
colour_clusters : descendTree: no visible global function definition
  for 'dendrapply'
labels<-.dendrogram : replaceLabel: no visible global function
  definition for 'is.leaf'
labels<-.dendrogram: no visible global function definition for
  'dendrapply'
leaf_colors : leaf_col: no visible global function definition for
  'is.leaf'
leaf_colors: no visible global function definition for 'dendrapply'
leaf_colours : leaf_col: no visible global function definition for
  'is.leaf'
leaf_colours: no visible global function definition for 'dendrapply'
set_leaf_colors : leaf_col: no visible global function definition for
  'is.leaf'
set_leaf_colors: no visible global function definition for 'dendrapply'
set_leaf_colours : leaf_col: no visible global function definition for
  'is.leaf'
set_leaf_colours: no visible global function definition for
  'dendrapply'
slice.dendrogram: no visible global function definition for 'as.hclust'
slice.hclust: no visible global function definition for 'cutree'
Undefined global functions or variables:
  as.dendrogram as.hclust cutree dendrapply is.leaf rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("stats", "as.dendrogram", "as.hclust", "cutree",
             "dendrapply", "is.leaf")
to your NAMESPACE file.
DendSer: no visible global function definition for 'getFromNamespace'
crit2cost : <anonymous>: no visible global function definition for
  'as.dist'
dser.dist: no visible global function definition for 'hclust'
dser.matrix: no visible global function definition for 'dist'
plotAsColor: no visible global function definition for 'image'
plotAsColor: no visible global function definition for 'box'
plotAsColor: no visible global function definition for 'axis'
seriation_method_dist_dser: no visible global function definition for
  'hclust'
seriation_method_dist_dser: no visible global function definition for
  'modifyList'
seriation_method_leafsort: no visible global function definition for
  'modifyList'
Undefined global functions or variables:
  as.dist axis box dist getFromNamespace hclust image modifyList
Consider adding
  importFrom("graphics", "axis", "box", "image")
  importFrom("stats", "as.dist", "dist", "hclust")
  importFrom("utils", "getFromNamespace", "modifyList")
to your NAMESPACE file.
descomponer: no visible global function definition for 'lm'
gdescomponer: no visible global function definition for 'ts'
gdescomponer: no visible global function definition for 'par'
gdescomponer: no visible global function definition for 'plot'
gperiodograma: no visible global function definition for 'plot'
Undefined global functions or variables:
  lm par plot ts
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "lm", "ts")
to your NAMESPACE file.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.7Mb
    help   1.3Mb
    libs   1.5Mb
Packages suggested but not available for checking: 'Rmosek' 'gurobi'
Package unavailable to check Rd xrefs: 'Rmosek'
Package in Depends field not imported from: 'dplR'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.get' 'InteractiveDetrending' 'RemoveTrend'
simulate_dataframe : generate_dumb_answer: no visible global function
  definition for 'rbinom'
simulate_dataframe : generate_dumb_answer: no visible global function
  definition for 'rnorm'
simulate_dataframe : generate_initial: no visible global function
  definition for 'rbinom'
simulate_dataframe: no visible binding for global variable 'randu'
simulate_dataframe: no visible global function definition for 'rbinom'
simulate_dataframe: no visible global function definition for 'rnorm'
simulate_dataframe: no visible global function definition for 'rpois'
simulate_dataframe : add_NAs: no visible global function definition for
  'rbinom'
Undefined global functions or variables:
  randu rbinom rnorm rpois
Consider adding
  importFrom("datasets", "randu")
  importFrom("stats", "rbinom", "rnorm", "rpois")
to your NAMESPACE file.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
makeAdjMatrix: no visible global function definition for 'combn'
plotPosteriorN: no visible global function definition for 'plot'
plotPosteriorN: no visible global function definition for 'title'
plotPosteriorN: no visible global function definition for 'lines'
plotPosteriorN: no visible global function definition for 'legend'
venn3: no visible global function definition for 'plot'
venn3: no visible global function definition for 'runif'
venn3: no visible global function definition for 'points'
venn3: no visible global function definition for 'lines'
venn3: no visible global function definition for 'text'
venn4: no visible global function definition for 'plot'
venn4: no visible global function definition for 'lines'
venn4: no visible global function definition for 'runif'
venn4: no visible global function definition for 'points'
Undefined global functions or variables:
  combn legend lines plot points runif text title
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points", "text",
             "title")
  importFrom("stats", "runif")
  importFrom("utils", "combn")
to your NAMESPACE file.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    bin   3.1Mb
    doc   1.7Mb
L2eV: no visible binding for global variable 'constants'
L2w: no visible binding for global variable 'constants'
dielectric: no visible global function definition for 'new'
dielectric2plot: no visible global function definition for 'reshape'
eV2L: no visible binding for global variable 'constants'
t2eV: no visible binding for global variable 'constants'
Undefined global functions or variables:
  constants new reshape
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "reshape")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
adapreg: no visible global function definition for 'optimize'
adapreg: no visible global function definition for 'runif'
adapreg.m: no visible global function definition for 'lm'
epsilonCompute: no visible global function definition for 'median'
plot.dmap: no visible global function definition for 'plot'
plot.dmap: no visible global function definition for 'stripchart'
Undefined global functions or variables:
  lm median optimize plot runif stripchart
Consider adding
  importFrom("graphics", "plot", "stripchart")
  importFrom("stats", "lm", "median", "optimize", "runif")
to your NAMESPACE file.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    5.1Mb
    libs   1.4Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    5.6Mb
    libs   1.4Mb
'library' or 'require' calls to packages already attached by Depends:
  'maptools' 'spatstat' 'spdep'
  Please remove these calls from your code.
fAssocmatrix : fAssocmatrix1: no visible global function definition for
  'coordinates<-'
fAssocplot: no visible global function definition for 'plot'
fAssocplot: no visible global function definition for 'coordinates'
fAssocplot: no visible global function definition for 'text'
fAssocplot: no visible global function definition for 'box'
fDrawfigure: no visible global function definition for 'slot'
fDrawfigure : <anonymous>: no visible global function definition for
  'slot'
fDrawfigure: no visible global function definition for
  'SpatialPolygons'
fDrawfigure: no visible global function definition for 'spsample'
fDrawfigure: no visible global function definition for 'plot'
fDrawfigure: no visible global function definition for 'image'
fDrawfigure: no visible global function definition for
  'colorRampPalette'
fDrawfigure: no visible global function definition for 'points'
fRanXY : <anonymous>: no visible global function definition for 'slot'
fRanXY : <anonymous>: no visible global function definition for
  'spsample'
Undefined global functions or variables:
  SpatialPolygons box colorRampPalette coordinates coordinates<- image
  plot points slot spsample text
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "box", "image", "plot", "points", "text")
  importFrom("methods", "slot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages in Depends field not imported from:
  'Rcpp' 'igraph'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following hidden files and directories:
  .directory
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
distSegment: no visible global function definition for 'dist'
distShape: no visible global function definition for 'dist'
distTriangle: no visible global function definition for 'dist'
exactHausdorff: no visible global function definition for 'aggregate'
Undefined global functions or variables:
  aggregate dist
Consider adding
  importFrom("stats", "aggregate", "dist")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'car' 'prettyGraphs'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Chi2DistanceFromSort: no visible global function definition for
  'model.matrix'
GraphDistatisAll: no visible global function definition for
  'createColorVectorsByDesign'
GraphDistatisBoot: no visible global function definition for
  'createColorVectorsByDesign'
GraphDistatisBoot: no visible global function definition for
  'dataEllipse'
GraphDistatisBoot: no visible global function definition for
  'peeledHull'
GraphDistatisCompromise: no visible global function definition for
  'createColorVectorsByDesign'
GraphDistatisCompromise: no visible global function definition for
  'prettyPlot'
GraphDistatisPartial: no visible global function definition for
  'createColorVectorsByDesign'
GraphDistatisPartial: no visible global function definition for
  'points'
GraphDistatisPartial: no visible global function definition for
  'prettyPlot'
GraphDistatisRv: no visible global function definition for
  'createColorVectorsByDesign'
GraphDistatisRv: no visible global function definition for 'prettyPlot'
Undefined global functions or variables:
  createColorVectorsByDesign dataEllipse model.matrix peeledHull points
  prettyPlot
Consider adding
  importFrom("graphics", "points")
  importFrom("stats", "model.matrix")
to your NAMESPACE file.
'library' or 'require' call to 'glmnet' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'glmnet' 'tcltk'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    include  19.3Mb
    libs      1.3Mb
'library' or 'require' calls in package code:
  'FKF' 'dlm'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
dlmodeler.extract: no visible global function definition for 'qnorm'
dlmodeler.fit.MAD: no visible global function definition for 'optim'
dlmodeler.fit.MAPE: no visible global function definition for 'optim'
dlmodeler.fit.MLE: no visible global function definition for 'optim'
dlmodeler.fit.MSE: no visible global function definition for 'optim'
dlmodeler.fit.sigma : fit.fun: no visible global function definition
  for 'var'
dlmodeler.fit.sigma: no visible global function definition for 'optim'
dlmodeler.forecast: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  optim qnorm var
Consider adding
  importFrom("stats", "optim", "qnorm", "var")
to your NAMESPACE file.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   1.4Mb
Package suggested but not available for checking: 'rPython'
Warning: no function found corresponding to methods exports from 'DMwR' 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.
Packages in Depends field not imported from:
  'grid' 'lattice' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Missing object imported by a ':::' call: 'rpart:::rpconvert'
Unexported objects imported by ':::' calls:
  'rpart:::rpart.branch' 'rpart:::rpartco'
  'rpart:::string.bounding.box'
  See the note in ?`:::` about the use of this operator.
network.modules: no visible global function definition for
  'graph.empty'
network.modules: no visible global function definition for
  'add.vertices'
network.modules: no visible global function definition for 'add.edges'
network.modules: no visible global function definition for 'tkplot'
network.modules: no visible global function definition for 'V'
Undefined global functions or variables:
  V add.edges add.vertices graph.empty tkplot
.ccd.1.41: no visible global function definition for 'rnorm'
.ccd.1.41: no visible global function definition for 'formula'
.ccd.1.41: no visible global function definition for 'coef'
.ccd.1.41: no visible global function definition for 'runif'
.ccd.1.41 : <anonymous>: no visible global function definition for
  'as.formula'
.gen.des.old.way: no visible global function definition for 'runif'
.randomize: no visible global function definition for '[.coded.data'
Dopt.augment: no visible global function definition for 'rnorm'
Dopt.augment: no visible global function definition for 'as.formula'
Dopt.augment: no visible global function definition for 'model.matrix'
Dopt.design: no visible global function definition for 'as.formula'
Dopt.design: no visible global function definition for 'model.matrix'
Scalc: no visible global function definition for 'dist'
bbd.design: no visible global function definition for 'model.matrix'
ccd.augment: no visible global function definition for 'as.formula'
ccd.augment: no visible global function definition for 'model.matrix'
ccd.augment: no visible global function definition for 'model.frame'
ccd.augment: no visible binding for global variable 'na.pass'
generators.from.design: no visible global function definition for
  'formula'
generators.from.design : <anonymous>: no visible global function
  definition for 'as.formula'
lhs.design: no visible global function definition for 'cor'
rsm.design: no visible global function definition for 'as.formula'
rsmformula: no visible global function definition for 'formula'
Undefined global functions or variables:
  [.coded.data as.formula coef cor dist formula model.frame
  model.matrix na.pass rnorm runif
Consider adding
  importFrom("stats", "as.formula", "coef", "cor", "dist", "formula",
             "model.frame", "model.matrix", "na.pass", "rnorm", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: running command 'domino help' had status 127
See 'd:/Rcompile/CRANpkg/local/3.3/domino.Rcheck/00install.out' for details.
Running 'testthat.R' [0s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
    -  Login failed
  1: domino.login(Sys.getenv("TESTUSER"), Sys.getenv("TESTUSERPASS"), FALSE, "https://app.dominodatalab.com") at testthat/test-login.R:5
  2: domino.runCommand(loginCommand, domino.OK, "Login failed", theinput)
  3: domino.runCommandFromDefaultPath(commandAndArgs, successCallback, failureMessage, 
         stdInput)
  4: domino.handleCommandNotFound(failureMessage)
  5: stop(paste("Couldn't find domino client in the PATH or in default locations.\n  Add domino client directory path to PATH environment variable.\n  If you don't have domino client installed follow instructions on 'http://help.dominodatalab.com/client'.\n  If you use R-Studio Domino on GNU/Linux through a desktop launcher, add domino path to the .desktop file.\n\n  If you need more help, email support@dominodatalab.com or visit http://help.dominodatalab.com/troubleshooting\n\n  - ", 
         failureMessage), call. = FALSE)
  
  testthat results ================================================================
  OK: 1 SKIPPED: 0 FAILED: 1
  1. Error: The login command works (@test-login.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
.collapse: no visible global function definition for 'head'
Undefined global functions or variables:
  head
Consider adding
  importFrom("utils", "head")
to your NAMESPACE file.
Running 'doRUnit.R' [6s]
Running the tests in 'tests/doRUnit.R' failed.
Last 13 lines of output:
   done successfully.
  
  
  
  Executing test function test.registerDoRNG  ...  done successfully.
  
  ------------------- UNIT TEST SUMMARY ---------------------
  
  Error in .local(x, ...) : Functions: 2 | Errors: 1 | Failures: 0 
  ERROR in runit.dorng.R::test.dorng: Error in mpi.comm.spawn(slave = rscript, slavearg = args, nslaves = count,  : 
    Other MPI error, error stack:
  MPI_Comm_spawn(cmd="D:/RCompile/recent/R-33~1.3/bin/Rscript", argv=0x0000000006E95F08, maxprocs=2, MPI_INFO_NULL, root=0, MPI_COMM_SELF, intercomm=0x000000000A06BF08, errors=0x000000000A604E88) failed
  Function not implemented
  Calls: <Anonymous> -> <Anonymous> -> .local -> utest -> utest -> .local
  Execution halted
dostats: no visible binding for global variable 'na.fail'
first: no visible global function definition for 'head'
last: no visible global function definition for 'tail'
pval.default: no visible global function definition for '.hasSlot'
pval.lm: no visible global function definition for 'anova'
Undefined global functions or variables:
  .hasSlot anova head na.fail tail
Consider adding
  importFrom("methods", ".hasSlot")
  importFrom("stats", "anova", "na.fail")
  importFrom("utils", "head", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
compute_xsq: no visible global function definition for 'chisq.test'
Undefined global functions or variables:
  chisq.test
Consider adding
  importFrom("stats", "chisq.test")
to your NAMESPACE file.
DCEA: no visible global function definition for 'p.adjust'
DS: no visible global function definition for 'p.adjust'
DS: no visible global function definition for 'pdf'
DS: no visible global function definition for 'plot'
DS: no visible global function definition for 'dev.off'
LFC: no visible global function definition for 'glm'
LFC: no visible global function definition for 'predict'
PartialCor: no visible global function definition for 'na.omit'
comDCGLplot: no visible global function definition for 'pdf'
comDCGLplot: no visible global function definition for 'plot'
comDCGLplot: no visible global function definition for 'dev.off'
percentLinkfilter: no visible global function definition for 'cor'
qLinkfilter: no visible global function definition for 'cor'
qLinkfilter: no visible global function definition for 'pt'
qLinkfilter: no visible global function definition for 'p.adjust'
rLinkfilter: no visible global function definition for 'cor'
varianceBasedfilter: no visible binding for global variable 'var'
varianceBasedfilter: no visible global function definition for 'median'
varianceBasedfilter: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  cor dev.off glm median na.omit p.adjust pchisq pdf plot predict pt
  var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "plot")
  importFrom("stats", "cor", "glm", "median", "na.omit", "p.adjust",
             "pchisq", "predict", "pt", "var")
to your NAMESPACE file.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    2.9Mb
    libs   2.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    models   4.3Mb
NB: this package is only installed for sub-architecture 'x64'
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.
.file_attachment: no visible global function definition for
  'base64encode'
.plot_attachment: no visible global function definition for 'dev.off'
.update_list: no visible global function definition for 'modifyList'
easyHtmlReport: no visible global function definition for 'knit'
easyHtmlReport: no visible global function definition for
  'markdownToHTML'
mime_part.data.frame: no visible global function definition for
  'write.table'
mime_part.ggplot: no visible binding for global variable 'pdf'
mime_part.matrix: no visible global function definition for
  'write.table'
mime_part.trellis: no visible binding for global variable 'pdf'
simpleHtmlReport : <anonymous>: no visible global function definition
  for 'write.table'
Undefined global functions or variables:
  base64encode dev.off knit markdownToHTML modifyList pdf write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("utils", "modifyList", "write.table")
to your NAMESPACE file.
MARK.MCMC : Model.Creator: no visible global function definition for
  'combn'
MARK.MCMC : formula.Maker: no visible global function definition for
  'combn'
Simulate.CH: no visible global function definition for 'rnorm'
Simulate.CH: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  combn rbinom rnorm
Consider adding
  importFrom("stats", "rbinom", "rnorm")
  importFrom("utils", "combn")
to your NAMESPACE file.
ecipex: no visible binding for global variable 'nistiso'
ecipex : <anonymous>: no visible global function definition for 'nextn'
ecipex : <anonymous>: no visible global function definition for 'fft'
ecipex : <anonymous> : <anonymous>: no visible global function
  definition for 'fft'
Undefined global functions or variables:
  fft nextn nistiso
Consider adding
  importFrom("stats", "fft", "nextn")
to your NAMESPACE file.
UCexactTest: no visible global function definition for 'is'
UCexactTest: no visible global function definition for 'new'
pvalue: no visible global function definition for 'dnbinom'
pvalue: no visible global function definition for 'pnbinom'
sup.mu: no visible global function definition for 'predict'
Undefined global functions or variables:
  dnbinom is new pnbinom predict
Consider adding
  importFrom("methods", "is", "new")
  importFrom("stats", "dnbinom", "pnbinom", "predict")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
as.character.cateditmatrix: no visible global function definition for
  'str'
datamodel: no visible global function definition for 'stack'
localize: no visible global function definition for 'flush.console'
perturbWeights: no visible global function definition for 'runif'
plot.errorLocation: no visible global function definition for 'par'
plot.errorLocation: no visible global function definition for 'barplot'
plot.errorLocation: no visible global function definition for 'plot'
plot.errorLocation: no visible global function definition for 'grid'
plot.errorLocation: no visible global function definition for 'mtext'
plot.errorLocation: no visible global function definition for 'density'
plot.errorLocation: no visible global function definition for 'lines'
plot.errorLocation: no visible global function definition for 'axis'
plot.violatedEdits: no visible global function definition for 'par'
plot.violatedEdits: no visible global function definition for 'barplot'
plot.violatedEdits: no visible global function definition for 'plot'
plot.violatedEdits: no visible global function definition for 'mtext'
plotEditGraph: no visible global function definition for 'plot'
print.backtracker: no visible global function definition for 'ls.str'
removeRedundantDummies: no visible global function definition for
  'dist'
summary.errorLocation: no visible global function definition for
  'quantile'
summary.errorLocation : <anonymous>: no visible global function
  definition for 'quantile'
Undefined global functions or variables:
  axis barplot density dist flush.console grid lines ls.str mtext par
  plot quantile runif stack str
Consider adding
  importFrom("graphics", "axis", "barplot", "grid", "lines", "mtext",
             "par", "plot")
  importFrom("stats", "density", "dist", "quantile", "runif")
  importFrom("utils", "flush.console", "ls.str", "stack", "str")
to your NAMESPACE file.
.gdf : find_loss: no visible global function definition for 'rnorm'
.p.values : <anonymous>: no visible global function definition for
  'pnorm'
.relist.dwt: no visible global function definition for 'relist'
.relist.dwt: no visible global function definition for 'as'
.std.wav.coeff : <anonymous>: no visible global function definition for
  'mad'
regrid: no visible global function definition for 'predict'
regrid: no visible global function definition for 'var'
regrid: no visible global function definition for 'medpolish'
Undefined global functions or variables:
  as mad medpolish pnorm predict relist rnorm var
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "mad", "medpolish", "pnorm", "predict", "rnorm",
             "var")
  importFrom("utils", "relist")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' call to 'sna' which was already attached by Depends.
  Please remove these calls from your code.
read.egonet: no visible global function definition for 'read.csv'
Undefined global functions or variables:
  read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'class' 'quantreg'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cluster.segment: no visible global function definition for 'kmeans'
cluster.segment: no visible global function definition for 'knn'
comp.anc.dist: no visible global function definition for 'wilcox.test'
eila: no visible global function definition for 'hasArg'
get.prob.score: no visible global function definition for 'glm'
get.prob.score: no visible global function definition for 'binomial'
get.prob.score: no visible binding for global variable 'logit'
get.prob.score: no visible global function definition for 'predict'
quantreg.est: no visible global function definition for 'rnorm'
quantreg.est: no visible global function definition for 'rq.fit.fnb'
Undefined global functions or variables:
  binomial glm hasArg kmeans knn logit predict rnorm rq.fit.fnb
  wilcox.test
Consider adding
  importFrom("methods", "hasArg")
  importFrom("stats", "binomial", "glm", "kmeans", "predict", "rnorm",
             "wilcox.test")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    examples   4.5Mb
Likelihood: no visible global function definition for
  'makePSOCKcluster'
Likelihood: no visible global function definition for 'clusterExport'
Likelihood: no visible global function definition for 'makeForkCluster'
Likelihood.first.run: no visible global function definition for
  'clusterApply'
Likelihood.next.runs: no visible global function definition for
  'clusterApply'
es.stopCluster: no visible global function definition for 'stopCluster'
plot.es.pedigree: no visible global function definition for 'hasArg'
Undefined global functions or variables:
  clusterApply clusterExport hasArg makeForkCluster makePSOCKcluster
  stopCluster
Consider adding
  importFrom("methods", "hasArg")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    xsd   5.5Mb
'library' or 'require' calls to packages already attached by Depends:
  'clusterSim' 'earth'
  Please remove these calls from your code.
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.
distance: no visible global function definition for
  'data.Normalization'
emmatn: no visible global function definition for 'runif'
estimateModel: no visible global function definition for 'as.formula'
estimateModel: no visible global function definition for 'earth'
estimateModel: no visible global function definition for 'plotmo'
estimateModel: no visible global function definition for 'predict'
mutation: no visible global function definition for 'runif'
plot.emma: no visible global function definition for 'colorRampPalette'
plot.emma: no visible global function definition for 'par'
plot.emma: no visible global function definition for 'persp'
plot.emma: no visible global function definition for 'points'
plot.emma: no visible global function definition for 'trans3d'
Undefined global functions or variables:
  as.formula colorRampPalette data.Normalization earth par persp plotmo
  points predict runif trans3d
Consider adding
  importFrom("grDevices", "colorRampPalette", "trans3d")
  importFrom("graphics", "par", "persp", "points")
  importFrom("stats", "as.formula", "predict", "runif")
to your NAMESPACE file.
'library' or 'require' call to 'RColorBrewer' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'Rcmdr' 'gWidgets' 'gWidgetstcltk'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'Hmisc' 'RColorBrewer' 'vcd'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages in Depends field not imported from:
  'FactoMineR' 'MASS' 'Rcmdr' 'SensoMineR'
  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 'chron' which was already attached by Depends.
  Please remove these calls from your code.
cdf.ensembleMOSnormal: no visible global function definition for 'var'
cdf.ensembleMOSnormal: no visible global function definition for
  'pnorm'
cdf.fitMOSnormal: no visible binding for global variable 'var'
cdf.fitMOSnormal: no visible global function definition for 'pnorm'
crps.ensembleMOSnormal : crpsFunc: no visible global function
  definition for 'pnorm'
crps.ensembleMOSnormal : crpsFunc: no visible global function
  definition for 'dnorm'
crps.ensembleMOSnormal: no visible global function definition for 'var'
crps.fitMOSnormal : crpsFunc: no visible global function definition for
  'pnorm'
crps.fitMOSnormal : crpsFunc: no visible global function definition for
  'dnorm'
crps.fitMOSnormal: no visible global function definition for 'var'
fitMOSnormal: no visible global function definition for 'lm'
fitMOSnormal : objectiveFUN: no visible global function definition for
  'pnorm'
fitMOSnormal : objectiveFUN: no visible global function definition for
  'dnorm'
fitMOSnormal: no visible global function definition for 'optim'
quantileForecast.ensembleMOSnormal: no visible global function
  definition for 'var'
quantileForecast.ensembleMOSnormal: no visible global function
  definition for 'qnorm'
quantileForecast.fitMOSnormal: no visible binding for global variable
  'var'
quantileForecast.fitMOSnormal: no visible global function definition
  for 'qnorm'
Undefined global functions or variables:
  dnorm lm optim pnorm qnorm var
Consider adding
  importFrom("stats", "dnorm", "lm", "optim", "pnorm", "qnorm", "var")
to your NAMESPACE file.
'library' or 'require' call to 'plotrix' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'Hmisc' 'survival'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'plotrix'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'a.alpha.ade' 'a.coladd.ade' 'a.getcol.ade' 'a.glc'
plot.eb: no visible global function definition for 'plot'
plot.eb : <anonymous>: no visible global function definition for
  'lines'
plot.ebhistorical: no visible global function definition for 'palette'
plot.ebhistorical: no visible global function definition for 'dev.new'
plot.ebhistorical: no visible global function definition for 'par'
plot.ebhistorical: no visible global function definition for
  'topo.colors'
plot.ebhistorical: no visible global function definition for 'plot'
plot.ebhistorical: no visible global function definition for 'curve'
plot.ebhistorical: no visible global function definition for 'lines'
plot.ebhistoricalsummary: no visible global function definition for
  'topo.colors'
plot.ebhistoricalsummary: no visible global function definition for
  'dev.new'
plot.ebhistoricalsummary: no visible global function definition for
  'plot'
plot.ebhistoricalsummary: no visible global function definition for
  'axis'
plot.ebhistoricalsummary: no visible global function definition for
  'lines'
plot.ebhistoricalsummary: no visible global function definition for
  'legend'
Undefined global functions or variables:
  axis curve dev.new legend lines palette par plot topo.colors
Consider adding
  importFrom("grDevices", "dev.new", "palette", "topo.colors")
  importFrom("graphics", "axis", "curve", "legend", "lines", "par",
             "plot")
to your NAMESPACE file.
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.
eqs2lavaan: no visible binding for global variable 'r'
eqsCorr: no visible global function definition for 'cov2cor'
plotCov: no visible global function definition for 'cov2cor'
plotCov: no visible global function definition for 'par'
plotCov: no visible global function definition for 'image'
plotCov: no visible global function definition for 'axis'
Undefined global functions or variables:
  axis cov2cor image par r
Consider adding
  importFrom("graphics", "axis", "image", "par")
  importFrom("stats", "cov2cor")
to your NAMESPACE file.
ESEA.Main: no visible global function definition for 'rnorm'
ESEA.Main: no visible global function definition for 'sd'
ESEA.Main: no visible global function definition for 'p.adjust'
PlotGlobEdgeCorProfile: no visible global function definition for
  'plot'
PlotGlobEdgeCorProfile: no visible global function definition for
  'lines'
PlotGlobEdgeCorProfile: no visible global function definition for
  'colors'
PlotGlobEdgeCorProfile: no visible global function definition for
  'points'
PlotGlobEdgeCorProfile: no visible global function definition for
  'legend'
PlotGlobEdgeCorProfile: no visible global function definition for
  'text'
PlotPathwayGraph: no visible global function definition for 'par'
PlotPathwayGraph: no visible global function definition for 'plot'
PlotRunEnrichment: no visible global function definition for 'plot'
PlotRunEnrichment: no visible global function definition for 'lines'
PlotRunEnrichment: no visible global function definition for 'colors'
PlotRunEnrichment: no visible global function definition for 'text'
SavePathway2File: no visible global function definition for 'is'
calEdgeCorScore: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  colors is legend lines na.omit p.adjust par plot points rnorm sd text
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "legend", "lines", "par", "plot", "points",
             "text")
  importFrom("methods", "is")
  importFrom("stats", "na.omit", "p.adjust", "rnorm", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages in Depends field not imported from:
  'Hmisc' 'xtable'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
corr_p_cell: no visible global function definition for 'cov.wt'
iqr_cell: no visible global function definition for 'quantile'
iqr_cell: no visible global function definition for 'wtd.quantile'
mean_sd_cell: no visible global function definition for 'wtd.mean'
mean_sd_cell: no visible global function definition for 'wtd.var'
mode_cell: no visible global function definition for 'wtd.table'
quantile_cell: no visible global function definition for 'wtd.quantile'
quantile_cell: no visible global function definition for 'quantile'
stat_cell: no visible global function definition for 'quantile'
stat_cell: no visible global function definition for 'wtd.quantile'
stat_cell: no visible global function definition for 'wtd.mean'
stat_cell: no visible global function definition for 'wtd.var'
stat_cell: no visible global function definition for 'mad'
stat_cell: no visible global function definition for 'wtd.table'
Undefined global functions or variables:
  cov.wt mad quantile wtd.mean wtd.quantile wtd.table wtd.var
Consider adding
  importFrom("stats", "cov.wt", "mad", "quantile")
to your NAMESPACE file.
Running examples in 'etl-Ex.R' failed
The error most likely occurred in:

> ### Name: smart_download
> ### Title: Download only those files that don't already exist
> ### Aliases: smart_download
> 
> ### ** Examples
> 
> cars <- etl("mtcars")
Not a valid src. Creating a src_sqlite for you at:
D:\temp\RtmpC8qzAq\file283c1ba5348c.sqlite3
> urls <- c("http://www.google.com", "http://www.nytimes.com")
> smart_download(cars, src = urls)
trying URL 'http://www.google.com'
Content type 'text/html; charset=ISO-8859-1' length unknown
.......... 
downloaded 10 KB

trying URL 'http://www.nytimes.com'
Error in download.file(url, method = method, ...) : 
  cannot open URL 'http://www.nytimes.com'
Calls: smart_download -> mapply -> <Anonymous>
Execution halted
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
         }
         else {
             download.file(url, ...)
         }
     })(dots[[1L]][[2L]], dots[[2L]][[2L]])
  9: suppressWarnings(download.file(url, method = method, ...))
  10: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  11: download.file(url, method = method, ...)
  
  testthat results ================================================================
  OK: 22 SKIPPED: 0 FAILED: 1
  1. Error: smart_download works (@test-etl.R#103) 
  
  Error: testthat unit tests failed
  Execution halted
avec.cov: no visible global function definition for 'qnorm'
closPseudo: no visible global function definition for 'terms'
etmCIF: no visible global function definition for 'model.extract'
lines.etm: no visible global function definition for 'lines'
phiPseudo: no visible global function definition for 'terms'
plot.clos.etm: no visible global function definition for 'par'
plot.clos.etm: no visible global function definition for 'split.screen'
plot.clos.etm: no visible global function definition for 'screen'
plot.clos.etm: no visible global function definition for 'plot'
plot.clos.etm: no visible global function definition for 'axis'
plot.clos.etm: no visible global function definition for 'box'
plot.clos.etm: no visible global function definition for 'lines'
plot.clos.etm: no visible global function definition for 'close.screen'
plot.etm: no visible global function definition for 'plot'
plot.etm: no visible global function definition for 'lines'
plot.etmCIF: no visible global function definition for 'plot'
plot.etmCIF: no visible global function definition for 'lines'
plot.etmCIF: no visible global function definition for 'segments'
print.summary.etm: no visible global function definition for 'quantile'
print.summary.etmCIF: no visible global function definition for
  'quantile'
Undefined global functions or variables:
  axis box close.screen lines model.extract par plot qnorm quantile
  screen segments split.screen terms
Consider adding
  importFrom("graphics", "axis", "box", "close.screen", "lines", "par",
             "plot", "screen", "segments", "split.screen")
  importFrom("stats", "model.extract", "qnorm", "quantile", "terms")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'boot' 'xts' 'zoo'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages in Depends field not imported from:
  'lars' 'ncvreg'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plot.path: no visible global function definition for 'par'
plot.path: no visible global function definition for 'plot'
plot.path: no visible global function definition for 'axis'
plot.path: no visible global function definition for 'points'
plot.path: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline axis par plot points
Consider adding
  importFrom("graphics", "abline", "axis", "par", "plot", "points")
to your NAMESPACE file.
countBamInGRanges.exomeDepth: 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 'fields' 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: '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 'spatstat' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
eppSimDat: no visible global function definition for 'rnorm'
eppSimDat: no visible global function definition for 'rpois'
DirichletPolygons,SpatialPointsBreeding-missing: no visible global
  function definition for 'ripras'
barplot,epp: no visible global function definition for 'axis'
barplot,epp: no visible global function definition for 'par'
plot,SpatialPointsBreeding-eppMatrix: no visible global function
  definition for 'points'
plot,SpatialPointsBreeding-eppMatrix: no visible global function
  definition for 'text'
plot,SpatialPointsBreeding-eppMatrix: no visible global function
  definition for 'arrows'
plot,SpatialPointsBreeding-missing: no visible global function
  definition for 'points'
plot,SpatialPointsBreeding-missing: no visible global function
  definition for 'text'
Undefined global functions or variables:
  arrows axis par points ripras rnorm rpois text
Consider adding
  importFrom("graphics", "arrows", "axis", "par", "points", "text")
  importFrom("stats", "rnorm", "rpois")
to your NAMESPACE file.
index.citations: no visible global function definition for
  'txtProgressBar'
read.exsic: no visible global function definition for 'read.csv'
update.pb: no visible global function definition for
  'setTxtProgressBar'
Undefined global functions or variables:
  read.csv setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "read.csv", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
toJavaMatrix2D: no visible global function definition for 'is'
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
createFormula: no visible global function definition for 'tail'
createFormula: no visible global function definition for 'head'
createFormula: no visible global function definition for 'as.formula'
ezsim: no visible global function definition for 'runif'
plot.ezsim: no visible global function definition for 'quantile'
plot.ezsim: no visible global function definition for 'head'
plot.ezsim: no visible global function definition for 'tail'
plot.ezsim: no visible global function definition for 'plot'
plot.ezsim: no visible binding for global variable 'dnorm'
plot.ezsim: no visible binding for global variable 'pdf'
plot.ezsim: no visible global function definition for 'dev.off'
plot.ezsim : <anonymous>: no visible global function definition for
  'dev.new'
plot.summary.ezsim: no visible global function definition for 'head'
plot.summary.ezsim: no visible global function definition for 'tail'
plot.summary.ezsim: no visible binding for global variable 'pdf'
plot.summary.ezsim: no visible global function definition for 'dev.off'
plot.summary.ezsim : <anonymous>: no visible global function definition
  for 'dev.new'
Undefined global functions or variables:
  as.formula dev.new dev.off dnorm head pdf plot quantile runif tail
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf")
  importFrom("graphics", "plot")
  importFrom("stats", "as.formula", "dnorm", "quantile", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'Rgraphviz' 'corpcor' 'energy' 'mvnmle' 'mvnormtest' 'nFactors'
  'polycor'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/FamEvent.Rcheck/00install.out' for details.
Aggregation : foo: no visible global function definition for
  'weighted.mean'
Aggregation: no visible global function definition for 'txtProgressBar'
Aggregation: no visible global function definition for
  'setTxtProgressBar'
constructSYB: no visible global function definition for 'str'
fillCountryCode: no visible global function definition for 'na.omit'
getFAO: no visible global function definition for 'read.csv'
getWDImetaData: no visible global function definition for 'write.csv'
getWDItoSYB: no visible global function definition for 'na.omit'
lsgr: no visible global function definition for 'na.omit'
lsgr: no visible global function definition for 'coef'
lsgr: no visible global function definition for 'lm'
Undefined global functions or variables:
  coef lm na.omit read.csv setTxtProgressBar str txtProgressBar
  weighted.mean write.csv
Consider adding
  importFrom("stats", "coef", "lm", "na.omit", "weighted.mean")
  importFrom("utils", "read.csv", "setTxtProgressBar", "str",
             "txtProgressBar", "write.csv")
to your NAMESPACE file.
FHCSpsdo: no visible global function definition for 'is'
FastHCS: no visible global function definition for 'complete.cases'
compPcaParams: no visible global function definition for 'quantile'
compPcaParams: no visible global function definition for 'qchisq'
compPcaParams: no visible global function definition for 'qnorm'
compPcaParams: no visible global function definition for 'sd'
plot.FastHCS: no visible global function definition for 'plot'
plot.FastHCS: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline complete.cases is plot qchisq qnorm quantile sd
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("methods", "is")
  importFrom("stats", "complete.cases", "qchisq", "qnorm", "quantile",
             "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
FastPCS: no visible global function definition for 'complete.cases'
FastPCS: no visible global function definition for 'cov'
FastPCS: no visible global function definition for 'mahalanobis'
FastPCS: no visible global function definition for 'qchisq'
FastPCS: no visible global function definition for 'quantile'
plot.FastPCS: no visible global function definition for 'plot'
plot.FastPCS: no visible global function definition for 'abline'
plot.FastPCS: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  abline complete.cases cov mahalanobis plot qchisq quantile
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("stats", "complete.cases", "cov", "mahalanobis", "qchisq",
             "quantile")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/FastRWeb.Rcheck/00install.out' for details.
'library' or 'require' calls in package code:
  'RCurl' 'RJSONIO' 'XML' 'glmnet' 'httr' 'speedglm' 'tcltk' 'xtable'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'MASS' 'combinat' 'glmnet'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fcd.cluster: no visible global function definition for 'kmeans'
fcd.start: no visible global function definition for 'ginv'
fcd.start: no visible global function definition for 'glmnet'
gen.dcbm: no visible global function definition for 'rbinom'
gen.sbm: no visible global function definition for 'rbinom'
mis.cluster: no visible global function definition for 'permn'
spectral.clustering: no visible global function definition for 'kmeans'
Undefined global functions or variables:
  ginv glmnet kmeans permn rbinom
Consider adding
  importFrom("stats", "kmeans", "rbinom")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'R.matlab' 'RCurl' 'nlme' 'quadprog'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
FDRreg: no visible global function definition for 'dnorm'
colnormalize: no visible global function definition for 'sd'
efron: no visible global function definition for 'median'
efron: no visible global function definition for 'hist'
efron: no visible global function definition for 'glm'
efron: no visible binding for global variable 'poisson'
efron: no visible global function definition for 'qchisq'
efron: no visible global function definition for 'predict'
efron: no visible global function definition for 'quantile'
efron: no visible global function definition for 'lm'
efron: no visible global function definition for 'coef'
make.bspline.matrix: no visible global function definition for
  'quantile'
plotFDR: no visible global function definition for 'hist'
plotFDR: no visible global function definition for 'par'
plotFDR: no visible global function definition for 'plot'
plotFDR: no visible global function definition for 'axis'
plotFDR: no visible global function definition for 'lines'
plotFDR: no visible global function definition for 'legend'
plotFDR: no visible global function definition for 'rug'
plotFDR: no visible global function definition for 'title'
Undefined global functions or variables:
  axis coef dnorm glm hist legend lines lm median par plot poisson
  predict qchisq quantile rug sd title
Consider adding
  importFrom("graphics", "axis", "hist", "legend", "lines", "par",
             "plot", "rug", "title")
  importFrom("stats", "coef", "dnorm", "glm", "lm", "median", "poisson",
             "predict", "qchisq", "quantile", "sd")
to your NAMESPACE file.
read.hmd: no visible global function definition for 'read.table'
Undefined global functions or variables:
  read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
FeaLect: no visible global function definition for 'plot'
compute.logistic.score: no visible global function definition for
  'coef'
ignore.redundant: no visible global function definition for 'var'
train.doctor: no visible global function definition for 'coef'
train.doctor: no visible global function definition for 'predict'
Undefined global functions or variables:
  coef plot predict var
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "coef", "predict", "var")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'ggplot2' 'gridExtra'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
FFieldPtRepDemo: no visible global function definition for 'ggplot'
FFieldPtRepDemo: no visible binding for global variable 'mtcars'
FFieldPtRepDemo: no visible global function definition for 'aes'
FFieldPtRepDemo: no visible binding for global variable 'mpg'
FFieldPtRepDemo: no visible global function definition for 'geom_point'
FFieldPtRepDemo: no visible global function definition for 'geom_text'
FFieldPtRepDemo: no visible global function definition for 'ggtitle'
FFieldPtRepDemo: no visible global function definition for
  'geom_segment'
FFieldPtRepDemo: no visible global function definition for
  'grid.arrange'
Undefined global functions or variables:
  aes geom_point geom_segment geom_text ggplot ggtitle grid.arrange mpg
  mtcars
Consider adding
  importFrom("datasets", "mtcars")
to your NAMESPACE file.
bigsample.default: no visible global function definition for 'runif'
cmedian: no visible binding for global variable 'median'
cquantile: no visible binding for global variable 'quantile'
read.table.ffdf: no visible binding for global variable 'read.fwf'
read.table.ffdf: no visible binding for global variable 'read.table'
regtest.fforder: no visible global function definition for 'runif'
str.ff: no visible global function definition for 'str'
str.ffdf: no visible global function definition for 'str'
str.hi: no visible global function definition for 'str'
write.csv: no visible binding for global variable 'write.table'
write.csv2: no visible binding for global variable 'write.table'
Undefined global functions or variables:
  median quantile read.fwf read.table runif str write.table
Consider adding
  importFrom("stats", "median", "quantile", "runif")
  importFrom("utils", "read.fwf", "read.table", "str", "write.table")
to your NAMESPACE file.
fgeasy: no visible global function definition for 'dist'
fgeasy : cor.est: no visible global function definition for 'cor.test'
fgeasy: no visible binding for global variable 'var'
fgperm : runrand: no visible global function definition for 'runif'
fgperm : runrand: no visible global function definition for 'ave'
fgploc : runrand: no visible global function definition for 'runif'
fgploc : runrand: no visible global function definition for 'ave'
fyshuffle: no visible global function definition for 'runif'
plot.fg: no visible global function definition for 'par'
plot.fg: no visible global function definition for 'plot'
plot.fg: no visible global function definition for 'segments'
plot.fg: no visible binding for global variable 'quantile'
plot.fg: no visible global function definition for 'abline'
plot.fg: no visible global function definition for 'axis'
summary.fg: no visible binding for global variable 'quantile'
Undefined global functions or variables:
  abline ave axis cor.test dist par plot quantile runif segments var
Consider adding
  importFrom("graphics", "abline", "axis", "par", "plot", "segments")
  importFrom("stats", "ave", "cor.test", "dist", "quantile", "runif",
             "var")
to your NAMESPACE file.
fieldsim: no visible global function definition for 'rnorm'
midpoint: no visible global function definition for 'rnorm'
setAtlas_under: no visible global function definition for 'runif'
setCovf_under : Ibeta: no visible global function definition for
  'pbeta'
visualize: no visible global function definition for 'colorRampPalette'
Undefined global functions or variables:
  colorRampPalette pbeta rnorm runif
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "pbeta", "rnorm", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'filehash' 'DBI'
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  'RSQLite' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
createSQLite: no visible global function definition for 'dbDriver'
createSQLite: no visible global function definition for 'dbConnect'
createSQLite: no visible global function definition for
  'dbUnloadDriver'
createSQLite: no visible global function definition for 'dbGetQuery'
initializeSQLite: no visible global function definition for 'dbDriver'
initializeSQLite: no visible global function definition for 'dbConnect'
initializeSQLite: no visible global function definition for 'new'
dbDelete,filehashSQLite-character: no visible global function
  definition for 'dbGetQuery'
dbDisconnect,filehashSQLite: no visible global function definition for
  'dbUnloadDriver'
dbFetch,filehashSQLite-character: no visible global function definition
  for 'dbGetQuery'
dbInsert,filehashSQLite-character: no visible global function
  definition for 'dbGetQuery'
dbList,filehashSQLite: no visible global function definition for
  'dbGetQuery'
dbMultiFetch,filehashSQLite-character: no visible global function
  definition for 'dbGetQuery'
Undefined global functions or variables:
  dbConnect dbDriver dbGetQuery dbUnloadDriver new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' calls in package code:
  'XML' 'foreach' 'its' 'timeSeries' 'utils'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
'library' or 'require' calls in package code:
  'e1071' 'fUnitRoots' 'polynom'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
lsmacof: no visible global function definition for 'cmdscale'
plotInc: no visible global function definition for 'rainbow'
plotInc: no visible global function definition for 'plot'
prepareCalib: no visible global function definition for 'lm'
Undefined global functions or variables:
  cmdscale lm plot rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "plot")
  importFrom("stats", "cmdscale", "lm")
to your NAMESPACE file.
fishmove : coefs: no visible global function definition for 'coef'
fishmove : coefs: no visible global function definition for 'pf'
fishmove: no visible global function definition for 'lm'
fishmove: no visible global function definition for 'predict.lm'
fishmove.estimate: no visible global function definition for 'quantile'
fishmove.estimate : ddoublenorm: no visible global function definition
  for 'dnorm'
fishmove.query: no visible global function definition for 'hasArg'
fishmove.query : f: no visible global function definition for 'pnorm'
fishmove.query: no visible global function definition for 'uniroot'
pdk: no visible global function definition for 'hasArg'
pdk : eq: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  coef dnorm hasArg lm pf pnorm predict.lm quantile uniroot
Consider adding
  importFrom("methods", "hasArg")
  importFrom("stats", "coef", "dnorm", "lm", "pf", "pnorm", "predict.lm",
             "quantile", "uniroot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' call to 'clue' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'getData' 'newKccaObject'
Missing or unexported object: 'lme4::sigma'
FlimFormula: no visible global function definition for 'is'
FlimFormula: no visible global function definition for 'terms'
FlimFormula: no visible global function definition for 'reformulate'
ImputateMissingValues : RegFun: no visible global function definition
  for 'lm'
ImputateMissingValues : RegFun: no visible binding for global variable
  'na.omit'
ImputateMissingValues: no visible global function definition for
  'predict'
ImputateMissingValues: no visible global function definition for
  'model.matrix'
ImputateMissingValues: no visible global function definition for 'coef'
flimList: no visible global function definition for 'coef'
flimSD: no visible binding for global variable 'sd'
plot.flim: no visible global function definition for 'plot'
plot.flim: no visible global function definition for 'lines'
plot.flim: no visible global function definition for 'points'
plot.flimList: no visible global function definition for 'par'
plot.flimList: no visible global function definition for 'plot'
plot.flimboot: no visible global function definition for 'plot'
plot.flimboot: no visible global function definition for 'points'
plot.flimboot: no visible global function definition for 'lines'
spaplot: no visible global function definition for 'plot'
spaplot: no visible global function definition for 'lines'
Undefined global functions or variables:
  coef is lines lm model.matrix na.omit par plot points predict
  reformulate sd terms
Consider adding
  importFrom("graphics", "lines", "par", "plot", "points")
  importFrom("methods", "is")
  importFrom("stats", "coef", "lm", "model.matrix", "na.omit", "predict",
             "reformulate", "sd", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' call to 'rgl' which was already attached by Depends.
  Please remove these calls from your code.
Running 'testthat.R' [10m]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Cross validating the nnetar model
  Cross validating the stlm model
  Cross validating the tbats model
  Fitting the auto.arima model
  Fitting the nnetar model
  Fitting the stlm model
  Fitting the tbats model
  Fitting the ets model
  Fitting the thetam model
  testthat results ================================================================
  OK: 110 SKIPPED: 0 FAILED: 1
  1. Failure: Testing is.hybridModel(), fitted.hybridModel(), residuals.hybridModel(), and accuracy.hybridModel() (@test-hybridModel.R#73) 
  
  Error: testthat unit tests failed
  Execution halted
ForImp: no visible global function definition for 'head'
ForImp: no visible global function definition for 'tail'
ForImp: no visible global function definition for 'dist'
medianimp: no visible global function definition for 'quantile'
rancatmat: no visible global function definition for 'runif'
transfmatcat: no visible global function definition for 'qnorm'
transfmatcat: no visible global function definition for 'sd'
Undefined global functions or variables:
  dist head qnorm quantile runif sd tail
Consider adding
  importFrom("stats", "dist", "qnorm", "quantile", "runif", "sd")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
ForwardSearch.fit: no visible global function definition for 'glm.fit'
ForwardSearch.plot: no visible global function definition for 'lines'
ForwardSearch.pointwise.asymptotics: no visible global function
  definition for 'qnorm'
ForwardSearch.pointwise.asymptotics: no visible global function
  definition for 'dnorm'
Undefined global functions or variables:
  dnorm glm.fit lines qnorm
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "dnorm", "glm.fit", "qnorm")
to your NAMESPACE file.
GenObs: no visible global function definition for 'rnorm'
GenObs.T: no visible global function definition for 'rt'
MeasL: no visible global function definition for 'rbeta'
OutDet: no visible global function definition for 'median'
RanCur: no visible global function definition for 'rnorm'
init: no visible global function definition for 'prcomp'
Undefined global functions or variables:
  median prcomp rbeta rnorm rt
Consider adding
  importFrom("stats", "median", "prcomp", "rbeta", "rnorm", "rt")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'Rsocp' 'Rnlminb2' 'Rdonlp2'
'library' or 'require' calls in package code:
  'Rdonlp2' 'Rnlminb2' 'bcp' 'dplR' 'fGarch' 'mvoutlier'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'futile.any' 'futile.logger' 'quantmod' 'timeDate'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/frair.Rcheck/00install.out' for details.
.corfreq: no visible global function definition for 'complete.cases'
.covfreq: no visible global function definition for 'complete.cases'
.hclustvfreq: no visible global function definition for
  'complete.cases'
.quantilefreq : <anonymous>: no visible global function definition for
  'approx'
coef.biglmfreq: no visible global function definition for 'coef'
predict.biglmfreq: no visible global function definition for 'predict'
predict.lmfreq: no visible global function definition for 'predict'
summary.lmfreq: no visible global function definition for 'coef'
summary.lmfreq: no visible global function definition for 'pt'
summary.lmfreq: no visible global function definition for 'AIC'
update.biglmfreq: no visible global function definition for 'update'
Undefined global functions or variables:
  AIC approx coef complete.cases predict pt update
Consider adding
  importFrom("stats", "AIC", "approx", "coef", "complete.cases",
             "predict", "pt", "update")
to your NAMESPACE file.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    1.6Mb
    libs   1.4Mb
ROCscore: no visible global function definition for 'par'
ROCscore: no visible global function definition for 'axis'
ROCscore: no visible global function definition for 'mtext'
ROCscore: no visible global function definition for 'legend'
alphafrontier.2d: no visible global function definition for 'par'
alphafrontier.2d: no visible global function definition for 'polygon'
alphafrontier.2d: no visible global function definition for 'lines'
alphafrontier.2d: no visible global function definition for 'points'
alphafrontier.3d: no visible global function definition for 'layout'
alphafrontier.3d: no visible global function definition for 'barplot'
alphafrontier.3d: no visible global function definition for 'axis'
alphafrontier.3d: no visible global function definition for 'lines'
alphafrontier.3d: no visible global function definition for 'na.omit'
ordermfrontier.2d: no visible global function definition for 'par'
ordermfrontier.2d: no visible global function definition for 'polygon'
ordermfrontier.2d: no visible global function definition for 'lines'
ordermfrontier.2d: no visible global function definition for 'points'
ordermscore.boot: no visible global function definition for 'sd'
Undefined global functions or variables:
  axis barplot layout legend lines mtext na.omit par points polygon sd
Consider adding
  importFrom("graphics", "axis", "barplot", "layout", "legend", "lines",
             "mtext", "par", "points", "polygon")
  importFrom("stats", "na.omit", "sd")
to your NAMESPACE file.
cor.by.row: no visible global function definition for 'cor'
plot.fts: no visible global function definition for 'plot'
plot.fts: no visible global function definition for 'xy.coords'
plot.fts: no visible binding for global variable 'plot.xy'
read.csv.fts: no visible global function definition for 'read.csv'
write.csv.fts: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  cor plot plot.xy read.csv write.csv xy.coords
Consider adding
  importFrom("grDevices", "xy.coords")
  importFrom("graphics", "plot", "plot.xy")
  importFrom("stats", "cor")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
'library' or 'require' call to 'foreach' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
fxreturns: no visible binding for global variable 'FXRatesCHF'
fxreturns : <anonymous>: no visible global function definition for
  'tail'
gbreakpoints: no visible global function definition for '%dopar%'
gbreakpoints: no visible global function definition for 'foreach'
Undefined global functions or variables:
  %dopar% FXRatesCHF foreach tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'MASS' 'igraph'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
DBNScoreStep1: no visible global function definition for 'lm'
DBNScoreStep1: no visible global function definition for 'rlm'
DBNScoreStep1: no visible global function definition for 'pt'
DBNScoreStep2: no visible global function definition for 'lm'
DBNScoreStep2: no visible global function definition for 'rlm'
DBNScoreStep2: no visible global function definition for 'pt'
SimulGeneExpressionAR1: no visible global function definition for
  'rnorm'
SimulGeneExpressionAR1: no visible global function definition for 'ts'
SimulNetworkAdjMatrix: no visible global function definition for
  'runif'
Undefined global functions or variables:
  lm pt rlm rnorm runif ts
Consider adding
  importFrom("stats", "lm", "pt", "rnorm", "runif", "ts")
to your NAMESPACE file.
cvriskMSM: no visible global function definition for 'predict'
plotcvriskMSM: no visible global function definition for 'plot'
plotcvriskMSM: no visible binding for global variable 'lines'
plotcvriskMSM: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines plot predict
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "predict")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/gamsel.Rcheck/00install.out' for details.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    data    3.7Mb
    doc     2.9Mb
    tests   2.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      3.2Mb
contindic.gb2: no visible global function definition for 'contour'
contindic.gb2: no visible global function definition for 'box'
contindic.gb2: no visible global function definition for 'mtext'
contprof.gb2: no visible global function definition for 'image'
contprof.gb2: no visible global function definition for 'heat.colors'
contprof.gb2: no visible global function definition for 'contour'
contprof.gb2: no visible global function definition for 'text'
contprof.gb2: no visible global function definition for 'box'
dplot.cavgb2: no visible global function definition for 'par'
dplot.cavgb2: no visible global function definition for 'curve'
dplot.cavgb2: no visible global function definition for 'legend'
dplot.cavgb2: no visible global function definition for 'plot'
dplot.cavgb2: no visible global function definition for 'lines'
dplot.cgb2: no visible global function definition for 'curve'
dplot.cgb2: no visible global function definition for 'lines'
dplot.cgb2: no visible global function definition for 'legend'
plotsML.gb2: no visible global function definition for 'par'
plotsML.gb2: no visible global function definition for 'plot'
plotsML.gb2: no visible global function definition for 'abline'
plotsML.gb2: no visible global function definition for 'curve'
plotsML.gb2: no visible global function definition for 'legend'
saveplot : <local>: no visible global function definition for 'dev.set'
saveplot : <local>: no visible global function definition for
  'dev.print'
saveplot : <local>: no visible binding for global variable 'pdf'
Undefined global functions or variables:
  abline box contour curve dev.print dev.set heat.colors image legend
  lines mtext par pdf plot text
Consider adding
  importFrom("grDevices", "dev.print", "dev.set", "heat.colors", "pdf")
  importFrom("graphics", "abline", "box", "contour", "curve", "image",
             "legend", "lines", "mtext", "par", "plot", "text")
to your NAMESPACE file.
Package in Depends field not imported from: 'tools'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
DownloadGdelt: no visible global function definition for
  'packageVersion'
DownloadGdelt: no visible global function definition for
  'download.file'
GdeltZipToDataframe: no visible global function definition for
  'read.delim'
GdeltZipToDataframe: no visible global function definition for 'unzip'
GetSizeOfGDELT: no visible global function definition for 'read.delim'
IsValidGDELT: no visible global function definition for 'read.delim'
IsValidGDELT: no visible global function definition for 'md5sum'
NormEventCounts: no visible global function definition for
  'download.file'
NormEventCounts: no visible global function definition for 'read.csv'
Undefined global functions or variables:
  download.file md5sum packageVersion read.csv read.delim unzip
Consider adding
  importFrom("utils", "download.file", "packageVersion", "read.csv",
             "read.delim", "unzip")
to your NAMESPACE file.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.3Mb
Warning: no function found corresponding to methods exports from 'GenABEL' 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:
  'DatABEL' 'genetics' 'haplo.stats' 'hglm' 'qvalue'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'GenABEL.data' 'MASS' 'methods'
  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: 'genderdata'
Package suggested but not available for checking: 'RHugin'
fit.dbn: no visible global function definition for 'as'
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' calls to packages already attached by Depends:
  'igraph' 'splines'
  Please remove these calls from your code.
timedelay.lm: no visible global function definition for 'lm'
timedelay.lm: no visible global function definition for 'AIC'
timedelay.lm: no visible global function definition for 'pdf'
timedelay.lm: no visible global function definition for 'x11'
timedelay.lm: no visible global function definition for 'rainbow'
timedelay.lm: no visible global function definition for 'title'
timedelay.lm: no visible global function definition for 'lines'
timedelay.lm: no visible global function definition for 'predict'
timedelay.lm: no visible global function definition for 'points'
timedelay.lm: no visible global function definition for 'legend'
timedelay.lm: no visible global function definition for 'dev.off'
timedelay.univariate.lm: no visible global function definition for 'lm'
timedelay.univariate.lm: no visible global function definition for
  'AIC'
ts.bspline: no visible global function definition for 'lm'
ts.bspline: no visible global function definition for 'predict'
Undefined global functions or variables:
  AIC dev.off legend lines lm pdf points predict rainbow title x11
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "rainbow", "x11")
  importFrom("graphics", "legend", "lines", "points", "title")
  importFrom("stats", "AIC", "lm", "predict")
to your NAMESPACE file.
checkrows: no visible global function definition for 'rnorm'
cv.trendfilter: no visible binding for global variable 'sd'
plot.cv.trendfilter: no visible global function definition for 'plot'
plot.cv.trendfilter: no visible global function definition for 'lines'
plot.cv.trendfilter: no visible global function definition for 'points'
plot.cv.trendfilter: no visible global function definition for 'legend'
plot.gcv.genlasso: no visible global function definition for 'plot'
plot.gcv.genlasso: no visible global function definition for 'points'
plot.genlasso: no visible global function definition for 'par'
plot.genlasso: no visible global function definition for 'rainbow'
plot.genlasso: no visible global function definition for 'plot'
plot.genlasso: no visible global function definition for 'matplot'
plot.genlasso: no visible global function definition for 'abline'
plot.genlasso: no visible global function definition for 'text'
plot.genlasso: no visible global function definition for 'lines'
plot.trendfilter: no visible global function definition for 'plot'
plot.trendfilter: no visible global function definition for 'matplot'
predict.genlasso: no visible global function definition for 'coef'
softthresh: no visible global function definition for 'coef'
Undefined global functions or variables:
  abline coef legend lines matplot par plot points rainbow rnorm sd
  text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "legend", "lines", "matplot", "par",
             "plot", "points", "text")
  importFrom("stats", "coef", "rnorm", "sd")
to your NAMESPACE file.
GESTr: no visible global function definition for 'rnorm'
GESTr: no visible global function definition for 'sd'
GESTr : <anonymous>: no visible global function definition for 'pnorm'
TranSAM : magChange: no visible global function definition for 'median'
TranSAM : dstat: no visible global function definition for 'sd'
TranSAM: no visible binding for global variable 'sd'
TranSAM: no visible global function definition for 'quantile'
findReplicateGroups: no visible global function definition for 'qnorm'
findReplicateGroups: no visible global function definition for 'sd'
fitGMM : simulateData: no visible global function definition for
  'rnorm'
fitGMM : simulateData: no visible global function definition for 'sd'
fitGMM: no visible global function definition for 'median'
fitGMM: no visible global function definition for 'ks.test'
fitRockeDurbin: no visible global function definition for 'dist'
fitRockeDurbin : findLowGenes: no visible global function definition
  for 'median'
fitRockeDurbin : findLowGenes: no visible global function definition
  for 'mad'
fitRockeDurbin: no visible binding for global variable 'sd'
getMonotonicConfidences_multiclass: no visible global function
  definition for 'pnorm'
getMonotonicConfidences_multiclass: no visible global function
  definition for 'sd'
Undefined global functions or variables:
  dist ks.test mad median pnorm qnorm quantile rnorm sd
Consider adding
  importFrom("stats", "dist", "ks.test", "mad", "median", "pnorm",
             "qnorm", "quantile", "rnorm", "sd")
to your NAMESPACE file.
getopt: 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.
example.alpha: no visible global function definition for 'rnorm'
example.quadratic.approx: no visible global function definition for
  'rnorm'
generate_nnm: no visible global function definition for 'rnorm'
generate_nnm: no visible global function definition for 'rgamma'
generate_nnm: no visible global function definition for 'dnorm'
plot_nnm: no visible global function definition for 'stack'
testmatrix: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  dnorm rgamma rnorm stack
Consider adding
  importFrom("stats", "dnorm", "rgamma", "rnorm")
  importFrom("utils", "stack")
to your NAMESPACE file.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.6Mb
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'ggplot2'
A package should be listed in only one of these fields.
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.
ggroc: no visible global function definition for 'ggplot'
ggroc: no visible global function definition for 'aes'
ggroc: no visible global function definition for 'geom_point'
ggroc: no visible global function definition for 'geom_line'
ggroc: no visible global function definition for 'theme'
ggroc: no visible global function definition for 'element_text'
ggroc: no visible global function definition for 'labs'
ggroc: no visible global function definition for 'ggsave'
Undefined global functions or variables:
  aes element_text geom_line geom_point ggplot ggsave labs theme
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg18.masked'
  'BSgenome.Hsapiens.UCSC.hg19.masked'
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  21.0Mb
Package in Depends field not imported from: 'glmnet'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
glmnet.cr: no visible global function definition for 'glmnet'
plot.glmnet.cr: no visible binding for global variable 'sd'
plot.glmnet.cr: no visible global function definition for 'predict'
plot.glmnet.cr: no visible global function definition for 'plot'
plot.glmnet.cr: no visible global function definition for 'title'
plot.glmnet.cr: no visible global function definition for 'matplot'
plot.glmnet.cr: no visible global function definition for 'abline'
plot.glmnet.cr: no visible global function definition for 'axis'
Undefined global functions or variables:
  abline axis glmnet matplot plot predict sd title
Consider adding
  importFrom("graphics", "abline", "axis", "matplot", "plot", "title")
  importFrom("stats", "predict", "sd")
to your NAMESPACE file.
globalboosttest: no visible global function definition for 'predict'
globalboosttest: no visible global function definition for 'lm'
globalboosttest: no visible global function definition for 'glm'
globalboosttest: no visible binding for global variable 'binomial'
globalboosttest: no visible global function definition for 'points'
globalboosttest: no visible global function definition for 'AIC'
Undefined global functions or variables:
  AIC binomial glm lm points predict
Consider adding
  importFrom("graphics", "points")
  importFrom("stats", "AIC", "binomial", "glm", "lm", "predict")
to your NAMESPACE file.
'library' or 'require' call to 'fxregime' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
refit.breakpoints.glogisfit: no visible binding for global variable
  'head'
refit.breakpoints.glogisfit: no visible binding for global variable
  'tail'
summary.glogisfit: no visible global function definition for 'tail'
Undefined global functions or variables:
  head tail
Consider adding
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
estfun.gmmFct: no visible global function definition for 'is'
getModel.baseGel: no visible global function definition for 'is'
getModel.baseGmm: no visible global function definition for 'is'
getModel.constGmm: no visible global function definition for 'is'
plot.gel: no visible binding for global variable 'panel.smooth'
plot.gel: no visible binding for global variable 'points'
plot.gel: no visible global function definition for 'par'
plot.gel: no visible global function definition for 'dev.interactive'
plot.gel: no visible global function definition for 'plot'
plot.gmm: no visible binding for global variable 'panel.smooth'
plot.gmm: no visible binding for global variable 'points'
plot.gmm: no visible global function definition for 'par'
plot.gmm: no visible global function definition for 'dev.interactive'
plot.gmm: no visible global function definition for 'devAskNewPage'
plot.gmm: no visible global function definition for 'extendrange'
plot.gmm: no visible global function definition for 'plot'
plot.gmm: no visible global function definition for 'abline'
plot.gmm: no visible global function definition for 'lines'
plot.gmm: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline dev.interactive devAskNewPage extendrange is legend lines
  panel.smooth par plot points
Consider adding
  importFrom("grDevices", "dev.interactive", "devAskNewPage",
             "extendrange")
  importFrom("graphics", "abline", "legend", "lines", "panel.smooth",
             "par", "plot", "points")
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/gmum.r.Rcheck/00install.out' for details.
'library' or 'require' calls in package code:
  'lava' 'numDeriv' 'survival'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
cumres.lvmfit : myres: no visible global function definition for 'vars'
cumres.lvmfit: no visible global function definition for 'iid'
plot.cumres : sampleproc: no visible global function definition for
  'lines'
plot.cumres : predband : <anonymous>: no visible binding for global
  variable 'rgb'
plot.cumres : predband : <anonymous>: no visible global function
  definition for 'col2rgb'
plot.cumres : predband: no visible global function definition for
  'lines'
plot.cumres : predband: no visible global function definition for
  'polygon'
Undefined global functions or variables:
  col2rgb iid lines polygon rgb vars
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
  importFrom("graphics", "lines", "polygon")
to your NAMESPACE file.
gpairs: no visible global function definition for 'hclust'
gpairs: no visible global function definition for 'dist'
gpairs : scatterplot.panel: no visible global function definition for
  'lm'
gpairs : scatterplot.panel: no visible global function definition for
  'predict'
gpairs : scatterplot.panel: no visible global function definition for
  'prcomp'
gpairs : scatterplot.panel: no visible global function definition for
  'cor'
gpairs : scatterplot.panel: no visible global function definition for
  'cor.test'
gpairs : scatterplot.panel: no visible global function definition for
  'hsv'
gpairs : scatterplot.panel: no visible global function definition for
  'na.omit'
gpairs : scatterplot.panel: no visible global function definition for
  'pf'
gpairs : scatterplot.panel: no visible global function definition for
  'grey'
Undefined global functions or variables:
  cor cor.test dist grey hclust hsv lm na.omit pf prcomp predict
Consider adding
  importFrom("grDevices", "grey", "hsv")
  importFrom("stats", "cor", "cor.test", "dist", "hclust", "lm",
             "na.omit", "pf", "prcomp", "predict")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from 'gpclib' for: 'coerce', 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
read.polyfile: no visible global function definition for 'as'
write.polyfile: no visible global function definition for 'is'
write.polyfile: no visible global function definition for 'as'
[,gpc.poly: no visible global function definition for 'new'
append.poly,gpc.poly-gpc.poly: no visible global function definition
  for 'new'
coerce,data.frame-gpc.poly: no visible global function definition for
  'as'
coerce,list-gpc.poly: no visible global function definition for 'as'
coerce,matrix-gpc.poly: no visible global function definition for 'new'
coerce,numeric-gpc.poly: no visible global function definition for
  'new'
coerce,numeric-gpc.poly.nohole: no visible global function definition
  for 'new'
intersect,gpc.poly-gpc.poly: no visible global function definition for
  'as'
intersect,gpc.poly-gpc.poly: no visible global function definition for
  'new'
setdiff,gpc.poly-gpc.poly: no visible global function definition for
  'as'
setdiff,gpc.poly-gpc.poly: no visible global function definition for
  'new'
tristrip,gpc.poly: no visible global function definition for 'as'
union,gpc.poly-gpc.poly: no visible global function definition for 'as'
union,gpc.poly-gpc.poly: no visible global function definition for
  'new'
Undefined global functions or variables:
  as is new
Consider adding
  importFrom("methods", "as", "is", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running the tests in 'tests/bug1.R' failed.
Last 13 lines of output:
  'help.start()' for an HTML browser interface to help.
  Type 'q()' to quit R.
  
  > suppressMessages(library(gpclib))
  > to_numeric <- selectMethod(coerce, c("gpc.poly", "numeric"))
  > load("bug1_data.RData")
  > plot(p)  ## loads a polygon, looks fine
  > plot(as(vec, "gpc.poly"))  ## looks fine
  > clip <- to_numeric(p); str(clip)
   num [1:17] 1 7 0 570545 7890092 ...
  > 
  > ## Crashes R 2.14 and 2.15 (32-bit) on Windows
  > vec <- .Call("Rgpc_polygon_clip", vec, clip, 3, PACKAGE="gpclib")
Namespaces with empty importFrom:
  'scatterplot3d' 'sqldf'
Resdata : prepdata: no visible global function definition for 'sqldf'
gpca : Build3d: no visible global function definition for 'dev.new'
gpca : Build3d: no visible global function definition for
  'scatterplot3d'
gpca : Build3d: no visible global function definition for 'text'
gpca : Build3d: no visible global function definition for 'plot'
gpca : Build3d: no visible global function definition for 'abline'
gpca : Build3d: no visible global function definition for 'rect'
gpca: no visible global function definition for 'cor'
gpca: no visible global function definition for 'dev.new'
gpca: no visible global function definition for 'plot'
gpca: no visible global function definition for 'text'
gpca: no visible global function definition for 'abline'
gpca: no visible global function definition for 'rect'
gpca: no visible global function definition for 'scatterplot3d'
gpca: no visible global function definition for 'segments'
gpca: no visible global function definition for 'points'
gpca: no visible global function definition for 'write.table'
Undefined global functions or variables:
  abline cor dev.new plot points rect scatterplot3d segments sqldf text
  write.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "plot", "points", "rect", "segments",
             "text")
  importFrom("stats", "cor")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'foreach' 'ggplot2' 'isotone' 'plyr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/gpuR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/gputools.Rcheck/00install.out' for details.
Package in Depends field not imported from: 'dismo'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' calls in package code:
  'mgcv' 'rgl' 'tcltk'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
KL: no visible global function definition for 'complete.cases'
MergeNodes: no visible global function definition for 'colors'
cross.validate: no visible global function definition for 'runif'
fit.APFA: no visible global function definition for 'complete.cases'
fit.APFA: no visible global function definition for 'aggregate'
select.beagle: no visible global function definition for 'write.table'
select.beagle: no visible global function definition for 'aggregate'
select.beagle: no visible global function definition for 'colors'
simulateAPFA: no visible global function definition for 'runif'
st: no visible global function definition for 'colors'
Undefined global functions or variables:
  aggregate colors complete.cases runif write.table
Consider adding
  importFrom("grDevices", "colors")
  importFrom("stats", "aggregate", "complete.cases", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file.
accrualReport: multiple local function definitions for 'gg' with
  different formal arguments
bestcut2: no visible global function definition for 'pchisq'
cov.func: no visible global function definition for 'rbinom'
cov.func: no visible global function definition for 'cov'
cov.func: no visible global function definition for 'pnorm'
cox.summary: no visible global function definition for 'predict'
em.func: no visible global function definition for 'quantile'
genSurvData: no visible global function definition for 'rweibull'
greyzone.func: no visible global function definition for 'points'
greyzone.func: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline cov pchisq pnorm points predict quantile rbinom rweibull
Consider adding
  importFrom("graphics", "abline", "points")
  importFrom("stats", "cov", "pchisq", "pnorm", "predict", "quantile",
             "rbinom", "rweibull")
to your NAMESPACE file.
PostScriptTrace: no visible global function definition for
  'shortPathName'
pictureHull: no visible global function definition for 'chull'
picturePaths: no visible global function definition for 'n2mfrow'
readPicture : funPath: no visible global function definition for 'rgb'
drawPath,PictureChar: no visible global function definition for
  'polypath'
drawPath,PictureFill: no visible global function definition for
  'polypath'
drawPath,PictureStroke: no visible global function definition for
  'xinch'
drawPath,PictureStroke: no visible global function definition for
  'lines'
drawPath,PictureText: no visible global function definition for 'text'
Undefined global functions or variables:
  chull lines n2mfrow polypath rgb shortPathName text xinch
Consider adding
  importFrom("grDevices", "chull", "n2mfrow", "rgb")
  importFrom("graphics", "lines", "polypath", "text", "xinch")
  importFrom("utils", "shortPathName")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'gRain' 'gRbase' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plotgsCP: no visible global function definition for 'opts'
plotgsPower: no visible global function definition for 'opts'
qplotit: no visible global function definition for 'opts'
Undefined global functions or variables:
  opts
binding: no visible global function definition for 'rnorm'
binding: no visible binding for global variable 'var'
binding: no visible global function definition for 'uniroot'
equivonly: no visible global function definition for 'rnorm'
equivonly: no visible binding for global variable 'var'
equivonly: no visible global function definition for 'uniroot'
figureE: no visible global function definition for 'rgb'
figureEF: no visible global function definition for 'rgb'
nfix : f: no visible global function definition for 'pnorm'
nfix : f: no visible global function definition for 'qnorm'
nfix: no visible global function definition for 'uniroot'
nonbinding: no visible global function definition for 'rnorm'
nonbinding: no visible binding for global variable 'var'
nonbinding: no visible global function definition for 'uniroot'
oc: no visible global function definition for 'rnorm'
oc: no visible global function definition for 'var'
Undefined global functions or variables:
  pnorm qnorm rgb rnorm uniroot var
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "pnorm", "qnorm", "rnorm", "uniroot", "var")
to your NAMESPACE file.
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  
  2. Failure: segm returns correct output (@test_segm.R#17) ----------------------
  dim(dat$cna) not equal to c(104, 6).
  1/2 mismatches
  [1] 103 - 104 == -1
  
  
  testthat results ================================================================
  OK: 29 SKIPPED: 0 FAILED: 2
  1. Failure: cnv returns correct output (@test_cnv.R#18) 
  2. Failure: segm returns correct output (@test_segm.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
read.pattern: 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.
Error in re-building vignettes:
  ...
Loading required package: survival
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "ashg2012.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.3/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'ashg2012.tex' failed

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

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
Execution halted
PermanovaG: no visible global function definition for 'as.dist'
PermanovaG: no visible global function definition for 'as.formula'
Undefined global functions or variables:
  as.dist as.formula
Consider adding
  importFrom("stats", "as.dist", "as.formula")
to your NAMESPACE file.
Running 'testthat.R' [15s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  
  testthat results ================================================================
  OK: 50 SKIPPED: 0 FAILED: 8
  1. Error: gutenberg_get_mirror works (@test-download.R#13) 
  2. Failure: Can download Charles Dickens' Christmas Carol and Jane Austen's Persuasion (@test-download.R#22) 
  3. Failure: Can download Charles Dickens' Christmas Carol and Jane Austen's Persuasion (@test-download.R#23) 
  4. Failure: Can download Charles Dickens' Christmas Carol and Jane Austen's Persuasion (@test-download.R#31) 
  5. Failure: Can download Charles Dickens' Christmas Carol and Jane Austen's Persuasion (@test-download.R#32) 
  6. Failure: Can download books from a data frame with gutenberg_id column (@test-download.R#43) 
  7. Failure: We can download a file that only has a -8 version (@test-download.R#50) 
  8. Failure: read_zip_url can download and read a zip file (@test-utils.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
browseDataAsCSV: no visible global function definition for 'write.csv'
browseDataAsCSV: no visible global function definition for 'browseURL'
tcltkDialog: no visible global function definition for 'runif'
tl_get_column_name: no visible global function definition for 'tail'
.add,gTexttcltk-guiWidgetsToolkittcltk-character: no visible global
  function definition for 'rnorm'
.font<-,gTexttcltk-guiWidgetsToolkittcltk: no visible global function
  definition for 'rnorm'
.font<-,tcltkObject-guiWidgetsToolkittcltk: no visible global function
  definition for 'rnorm'
.gdf,guiWidgetsToolkittcltk: no visible global function definition for
  'head'
.visible<-,gGraphicstcltk-guiWidgetsToolkittcltk-ANY: no visible global
  function definition for 'dev.set'
Undefined global functions or variables:
  browseURL dev.set head rnorm runif tail write.csv
Consider adding
  importFrom("grDevices", "dev.set")
  importFrom("stats", "rnorm", "runif")
  importFrom("utils", "browseURL", "head", "tail", "write.csv")
to your NAMESPACE file.
GWLelast.est: no visible global function definition for 'dist'
GWLelast.inner: no visible global function definition for 'predict'
GWLelast.inner.parallel: no visible global function definition for
  'predict'
GWLelast.sel.bw: no visible global function definition for 'dist'
GWLelast.sel.bw: no visible global function definition for 'optimize'
Undefined global functions or variables:
  dist optimize predict
Consider adding
  importFrom("stats", "dist", "optimize", "predict")
to your NAMESPACE file.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
clustersG: no visible global function definition for 'combn'
pairneidist: no visible global function definition for 'as.dist'
pairneidist: no visible global function definition for 'combn'
steplimit : .TempletonProb: no visible global function definition for
  'integrate'
distance,Dna: no visible global function definition for 'dist'
distance,Dna: no visible global function definition for 'combn'
distance,Dna: no visible global function definition for 'as.dist'
pairnei,matrix: no visible global function definition for 'as.dist'
show,Dna: no visible global function definition for 'head'
Undefined global functions or variables:
  as.dist combn dist head integrate
Consider adding
  importFrom("stats", "as.dist", "dist", "integrate")
  importFrom("utils", "combn", "head")
to your NAMESPACE file.
Namespace with empty importFrom: 'utils'
hash: no visible global function definition for 'new'
is.hash: no visible global function definition for 'is'
Undefined global functions or variables:
  is new
Consider adding
  importFrom("methods", "is", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
extract_hazus_functions: no visible global function definition for
  'data'
Undefined global functions or variables:
  data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/hBayesDM.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/hdnom.Rcheck/00install.out' for details.
Packages in Depends field not imported from:
  'grplasso' 'lattice' 'rgl' 'splines'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
HubNetwork: no visible global function definition for 'rbinom'
HubNetwork: no visible global function definition for 'runif'
HubNetwork: no visible global function definition for 'cov2cor'
binaryMCMC: no visible global function definition for 'rbinom'
image.hbn: no visible global function definition for 'col2rgb'
image.hbn: no visible global function definition for 'rgb'
image.hbn: no visible global function definition for 'dev.new'
image.hbn: no visible global function definition for 'par'
image.hbn: no visible global function definition for 'image'
image.hcov: no visible global function definition for 'col2rgb'
image.hcov: no visible global function definition for 'rgb'
image.hcov: no visible global function definition for 'dev.new'
image.hcov: no visible global function definition for 'par'
image.hcov: no visible global function definition for 'image'
image.hglasso: no visible global function definition for 'col2rgb'
image.hglasso: no visible global function definition for 'rgb'
image.hglasso: no visible global function definition for 'dev.new'
image.hglasso: no visible global function definition for 'par'
image.hglasso: no visible global function definition for 'image'
plot.hbn: no visible global function definition for 'rgb'
plot.hbn: no visible global function definition for 'plot'
plot.hcov: no visible global function definition for 'rgb'
plot.hcov: no visible global function definition for 'plot'
plot.hglasso: no visible global function definition for 'rgb'
plot.hglasso: no visible global function definition for 'plot'
Undefined global functions or variables:
  col2rgb cov2cor dev.new image par plot rbinom rgb runif
Consider adding
  importFrom("grDevices", "col2rgb", "dev.new", "rgb")
  importFrom("graphics", "image", "par", "plot")
  importFrom("stats", "cov2cor", "rbinom", "runif")
to your NAMESPACE file.
Running examples in 'HiCfeat-Ex.R' failed
The error most likely occurred in:

> ### Name: borderAnalysisFun
> ### Title: Multivariate enrichment test for chromatin domain borders
> ### Aliases: borderAnalysisFun
> 
> ### ** Examples
> 
> # Load library HiCfeat
> library(HiCfeat)
> 
> # Load data example.
> data(dataExample) 
> 
> # Multiple logistic regression estimated by maximum likelihood
> print("Multiple logistic regression estimated by maximum likelihood")
[1] "Multiple logistic regression estimated by maximum likelihood"
> BA_res=borderAnalysisFun(genomicFeatureList.GR=dataExample$GenomicFeatureList.GR,
+ 	GFDataType="bed",annotNames=dataExample$AnnotNames,domains.GR=dataExample$Domains.GR,
+ 	seqInfoChr=dataExample$SeqInfoChr,analysisMode="MLR",binSize=500,borderSize=5e3,
+ 	LRT=FALSE,interactionTerms="",verbose=FALSE)
Error in .Primitive("c")(<S4 object of class "IRanges">) : 
  could not find symbol "recursive" in environment of the generic function
Calls: borderAnalysisFun ... compress_listData -> do.call -> do.call -> <Anonymous>
Execution halted
build.clusters.spatial: no visible global function definition for
  'kmeans'
build.clusters.spatial: no visible global function definition for
  'points'
mubz.copula: no visible global function definition for 'integrate'
perspcolor: no visible global function definition for 'terrain.colors'
rCMS: no visible global function definition for 'runif'
rSchlatherExcess: no visible global function definition for 'runif'
simul.maxlik.maxstable: no visible global function definition for
  'runif'
Undefined global functions or variables:
  integrate kmeans points runif terrain.colors
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "points")
  importFrom("stats", "integrate", "kmeans", "runif")
to your NAMESPACE file.
Unexported objects imported by ':::' calls:
  'ggplot2:::build_guides' 'ggplot2:::guide_axis'
  'ggplot2:::scales_list'
  See the note in ?`:::` about the use of this operator.
banded: no visible global function definition for 'toeplitz'
gpband: no visible global function definition for 'toeplitz'
hierband.cv: no visible global function definition for 'cov'
hierband.cv: no visible binding for global variable 'sd'
subdiag.thresh: no visible global function definition for 'uniroot'
subdiag.thresh: no visible global function definition for 'toeplitz'
Undefined global functions or variables:
  cov sd toeplitz uniroot
Consider adding
  importFrom("stats", "cov", "sd", "toeplitz", "uniroot")
to your NAMESPACE file.
Func.ABOD: no visible global function definition for 'combn'
Func.ABOD: no visible global function definition for 'var'
Func.SOD: no visible global function definition for 'var'
Func.trans : erf: no visible global function definition for 'pnorm'
Func.trans: no visible global function definition for 'sd'
Undefined global functions or variables:
  combn pnorm sd var
Consider adding
  importFrom("stats", "pnorm", "sd", "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
occupancy: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
PlotOptPower: no visible global function definition for 'bmp'
PlotOptPower: no visible global function definition for
  'filled.contour'
PlotOptPower: no visible global function definition for 'title'
PlotOptPower: no visible global function definition for 'grey.colors'
PlotOptPower: no visible global function definition for 'axis'
PlotOptPower: no visible global function definition for 'polygon'
PlotOptPower: no visible global function definition for 'legend'
PlotOptPower: no visible global function definition for 'mtext'
PlotOptPower: no visible global function definition for 'dev.off'
PlotOptPower: no visible global function definition for
  'terrain.colors'
ShowOptDesign: no visible global function definition for 'head'
diffVariantError: no visible global function definition for 'pbinom'
predictPoolNCP: no visible global function definition for 'data'
probDetEqual3: no visible global function definition for 'dbinom'
probDetEqual3: no visible global function definition for 'pbinom'
Undefined global functions or variables:
  axis bmp data dbinom dev.off filled.contour grey.colors head legend
  mtext pbinom polygon terrain.colors title
Consider adding
  importFrom("grDevices", "bmp", "dev.off", "grey.colors",
             "terrain.colors")
  importFrom("graphics", "axis", "filled.contour", "legend", "mtext",
             "polygon", "title")
  importFrom("stats", "dbinom", "pbinom")
  importFrom("utils", "data", "head")
to your NAMESPACE file.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.2Mb
File 'hSDM/libs/i386/hSDM.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'useful.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'hSDM.Nmixture.o', 'hSDM.Nmixture.iCAR.o', 'hSDM.ZIB.o',
      'hSDM.ZIB.iCAR.alteration.o', 'hSDM.ZIB.iCAR.o', 'hSDM.ZIP.o',
      'hSDM.ZIP.iCAR.alteration.o', 'hSDM.ZIP.iCAR.o',
      'hSDM.binomial.o', 'hSDM.binomial.iCAR.o', 'hSDM.poisson.o',
      'hSDM.poisson.iCAR.o', 'hSDM.siteocc.o', 'hSDM.siteocc.iCAR.o'
File 'hSDM/libs/x64/hSDM.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'useful.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'hSDM.Nmixture.o', 'hSDM.Nmixture.iCAR.o', 'hSDM.ZIB.o',
      'hSDM.ZIB.iCAR.alteration.o', 'hSDM.ZIB.iCAR.o', 'hSDM.ZIP.o',
      'hSDM.ZIP.iCAR.alteration.o', 'hSDM.ZIP.iCAR.o',
      'hSDM.binomial.o', 'hSDM.binomial.iCAR.o', 'hSDM.poisson.o',
      'hSDM.poisson.iCAR.o', 'hSDM.siteocc.o', 'hSDM.siteocc.iCAR.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Package in Depends field not imported from: 'testthat'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in 'humarray-Ex.R' failed
The error most likely occurred in:

> ### Name: chip.support
> ### Title: Retrieve current ChipInfo annotation object
> ### Aliases: chip.support
> 
> ### ** Examples
> 
> chip.support() # shows the current ChipInfo object (default is 'ImmunoChip' build 37)
ChipInfo for ImmunoChip with 196524 SNPs using hg19 coordinates:
             chr                  pos   |   A1   A2 QCcode        rs.id
imm_1_898835   1   [ 908972,  908972]   |    A <NA>   pass imm_1_898835
vh_1_1108138   1   [1118275, 1118275]   |    C    T   pass   rs61733845
vh_1_1110294   1   [1120431, 1120431]   |    A    G   pass    rs1320571
   rs9729550   1   [1135242, 1135242]   |    A    C   pass    rs9729550
   rs1815606   1   [1140435, 1140435]   |    G    T   pass    rs1815606
         ... ...                  ... ...  ...  ...    ...          ...
   rs2334082   Y [59032457, 59032457]   | <NA> <NA>   pass    rs2334082
   rs9724531   Y [59032665, 59032665]   | <NA> <NA>   pass    rs9724531
   rs4047358   Y [59032685, 59032685]   | <NA> <NA>   pass    rs4047358
   rs9724555   Y [59032785, 59032785]   | <NA> <NA>   pass    rs9724555
   rs9724556   Y [59032809, 59032809]   | <NA> <NA>   pass    rs9724556
> #/donttest{
> chip.support(build=36) # gives warning as hg19 version is currently loaded
Error in c(<S4 object of class "GRanges">, <S4 object of class "GRanges">,  : 
  could not find symbol "recursive" in environment of the generic function
Calls: chip.support ... liftOver -> liftOver -> .local -> unlist -> GRangesList
Execution halted
Calculate3D: no visible global function definition for 'persp'
CalculateHUM_Ex: no visible global function definition for 'combn'
CalculateHUM_Plot: no visible global function definition for 'plot'
CalculateHUM_Plot: no visible global function definition for 'polygon'
CalculateHUM_Plot: no visible global function definition for 'text'
CalculateHUM_Plot: no visible global function definition for 'points'
CalculateHUM_Plot: no visible global function definition for 'lines'
Undefined global functions or variables:
  combn lines persp plot points polygon text
Consider adding
  importFrom("graphics", "lines", "persp", "plot", "points", "polygon",
             "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
trying URL 'https://arxiv.org/e-print/1406.4806v1'
Content type 'application/x-eprint-tar' length 29273 bytes (28 KB)
==================================================
downloaded 28 KB

Quitting from lines 153-159 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: 'hurricaneexposuredata'
'library' or 'require' calls in package code:
  'hydroGOF' 'hydroTSM' 'parallel' 'vioplot'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
'library' or 'require' calls in package code:
  'lattice' 'maptools'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
maxmult: no visible global function definition for 'cov'
maxmult: no visible global function definition for 'nlm'
maxmult: no visible global function definition for 'optim'
mle: no visible global function definition for 'optim'
mle_restricted: no visible global function definition for 'optim'
rhyperdirichlet: no visible global function definition for 'runif'
triplot: no visible global function definition for 'quantile'
triplot: no visible global function definition for 'image'
triplot: no visible global function definition for 'contour'
triplot: no visible global function definition for 'segments'
triplot: no visible global function definition for 'text'
Undefined global functions or variables:
  contour cov image nlm optim quantile runif segments text
Consider adding
  importFrom("graphics", "contour", "image", "segments", "text")
  importFrom("stats", "cov", "nlm", "optim", "quantile", "runif")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'R.utils' 'ape'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
requiprobable: no visible global function definition for 'extract'
requiprobable : make.tree: no visible global function definition for
  'extract'
requiprobable : make.tree: no visible global function definition for
  'runif'
rgenetree: no visible global function definition for 'dbinom'
rgenetree: no visible global function definition for 'dnbinom'
rgenetree: no visible global function definition for 'runif'
rgenetree: no visible global function definition for 'rbinom'
rgenetree: no visible global function definition for 'rnbinom'
Undefined global functions or variables:
  dbinom dnbinom extract rbinom rnbinom runif
Consider adding
  importFrom("stats", "dbinom", "dnbinom", "rbinom", "rnbinom", "runif")
to your NAMESPACE file.
Dscores: no visible global function definition for 'filter'
Dscores: no visible global function definition for 'sd'
Gscores: no visible global function definition for 'filter'
MiniDscores: no visible global function definition for 'filter'
MiniDscores: no visible global function definition for 'object.size'
RobustScores: no visible global function definition for 'filter'
SplitHalf: no visible global function definition for 'cor'
TestRetest: no visible global function definition for 'filter'
TestRetest: no visible global function definition for 'cor'
WPRscores: no visible global function definition for 'filter'
WPRscores: no visible global function definition for 'quantile'
WPRscores: no visible global function definition for 'sd'
computeMinid: no visible global function definition for 'sd'
doP1P2: no visible global function definition for 'filter'
doP1P2: no visible global function definition for 'sd'
doP1P2P3P4: no visible global function definition for 'filter'
specialvar: no visible global function definition for 'var'
Undefined global functions or variables:
  cor filter object.size quantile sd var
Consider adding
  importFrom("stats", "cor", "filter", "quantile", "sd", "var")
  importFrom("utils", "object.size")
to your NAMESPACE file.
NLIP: no visible global function definition for 'combn'
aov.ibd: no visible global function definition for 'lm'
detect: no visible global function definition for 'combn'
ibdgen: no visible global function definition for 'winProgressBar'
ibdgen: no visible global function definition for 'txtProgressBar'
ibdgen: no visible global function definition for 'setWinProgressBar'
ibdgen: no visible global function definition for 'setTxtProgressBar'
Undefined global functions or variables:
  combn lm setTxtProgressBar setWinProgressBar txtProgressBar
  winProgressBar
Consider adding
  importFrom("stats", "lm")
  importFrom("utils", "combn", "setTxtProgressBar", "setWinProgressBar",
             "txtProgressBar", "winProgressBar")
to your NAMESPACE file.
CreateVoronoi: no visible global function definition for 'slot'
CreateVoronoi : <anonymous>: no visible global function definition for
  'slot'
CreateVoronoi: no visible global function definition for 'chull'
ExtractIMFi2D: no visible global function definition for 'par'
LocatedAtBoundary: no visible global function definition for
  'txtProgressBar'
LocatedAtBoundary: no visible global function definition for
  'setTxtProgressBar'
PlotFit: no visible global function definition for 'par'
iBEEMD: no visible global function definition for 'is'
iBEEMD: no visible global function definition for 'sd'
iBEEMD: no visible global function definition for 'txtProgressBar'
iBEEMD: no visible global function definition for 'rnorm'
iBEEMD: no visible global function definition for 'setTxtProgressBar'
iBEEMD: no visible global function definition for 'terrain.colors'
rbfcreate: no visible global function definition for 'is'
rbfcreate : rbfAssemble: no visible global function definition for
  'dist'
rbfinterp: no visible global function definition for 'is'
rbfinterp: no visible global function definition for 'dist'
Undefined global functions or variables:
  chull dist is par rnorm sd setTxtProgressBar slot terrain.colors
  txtProgressBar
Consider adding
  importFrom("grDevices", "chull", "terrain.colors")
  importFrom("graphics", "par")
  importFrom("methods", "is", "slot")
  importFrom("stats", "dist", "rnorm", "sd")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
..placeOrder: no visible global function definition for 'str'
.reqMktData.vignette: no visible global function definition for
  'flush.console'
e_portfolio_value: no visible global function definition for 'str'
print.eventPortfolioValue: no visible global function definition for
  'str'
print.twsContract: no visible global function definition for 'str'
print.twsContractDetails: no visible global function definition for
  'str'
print.twsOrder: no visible global function definition for 'str'
print.twsOrderState: no visible global function definition for 'str'
print.twsScannerSubscription: no visible global function definition for
  'str'
reqAccountUpdates: no visible binding for global variable 'timestamp'
reqContractDetails: no visible binding for global variable 'timestamp'
reqHistoricalData: no visible global function definition for
  'flush.console'
reqHistoricalData: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  flush.console str timestamp write.table
Consider adding
  importFrom("utils", "flush.console", "str", "timestamp", "write.table")
to your NAMESPACE file.
'library' or 'require' call to 'R2jags' 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:
  'R2WinBUGS' 'gWidgetsRGtk2'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.1Mb
    libs   1.1Mb
NB: this package is only installed for sub-architecture 'x64'
Packages in Depends field not imported from:
  'XML' 'vegan'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Error in re-building vignettes:
  ...
Quitting from lines 1546-1553 (pritikin-schmidt.Rnw) 
Error: processing vignette 'pritikin-schmidt.Rnw' failed with diagnostics:
Not implemented yet
Execution halted
UpdateSweepDataFrame: no visible global function definition for
  'read.csv'
UpdateSweepDataFrame: no visible global function definition for
  'write.csv'
WaveToTimeSeries: no visible global function definition for 'ts'
Undefined global functions or variables:
  read.csv ts write.csv
Consider adding
  importFrom("stats", "ts")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    help   1.2Mb
    libs  13.4Mb
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       4.2Mb
    extdata   1.0Mb
    include   2.8Mb
    libs     11.5Mb
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'count_compare'
heal_data: no visible global function definition for 'optimum_k'
heal_data: no visible global function definition for 'optimum_w'
heal_data: no visible global function definition for 'pred_for_w'
Undefined global functions or variables:
  optimum_k optimum_w pred_for_w
'library' or 'require' call to 'xtable' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'Rmpi' 'rsprng' 'snow'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
A.dep.tests: no visible global function definition for 'combn'
A.dep.tests: no visible global function definition for 'pchisq'
dependogram: no visible global function definition for 'makeCluster'
dependogram: no visible global function definition for
  'clusterSetupSPRNG'
dependogram: no visible global function definition for 'clusterCall'
dependogram: no visible global function definition for 'stopCluster'
dependogram: no visible global function definition for 'combn'
dependogram: no visible global function definition for 'plot'
dependogram: no visible global function definition for 'points'
dependogram: no visible global function definition for 'segments'
Undefined global functions or variables:
  clusterCall clusterSetupSPRNG combn makeCluster pchisq plot points
  segments stopCluster
Consider adding
  importFrom("graphics", "plot", "points", "segments")
  importFrom("stats", "pchisq")
  importFrom("utils", "combn")
to your NAMESPACE file.
interference: no visible global function definition for 'binomial'
interference: no visible global function definition for 'terms'
interference: no visible global function definition for 'coef'
interference: no visible global function definition for 'model.matrix'
ipw_interference: no visible binding for global variable 'integrate'
log_likelihood: no visible binding for global variable 'integrate'
log_likelihood: no visible global function definition for 'is'
logit_integrand: no visible global function definition for 'plogis'
logit_integrand: no visible global function definition for 'dbinom'
logit_integrand: no visible global function definition for 'dnorm'
print.interference: no visible global function definition for
  'quantile'
score_calc: no visible binding for global variable 'integrate'
score_calc : <anonymous>: no visible global function definition for
  'is'
score_matrix: no visible binding for global variable 'integrate'
wght_calc: no visible binding for global variable 'integrate'
wght_calc: no visible global function definition for 'is'
wght_deriv_calc: no visible binding for global variable 'integrate'
wght_deriv_calc : <anonymous>: no visible global function definition
  for 'is'
Undefined global functions or variables:
  binomial coef dbinom dnorm integrate is model.matrix plogis quantile
  terms
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "binomial", "coef", "dbinom", "dnorm", "integrate",
             "model.matrix", "plogis", "quantile", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
cgrad: no visible global function definition for 'res'
doshade: no visible global function definition for 'projection'
doshade: no visible global function definition for 'extent'
doshade: no visible global function definition for 'res'
doshade: no visible global function definition for 'raster'
doshade: no visible global function definition for 'extent<-'
Undefined global functions or variables:
  extent extent<- projection raster res
'library' or 'require' call to 'rgdal' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Missing or unexported object: 'rgdal::spTransform'
Unexported objects imported by ':::' calls:
  'intamap:::commonArea' 'intamap:::estimateAnisotropySc'
  See the note in ?`:::` about the use of this operator.
ClearBottomMenuPlot: no visible global function definition for 'rect'
InteractiveIGraph : mousedown: no visible global function definition
  for 'grconvertX'
InteractiveIGraph : mousedown: no visible global function definition
  for 'grconvertY'
InteractiveIGraph : dragmousemove: no visible global function
  definition for 'grconvertX'
InteractiveIGraph : dragmousemove: no visible global function
  definition for 'grconvertY'
InteractiveIGraph : dragmousemove: no visible global function
  definition for 'polygon'
InteractiveIGraph : mouseup: no visible global function definition for
  'grconvertX'
InteractiveIGraph : mouseup: no visible global function definition for
  'grconvertY'
InteractiveIGraph : keybd: no visible global function definition for
  'readClipboard'
InteractiveIGraph : keybd: no visible global function definition for
  'par'
PlotRegionGeneral: no visible global function definition for 'polygon'
plot.InteractiveIGraph: no visible global function definition for
  'plot'
plot.InteractiveIGraph: no visible global function definition for 'par'
plot.Menu: no visible global function definition for 'par'
plot.Menu: no visible binding for global variable 'rect'
plot.MenuItem: no visible binding for global variable 'strwidth'
plot.MenuItem: no visible binding for global variable 'strheight'
plot.MenuItem: no visible binding for global variable 'rect'
plot.MenuItem: no visible binding for global variable 'text'
plot.MenuLine: no visible binding for global variable 'rect'
Undefined global functions or variables:
  grconvertX grconvertY par plot polygon readClipboard rect strheight
  strwidth text
Consider adding
  importFrom("graphics", "grconvertX", "grconvertY", "par", "plot",
             "polygon", "rect", "strheight", "strwidth", "text")
  importFrom("utils", "readClipboard")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'chron' 'date'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Mo.Th.Ra.: no visible global function definition for 'aggregate'
daily_mean: no visible global function definition for 'aggregate'
date.time: no visible global function definition for 'chron'
date.time: no visible global function definition for 'years'
date.time: no visible global function definition for 'days'
date.time: no visible global function definition for 'hours'
par_calibration: no visible global function definition for 'date.mdy'
par_calibration: no visible global function definition for 'as.date'
par_calibration: no visible global function definition for 'aggregate'
plot_meas_sim: no visible global function definition for 'as.date'
plot_meas_sim: no visible global function definition for 'date.mdy'
plot_meas_sim: no visible global function definition for 'plot'
plot_meas_sim: no visible global function definition for 'par'
plot_meas_sim: no visible global function definition for 'legend'
shape_calibration: no visible global function definition for 'date.mdy'
shape_calibration: no visible global function definition for 'as.date'
shape_calibration: no visible global function definition for
  'aggregate'
Undefined global functions or variables:
  aggregate as.date chron date.mdy days hours legend par plot years
Consider adding
  importFrom("graphics", "legend", "par", "plot")
  importFrom("stats", "aggregate")
to your NAMESPACE file.
dataSimulate: no visible global function definition for 'runif'
dataSimulate: no visible global function definition for 'quantile'
dicretizeVector: no visible global function definition for 'quantile'
getFreqPattern: no visible global function definition for 'as'
measureRule: no visible global function definition for 'median'
voteAllRules: no visible global function definition for 'median'
Undefined global functions or variables:
  as median quantile runif
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "median", "quantile", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File 'iotools/libs/i386/iotools.dll':
  Found non-API call to R: 'getConnection'
File 'iotools/libs/x64/iotools.dll':
  Found non-API call to R: 'getConnection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'library' or 'require' calls in package code:
  'MCMCpack' 'mvtnorm' 'truncnorm'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
code.simple.gaps: no visible global function definition for 'tail'
multistateMCMC: no visible global function definition for 'write.table'
multistateMCMC: no visible global function definition for 'read.table'
multistateMCMC: no visible global function definition for 'tail'
multistateML: no visible global function definition for 'tail'
multistateML: no visible global function definition for 'write.table'
multistateML: no visible global function definition for 'read.table'
phylo2mafft: no visible global function definition for 'write.table'
read.beast : foo: no visible global function definition for 'head'
read.beast: no visible global function definition for 'tail'
read.starbeast: no visible global function definition for 'head'
trimEnds : replaceWithN : getIndex: no visible global function
  definition for 'head'
unresolve.clade: no visible global function definition for 'tail'
unresolve.clade: no visible global function definition for 'head'
write.fas: no visible global function definition for 'tail'
Undefined global functions or variables:
  head read.table tail write.table
Consider adding
  importFrom("utils", "head", "read.table", "tail", "write.table")
to your NAMESPACE file.
'library' or 'require' call to 'HH' 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:
  'RBGL' 'graph' 'igraph'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
convert_MITAB_to_edgeList: no visible global function definition for
  'combn'
convert_edgeList_to_graph: no visible global function definition for
  'ftM2graphNEL'
convert_edgeList_to_graph: no visible global function definition for
  'graph.data.frame'
convert_graph_to_edgeList: no visible global function definition for
  'edgeWeights'
convert_graph_to_edgeList: no visible global function definition for
  'get.edgelist'
convert_graph_to_edgeList: no visible global function definition for
  'E'
create_id_conversion_table: no visible global function definition for
  'write.table'
get_irefindex: no visible global function definition for 'read.table'
get_irefindex: no visible global function definition for
  'download.file'
get_irefindex: no visible global function definition for 'unzip'
summary_graph: no visible global function definition for
  'connectedComp'
summary_graph: no visible global function definition for 'subGraph'
summary_graph: no visible global function definition for 'clusters'
summary_graph: no visible global function definition for 'subgraph'
summary_graph: no visible global function definition for 'plot'
summary_graph: no visible binding for global variable
  'layout.fruchterman.reingold'
Undefined global functions or variables:
  E clusters combn connectedComp download.file edgeWeights ftM2graphNEL
  get.edgelist graph.data.frame layout.fruchterman.reingold plot
  read.table subGraph subgraph unzip write.table
Consider adding
  importFrom("graphics", "plot")
  importFrom("utils", "combn", "download.file", "read.table", "unzip",
             "write.table")
to your NAMESPACE file.
dendrify: no visible binding for global variable 'item'
dendrify: no visible binding for global variable 'node'
dendrify: no visible binding for global variable 'value'
exogenize: no visible binding for global variable 'item'
Undefined global functions or variables:
  item node value
EstimateIsingLL: no visible global function definition for 'combn'
EstimateIsingLL: no visible global function definition for 'loglin'
EstimateIsingPL: no visible global function definition for 'nlm'
EstimateIsingUni : <anonymous>: no visible global function definition
  for 'glm'
EstimateIsingUni : <anonymous>: no visible binding for global variable
  'binomial'
EstimateIsingUni: no visible binding for global variable 'coef'
Undefined global functions or variables:
  binomial coef combn glm loglin nlm
Consider adding
  importFrom("stats", "binomial", "coef", "glm", "loglin", "nlm")
  importFrom("utils", "combn")
to your NAMESPACE file.
'library' or 'require' call to 'proxy' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
isopam : core: no visible global function definition for 'dist'
isopam : core: no visible global function definition for 'write.table'
isopam : core: no visible global function definition for 'as.dist'
isopam : core: no visible global function definition for
  'txtProgressBar'
isopam : core: no visible global function definition for
  'setTxtProgressBar'
isopam : core: no visible global function definition for 'aggregate'
isopam: no visible binding for global variable 'var'
isopam: no visible global function definition for 'na.omit'
isopam: no visible global function definition for 'write.table'
isopam: no visible global function definition for 'bmp'
isopam: no visible global function definition for 'dev.off'
isotab: no visible global function definition for 'aggregate'
isotab : fshtest: no visible global function definition for 'dhyper'
isotab : fshtest : pnhyper: no visible global function definition for
  'phyper'
Undefined global functions or variables:
  aggregate as.dist bmp dev.off dhyper dist na.omit phyper
  setTxtProgressBar txtProgressBar var write.table
Consider adding
  importFrom("grDevices", "bmp", "dev.off")
  importFrom("stats", "aggregate", "as.dist", "dhyper", "dist",
             "na.omit", "phyper", "var")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar",
             "write.table")
to your NAMESPACE file.
Depends: includes the non-default packages:
  'partitions' 'VGAM' 'MASS' 'ape' 'apTreeshape' 'geiger' 'gtools'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  'MASS' 'VGAM' 'apTreeshape' 'ape' 'geiger' 'gtools' 'partitions'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
clusterVCV: no visible global function definition for 'estfun'
covc: no visible global function definition for 'sandwich'
ftest: no visible global function definition for 'vcovHC'
Undefined global functions or variables:
  estfun sandwich vcovHC
ARsensitivity.ci: no visible global function definition for 'residuals'
ARsensitivity.ci: no visible global function definition for 'lm'
ARsensitivity.ci: no visible global function definition for 'qf'
ARsensitivity.ci: no visible global function definition for 'fitted'
ARsensitivity.power: no visible global function definition for 'qf'
ARsensitivity.power: no visible global function definition for 'pf'
ARsensitivity.size: no visible global function definition for 'qf'
ARsensitivity.size: no visible global function definition for 'pf'
anderson.rubin.ci: no visible global function definition for 'qf'
anderson.rubin.ci: no visible global function definition for 'fitted'
anderson.rubin.ci: no visible global function definition for 'lm'
power.iv: no visible global function definition for 'qf'
power.iv: no visible global function definition for 'pf'
Undefined global functions or variables:
  fitted lm pf qf residuals
Consider adding
  importFrom("stats", "fitted", "lm", "pf", "qf", "residuals")
to your NAMESPACE file.
boxplot.james: no visible global function definition for 'mtext'
getBestSolutionValues.james : <anonymous>: no visible global function
  definition for 'tail'
isMinimizing: no visible global function definition for 'head'
isMinimizing: no visible global function definition for 'tail'
mergeJAMES.james: no visible global function definition for 'glob2rx'
plotConvergence.james : <anonymous> : <anonymous>: no visible global
  function definition for 'tail'
plotConvergence.james: no visible global function definition for 'tail'
plotConvergence.james: no visible global function definition for 'head'
plotConvergence.james : <anonymous>: no visible global function
  definition for 'tail'
plotConvergence.james: no visible global function definition for
  'matplot'
plotConvergence.james: no visible global function definition for
  'mtext'
summary.james: no visible global function definition for 'sd'
summary.james: no visible global function definition for 'median'
summary.james: no visible global function definition for 'IQR'
Undefined global functions or variables:
  IQR glob2rx head matplot median mtext sd tail
Consider adding
  importFrom("graphics", "matplot", "mtext")
  importFrom("stats", "IQR", "median", "sd")
  importFrom("utils", "glob2rx", "head", "tail")
to your NAMESPACE file.
getSysinfo: no visible global function definition for 'sessionInfo'
getVecInfo: no visible global function definition for 'sd'
isSeriesConstant: no visible global function definition for 'median'
labelMargins: no visible global function definition for 'mtext'
plotBG: no visible global function definition for 'plot'
plotBG: no visible global function definition for 'polygon'
plotBG: no visible global function definition for 'par'
plotColorScale: no visible global function definition for 'par'
plotColorScale: no visible global function definition for 'text'
plotImageRotated: no visible global function definition for
  'heat.colors'
plotImageRotated: no visible global function definition for 'par'
plotImageRotated: no visible global function definition for 'plot'
plotImageRotated: no visible global function definition for 'image'
plotImageRotated: no visible global function definition for 'axis'
plotNLines: no visible global function definition for 'par'
plotNLines: no visible global function definition for 'plot'
plotNLines: no visible global function definition for 'mtext'
plotNLines: no visible global function definition for 'axis'
plotNLines: no visible global function definition for 'points'
plotNLines: no visible global function definition for 'sd'
userCoords: no visible global function definition for 'par'
Undefined global functions or variables:
  axis heat.colors image median mtext par plot points polygon sd
  sessionInfo text
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "axis", "image", "mtext", "par", "plot",
             "points", "polygon", "text")
  importFrom("stats", "median", "sd")
  importFrom("utils", "sessionInfo")
to your NAMESPACE file.
Package unavailable to check Rd xrefs: 'doMC'
'library' or 'require' call to 'igraph' which was already attached by Depends.
  Please remove these calls from your code.
JGL: no visible global function definition for 'cov'
admm.iters: no visible global function definition for 'cov'
admm.iters.unconnected: no visible global function definition for 'var'
plot.jgl: no visible global function definition for 'plot'
Undefined global functions or variables:
  cov plot var
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "cov", "var")
to your NAMESPACE file.
.generate.mac.script: no visible global function definition for
  'download.file'
.generate.windows.script: no visible global function definition for
  'download.file'
JGR: no visible global function definition for 'install.packages'
installPackages: no visible global function definition for
  'available.packages'
installPackages: no visible global function definition for
  'contrib.url'
print.hsearch: no visible global function definition for 'browseURL'
Undefined global functions or variables:
  available.packages browseURL contrib.url download.file
  install.packages
Consider adding
  importFrom("utils", "available.packages", "browseURL", "contrib.url",
             "download.file", "install.packages")
to your NAMESPACE file.
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    dict  19.2Mb
JBTest: no visible global function definition for 'pchisq'
generateSignificance: no visible global function definition for 'pnorm'
packages: no visible global function definition for 'install.packages'
shift: no visible global function definition for 'tail'
shift: no visible global function definition for 'head'
splitBy: no visible global function definition for 'head'
Undefined global functions or variables:
  head install.packages pchisq pnorm tail
Consider adding
  importFrom("stats", "pchisq", "pnorm")
  importFrom("utils", "head", "install.packages", "tail")
to your NAMESPACE file.
sonarCSV: 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.
qtls: no visible global function definition for 'quantile'
qtls: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm quantile
Consider adding
  importFrom("stats", "pnorm", "quantile")
to your NAMESPACE file.
as.matrix.multiPhylo : tip2tip: no visible global function definition
  for 'cophenetic'
bw.nn : <anonymous>: no visible global function definition for
  'quantile'
dist.diss: no visible binding for global variable 'median'
dist.diss: no visible global function definition for 'dist'
hist.kdetrees: no visible binding for global variable 'density'
kdetrees : cutoff: no visible global function definition for 'quantile'
kdetrees.complete: no visible global function definition for 'plot'
kdetrees.complete: no visible global function definition for 'hist'
kdetrees.complete: no visible global function definition for
  'write.csv'
plot.kdetrees: no visible binding for global variable 'density'
Undefined global functions or variables:
  cophenetic density dist hist median plot quantile write.csv
Consider adding
  importFrom("graphics", "hist", "plot")
  importFrom("stats", "cophenetic", "density", "dist", "median",
             "quantile")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Checking should be performed on sources prepared by 'R CMD build'.
Packages in Depends field not imported from:
  'chron' 'date' 'evir'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ALbw: no visible global function definition for 'sd'
ALbw: no visible global function definition for 'quantile'
CVbw: no visible global function definition for 'quantile'
PBbw: no visible global function definition for 'sd'
PBbw: no visible global function definition for 'IQR'
kernel_function: no visible global function definition for 'dnorm'
kernel_function_distribution: no visible global function definition for
  'pnorm'
simp_int: no visible global function definition for 'approx'
Undefined global functions or variables:
  IQR approx dnorm pnorm quantile sd
Consider adding
  importFrom("stats", "IQR", "approx", "dnorm", "pnorm", "quantile",
             "sd")
to your NAMESPACE file.
installed size is 45.9Mb
  sub-directories of 1Mb or more:
    visit_1  23.0Mb
    visit_2  22.8Mb
kissmigDummyS: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
distrct.analysis : <anonymous> : <anonymous>: no visible global
  function definition for 'cor'
grand.table: no visible global function definition for 'write.csv2'
grand.table: no visible global function definition for 'write.csv'
klausur: no visible global function definition for 'sd'
klausur: no visible global function definition for 'na.omit'
klausur.gen.marks : suggestion : <anonymous>: no visible global
  function definition for 'qnorm'
klausur.mufo: no visible global function definition for 'sd'
klausur.report: no visible global function definition for 'dev.off'
klausur.report : tabellenbau: no visible global function definition for
  'capture.output'
plot,klausuR-missing: no visible global function definition for
  'na.omit'
plot,klausuR-missing: no visible global function definition for 'sd'
plot,klausuR-missing : <anonymous>: no visible global function
  definition for 'dnorm'
Undefined global functions or variables:
  capture.output cor dev.off dnorm na.omit qnorm sd write.csv
  write.csv2
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("stats", "cor", "dnorm", "na.omit", "qnorm", "sd")
  importFrom("utils", "capture.output", "write.csv", "write.csv2")
to your NAMESPACE file.
C_zero : <anonymous>: no visible global function definition for 'runif'
get_extra_centroid_index: no visible global function definition for
  'head'
get_within_cluster_ss: no visible global function definition for
  'aggregate'
kmod: no visible global function definition for 'head'
kmod: no visible global function definition for 'tail'
Undefined global functions or variables:
  aggregate head runif tail
Consider adding
  importFrom("stats", "aggregate", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
knockoff.filter: no visible global function definition for 'rnorm'
random_problem : y.sample: no visible global function definition for
  'rnorm'
rnorm_matrix: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   2.1Mb
kselection: no visible global function definition for 'txtProgressBar'
kselection: no visible global function definition for
  'setTxtProgressBar'
plot.Kselection: no visible global function definition for 'plot'
plot.Kselection: no visible global function definition for 'lines'
plot.Kselection: no visible global function definition for 'legend'
Undefined global functions or variables:
  legend lines plot setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
auc: no visible global function definition for 'approx'
kulife.colors: no visible global function definition for 'palette'
rootonorm: no visible global function definition for 'sd'
rootonorm: no visible global function definition for 'hist'
rootonorm: no visible global function definition for 'pnorm'
rootonorm: no visible global function definition for 'dnorm'
rootonorm: no visible global function definition for 'plot'
rootonorm: no visible global function definition for 'rect'
rootonorm: no visible global function definition for 'lines'
rootonorm: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline approx dnorm hist lines palette plot pnorm rect sd
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "abline", "hist", "lines", "plot", "rect")
  importFrom("stats", "approx", "dnorm", "pnorm", "sd")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'GPArotation' 'mice'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
angoff: no visible global function definition for 'cov2cor'
angoff: no visible global function definition for 'runif'
cov.lambda4: no visible global function definition for 'cov2cor'
cov.lambda4: no visible global function definition for 'median'
guttman: no visible global function definition for 'cov2cor'
impute.cov: no visible global function definition for 'cov'
impute.cov: no visible global function definition for 'complete'
impute.cov: no visible global function definition for 'mice'
kristof: no visible global function definition for 'cov2cor'
kristof: no visible global function definition for 'runif'
lambda1: no visible global function definition for 'cov2cor'
lambda2: no visible global function definition for 'cov2cor'
lambda3: no visible global function definition for 'cov2cor'
lambda3: no visible binding for global variable 'sd'
lambda5: no visible global function definition for 'cov2cor'
lambda6: no visible global function definition for 'cov2cor'
omega.tot: no visible global function definition for 'cov2cor'
omega.tot: no visible global function definition for 'factanal'
quant.lambda4: no visible global function definition for 'cov2cor'
quant.lambda4: no visible global function definition for 'runif'
quant.lambda4: no visible global function definition for 'quantile'
raju: no visible global function definition for 'cov2cor'
raju: no visible global function definition for 'runif'
user.lambda4: no visible global function definition for 'runif'
user.lambda4: no visible binding for global variable 'sd'
Undefined global functions or variables:
  complete cov cov2cor factanal median mice quantile runif sd
Consider adding
  importFrom("stats", "cov", "cov2cor", "factanal", "median", "quantile",
             "runif", "sd")
to your NAMESPACE file.
Versioned 'LinkingTo' value for 'RcppParallel' is only usable in R >= 3.0.2
getGO: no visible global function definition for 'new'
getGO: no visible global function definition for 'getGeneric'
graph.kd: no visible global function definition for 'as'
Undefined global functions or variables:
  as getGeneric new
Consider adding
  importFrom("methods", "as", "getGeneric", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' calls in package code:
  'MASS' 'lattice' 'lme4' 'rms' 'zipfR'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs           3.1Mb
    testdata       1.8Mb
    vignettedata   2.0Mb
glassoscore: no visible global function definition for 'var'
glassoscore: no visible global function definition for 'pchisq'
lassoscore: no visible global function definition for 'txtProgressBar'
lassoscore: no visible global function definition for
  'setTxtProgressBar'
lassoscore: no visible global function definition for 'pchisq'
plot.glassoscore: no visible global function definition for 'legend'
plot.lassoscore: no visible global function definition for 'legend'
plot.mbscore: no visible global function definition for 'legend'
qqpval: no visible global function definition for 'ppoints'
qqpval: no visible global function definition for 'qbeta'
qqpval: no visible global function definition for 'points'
qqpval: no visible global function definition for 'plot'
qqpval: no visible global function definition for 'abline'
qqpval: no visible global function definition for 'polygon'
Undefined global functions or variables:
  abline legend pchisq plot points polygon ppoints qbeta
  setTxtProgressBar txtProgressBar var
Consider adding
  importFrom("graphics", "abline", "legend", "plot", "points", "polygon")
  importFrom("stats", "pchisq", "ppoints", "qbeta", "var")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    dataset   1.4Mb
    include   3.8Mb
    libs      2.0Mb
'library' or 'require' calls to packages already attached by Depends:
  'spam' 'spatstat' 'spdep' 'splancs'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'spam' 'spatstat' 'spdep' 'splancs'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' calls to packages already attached by Depends:
  'mvtnorm' 'survival'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'lava' 'mvtnorm' 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dens.norm: no visible global function definition for 'dnorm'
init.norm: no visible global function definition for 'var'
init.norm: no visible global function definition for 'cutree'
init.norm: no visible global function definition for 'hclust'
init.norm: no visible global function definition for 'dist'
optim.const.ordi: no visible binding for global variable 'k'
optim.const.ordi: no visible global function definition for 'coef'
Undefined global functions or variables:
  coef cutree dist dnorm hclust k var
Consider adding
  importFrom("stats", "coef", "cutree", "dist", "dnorm", "hclust", "var")
to your NAMESPACE file.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    geojson  12.1Mb
Package in Depends field not imported from: 'IndependenceTests'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/lgcp.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      3.4Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
LinearizedSVRTrain: no visible global function definition for 'kmeans'
sigma.est: no visible global function definition for 'median'
sigma.est: no visible global function definition for 'dist'
Undefined global functions or variables:
  dist kmeans median
Consider adding
  importFrom("stats", "dist", "kmeans", "median")
to your NAMESPACE file.
'library' or 'require' call to 'scatterplot3d' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to 'rgl' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc        1.8Mb
    libs       2.1Mb
    testdata   1.5Mb
AnalyticalOptim: no visible global function definition for 'optim'
LLConstructor : LL: no visible global function definition for 'dpois'
MixtureDensity: no visible global function definition for 'glm'
MixtureDensity : f_hat: no visible global function definition for
  'predict'
NullDensity : f0: no visible global function definition for 'dpois'
Undefined global functions or variables:
  dpois glm optim predict
Consider adding
  importFrom("stats", "dpois", "glm", "optim", "predict")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'mclust' 'rgl' 'tkrplot'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
amendColumns: no visible global function definition for 'setNames'
fillColumns: no visible global function definition for 'setNames'
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
TOS2D: no visible global function definition for 'medpolish'
countTextures: no visible global function definition for 'medpolish'
plot.imageQT: no visible global function definition for 'segments'
simTexture: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  medpolish rnorm segments
Consider adding
  importFrom("graphics", "segments")
  importFrom("stats", "medpolish", "rnorm")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'R2wd' 'ggplot2' 'metafor'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is 41.3Mb
  sub-directories of 1Mb or more:
    doc    6.9Mb
    libs  34.2Mb
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.3/maps/libs/i386/maps.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.3/maps/libs/x64/maps.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
':::' call which should be '::': 'leaflet:::getMapData'
  See the note in ?`:::` about the use of this operator.
'library' or 'require' call to 'MARSS' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'tcltk'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: 'MARSS:::is.diagonal'
  See the note in ?`:::` about the use of this operator.
.b64EncodeImages : .b64EncodeImgSrc: no visible global function
  definition for 'URLdecode'
Undefined global functions or variables:
  URLdecode
Consider adding
  importFrom("utils", "URLdecode")
to your NAMESPACE file.
Running 'testthat.R' [11s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  Loading required package: survival
  testthat results ================================================================
  OK: 97 SKIPPED: 0 FAILED: 1
  1. Failure: Check steadyStates (@testSteadyStates.R#39) 
  
  Error: testthat unit tests failed
  In addition: Warning messages:
  1: In markovchainFit(mix_seq, "map", sanitize = TRUE, possibleStates = c("d")) :
    
  'estimate' is the MAP set of parameters where as 'expectedValue' 
  is the expectation of the parameters with respect to the posterior.
  The confidence intervals are given for 'estimate'.
  2: In data(cav) : data set 'cav' not found
  Execution halted
'library' or 'require' calls in package code:
  'Hmisc' 'stringr'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
CSEGtmufigure: no visible global function definition for 'contourLines'
build.eqn.tex: no visible global function definition for 'str_detect'
build.eqn.tex: no visible global function definition for 'str_trim'
get.mat.tex : tmp.fun: no visible global function definition for
  'latexTranslate'
get.mat.tex : tmp.fun.2: no visible global function definition for
  'str_replace_all'
get.mat.tex: no visible global function definition for 'latexTabular'
get.mat.tex: no visible global function definition for
  'str_replace_all'
parameters.time.varying: no visible global function definition for
  'str_detect'
parameters.time.varying: no visible global function definition for
  'str_trim'
toLatex.marssMODEL: no visible global function definition for
  'str_detect'
toLatex.marssMODEL: no visible global function definition for
  'str_trim'
toLatex.marssMODEL: no visible global function definition for 'str_sub'
toLatex.marssMODEL: no visible global function definition for 'sys'
toLatex.marssMODEL: no visible global function definition for
  'str_replace'
Undefined global functions or variables:
  contourLines latexTabular latexTranslate str_detect str_replace
  str_replace_all str_sub str_trim sys
Consider adding
  importFrom("grDevices", "contourLines")
to your NAMESPACE file.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   2.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Depends: includes the non-default packages:
  'lattice' 'locfit' 'maptools' 'quantreg' 'RANN' 'SparseM'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' call to 'lattice' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'RColorBrewer' 'car' 'spatstat' 'spdep'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'RANN' 'maptools'
  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:
  'MASS' 'boot' 'RColorBrewer' 'scatterplot3d' 'tcltk' 'tcltk2'
  'tkrplot' 'rpanel' 'rgl'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/medSTC.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'seqinr' 'pcaMethods' 'Matrix' 'ROCR' 'Hmisc' 'KernSmooth' 'seqLogo'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' calls to packages already attached by Depends:
  'Hmisc' 'KernSmooth' 'Matrix' 'ROCR' 'methods' 'pcaMethods' 'seqLogo'
  'seqinr'
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'adegenet' 'geosphere'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
dometa: no visible global function definition for 'qchisq'
dometa: no visible global function definition for 'median'
dometa: no visible global function definition for 'pchisq'
forestplot: no visible global function definition for 'pchisq'
forestplot: no visible global function definition for 'qnorm'
forestplot: no visible global function definition for 'plot'
forestplot: no visible global function definition for 'points'
forestplot: no visible global function definition for 'text'
metagwa.files: no visible global function definition for 'read.csv'
metagwa.files: no visible global function definition for 'write.csv'
metagwa.tables: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  median pchisq plot points qchisq qnorm read.csv text write.csv
Consider adding
  importFrom("graphics", "plot", "points", "text")
  importFrom("stats", "median", "pchisq", "qchisq", "qnorm")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
bcgVaccineData: no visible global function definition for 'data'
bcgVaccineData: no visible global function definition for 'qnorm'
hConfidence: no visible global function definition for 'qchisq'
intervalEstimates_OneSgnf : crt: no visible global function definition
  for 'qt'
intervalEstimates_OneSgnf: no visible binding for global variable
  'qnorm'
metagenGeneralised: no visible binding for global variable 'quantile'
performancePointH : property: no visible global function definition for
  'var'
performancePointR : property: no visible global function definition for
  'var'
pfunc : pfun: no visible global function definition for 'uniroot'
pivotalStream: no visible global function definition for 'rchisq'
pivotalStream : <anonymous>: no visible global function definition for
  'rchisq'
pivotalStream: no visible global function definition for 'rnorm'
rBinomGauss: no visible global function definition for 'rnorm'
rBinomGauss: no visible global function definition for 'rbinom'
rD: no visible global function definition for 'rchisq'
rY: no visible global function definition for 'rnorm'
render: no visible global function definition for 'pdf'
render: no visible global function definition for 'dev.off'
renderSVG: no visible global function definition for 'svg'
renderSVG: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  data dev.off pdf qchisq qnorm qt quantile rbinom rchisq rnorm svg
  uniroot var
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "svg")
  importFrom("stats", "qchisq", "qnorm", "qt", "quantile", "rbinom",
             "rchisq", "rnorm", "uniroot", "var")
  importFrom("utils", "data")
to your NAMESPACE file.
'library' or 'require' call to 'survival' 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:
  'foreach' 'iterators' 'proto'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fit.bivar: no visible binding for global variable 'binomial'
summary.fit.bivar: no visible global function definition for 'qt'
summary.fit.bivar: no visible global function definition for 'pt'
Undefined global functions or variables:
  binomial pt qt
Consider adding
  importFrom("stats", "binomial", "pt", "qt")
to your NAMESPACE file.
crosssection: no visible global function definition for
  'colorRampPalette'
crosssection: no visible global function definition for
  'filled.contour'
crosssection: no visible global function definition for 'axis'
crosssection: no visible global function definition for 'par'
crosssection: no visible global function definition for 'contour'
temperatures: no visible binding for global variable 'time'
Undefined global functions or variables:
  axis colorRampPalette contour filled.contour par time
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "contour", "filled.contour", "par")
  importFrom("stats", "time")
to your NAMESPACE file.
'library' or 'require' call to 'nlme' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'BRugs' 'R2WinBUGS' 'coda' 'rjags'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'nlme'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'nlme:::VarCorr'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'VC.est.fixed' 'VC.est.random'
getdata: no visible global function definition for 'read.csv'
plotdata: no visible global function definition for 'head'
Undefined global functions or variables:
  head read.csv
Consider adding
  importFrom("utils", "head", "read.csv")
to your NAMESPACE file.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
    misc   1.1Mb
Package suggested but not available for checking: 'RTisean'
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'
CatMaps: no visible binding for global variable 'poly'
RankMaps: no visible binding for global variable 'poly'
RankMaps: no visible global function definition for 'median'
alterForMedian: no visible binding for global variable 'median'
assimilatePlot: no visible global function definition for 'gray'
bar_build: no visible global function definition for 'median'
bar_cl_build: no visible global function definition for 'median'
box_summary_build: no visible global function definition for 'median'
create_DF_rank: no visible global function definition for 'aggregate'
create_map_table: no visible binding for global variable 'poly'
dot_att: no visible global function definition for 'gray'
dot_build: no visible global function definition for 'median'
dot_cl_att: no visible global function definition for 'gray'
dot_cl_build: no visible global function definition for 'median'
lmplot: no visible global function definition for 'gray'
map_att: no visible global function definition for 'gray'
mmgroupedplot: no visible global function definition for 'median'
mmplot: no visible global function definition for 'gray'
mmplot: no visible global function definition for 'median'
print.mm: no visible global function definition for 'dev.new'
print.mm: no visible global function definition for 'pdf'
print.mm: no visible global function definition for 'tiff'
print.mm: no visible global function definition for 'jpeg'
print.mm: no visible global function definition for 'png'
print.mm: no visible global function definition for 'postscript'
print.mm: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  aggregate dev.new dev.off gray jpeg median pdf png poly postscript
  tiff
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "gray", "jpeg", "pdf",
             "png", "postscript", "tiff")
  importFrom("stats", "aggregate", "median", "poly")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'SDMTools' 'raster'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
MigClim.genClust: no visible global function definition for 'raster'
MigClim.migrate: no visible global function definition for 'raster'
MigClim.migrate: no visible global function definition for
  'dataframe2asc'
MigClim.migrate: no visible global function definition for
  'writeRaster'
MigClim.migrate: no visible global function definition for 'cellStats'
MigClim.migrate: no visible global function definition for 'read.table'
MigClim.migrate: no visible global function definition for
  'write.table'
MigClim.plot: no visible global function definition for 'raster'
MigClim.plot: no visible global function definition for 'rainbow'
MigClim.plot: no visible global function definition for 'jpeg'
MigClim.plot: no visible global function definition for 'ymax'
MigClim.plot: no visible global function definition for 'ymin'
MigClim.plot: no visible global function definition for 'xmax'
MigClim.plot: no visible global function definition for 'xmin'
MigClim.plot: no visible global function definition for 'image'
MigClim.plot: no visible global function definition for 'dev.off'
MigClim.plot: no visible global function definition for 'png'
MigClim.plot: no visible global function definition for 'dev.new'
MigClim.plot: no visible global function definition for 'plot'
Undefined global functions or variables:
  cellStats dataframe2asc dev.new dev.off image jpeg plot png rainbow
  raster read.table write.table writeRaster xmax xmin ymax ymin
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "jpeg", "png", "rainbow")
  importFrom("graphics", "image", "plot")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
File 'MigClim/libs/i386/MigClim.dll':
  Found 'rand', possibly from 'rand' (C)
    Objects: 'genclust.o', 'migrate.o', 'src_cell.o', 'validate.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'genclust.o', 'migrate.o'
File 'MigClim/libs/x64/MigClim.dll':
  Found 'rand', possibly from 'rand' (C)
    Objects: 'genclust.o', 'migrate.o', 'src_cell.o', 'validate.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'genclust.o', 'migrate.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
MImix.default: no visible binding for global variable 'coef'
MImix.default: no visible binding for global variable 'vcov'
MImix.one: no visible global function definition for 'qnorm'
MImix.one: no visible global function definition for 'uniroot'
mixcdf.target: no visible global function definition for 'pnorm'
print.MImixresult: no visible global function definition for 'coef'
print.MImixresult: no visible global function definition for 'vcov'
summary.MImixresult: no visible global function definition for 'coef'
summary.MImixresult: no visible global function definition for 'vcov'
summary.MImixresult: no visible global function definition for 'qt'
Undefined global functions or variables:
  coef pnorm qnorm qt uniroot vcov
Consider adding
  importFrom("stats", "coef", "pnorm", "qnorm", "qt", "uniroot", "vcov")
to your NAMESPACE file.
read_design: no visible global function definition for 'model.frame'
read_design: no visible global function definition for 'read.table'
read_design: no visible global function definition for 'model.matrix'
read_response: no visible global function definition for 'read.table'
update_beta: no visible global function definition for 'update'
update_beta: no visible global function definition for 'glm'
update_beta: no visible global function definition for 'poisson'
Undefined global functions or variables:
  glm model.frame model.matrix poisson read.table update
Consider adding
  importFrom("stats", "glm", "model.frame", "model.matrix", "poisson",
             "update")
  importFrom("utils", "read.table")
to your NAMESPACE file.
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.
'library' or 'require' calls in package code:
  'rgl' 'tkrplot'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'canonicalizeAndMergeScene' 'colorScene' 't2ve' 'vertexNormals'
  'vertexTriangles'
MIcombine.default: no visible binding for global variable 'vcov'
MIcombine.default: no visible binding for global variable 'coef'
MIcombine.default: no visible global function definition for 'var'
MIcombine.imputationResultList: no visible binding for global variable
  'vcov'
MIcombine.imputationResultList: no visible binding for global variable
  'coef'
close.DBimputationList: no visible global function definition for 'is'
getvars: no visible global function definition for 'is'
print.MIresult: no visible global function definition for 'coef'
print.MIresult: no visible global function definition for 'vcov'
summary.MIresult: no visible global function definition for 'coef'
summary.MIresult: no visible global function definition for 'vcov'
summary.MIresult: no visible global function definition for 'qt'
Undefined global functions or variables:
  coef is qt var vcov
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "coef", "qt", "var", "vcov")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Error in re-building vignettes:
  ...
Loading required package: rtkore
Loading required package: Rcpp

Attaching package: 'rtkore'

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

    LdFlags


Error: processing vignette 'Introduction-Mixtures.Rnw' failed with diagnostics:
 chunk 13 
Error in cov.wt(as.matrix(Y), x@tik[, k], method = "ML") : 
  'x' must contain finite values only
Execution halted
Packages in Depends field not imported from:
  'methods' 'seqinr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Missing or unexported object: 'kohonen::bdk'
Found the following significant warnings:
  mmap.c:223:48: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  mmap.c:226:46: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.3/mmap.Rcheck/00install.out' for details.
get.score: no visible global function definition for 'sd'
get.score: no visible global function definition for 'coef'
get.score: no visible global function definition for 'as'
get.score.main: no visible global function definition for 'sd'
get.score.main: no visible global function definition for 'coef'
get.subgroup: no visible global function definition for 'sd'
sample.tte: no visible global function definition for 'runif'
Undefined global functions or variables:
  as coef runif sd
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "coef", "runif", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
.onAttach: no visible global function definition for
  'packageDescription'
MM2: no visible global function definition for 'lm'
lassop_diag: no visible global function definition for 'var'
lassop_nodiag: no visible global function definition for 'var'
lmme_diag: no visible global function definition for 'lm'
lmme_diag: no visible global function definition for 'var'
lmme_nodiag: no visible global function definition for 'lm'
mhtp_diag: no visible global function definition for 'runif'
mhtp_diag: no visible global function definition for 'lm'
mhtp_diag: no visible global function definition for 'var'
mhtp_nodiag: no visible global function definition for 'runif'
mhtp_nodiag: no visible global function definition for 'lm'
mhtp_nodiag: no visible global function definition for 'var'
refit.mhtp_diag: no visible global function definition for 'runif'
refit.mhtp_diag: no visible global function definition for 'lm'
refit.mhtp_diag: no visible global function definition for 'var'
refit.mhtp_nodiag: no visible global function definition for 'runif'
refit.mhtp_nodiag: no visible global function definition for 'lm'
refit.mhtp_nodiag: no visible global function definition for 'var'
Undefined global functions or variables:
  lm packageDescription runif var
Consider adding
  importFrom("stats", "lm", "runif", "var")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
bin.by.date: no visible binding for global variable 'quantile'
bin.by.date: no visible global function definition for 'na.omit'
biplot: no visible global function definition for 'na.omit'
biplot.character: no visible global function definition for 'runif'
biplot.character: no visible global function definition for 'opts'
biplot.character: no visible global function definition for
  'theme_blank'
distributionplot: no visible global function definition for 'na.omit'
distributionplot.character: no visible global function definition for
  'head'
distributionplot.factor: no visible global function definition for
  'opts'
distributionplot.factor: no visible global function definition for
  'theme_text'
mapmobility: no visible global function definition for 'lines'
responseplot: no visible global function definition for 'na.omit'
scatterplot: no visible global function definition for 'na.omit'
scatterplot: no visible global function definition for 'opts'
scatterplot: no visible global function definition for 'theme_text'
sharedtimeplot: no visible global function definition for 'na.omit'
timeplot: no visible global function definition for 'na.omit'
timeplot: no visible global function definition for 'opts'
timeplot.character: no visible global function definition for 'runif'
timeplot.character: no visible global function definition for 'rnorm'
timeplot.character: no visible binding for global variable 'text'
userplot: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  head lines na.omit opts quantile rnorm runif text theme_blank
  theme_text
Consider adding
  importFrom("graphics", "lines", "text")
  importFrom("stats", "na.omit", "quantile", "rnorm", "runif")
  importFrom("utils", "head")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'MASS' 'parallel'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
'library' or 'require' call to 'glmnet' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.4Mb
Mort1Dsmooth: no visible global function definition for 'time'
Mort1Dsmooth: no visible global function definition for 'glm'
Mort1Dsmooth: no visible binding for global variable 'poisson'
Mort1Dsmooth_optimize: no visible global function definition for
  'median'
Mort2Dsmooth: no visible global function definition for 'glm'
Mort2Dsmooth: no visible binding for global variable 'poisson'
Mort2Dsmooth: no visible global function definition for 'median'
Mort2Dsmooth_optimize: no visible global function definition for
  'median'
plot.HMDdata: no visible global function definition for 'plot'
plot.Mort1Dsmooth: no visible global function definition for 'matplot'
plot.Mort2Dsmooth: no visible global function definition for 'quantile'
predict.Mort1Dsmooth: no visible global function definition for 'glm'
predict.Mort1Dsmooth: no visible binding for global variable 'poisson'
predict.Mort2Dsmooth: no visible global function definition for 'glm'
predict.Mort2Dsmooth: no visible binding for global variable 'poisson'
print.summary.Mort1Dsmooth: no visible global function definition for
  'quantile'
print.summary.Mort2Dsmooth: no visible global function definition for
  'quantile'
Undefined global functions or variables:
  glm matplot median plot poisson quantile time
Consider adding
  importFrom("graphics", "matplot", "plot")
  importFrom("stats", "glm", "median", "poisson", "quantile", "time")
to your NAMESPACE file.
mMap: no visible binding for global variable 'facet'
mScatter: no visible binding for global variable 'facet'
mUniplot: no visible binding for global variable 'facet'
Undefined global functions or variables:
  facet
'library' or 'require' calls in package code:
  'R.devices' 'R.filesets' 'R.methodsS3' 'R.oo' 'aroma.affymetrix'
  'aroma.cn' 'aroma.core' 'aroma.light' 'matrixStats' 'snowfall'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: 'cghseg:::segmeanCO'
  See the note in ?`:::` about the use of this operator.
runModels_Interactive : onBrowse: no visible global function definition
  for 'choose.dir'
Undefined global functions or variables:
  choose.dir
Consider adding
  importFrom("utils", "choose.dir")
to your NAMESPACE file.
msap: no visible global function definition for 'packageVersion'
msap: no visible global function definition for 'read.csv'
msap: no visible global function definition for 'write.csv'
msap: no visible global function definition for 'sd'
msap: no visible global function definition for 'wilcox.test'
msap: no visible global function definition for 'dist'
msap: no visible global function definition for 'rainbow'
msap: no visible global function definition for 'png'
msap: no visible global function definition for 'legend'
msap: no visible global function definition for 'dev.off'
pcoa: no visible global function definition for 'cmdscale'
pcoa: no visible global function definition for 'png'
pcoa: no visible global function definition for 'par'
pcoa: no visible global function definition for 'plot'
pcoa: no visible global function definition for 'rainbow'
pcoa: no visible global function definition for 'points'
pcoa: no visible global function definition for 'dev.off'
pcoa: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  cmdscale dev.off dist legend packageVersion par plot png points
  rainbow read.csv sd wilcox.test write.csv
Consider adding
  importFrom("grDevices", "dev.off", "png", "rainbow")
  importFrom("graphics", "legend", "par", "plot", "points")
  importFrom("stats", "cmdscale", "dist", "sd", "wilcox.test")
  importFrom("utils", "packageVersion", "read.csv", "write.csv")
to your NAMESPACE file.
Depends: includes the non-default packages:
  'amap' 'clValid' 'cluster' 'fpc' 'mzR' 'xcms'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' calls to packages already attached by Depends:
  'amap' 'clValid' 'cluster' 'fpc' 'xcms'
  Please remove these calls from your code.
'library' or 'require' call to 'tcltk' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'mzR' 'xcms'
  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:
  'MSeasy' 'tcltk'
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'grDevices' 'xcms'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
MSIseq.classify: no visible global function definition for 'predict'
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
bothsidesmodel: no visible global function definition for 'lm'
bothsidesmodel.chisquare: no visible global function definition for
  'pchisq'
bothsidesmodel.hotelling: no visible global function definition for
  'pf'
bothsidesmodel.hotelling: no visible global function definition for
  'pchisq'
bothsidesmodel.lrt: no visible global function definition for 'pchisq'
bsm.fit: no visible global function definition for 'lm'
bsm.fit: no visible global function definition for 'cov'
lda: no visible global function definition for 'var'
negent3D: no visible global function definition for 'runif'
negent3D: no visible global function definition for 'optim'
qda: no visible global function definition for 'var'
Undefined global functions or variables:
  cov lm optim pchisq pf runif var
Consider adding
  importFrom("stats", "cov", "lm", "optim", "pchisq", "pf", "runif",
             "var")
to your NAMESPACE file.
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  3    z_pos nist_testbed_GF_Agie_1<Device>:path_pos_z<PATH_POSITION>
  Normalized Distance: 27.4341489022279
  Error: `mapped_plot` not equal to lazyLoadDBfetch(c(36520L, 320L), datafile, compressed, envhook).
  Component "layers": Component 1: Component 3: Component 2: Modes of target, current: function, environment
  Component "layers": Component 1: Component 3: Component 2: target, current do not match when deparsed
  Component "layers": Component 1: Component 7: Component 2: Modes of target, current: function, environment
  Component "layers": Component 1: Component 7: Component 2: target, current do not match when deparsed
  Component "layers": Component 1: Component 9: Component 2: Modes of target, current: function, environment
  Component "layers": Component 1: Component 9: Component 2: target, current do not match when deparsed
  Component "layers": Component 1: Component 12: Modes of target, current: function, environment
  Component "layers": Component 1: Component 12: target, current do not match when deparsed
  Component "layers": Component 2: Component 3: Component 2: Modes of target, current: fun
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
Designer.sobol: no visible global function definition for 'runif'
basicMonteCarlo: no visible global function definition for 'runif'
lhs003: no visible global function definition for 'runif'
plmm.mtk : GenereXplmm: no visible binding for global variable 'poly'
plmm.mtk : calc.plm: no visible global function definition for 'lm.fit'
plmm.mtk: no visible global function definition for 'var'
plmm.mtk: no visible global function definition for 'lm'
plmm.mtk: no visible global function definition for 'formula'
plmm.mtk: no visible global function definition for 'update'
plmm.mtk: no visible global function definition for 'stepAIC'
plot.plmm: no visible global function definition for 'par'
plot.plmm: no visible global function definition for 'barplot'
plot.plmm: no visible global function definition for 'segments'
plot.plmm: no visible global function definition for 'abline'
plot.plmm: no visible global function definition for 'title'
plot.plmm: no visible global function definition for 'legend'
plot.regressionSI: no visible global function definition for 'par'
plot.regressionSI: no visible global function definition for 'title'
plot.regressionSI: no visible global function definition for 'abline'
plot,mtkProcess: no visible global function definition for 'dev.new'
Undefined global functions or variables:
  abline barplot dev.new formula legend lm lm.fit par poly runif
  segments stepAIC title update var
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "barplot", "legend", "par",
             "segments", "title")
  importFrom("stats", "formula", "lm", "lm.fit", "poly", "runif",
             "update", "var")
to your NAMESPACE file.
'library' or 'require' call to 'XML' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'NightDay' 'RSQLite' 'XML' 'geosphere' 'sp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
drawMap: no visible global function definition for 'plot'
drawMap: no visible global function definition for 'box'
drawMap: no visible global function definition for 'points'
getFlights: no visible binding for global variable 'htmlTreeParse'
getFlights: no visible binding for global variable 'xpathSApply'
getFlights: no visible binding for global variable 'xmlAttrs'
getFlights: no visible binding for global variable 'free'
movie.routes: no visible global function definition for
  'txtProgressBar'
movie.routes: no visible global function definition for 'jpeg'
movie.routes: no visible global function definition for 'plot'
movie.routes: no visible global function definition for
  'setTxtProgressBar'
movie.routes: no visible global function definition for 'dev.off'
plot.routes: no visible global function definition for 'plot'
plot.routes: no visible global function definition for 'points'
plot.routes: no visible global function definition for 'mtext'
plot.routes : a: no visible global function definition for 'points'
plot.routes : a: no visible global function definition for 'text'
plot.routes : a: no visible global function definition for
  'gcIntermediate'
plot.routes : a: no visible global function definition for 'lines'
routes: no visible global function definition for 'data'
routes: no visible global function definition for 'distHaversine'
routes: no visible global function definition for 'gcIntermediate'
Undefined global functions or variables:
  box data dev.off distHaversine free gcIntermediate htmlTreeParse jpeg
  lines mtext plot points setTxtProgressBar text txtProgressBar
  xmlAttrs xpathSApply
Consider adding
  importFrom("grDevices", "dev.off", "jpeg")
  importFrom("graphics", "box", "lines", "mtext", "plot", "points",
             "text")
  importFrom("utils", "data", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
betas_plot: no visible global function definition for 'cov2cor'
betas_plot: no visible global function definition for
  'colorRampPalette'
betas_plot: no visible global function definition for 'pdf'
betas_plot: no visible global function definition for 'dev.off'
mhplot: no visible global function definition for 'read.table'
mhplot: no visible global function definition for 'pdf'
mhplot: no visible global function definition for 'plot'
mhplot: no visible global function definition for 'points'
mhplot: no visible global function definition for 'abline'
mhplot: no visible global function definition for 'axis'
mhplot: no visible global function definition for 'dev.off'
multi_meta: no visible global function definition for 'write.table'
multi_meta: no visible global function definition for 'read.table'
multi_meta: no visible global function definition for 'pchisq'
qqplotter: no visible global function definition for 'read.table'
qqplotter: no visible global function definition for 'qchisq'
qqplotter: no visible global function definition for 'ppoints'
qqplotter: no visible global function definition for 'median'
qqplotter: no visible global function definition for 'pchisq'
qqplotter: no visible global function definition for 'pdf'
qqplotter: no visible global function definition for 'plot'
qqplotter: no visible global function definition for 'abline'
qqplotter: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  abline axis colorRampPalette cov2cor dev.off median pchisq pdf plot
  points ppoints qchisq read.table write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf")
  importFrom("graphics", "abline", "axis", "plot", "points")
  importFrom("stats", "cov2cor", "median", "pchisq", "ppoints", "qchisq")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: replacing previous import 'class::somgrid' by 'kohonen::somgrid' when loading 'multisom'
See 'd:/Rcompile/CRANpkg/local/3.3/multisom.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/MXM.Rcheck/00install.out' for details.
mycor.formula: no visible global function definition for 'terms'
mylm: no visible global function definition for 'cor.test'
mylm: no visible global function definition for 'lm'
panel.cor: no visible global function definition for 'par'
panel.cor: no visible global function definition for 'cor'
panel.cor: no visible global function definition for 'strwidth'
panel.cor: no visible global function definition for 'text'
panel.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'
plot.mycor: no visible global function definition for 'pairs'
plot.mycor: no visible binding for global variable 'panel.smooth'
Undefined global functions or variables:
  cor cor.test hist lm pairs panel.smooth par rect strwidth terms text
Consider adding
  importFrom("graphics", "hist", "pairs", "panel.smooth", "par", "rect",
             "strwidth", "text")
  importFrom("stats", "cor", "cor.test", "lm", "terms")
to your NAMESPACE file.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.3Mb
    libs   1.4Mb
NAPPA: no visible binding for global variable 'sd'
NAPPA: no visible global function definition for 'sd'
calibrate.sigmoid.curve : <anonymous> : <anonymous>: no visible global
  function definition for 'coef'
calibrate.sigmoid.curve : <anonymous> : <anonymous>: no visible global
  function definition for 'lm'
calibrate.sigmoid.curve: no visible global function definition for
  'nls'
calibrate.sigmoid.curve: no visible binding for global variable
  'weights'
calibrate.sigmoid.curve: no visible global function definition for
  'coef'
calibrate.sigmoid.curve: no visible global function definition for
  'plot'
calibrate.sigmoid.curve: no visible global function definition for
  'rgb'
calibrate.sigmoid.curve: no visible global function definition for
  'box'
calibrate.sigmoid.curve: no visible global function definition for
  'axis'
calibrate.sigmoid.curve: no visible global function definition for
  'abline'
calibrate.sigmoid.curve: no visible global function definition for
  'lines'
calibrate.sigmoid.curve: no visible global function definition for
  'predict'
calibrate.sigmoid.curve: no visible global function definition for
  'smooth.spline'
calibrate.sigmoid.curve : <anonymous>: no visible global function
  definition for 'nls'
calibrate.sigmoid.curve : <anonymous>: no visible binding for global
  variable 'weights'
calibrate.sigmoid.curve: no visible binding for global variable 'coef'
calibrate.sigmoid.curve: no visible global function definition for 'pf'
calibrate.sigmoid.curve: no visible global function definition for
  'legend'
Undefined global functions or variables:
  abline axis box coef legend lines lm nls pf plot predict rgb sd
  smooth.spline weights
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "abline", "axis", "box", "legend", "lines",
             "plot")
  importFrom("stats", "coef", "lm", "nls", "pf", "predict", "sd",
             "smooth.spline", "weights")
to your NAMESPACE file.
data.reduction: no visible global function definition for 'prcomp'
data.reduction: no visible global function definition for 'hclust'
data.reduction: no visible global function definition for 'as.dist'
data.reduction: no visible global function definition for 'cor'
data.reduction: no visible global function definition for 'dist'
heatmap1: no visible global function definition for 'sd'
lineplot: no visible global function definition for 'sd'
normalize: no visible global function definition for 'sd'
profileplot3d : ColorFunction: no visible global function definition
  for 'rgb'
profileplot3d : ColorFunction: no visible global function definition
  for 'colorRamp'
profileplot3d: no visible global function definition for 'sd'
profileplot3d: no visible global function definition for 'gray'
Undefined global functions or variables:
  as.dist colorRamp cor dist gray hclust prcomp rgb sd
Consider adding
  importFrom("grDevices", "colorRamp", "gray", "rgb")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "prcomp", "sd")
to your NAMESPACE file.
File 'NeatMap/libs/i386/NeatMap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'nMDS_R.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'nMDS_R.o'
File 'NeatMap/libs/x64/NeatMap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'nMDS_R.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'nMDS_R.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
nestedRanksTest.default: no visible global function definition for
  'setNames'
nestedRanksTest.default: no visible global function definition for
  'quantile'
nestedRanksTest.formula: no visible global function definition for
  'terms'
plot.htest_boot: no visible global function definition for 'hist'
plot.htest_boot: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline hist quantile setNames terms
Consider adding
  importFrom("graphics", "abline", "hist")
  importFrom("stats", "quantile", "setNames", "terms")
to your NAMESPACE file.
clustConfigurations: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   2.1Mb
Running examples in 'netdiffuseR-Ex.R' failed
The error most likely occurred in:

> ### Name: exposure
> ### Title: Ego exposure
> ### Aliases: exposure
> ### Keywords: univar
> 
> ### ** Examples
> 
> # Calculating the exposure based on Structural Equivalence ------------------
> set.seed(113132)
> graph <- rdiffnet(100, 10)
> 
> SE <- lapply(struct_equiv(graph), "[[", "SE")
> SE <- lapply(SE, function(x) {
+    x <- 1/x
+    x[!is.finite(x)] <- 0
+    x
+ })
> 
> # Recall setting valued equal to TRUE!
> expo_se <- exposure(graph, alt.graph=SE , valued=TRUE)
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   2.0Mb
'library' or 'require' call to 'igraph' 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: 'Rcpp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File 'NetSim/libs/i386/NetSim.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'utils/Random.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'utils/Random.o'
File 'NetSim/libs/x64/NetSim.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'utils/Random.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'utils/Random.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/NetworkRiskMeasures.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'NFPdata'
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    CppCode   1.8Mb
    R         2.4Mb
    include   3.7Mb
    libs      1.5Mb
Pwr.lme: no visible global function definition for 'anova'
Pwr.lme: no visible global function definition for 'qf'
Pwr.lme: no visible global function definition for 'pf'
logLik1.lme: no visible global function definition for 'coef'
logLik1.lme: no visible global function definition for 'model.matrix'
logLik1.lme: no visible global function definition for 'predict'
logLik1.lme: no visible global function definition for 'formula'
runScript: no visible binding for global variable 'example'
sigmaTolme: no visible global function definition for 'vcov'
simulateY.lme: no visible global function definition for 'runif'
simulateY.lme: no visible global function definition for 'fitted'
simulateY.lme: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  anova coef example fitted formula model.matrix pf predict qf rnorm
  runif vcov
Consider adding
  importFrom("stats", "anova", "coef", "fitted", "formula",
             "model.matrix", "pf", "predict", "qf", "rnorm", "runif",
             "vcov")
  importFrom("utils", "example")
to your NAMESPACE file.
Running 'test-all.R' [2s]
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
  1/2 mismatches
  [1] 3 - 1 == 2
  
  
  2. Failure: Test HS023. (@test-hs023.R#95) -------------------------------------
  all(eval_g_ineq(res$solution)$constr <= res$options$tol_constraints_ineq) isn't true.
  
  
  testthat results ================================================================
  OK: 41 SKIPPED: 0 FAILED: 2
  1. Failure: Test HS023. (@test-hs023.R#90) 
  2. Failure: Test HS023. (@test-hs023.R#95) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.3Mb
Package suggested but not available for checking: 'synchronicity'
algorithm,NMFStrategyOctave: no visible global function definition for
  'fstop'
evar,ANY: no visible binding for global variable 'Biobase'
nmf,matrix-numeric-NMFStrategy : run.all: no visible binding for global
  variable 'n'
nmf,matrix-numeric-NMFStrategy : run.all: no visible binding for global
  variable 'RNGobj'
rss,matrix: no visible binding for global variable 'Biobase'
Undefined global functions or variables:
  Biobase RNGobj fstop n
Error in re-building vignettes:
  ...
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "nonrandom.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.3/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'nonrandom.tex' failed

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

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

Execution halted
CIPW: no visible global function definition for 'data'
CIPW: no visible binding for global variable 'AtomWeight'
CIPW: no visible binding for global variable 'MinWeight'
CIPW: no visible binding for global variable 'OxiWeight'
CIPW.trace: no visible global function definition for 'data'
CIPW.trace: no visible binding for global variable 'AtomWeight'
CIPW.trace: no visible binding for global variable 'MinWeight'
CIPW.trace: no visible binding for global variable 'OxiWeight'
Undefined global functions or variables:
  AtomWeight MinWeight OxiWeight data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
BoundingRA: no visible global function definition for 'rnorm'
check_y_estimator: no visible global function definition for 'rnorm'
genNORTARA: no visible global function definition for 'rnorm'
genNORTARA: no visible global function definition for 'pnorm'
valid_input_cormat: no visible global function definition for 'rnorm'
valid_input_cormat: no visible global function definition for 'pnorm'
valid_input_cormat: no visible global function definition for 'cor'
y_control_estimator: no visible global function definition for 'pnorm'
y_control_estimator: no visible global function definition for 'cor'
y_control_estimator : <anonymous>: no visible global function
  definition for 'cor'
y_control_estimator: no visible global function definition for 'cov'
y_control_estimator: no visible global function definition for 'var'
y_crude_estimator: no visible global function definition for 'pnorm'
y_crude_estimator: no visible global function definition for 'cor'
Undefined global functions or variables:
  cor cov pnorm rnorm var
Consider adding
  importFrom("stats", "cor", "cov", "pnorm", "rnorm", "var")
to your NAMESPACE file.
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.
Depends: includes the non-default packages:
  'R.methodsS3' 'MASS' 'matrixStats' 'R.oo' 'R.utils' 'aroma.core'
  'aroma.affymetrix' 'DNAcopy'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  'DNAcopy' 'MASS' 'R.methodsS3' 'R.oo' 'aroma.affymetrix' 'aroma.core'
  'matrixStats'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
acor: no visible global function definition for 'cor'
macor: no visible global function definition for 'cor'
mcancor: no visible global function definition for 'cor'
mcc_inner: no visible global function definition for 'rnorm'
nscancor: no visible global function definition for 'cor'
nscc_inner: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  cor rnorm
Consider adding
  importFrom("stats", "cor", "rnorm")
to your NAMESPACE file.
box_dist: no visible global function definition for 'quantile'
calc_mean_dist: no visible global function definition for 'filter'
n: no visible global function definition for 'resid'
null_dist : <anonymous>: no visible global function definition for
  'coef'
null_lm : <anonymous>: no visible global function definition for
  'predict'
reg_dist: no visible global function definition for 'coef'
reg_dist: no visible global function definition for 'lm'
resid_boot: no visible global function definition for 'resid'
resid_pboot: no visible global function definition for 'rnorm'
resid_rotate: no visible global function definition for 'rnorm'
resid_rotate: no visible global function definition for 'update'
resid_rotate: no visible global function definition for 'resid'
resid_sigma: no visible global function definition for 'rnorm'
rorschach: no visible global function definition for 'rbinom'
rss: no visible global function definition for 'resid'
sep_dist: no visible global function definition for 'dist'
sep_dist: no visible global function definition for 'cutree'
sep_dist: no visible global function definition for 'hclust'
uni_dist: no visible global function definition for 'sd'
Undefined global functions or variables:
  coef cutree dist filter hclust lm predict quantile rbinom resid rnorm
  sd update
Consider adding
  importFrom("stats", "coef", "cutree", "dist", "filter", "hclust", "lm",
             "predict", "quantile", "rbinom", "resid", "rnorm", "sd",
             "update")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'nutshell.audioscrobbler' 'nutshell.bbdb'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ### Aliases: weight_polls
> 
> ### ** Examples
> 
> polldates <- tail(unique(polls$MidDate), 20)
> weight_polls(polldates, method = "curia")
 [1] NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
[20] NaN
> weight_polls(polldates, method = "pundit")
 [1] 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
 [7] 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
[13] 0.00000000 0.00000000 0.00000000 0.03960526 0.06044955 0.15833013
[19] 0.33013825 0.41147682
> 
> 
> 
> ### * <FOOTER>
> ###
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  8.27 0.14 8.62 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    help   2.1Mb
    libs   1.2Mb
Packages in Depends field not imported from:
  'DBI' 'RJDBC' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
OLScurve: no visible global function definition for 'as.formula'
OLScurve: no visible global function definition for 'na.omit'
OLScurve: no visible global function definition for 'lm'
OLScurve: no visible global function definition for 'predict'
OLScurve: no visible global function definition for 'residuals'
OLScurve: no visible global function definition for 'model.frame'
OLScurve: no visible global function definition for 'model.matrix'
plot.OLScurve : plotOLScurve: no visible global function definition for
  'reshape'
print.OLScurve: no visible global function definition for 'na.omit'
print.OLScurve: no visible global function definition for 'model.frame'
print.OLScurve: no visible global function definition for
  'model.matrix'
print.OLScurve: no visible global function definition for 'cov'
print.OLScurve: no visible global function definition for 'cor'
print.OLScurve: no visible global function definition for 'sd'
subjplot.OLScurve : plotOLScurve: no visible global function definition
  for 'devAskNewPage'
subjplot.OLScurve : plotOLScurve: no visible global function definition
  for 'reshape'
subjplot.OLScurve : plotOLScurve : mypanel: no visible global function
  definition for 'gray'
subjplot.OLScurve: no visible global function definition for
  'devAskNewPage'
Undefined global functions or variables:
  as.formula cor cov devAskNewPage gray lm model.frame model.matrix
  na.omit predict reshape residuals sd
Consider adding
  importFrom("grDevices", "devAskNewPage", "gray")
  importFrom("stats", "as.formula", "cor", "cov", "lm", "model.frame",
             "model.matrix", "na.omit", "predict", "reshape",
             "residuals", "sd")
to your NAMESPACE file.
MLparameters: no visible global function definition for 'optim'
comp.freq: no visible global function definition for 'x11'
comp.freq: no visible global function definition for 'par'
comp.freq: no visible global function definition for 'plot'
Undefined global functions or variables:
  optim par plot x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "par", "plot")
  importFrom("stats", "optim")
to your NAMESPACE file.
ComputeDependencies: no visible global function definition for 'find'
Fetch: no visible global function definition for 'find'
Q0.025: no visible global function definition for 'quantile'
Q0.975: no visible global function definition for 'quantile'
interpf: no visible global function definition for 'qnorm'
interpf: no visible global function definition for 'rnorm'
interpf: no visible global function definition for 'runif'
oapply: no visible global function definition for 'aggregate'
odebug: no visible global function definition for 'combn'
odebug: no visible global function definition for 'aov'
odebug: no visible global function definition for 'as.formula'
opasnet.csv: no visible global function definition for 'read.table'
opbase.locations: no visible global function definition for 'URLencode'
opbase.parse_locations: no visible global function definition for
  'URLencode'
opbase.parse_range: no visible global function definition for
  'URLencode'
rdirichlet: no visible global function definition for 'rgamma'
tidy: no visible global function definition for 'reshape'
Undefined global functions or variables:
  URLencode aggregate aov as.formula combn find qnorm quantile
  read.table reshape rgamma rnorm runif
Consider adding
  importFrom("stats", "aggregate", "aov", "as.formula", "qnorm",
             "quantile", "reshape", "rgamma", "rnorm", "runif")
  importFrom("utils", "URLencode", "combn", "find", "read.table")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/OpenCL.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'RAppArmor'
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs     5.4Mb
    models   4.7Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   4.9Mb
avg2Lower: no visible global function definition for 'optimize'
classificationError.data.frame: no visible binding for global variable
  'na.omit'
classificationError.data.frame: no visible global function definition
  for 'terms'
classificationError.data.frame: no visible binding for global variable
  'predict'
classpredict.lda: no visible global function definition for 'predict'
simData: no visible global function definition for 'rnorm'
simData: no visible global function definition for 'runif'
simData: no visible global function definition for 'var'
tnormAvg: no visible global function definition for 'dnorm'
tnormAvg: no visible global function definition for 'pnorm'
yapprox: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx dnorm na.omit optimize pnorm predict rnorm runif terms var
Consider adding
  importFrom("stats", "approx", "dnorm", "na.omit", "optimize", "pnorm",
             "predict", "rnorm", "runif", "terms", "var")
to your NAMESPACE file.
Package required but not available: 'ROracle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
error.bars: no visible global function definition for 'segments'
lambda.interp: no visible global function definition for 'approx'
orderedLasso: no visible binding for global variable 'sd'
orderedLasso.cv: no visible binding for global variable 'var'
plot.orderedLasso.cv: no visible global function definition for 'par'
plot.orderedLasso.cv: no visible global function definition for 'plot'
plot.orderedLasso.cv: no visible global function definition for 'axis'
plot.orderedLasso.cv: no visible global function definition for 'mtext'
plot.orderedLasso.cv: no visible global function definition for
  'points'
plot.orderedLasso.cv: no visible global function definition for
  'abline'
plot.timeLagLasso.cv: no visible global function definition for 'par'
plot.timeLagLasso.cv: no visible global function definition for 'plot'
plot.timeLagLasso.cv: no visible global function definition for 'axis'
plot.timeLagLasso.cv: no visible global function definition for 'mtext'
plot.timeLagLasso.cv: no visible global function definition for
  'points'
plot.timeLagLasso.cv: no visible global function definition for
  'abline'
timeLagLasso: no visible binding for global variable 'sd'
timeLagLasso.cv: no visible binding for global variable 'sd'
timeLagLasso.cv: no visible binding for global variable 'var'
timeLagLasso.path: no visible binding for global variable 'sd'
Undefined global functions or variables:
  abline approx axis mtext par plot points sd segments var
Consider adding
  importFrom("graphics", "abline", "axis", "mtext", "par", "plot",
             "points", "segments")
  importFrom("stats", "approx", "sd", "var")
to your NAMESPACE file.
boat3d: no visible global function definition for 'rgl.cur'
boat3d: no visible global function definition for 'open3d'
boat3d: no visible global function definition for 'clear3d'
boat3d: no visible global function definition for 'bg3d'
boat3d: no visible global function definition for 'rgl.set'
boat3d: no visible global function definition for 'triangles3d'
boat3d: no visible global function definition for 'quads3d'
boat3d: no visible global function definition for 'decorate3d'
boat3d: no visible global function definition for 'scatterplot3d'
orientlm: no visible global function definition for 'model.matrix'
orientlm: no visible global function definition for 'lm'
Undefined global functions or variables:
  bg3d clear3d decorate3d lm model.matrix open3d quads3d rgl.cur
  rgl.set scatterplot3d triangles3d
Consider adding
  importFrom("stats", "lm", "model.matrix")
to your NAMESPACE file.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    nifti   3.8Mb
odm: no visible binding for global variable 'sd'
odm : <anonymous>: no visible global function definition for 'sd'
odm : <anonymous>: no visible global function definition for 'quantile'
odm: no visible global function definition for 'prcomp'
quant.const: no visible global function definition for 'quantile'
quant.const.D: no visible global function definition for 'reshape'
quant.const.D: no visible global function definition for 'quantile'
quant.linear.D: no visible global function definition for 'reshape'
quant.nonlin : FrankModel: no visible global function definition for
  'qt'
quant.nonlin : FrankModel: no visible global function definition for
  'pt'
quant.nonlin: no visible global function definition for 'predict'
quant.nonlin.D: no visible global function definition for 'reshape'
quant.nonlin.D: no visible global function definition for 'predict'
quant.nonpar.D: no visible global function definition for 'reshape'
rgrubbs.test: no visible global function definition for 'sd'
plot,OutlierDM-missing: no visible binding for global variable 'pch'
summary,OutlierDM: no visible global function definition for 'head'
Undefined global functions or variables:
  head pch prcomp predict pt qt quantile reshape sd
Consider adding
  importFrom("stats", "prcomp", "predict", "pt", "qt", "quantile",
             "reshape", "sd")
  importFrom("utils", "head")
to your NAMESPACE file.
Electre3_AlphaBetaThresholds: no visible global function definition for
  'plot'
Electre3_SimpleThresholds: no visible global function definition for
  'plot'
Electre_1: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Warning: invalid input found on input connection 'PAFit-Ex.R'
CalGIF: no visible binding for global variable 'PAGIData'
CalGIF2: no visible binding for global variable 'PAGIData'
PAGI.Main: no visible binding for global variable 'PAGIData'
PAGI.Main: no visible global function definition for 'p.adjust'
PAGI.Main: no visible global function definition for 'pt'
getclass.labels: no visible binding for global variable 'ExampleData'
getdataset: no visible binding for global variable 'ExampleData'
Undefined global functions or variables:
  ExampleData PAGIData p.adjust pt
Consider adding
  importFrom("stats", "p.adjust", "pt")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'gld' 'mvtnorm'
  Please remove these calls from your code.
pairsD3: no visible global function definition for 'gray.colors'
Undefined global functions or variables:
  gray.colors
Consider adding
  importFrom("grDevices", "gray.colors")
to your NAMESPACE file.
Running examples in 'paleofire-Ex.R' failed
The error most likely occurred in:

> ### Name: plot.CHAR
> ### Title: Plot CHAR
> ### Aliases: plot.CHAR
> 
> ### ** Examples
> 
> 
> ## In this example we will use the charcoal record of the Lac du Loup (Blarquez et al. 2010)
> ## Load raw charcoal data in mm^2
> A=read.csv("http://blarquez.com/public/code/loupchar.csv")
Warning in file(file, "rt") :
  cannot open URL 'http://blarquez.com/public/code/loupchar.csv': HTTP status was '404 Not Found'
Error in file(file, "rt") : cannot open the connection
Calls: read.csv -> read.table -> file
Execution halted
Missing or unexported object: 'rms::reVector'
grow.forest: no visible global function definition for 'model.frame'
grow.tree: no visible global function definition for 'model.frame'
predict.forest: no visible global function definition for 'model.frame'
predict.tree: no visible global function definition for 'model.frame'
predict,forest: no visible global function definition for 'model.frame'
predict,tree: no visible global function definition for 'model.frame'
Undefined global functions or variables:
  model.frame
Consider adding
  importFrom("stats", "model.frame")
to your NAMESPACE file.
parallelExport: no visible global function definition for 'setNames'
parallelGetOptions: no visible global function definition for
  'setNames'
parallelStop: no visible global function definition for
  'getFromNamespace'
stopWithJobErrorMessages: no visible global function definition for
  'head'
Undefined global functions or variables:
  getFromNamespace head setNames
Consider adding
  importFrom("stats", "setNames")
  importFrom("utils", "getFromNamespace", "head")
to your NAMESPACE file.
.formula.make: no visible global function definition for 'formula'
regress: no visible global function definition for 'lm'
regress: no visible global function definition for 'model.matrix'
Undefined global functions or variables:
  formula lm model.matrix
Consider adding
  importFrom("stats", "formula", "lm", "model.matrix")
to your NAMESPACE file.
'library' or 'require' call to 'glmnet' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'glmnet'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cv_nfold: no visible global function definition for 'predict'
cv_nfold: no visible global function definition for 'cv.glmnet'
cv_nfold: no visible global function definition for 'coef'
cv_nfold: no visible global function definition for 'var'
getoptbinsize: no visible global function definition for 'var'
getoptbinsize: no visible global function definition for 'cor'
glmcvbeta: no visible global function definition for 'cv.glmnet'
myhistplot: no visible global function definition for 'par'
myhistplot: no visible global function definition for 'plot'
myhistplot: no visible global function definition for 'axis'
plot.binmod: no visible global function definition for 'par'
plot.binmod: no visible global function definition for 'layout'
plot.binmod: no visible global function definition for 'dev.off'
plot.binmod: no visible binding for global variable 'plot.new'
plot.binmod: no visible global function definition for 'postscript'
plot.binmod: no visible global function definition for 'plot'
plot.binmod: no visible global function definition for 'mtext'
plot.binmod: no visible global function definition for 'legend'
plot.binmod: no visible global function definition for 'arrows'
predict.binmod: no visible global function definition for 'predict'
singlemarkanalysis: no visible global function definition for 'glm'
singlemarkanalysis: no visible global function definition for 'var'
weightedx: no visible global function definition for 'na.exclude'
Undefined global functions or variables:
  arrows axis coef cor cv.glmnet dev.off glm layout legend mtext
  na.exclude par plot plot.new postscript predict var
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "arrows", "axis", "layout", "legend", "mtext",
             "par", "plot", "plot.new")
  importFrom("stats", "coef", "cor", "glm", "na.exclude", "predict",
             "var")
to your NAMESPACE file.
SweaveAll: no visible global function definition for 'file_test'
texi2dvi: no visible global function definition for 'file_test'
Undefined global functions or variables:
  file_test
Consider adding
  importFrom("utils", "file_test")
to your NAMESPACE file.
Package in Depends field not imported from: 'shape'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
arrow: no visible global function definition for 'arrows'
draw: no visible global function definition for 'rect'
draw: no visible global function definition for 'text'
draw: no visible global function definition for 'plotellipse'
wall: no visible global function definition for 'plot.new'
wall: no visible global function definition for 'plot.window'
Undefined global functions or variables:
  arrows plot.new plot.window plotellipse rect text
Consider adding
  importFrom("graphics", "arrows", "plot.new", "plot.window", "rect",
             "text")
to your NAMESPACE file.
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  1. Failure: standardize_path works with missing files with ./ prefix (@test_standardize_path.R#198) 
  standardize_path(x) not equal to `expected`.
  1/2 mismatches
  x[1]: "D:/RCompile/CRANpkg/local/3.3/pathological.Rcheck/tests/testthat/test_dec
  x[1]: ompose_path.R"
  y[1]: "D:/Rcompile/CRANpkg/local/3.3/pathological.Rcheck/tests/testthat/test_dec
  y[1]: ompose_path.R"
  
  
  testthat results ================================================================
  OK: 187 SKIPPED: 15 FAILED: 1
  1. Failure: standardize_path works with missing files with ./ prefix (@test_standardize_path.R#198) 
  
  Error: testthat unit tests failed
  Execution halted
add_noise: no visible global function definition for 'rnorm'
estimate_risk_dream6 : <anonymous>: no visible global function
  definition for 'var'
generate_sample: no visible global function definition for 'rnorm'
generate_sample: no visible global function definition for 'runif'
sample_function: no visible global function definition for 'runif'
sample_function : <anonymous>: no visible global function definition
  for 'var'
sample_function_multi_mod_weight: no visible global function definition
  for 'runif'
sample_function_multi_mod_weight : <anonymous>: no visible global
  function definition for 'var'
sample_function_single_mod: no visible global function definition for
  'runif'
Undefined global functions or variables:
  rnorm runif var
Consider adding
  importFrom("stats", "rnorm", "runif", "var")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from 'PAWL' 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 to packages already attached by Depends:
  'foreach' 'ggplot2' 'reshape'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'foreach' 'ggplot2' 'methods' 'mvtnorm' 'reshape'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    lib    5.5Mb
    libs   4.5Mb
dotplot.pbo: no visible global function definition for 'reorder'
pbo: no visible global function definition for '%dopar%'
pbo: no visible global function definition for 'foreach'
pbo: no visible global function definition for 'lm'
xyplot.pbo: no visible global function definition for 'ecdf'
xyplot.pbo: no visible global function definition for 'doubleYScale'
xyplot.pbo: no visible global function definition for 'reorder'
Undefined global functions or variables:
  %dopar% doubleYScale ecdf foreach lm reorder
Consider adding
  importFrom("stats", "ecdf", "lm", "reorder")
to your NAMESPACE file.
draw.pcaBootPlot: no visible global function definition for 'plot'
draw.pcaBootPlot: no visible global function definition for 'grid'
draw.pcaBootPlot: no visible global function definition for 'points'
draw.pcaBootPlot: no visible global function definition for 'symbols'
draw.pcaBootPlot: no visible global function definition for 'legend'
pcaBootPlot: no visible global function definition for 'prcomp'
pcaBootPlot: no visible global function definition for 'cor'
pcaBootPlot: no visible global function definition for 'quantile'
pcaBootPlot: no visible global function definition for 'pdf'
pcaBootPlot: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  cor dev.off grid legend pdf plot points prcomp quantile symbols
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "grid", "legend", "plot", "points", "symbols")
  importFrom("stats", "cor", "prcomp", "quantile")
to your NAMESPACE file.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    data   2.1Mb
    libs   2.2Mb
Packages in Depends field not imported from:
  'Rcpp' 'RcppArmadillo' 'ggplot2'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
AssoTestProc: no visible global function definition for 'rbinom'
AssoTestProc: no visible global function definition for 'princomp'
AssoTestProc: no visible global function definition for 'loadings'
AssoTestProc: no visible global function definition for 'lm'
CNVtypeAnay: no visible global function definition for 'cov'
ClusProc: no visible global function definition for 'princomp'
ClusProc: no visible global function definition for 'prcomp'
ClusProc0: no visible global function definition for 'kmeans'
ClusProc0: no visible global function definition for 'cov'
Inde: no visible global function definition for 'lm'
Inde: no visible global function definition for 'var'
STE: no visible global function definition for 'pchisq'
STIM: no visible global function definition for 'cor'
STIM: no visible global function definition for 'pchisq'
plot.clust: no visible global function definition for 'princomp'
plot.clust: no visible global function definition for 'loadings'
plot.clust: no visible global function definition for 'qplot'
plot.clust: no visible global function definition for 'geom_histogram'
plot.clust: no visible global function definition for 'aes_string'
plot.clust: no visible global function definition for 'barplot'
plot.clust: no visible global function definition for 'title'
plot.clust: no visible global function definition for 'mtext'
plot.clust: no visible global function definition for 'text'
Undefined global functions or variables:
  aes_string barplot cor cov geom_histogram kmeans lm loadings mtext
  pchisq prcomp princomp qplot rbinom text title var
Consider adding
  importFrom("graphics", "barplot", "mtext", "text", "title")
  importFrom("stats", "cor", "cov", "kmeans", "lm", "loadings", "pchisq",
             "prcomp", "princomp", "rbinom", "var")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'MASS' 'gamlss' 'quantreg' 'robustbase'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
hasMethod: no visible global function definition for 'getS3method'
Undefined global functions or variables:
  getS3method
Consider adding
  importFrom("utils", "getS3method")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'ggplot2' 'reshape'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plot.phtMCMC: no visible global function definition for 'ggplot'
plot.phtMCMC: no visible global function definition for 'melt'
plot.phtMCMC: no visible global function definition for 'geom_line'
plot.phtMCMC: no visible global function definition for 'aes_string'
plot.phtMCMC: no visible global function definition for 'geom_smooth'
plot.phtMCMC: no visible global function definition for 'facet_wrap'
plot.phtMCMC: no visible global function definition for 'ggtitle'
plot.phtMCMC: no visible global function definition for 'xlab'
plot.phtMCMC: no visible global function definition for 'ylab'
plot.phtMCMC: no visible global function definition for 'geom_density'
Undefined global functions or variables:
  aes_string facet_wrap geom_density geom_line geom_smooth ggplot
  ggtitle melt xlab ylab
File 'PhaseType/libs/i386/PhaseType.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'LJMA_arms.o'
File 'PhaseType/libs/x64/PhaseType.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'LJMA_arms.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Packages in Depends field not imported from:
  'ARTP' 'snowfall' 'survival' 'xtable'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' calls in package code:
  'argparse' 'devtools' 'knitr'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Depends: includes the non-default packages:
  'RGtk2' 'gWidgetsRGtk2' 'cairoDevice' 'lattice' 'rggobi' 'ggplot2'
  'proto'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'RGtk2' 'gWidgetsRGtk2'
A package should be listed in only one of these fields.
Package in Depends field not imported from: 'cairoDevice'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
PKadjust: no visible binding for global variable 'jpeg'
PKadjust: no visible binding for global variable 'bmp'
PKadjust: no visible binding for global variable 'png'
PKadjust: no visible binding for global variable 'tiff'
PKadjust: no visible binding for global variable 'dev.new'
PKadjust: no visible global function definition for 'dev.off'
PKfigure: no visible global function definition for 'dev.cur'
PKfigure: no visible global function definition for 'dev.off'
PKoutput: no visible global function definition for 'heatmap'
PKoutput: no visible global function definition for
  'packageDescription'
PKshow: no visible global function definition for 'browseURL'
addList1: no visible global function definition for 'formula'
addList1.old: no visible global function definition for 'formula'
addList2: no visible global function definition for 'formula'
generate.plot: no visible global function definition for 'dev.off'
writeHTML: no visible global function definition for
  'packageDescription'
writeLst: no visible global function definition for
  'packageDescription'
writeLst.tab: no visible global function definition for
  'packageDescription'
writeTable: no visible global function definition for
  'packageDescription'
writeTable: no visible global function definition for 'quantile'
initialize,nonmem: no visible global function definition for
  'read.table'
Undefined global functions or variables:
  bmp browseURL dev.cur dev.new dev.off formula heatmap jpeg
  packageDescription png quantile read.table tiff
Consider adding
  importFrom("grDevices", "bmp", "dev.cur", "dev.new", "dev.off", "jpeg",
             "png", "tiff")
  importFrom("stats", "formula", "heatmap", "quantile")
  importFrom("utils", "browseURL", "packageDescription", "read.table")
to your NAMESPACE file.
'library' or 'require' call to 'lattice' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to 'latticist' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'cairoDevice' 'gWidgetsRGtk2' 'grid' 'lattice'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  'lattice:::lattice.getStatus' 'stats:::biplot.prcomp'
  See the note in ?`:::` about the use of this operator.
S3 methods shown with full name in documentation object 'plotCoords':
  'plotCoords.plot' 'plotCoords.biplot'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   1.6Mb
Packages in Depends field not imported from:
  'impute' 'plyr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' call to 'rgenoud' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.sigma: no visible global function definition for 'plot'
smooth: no visible global function definition for 'genoud'
Undefined global functions or variables:
  genoud plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
as.popgraph: no visible global function definition for 'is'
centroid_distance: no visible global function definition for 'is'
centroid_variance: no visible global function definition for 'is'
centroid_variance: no visible global function definition for 'cov'
decorate_graph: no visible global function definition for 'is'
overlay_popgraph: no visible global function definition for 'is'
overlay_popgraph: no visible global function definition for 'lines'
overlay_popgraph: no visible global function definition for 'points'
overlay_popgraph: no visible global function definition for 'text'
permute_popgraph: no visible global function definition for 'is'
popgraph: no visible global function definition for 'is'
popgraph: no visible global function definition for 'qchisq'
popgraph: no visible global function definition for 'prcomp'
popgraph: no visible global function definition for 'var'
read.popgraph: no visible global function definition for 'read.table'
test_congruence: no visible global function definition for 'cor.test'
to_data.frame: no visible global function definition for 'is'
to_pgraph: no visible global function definition for 'is'
write_popgraph: no visible global function definition for 'is'
write_popgraph : <anonymous>: no visible global function definition for
  'write.csv'
Undefined global functions or variables:
  cor.test cov is lines points prcomp qchisq read.table text var
  write.csv
Consider adding
  importFrom("graphics", "lines", "points", "text")
  importFrom("methods", "is")
  importFrom("stats", "cor.test", "cov", "prcomp", "qchisq", "var")
  importFrom("utils", "read.table", "write.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Error in re-building vignettes:
  ...
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

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

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'VariantAnnotation'

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

    tabulate


Error: processing vignette 'poplite.Rnw' failed with diagnostics:
 chunk 15 
Error in c(DataFrameList(META = meta), tbls[unique(tags)]) : 
  could not find symbol "recursive" in environment of the generic function
Execution halted
estMod.rinvGamma.mar29: no visible global function definition for
  'rgamma'
life.expectancy.stationary: no visible global function definition for
  'head'
life.expectancy.stationary: no visible global function definition for
  'tail'
log.lhood.mar29: no visible global function definition for 'dnorm'
log.post.mar29: no visible global function definition for 'dnorm'
popRecon.sampler: no visible global function definition for 'rnorm'
popRecon.sampler: no visible global function definition for 'runif'
Undefined global functions or variables:
  dnorm head rgamma rnorm runif tail
Consider adding
  importFrom("stats", "dnorm", "rgamma", "rnorm", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Packages which this enhances but not available for checking:
  'org.Ag.eg.db' 'org.Pt.eg.db' 'org.Ss.eg.db' 'org.Bt.eg.db'
  'org.Ce.eg.db' 'org.Cf.eg.db' 'org.Dr.eg.db' 'org.EcK12.eg.db'
  'org.EcSakai.eg.db' 'org.Gg.eg.db' 'org.Mmu.eg.db' 'org.Pf.plasmo.db'
  'org.Xl.eg.db'
JKpp.fourpl: no visible global function definition for 'packageVersion'
JKpp.gpcm: no visible global function definition for 'packageVersion'
JKpp.gpcm4pl: no visible global function definition for
  'packageVersion'
PP_4pl: no visible global function definition for 'packageVersion'
PP_gpcm: no visible global function definition for 'packageVersion'
PPall: no visible global function definition for 'packageVersion'
PV.fourpl: no visible global function definition for 'packageVersion'
PV.fourpl : <anonymous>: no visible global function definition for
  'rnorm'
PV.fourpl : <anonymous>: no visible global function definition for
  'dnorm'
PV.fourpl : <anonymous>: no visible global function definition for
  'runif'
PV.gpcm: no visible global function definition for 'packageVersion'
PV.gpcm : <anonymous>: no visible global function definition for
  'rnorm'
PV.gpcm : <anonymous>: no visible global function definition for
  'dnorm'
PV.gpcm : <anonymous>: no visible global function definition for
  'runif'
PV.gpcm4pl: no visible global function definition for 'packageVersion'
PV.gpcm4pl : <anonymous>: no visible global function definition for
  'rnorm'
PV.gpcm4pl : <anonymous>: no visible global function definition for
  'dnorm'
PV.gpcm4pl : <anonymous>: no visible global function definition for
  'runif'
cco : <anonymous>: no visible global function definition for 'median'
cco : <anonymous>: no visible global function definition for 'optim'
quadIT : <anonymous>: no visible global function definition for 'dnorm'
stdrdize_hist: no visible global function definition for
  'weighted.mean'
Undefined global functions or variables:
  dnorm median optim packageVersion rnorm runif weighted.mean
Consider adding
  importFrom("stats", "dnorm", "median", "optim", "rnorm", "runif",
             "weighted.mean")
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
Missing or unexported object: 'cowplot::switch_axis_position'
getCandidates: no visible binding for global variable 'envData'
getGraph: no visible binding for global variable 'envData'
getProvidedDiseaseName: no visible binding for global variable
  'envData'
getSeed: no visible binding for global variable 'envData'
getTopDiseaseMetabolites: no visible binding for global variable
  'envData'
Undefined global functions or variables:
  envData
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    extdata  10.9Mb
    libs      1.5Mb
.simplify : <anonymous>: no visible binding for global variable 'hist'
.simplify : <anonymous>: no visible binding for global variable 'start'
.simplify: no visible binding for global variable 'start'
.simplify: no visible binding for global variable 'end'
ggplot.profr: no visible global function definition for 'ggplot'
ggplot.profr: no visible global function definition for 'geom_rect'
ggplot.profr: no visible global function definition for 'aes'
ggplot.profr: no visible binding for global variable 'start'
ggplot.profr: no visible binding for global variable 'end'
ggplot.profr: no visible global function definition for 'geom_text'
ggplot.profr: no visible binding for global variable 'time'
ggplot.profr: no visible global function definition for
  'scale_y_continuous'
ggplot.profr: no visible global function definition for
  'scale_x_continuous'
plot.profr: no visible global function definition for 'plot'
plot.profr: no visible global function definition for 'rect'
plot.profr: no visible binding for global variable 'time'
plot.profr: no visible global function definition for 'text'
profr: no visible global function definition for 'Rprof'
Undefined global functions or variables:
  Rprof aes end geom_rect geom_text ggplot hist plot rect
  scale_x_continuous scale_y_continuous start text time
Consider adding
  importFrom("graphics", "hist", "plot", "rect", "text")
  importFrom("stats", "end", "start", "time")
  importFrom("utils", "Rprof")
to your NAMESPACE file.
Package suggested but not available for checking: 'qtbase'
Cul: no visible global function definition for 'qf'
blockScale: no visible binding for global variable 'sd'
cochranTest: no visible global function definition for 'prcomp'
cochranTest: no visible binding for global variable 'var'
cochranTest: no visible global function definition for 'matplot'
cochranTest: no visible global function definition for 'legend'
continuumRemoval : crfun: no visible global function definition for
  'chull'
continuumRemoval : crfun: no visible global function definition for
  'approx'
continuumRemoval : crfun: no visible global function definition for
  'splinefun'
detrend: no visible binding for global variable 'sd'
duplex: no visible global function definition for 'prcomp'
e2m: no visible global function definition for 'cov'
kenStone: no visible global function definition for 'prcomp'
naes: no visible global function definition for 'prcomp'
naes: no visible global function definition for 'kmeans'
puchwein: no visible global function definition for 'prcomp'
readASD: no visible global function definition for 'read.table'
resample : resfun: no visible global function definition for 'approx'
resample : resfun: no visible global function definition for
  'splinefun'
shenkWest: no visible global function definition for 'prcomp'
spliceCorrection : extrapfun: no visible global function definition for
  'lm'
standardNormalVariate: no visible binding for global variable 'sd'
Undefined global functions or variables:
  approx chull cov kmeans legend lm matplot prcomp qf read.table sd
  splinefun var
Consider adding
  importFrom("grDevices", "chull")
  importFrom("graphics", "legend", "matplot")
  importFrom("stats", "approx", "cov", "kmeans", "lm", "prcomp", "qf",
             "sd", "splinefun", "var")
  importFrom("utils", "read.table")
to your NAMESPACE file.
addIonSatistics: no visible binding for global variable 'median'
adjustOne: no visible binding for global variable 'median'
attachModifications: no visible global function definition for
  'na.omit'
avrgLoadingCalculation: no visible binding for global variable 'median'
channelResponses : estimate: no visible binding for global variable
  'var'
responseStatisics : func: no visible global function definition for
  'aggregate'
testing: no visible global function definition for 'aov'
testingOneshot: no visible global function definition for 'anova'
testingTukey: no visible global function definition for 'TukeyHSD'
Undefined global functions or variables:
  TukeyHSD aggregate anova aov median na.omit var
Consider adding
  importFrom("stats", "TukeyHSD", "aggregate", "anova", "aov", "median",
             "na.omit", "var")
to your NAMESPACE file.
'library' or 'require' call to 'class' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'class'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
addcircle: no visible global function definition for 'lines'
addclassifierboundary: no visible global function definition for 'par'
addclassifierboundary: no visible global function definition for
  'contour'
plot.protoclass: no visible global function definition for 'plot'
plot.protoclass: no visible global function definition for 'box'
plot.protoclass: no visible global function definition for 'rgb2hsv'
plot.protoclass: no visible global function definition for 'col2rgb'
plot.protoclass: no visible global function definition for 'points'
plot.protoclass: no visible global function definition for 'hsv'
predict.protoclass: no visible global function definition for 'knn1'
Undefined global functions or variables:
  box col2rgb contour hsv knn1 lines par plot points rgb2hsv
Consider adding
  importFrom("grDevices", "col2rgb", "hsv", "rgb2hsv")
  importFrom("graphics", "box", "contour", "lines", "par", "plot",
             "points")
to your NAMESPACE file.
plot.PRROC: no visible global function definition for 'hsv'
plot.PRROC: no visible global function definition for 'grey'
plot.PRROC: no visible global function definition for 'lcm'
plot.PRROC: no visible global function definition for 'layout'
plot.PRROC: no visible global function definition for 'plot'
plot.PRROC: no visible global function definition for 'polygon'
plot.PRROC: no visible global function definition for 'lines'
plot.PRROC: no visible global function definition for 'segments'
plot.PRROC: no visible global function definition for 'par'
plot.PRROC: no visible global function definition for 'image'
plot.PRROC: no visible global function definition for 'axis'
Undefined global functions or variables:
  axis grey hsv image layout lcm lines par plot polygon segments
Consider adding
  importFrom("grDevices", "grey", "hsv")
  importFrom("graphics", "axis", "image", "layout", "lcm", "lines",
             "par", "plot", "polygon", "segments")
to your NAMESPACE file.
compare_size: no visible global function definition for 'object.size'
f: no visible global function definition for 'setNames'
internal_generics: no visible global function definition for
  'getGroupMembers'
method_from_call: no visible global function definition for
  'getGeneric'
method_from_call: no visible global function definition for
  'selectMethod'
names_c: no visible global function definition for 'read.csv'
primitive_name: no visible global function definition for
  'capture.output'
show_c_source: no visible global function definition for 'URLencode'
show_c_source: no visible global function definition for 'browseURL'
Undefined global functions or variables:
  URLencode browseURL capture.output getGeneric getGroupMembers
  object.size read.csv selectMethod setNames
Consider adding
  importFrom("methods", "getGeneric", "getGroupMembers", "selectMethod")
  importFrom("stats", "setNames")
  importFrom("utils", "URLencode", "browseURL", "capture.output",
             "object.size", "read.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
mahalanobisComposite: no visible global function definition for
  'princomp'
prepareComposite: no visible global function definition for 'cov'
winsorizor : f: no visible global function definition for 'quantile'
Undefined global functions or variables:
  cov princomp quantile
Consider adding
  importFrom("stats", "cov", "princomp", "quantile")
to your NAMESPACE file.
Package suggested but not available for checking: 'printr'
Packages in Depends field not imported from:
  'R.utils' 'rmeta'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ChisqTest_expect: no visible global function definition for 'pchisq'
plot_chase_observed_expected: no visible global function definition for
  'meta.MH'
plot_chase_observed_expected: no visible global function definition for
  'txtProgressBar'
plot_chase_observed_expected: no visible global function definition for
  'setTxtProgressBar'
test.one.treated: no visible global function definition for
  'fisher.test'
test_one: no visible global function definition for 'rbinom'
test_one: no visible global function definition for 'fisher.test'
Undefined global functions or variables:
  fisher.test meta.MH pchisq rbinom setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "fisher.test", "pchisq", "rbinom")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
CandidateBio.getBio : <anonymous>: no visible global function
  definition for 'na.omit'
Committee.getCommittee : <anonymous>: no visible global function
  definition for 'na.omit'
getAllBios: no visible global function definition for 'txtProgressBar'
getAllBios: no visible global function definition for
  'setTxtProgressBar'
getAllLocalOfficials: no visible global function definition for
  'txtProgressBar'
getAllLocalOfficials: no visible global function definition for
  'setTxtProgressBar'
getAllVotes: no visible global function definition for 'txtProgressBar'
getAllVotes: no visible global function definition for
  'setTxtProgressBar'
Undefined global functions or variables:
  na.omit setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
dmm_fn: no visible global function definition for 'dnorm'
dmm_noweights_fn: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Quitting from lines 110-111 (orthography_processing.Rmd) 
Error: processing vignette 'orthography_processing.Rmd' failed with diagnostics:
undefined columns selected
Execution halted
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    data  11.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/qtbase.Rcheck/00install.out' for details.
Package required but not available: 'qtbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' call to 'Rmpfr' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
adjacencyMatrix: no visible global function definition for 'as'
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
alphaf: no visible global function definition for 'pchisq'
alphaf: no visible global function definition for 'dbinom'
conout: no visible global function definition for 'sd'
ibgaout: no visible global function definition for 'qnorm'
ibgaout: no visible global function definition for 'pnorm'
plot.qualint: no visible global function definition for 'qnorm'
powerval: no visible global function definition for 'rnorm'
powerval: no visible global function definition for 'qnorm'
powerval: no visible global function definition for 'pnorm'
print.expplot: no visible global function definition for 'gray'
print.expplot: no visible binding for global variable 'coef'
print.outplot: no visible global function definition for 'gray'
print.outplot: no visible binding for global variable 'coef'
qualint: no visible global function definition for 'qnorm'
qualint: no visible global function definition for 'plot'
qualval: no visible global function definition for 'qnorm'
qualval: no visible global function definition for 'plot'
surout: no visible global function definition for 'tail'
surout: no visible global function definition for 'coef'
Undefined global functions or variables:
  coef dbinom gray pchisq plot pnorm qnorm rnorm sd tail
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "plot")
  importFrom("stats", "coef", "dbinom", "pchisq", "pnorm", "qnorm",
             "rnorm", "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    2.3Mb
    libs   2.4Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   1.9Mb
draw_legend: no visible global function definition for 'legend'
draw_legend: no visible global function definition for 'par'
draw_nodes: no visible global function definition for 'lines'
draw_nodes: no visible global function definition for 'points'
draw_nodes: no visible global function definition for 'text'
draw_vertical_lines: no visible global function definition for 'lines'
draw_vertical_lines: no visible global function definition for 'abline'
layout_large_plot: no visible global function definition for 'par'
layout_large_plot: no visible global function definition for 'mtext'
layout_large_plot: no visible global function definition for 'axis'
layout_large_plot: no visible global function definition for 'lines'
layout_small_plot: no visible global function definition for 'par'
rquipu: no visible global function definition for 'colors'
rquipu: no visible global function definition for 'jpeg'
rquipu: no visible global function definition for 'png'
rquipu: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  abline axis colors dev.off jpeg legend lines mtext par png points
  text
Consider adding
  importFrom("grDevices", "colors", "dev.off", "jpeg", "png")
  importFrom("graphics", "abline", "axis", "legend", "lines", "mtext",
             "par", "points", "text")
to your NAMESPACE file.
File 'qVarSel/libs/i386/qVarSel.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'qVarSelH.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'qVarSelH.o'
File 'qVarSel/libs/x64/qVarSel.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'qVarSelH.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'qVarSelH.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    Output   2.2Mb
    bin      9.3Mb
'library' or 'require' call to 'rgl' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'lattice' 'leaps' 'rgl' 's20x'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cpc_get_rawdata: no visible global function definition for
  'download.file'
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
altmetric_data: no visible global function definition for 'is'
plot.altmetric: no visible global function definition for 'is'
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
plot.rsm: no visible global function definition for 'par'
plot.rsm: no visible global function definition for 'abline'
plot.rsm: no visible global function definition for 'barplot'
Undefined global functions or variables:
  abline barplot par
Consider adding
  importFrom("graphics", "abline", "barplot", "par")
to your NAMESPACE file.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   6.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   2.6Mb
BruteAggreg: no visible global function definition for 'median'
RankAggreg: no visible global function definition for 'median'
RankAggreg: no visible global function definition for 'runif'
mcmcProc: no visible global function definition for 'runif'
plot.raggr: no visible global function definition for 'layout'
plot.raggr: no visible global function definition for 'plot'
plot.raggr: no visible global function definition for 'legend'
plot.raggr: no visible global function definition for 'hist'
plot.raggr: no visible global function definition for 'runif'
plot.raggr: no visible global function definition for 'axis'
plot.raggr: no visible global function definition for 'lines'
plotUpdate: no visible global function definition for 'layout'
plotUpdate: no visible global function definition for 'plot'
plotUpdate: no visible global function definition for 'legend'
rmult: no visible global function definition for 'runif'
Undefined global functions or variables:
  axis hist layout legend lines median plot runif
Consider adding
  importFrom("graphics", "axis", "hist", "layout", "legend", "lines",
             "plot")
  importFrom("stats", "median", "runif")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Loading required package: cluster
Loading required package: kohonen
Loading required package: mclust
Package 'mclust' version 5.2.3
Type 'citation("mclust")' for citing this R package in publications.

Attaching package: 'mclust'

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

    map

Warning in fanny(DistDel, nc, ...) :
  FANNY algorithm has not converged in 'maxit' = 500 iterations

Error: processing vignette 'RankAggreg.Rnw' failed with diagnostics:
 chunk 4 
Error in !toroidal : invalid argument type
Execution halted
'library' or 'require' call to 'BSgenome.Hsapiens.UCSC.hg19' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages suggested but not available for checking: 'gurobi' 'rgurobi'
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.7Mb
    libs   2.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   1.6Mb
Error in re-building vignettes:
  ...
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "rattle.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.3/share/texmf/bibtex/bst"' had status 1
Error in find_vignette_product(name, by = "texi2pdf", engine = engine) : 
  Failed to locate the 'texi2pdf' output file (by engine 'utils::Sweave') for vignette with name 'rattle'. The following files exist in directory '.': 'rattle.Rnw', 'rattle.tex'
Calls: buildVignettes -> find_vignette_product
Execution halted
.avisApiBusAvanzada: no visible global function definition for
  'read.csv'
.avisRenderMapAdmin: no visible global function definition for 'points'
.avisRenderMapAdmin: no visible global function definition for 'rect'
.avisRenderMapPhysical: no visible global function definition for
  'points'
avisMap: no visible global function definition for 'par'
avisMap: no visible global function definition for 'layout'
Undefined global functions or variables:
  layout par points read.csv rect
Consider adding
  importFrom("graphics", "layout", "par", "points", "rect")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
.parse.rhea: no visible global function definition for 'tail'
get.chebi.all: no visible global function definition for
  'download.file'
get.chebi.all: no visible global function definition for 'read.delim'
get.rhea.all: no visible global function definition for 'download.file'
get.unipathway.all: no visible global function definition for
  'download.file'
Undefined global functions or variables:
  download.file read.delim tail
Consider adding
  importFrom("utils", "download.file", "read.delim", "tail")
to your NAMESPACE file.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
find_available_versions: no visible global function definition for
  'contrib.url'
find_available_versions: no visible global function definition for
  'available.packages'
install_version: no visible global function definition for
  'contrib.url'
install_version: no visible global function definition for
  'available.packages'
install_version: no visible global function definition for
  'install_url'
load_available_packages: no visible global function definition for
  'contrib.url'
validate_installed_package: no visible global function definition for
  'installed.packages'
Undefined global functions or variables:
  available.packages contrib.url install_url installed.packages
Consider adding
  importFrom("utils", "available.packages", "contrib.url",
             "installed.packages")
to your NAMESPACE file.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
get_ClinicalCodes: no visible global function definition for 'read.csv'
get_ClinicalCodes : <anonymous>: no visible global function definition
  for 'read.csv'
Undefined global functions or variables:
  read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
.onAttach: no visible global function definition for 'palette'
.onAttach: no visible global function definition for 'dev.off'
helpAboutBCA: no visible global function definition for 'help'
Undefined global functions or variables:
  dev.off help palette
Consider adding
  importFrom("grDevices", "dev.off", "palette")
  importFrom("utils", "help")
to your NAMESPACE file.
Depends: includes the non-default packages:
  'biclust' 'fabia' 'iBBiG' 'superbiclust' 'BcDiag' 'rqubic' 'BicARE'
  's4vd' 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
enterTableMHTest : onOK: no visible global function definition for
  'na.omit'
startStop: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Namespace with empty importFrom: 'tcltk'
'library' or 'require' calls to packages already attached by Depends:
  'depthTools' 'tcltk'
  Please remove these calls from your code.
computeMBD : OnOutput: no visible global function definition for
  'tkbutton'
computeMBD: no visible global function definition for 'tkbutton'
computeMBD : OnPlot: no visible global function definition for
  'tkcanvas'
computeMBD : OnPlot: no visible global function definition for
  'tkbutton'
computeTmean: no visible global function definition for 'tkcanvas'
computeTmean: no visible global function definition for 'tkbutton'
computeTmean : onOK: no visible global function definition for 'par'
plotCentralCurves: no visible global function definition for 'tkcanvas'
plotCentralCurves: no visible global function definition for 'tkbutton'
plotCentralCurves : onOK: no visible global function definition for
  'par'
Undefined global functions or variables:
  par tkbutton tkcanvas
Consider adding
  importFrom("graphics", "par")
to your NAMESPACE file.
'library' or 'require' call to 'FrF2.catlg128' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'Rcmdr' 'multcomp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Depends: includes the non-default packages:
  'Rcmdr' 'TeachingDemos' 'tseries' 'abind' 'MASS' 'xts' 'forecast'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'tseries'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'MASS' 'Rcmdr' 'TeachingDemos' 'abind' 'forecast' 'tseries' 'xts'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' calls in package code:
  'abind' 'e1071' 'qcc'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'ENmisc' 'Hmisc' 'Rcmdr' 'vcd'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.onAttach: no visible global function definition for 'getRcmdr'
.onAttach: no visible global function definition for 'closeCommander'
.onAttach: no visible global function definition for 'Commander'
mosaicMenuItem: no visible global function definition for
  'mosaicSelectDialog'
mosaicMenuItem: no visible global function definition for 'Message'
Undefined global functions or variables:
  Commander Message closeCommander getRcmdr mosaicSelectDialog
Packages in Depends field not imported from:
  'orloca' 'orloca.es'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rcmdr.new.loca.p: no visible binding for global variable 'top'
Rcmdr.new.loca.p: no visible binding for global variable 'buttonsFrame'
Rcmdr.orloca.norm: no visible binding for global variable 'top'
Rcmdr.orloca.norm : onOK: no visible binding for global variable
  'normaVariable'
Rcmdr.orloca.norm: no visible binding for global variable 'normaFrame'
Rcmdr.orloca.norm: no visible binding for global variable
  'buttonsFrame'
Rcmdr.rloca.p: no visible binding for global variable 'top'
Rcmdr.rloca.p: no visible binding for global variable 'buttonsFrame'
Rcmdr.zsum: no visible binding for global variable 'top'
Rcmdr.zsum: no visible binding for global variable 'buttonsFrame'
Rcmdr.zsummin: no visible binding for global variable 'top'
Rcmdr.zsummin : onOK: no visible binding for global variable
  'algorithmVariable'
Rcmdr.zsummin : onOK: no visible binding for global variable '.sol'
Rcmdr.zsummin: no visible binding for global variable 'algorithmFrame'
Rcmdr.zsummin: no visible binding for global variable 'buttonsFrame'
Undefined global functions or variables:
  .sol algorithmFrame algorithmVariable buttonsFrame normaFrame
  normaVariable top
BOXWP: no visible binding for global variable 'top'
BOXWP: no visible binding for global variable 'buttonsFrame'
HIST: no visible binding for global variable 'top'
HIST: no visible binding for global variable 'buttonsFrame'
QQN: no visible binding for global variable 'top'
QQN: no visible binding for global variable 'buttonsFrame'
Undefined global functions or variables:
  buttonsFrame top
Namespaces with empty importFrom:
  'stats' 'tcltk'
fncLRpROC: no visible global function definition for 'palette'
fncLRpROC : onOK : convert: no visible global function definition for
  'col2rgb'
fncLRpROC : onOK : convert: no visible global function definition for
  'rgb'
fncPairedpROC: no visible global function definition for 'palette'
fncPairedpROC : onOK : convert: no visible global function definition
  for 'col2rgb'
fncPairedpROC : onOK : convert: no visible global function definition
  for 'rgb'
fncUnpairedpROC: no visible global function definition for 'palette'
fncUnpairedpROC : onOK : convert: no visible global function definition
  for 'col2rgb'
fncUnpairedpROC : onOK : convert: no visible global function definition
  for 'rgb'
fncvpROC: no visible global function definition for 'palette'
fncvpROC : onOK : convert: no visible global function definition for
  'col2rgb'
fncvpROC : onOK : convert: no visible global function definition for
  'rgb'
Undefined global functions or variables:
  col2rgb palette rgb
Consider adding
  importFrom("grDevices", "col2rgb", "palette", "rgb")
to your NAMESPACE file.
SampleSizes: no visible global function definition for 'xtabs'
SampleSizes: no visible global function definition for 'weighted.mean'
SampleSizes: no visible global function definition for 'reshape'
stage1Sample.fn: no visible global function definition for 'runif'
stage2Sample.fn: no visible global function definition for 'runif'
strata.options : onOK: no visible global function definition for
  'packageDescription'
Undefined global functions or variables:
  packageDescription reshape runif weighted.mean xtabs
Consider adding
  importFrom("stats", "reshape", "runif", "weighted.mean", "xtabs")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'Rcmdr' 'seeg' 'sgeostat' 'spatstat'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' call to 'SLC' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'SLC'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Depends: includes the non-default packages:
  'Rcmdr' 'tcltk' 'car' 'RColorBrewer' 'colorspace' 'vcd'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' call to 'car' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'RColorBrewer' 'Rcmdr' 'car' 'colorspace' 'vcd'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rcmdr.steeptestDij : onOK: no visible binding for global variable
  'replications'
Rcmdr.steeptestPij : onOK: no visible binding for global variable
  'replications'
Undefined global functions or variables:
  replications
Consider adding
  importFrom("stats", "replications")
to your NAMESPACE file.
Package suggested but not available for checking: 'ROpenOffice'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/Rcplex.Rcheck/00install.out' for details.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    include   4.7Mb
    libs      1.6Mb
Gauss: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/RcppOctave.Rcheck/00install.out' for details.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib       8.0Mb
    libs      1.0Mb
get_rollit_source: no visible global function definition for
  'file.edit'
Undefined global functions or variables:
  file.edit
Consider adding
  importFrom("utils", "file.edit")
to your NAMESPACE file.
installed size is 30.1Mb
  sub-directories of 1Mb or more:
    include   4.5Mb
    lib      21.6Mb
    libs      3.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/RDieHarder.Rcheck/00install.out' for details.
ip2coordinates: no visible global function definition for 'URLencode'
street2coordinates: no visible global function definition for
  'URLencode'
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
checkForVServer: no visible global function definition for
  'download.file'
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
Package required but not available: 'Rmosek'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
allocationTable_offline: no visible global function definition for
  'read.csv'
exportArms.redcapApiConnection: no visible global function definition
  for 'read.csv'
exportEvents.redcapApiConnection: no visible global function definition
  for 'read.csv'
exportInstruments.redcapApiConnection: no visible global function
  definition for 'read.csv'
exportMappings.redcapApiConnection: no visible global function
  definition for 'read.csv'
exportMetaData.redcapApiConnection: no visible global function
  definition for 'read.csv'
exportRecords.redcapApiConnection: no visible global function
  definition for 'read.csv'
exportRecords.redcapApiConnection : <anonymous>: no visible global
  function definition for 'read.csv'
exportRecords_offline: no visible global function definition for
  'read.csv'
exportReports.redcapApiConnection: no visible global function
  definition for 'read.csv'
exportUsers.redcapApiConnection: no visible global function definition
  for 'read.csv'
importRecords.redcapApiConnection : <anonymous>: no visible global
  function definition for 'capture.output'
importRecords.redcapApiConnection : <anonymous>: no visible global
  function definition for 'write.table'
importRecords.redcapApiConnection: no visible global function
  definition for 'capture.output'
importRecords.redcapApiConnection: no visible global function
  definition for 'write.table'
validateImport : printLog: no visible global function definition for
  'write.table'
validateImport: no visible binding for global variable 'tail'
validateImport: no visible binding for global variable 'head'
Undefined global functions or variables:
  capture.output head read.csv tail write.table
Consider adding
  importFrom("utils", "capture.output", "head", "read.csv", "tail",
             "write.table")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Quitting from lines 42-45 (BasicREDCapROperations.Rmd) 
Error: processing vignette 'BasicREDCapROperations.Rmd' failed with diagnostics:
object 'ds' not found
Execution halted
mergeNamespace_roclet: no visible global function definition for
  'new_roclet'
Undefined global functions or variables:
  new_roclet
AutoCorrelationLRtest: no visible global function definition for
  'logLik'
AutoCorrelationLRtest: no visible global function definition for
  'pchisq'
REEMtree: no visible global function definition for 'terms'
REEMtree: no visible binding for global variable 'SubsetVector'
REEMtree: no visible global function definition for 'predict'
REEMtree: no visible global function definition for 'logLik'
fitted.REEMtree: no visible global function definition for 'fitted'
plot.REEMtree: no visible global function definition for 'plot'
predict.REEMtree: no visible global function definition for 'predict'
residuals.REEMtree: no visible global function definition for
  'residuals'
Undefined global functions or variables:
  SubsetVector fitted logLik pchisq plot predict residuals terms
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "fitted", "logLik", "pchisq", "predict",
             "residuals", "terms")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'fitted.REEMtree':
  'fitted.REEMtree'

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

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

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

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

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

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Foreign function call to a different package:
  .External("do_read_bib", ..., PACKAGE = "bibtex")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
CapDistSlope: no visible global function definition for 'coef'
CapDistSlope: no visible global function definition for 'lm'
EnergyEntropyDecomp: no visible global function definition for 'legend'
FernholzDecomp: no visible global function definition for 'legend'
Invest: no visible global function definition for 'par'
Invest: no visible global function definition for 'legend'
SimMarketModel: no visible global function definition for 'rnorm'
plot.capdist: no visible global function definition for 'plot'
plot.capdist: no visible global function definition for 'abline'
plot.capdist: no visible global function definition for 'lm'
plot.toymkt: no visible global function definition for 'par'
plot.toymkt: no visible global function definition for 'plot'
plot.toymkt: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline coef legend lm par plot rnorm
Consider adding
  importFrom("graphics", "abline", "legend", "par", "plot")
  importFrom("stats", "coef", "lm", "rnorm")
to your NAMESPACE file.
MakeHierarchyTree: no visible global function definition for
  'as.formula'
Undefined global functions or variables:
  as.formula
Consider adding
  importFrom("stats", "as.formula")
to your NAMESPACE file.
plot.k2w: no visible global function definition for 'short.deparse'
Undefined global functions or variables:
  short.deparse
CA: no visible global function definition for 'readClipboard'
LL: no visible global function definition for 'readClipboard'
US: no visible global function definition for 'readClipboard'
delete: no visible global function definition for 'menu'
doc_temp: no visible global function definition for 'menu'
html5: no visible global function definition for 'na.omit'
install_pandoc: no visible global function definition for
  'download.file'
latexlist: no visible global function definition for 'readClipboard'
new_report: no visible global function definition for 'tail'
new_report: no visible global function definition for 'head'
new_report: no visible global function definition for 'menu'
presentation: no visible global function definition for 'head'
presentation: no visible global function definition for 'tail'
presentation: no visible global function definition for 'menu'
repo2github: no visible global function definition for 'download.file'
repo2github: no visible global function definition for 'unzip'
reveal.js: no visible global function definition for 'na.omit'
strWrap: no visible global function definition for 'readClipboard'
update_bib: no visible global function definition for 'tail'
update_bib: no visible global function definition for 'menu'
Undefined global functions or variables:
  download.file head menu na.omit readClipboard tail unzip
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "download.file", "head", "menu", "readClipboard",
             "tail", "unzip")
to your NAMESPACE file.
Package suggested but not available for checking: 'rsolr'
GUI_template : onHelp: no visible global function definition for 'help'
Undefined global functions or variables:
  help
Consider adding
  importFrom("utils", "help")
to your NAMESPACE file.
Running 'getFuns.R' [1s]
  Comparing 'getFuns.Rout' to 'getFuns.Rout.save' ... OK
  Running 'ijroi-format.R' [2s]
  Comparing 'ijroi-format.Rout' to 'ijroi-format.Rout.save' ... OK
  Running 'reconstruct.R' [2s]
Running the tests in 'tests/reconstruct.R' failed.
Last 13 lines of output:
    Backwards path
      i = 377 ; sf/Sf = 0.5 ; sf = 368.306937214058
        k =   34 ; sb/Sb = 0 ; sb = 0
        k =  414 ; sb/Sb = 0.60237132329825 ; sb = 387.816744112795
        Creating new point: f = 0.830052794117553
  Triangulating...
  Internal error in finddirection():  Unable to find a
    triangle leading from (-195.467775468, 4725.74636175) to  (192.266112266, 4832.37318087).
    Please report this bug to jrs@cs.berkeley.edu
    Include the message above, your input data set, and the exact
      command line you used to run Triangle.
  Error in RTriangle::triangulate(RTriangle::pslg(P = out$P, S = out$S[out$SB ==  : 
    Triangle exit, code $i
  Calls: retistruct.reconstruct ... ReconstructedOutline -> TriangulatedOutline -> <Anonymous> -> .Call
  Execution halted
fs_author_ids : <anonymous>: no visible global function definition for
  'select.list'
fs_download : <anonymous>: no visible global function definition for
  'download.file'
Undefined global functions or variables:
  download.file select.list
Consider adding
  importFrom("utils", "download.file", "select.list")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.6Mb
Error in re-building vignettes:
  ...
Quitting from lines 101-111 (a-intro.Rmd) 
Error: processing vignette 'a-intro.Rmd' failed with diagnostics:
No data returned by WHO GHO server.
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc     2.6Mb
    fonts   1.5Mb
    libs    2.0Mb
Error in re-building vignettes:
  ...
mpiler/texmf/fonts/type1/public/amsfonts/cm/cmr8.pfb><D:/Compiler/texmf/fonts/t
ype1/public/amsfonts/cm/cmr9.pfb><D:/Compiler/texmf/fonts/type1/public/amsfonts
/cm/cmsltt10.pfb><D:/Compiler/texmf/fonts/type1/public/amsfonts/cm/cmss10.pfb><
D:/Compiler/texmf/fonts/type1/public/amsfonts/cm/cmss8.pfb><D:/Compiler/texmf/f
onts/type1/public/amsfonts/cm/cmss9.pfb><D:/Compiler/texmf/fonts/type1/public/a
msfonts/cm/cmsy10.pfb><D:/Compiler/texmf/fonts/type1/public/amsfonts/cm/cmti10.
pfb><D:/Compiler/texmf/fonts/type1/public/amsfonts/cm/cmti12.pfb><D:/Compiler/t
exmf/fonts/type1/public/amsfonts/cm/cmtt10.pfb><D:/Compiler/texmf/fonts/type1/p
ublic/amsfonts/cm/cmtt8.pfb><D:/Compiler/texmf/fonts/type1/public/mathpazo/fplm
ri.pfb><D:/Compiler/texmf/fonts/type1/public/cm-super/sfrm0900.pfb><D:/Compiler
/texmf/fonts/type1/public/cm-super/sfrm1000.pfb><D:/Compiler/texmf/fonts/type1/
urw/palatino/uplr8a.pfb><D:/Compiler/texmf/fonts/type1/urw/palatino/uplri8a.pfb
>
Output written on rgp_introduction.pdf (16 pages, 430970 bytes).
Transcript written on rgp_introduction.log.
"D:/RCompile/recent/R-33~1.3/bin/Rscript" -e "tools::compactPDF('rgp_introduction.pdf', gs_quality='ebook')"
  compacted 'rgp_introduction.pdf' from 421Kb to 205Kb
rm -f Rplots.pdf
rm: cannot remove 'Rplots.pdf': Device or resource busy
make[1]: *** [pdf] Error 1
make[1]: Leaving directory `/cygdrive/d/RCompile/CRANpkg/local/3.3/rgp.Rcheck/vign_test/rgp/vignettes'
Warning: running command 'make' had status 2
Error in buildVignettes(dir = "d:/Rcompile/CRANpkg/local/3.3/rgp.Rcheck/vign_test/rgp") : 
  running 'make' failed
Execution halted
.onAttach: no visible global function definition for 'sessionInfo'
rescaleIndividual: no visible global function definition for 'cov'
rescaleIndividual: no visible global function definition for 'var'
server: no visible global function definition for 'mcparallel'
server: no visible global function definition for 'read.csv'
server: no visible global function definition for 'tail'
server: no visible global function definition for 'as.formula'
server: no visible global function definition for 'terms'
server: no visible global function definition for 'plot'
server: no visible global function definition for 'legend'
server: no visible global function definition for 'lines'
server: no visible global function definition for 'par'
server: no visible global function definition for 'layout'
server: no visible global function definition for 'points'
server: no visible global function definition for 'barplot'
workerProcessRun: no visible global function definition for
  'as.formula'
workerProcessRun : <anonymous>: no visible global function definition
  for 'runif'
workerProcessRun : progressMonitor: no visible global function
  definition for 'alarm'
workerProcessRun : progressMonitor: no visible global function
  definition for 'runif'
Undefined global functions or variables:
  alarm as.formula barplot cov layout legend lines mcparallel par plot
  points read.csv runif sessionInfo tail terms var
Consider adding
  importFrom("graphics", "barplot", "layout", "legend", "lines", "par",
             "plot", "points")
  importFrom("stats", "as.formula", "cov", "runif", "terms", "var")
  importFrom("utils", "alarm", "read.csv", "sessionInfo", "tail")
to your NAMESPACE file.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    extra   9.3Mb
Found the following significant warnings:
  gdkFuncs.c:1466:31: warning: passing argument 1 of 'gdk_drag_get_protocol' makes pointer from integer without a cast
  gdkFuncs.c:1510:52: warning: passing argument 2 of 'gdk_drag_get_protocol_for_display' makes pointer from integer without a cast
See 'd:/Rcompile/CRANpkg/local/3.3/RGtk2.Rcheck/00install.out' for details.
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    help  10.6Mb
    libs   4.7Mb
dbConnect,H2Driver: no visible global function definition for '.jgetEx'
dbSendQuery,H2Connection-character: no visible global function
  definition for '.jfield'
Undefined global functions or variables:
  .jfield .jgetEx
.quick_fetch: no visible global function definition for 'POST'
.quick_fetch: no visible global function definition for 'add_headers'
.quick_fetch: no visible global function definition for
  'stop_for_status'
.quick_fetch: no visible global function definition for 'content'
fetch_healthdata: no visible binding for global variable 'resources'
fetch_healthdata : <anonymous>: no visible binding for global variable
  'filters'
Undefined global functions or variables:
  POST add_headers content filters resources stop_for_status
plot.ijzip: no visible global function definition for 'plot'
plot.ijzip : <anonymous>: no visible global function definition for
  'plot'
plot.ijzip: no visible global function definition for 'axis'
read.ijzip: no visible global function definition for 'unzip'
Undefined global functions or variables:
  axis plot unzip
Consider adding
  importFrom("graphics", "axis", "plot")
  importFrom("utils", "unzip")
to your NAMESPACE file.
rite : exitWiz: no visible global function definition for 'bringToTop'
rite : loadHistory: no visible global function definition for
  'savehistory'
rite : saveGist: no visible global function definition for 'browseURL'
rite : uploadToRPubs : processEntry: no visible global function
  definition for 'browseURL'
rite : runCode: no visible global function definition for 'savehistory'
rite : runCode: no visible global function definition for 'loadhistory'
rite : knittxt: no visible global function definition for 'Sweave'
rite : knittxt: no visible global function definition for 'browseURL'
rite : addHighlighting : addHighlight: no visible global function
  definition for 'packageDescription'
rite : addHighlighting : addHighlight: no visible global function
  definition for 'na.omit'
rite : about : <anonymous>: no visible global function definition for
  'browseURL'
rite : <anonymous>: no visible global function definition for
  'capture.output'
rite : <anonymous>: no visible global function definition for
  'update.packages'
rite : <anonymous>: no visible global function definition for 'help'
rite : f1: no visible global function definition for 'help'
rite : f1: no visible global function definition for 'help.search'
rite : commandCompletion: no visible global function definition for
  'apropos'
rite : findreplace : <anonymous>: no visible global function definition
  for 'browseURL'
Undefined global functions or variables:
  Sweave apropos bringToTop browseURL capture.output help help.search
  loadhistory na.omit packageDescription savehistory update.packages
Consider adding
  importFrom("grDevices", "bringToTop")
  importFrom("stats", "na.omit")
  importFrom("utils", "Sweave", "apropos", "browseURL", "capture.output",
             "help", "help.search", "loadhistory", "packageDescription",
             "savehistory", "update.packages")
to your NAMESPACE file.
Found the following significant warnings:
  jri.h:21:20: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  jri.c:308:27: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  jri_glue.c:24:15: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.3/rJava.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available


See 'Writing portable packages' in the 'Writing R Extensions' manual.
Undocumented S4 methods:
  generic 'dbReadTable' and siglist 'JDBCConnection,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is 45.1Mb
  sub-directories of 1Mb or more:
    exe  45.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    java   4.5Mb
CI: no visible global function definition for 'sd'
CI: no visible global function definition for 'qt'
L: no visible global function definition for 'sd'
L: no visible global function definition for 'residuals'
Qa: no visible global function definition for 'logLik'
Qb: no visible global function definition for 'residuals'
Qc: no visible global function definition for 'residuals'
Qc: no visible global function definition for 'logLik'
STDERR: no visible global function definition for 'sd'
group.UCL: no visible global function definition for 'aggregate'
lr.glover: no visible binding for global variable 'logLik'
lr.glover: no visible binding for global variable 'update'
lr.glover : nobs0: no visible binding for global variable 'nobs'
lr.glover : nobs0 : nobs2: no visible global function definition for
  'residuals'
lr.glover : tlab: no visible global function definition for 'terms'
lr.glover : name: no visible global function definition for 'formula'
lr.glover : modelUpdate: no visible global function definition for
  'as.formula'
lr.glover: no visible global function definition for 'model.frame'
lr.glover: no visible binding for global variable 'AIC'
lr.glover: no visible binding for global variable 'BIC'
summarySE : <anonymous>: no visible global function definition for 'sd'
summarySE: no visible global function definition for 'qt'
Undefined global functions or variables:
  AIC BIC aggregate as.formula formula logLik model.frame nobs qt
  residuals sd terms update
Consider adding
  importFrom("stats", "AIC", "BIC", "aggregate", "as.formula", "formula",
             "logLik", "model.frame", "nobs", "qt", "residuals", "sd",
             "terms", "update")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/Rmosek.Rcheck/00install.out' for details.
CoeffYWeq: no visible global function definition for 'index'
fitdistrForPrecipitation: no visible global function definition for
  'fitdistr'
generate.CCGammaObject: no visible binding for global variable 'rnorm'
generate.CCGammaObject: no visible global function definition for
  'pnorm'
generate.YuleWalkerCoefficientBlockmatrices: no visible binding for
  global variable 'rnorm'
generate.YuleWalkerCoefficientBlockmatricesPerEachMonth: no visible
  binding for global variable 'rnorm'
generatePrecipitationAmount: no visible global function definition for
  'str'
omega_inv: no visible global function definition for 'uniroot'
qqfit: no visible binding for global variable 'qexp'
qqfit: no visible global function definition for 'ecdf'
Undefined global functions or variables:
  ecdf fitdistr index pnorm qexp rnorm str uniroot
Consider adding
  importFrom("stats", "ecdf", "pnorm", "qexp", "rnorm", "uniroot")
  importFrom("utils", "str")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'DESeq' 'seqinr' 'topGO'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: 'rnaturalearthhires'
.isPath: no visible global function definition for 'tail'
.isPath: no visible global function definition for 'head'
navGraph : <anonymous>: no visible global function definition for
  'tail'
navGraph : <anonymous>: no visible global function definition for 'sd'
navGraph: no visible global function definition for 'colors'
ng_image_array_gray : <anonymous>: no visible global function
  definition for 'grey'
scagGraph: no visible global function definition for 'quantile'
closeViz,NG_Viz2DAxis: no visible global function definition for
  'dev.off'
initializeViz,NG_Viz2DAxis: no visible global function definition for
  'dev.new'
initializeViz,NG_Viz2DAxis: no visible global function definition for
  'dev.cur'
plot,NG_graph-ANY: no visible global function definition for 'box'
plot,NG_graph-ANY: no visible global function definition for 'axis'
plot,NG_graph-ANY: no visible global function definition for 'points'
plot,NG_graph-ANY: no visible global function definition for 'text'
plot,NG_graph-ANY: no visible global function definition for 'segments'
updateViz,NG_Viz2DAxis: no visible global function definition for
  'dev.set'
Undefined global functions or variables:
  axis box colors dev.cur dev.new dev.off dev.set grey head points
  quantile sd segments tail text
Consider adding
  importFrom("grDevices", "colors", "dev.cur", "dev.new", "dev.off",
             "dev.set", "grey")
  importFrom("graphics", "axis", "box", "points", "segments", "text")
  importFrom("stats", "quantile", "sd")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
.collapse: no visible global function definition for 'head'
RNGinfo: no visible global function definition for 'setNames'
RNGlibs: no visible global function definition for 'tail'
RNGseq : <anonymous>: no visible global function definition for
  'nextRNGStream'
RNGseq: no visible global function definition for 'nextRNGStream'
RNGseq_seed: no visible global function definition for 'runif'
RNGseq_seed: no visible global function definition for 'nextRNGStream'
checkRNG: no visible global function definition for 'checkTrue'
nextRNG: no visible global function definition for 'runif'
.setRNG,numeric: no visible global function definition for 'runif'
Undefined global functions or variables:
  checkTrue head nextRNGStream runif setNames tail
Consider adding
  importFrom("stats", "runif", "setNames")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      5.3Mb
Nnls.trimW : fun1: no visible global function definition for 'runif'
initM: no visible global function definition for 'runif'
rnmf: no visible global function definition for 'txtProgressBar'
rnmf: no visible global function definition for 'setTxtProgressBar'
see: no visible global function definition for 'heat.colors'
see: no visible global function definition for 'colorRampPalette'
see: no visible global function definition for 'grey'
see: no visible global function definition for 'par'
see: no visible global function definition for 'image'
see: no visible global function definition for 'mtext'
simtum: no visible global function definition for 'runif'
simtum: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  colorRampPalette grey heat.colors image mtext par rnorm runif
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("grDevices", "colorRampPalette", "grey", "heat.colors")
  importFrom("graphics", "image", "mtext", "par")
  importFrom("stats", "rnorm", "runif")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
cluster_em_outlier: no visible global function definition for 'qchisq'
jth_dsty: no visible global function definition for 'mahalanobis'
k_means: no visible global function definition for 'kmeans'
mix_rcm: no visible global function definition for 'median'
Undefined global functions or variables:
  kmeans mahalanobis median qchisq
Consider adding
  importFrom("stats", "kmeans", "mahalanobis", "median", "qchisq")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/ROracle.Rcheck/00install.out' for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.1Mb
bestFM: no visible global function definition for 'data'
gaRoth: no visible global function definition for 'data'
ros: no visible global function definition for 'na.omit'
rosunc: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  data na.omit rnorm
Consider adding
  importFrom("stats", "na.omit", "rnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Quitting from lines 47-57 (meta-analysis.Rmd) 
Error: processing vignette 'meta-analysis.Rmd' failed with diagnostics:
SI number '1' greater than number of detected SIs (0)
Execution halted
mfix : m4m: no visible global function definition for 'median'
rrfa: no visible global function definition for 'predict'
rrfb: no visible global function definition for 'predict'
rrfc1: no visible global function definition for 'predict'
rrfc2: no visible global function definition for 'predict'
rrfc3: no visible global function definition for 'predict'
rrfc4: no visible global function definition for 'predict'
rrfc5 : regdat: no visible global function definition for 'predict'
rrfc5 : regdat: no visible global function definition for 'glm'
rrfc5: no visible global function definition for 'predict'
rrfc6: no visible global function definition for 'predict'
rrfc7: no visible global function definition for 'predict'
rrfd: no visible global function definition for 'predict'
rrfe : rdms: no visible global function definition for 'rbinom'
rrfe: no visible global function definition for 'predict'
Undefined global functions or variables:
  glm median predict rbinom
Consider adding
  importFrom("stats", "glm", "median", "predict", "rbinom")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'MASS' 'RandomFields' 'akima' 'denstrip' 'geoR' 'lattice' 'maps'
  'mgcv' 'rgl' 'sm' 'tkrplot'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'tcltk'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cell.density.default: no visible binding for global variable
  'universalConstants'
conect.pdb: no visible binding for global variable 'elements'
masses.default: no visible binding for global variable 'elements'
toSymbols.character: no visible binding for global variable 'elements'
toSymbols.integer: no visible binding for global variable 'elements'
visualize.coords: no visible binding for global variable 'elements'
visualize.coords: no visible binding for global variable 'rgb'
Undefined global functions or variables:
  elements rgb universalConstants
Consider adding
  importFrom("grDevices", "rgb")
to your NAMESPACE file.
postgresqlImportFile: no visible global function definition for
  'count.fields'
postgresqlImportFile: no visible global function definition for
  'read.table'
Undefined global functions or variables:
  count.fields read.table
Consider adding
  importFrom("utils", "count.fields", "read.table")
to your NAMESPACE file.
but_last: no visible global function definition for 'head'
first: no visible global function definition for 'head'
last: no visible global function definition for 'tail'
preview_frames: no visible global function definition for 'str'
print.EprimeFrame: no visible global function definition for 'str'
print.FrameList: no visible global function definition for 'str'
Undefined global functions or variables:
  head str tail
Consider adding
  importFrom("utils", "head", "str", "tail")
to your NAMESPACE file.
rpygeo.geoprocessor: warning in system(py.call, invisible = TRUE,
  minimize = TRUE, wait = wait): partial argument match of 'minimize'
  to 'minimized'
Package which this enhances but not available for checking: 'rjpod'
Found the following significant warnings:
  d:/RCompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:824:13: warning: this decimal constant is unsigned only in ISO C90
  d:/RCompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:842:13: warning: this decimal constant is unsigned only in ISO C90
  d:/RCompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomlosslatentmodel.hpp:84:13: warning: this decimal constant is unsigned only in ISO C90
  d:/Rcompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:824:13: warning: this decimal constant is unsigned only in ISO C90
  d:/Rcompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:842:13: warning: this decimal constant is unsigned only in ISO C90
  d:/Rcompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomlosslatentmodel.hpp:84:13: warning: this decimal constant is unsigned only in ISO C90
See 'd:/Rcompile/CRANpkg/local/3.3/RQuantLib.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/RSAP.Rcheck/00install.out' for details.
stripslash: 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 Please include winsock2.h before windows.h
  qap_decode.c:200:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:200:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:55: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:60: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.3/Rserve.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'biwt' 'cairoDevice' 'fBasics' 'gplots' 'gWidgets' 'gWidgetsRGtk2'
  'minerva' 'parmigene' 'stringr' 'snowfall'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' calls to packages already attached by Depends:
  'grDevices' 'snowfall'
  Please remove these calls from your code.
'library' or 'require' call to 'ctc' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'biwt' 'cairoDevice' 'fBasics' 'gWidgets' 'gWidgetsRGtk2' 'gplots'
  'minerva' 'parmigene' 'snowfall' 'stringr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' calls in package code:
  'MASS' 'codetools' 'lattice' 'network' 'parallel' 'tcltk' 'xtable'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: 'utils:::edit.data.frame'
  See the note in ?`:::` about the use of this operator.
Found the following significant warnings:
  Warning: replacing previous import 'kohonen::somgrid' by 'class::somgrid' when loading 'Rsomoclu'
See 'd:/Rcompile/CRANpkg/local/3.3/Rsomoclu.Rcheck/00install.out' for details.
negbin.pow : negbin.disp: no visible global function definition for
  'rpois'
negbin.pow : negbin.disp: no visible global function definition for
  'rnbinom'
negbin.pow : inner.fcn: no visible global function definition for
  'na.omit'
negbin.pow : inner.fcn: no visible global function definition for
  'quantile'
negbin.pow: no visible global function definition for 'txtProgressBar'
negbin.pow: no visible global function definition for
  'setTxtProgressBar'
poiss.pow : inner.fcn: no visible global function definition for
  'rpois'
poiss.pow : inner.fcn: no visible global function definition for
  'quantile'
poiss.pow: no visible global function definition for 'txtProgressBar'
poiss.pow: no visible global function definition for
  'setTxtProgressBar'
Undefined global functions or variables:
  na.omit quantile rnbinom rpois setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit", "quantile", "rnbinom", "rpois")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   9.0Mb
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:

======== End of example output (where/before crash/hang up occured ?) ========
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
RStorm: no visible global function definition for 'alply'
Undefined global functions or variables:
  alply
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
getSVGToolTipMode: no visible global function definition for 'dev.cur'
setSVGShapeContents: no visible global function definition for
  'dev.cur'
setSVGShapeToolTip: no visible global function definition for 'dev.cur'
setSVGShapeURL: no visible global function definition for 'dev.cur'
Undefined global functions or variables:
  dev.cur
Consider adding
  importFrom("grDevices", "dev.cur")
to your NAMESPACE file.
Running examples in 'RSVGTipsDevice-Ex.R' failed
The error most likely occurred in:

> ### Name: RSVGTipsDevice
> ### Title: A SVG Graphics Driver with dynamic tips
> ### Aliases: RSVGTipsDevice
> ### Keywords: device package
> 
> ### ** Examples
> 
> library("RSVGTipsDevice")
> sessionInfo()
R version 3.3.0 beta (2016-04-13 r70476)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server 2008 x64 (build 6002) Service Pack 2

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

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

other attached packages:
[1] RSVGTipsDevice_1.0-4
> devSVGTips("svgplot1.svg", toolTipMode=1,
+     title="SVG example plot 1: shapes and points, tooltips are title + 1 line")
> plot(c(0,10),c(0,10), type="n", xlab="x", ylab="y",
+     main="Example SVG plot with title + 1 line tips (mode=1)")
> setSVGShapeToolTip(title="A rectangle", desc="that is yellow")
> rect(1,1,4,6, col='yellow')
> setSVGShapeToolTip(title="1st circle with title only")
> points(5.5,7.5,cex=20,pch=19,col='red')
> setSVGShapeToolTip(title="A triangle", desc="big and green")
> polygon(c(3,6,8), c(3,6,3), col='green')
> # no tooltips on these points
> points(2:8, 8:2, cex=3, pch=19, col='black')
> # tooltips on each these points
> invisible(sapply(1:7, function(x)
+ {setSVGShapeToolTip(title=paste("point", x))
+  points(x+1, 8-x, cex=3, pch=1, col='black')}))
> setSVGShapeToolTip(title="Text", desc="can have a tool tip too!")
> text(x=4, y=9, lab="Poke me!", col="blue")
> dev.off()
classify_model: no visible global function definition for 'predict'
cross_validate: no visible global function definition for 'predict'
read_data: no visible global function definition for 'read.csv'
read_data: no visible global function definition for 'read.delim'
Undefined global functions or variables:
  predict read.csv read.delim
Consider adding
  importFrom("stats", "predict")
  importFrom("utils", "read.csv", "read.delim")
to your NAMESPACE file.
.forest.plot: no visible global function definition for 'par'
.forest.plot: no visible global function definition for 'plot'
.forest.plot: no visible global function definition for 'abline'
.forest.plot: no visible global function definition for 'arrows'
.forest.plot: no visible global function definition for 'points'
.forest.plot.scale: no visible global function definition for 'par'
.forest.plot.scale: no visible global function definition for 'plot'
.forest.plot.scale: no visible global function definition for 'axTicks'
.forest.plot.scale : <anonymous>: no visible global function definition
  for 'lines'
.forest.plot.scale: no visible global function definition for 'lines'
.forest.plot.scale: no visible global function definition for 'text'
.rtf.plot: no visible global function definition for 'png'
.rtf.plot: no visible global function definition for 'dev.off'
.rtf.trellis.object: no visible global function definition for 'png'
.rtf.trellis.object: no visible global function definition for
  'dev.off'
addSessionInfo.RTF: no visible global function definition for
  'sessionInfo'
Undefined global functions or variables:
  abline arrows axTicks dev.off lines par plot png points sessionInfo
  text
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "abline", "arrows", "axTicks", "lines", "par",
             "plot", "points", "text")
  importFrom("utils", "sessionInfo")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/RVAideMemoire.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
'library' or 'require' call to 'pixmap' which was already attached by Depends.
  Please remove these calls from your code.
rvideopoker: warning in rp.radiogroup(mypanel, var =
  state$penny.nickel.quarter.dollar, initval = 1, values = c(1, 5, 25,
  100), title = "Bet (in Cents)", action = setbet): partial argument
  match of 'var' to 'variable'
rvideopoker: warning in rp.slider(mypanel, var = state$no.of.credits,
  from = 1, to = 5, initval = 1, title = "How many Credits?",
  resolution = 1, action = creditset, showvalue = TRUE): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC1, action = card1check, title = "Keep Card 1?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC2, action = card2check, title = "Keep Card 2?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC3, action = card3check, title = "Keep Card 3?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC4, action = card4check, title = "Keep Card 4?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC5, action = card5check, title = "Keep Card 5?"): partial
  argument match of 'var' to 'variable'
rvideopoker : plotFrame: no visible global function definition for
  'par'
rvideopoker : showBack: no visible global function definition for
  'title'
rvideopoker : showCardsInitially: no visible global function definition
  for 'title'
Undefined global functions or variables:
  par title
Consider adding
  importFrom("graphics", "par", "title")
to your NAMESPACE file.
Package suggested but not available for checking: 'gpuR'
LASSO: no visible global function definition for 'lm'
LASSO: no visible global function definition for 'anova'
LASSO: no visible global function definition for 'glm'
LASSO: no visible global function definition for 'pchisq'
LASSO : <anonymous>: no visible global function definition for
  'extractAIC'
PCR : <anonymous>: no visible global function definition for 'cor'
PLS : <anonymous>: no visible global function definition for 'cor'
RR : RRscore: no visible binding for global variable 'sd'
SPLS: no visible global function definition for 'lm'
SPLS: no visible global function definition for 'anova'
SPLS : <anonymous>: no visible global function definition for
  'extractAIC'
VTWOD : getScores: no visible global function definition for 'sd'
VTWOD : getScores: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  anova cor extractAIC glm lm pchisq pnorm sd
Consider adding
  importFrom("stats", "anova", "cor", "extractAIC", "glm", "lm",
             "pchisq", "pnorm", "sd")
to your NAMESPACE file.
check_ISO_code: no visible binding for global variable 'NoAm_country'
check_ISO_code: no visible binding for global variable 'SoAm_country'
check_ISO_code: no visible binding for global variable 'Oceana_country'
check_ISO_code: no visible binding for global variable 'Africa_country'
check_ISO_code: no visible binding for global variable 'Asia_country'
check_ISO_code: no visible binding for global variable 'Eur_country'
climate_map: no visible binding for global variable 'data'
date_correct: no visible global function definition for 'tail'
Undefined global functions or variables:
  Africa_country Asia_country Eur_country NoAm_country Oceana_country
  SoAm_country data tail
Consider adding
  importFrom("utils", "data", "tail")
to your NAMESPACE file.
RWBP.default: no visible global function definition for 'na.omit'
RWBP.default: no visible global function definition for 'kmeans'
RWBP.formula: no visible global function definition for 'model.extract'
plot.RWBP: no visible global function definition for 'plot'
predict.RWBP: no visible global function definition for 'head'
Undefined global functions or variables:
  head kmeans model.extract na.omit plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "kmeans", "model.extract", "na.omit")
  importFrom("utils", "head")
to your NAMESPACE file.
'library' or 'require' call to 'vcd' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'foreign' 'ggplot2' 'grid' 'psych'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: 'foreign:::adQuote'
  See the note in ?`:::` about the use of this operator.
.onAttach: no visible global function definition for 'winMenuAdd'
.onAttach: no visible global function definition for 'winMenuAddItem'
calc.hist.breaks: no visible global function definition for
  'nclass.Sturges'
calc.hist.breaks: no visible global function definition for 'nclass.FD'
calc.hist.breaks: no visible global function definition for
  'nclass.scott'
check.class: no visible global function definition for 'as.formula'
gtkColorSelectionForPlotGetColor: no visible global function definition
  for 'rgb'
gtkColorSelectionWidgetNew: no visible global function definition for
  'colors'
gtkFileChooserDialogFilteredActivate: no visible binding for global
  variable 'theme_grey'
localize: no visible global function definition for 'localeToCharset'
summary.CrossTable : twoDimTable: no visible global function definition
  for 'addmargins'
summary.CrossTable: no visible global function definition for
  'assocstats'
write.spss: no visible global function definition for 'write.table'
write.stata: no visible global function definition for 'write.table'
Undefined global functions or variables:
  addmargins as.formula assocstats colors localeToCharset nclass.FD
  nclass.Sturges nclass.scott rgb theme_grey winMenuAdd winMenuAddItem
  write.table
Consider adding
  importFrom("grDevices", "colors", "nclass.FD", "nclass.Sturges",
             "nclass.scott", "rgb")
  importFrom("stats", "addmargins", "as.formula")
  importFrom("utils", "localeToCharset", "winMenuAdd", "winMenuAddItem",
             "write.table")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    sample_data   3.2Mb
fitSBSA: no visible binding for global variable 'var'
fitSBSA: no visible global function definition for 'var'
fitSBSA: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  qnorm var
Consider adding
  importFrom("stats", "qnorm", "var")
to your NAMESPACE file.
ChooseBest: no visible global function definition for 'head'
GetScores: no visible global function definition for 'write.table'
ReportTable: no visible binding for global variable 'sd'
ReportTable: no visible global function definition for 'write.table'
Undefined global functions or variables:
  head sd write.table
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "head", "write.table")
to your NAMESPACE file.
c,scidbdf: warning in build_dim_schema(x, newname = j): partial
  argument match of 'newname' to 'newnames'
.format: no visible global function definition for 'capture.output'
.scidbstr: no visible global function definition for 'capture.output'
glm.fit_scidb: no visible global function definition for 'gaussian'
glm.fit_scidb: no visible global function definition for 'pnorm'
glm_scidb: no visible global function definition for 'gaussian'
glm_scidb: no visible global function definition for 'as.formula'
iqiter : nextEl: no visible global function definition for 'read.table'
iquery: no visible global function definition for 'read.table'
model_scidb: no visible global function definition for 'as.formula'
model_scidb: no visible global function definition for 'terms'
model_scidb: no visible global function definition for 'drop.terms'
predict.glm_scidb: no visible global function definition for 'coef'
print.glm_scidb: no visible global function definition for 'coef'
summary.glm_scidb: no visible global function definition for 'coef'
glm.fit,scidb-ANY-MNSN: no visible global function definition for
  'gaussian'
glm.fit,scidb-ANY-MNSN: no visible global function definition for
  'pnorm'
glm,ANY-ANY-scidbdf: no visible global function definition for
  'gaussian'
glm,ANY-ANY-scidbdf: no visible global function definition for
  'as.formula'
image,scidb: no visible global function definition for 'axis'
Undefined global functions or variables:
  as.formula axis capture.output coef drop.terms gaussian pnorm
  read.table terms
Consider adding
  importFrom("graphics", "axis")
  importFrom("stats", "as.formula", "coef", "drop.terms", "gaussian",
             "pnorm", "terms")
  importFrom("utils", "capture.output", "read.table")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'MASS' 'oligoClasses'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
lahiri.design: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'raster' 'sp'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.5Mb
Found the following significant warnings:
  Warning: S3 methods '[.xml_missing', '[.xml_nodeset', '[[.xml_missing', 'xml_attr<-.xml_missing', 'xml_attr<-.xml_node', 'xml_attr<-.xml_nodeset', 'xml_attrs<-.xml_missing', 'xml_attrs<-.xml_node', 'xml_attrs<-.xml_nodeset', 'xml_name<-.xml_missing', 'xml_name<-.xml_node', 'xml_name<-.xml_nodeset', 'xml_text<-.xml_missing', 'xml_text<-.xml_node', 'xml_text<-.xml_nodeset', 'as.character.xml_document', 'as.character.xml_missing', 'as.character.xml_node', 'as.character.xml_nodeset', 'as_list.xml_missing', 'as_list.xml_node', 'as_list.xml_nodeset', 'as_xml_document.character', 'as_xml_document.connection', 'as_xml_document.list', 'as_xml_document.raw', 'as_xml_document.response', 'as_xml_document.xml_document', 'as_xml_document.xml_node', 'as_xml_document.xml_nodeset', 'format.xml_node', 'is.na.xml_missing', 'is.na.xml_node', 'is.na.xml_nodeset', 'nodeset_apply.xml_document', 'nodeset_apply.xml_missing', 'nodeset_apply.xml_node', 'nodeset_apply.xml_nodeset', 'print.xml_document', 'print.xml_missing [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.3/selectr.Rcheck/00install.out' for details.
get_statistics_from_file: no visible global function definition for
  'read.csv'
glm_anova: no visible global function definition for 'aov'
glm_anova: no visible global function definition for 'glm'
glm_anova: no visible global function definition for 'gaussian'
glm_anova: no visible global function definition for 'anova'
glm_anova: no visible global function definition for 'quasipoisson'
glm_anova: no visible global function definition for 'sd'
glm_anova: no visible global function definition for 'p.adjust'
ttest_cohens_d: no visible global function definition for 't.test'
ttest_cohens_d: no visible global function definition for 'sd'
Undefined global functions or variables:
  anova aov gaussian glm p.adjust quasipoisson read.csv sd t.test
Consider adding
  importFrom("stats", "anova", "aov", "gaussian", "glm", "p.adjust",
             "quasipoisson", "sd", "t.test")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.7Mb
Unexported objects imported by ':::' calls:
  'igraph:::.igraph.shapes' 'igraph:::i.get.arrow.mode'
  'igraph:::i.parse.plot.params' 'igraph:::igraph.Arrows'
  'igraph:::igraph.check.shapes' 'igraph:::igraph.polygon'
  See the note in ?`:::` about the use of this operator.
installed size is 65.9Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    gdal   3.2Mb
    libs  51.8Mb
    proj   5.0Mb
.computePStar: no visible global function definition for 'uniroot'
plotBoundary: no visible global function definition for
  'scale_y_continuous'
Undefined global functions or variables:
  scale_y_continuous uniroot
Consider adding
  importFrom("stats", "uniroot")
to your NAMESPACE file.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    www   9.5Mb
popify: no visible global function definition for 'runif'
tipify: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    www   6.2Mb
get_selected_names: no visible global function definition for 'tail'
get_selected_names: no visible global function definition for 'head'
Undefined global functions or variables:
  head tail
Consider adding
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Missing or unexported object: 'spatstat::overlap.xypolygon'
Running examples in 'SIBER-Ex.R' failed
The error most likely occurred in:

> ### Name: maxLikOverlap
> ### Title: Calculate the overlap between two ellipses based on the maximum
> ###   likelihood fitted ellipses.
> ### Aliases: maxLikOverlap
> 
> ### ** Examples
> 
> # load in the included demonstration dataset data("demo.siber.data")
> siber.example <- createSiberObject(demo.siber.data) 
> 
> # The first ellipse is referenced using a character string representation 
> # where in "x.y", "x" is the community, and "y" is the group within that 
> # community.
> ellipse1 <- "1.2" 
> 
> # Ellipse two is similarly defined: community 1, group3 
> ellipse2 <- "1.3"
> 
> # the overlap betweeen the corresponding 95% prediction ellipses is given by: 
> ellipse95.overlap <- maxLikOverlap(ellipse1, ellipse2, siber.example,
+ p.interval = 0.95, n = 100)
Error: 'overlap.xypolygon' is not an exported object from 'namespace:spatstat'
Execution halted
Error in re-building vignettes:
  ...
Warning in buildVignettes(dir = "d:/Rcompile/CRANpkg/local/3.3/SIBER.Rcheck/vign_test/SIBER") :
  Files named as vignettes but with no recognized vignette engine:
   'vignettes/test-nonnumeric-community-labels.Rmd'
   'vignettes/test-nonnumeric-group-labels.Rmd'
(Is a VignetteBuilder field missing?)
Quitting from lines 89-115 (Ellipse-Overlap.Rmd) 
Error: processing vignette 'Ellipse-Overlap.Rmd' failed with diagnostics:
'overlap.xypolygon' is not an exported object from 'namespace:spatstat'
Execution halted
Packages in Depends field not imported from:
  'ade4' 'corpcor'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
filter.PCA.default: no visible global function definition for
  'princomp'
filter.mRMR.default: no visible global function definition for
  'discretize'
gaussian.default: no visible global function definition for 'cov'
gaussian.default: no visible global function definition for
  'cov.shrink'
plot.verify.cv: no visible global function definition for 'plot'
plot.verify.cv: no visible global function definition for 'points'
plot.verify.ho: no visible global function definition for 'plot'
plot.verify.ho: no visible global function definition for 'points'
plot.verify.loo: no visible global function definition for 'plot'
plot.verify.loo: no visible global function definition for 'points'
predict.dpa1: no visible global function definition for 'cor'
predict.filter.PCA: no visible global function definition for 'predict'
predict.filter.RegressionTreeFilter: no visible global function
  definition for 'is.struct'
predict.filter.RegressionTreeFilter: no visible global function
  definition for 'var'
simulator.Simple1: no visible global function definition for 'rnorm'
verify.ho.default: no visible global function definition for 'predict'
verify.loo.default: no visible global function definition for 'predict'
Undefined global functions or variables:
  cor cov cov.shrink discretize is.struct plot points predict princomp
  rnorm var
Consider adding
  importFrom("graphics", "plot", "points")
  importFrom("stats", "cor", "cov", "predict", "princomp", "rnorm",
             "var")
to your NAMESPACE file.
dSepAdji: no visible global function definition for 'as'
dag2cpdagAdj: no visible global function definition for 'as'
randomDAG: no visible global function definition for 'rbinom'
structIntervDist: no visible global function definition for 'as'
Undefined global functions or variables:
  as rbinom
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "rbinom")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' calls in package code:
  'gdata' 'splines'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.SII: no visible global function definition for 'plot'
plot.SII: no visible global function definition for 'lines'
plot.SII: no visible global function definition for 'abline'
plot.SII: no visible global function definition for 'legend'
sii : approx.l: no visible global function definition for 'approx'
sii.excel: no visible global function definition for 'predict'
sii.excel : approx.l: no visible global function definition for
  'approx'
Undefined global functions or variables:
  abline approx legend lines plot predict
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "plot")
  importFrom("stats", "approx", "predict")
to your NAMESPACE file.
Package in Depends field not imported from: 'mclust'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Simpsons: no visible global function definition for 'Mclust'
Simpsons: no visible global function definition for 'lm'
Simpsons: no visible global function definition for 'plot'
Simpsons: no visible global function definition for 'abline'
Simpsons: no visible global function definition for 'par'
Simpsons: no visible global function definition for 'legend'
Simpsons: no visible global function definition for 'txtProgressBar'
Simpsons: no visible global function definition for 'setTxtProgressBar'
Simpsons: no visible global function definition for 'quantile'
plot.Simpson: no visible global function definition for 'plot'
plot.Simpson: no visible global function definition for 'lm'
plot.Simpson: no visible global function definition for 'abline'
plot.Simpson: no visible global function definition for 'par'
plot.Simpson: no visible global function definition for 'legend'
Undefined global functions or variables:
  Mclust abline legend lm par plot quantile setTxtProgressBar
  txtProgressBar
Consider adding
  importFrom("graphics", "abline", "legend", "par", "plot")
  importFrom("stats", "lm", "quantile")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
evalGrids: no visible global function definition for 'sessionInfo'
meanAndNormCI: no visible global function definition for 'sd'
Undefined global functions or variables:
  sd sessionInfo
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "sessionInfo")
to your NAMESPACE file.
plot.sla: no visible global function definition for 'title'
plot.sla: no visible global function definition for 'abline'
print.sla: no visible global function definition for 'coef'
sla.default: no visible global function definition for 'lm'
sla.default: no visible global function definition for 'anova'
Undefined global functions or variables:
  abline anova coef lm title
Consider adding
  importFrom("graphics", "abline", "title")
  importFrom("stats", "anova", "coef", "lm")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/slimrec.Rcheck/00install.out' for details.
'library' or 'require' calls to packages already attached by Depends:
  'ggplot2' 'reshape'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'corpcor' 'ggplot2' 'reshape'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' calls in package code:
  'MASS' 'survival'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
lines.SmithWilsonYieldCurve: no visible global function definition for
  'lines'
plot.SmithWilsonYieldCurve: no visible global function definition for
  'plot'
points.SmithWilsonYieldCurve: no visible global function definition for
  'points'
Undefined global functions or variables:
  lines plot points
Consider adding
  importFrom("graphics", "lines", "plot", "points")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'akima' 'misc3d' 'rgl' 'rpanel' 'tkrplot'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
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.
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.
Package suggested but not available for checking: 'fastshp'
span: no visible global function definition for 'complete.cases'
spanr: no visible global function definition for 'model.frame'
spanr: no visible global function definition for 'complete.cases'
spanr.hull: no visible global function definition for 'par'
spanr.hull: no visible global function definition for 'plot.new'
spanr.hull: no visible global function definition for 'plot.window'
spanr.hull: no visible global function definition for 'axis'
spanr.hull: no visible global function definition for 'title'
spanr.hull: no visible global function definition for 'points'
spanr.hull: no visible global function definition for 'lines'
spanr.hull: no visible global function definition for 'abline'
spanr.hull: no visible global function definition for 'text'
spanr.hull: no visible global function definition for 'segments'
spanr.hull: no visible global function definition for 'box'
Undefined global functions or variables:
  abline axis box complete.cases lines model.frame par plot.new
  plot.window points segments text title
Consider adding
  importFrom("graphics", "abline", "axis", "box", "lines", "par",
             "plot.new", "plot.window", "points", "segments", "text",
             "title")
  importFrom("stats", "complete.cases", "model.frame")
to your NAMESPACE file.
rmvn.sparse: no visible global function definition for 'rnorm'
rmvn.sparse: no visible global function definition for 'as'
Undefined global functions or variables:
  as rnorm
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "rnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Missing or unexported object: 'spatstat::check.range'
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    data   3.4Mb
    doc    4.6Mb
    help   5.0Mb
    libs   1.2Mb
Missing or unexported object: 'ChemoSpec::readJDX'
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.
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.
ffmpeg version N-34549-g13b7781, Copyright (c) 2000-2011 the FFmpeg developers
  built on Nov  6 2011 22:02:08 with gcc 4.6.1
  configuration: --enable-gpl --enable-version3 --disable-w32threads --enable-runtime-cpudetect --enable-avisynth --enable-bzlib --enable-frei0r --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libfreetype --enable-libgsm --enable-libmp3lame --enable-libopenjpeg --enable-librtmp --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvo-aacenc --enable-libvo-amrwbenc --enable-libvorbis --enable-libvpx --enable-libx264 --enable-libxavs --enable-libxvid --enable-zlib
  libavutil    51. 24. 0 / 51. 24. 0
  libavcodec   53. 28. 0 / 53. 28. 0
  libavformat  53. 19. 0 / 53. 19. 0
  libavdevice  53.  4. 0 / 53.  4. 0
  libavfilter   2. 47. 0 /  2. 47. 0
  libswscale    2.  1. 0 /  2.  1. 0
  libpostproc  51.  2. 0 / 51.  2. 0
ffmpeg version N-34549-g13b7781, Copyright (c) 2000-2011 the FFmpeg developers
  built on Nov  6 2011 22:02:08 with gcc 4.6.1
  configuration: --enable-gpl --enable-version3 --disable-w32threads --enable-runtime-cpudetect --enable-avisynth --enable-bzlib --enable-frei0r --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libfreetype --enable-libgsm --enable-libmp3lame --enable-libopenjpeg --enable-librtmp --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvo-aacenc --enable-libvo-amrwbenc --enable-libvorbis --enable-libvpx --enable-libx264 --enable-libxavs --enable-libxvid --enable-zlib
  libavutil    51. 24. 0 / 51. 24. 0
  libavcodec   53. 28. 0 / 53. 28. 0
  libavformat  53. 19. 0 / 53. 19. 0
  libavdevice  53.  4. 0 / 53.  4. 0
  libavfilter   2. 47. 0 /  2. 47. 0
  libswscale    2.  1. 0 /  2.  1. 0
  libpostproc  51.  2. 0 / 51.  2. 0
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
ffmpeg version N-34549-g13b7781, Copyright (c) 2000-2011 the FFmpeg developers
  built on Nov  6 2011 22:02:08 with gcc 4.6.1
  configuration: --enable-gpl --enable-version3 --disable-w32threads --enable-runtime-cpudetect --enable-avisynth --enable-bzlib --enable-frei0r --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libfreetype --enable-libgsm --enable-libmp3lame --enable-libopenjpeg --enable-librtmp --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvo-aacenc --enable-libvo-amrwbenc --enable-libvorbis --enable-libvpx --enable-libx264 --enable-libxavs --enable-libxvid --enable-zlib
  libavutil    51. 24. 0 / 51. 24. 0
  libavcodec   53. 28. 0 / 53. 28. 0
  libavformat  53. 19. 0 / 53. 19. 0
  libavdevice  53.  4. 0 / 53.  4. 0
  libavfilter   2. 47. 0 /  2. 47. 0
  libswscale    2.  1. 0 /  2.  1. 0
  libpostproc  51.  2. 0 / 51.  2. 0
The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
ffmpeg version N-34549-g13b7781, Copyright (c) 2000-2011 the FFmpeg developers
  built on Nov  6 2011 22:02:08 with gcc 4.6.1
  configuration: --enable-gpl --enable-version3 --disable-w32threads --enable-runtime-cpudetect --enable-avisynth --enable-bzlib --enable-frei0r --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libfreetype --enable-libgsm --enable-libmp3lame --enable-libopenjpeg --enable-librtmp --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvo-aacenc --enable-libvo-amrwbenc --enable-libvorbis --enable-libvpx --enable-libx264 --enable-libxavs --enable-libxvid --enable-zlib
  libavutil    51. 24. 0 / 51. 24. 0
  libavcodec   53. 28. 0 / 53. 28. 0
  libavformat  53. 19. 0 / 53. 19. 0
  libavdevice  53.  4. 0 / 53.  4. 0
  libavfilter   2. 47. 0 /  2. 47. 0
  libswscale    2.  1. 0 /  2.  1. 0
  libpostproc  51.  2. 0 / 51.  2. 0
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
ffmpeg version N-34549-g13b7781, Copyright (c) 2000-2011 the FFmpeg developers
  built on Nov  6 2011 22:02:08 with gcc 4.6.1
  configuration: --enable-gpl --enable-version3 --disable-w32threads --enable-runtime-cpudetect --enable-avisynth --enable-bzlib --enable-frei0r --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libfreetype --enable-libgsm --enable-libmp3lame --enable-libopenjpeg --enable-librtmp --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvo-aacenc --enable-libvo-amrwbenc --enable-libvorbis --enable-libvpx --enable-libx264 --enable-libxavs --enable-libxvid --enable-zlib
  libavutil    51. 24. 0 / 51. 24. 0
  libavcodec   53. 28. 0 / 53. 28. 0
  libavformat  53. 19. 0 / 53. 19. 0
  libavdevice  53.  4. 0 / 53.  4. 0
  libavfilter   2. 47. 0 /  2. 47. 0
  libswscale    2.  1. 0 /  2.  1. 0
  libpostproc  51.  2. 0 / 51.  2. 0
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
ffmpeg version N-34549-g13b7781, Copyright (c) 2000-2011 the FFmpeg developers
  built on Nov  6 2011 22:02:08 with gcc 4.6.1
  configuration: --enable-gpl --enable-version3 --disable-w32threads --enable-runtime-cpudetect --enable-avisynth --enable-bzlib --enable-frei0r --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libfreetype --enable-libgsm --enable-libmp3lame --enable-libopenjpeg --enable-librtmp --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvo-aacenc --enable-libvo-amrwbenc --enable-libvorbis --enable-libvpx --enable-libx264 --enable-libxavs --enable-libxvid --enable-zlib
  libavutil    51. 24. 0 / 51. 24. 0
  libavcodec   53. 28. 0 / 53. 28. 0
  libavformat  53. 19. 0 / 53. 19. 0
  libavdevice  53.  4. 0 / 53.  4. 0
  libavfilter   2. 47. 0 /  2. 47. 0
  libswscale    2.  1. 0 /  2.  1. 0
  libpostproc  51.  2. 0 / 51.  2. 0
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
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.
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.
'library' or 'require' call to 'tcltk' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
read.csv.sql: no visible global function definition for 'download.file'
sqldf: no visible global function definition for 'modifyList'
sqldf: no visible global function definition for 'head'
Undefined global functions or variables:
  download.file head modifyList
Consider adding
  importFrom("utils", "download.file", "head", "modifyList")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'RJDBC' 'RMySQL' 'RODBC' 'RPostgreSQL' 'RSQLite' 'tcltk'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
cacheQuery: no visible global function definition for 'read.csv'
cacheQuery: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  read.csv write.csv
Consider adding
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
SQN: no visible binding for global variable 'median'
SQN: no visible global function definition for 'quantile'
SQN.demo.data: no visible global function definition for 'rnorm'
mix.qn: no visible global function definition for 'ecdf'
mix.qn: no visible global function definition for 'quantile'
Undefined global functions or variables:
  ecdf median quantile rnorm
Consider adding
  importFrom("stats", "ecdf", "median", "quantile", "rnorm")
to your NAMESPACE file.
draw.srd: no visible global function definition for 'complete.cases'
draw.srd: no visible global function definition for 'runif'
draw.srd: no visible global function definition for 'arrows'
draw.srd: no visible global function definition for 'text'
draw.srd: no visible global function definition for 'segments'
draw.srd.enc: no visible global function definition for 'par'
draw.srd.enc: no visible global function definition for 'plot.new'
draw.srd.enc: no visible global function definition for 'plot.window'
draw.srd.enc: no visible global function definition for 'rgb'
draw.srd.enc: no visible global function definition for 'polygon'
draw.srd.enc: no visible global function definition for 'pchisq'
draw.srd.enc: no visible global function definition for 'text'
draw.srd.enc: no visible global function definition for 'title'
draw.srd.enc: no visible global function definition for 'arrows'
drawcell: no visible global function definition for 'polygon'
drawcell: no visible global function definition for 'segments'
rotate.srd: no visible global function definition for 'devAskNewPage'
srd: no visible global function definition for 'devAskNewPage'
Undefined global functions or variables:
  arrows complete.cases devAskNewPage par pchisq plot.new plot.window
  polygon rgb runif segments text title
Consider adding
  importFrom("grDevices", "devAskNewPage", "rgb")
  importFrom("graphics", "arrows", "par", "plot.new", "plot.window",
             "polygon", "segments", "text", "title")
  importFrom("stats", "complete.cases", "pchisq", "runif")
to your NAMESPACE file.
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.
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.
.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.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   5.0Mb
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.
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.
Error in re-building vignettes:
  ...
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "VignetteforSTPGA.ltx" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.3/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'VignetteforSTPGA.ltx' failed with diagnostics:
running 'texi2dvi' on 'VignetteforSTPGA.ltx' failed

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

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

Execution halted
'library' or 'require' calls in package code:
  'rgl' 'rpanel'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
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.
Package which this enhances but not available for checking: 'gputools'
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   1.6Mb
dropout : <anonymous>: no visible global function definition for
  'na.omit'
encToInt: no visible global function definition for 'localeToCharset'
intToEnc: no visible global function definition for 'localeToCharset'
Undefined global functions or variables:
  localeToCharset na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "localeToCharset")
to your NAMESPACE file.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.6Mb
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.
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/sybilSBML.Rcheck/00install.out' for details.
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.
Namespaces with empty importFrom:
  'Rcpp' 'methods'
'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.
'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.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.9Mb
    libs   1.4Mb
cluster_cutoff_at_first_empty_bin: no visible global function
  definition for 'hist'
mapper1D: no visible global function definition for 'dist'
mapper1D: no visible global function definition for 'as.dist'
mapper1D: no visible global function definition for 'hclust'
mapper1D: no visible global function definition for 'cutree'
mapper2D: no visible global function definition for 'dist'
mapper2D: no visible global function definition for 'as.dist'
mapper2D: no visible global function definition for 'hclust'
mapper2D: no visible global function definition for 'cutree'
Undefined global functions or variables:
  as.dist cutree dist hclust hist
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "as.dist", "cutree", "dist", "hclust")
to your NAMESPACE file.
makeCircles: no visible global function definition for 'quantile'
targetDiagram: no visible global function definition for 'as.formula'
targetDiagram: no visible global function definition for 'modifyList'
targetDiagram: no visible global function definition for 'extendrange'
tdStats : sdo: no visible global function definition for 'sd'
tdStats : sdm: no visible global function definition for 'sd'
tdStats : r2: no visible global function definition for 'cor'
Undefined global functions or variables:
  as.formula cor extendrange modifyList quantile sd
Consider adding
  importFrom("grDevices", "extendrange")
  importFrom("stats", "as.formula", "cor", "quantile", "sd")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
aniplotevents: no visible global function definition for 'plot'
aniplotevents: no visible global function definition for 'lines'
cbfs: no visible global function definition for 'rnorm'
cbfs: no visible global function definition for 'runif'
cbfs_red: no visible global function definition for 'arima.sim'
cbfs_red: no visible global function definition for 'runif'
eventCluster: no visible global function definition for 'princomp'
eventCluster: no visible global function definition for 'kmeans'
measures: no visible global function definition for 'sd'
measures: no visible global function definition for 'var'
measures: no visible global function definition for 'PP.test'
noiseTests: no visible global function definition for 'Box.test'
noiseTests: no visible global function definition for 'PP.test'
noiseTests: no visible global function definition for 'ar'
plotevents: no visible global function definition for 'plot'
plotevents: no visible global function definition for 'lines'
ur.za.fast : roll: no visible global function definition for 'coef'
ur.za.fast : roll: no visible global function definition for 'lm'
Undefined global functions or variables:
  Box.test PP.test ar arima.sim coef kmeans lines lm plot princomp
  rnorm runif sd var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "Box.test", "PP.test", "ar", "arima.sim", "coef",
             "kmeans", "lm", "princomp", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
installed size is 43.4Mb
  sub-directories of 1Mb or more:
    libs      12.4Mb
    tessdata  30.9Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    3.5Mb
    libs   2.2Mb
newTiddler: no visible global function definition for 'new'
twImage: no visible global function definition for 'new'
twLink: no visible global function definition for 'new'
twList: no visible global function definition for 'new'
twTable: no visible global function definition for 'new'
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
read_json: no visible global function definition for 'tail'
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
'library' or 'require' call to 'ggplot2' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'microbenchmark'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
determine_replications: no visible global function definition for
  'microbenchmark'
do_timeit: no visible global function definition for 'Rprof'
do_timeit: no visible global function definition for 'summaryRprof'
mean.timeit: no visible global function definition for 'aggregate'
plot.timeit: no visible global function definition for 'ggplot'
plot.timeit: no visible global function definition for 'aes'
plot.timeit: no visible global function definition for 'geom_boxplot'
plot.timeit: no visible global function definition for 'geom_point'
plot.timeit: no visible global function definition for 'xlab'
plot.timeit: no visible global function definition for 'ylab'
plot.timeit: no visible global function definition for 'ggtitle'
plot.timeit: no visible global function definition for 'coord_flip'
timeit: no visible binding for global variable 'median'
Undefined global functions or variables:
  Rprof aes aggregate coord_flip geom_boxplot geom_point ggplot ggtitle
  median microbenchmark summaryRprof xlab ylab
Consider adding
  importFrom("stats", "aggregate", "median")
  importFrom("utils", "Rprof", "summaryRprof")
to your NAMESPACE file.
'library' or 'require' call to 'shiny' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'ggplot2'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
timeline: no visible global function definition for 'ggplot'
timeline: no visible global function definition for 'geom_segment'
timeline: no visible global function definition for 'aes_string'
timeline: no visible global function definition for 'geom_rect'
timeline: no visible global function definition for 'geom_text'
timeline: no visible global function definition for 'theme'
timeline: no visible global function definition for 'element_blank'
timeline: no visible global function definition for 'xlab'
timeline: no visible global function definition for 'ylab'
timeline: no visible global function definition for 'xlim'
timeline: no visible global function definition for
  'scale_y_continuous'
timeline: no visible global function definition for 'geom_point'
timeline: no visible global function definition for 'scale_color_grey'
timeline: no visible global function definition for 'geom_hline'
Undefined global functions or variables:
  aes_string element_blank geom_hline geom_point geom_rect geom_segment
  geom_text ggplot scale_color_grey scale_y_continuous theme xlab xlim
  ylab
'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
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.
ls.tree: no visible global function definition for 'lm'
ls.tree: no visible global function definition for 'coef'
Undefined global functions or variables:
  coef lm
Consider adding
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'rgl' 'tcltk'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
'library' or 'require' calls to packages already attached by Depends:
  'Cairo' 'RGtk2' 'colorspace' 'gWidgets' 'tourr'
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'TeachingDemos' 'ash'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'Cairo' 'RGtk2' 'colorspace' 'gWidgets' 'tourr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' calls in package code:
  'TeachingDemos' 'ash'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
DeadReckoning: no visible global function definition for 'filter'
DeadReckoning: no visible global function definition for 'approx'
DeadReckoning: no visible global function definition for 'lm'
Mapper: no visible global function definition for 'colorRampPalette'
Mapper: no visible global function definition for 'terrain.colors'
Mapper: no visible global function definition for 'points'
Mapper: no visible global function definition for 'axis'
Standardize: no visible global function definition for 'lm'
Undefined global functions or variables:
  approx axis colorRampPalette filter lm points terrain.colors
Consider adding
  importFrom("grDevices", "colorRampPalette", "terrain.colors")
  importFrom("graphics", "axis", "points")
  importFrom("stats", "approx", "filter", "lm")
to your NAMESPACE file.
microsoftTranslate: no visible global function definition for
  'URLencode'
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
rtrapezoid: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.4Mb
binary.hess: no visible global function definition for 'as'
trust.optim: no visible global function definition for 'as'
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
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.
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.
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.
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/TSPred.Rcheck/00install.out' for details.
TSgetSQL: no visible global function definition for 'ts'
TSputSQL: no visible global function definition for 'is.ts'
TSputSQL: no visible global function definition for 'frequency'
TSputSQL: no visible global function definition for 'time'
TSquery: no visible global function definition for 'ts'
Undefined global functions or variables:
  frequency is.ts time ts
Consider adding
  importFrom("stats", "frequency", "is.ts", "time", "ts")
to your NAMESPACE file.
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.
turf: no visible global function definition for 'read.table'
turf: no visible global function definition for 'flush.console'
turf.combos: no visible global function definition for 'combn'
Undefined global functions or variables:
  combn flush.console read.table
Consider adding
  importFrom("utils", "combn", "flush.console", "read.table")
to your NAMESPACE file.
turtle_param: no visible global function definition for 'col2rgb'
Undefined global functions or variables:
  col2rgb
Consider adding
  importFrom("grDevices", "col2rgb")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/uaparserjs.Rcheck/00install.out' for details.
rmd2pdf: no visible global function definition for 'tail'
rnw2pdf: no visible global function definition for 'tail'
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
ubRacing : predCandidate: no visible global function definition for
  'predict'
ubRacing : aux2.friedman.edit: no visible global function definition
  for 'pchisq'
ubRacing : aux2.friedman.edit: no visible global function definition
  for 'qt'
ubRacing : aux.friedman.edit: no visible global function definition for
  'wilcox.test'
ubRacing : aux.ttest.edit: no visible global function definition for
  't.test'
ubRacing : aux.ttest.edit: no visible global function definition for
  'p.adjust'
ubRacing : idFolds: no visible global function definition for
  'quantile'
ubRacing: no visible binding for global variable 'sd'
ubSmoteExs: no visible global function definition for 'runif'
Undefined global functions or variables:
  p.adjust pchisq predict qt quantile runif sd t.test wilcox.test
Consider adding
  importFrom("stats", "p.adjust", "pchisq", "predict", "qt", "quantile",
             "runif", "sd", "t.test", "wilcox.test")
to your NAMESPACE file.
plot.upclassfit: no visible global function definition for 'frame'
plot.upclassfit: no visible global function definition for 'par'
plot.upclassfit: no visible global function definition for 'axis'
plot.upclassfit: no visible global function definition for 'matplot'
plot.upclassfit: no visible global function definition for 'legend'
plot.upclassfit: no visible global function definition for 'title'
Undefined global functions or variables:
  axis frame legend matplot par title
Consider adding
  importFrom("graphics", "axis", "frame", "legend", "matplot", "par",
             "title")
to your NAMESPACE file.
UPMASKfile: no visible global function definition for 'read.table'
UPMASKfile: no visible global function definition for 'write.table'
analyse_randomKde2d: no visible global function definition for 'hist'
analyse_randomKde2d: no visible global function definition for 'lines'
analyse_randomKde2d_AutoCalibrated: no visible global function
  definition for 'hist'
analyse_randomKde2d_AutoCalibrated: no visible global function
  definition for 'lines'
create_randomKde2d: no visible global function definition for 'image'
create_randomKde2d: no visible global function definition for 'points'
getStarsAtHighestDensityRegion: no visible global function definition
  for 'rgb'
getStarsAtHighestDensityRegion: no visible global function definition
  for 'dev.new'
getStarsAtHighestDensityRegion: no visible global function definition
  for 'plot'
getStarsAtHighestDensityRegion: no visible global function definition
  for 'image'
getStarsAtHighestDensityRegion: no visible global function definition
  for 'contour'
getStarsAtHighestDensityRegion: no visible global function definition
  for 'points'
innerLoop: no visible global function definition for 'dev.new'
innerLoop: no visible global function definition for 'par'
innerLoop: no visible global function definition for 'pairs'
innerLoop: no visible global function definition for 'rainbow'
kde2dForSubset: no visible global function definition for 'image'
kde2dForSubset: no visible global function definition for 'points'
Undefined global functions or variables:
  contour dev.new hist image lines pairs par plot points rainbow
  read.table rgb write.table
Consider adding
  importFrom("grDevices", "dev.new", "rainbow", "rgb")
  importFrom("graphics", "contour", "hist", "image", "lines", "pairs",
             "par", "plot", "points")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/uroot.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'USAboundariesData'
readSEER: no visible global function definition for 'read.fwf'
Undefined global functions or variables:
  read.fwf
Consider adding
  importFrom("utils", "read.fwf")
to your NAMESPACE file.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   6.2Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
Packages suggested but not available for checking: 'vaers' 'vaersND'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   2.2Mb
cv.vda.le.default: no visible global function definition for 'predict'
cv.vda.r.default: no visible global function definition for 'predict'
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
DrawDensity3D: no visible global function definition for 'colorRamp'
DrawDensity3D: no visible global function definition for 'rgb'
ReadFromFile3D: no visible global function definition for 'read.table'
Undefined global functions or variables:
  colorRamp read.table rgb
Consider adding
  importFrom("grDevices", "colorRamp", "rgb")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Running examples in 'vegalite-Ex.R' failed
The error most likely occurred in:

> ### Name: from_spec
> ### Title: Take a JSON Vega-Lite Spec and render as an htmlwidget
> ### Aliases: from_spec
> 
> ### ** Examples
> 
> from_spec("http://rud.is/dl/embedded.json")
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in file(con, "r") : cannot open the connection
Calls: from_spec -> readLines -> file
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.2Mb
    help   2.6Mb
'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.
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.
Running examples in 'VSE-Ex.R' failed
The error most likely occurred in:

> ### Name: avsSize
> ### Title: avsSize
> ### Aliases: avsSize
> ### Keywords: AVS,Granges
> 
> ### ** Examples
> 
> ld<-loadLd(file.path(system.file("extdata", "ld_BCa_raggr.csv", package="VSE")), type="raggr")
> avs<-makeAVS(ld)
Error in c(<S4 object of class "GRanges">) : 
  could not find symbol "recursive" in environment of the generic function
Calls: makeAVS -> GRangesList
Execution halted
Error in re-building vignettes:
  ...

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

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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Quitting from lines 74-84 (my-vignette.Rmd) 
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
could not find symbol "recursive" in environment of the generic function
Execution halted
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 suggested but not available for checking: 'AnomalyDetection'
Running examples in 'WikipediR-Ex.R' failed
The error most likely occurred in:

> ### Name: page_links
> ### Title: Retrieve a page's links
> ### Aliases: page_links
> 
> ### ** Examples
> 
> #Links
> links <- page_links("en","wikipedia", page = "Aaron Halfaker")
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Error in the HTTP2 framing layer
Calls: page_links ... request_fetch -> request_fetch.write_memory -> <Anonymous> -> .Call
Execution halted
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.
.__A__.1 : <anonymous>: no visible binding for global variable '.hwnd'
Undefined global functions or variables:
  .hwnd
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    5.0Mb
    libs   1.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
R5.value.default: no visible binding for global variable 'data.table'
R5.value.default: no visible global function definition for
  'as.data.table'
R5.value.parse: no visible binding for global variable 'data.table'
R5.value.parse: no visible global function definition for
  'is.data.table'
R5.value.parse: no visible global function definition for
  'as.data.table'
stampme: no visible global function definition for 'flush.console'
stampmsg: no visible global function definition for 'flush.console'
write.data.table: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  as.data.table data.table flush.console is.data.table write.table
Consider adding
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE file.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    exampleData   1.4Mb
    examples      4.5Mb
    libs          4.2Mb
newXMLDoc: no visible binding for global variable 'doc'
xmlFlatListTree : f: no visible binding for global variable 'nodeNames'
xmlFlatListTree : f: no visible binding for global variable 'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'nodeSet'
xmlFlatListTree : addNode: no visible binding for global variable
  'nodeSet'
xmlFlatListTree : addNode: no visible binding for global variable 'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'nodeNames'
xmlFlatListTree : addNode: no visible binding for global variable
  'nodeNames'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'parentCount'
xmlFlatListTree : addNode: no visible binding for global variable
  'parentCount'
xmlFlatListTree : <anonymous>: no visible binding for global variable
  'e'
xmlFlatTree : <anonymous>: no visible binding for global variable 'e'
[[,XMLCodeFile: possible error in updateIds(doc, save = x): unused
  argument (save = x)
Undefined global functions or variables:
  doc e idx nodeNames nodeSet parentCount
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.
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.
BFD_Processor: no visible global function definition for 'levelplot'
BFD_Processor: no visible global function definition for 'corrplot'
FBA_solve: no visible global function definition for 'Rglpk_solve_LP'
PHPP: no visible global function definition for 'levelplot'
PHPP: no visible global function definition for 'persp3d'
PHPP: no visible global function definition for 'play3d'
PHPP: no visible global function definition for 'spin3d'
Found the following significant warnings:
  Warning: D:/temp/RtmpCSymOm/R.INSTALL3d4455d542a2/ACEt/man/ACEt-package.Rd:1: All text must be in a section
See 'd:/Rcompile/CRANpkg/local/3.2/ACEt.Rcheck/00install.out' for details.
clusters: no visible global function definition for 'write.matrix'
copNormal : pcopula: no visible global function definition for
  'pmvnorm'
copNormal : rcopula: no visible global function definition for
  'rmvnorm'
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    R  14.3Mb
Namespaces in Imports field not imported from:
  'plotly' 'shinydashboard'
  All declared Imports should be used.
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'
rCSL: no visible global function definition for 'ginv'
rCSL: no visible global function definition for 'expand'
rCSL: no visible global function definition for 'lu'
adaptiveGMRF2COVAR: no visible global function definition for
  'mcparallel'
adaptiveGMRF2COVAR: no visible global function definition for
  'mccollect'
sim.adaptiveGMRF2COVAR: no visible global function definition for
  'mcparallel'
sim.adaptiveGMRF2COVAR: no visible global function definition for
  'mccollect'
ov.p.grid: no visible global function definition for 'cloud'
ov.p.grid: no visible global function definition for 'wireframe'
Namespace in Imports field not imported from: 'filehash'
  All declared Imports should be used.
denoise: no visible global function definition for 'ebayesthresh'
denoise2: no visible global function definition for 'ebayesthresh'
denoisehetero: no visible global function definition for 'ebayesthresh'
denoisehetero2: no visible global function definition for
  'ebayesthresh'
denoiseheteromp: no visible global function definition for
  'ebayesthresh'
denoiseheteroprop: no visible global function definition for
  'ebayesthresh'
denoiseheteroprop2: no visible global function definition for
  'ebayesthresh'
Namespaces in Imports field not imported from:
  'fields' 'knitr'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/agRee.Rcheck/00install.out' for details.
backfit.logistic.interaction: warning in glm(y ~ trt, family =
  "binomial", weight = wt): partial argument match of 'weight' to
  'weights'
backfit.logistic.main: warning in glm(y ~ 1, family = "binomial",
  weight = wt): partial argument match of 'weight' to 'weights'
logistic.interaction: warning in glm(y ~ trt, family = "binomial",
  weight = wt): partial argument match of 'weight' to 'weights'
logistic.main: warning in glm(y ~ 1, family = "binomial", weight = wt):
  partial argument match of 'weight' to 'weights'
backfit.cox.interaction: no visible global function definition for
  'coxph'
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'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/AlignStat.Rcheck/00install.out' for details.
pedigree.summary: no visible global function definition for 'orderPed'
pedigree.summary: no visible global function definition for
  'calcInbreeding'
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'
sigma.hat: no visible global function definition for 'sigmaHat'
Namespace in Imports field not imported from: 'unmarked'
  All declared Imports should be used.
Package required and available but unsuitable version: 'tcltk'

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

> ### Name: authenticate
> ### Title: authenticate
> ### Aliases: authenticate
> 
> ### ** Examples
> 
> username <- "demo.user@demoanametrix.com"
> password <- "password"
> auth     <- authenticate("https://demo.anametrix.com/api", username, password)
Failed to authenticate with Anametrix API 
Error: Failed to connect to demo.anametrix.com port 443: Timed out 
Error in xmlTreeParse(resp) : object 'resp' not found
Calls: authenticate -> xmlTreeParse
Execution halted
LBI: warning in png(file = paste(graphout, ".png", sep = "")): partial
  argument match of 'file' to 'filename'
normalisation: warning in read.table(as.character(nom[i]), nrow = 1,
  skip = 1, sep = sep): partial argument match of 'nrow' to 'nrows'
aode: no visible global function definition for 'Compose'
mdl: no visible global function definition for 'cutPoints'
setVar: no visible global function definition for 'Compose'
plot,ANFIS : .local: no visible binding for global variable 'X'
Namespaces in Imports field not imported from:
  'RColorBrewer' 'gplots' 'tidyverse'
  All declared Imports should be used.
varbin: no visible global function definition for 'boot'
parse.php.msgs: no visible global function definition for 'startsWith'
read.multiple.apache.access.log: no visible global function definition
  for 'endsWith'
read.multiple.apache.error.log: no visible global function definition
  for 'endsWith'
Running examples in 'ApacheLogProcessor-Ex.R' failed
The error most likely occurred in:

> ### Name: parse.php.msgs
> ### Title: Parses PHP mesages and store its parts in a data frame that
> ###   contains level, message, file, line number and referer.
> ### Aliases: parse.php.msgs
> 
> ### ** Examples
> 
> 
> #Loads the path of the erro log
> path <- system.file("examples", "error_log.log", package = "ApacheLogProcessor")
> 
> #Loads the error log to a data frame
> dfELog <- read.apache.error.log(path)
> 
> dfPHPMsgs <- parse.php.msgs(dfELog)
Error: could not find function "startsWith"
Execution halted
apple: no visible global function definition for 'ginv'
deri: no visible global function definition for 'ginv'
y.app: no visible global function definition for 'ginv'
bookTheme: no visible global function definition for 'trellis.par.set'
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'
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'
runAPSIM: warning in scan(reports_file[i], "", sep = "", skip =
  length(temp), nline = 1): partial argument match of 'nline' to
  'nlines'
apsrtableSummary.lrm: no visible binding for global variable 'est.exp'
pval.note: no visible binding for global variable 'se'
se.note: no visible binding for global variable 'se'
se.note: no visible binding for global variable 'nmodels'
stars.note: no visible binding for global variable 'lev'
aqDayOfWeekStat: no visible global function definition for 'index'
aqDropHour: no visible global function definition for 'index'
aqHourIndex: no visible global function definition for 'index'
aqHourlyStat: no visible global function definition for 'index'
aqStoreSeriesField: no visible global function definition for 'index'
ginv.zalphasfn: no visible global function definition for 'ginv'
tspsimplex_projection: no visible global function definition for
  'solve_TSP'
tspsimplex_projection: no visible global function definition for 'TSP'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.4Mb
Package required and available but unsuitable version: 'arules'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    bin   11.7Mb
    misc   2.1Mb
Found the following significant warnings:
  Warning: failed to assign NativeSymbolInfo for lhs since lhs is already defined in the 'lazyeval' namespace
  Warning: failed to assign NativeSymbolInfo for rhs since rhs is already defined in the 'lazyeval' namespace
See 'd:/Rcompile/CRANpkg/local/3.2/arulesViz.Rcheck/00install.out' for details.
Asciidoc: no visible binding for global variable 'RweaveAsciidoc'
Org: no visible binding for global variable 'RweaveOrg'
Pandoc: no visible binding for global variable 'RweavePandoc'
ReST: no visible binding for global variable 'RweaveReST'
T2t: no visible binding for global variable 'RweaveT2t'
Textile: no visible binding for global variable 'RweaveTextile'
weaverAsciiFinish: no visible global function definition for
  'resetStorage'
weaverAsciiFinish: no visible binding for global variable 'cache_expr'
weaverAsciiRuncode: Error while checking: object 'weaverEvalWithOpt'
  not found
weaverAsciiSetup: no visible global function definition for 'log_debug'
weaverOrgSetup: no visible global function definition for 'log_debug'
weaverPandocSetup: no visible global function definition for
  'log_debug'
weaverReSTSetup: no visible global function definition for 'log_debug'
weaverT2tSetup: no visible global function definition for 'log_debug'
weaverTextileSetup: no visible global function definition for
  'log_debug'
CF: no visible binding for global variable 'activities'
CF2PTS: no visible binding for global variable 'activities'
CF2PTS: no visible binding for global variable 'activities2'
CMD: no visible binding for global variable 'activities'
CMD: no visible global function definition for 'gridpts'
calc_box: no visible binding for global variable 'activities'
calc_box: no visible global function definition for 'wtd.var'
calc_sdd: no visible binding for global variable 'activities'
calc_sde: no visible binding for global variable 'activities'
distances: no visible binding for global variable 'centre'
distances: no visible binding for global variable 'activities'
mean_centre: no visible binding for global variable 'activities'
median_centre: no visible binding for global variable 'activities'
plot_box: no visible binding for global variable 'r.BOX'
plot_centres: no visible binding for global variable 'r.SDE'
plot_centres: no visible binding for global variable 'r.CF'
plot_centres: no visible binding for global variable 'r.median'
plot_centres: no visible binding for global variable 'r.CMD'
plot_centres: no visible binding for global variable 'r.CF2PTS'
plot_sdd: no visible binding for global variable 'r.SDD'
plot_sde: no visible binding for global variable 'r.SDE'
Missing link or links in documentation object 'is_s3_generic.Rd':
  '[utils]{isS3method}'

See section 'Cross-references' in the 'Writing R Extensions' manual.
my_uminp_method: no visible global function definition for 'pmvnorm'
audioHist: no visible global function definition for 'rescale'
audioHist: no visible global function definition for 'toJSON'
audioScatter: no visible global function definition for 'hexbinplot'
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 : <anonymous>: no visible global function definition for
  'toJSON'
matricize: no visible global function definition for 'hexbin'
panel.audiolyzR: no visible global function definition for
  'panel.hexbinplot'
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/3.2/audio.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/auRoc.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'gpclib'
cv.compare.ggplot: no visible global function definition for 'ggplot'
cv.compare.ggplot: no visible global function definition for
  'aes_string'
cv.compare.ggplot: no visible global function definition for
  'facet_wrap'
cv.compare.ggplot: no visible global function definition for
  'scale_x_continuous'
cv.compare.ggplot: no visible global function definition for
  'scale_y_continuous'
cv.compare.ggplot: no visible global function definition for
  'coord_equal'
cv.compare.ggplot: no visible global function definition for
  'scale_color_gradient2'
cv.compare.ggplot: no visible global function definition for
  'scale_size_continuous'
cv.compare.ggplot: no visible global function definition for 'fortify'
cv.compare.ggplot: no visible global function definition for
  'geom_path'
cv.compare.ggplot: no visible global function definition for
  'geom_point'
Namespace in Imports field not imported from: 'EBImage'
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/BACCT.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'osd'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/bamdit.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/BANOVA.Rcheck/00install.out' for details.
Loading required package: gcrma
Loading required package: preprocessCore
Loading required package: gcrma
Loading required package: preprocessCore
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
Loading required package: gcrma
Loading required package: preprocessCore
The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
Loading required package: gcrma
Loading required package: preprocessCore
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
Loading required package: gcrma
Loading required package: preprocessCore
Loading required package: gcrma
Loading required package: preprocessCore
Loading required package: gcrma
Loading required package: preprocessCore
Loading required package: gcrma
Loading required package: preprocessCore
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.
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 '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'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/bayescount.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'Rcpp'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/BayesMed.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/bayesmix.Rcheck/00install.out' for details.
gibbs: no visible global function definition for 'permn'
hmflatlogit: no visible global function definition for 'rmnorm'
hmflatloglin: no visible global function definition for 'mvrnorm'
hmflatprobit: no visible global function definition for 'rmnorm'
hmnoinflogit: no visible global function definition for 'rmnorm'
hmnoinfloglin: no visible global function definition for 'mvrnorm'
hmnoinfprobit: no visible global function definition for 'rmnorm'
ACGaussian: no visible global function definition for 'ginv'
ACGaussian: no visible global function definition for 'rmvnorm'
ACt: no visible global function definition for 'ginv'
ACt: no visible global function definition for 'rmvnorm'
MCGaussian: no visible global function definition for 'ginv'
MCGaussian: no visible global function definition for 'rmvnorm'
MCGaussian: no visible global function definition for 'vec'
MCt: no visible global function definition for 'ginv'
MCt: no visible global function definition for 'rmvnorm'
MCt: no visible global function definition for 'vec'
NCGaussian: no visible global function definition for 'ginv'
NCGaussian: no visible global function definition for 'rmvnorm'
NCGaussian: no visible global function definition for 'rdiric'
NCt: no visible global function definition for 'ginv'
NCt: no visible global function definition for 'rmvnorm'
NCt: no visible global function definition for 'rdiric'
coef.Bayesthresh: no visible global function definition for 'mcmc'
lmerFactorList : <anonymous>: no visible binding for global variable
  'rBind'
lmerFactorList : <anonymous>: no visible global function definition for
  'drop0'
mkZt: no visible binding for global variable 'rBind'
predict.Bayesthresh: no visible global function definition for
  'rankMatrix'
random.effects: no visible global function definition for 'mcmc'
installed size is 25.1Mb
  sub-directories of 1Mb or more:
    libs  25.0Mb
BPSpost2mcmc: no visible global function definition for 'mcmc'
CPPpost2mcmc: no visible global function definition for 'mcmc'
LittleMCAR: no visible global function definition for 'mlest'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/BaySIC.Rcheck/00install.out' for details.
semimetric.deriv: no visible global function definition for
  'splineDesign'
BBRecap: no visible global function definition for 'arms'
LBRecap: no visible global function definition for 'findbars'
LBRecap: no visible global function definition for 'glmer'
LBRecap: no visible global function definition for 'fixef'
LBRecap: no visible global function definition for 'ranef'
plot,BCDating-ts : .local: no visible binding for global variable
  'na.rm'
Running examples in 'BCEA-Ex.R' failed
The error most likely occurred in:

> ### Name: evppi
> ### Title: Expected Value of Perfect Partial Information (EVPPI) for
> ###   selected parameters
> ### Aliases: evppi evppi.default
> ### Keywords: Health economic evaluation Expected value of partial
> ###   information
> 
> ### ** Examples
> 
> # See Baio G., Dawid A.P. (2011) for a detailed description of the 
> # Bayesian model and economic problem
> #
> # Load the processed results of the MCMC simulation model
> data(Vaccine)
Warning: namespace 'rjags' is not available and has been replaced
by .GlobalEnv when processing object 'vaccine'
> # 
> # Runs the health economic evaluation using BCEA
> m <- bcea(e,c,ref=2,interventions=treats)
> #
> # Computes the EVPPI for a bunch of parameters
> inp <- CreateInputs(vaccine)
Error in CreateInputs(vaccine) : 
  You need to install the package 'R2jags'. Please run in your R terminal:
 install.packages('R2jags')
Execution halted
Running examples in 'BCEs0-Ex.R' failed
The error most likely occurred in:

> ### Name: bces0
> ### Title: Bayesian Cost-Effectiveness models in the presence of structural
> ###   zeros
> ### Aliases: bces0 bces0.default
> ### Keywords: JAGS Markov Chain Monte Carlo Bayesian models for
> ###   cost-effectiveness analysis
> 
> ### ** Examples
> 
> data(acupuncture)
> m <- bces0(data,dist.c="gamma",dist.e="beta",n.iter=1000,n.burnin=500,n.chains=2)
> print(m)
NULL
> plot(m)
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Error in plot.window(...) : need finite 'xlim' values
Calls: plot -> plot.default -> localWindow -> plot.window
Execution halted
Namespace in Imports field not imported from: 'inline'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'ggplot2'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'readxl'
  All declared Imports should be used.
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'
Found the following significant warnings:
  Warning: 'loadRcppModules' is deprecated.
See 'd:/Rcompile/CRANpkg/local/3.2/beanz.Rcheck/00install.out' for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Found the following significant warnings:

  Warning: 'loadRcppModules' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
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.
boxplot.AlgorithmPerformance: no visible binding for global variable
  'algorithms'
boxplot.AlgorithmPerformance: no visible binding for global variable
  'value'
boxplot.AlgorithmPerformance: no visible binding for global variable
  'samples'
bsgraph0.dist: no visible global function definition for 'addEdge'
bsgraph0.graphNEL: no visible global function definition for
  'getDefaultAttrs'
bsgraph0.graphNEL: no visible global function definition for 'agopen'
densityplot.AlgorithmPerformance: no visible binding for global
  variable 'value'
densityplot.AlgorithmPerformance: no visible binding for global
  variable 'algorithms'
mi: no visible global function definition for 'mi.plugin'
patch.relation_class_ids: no visible global function definition for
  'relation_is_strict_weak_order'
plot.DatasetCharacterization: no visible binding for global variable
  'characteristics'
plot.DatasetCharacterization: no visible binding for global variable
  'value'
plot.DatasetCharacterization: no visible binding for global variable
  'samples'
plot.DatasetCharacterization: no visible global function definition for
  'theme_text'
plot.TestResult: no visible binding for global variable 'samples'
plot.TestResult: no visible binding for global variable 'value'
stripchart.AlgorithmPerformance: no visible binding for global variable
  'algorithms'
stripchart.AlgorithmPerformance: no visible binding for global variable
  'value'
stripchart.AlgorithmPerformance: no visible binding for global variable
  'samples'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/benchr.Rcheck/00install.out' for details.
bI: no visible global function definition for 'mpfr'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/BEST.Rcheck/00install.out' for details.
betafam: no visible global function definition for 'glmnet'
cca.pertables : cca.var: no visible binding for global variable
  'cca.formula'
cca.pertables: no visible binding for global variable 'cca.formula'
rda.pertables : rda.var: no visible binding for global variable
  'rda.formula'
rda.pertables: no visible binding for global variable 'rda.formula'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/betategarch.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'FinTS' 'Rcpp' 'TSA' 'TTR' 'colorspace' 'fpp' 'fracdiff' 'gtable'
  'htmlwidgets' 'lmtest' 'normtest' 'quadprog' 'rugarch' 'scales'
  'stringi' 'testthat' 'timeDate' 'tseries' 'viridis'
  All declared Imports should be used.
maxstudent2 : padj.fun: no visible global function definition for
  'pmvnorm'
pvstudent2 : padj.fun: no visible global function definition for
  'pmvnorm'
lasso.stars: no visible global function definition for 'glmnet'
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 : .local: no visible global function
  definition for 'dbSendQuery'
bigglm,ANY-DBIConnection : .local: no visible global function
  definition for 'dbClearResult'
bigglm,ANY-DBIConnection : .local : chunk: no visible global function
  definition for 'dbClearResult'
bigglm,ANY-DBIConnection : .local : chunk: no visible global function
  definition for 'dbSendQuery'
bigglm,ANY-DBIConnection : .local : chunk: no visible global function
  definition for 'fetch'
Namespace in Imports field not imported from: 'R6'
  All declared Imports should be used.
LDCAEst: no visible global function definition for 'glmnet'
cv.LDCA: no visible global function definition for 'cv.glmnet'
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'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
ebayesthresh.wavelet.wd: no visible global function definition for
  'ebayesthresh'
hfdenoise: no visible global function definition for
  'ebayesthresh.wavelet'
negloglik.laplace: no visible global function definition for 'wfromt'
negloglik.laplace: no visible global function definition for
  'beta.laplace'
wandafromx: no visible global function definition for 'wfromt'
HLtest.Rsq: warning in pchisq(X2, 10 - 2, lower = FALSE): partial
  argument match of 'lower' to 'lower.tail'
X2GOFtest.Rsq: warning in pnorm(abs(z), lower = FALSE): partial
  argument match of 'lower' to 'lower.tail'
Namespace in Imports field not imported from: 'utils'
  All declared Imports should be used.
Packages required and available but unsuitable versions:
  'spatstat' 'grDevices' 'stats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'stringi'
  All declared Imports should be used.
Packages required and available but unsuitable versions: 'stats' 'graphics'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
dis: no visible binding for global variable 'sub.mat'
mat.dis: no visible binding for global variable 'sub.mat'
mmds.3D.plot: no visible global function definition for 'box3d'
mmds.3D.plot: no visible global function definition for 'axes3d'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/BiSEp.Rcheck/00install.out' for details.
biwt.cor: no visible global function definition for 'covMcd'
biwt.est: no visible global function definition for 'covMcd'
Namespaces in Imports field not imported from:
  'glmnet' 'gtools' 'knitr' 'nnet' 'parallel' 'rJava' 'reshape'
  'rmarkdown' 'shinyjs'
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
'library' or 'require' calls in package code:
  'Matrix' 'sna'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: 'stats'
  All declared Imports should be used.
gplot1: warning in grep(pat = "block", search()): partial argument
  match of 'pat' to 'pattern'
gplot2: warning in grep(pat = "block", search()): partial argument
  match of 'pat' to 'pattern'
loadnetwork2: warning in grep(patt = "^ *$", x = as.character(line)):
  partial argument match of 'patt' to 'pattern'
loadpajek: warning in grep(patt = "^ *$", x = as.character(line)):
  partial argument match of 'patt' to 'pattern'
savecluster: warning in grep(patt = "w32", x = version["os"]): partial
  argument match of 'patt' to 'pattern'
savematrix: warning in grep(patt = "w32", x = version["os"]): partial
  argument match of 'patt' to 'pattern'
savenetwork: warning in grep(patt = "w32", x = version["os"]): partial
  argument match of 'patt' to 'pattern'
savepajek: warning in grep(patt = "w32", x = version["os"]): partial
  argument match of 'patt' to 'pattern'
savevector: warning in grep(patt = "w32", x = version["os"]): partial
  argument match of 'patt' to 'pattern'
check.these.par: no visible global function definition for
  'crit.fun.tmp'
check.these.par: no visible binding for global variable 'useM'
crit.fun: no visible global function definition for 'crit.fun.tmp'
crit.fun: no visible binding for global variable 'useM'
gen.crit.fun: no visible binding for global variable 's'
gplot1: no visible global function definition for 'gplot'
gplot2: no visible global function definition for 'gplot'
loadnetwork: no visible global function definition for 'Matrix'
loadnetwork2: no visible global function definition for 'Matrix'
opt.par: no visible global function definition for 'opt.par.tmp'
opt.random.par: no visible global function definition for 'opt.par.tmp'
opt.these.par: no visible global function definition for 'opt.par.tmp'
opt.these.par: no visible binding for global variable 'm'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
      as.Date, as.Date.numeric
  
  trying URL 'http://www.bls.gov/web/metro/laucntycur14.txt'
  Error in download.file("http://www.bls.gov/web/metro/laucntycur14.txt",  : 
    cannot open URL 'http://www.bls.gov/web/metro/laucntycur14.txt'
  Calls: test_check ... force -> source_file -> eval -> eval -> download.file
  In addition: Warning message:
  In download.file("http://www.bls.gov/web/metro/laucntycur14.txt",  :
    InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
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'
bmem.bs: no visible global function definition for 'sem'
bmem.em.rcov: no visible global function definition for 'cov.rob'
bmem.mi.cov: no visible global function definition for 'amelia'
bmem.sem: no visible global function definition for 'sem'
bmem.sobel: no visible global function definition for 'sem'
power.basic: no visible global function definition for 'simulateData'
power.basic: no visible global function definition for 'lavaanNames'
power.basic : runonce: no visible global function definition for
  'simulateData'
power.basic: no visible global function definition for 'sfInit'
power.basic: no visible global function definition for 'sfLibrary'
power.basic: no visible binding for global variable 'lavaan'
power.basic: no visible global function definition for 'sfLapply'
power.boot: no visible global function definition for 'simulateData'
power.boot: no visible global function definition for 'lavaanNames'
power.boot : runonce: no visible global function definition for
  'simulateData'
power.boot : runonce: no visible global function definition for
  'bootstrapLavaan'
power.boot: no visible global function definition for 'sfInit'
power.boot: no visible global function definition for 'sfLibrary'
power.boot: no visible binding for global variable 'lavaan'
power.boot: no visible global function definition for 'sfLapply'
summary.power: no visible global function definition for 'lavaanNames'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/bmeta.Rcheck/00install.out' for details.
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 global function definition for 'mcmc'
bmksummary: no visible global function definition for 'mcmc.list'
bmksummary: no visible global function definition for 'effectiveSize'
bmksummary: no visible global function definition for 'gelman.diag'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/bmlm.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'compiler'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/Boom.Rcheck/00install.out' for details.
Package required and available but unsuitable version: 'Boom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
alleleEnrichment.data.alleles : <anonymous>: no visible global function
  definition for 'allele.count'
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'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/boral.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'rgdal' 'tidyr'
  All declared Imports should be used.
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'
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'
confint.profile.brglm: no visible global function definition for
  'profConfint'
profile.brglm: no visible global function definition for 'profileModel'
Error in re-building vignettes:
  ...
Loading required package: rjags
Loading required package: coda
Error : .onLoad failed in loadNamespace() for 'rjags', details:
  call: fun(libname, pkgname)
  error: The environment variable JAGS_HOME is set to
c:/Program Files/JAGS/JAGS-4.0.0
but no JAGS installation can be found there

Quitting from lines 51-116 (bridgesampling_example.Rmd) 
Error: processing vignette 'bridgesampling_example.Rmd' failed with diagnostics:
package 'rjags' could not be loaded
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.
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 'univariate_calpha'
CIGLM: no visible global function definition for 'adjusted_calpha'
EDA: no visible global function definition for 'kurtosis'
EDA: no visible global function definition for 'skewness'
bs.design: no visible global function definition for 'spline.des'
Packages required and available but unsuitable versions:
  'BoomSpikeSlab' 'Boom' 'Boom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/BTSPAS.Rcheck/00install.out' for details.
CADFpvalues: no visible binding for global variable 'coeffs_ct'
CADFpvalues: no visible binding for global variable 'coeffs_c'
CADFpvalues: no visible binding for global variable 'coeffs_nc'
estmodel: no visible global function definition for 'dynlm'
estmodel: no visible global function definition for 'punitroot'
estmodel: no visible global function definition for 'kernHAC'
plot.CADFtest: no visible global function definition for
  'jarque.bera.test'
MH: no visible global function definition for 'rmvnorm'
computer.model: no visible global function definition for 'rmvnorm'
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'
bestBy: no visible global function definition for 'dbConnect'
bestBy: no visible global function definition for 'dbDriver'
bestBy: no visible global function definition for 'dbWriteTable'
bestBy: no visible global function definition for 'dbGetQuery'
dbWriteTable2: no visible global function definition for 'dbListFields'
dbWriteTable2: no visible global function definition for 'dbGetQuery'
dbWriteTable2: no visible global function definition for 'dbSendQuery'
dbWriteTable2: no visible global function definition for 'dbColumnInfo'
dbWriteTable2: no visible global function definition for
  'dbClearResult'
dbWriteTable2: no visible global function definition for 'dbWriteTable'
groupBy: no visible global function definition for 'dbConnect'
groupBy: no visible global function definition for 'dbDriver'
groupBy: no visible global function definition for 'dbWriteTable'
groupBy: no visible global function definition for 'dbGetQuery'
spie: no visible global function definition for 'grid.newpage'
spie: no visible global function definition for 'pushViewport'
spie: no visible global function definition for 'viewport'
spie: no visible global function definition for 'grid.layout'
spie: no visible global function definition for 'dataViewport'
spie: no visible global function definition for 'grid.circle'
spie: no visible global function definition for 'gpar'
spie: no visible global function definition for 'grid.polygon'
spie: no visible global function definition for 'grid.rect'
spie: no visible global function definition for 'stringWidth'
spie: no visible global function definition for 'stringHeight'
spie: no visible global function definition for 'grid.text'
spie: no visible global function definition for 'grid.lines'
spie: no visible global function definition for 'unit'
spie: no visible global function definition for 'upViewport'
Namespace in Imports field not imported from: 'Matrix'
  All declared Imports should be used.
File 'CausalGAM/R/zzz.R':
  .onAttach calls:
    cat("##\n## CausalGAM Package\n")
    cat("## Copyright (C) 2009", " Adam Glynn and Kevin Quinn\n",     sep = "")
    require(gam, quietly = TRUE)

Package startup functions should not change the search path.
Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
estim.regul: warning in matrix(res, nc = length(grid2)): partial
  argument match of 'nc' to 'ncol'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/CCTpack.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/cda.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'RCurl' 'rgdal'
  All declared Imports should be used.
fitVolDist: no visible global function definition for 'nls.lm'
fitVolDist: no visible global function definition for 'nls.lm.control'
centrality: no visible global function definition for 'vcount'
centrality: no visible global function definition for 'degree'
centrality: no visible global function definition for 'betweenness'
cepa.all.parallel.by.snow: no visible global function definition for
  'makeCluster'
cepa.all.parallel.by.snow: no visible global function definition for
  'clusterCall'
cepa.all.parallel.by.snow: no visible global function definition for
  'clusterApply'
cepa.all.parallel.by.snow: no visible global function definition for
  'stopCluster'
generate.pathway: no visible global function definition for
  'graph.edgelist'
pathway.nodes: no visible global function definition for 'vcount'
pathway.nodes: no visible global function definition for
  'get.vertex.attribute'
plot.igraph2: no visible binding for global variable 'layout.random'
plot.igraph2: no visible global function definition for 'V'
plot.igraph2: no visible global function definition for 'E'
plot.igraph2: no visible global function definition for 'get.edgelist'
plot.igraph2: no visible global function definition for 'ecount'
plotGraph: no visible global function definition for 'V'
plotGraph: no visible global function definition for 'V<-'
plotGraph: no visible global function definition for 'E'
plotGraph: no visible global function definition for 'E<-'
plotGraph : layout.method: no visible global function definition for
  'layout.reingold.tilford'
radiality: no visible global function definition for 'shortest.paths'
radiality: no visible global function definition for 'vcount'
radiality: no visible global function definition for 'diameter'
reach: no visible global function definition for 'E'
reach: no visible global function definition for 'shortest.paths'
report: no visible global function definition for 'write.graph'
spread: no visible global function definition for 'E'
spread: no visible global function definition for 'shortest.paths'
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'
L2L1ExpandFit: no visible global function definition for
  'L2L1PathExtract'
Namespace in Imports field not imported from: 'grDevices'
  All declared Imports should be used.
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'
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'
DPfitSamples: no visible global function definition for 'mclapply'
getCCF: no visible global function definition for 'mclapply'
getDiploidOrigin: no visible global function definition for 'mclapply'
getSegChr.CBS: no visible global function definition for 'mclapply'
getSegPurity: no visible global function definition for 'mclapply'
downloadMaster: no visible global function definition for
  'getURLContent'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/cheddar.Rcheck/00install.out' for details.
Running examples in 'chipPCR-Ex.R' failed
The error most likely occurred in:

> ### Name: amptest
> ### Title: Class '"amptest"'
> ### Aliases: amptest amptest-class summary.amptest summary,amptest-method
> ###   show.amptest show,amptest-method plot.amptest plot,amptest-method
> ###   plot,amptest,ANY-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> # Compare a positive and a negative amplification reaction.
> # First simulate positive reaction (fluo.pos) and than the 
> # negative reaction (fluo.neg).
> # Simulation of an amplifiaction curve with some noise and a high signal.
> 
> fluo.pos <- AmpSim(cyc = 1:40, noise = TRUE)[, 2]
> ampt.pos <- amptester(fluo.pos, manual = TRUE, background = c(0, 15), 
+ 		      noiselevel = 0.15)
Error in validObject(.Object) : 
  invalid class "amptest" object: superclass "replValueSp" not defined in the environment of the object's class
Calls: amptester -> new -> initialize -> initialize -> validObject
Execution halted
chngpt.test.2: no visible global function definition for 'startsWith'
sim.chngpt: no visible global function definition for 'startsWith'
sim.my: no visible global function definition for 'endsWith'
sim.my: no visible global function definition for 'startsWith'
Running examples in 'chngpt-Ex.R' failed
The error most likely occurred in:

> ### Name: chngpt.test
> ### Title: Change Point Tests
> ### Aliases: antoch.test chngpt.test plot.chngpt.test
> 
> ### ** Examples
> 
> 
> dat=sim.chngpt("sigmoid4", type="step", n=200, seed=1, beta=1, alpha=-1, x.distr="norm", e.=4)
Loading required namespace: mvtnorm
Error in sim.chngpt("sigmoid4", type = "step", n = 200, seed = 1, beta = 1,  : 
  could not find function "startsWith"
Execution halted
Running the tests in 'tests/doRUnit.R' failed.
Last 13 lines of output:
  
   
  1 Test Suite : 
  chngpt unit testing - 2 test functions, 2 errors, 0 failures
  ERROR in test.chngpt.test: Error in sim.chngpt("sigmoid4", type = "step", n = 250, seed = 1, beta = 0,  : 
    could not find function "startsWith"
  ERROR in test.chngptm: Error in sim.chngpt("sigmoid2", type = "hinge", n = 250, seed = 1, beta = log(0.4),  : 
    could not find function "startsWith"
  Error: 
  
  unit testing failed (#test failures: 0, #R errors: 2)
  
  Execution halted
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'
Namespaces in Imports field not imported from:
  'Matrix' 'stringr'
  All declared Imports should be used.
print.rao.spacing.test: no visible binding for global variable
  'rao.table'
cit.assignBcmst: no visible binding for global variable 'citbcmst'
cit.assignCcmst: no visible binding for global variable 'citccmst'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/classify.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'stats'
  All declared Imports should be used.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  5: eval(expr, envir, enclos)
  6: samplerate2d(tb$torigin)
  7: rbind(sample.rate.table, data.frame(item = stname2longname(code2stname(i)), hiccode = as.number(StdId(i)), 
         sr = sr))
  8: rbind(deparse.level, ...)
  9: stop("numbers of columns of arguments do not match")
  
  testthat results ================================================================
  OK: 207 SKIPPED: 0 FAILED: 1
  1. Error: calculate 2D sample rate (@test_report.r#36) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: 'survival'
  All declared Imports should be used.
cfly_dist: no visible global function definition for 'ggplot'
cfly_dist: no visible global function definition for 'aes_string'
cfly_dist: no visible global function definition for 'geom_density'
cfly_dist: no visible global function definition for 'facet_grid'
cfly_fluct: no visible global function definition for 'ggplot'
cfly_fluct: no visible global function definition for 'aes_string'
cfly_fluct: no visible global function definition for 'geom_tile'
cfly_fluct: no visible global function definition for
  'scale_y_discrete'
cfly_fluct: no visible global function definition for
  'scale_x_discrete'
cfly_fluct: no visible global function definition for 'theme'
cfly_pcp: no visible global function definition for 'ggplot'
cfly_pcp: no visible global function definition for 'aes_string'
cfly_pcp: no visible global function definition for 'geom_line'
cfly_pcp: no visible global function definition for 'facet_wrap'
som_iterate: no visible global function definition for 'unit.distances'
Package required but not available: 'OpenImageR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
    pdf   2.2Mb
Namespace in Imports field not imported from: 'tidyr'
  All declared Imports should be used.
BHI: no visible global function definition for 'getGO'
BHI: no visible binding for global variable 'dropECode'
BSI: no visible global function definition for 'getGO'
BSI: no visible binding for global variable 'dropECode'
vClusters: no visible global function definition for 'Mclust'
vClusters: no visible global function definition for 'som'
Error in re-building vignettes:
  ...
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Loading required package: XML

Attaching package: 'XML'

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

    toHTML

Loading required package: GO.db

Loading required package: moe430a.db
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'moe430a.db'
Loading required package: RankAggreg
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "clValid.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.2.5/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.2.5/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'clValid.tex' failed

LaTeX errors:
!pdfTeX error: pdflatex.EXE (file ./clValid-022.pdf): PDF inclusion: required p
age does not exist <0>
 ==> Fatal error occurred, no output PDF file produced!
Execution halted
ControlCharts: no visible global function definition for
  'com.log.density'
COBRA : COBRA.lars: no visible global function definition for 'lars'
COBRA : COBRA.lars: no visible global function definition for
  'predict.lars'
COBRA : COBRA.tree: no visible global function definition for 'tree'
COBRA : COBRA.ridge: no visible global function definition for
  'linearRidge'
COBRA : COBRA.randomForest: no visible global function definition for
  'randomForest'
COBRA: no visible global function definition for 'sfInit'
COBRA: no visible global function definition for 'sfLibrary'
COBRA: no visible global function definition for 'sfExportAll'
COBRA: no visible global function definition for 'sfSapply'
COBRA: no visible global function definition for 'sfStop'
autocorr1: no visible global function definition for 'is.mcmc'
autocorr1: no visible global function definition for 'as.mcmc'
autocorr1: no visible global function definition for 'autocorr'
bridgestat.diag: no visible global function definition for
  'is.mcmc.list'
bridgestat.diag: no visible global function definition for 'as.mcmc'
bridgestat.diag: no visible global function definition for 'nvar'
bridgestat.diag: no visible global function definition for 'varnames'
bridgestat.diag: no visible global function definition for 'niter'
bridgestat.diag: no visible global function definition for
  'spectrum0.ar'
transient.test: no visible global function definition for 'as.mcmc'
coloc.abf.snpStats: no visible global function definition for
  'single.snp.tests'
coloc.abf.snpStats: no visible global function definition for
  'col.summary'
fillin: no visible global function definition for 'col.summary'
fillin: no visible global function definition for 'snp.imputation'
fillin: no visible global function definition for 'impute.snps'
plot,colocPCs-missing : .local: no visible binding for global variable
  'object'
plotVenn2d : twoWayOverlap: no visible global function definition for
  'grid.polygon'
plotVenn2d : twoWayOverlap: no visible global function definition for
  'gpar'
plotVenn2d: no visible global function definition for 'grid.text'
plotVenn2d: no visible global function definition for 'gpar'
plotVenn2d: no visible global function definition for 'grid.polygon'
plotVenn3d : twoWayOverlap: no visible global function definition for
  'grid.polygon'
plotVenn3d : twoWayOverlap: no visible global function definition for
  'gpar'
plotVenn3d: no visible global function definition for 'grid.text'
plotVenn3d: no visible global function definition for 'gpar'
plotVenn3d: no visible global function definition for 'grid.polygon'
plotVenn4d : region.polygon: no visible global function definition for
  'grid.polygon'
plotVenn4d : region.polygon: no visible global function definition for
  'gpar'
plotVenn4d: no visible global function definition for 'grid.text'
plotVenn4d: no visible global function definition for 'gpar'
plotVenn4d: no visible global function definition for 'pushViewport'
plotVenn4d: no visible global function definition for 'viewport'
plotVenn4d: no visible global function definition for 'grid.polygon'
plotVenn4d: no visible global function definition for 'upViewport'
splitTrainTest: warning in ts(dat[1:numTrain], start = props[1], freq =
  props[3]): partial argument match of 'freq' to 'frequency'
splitTrainTest: warning in ts(dat[(numTrain + 1):length(dat)], start =
  (props[1] + numTrain/props[3]), freq = props[3]): partial argument
  match of 'freq' to 'frequency'
plot.msc : showResults: no visible global function definition for
  'rgl.open'
plot.msc : showResults: no visible global function definition for
  'rgl.clear'
plot.msc : showResults: no visible global function definition for
  'rgl.bg'
plot.msc : showResults: no visible global function definition for
  'rgl.light'
plot.msc : showResults: no visible global function definition for
  'rgl.bbox'
plot.msc : showResults: no visible global function definition for
  'rgl.surface'
plot.msc : showResults: no visible global function definition for
  'rgl.spheres'
plot.msc : showResults: no visible global function definition for
  'axes3d'
plot.msc : showResults: no visible global function definition for
  'title3d'
plot.msc : showResults: no visible global function definition for
  'rgl.viewpoint'
plot.msc: no visible global function definition for 'xyplot'
plot.msc : mypanel: no visible global function definition for
  'panel.fill'
plot.msc : mypanel: no visible global function definition for
  'panel.grid'
plot.msc : mypanel: no visible global function definition for
  'panel.levelplot'
plot.msc: no visible global function definition for 'levelplot'
plot.msc : <anonymous>: no visible global function definition for
  'axis.default'
plot.msc : <anonymous>: no visible global function definition for
  'panel.text'
plot.msc: no visible global function definition for 'shingle'
plot.msc: no visible global function definition for 'strip.custom'
Running examples in 'compareDF-Ex.R' failed
The error most likely occurred in:

> ### Name: compare_df
> ### Title: Compare Two dataframes
> ### Aliases: compare_df
> 
> ### ** Examples
> 
> old_df = data.frame(var1 = c("A", "B", "C"),
+                     val1 = c(1, 2, 3))
> new_df = data.frame(var1 = c("A", "B", "C"),
+                     val1 = c(1, 2, 4))
> ctable = compare_df(new_df, old_df, c("var1"))
Creating comparison table...
Loading required namespace: htmlTable
Creating HTML table for first 100 rows
Error in compare_df(new_df, old_df, c("var1")) : 
  Assertion failed. One of the following must apply:
 * check_matrix(css.cell): Must be of type 'matrix', not 'data.frame'
 * check_character(css.cell): Must be of type 'character', not
 * 'data.frame'
Calls: compare_df ... htmlTable.data.frame -> htmlTable.default -> assert -> mstop
Execution halted
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  Creating comparison table...
  Loading required namespace: htmlTable
  Creating HTML table for first 100 rows
  Error in test_check("compareDF") : 
    Assertion failed. One of the following must apply:
   * check_matrix(css.cell): Must be of type 'matrix', not 'data.frame'
   * check_character(css.cell): Must be of type 'character', not
   * 'data.frame'
  Calls: test_check ... htmlTable.data.frame -> htmlTable.default -> assert -> mstop
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
compareODM: no visible global function definition for 'xmlRoot'
compareODM: no visible global function definition for 'xmlTreeParse'
compareODM: no visible global function definition for 'xmlChildren'
compareODM: no visible global function definition for 'xmlAttrs'
compareODM: no visible global function definition for 'xmlValue'
dcomplnorm: no visible global function definition for 'grad'
pcomplnorm: no visible global function definition for 'grad'
qcomplnorm: no visible global function definition for 'grad'
arrows3D.default: no visible global function definition for 'texts3d'
arrows3D.default: no visible global function definition for
  'segments3d'
axis3D: no visible global function definition for 'bbox3d'
biplot3D.default: no visible global function definition for 'points3d'
biplot3D.default: no visible global function definition for 'texts3d'
biplot3D.princomp: no visible global function definition for 'texts3d'
biplot3D.princomp: no visible global function definition for 'par3d'
plot3D.acomp: no visible global function definition for 'points3d'
plot3D.acomp: no visible global function definition for 'lines3d'
plot3D.acomp: no visible global function definition for 'texts3d'
plot3D.acomp: no visible global function definition for 'rgl.viewpoint'
plot3D.acomp: no visible global function definition for 'bbox3d'
plot3D.default: no visible global function definition for 'rgl.bbox'
plot3D.rcomp: no visible global function definition for 'points3d'
plot3D.rcomp: no visible global function definition for 'lines3d'
plot3D.rcomp: no visible global function definition for 'texts3d'
plot3D.rcomp: no visible global function definition for 'rgl.viewpoint'
plot3D.rcomp: no visible global function definition for 'bbox3d'
plot3D.rmult: no visible global function definition for 'points3d'
plot3D.rmult: no visible global function definition for 'par3d'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/CompQuadForm.Rcheck/00install.out' for details.
dhpareto: no visible global function definition for 'pgpd'
dhpareto: no visible global function definition for 'dgpd'
hpareto.gamma: no visible global function definition for 'pgpd'
phpareto: no visible global function definition for 'pgpd'
qhpareto: no visible global function definition for 'qgpd'
rhpareto: no visible global function definition for 'qgpd'
rhpareto: no visible global function definition for 'pgpd'
Namespace in Imports field not imported from: 'graphics'
  All declared Imports should be used.
ConjointChecks: no visible global function definition for 'makeCluster'
ConjointChecks: no visible global function definition for
  'clusterSetRNGStream'
ConjointChecks: no visible global function definition for
  'clusterApply'
ConjointChecks: no visible global function definition for 'stopCluster'
Namespaces in Imports field not imported from:
  'Hmisc' 'MASS' 'geepack'
  All declared Imports should be used.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  preparing your full survey design to work with R convey package functions
  
  note that this function must be run on the full survey design object immediately after the svydesign() or svrepdesign() call.
  
  preparing your full survey design to work with R convey package functions
  
  note that this function must be run on the full survey design object immediately after the svydesign() or svrepdesign() call.
  
  Error: 'order_quant' must be a integer values in [0, 100]
  testthat results ================================================================
  OK: 251 SKIPPED: 0 FAILED: 0
  Execution halted
Namespace in Imports field not imported from: 'knitr'
  All declared Imports should be used.
Error in re-building vignettes:
  ...
  font family not found in Windows font database
Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call.graphics(L_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call.graphics(L_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call.graphics(L_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call.graphics(L_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Quitting from lines 775-800 (CopulaDTA_Vignette.Rmd) 
Error: processing vignette 'CopulaDTA_Vignette.Rmd' failed with diagnostics:
formal argument "axis.title.y" matched by multiple actual arguments
Execution halted
Namespaces in Imports field not imported from:
  'Rtsne' 'scatterplot3d'
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'loadRcppModules' is deprecated.
See 'd:/Rcompile/CRANpkg/local/3.2/CorrectOverloadedPeaks.Rcheck/00install.out' for details.
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.
correlogram: no visible global function definition for 'textxy'
correlogram: no visible global function definition for 'circle'
linangplot: no visible global function definition for 'rad2degree'
linangplot: no visible global function definition for 'ginv'
linangplot: no visible global function definition for 'calibrate'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Loading required package: corset
  1. Failure: Corset - class gts/hts  (@test-bezier.R#142) -----------------------
  `cx` not equal to structure(...).
  Component "bts": Mean relative difference: 0.8147274
  Component "histy": Mean relative difference: 0.1075422
  
  
  testthat results ================================================================
  OK: 23 SKIPPED: 3 FAILED: 1
  1. Failure: Corset - class gts/hts  (@test-bezier.R#142) 
  
  Error: testthat unit tests failed
  Execution halted
cosinor_analyzer: no visible binding for global variable 'vitamind'
AntiAR: no visible global function definition for 'first.last'
BootTOS: no visible global function definition for 'ewspec'
BootTOS : bsfn: no visible global function definition for 'LSWsim'
BootTOS : bsfn: no visible global function definition for 'ewspec'
EWSsmoothRM: no visible global function definition for 'accessD'
EWSsmoothRM: no visible global function definition for 'putD'
LCTS: no visible global function definition for 'ewspec'
LCTSres: no visible global function definition for 'ewspec'
coeftofn: no visible global function definition for 'wd'
coeftofn: no visible global function definition for 'wr'
findstysols: no visible global function definition for 'IsPowerOfTwo'
lacv: no visible global function definition for 'ewspec'
lacv: no visible global function definition for 'PsiJmat'
cotrend.default: no visible global function definition for 'coredata'
covLCA: no visible global function definition for 'ginv'
covLCA.initialAlphaGamma: no visible global function definition for
  'mlogit.data'
covLCA.initialAlphaGamma: no visible global function definition for
  'mlogit'
covLCA.initialBeta: no visible global function definition for 'poLCA'
covLCA.initialBeta: no visible global function definition for
  'mlogit.data'
covLCA.initialBeta: no visible global function definition for 'mlogit'
covLCA.paramVariance: no visible global function definition for 'ginv'
covLCA.varianceFirst: no visible global function definition for 'bdiag'
calcz02: no visible global function definition for 'coxph'
covTest: no visible global function definition for 'Surv'
CoxBoost: no visible global function definition for 'Matrix'
cv.CoxBoost: no visible global function definition for 'mclapply'
estimPVal: no visible global function definition for 'mclapply'
iCoxBoost: no visible global function definition for 'Matrix'
plot.coxr: warning in close.screen(all = TRUE): partial argument match
  of 'all' to 'all.screens'
cpa : OpenX: no visible global function definition for 'tclvalue'
cpa : OpenX: no visible global function definition for 'tkgetOpenFile'
cpa : OpenV: no visible global function definition for 'tclvalue'
cpa : OpenV: no visible global function definition for 'tkgetOpenFile'
cpa : OpenA: no visible global function definition for 'tclvalue'
cpa : OpenA: no visible global function definition for 'tkgetOpenFile'
cpa : Close: no visible global function definition for 'tkdestroy'
cpa : OnOK: no visible global function definition for 'tkmessageBox'
cpa : OnOK: no visible global function definition for 'tclvalue'
cpa : OnOK: no visible global function definition for 'tktoplevel'
cpa : OnOK: no visible global function definition for 'tclVar'
cpa : OnOK: no visible global function definition for 'tkentry'
cpa : OnOK: no visible global function definition for 'tkgrid'
cpa : OnOK: no visible global function definition for 'tklabel'
cpa : OnOK : Save: no visible global function definition for 'tclvalue'
cpa : OnOK : Save: no visible global function definition for
  'tkdestroy'
cpa : OnOK: no visible global function definition for 'tkbutton'
cpa : OnOK: no visible global function definition for 'tkbind'
cpa : OnOK: no visible global function definition for 'tkfocus'
cpa: no visible global function definition for 'tktoplevel'
cpa: no visible global function definition for 'tkwm.title'
cpa: no visible global function definition for 'tkbutton'
cpa: no visible global function definition for 'tkgrid'
cpa: no visible global function definition for 'tklabel'
cpa: no visible global function definition for 'tkfocus'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/crmPack.Rcheck/00install.out' for details.
getUrlsCRN: no visible global function definition for 'getURL'
BootC: no visible global function definition for 'boot'
BootC: no visible global function definition for 'boot.ci'
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Namespace in Imports field not imported from: 'httpcode'
  All declared Imports should be used.
GMLDfct: no visible global function definition for 'clusterApplyLB'
SNPgenmap: no visible binding for global variable 'RutgersMapB36'
doGeneDrops: no visible global function definition for 'write.pedfile'
doGeneDrops: no visible global function definition for 'GeneDrops'
doGeneDrops: no visible global function definition for 'read.pedfile'
flagAllPairs: no visible global function definition for 'showLabels'
flagPairs: no visible global function definition for 'showLabels'
gendrp: no visible global function definition for 'clusterApply'
get.ellipse: no visible global function definition for 'ellipse'
parfile.fitLD: no visible global function definition for
  'write.pedfile'
parfile.fitLD: no visible global function definition for
  'write.parfile'
parfile.fitLD: no visible global function definition for 'FitGMLD'
parfile.noLD: no visible global function definition for 'write.parfile'
snpfilter: no visible global function definition for 'row.summary'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/CuCubes.Rcheck/00install.out' for details.
cudiaDet: no visible global function definition for 'rdirichlet'
cudiaDet: no visible global function definition for 'lm.ridge'
getoptimalalpha: no visible global function definition for 'gcvplot'
.klogreg: no visible global function definition for 'Matrix'
.klogreg: no visible global function definition for 'kernelMatrix'
.klogreg: no visible global function definition for 'Diagonal'
.klogreg.predict: no visible global function definition for
  'kernelMult'
.krr: no visible global function definition for 'kernelMatrix'
.krr: no visible global function definition for 'Matrix'
.krr.predict: no visible global function definition for 'kernelMatrix'
constructSVMLearner : learn.svm: no visible global function definition
  for 'ksvm'
constructSVRLearner : learn.svr: no visible global function definition
  for 'ksvm'
cxxfunctionplus: no visible global function definition for 'getPlugin'
cxxfunctionplus: no visible global function definition for
  'cxxfunction'
get.trans: no visible global function definition for
  'create.bspline.basis'
get.trans: no visible global function definition for 'smooth.basis'
get.trans: no visible global function definition for 'deriv.fd'
get.trans: no visible global function definition for 'eval.fd'
initialize,D2C : .local: warning in sort(IM, decr = TRUE, ind = TRUE):
  partial argument match of 'decr' to 'decreasing'
updateD2C,D2C : .local: warning in sort(IM, decr = TRUE, ind = TRUE):
  partial argument match of 'decr' to 'decreasing'
compute,DAG.network : .local: no visible global function definition for
  'numNodes'
compute,DAG.network : .local: no visible global function definition for
  'inEdges'
initialize,D2C : .local: no visible binding for global variable 'i'
initialize,D2C : .local: no visible global function definition for
  'nodes'
initialize,D2C : .local: no visible global function definition for
  'subGraph'
initialize,D2C : .local: no visible global function definition for
  'inEdges'
initialize,simulatedDAG : .local: no visible binding for global
  variable 'i'
initialize,simulatedDAG : .local: no visible global function definition
  for 'edges'
updateD2C,D2C : .local: no visible binding for global variable 'i'
updateD2C,D2C : .local: no visible global function definition for
  'nodes'
updateD2C,D2C : .local: no visible global function definition for
  'subGraph'
updateD2C,D2C : .local: no visible global function definition for
  'inEdges'
compareModels: no visible binding for global variable 'fgl'
compareModels: no visible global function definition for 'rlm'
Daim: no visible global function definition for 'mclapply'
Daim: no visible global function definition for 'clusterSetRNGStream'
Daim: no visible global function definition for 'clusterEvalQ'
Daim: no visible global function definition for 'clusterApplyLB'
The following files are already in R: 'jss.bst', 'jss.cls'
Please remove them from your package.
.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'
meta,SftpLocation : .local: no visible global function definition for
  'basicTextGatherer'
meta,SftpLocation : .local: no visible binding for global variable
  'isdir'
meta,SftpLocation : .local: no visible binding for global variable
  'name'
put,BlogPostTarget-Blogger : .local: no visible global function
  definition for 'toJSON'
Package suggested but not available for checking: 'nanotime'
DAT : DATrun: no visible global function definition for 'rot90'
DAT : DATrun: no visible global function definition for 'locfit.robust'
DAT : DATrun: no visible global function definition for 'writeMat'
DAT: no visible binding for global variable 'DAT.simData'
plot.pcobiplot: no visible binding for global variable 'sveg'
getCutoff: no visible binding for global variable 'unifCut'
getCutoff: no visible binding for global variable 'normCut'
getCutoff: no visible binding for global variable 'distEqCut'
getPval: no visible binding for global variable 'unifCut'
getPval: no visible binding for global variable 'normCut'
getPval: no visible binding for global variable 'distEqCut'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/dbscan.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/dclone.Rcheck/00install.out' for details.
Plot.triangle: no visible global function definition for 'cloud'
Plot.triangle: no visible binding for global variable 'panel.3dbars'
Plot.triangle: no visible global function definition for 'level.colors'
Plot.triangle: no visible global function definition for 'do.breaks'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/dcmle.Rcheck/00install.out' for details.
plot,attribute.class-missing : .local: no visible binding for global
  variable 'attr.number'
plot,attribute.class-missing : .local: no visible binding for global
  variable 'mean.attr'
plot,attribute.profile.class-missing : .local: no visible binding for
  global variable 'attr.profile.number'
plot,attribute.profile.class-missing : .local: no visible binding for
  global variable 'mean.attr.profile'
summary,attribute.class : .local: no visible binding for global
  variable 'value'
summary,attribute.profile.class : .local: no visible binding for global
  variable 'max.class'
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
  > library(testthat)
  > test_check("dcmr")
  Loading required package: dcmr
  1. Failure: Test ScoreDCM outputs for Qmatrix with no interaction (@test_scoreDCM.R#18) 
  `rmse_class` is not strictly less than `tolerance`. Difference: 0.217
  
  
  testthat results ================================================================
  OK: 119 SKIPPED: 0 FAILED: 1
  1. Failure: Test ScoreDCM outputs for Qmatrix with no interaction (@test_scoreDCM.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
.onLoad: no visible binding for global variable 'jgr.addMenuItem'
.onLoad : gui.addSeperator: no visible global function definition for
  'jgr.addMenuSeparator'
.factorAnalysisRunFunction: no visible global function definition for
  'execute'
.onLoad: no visible binding for global variable '.deducer'
.onLoad: no visible global function definition for '.jnull'
.onLoad: no visible global function definition for '.jpackage'
.onLoad: no visible global function definition for '.registerDialog'
.onLoad: no visible global function definition for 'deducer.addMenu'
.onLoad: no visible global function definition for
  'deducer.addMenuItem'
.onLoad: no visible binding for global variable '.windowsGUI'
.onLoad: no visible binding for global variable '.jgr'
.onLoad: no visible global function definition for 'jgr.addMenu'
.onLoad: no visible global function definition for 'jgr.addMenuItem'
makeFactorAnalysisDialog: no visible binding for global variable
  'SimpleRDialog'
makeFactorAnalysisDialog: no visible binding for global variable
  'VariableSelectorWidget'
makeFactorAnalysisDialog: no visible global function definition for
  'addComponent'
makeFactorAnalysisDialog: no visible binding for global variable
  'VariableListWidget'
makeFactorAnalysisDialog: no visible binding for global variable
  'CheckBoxesWidget'
makeFactorAnalysisDialog: no visible global function definition for
  'toJava'
makeListExampleDialog: no visible binding for global variable
  'ListWidget'
makeListExampleDialog: no visible global function definition for
  'setSize'
makeListExampleDialog: no visible binding for global variable
  'AddRemoveButtons'
makeListExampleDialog: no visible binding for global variable
  'SimpleRDialog'
makeListExampleDialog: no visible global function definition for
  'addComponent'
makeListExampleDialog: no visible global function definition for
  'toJava'
makeScatterPlotDialog: no visible global function definition for 'J'
.makeICCDialog: no visible global function definition for 'J'
.makeICCDialog: no visible global function definition for '.jnull'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'J'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'toJava'
.makeNewLDADialog: no visible global function definition for 'J'
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for 'toJava'
.makeNewLDADialog: no visible global function definition for 'toJava'
.makeNewReliabilityDialog: no visible global function definition for
  'toJava'
.onLoad: no visible global function definition for '.jnull'
.onLoad: no visible global function definition for 'jgr.getMenuNames'
.onLoad: no visible global function definition for 'jgr.insertMenu'
.onLoad: no visible global function definition for 'jgr.addMenu'
.onLoad: no visible global function definition for 'jgr.addMenuItem'
'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.
.containedBy: no visible global function definition for
  'projectMercator'
.makeCensusDialog: no visible global function definition for 'J'
.makeCensusDialog: no visible global function definition for '.jnull'
.onLoad: no visible global function definition for '.jnull'
.onLoad: no visible global function definition for '.jpackage'
.onLoad: no visible global function definition for '.jengine'
.onLoad: no visible global function definition for 'J'
.subsetLines: no visible global function definition for
  'projectMercator'
.subsetPoints: no visible global function definition for
  'projectMercator'
.subsetPoly: no visible global function definition for
  'projectMercator'
spatialBubblePlot: no visible global function definition for
  'coordinates'
spatialChoropleth: no visible global function definition for
  'manual_pal'
spatialChoropleth: no visible global function definition for
  'gradient_n_pal'
spatialChoropleth: no visible global function definition for 'cscale'
spatialColoredPoints: no visible global function definition for
  'manual_pal'
spatialColoredPoints: no visible global function definition for
  'gradient_n_pal'
spatialColoredPoints: no visible global function definition for
  'cscale'
spatialTextPlot: no visible global function definition for
  'coordinates'
.CompareRunFunction: no visible global function definition for
  'execute'
.KMRunFunction: no visible global function definition for 'execute'
.onLoad: no visible binding for global variable '.deducer'
.onLoad: no visible global function definition for '.jnull'
.onLoad: no visible global function definition for '.jpackage'
.onLoad: no visible global function definition for '.registerDialog'
.onLoad: no visible global function definition for 'deducer.addMenu'
.onLoad: no visible global function definition for
  'deducer.addMenuItem'
.onLoad: no visible binding for global variable '.windowsGUI'
.onLoad: no visible binding for global variable '.jgr'
.onLoad: no visible global function definition for 'jgr.insertMenu'
.onLoad: no visible global function definition for 'jgr.addMenuItem'
makeCompareDialog: no visible binding for global variable
  'SimpleRDialog'
makeCompareDialog: no visible binding for global variable
  'VariableSelectorWidget'
makeCompareDialog: no visible global function definition for
  'addComponent'
makeCompareDialog: no visible binding for global variable
  'SingleVariableWidget'
makeCompareDialog: no visible binding for global variable
  'ButtonGroupWidget'
makeCompareDialog: no visible global function definition for 'toJava'
makeKMDialog: no visible binding for global variable 'SimpleRDialog'
makeKMDialog: no visible binding for global variable
  'VariableSelectorWidget'
makeKMDialog: no visible global function definition for 'addComponent'
makeKMDialog: no visible binding for global variable
  'SingleVariableWidget'
makeKMDialog: no visible binding for global variable 'TextAreaWidget'
makeKMDialog: no visible binding for global variable
  'ButtonGroupWidget'
makeKMDialog: no visible binding for global variable 'TextFieldWidget'
makeKMDialog: no visible global function definition for 'toJava'
.makeQuickWordcloud: no visible global function definition for 'J'
.makeQuickWordcloud: no visible global function definition for '.jnull'
.makeTextPlot: no visible global function definition for 'J'
.makeTextPlot: no visible global function definition for '.jnull'
.onLoad: no visible global function definition for '.jpackage'
.onLoad: no visible global function definition for '.jnew'
.onLoad: no visible global function definition for 'J'
bpstrip: no visible binding for global variable 'panel.polygon'
bpstrip: no visible binding for global variable 'panel.segments'
bpstrip: no visible global function definition for
  'current.panel.limits'
bpstrip: no visible global function definition for 'trellis.par.get'
cistrip: no visible binding for global variable 'panel.points'
cistrip: no visible binding for global variable 'panel.segments'
denstrip: no visible binding for global variable 'panel.rect'
denstrip: no visible binding for global variable 'panel.segments'
denstrip: no visible global function definition for
  'current.panel.limits'
denstrip: no visible global function definition for 'trellis.par.get'
denstrip.legend: no visible binding for global variable 'panel.polygon'
denstrip.legend: no visible binding for global variable
  'panel.segments'
denstrip.legend: no visible binding for global variable 'panel.text'
denstrip.legend: no visible global function definition for
  'current.panel.limits'
denstrip.legend: no visible global function definition for
  'trellis.last.object'
denstrip.legend: no visible global function definition for
  'trellis.par.get'
sectioned.density: no visible binding for global variable 'panel.rect'
sectioned.density: no visible global function definition for
  'current.panel.limits'
sectioned.density: no visible global function definition for
  'trellis.par.get'
vwstrip: no visible binding for global variable 'panel.polygon'
vwstrip: no visible binding for global variable 'panel.segments'
vwstrip: no visible global function definition for
  'current.panel.limits'
vwstrip: no visible global function definition for 'trellis.par.get'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/DEploid.Rcheck/00install.out' for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.7Mb
    help   1.3Mb
    libs   1.4Mb
Missing link or links in documentation object 'StrRep.Rd':
  'strrep'

See section 'Cross-references' in the 'Writing R Extensions' manual.
compute.p.values: no visible global function definition for 'ash2'
draw.single.detsel.graph: no visible global function definition for
  'ash2'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    bin   3.7Mb
    doc   1.7Mb
Namespace in Imports field not imported from: 'mgcv'
  All declared Imports should be used.
sectionview,function : .local: warning in sectionview.fun(fun = model,
  dim = dim, center = center, axis = axis, npoints = npoints, col =
  col, mfrow = mfrow, Xname = Xname, yname = yname, Xscale = Xscale,
  yscale = yscale, xlim = xlim, ylim = ylim, title = title, ...):
  partial argument match of 'col' to 'col_surf'
view,character-function : .local: warning in sectionview.fun(fun =
  model, dim = dim, center = center, axis = axis, npoints =
  ifelse(is.null(npoints), 100, npoints), col = col, mfrow = mfrow,
  Xname = Xname, yname = yname, Xscale = Xscale, yscale = yscale, xlim
  = xlim, ylim = ylim, title = title, ...): partial argument match of
  'col' to 'col_surf'
L2eV: no visible binding for global variable 'constants'
L2w: no visible binding for global variable 'constants'
eV2L: no visible binding for global variable 'constants'
t2eV: no visible binding for global variable 'constants'
diffpci: no visible global function definition for 'diffpropci.Wald.mp'
diffpci: no visible global function definition for 'diffpropci.mp'
diffpci: no visible global function definition for 'scoreci.mp'
wilson: no visible global function definition for 'uniroot.all'
wilson.cc: no visible global function definition for 'uniroot.all'
wilson.phi: no visible global function definition for 'uniroot.all'
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    5.1Mb
    libs   1.3Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    5.6Mb
    libs   1.3Mb
fAssocmatrix : fAssocmatrix1: no visible global function definition for
  'coordinates<-'
fAssocplot: no visible global function definition for 'coordinates'
fDrawfigure: no visible global function definition for
  'SpatialPolygons'
fDrawfigure: no visible global function definition for 'spsample'
fRanXY : <anonymous>: no visible global function definition for
  'spsample'
EdgelistFromIgraph: no visible global function definition for
  'get.adjacency'
EdgelistFromIgraph: no visible global function definition for 'V'
EdgelistFromIgraph: no visible global function definition for 'vcount'
IgraphFromEdgelist: no visible global function definition for
  'graph.adjacency'
IgraphFromEdgelist: no visible global function definition for 'V'
IgraphFromEdgelist: no visible global function definition for 'V<-'
MeasureNetworkInformation: no visible binding for global variable
  'betweenness'
MeasureNetworkInformation: no visible global function definition for
  'vcount'
MeasureNetworkInformation : SampleIgraph: no visible global function
  definition for 'ecount'
MeasureNetworkInformation : SampleIgraph: no visible global function
  definition for 'delete.edges'
MeasureNetworkInformation : SampleIgraph: no visible global function
  definition for 'E'
RelativeNetworkInformation: no visible binding for global variable
  'betweenness'
RssSuggestedNetwork: no visible global function definition for
  'get.adjacency'
RssSuggestedNetwork: no visible global function definition for
  'is.directed'
RssSuggestedNetwork: no visible global function definition for 'vcount'
RssSuggestedNetwork: no visible global function definition for
  'graph.adjacency'
RssSuggestedNetwork: no visible global function definition for
  'graph.density'
plot.discrimARTs: no visible global function definition for 'grid.text'
plot.discrimARTs: no visible global function definition for 'gpar'
GraphDistatisAll: no visible global function definition for
  'createColorVectorsByDesign'
GraphDistatisBoot: no visible global function definition for
  'createColorVectorsByDesign'
GraphDistatisBoot: no visible global function definition for
  'dataEllipse'
GraphDistatisBoot: no visible global function definition for
  'peeledHull'
GraphDistatisCompromise: no visible global function definition for
  'createColorVectorsByDesign'
GraphDistatisCompromise: no visible global function definition for
  'prettyPlot'
GraphDistatisPartial: no visible global function definition for
  'createColorVectorsByDesign'
GraphDistatisPartial: no visible global function definition for
  'prettyPlot'
GraphDistatisRv: no visible global function definition for
  'createColorVectorsByDesign'
GraphDistatisRv: no visible global function definition for 'prettyPlot'
momIntegrated: multiple local function definitions for 'ddist' with
  different formal arguments
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    include  18.9Mb
    libs      1.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   1.2Mb
hip: no visible global function definition for 'adiag'
.addEq: no visible global function definition for '.Eq'
.addSt: no visible global function definition for '.St'
plot.compExp: no visible global function definition for 'grid.newpage'
plot.compExp: no visible global function definition for 'pushViewport'
plot.compExp: no visible global function definition for 'viewport'
plot.compExp: no visible global function definition for 'grid.layout'
plot.compExp: no visible global function definition for 'bwplot'
plot.compExp : <anonymous>: no visible global function definition for
  'panel.grid'
plot.compExp : <anonymous>: no visible global function definition for
  'panel.bwplot'
plot.compExp: no visible global function definition for 'upViewport'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/DNAprofiles.Rcheck/00install.out' for details.
network.modules: no visible global function definition for
  'graph.empty'
network.modules: no visible global function definition for
  'add.vertices'
network.modules: no visible global function definition for 'add.edges'
network.modules: no visible global function definition for 'tkplot'
network.modules: no visible global function definition for 'V'
Namespaces in Imports field not imported from:
  'GOstats' 'caTools' 'fdrtool'
  All declared Imports should be used.
.randomize: no visible global function definition for '[.coded.data'
Found the following significant warnings:
  Warning: running command 'domino help' had status 127
See 'd:/Rcompile/CRANpkg/local/3.2/domino.Rcheck/00install.out' for details.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  2: domino.runCommand(loginCommand, domino.OK, "Login failed", theinput)
  3: domino.runCommandFromDefaultPath(commandAndArgs, successCallback, failureMessage, 
         stdInput)
  4: domino.handleCommandNotFound(failureMessage)
  5: stop(paste("Couldn't find domino client in the PATH or in default locations.\n  Add domino client directory path to PATH environment variable.\n  If you don't have domino client installed follow instructions on 'http://help.dominodatalab.com/client'.\n  If you use R-Studio Domino on GNU/Linux through a desktop launcher, add domino path to the .desktop file.\n\n  If you need more help, email support@dominodatalab.com or visit http://help.dominodatalab.com/troubleshooting\n\n  - ", 
         failureMessage), call. = FALSE)
  
  testthat results ================================================================
  OK: 1 SKIPPED: 0 FAILED: 1
  1. Error: The login command works (@test-login.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Running the tests in 'tests/doRUnit.R' failed.
Last 13 lines of output:
  
  
  Executing test function test.registerDoRNG  ...  done successfully.
  
  ------------------- UNIT TEST SUMMARY ---------------------
  
  Error in .local(x, ...) : Functions: 2 | Errors: 1 | Failures: 0 
  ERROR in runit.dorng.R::test.dorng: Error in mpi.comm.spawn(slave = rscript, slavearg = args, nslaves = count,  : 
    Other MPI error, error stack:
  MPI_Comm_spawn(cmd="D:/RCompile/recent/R-32~1.5/bin/Rscript", argv=0x000000000A669B90, maxprocs=2, MPI_INFO_NULL, root=0, MPI_COMM_SELF, intercomm=0x00000000069A42F8, errors=0x0000000009FD9500) failed
  Function not implemented
  Calls: <Anonymous> -> <Anonymous> -> .local -> utest -> utest -> .local
  Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
dpmixsim: no visible global function definition for 'clara'
postkcluster: no visible global function definition for 'clara'
readsliceimg: no visible global function definition for 'readNIfTI'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/dpmr.Rcheck/00install.out' for details.
depratio: warning in match.call(expand = FALSE): partial argument match
  of 'expand' to 'expand.dots'
drm: warning in match.call(expand = FALSE): partial argument match of
  'expand' to 'expand.dots'
Namespace in Imports field not imported from: 'shapefiles'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/dSVA.Rcheck/00install.out' for details.
perturbFBM: warning in circFBM(n, H, plot = FALSE): partial argument
  match of 'plot' to 'plotfBm'
filt: no visible global function definition for 'wavDaubechies'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/dynamichazard.Rcheck/00install.out' for details.
bootstrapCI: no visible global function definition for 'lpepa'
dynamicCorrelation: no visible global function definition for 'lpepa'
PredictPropen,modelObjFit-data.frame : .local: no visible global
  function definition for 'level'
PlotPotential: no visible global function definition for 'aes'
PlotPotential: no visible global function definition for 'geom_tile'
PlotPotential: no visible global function definition for
  'scale_fill_gradient'
PlotPotential: no visible global function definition for 'stat_contour'
PlotPotential: no visible global function definition for 'xlab'
PlotPotential: no visible global function definition for 'ylab'
PlotPotential: no visible global function definition for 'labs'
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.
.file_attachment: no visible global function definition for
  'base64encode'
easyHtmlReport: no visible global function definition for 'knit'
easyHtmlReport: no visible global function definition for
  'markdownToHTML'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/EasyMARK.Rcheck/00install.out' for details.
decdfHT: possible error in findInterval(x[i], ecdfHT.fit$xsort,
  rightmost.closed = TRUE, all.inside = TRUE, left.open = FALSE):
  unused argument (left.open = FALSE)
Running examples in 'ecdfHT-Ex.R' failed
The error most likely occurred in:

> ### Name: pecdfHT
> ### Title: Compute cdf, pdf, quantiles, and simulate from a fitted
> ###   distribution
> ### Aliases: decdfHT pecdfHT qecdfHT recdfHT
> 
> ### ** Examples
> 
> x <- rcauchy(1000)
> a <- ecdfHT( x, show.plot=FALSE )
> fit <- ecdfHT.fit( c(.1,.9), a, add.to.plot=FALSE )
> pecdfHT( -3:3, fit )
[1] 0.08621799 0.12705058 0.23166862 0.47955015 0.72400844 0.82998740 0.87927967
> decdfHT( -3:3, fit )
Error in findInterval(x[i], ecdfHT.fit$xsort, rightmost.closed = TRUE,  : 
  unused argument (left.open = FALSE)
Calls: decdfHT -> findInterval
Execution halted
Package required and available but unsuitable version: 'RSQLite'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
ecipex: no visible binding for global variable 'nistiso'
Namespace in Imports field not imported from: 'magrittr'
  All declared Imports should be used.
.echCusum1: no visible global function definition for 'xcusum.arl'
.echCusum2: no visible global function definition for 'xcusum.arl'
.echEwma1: no visible global function definition for 'xewma.arl'
.echEwma2: no visible global function definition for 'xewma.arl'
echCusum: no visible global function definition for 'xcusum.arl'
echEwma: no visible global function definition for 'xewma.arl'
ecoCusum: no visible global function definition for 'xcusum.arl'
ecoEwma: no visible global function definition for 'xewma.arl'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/eggCounts.Rcheck/00install.out' for details.
prepare_Rd: index.egonet.Rd:29-31: Dropping empty section \details
prepare_Rd: index.egonet.Rd:32-38: Dropping empty section \value
prepare_Rd: index.egonet.Rd:45-47: Dropping empty section \note
prepare_Rd: index.egonet.Rd:39-41: Dropping empty section \references
prepare_Rd: index.egonet.Rd:51-53: Dropping empty section \seealso
prepare_Rd: read.egonet.Rd:27-29: Dropping empty section \note
Y_impute: no visible binding for global variable 'pp_zq'
Y_impute: no visible binding for global variable 'Ranks'
Y_impute: no visible binding for global variable 'Z'
eigenmodel_setup: no visible binding for global variable 'Y'
rUL_fc: no visible binding for global variable 'Z'
rUL_fc: no visible binding for global variable 'X'
rUL_fc: no visible binding for global variable 'b'
rUL_fc: no visible binding for global variable 'UL'
rUL_fc: no visible binding for global variable 'R'
rUL_fc: no visible binding for '<<-' assignment to 'mean_u'
rUL_fc: no visible binding for global variable 'var_u'
rUL_fc: no visible binding for global variable 'pp_mu'
rUL_fc: no visible binding for global variable 'pm_mu'
rUL_fc: no visible binding for global variable 'n'
rUL_fc: no visible binding for global variable 'mean_u'
rUL_fc: no visible binding for global variable 'pp_l'
rZ_fc: no visible binding for global variable 'X'
rZ_fc: no visible binding for global variable 'b'
rZ_fc: no visible binding for global variable 'UL'
rZ_fc: no visible binding for global variable 'pp_zq'
rZ_fc: no visible binding for global variable 'Ranks'
rZ_fc: no visible binding for global variable 'uRanks'
rZ_fc: no visible binding for global variable 'n'
rb_fc: no visible binding for global variable 'Z'
rb_fc: no visible binding for global variable 'UL'
rb_fc: no visible binding for global variable 'pm_b'
rb_fc: no visible binding for global variable 'xtx'
rb_fc: no visible binding for global variable 'pp_b'
rb_fc: no visible binding for global variable 'tx'
cluster.segment: no visible global function definition for 'knn'
quantreg.est: no visible global function definition for 'rq.fit.fnb'
ei.MD.bayes: warning in BayesMDei2(formula, data, total = total,
  lambda1 = lambda1, lambda2 = lambda2, tune.alpha = tune.alpha,
  tune.beta = tune.beta, start.alpha = start.alphas, start.betas =
  start.betas, sample = sample, thin = thin, burnin = burnin, verbose =
  verbose, ret.beta = ret.beta, ret.mcmc = ret.mcmc, usrfun = usrfun):
  partial argument match of 'start.alpha' to 'start.alphas'
tuneMD: warning in ei.MD.bayes(formula, covariate = covariate, data =
  data, sample = sample, thin = thin, burnin = burnin, tune = tl, ...):
  partial argument match of 'tune' to 'tune.list'
bayes.regress : truncMVRnorm: no visible global function definition for
  'mvrnorm'
bayes.regress: no visible binding for global variable 'mvrnorm'
cover.plot: no visible global function definition for 'is.mcmc'
density.plot.lambdaMD: no visible global function definition for
  'is.mcmc'
density.plot.lambdaRegBayes: no visible global function definition for
  'is.mcmc'
lambda.MD: no visible global function definition for 'is.mcmc'
lambda.MD: no visible global function definition for 'mcpar'
mergeMD: no visible global function definition for 'mcmc'
print.eiMD: no visible global function definition for 'is.mcmc'
read.betas: no visible global function definition for 'as.mcmc'
summary.eiMD: no visible global function definition for 'is.mcmc'
summary.lambdaRegBayes: no visible global function definition for
  'is.mcmc'
BaB: no visible binding for global variable 'calc.pairwise.e_p'
BaB: no visible global function definition for 'weight.function'
BaB: no visible global function definition for 'compute.stark.t'
LKPBound: no visible binding for global variable 'calc.pairwise.e_p'
LKPBound: no visible global function definition for 'weight.function'
LKPBound: no visible global function definition for 'compute.stark.t'
eqValBound: no visible binding for global variable 'calc.pairwise.e_p'
eqValBound: no visible global function definition for 'weight.function'
eqValBound: no visible global function definition for 'compute.stark.t'
getEbsMargin: no visible global function definition for 'is.elec.data'
getEbsMargin: no visible global function definition for
  'maximumMarginBound'
makeStratObj: no visible global function definition for 'is.elec.data'
makeStratObj: no visible global function definition for
  'maximumMarginBound'
strat.elec.data: no visible global function definition for 'elec.data'
takeOutZeroMMB: no visible global function definition for
  'maximumMarginBound'
withReplaceBound: no visible binding for global variable
  'calc.pairwise.e_p'
withReplaceBound: no visible global function definition for
  'weight.function'
withReplaceBound: no visible global function definition for
  'compute.stark.t'
Namespaces in Imports field not imported from:
  'prettyunits' 'ratelimitr' 'rgdal'
  All declared Imports should be used.
Likelihood: no visible global function definition for
  'makePSOCKcluster'
Likelihood: no visible global function definition for 'clusterExport'
Likelihood: no visible global function definition for 'makeForkCluster'
Likelihood.first.run: no visible global function definition for
  'clusterApply'
Likelihood.next.runs: no visible global function definition for
  'clusterApply'
es.stopCluster: no visible global function definition for 'stopCluster'
################################################################################

Easy Microarray Analysis

EMA stable version

Current release : v1.4.4 - march 2014

################################################################################

All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
################################################################################

Easy Microarray Analysis

EMA stable version

Current release : v1.4.4 - march 2014

################################################################################

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Found the following significant warnings:
  Warning: S3 methods 'hist.Nests', 'hist.NestsResult', 'logLik.NestsResult', 'logLik.tsd', 'nobs.NestsResult', 'plot.NestsResult', 'plot.tsd', 'predict.tsd', 'summary.Nests' were declared in NAMESPACE but not found
  Warning: namespace 'embryogrowth' is not available and has been replaced
See 'd:/Rcompile/CRANpkg/local/3.2/embryogrowth.Rcheck/00install.out' for details.
File 'EMC/R/zzz.R':
  .onLoad calls:
    packageStartupMessage("##\n", "## Evolutionary Monte Carlo Package (EMC)\n",     "##\n", "## Functionality: random walk Metropolis, general Metropolis-Hastings\n",     "## parallel tempering, target oriented EMC (TOEMC), temperature ladder\n",     "## construction and placement\n", "##\n", "## Use: \"help(package = EMC)\" at the R prompt for more info\n",     "##\n", "## Copyright (C) 2006-", this.year, " Gopi Goswami\n",     "##\n", "##    Created by: Gopi Goswami <goswami@stat.harvard.edu>\n",     "## Maintained by: Gopi Goswami <grgoswami@gmail.com>\n",     "##\n")

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

CigarShapedFuncGenerator1 : logTarDensFunc: no visible global function
  definition for 'dmvnorm'
CigarShapedFuncGenerator2 : logTarDensFunc: no visible global function
  definition for 'dmvnorm'
VShapedFuncGenerator : logTarDensFunc : <anonymous>: no visible global
  function definition for 'dmvnorm'
WShapedFuncGenerator : logTarDensFunc : <anonymous>: no visible global
  function definition for 'dmvnorm'
threeDimNormalFuncGenerator : logTarDensFunc: no visible global
  function definition for 'dmvnorm'
threeDimNormalFuncGenerator : propNewFunc: no visible global function
  definition for 'mvrnorm'
twentyModeFuncGenerator : logTarDensFunc : <anonymous>: no visible
  global function definition for 'dmvnorm'
uniModeFuncGenerator : logTarDensFunc: no visible global function
  definition for 'dmvnorm'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.3Mb
'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.
distance: no visible global function definition for
  'data.Normalization'
estimateModel: no visible global function definition for 'earth'
estimateModel: no visible global function definition for 'plotmo'
MFFetch: no visible global function definition for 'melt'
drawScene.rgl: no visible global function definition for 'rgl.cur'
drawScene.rgl: no visible global function definition for 'open3d'
drawScene.rgl: no visible global function definition for 'clear3d'
drawScene.rgl: no visible global function definition for 'triangles3d'
fmmst.contour.3d: no visible global function definition for 'plot3d'
fmmst.contour.3d: no visible global function definition for 'points3d'
Error in re-building vignettes:
  ...
Quitting from lines 119-144 (emojifont.Rmd) 
Error: processing vignette 'emojifont.Rmd' failed with diagnostics:
StatTreeHorizontal was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
ENMCA : fn: no visible global function definition for 'assignCluster'
ENMCA : fn: no visible global function definition for 'catdes'
ENMCA : fn: no visible global function definition for 'plot.MCA'
ENdensity: no visible global function definition for 'kde2d'
ENlisib: no visible global function definition for 'plot.MCA'
MCA2: no visible global function definition for 'tab.disjonctif'
MCA2: no visible global function definition for 'PCA'
MCA2: no visible global function definition for 'CA'
MCA2: no visible global function definition for 'plot.MCA'
XvsYbarplot: possible error in hsv(h = 1, s = 1, v = 1, 1, 1): unused
  argument (1)
XvsYbarplot: possible error in hsv(h = 1, s = 0.4 + (height[i]/max) *
  0.6, v = 1, 1, 1): unused argument (1)
XvsYbarplot: possible error in hsv(h = a * i, s = 1, v = 1, 1, 1):
  unused argument (1)
barplot_function: possible error in hsv(h = a * m, s = 1, v = 1, 1, 1):
  unused argument (1)
barplot_function: possible error in hsv(h = a * m, s = 0.4 +
  (cont[j]/max) * 0.6, v = 1, 1, 1): unused argument (1)
barplot_sweave : set.X: no visible binding for global variable 'X'
chisq.function: no visible global function definition for 'coltable'
col.barplot: possible error in hsv(h = 1, s = 1, v = 1, 1, 1): unused
  argument (1)
col.barplot: possible error in hsv(h = 1, s = 0.4 + (height[i]/max) *
  0.6, v = 1, 1, 1): unused argument (1)
col.barplot: possible error in hsv(h = a * i, s = 1, v = 1, 1, 1):
  unused argument (1)
p_inertia: no visible global function definition for 'MCA'
tab_chi2: no visible global function definition for 'coltable'
KM.plot.ade : plot.box.ade: no visible global function definition for
  'axis.break'
KM.plot.ade: no visible global function definition for 'survfit'
KM.plot.ade: no visible global function definition for 'survdiff'
a.form.ade: no visible global function definition for 'cylindrect'
a.form.ade : sub.ellipse.ade : gradient.rect.ade: no visible global
  function definition for 'color.gradient'
box.plot.ade : a.draw.box: no visible global function definition for
  'cylindrect'
box.plot.wtd : wtd.sd: no visible global function definition for
  'wtd.var'
box.plot.wtd : a.draw.box: no visible global function definition for
  'wtd.mean'
box.plot.wtd : a.draw.box: no visible global function definition for
  'wtd.quantile'
box.plot.wtd : a.draw.box: no visible global function definition for
  'cylindrect'
histogram.ade: no visible global function definition for
  'weighted.hist'
pr2 : fa22: no visible global function definition for 'Anova'
eqs2lavaan: no visible binding for global variable 'r'
Namespace in Imports field not imported from: 'signal'
  All declared Imports should be used.
topoplot: no visible global function definition for 'interp'
esgplotshocks: no visible global function definition for 'geom_point'
esgplotshocks: no visible global function definition for 'aes'
esgplotshocks: no visible global function definition for 'theme'
esgplotshocks: no visible global function definition for
  'element_blank'
esgplotshocks: no visible global function definition for
  'scale_color_manual'
esgplotshocks: no visible global function definition for 'geom_density'
esgplotshocks: no visible global function definition for
  'scale_fill_manual'
esgplotshocks: no visible global function definition for 'coord_flip'
esgplotts: no visible global function definition for 'xlab'
esgplotts: no visible global function definition for 'ylab'
esgplotts: no visible global function definition for 'theme'
iqr_cell: no visible global function definition for 'wtd.quantile'
mean_sd_cell: no visible global function definition for 'wtd.mean'
mean_sd_cell: no visible global function definition for 'wtd.var'
mode_cell: no visible global function definition for 'wtd.table'
quantile_cell: no visible global function definition for 'wtd.quantile'
stat_cell: no visible global function definition for 'wtd.quantile'
stat_cell: no visible global function definition for 'wtd.mean'
stat_cell: no visible global function definition for 'wtd.var'
stat_cell: no visible global function definition for 'wtd.table'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
             download.file(url, ...)
         }
     })(dots[[1L]][[2L]], dots[[2L]][[2L]])
  9: suppressWarnings(download.file(url, method = method, ...))
  10: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  11: download.file(url, method = method, ...)
  
  testthat results ================================================================
  OK: 22 SKIPPED: 0 FAILED: 1
  1. Error: smart_download works (@test-etl.R#103) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: 'EnvStats'
  All declared Imports should be used.
read_eventdata : read_ed_file: warning in read.csv(d, sep = sep, head =
  head, strip.white = TRUE, colClasses = "character"): partial argument
  match of 'head' to 'header'
ees: no visible global function definition for 'zoo'
eesPlot: no visible global function definition for 'index'
gen.data: no visible global function definition for 'index'
gen.data: no visible global function definition for 'coredata'
get.clusters.formatted: no visible global function definition for 'xts'
get.clusters.formatted: no visible global function definition for 'zoo'
inference.Ecar: no visible global function definition for 'boot'
inference.change.boot: no visible global function definition for 'boot'
inference.change.boot: no visible global function definition for
  'boot.ci'
phys2eventtime : timeshift: no visible global function definition for
  'index'
phys2eventtime : timeshift: no visible global function definition for
  'zoo'
phys2eventtime: no visible global function definition for 'zoo'
phys2eventtime: no visible global function definition for 'na.locf'
sumstat: no visible global function definition for 'xts'
yearly.exevent.summary: no visible global function definition for
  'apply.yearly'
yearly.exevent.summary: no visible global function definition for 'xts'
yearly.exevent.summary: no visible global function definition for
  'index<-'
yearly.exevent.summary: no visible global function definition for
  'as.yearmon'
yearly.exevent.summary: no visible global function definition for
  'index'
Package required but not available: 'filesstrings'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'polynom'
  All declared Imports should be used.
expectreg.boost: no visible global function definition for 'mclapply'
expectreg.boost: no visible global function definition for
  'detectCores'
laws: no visible global function definition for 'mclapply'
laws: no visible global function definition for 'detectCores'
quant.boost: no visible global function definition for 'mclapply'
quant.boost: no visible global function definition for 'detectCores'
rb: no visible global function definition for 'cover.design'
ATEbounds: no visible global function definition for 'boot'
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'
computeConstraints: no visible global function definition for
  'minmaxHelper'
coreCA: no visible global function definition for 'repmat'
coreMDS: no visible global function definition for 'repmat'
corePCA: no visible global function definition for 'repmat'
epGraphs: no visible global function definition for
  'createColorVectorsByDesign'
epGraphs: no visible global function definition for 'prettyPlot'
epGraphs: no visible global function definition for 'contributionBars'
makeNominalData: no visible global function definition for 'repmat'
mca.eigen.fix: no visible global function definition for 'repmat'
pcaSupplementaryColsPreProcessing: no visible global function
  definition for 'repmat'
pcaSupplementaryRowsPreProcessing: no visible global function
  definition for 'repmat'
rowNorms: no visible global function definition for 'repmat'
supplementalProjection: no visible global function definition for
  'repmat'
node.age: no visible global function definition for 'is.binary.tree'
node.age: no visible global function definition for 'multi2di'
DirichletPolygons,SpatialPointsBreeding-missing: no visible global
  function definition for 'ripras'
Namespace in Imports field not imported from: 'affy'
  All declared Imports should be used.
extfunnel: no visible global function definition for 'meta.summaries'
misc : q: no visible global function definition for 'name'
Namespace in Imports field not imported from: 'FactoMineR'
  All declared Imports should be used.
bayesQR : captureFormula: warning in match.call(expand = FALSE):
  partial argument match of 'expand' to 'expand.dots'
bayesQR: warning in matrix(beta, nc = 1): partial argument match of
  'nc' to 'ncol'
factorQR : captureFormula: warning in match.call(expand = FALSE):
  partial argument match of 'expand' to 'expand.dots'
factorQR: warning in matrix(rnorm(nObs * nFact), nr = nObs): partial
  argument match of 'nr' to 'nrow'
factorQR: warning in matrix(0, nr = nFact + xBetLen + numManInd, nc =
  nFact + xBetLen + numManInd): partial argument match of 'nr' to
  'nrow'
factorQR: warning in matrix(0, nr = nFact + xBetLen + numManInd, nc =
  nFact + xBetLen + numManInd): partial argument match of 'nc' to
  'ncol'
factorQR: warning in matrix(0, nr = nFact + xBetLen + 1, nc = nFact +
  xBetLen + 1): partial argument match of 'nr' to 'nrow'
factorQR: warning in matrix(0, nr = nFact + xBetLen + 1, nc = nFact +
  xBetLen + 1): partial argument match of 'nc' to 'ncol'
factorQR: warning in matrix(0, nr = xLength, nc = nFact): partial
  argument match of 'nr' to 'nrow'
factorQR: warning in matrix(0, nr = xLength, nc = nFact): partial
  argument match of 'nc' to 'ncol'
makeData: warning in matrix(0, nr = xLength, nc = nFact): partial
  argument match of 'nr' to 'nrow'
makeData: warning in matrix(0, nr = xLength, nc = nFact): partial
  argument match of 'nc' to 'ncol'
makeData: warning in matrix(rnorm(N * nFact), nc = nFact): partial
  argument match of 'nc' to 'ncol'
makeData: warning in matrix(rnorm(N * xLength), nc = xLength): partial
  argument match of 'nc' to 'ncol'
plot.bayesQR: warning in matrix(sampledVals, nc = 1): partial argument
  match of 'nc' to 'ncol'
plot.factorQR: warning in matrix(sampledVals, nc = 1): partial argument
  match of 'nc' to 'ncol'
factualGetSchema: no visible global function definition for 'fromJSON'
factualRead: no visible global function definition for 'curlEscape'
factualRead: no visible global function definition for 'fromJSON'
as.FAMTdata: no visible global function definition for 'impute.knn'
nbfactors : bivprob : <anonymous>: no visible global function
  definition for 'biv.nt.prob'
File 'fANCOVA/R/onload.R':
  .onLoad calls:
    packageStartupMessage("fANCOVA 0.5-1 loaded")

See section 'Good practice' in '?.onAttach'.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  > library("testthat")
  > library("FastImputation")
  > 
  > test_check("FastImputation")
  Error in `[<-.data.frame`(`*tmp*`, i_row, cols_to_impute, value = <S4 object of class "dgeMatrix">) : 
    incompatible types (from S4 to double) in subassignment type fix
  Calls: test_check ... eval -> eval -> FastImputation -> [<- -> [<-.data.frame
  In addition: Warning message:
  In FUN(X[[i]], ...) : More than one constraint specified for variable 1
  testthat results ================================================================
  OK: 32 SKIPPED: 0 FAILED: 0
  Execution halted
.run: no visible binding for global variable 'init'
.run: no visible global function definition for 'init'
.run: no visible binding for global variable 'run'
Namespace in Imports field not imported from: 'whisker'
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.5Mb
fcd.start: no visible global function definition for 'ginv'
fcd.start: no visible global function definition for 'glmnet'
mis.cluster: no visible global function definition for 'permn'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/fcros.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/fdasrvf.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/feather.Rcheck/00install.out' for details.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'base' 'graphics' 'stats'
A package should be listed in only one of these fields.
Namespace in Imports field not imported from: 'base'
  All declared Imports should be used.
Conditional.MonteCarlo.ExpressCertificate.Classic: no visible global
  function definition for 'rnorm.halton'
Conditional.MonteCarlo.ExpressCertificate.Classic: no visible global
  function definition for 'rnorm.sobol'
EasyExpressCertificate: no visible global function definition for
  'CashOrNothingOption'
EasyExpressCertificate: no visible global function definition for
  'GBSOption'
ExpressCertificate: no visible global function definition for
  'GBSOption'
FFieldPtRepDemo: no visible global function definition for 'ggplot'
FFieldPtRepDemo: no visible global function definition for 'aes'
FFieldPtRepDemo: no visible binding for global variable 'mpg'
FFieldPtRepDemo: no visible global function definition for 'geom_point'
FFieldPtRepDemo: no visible global function definition for 'geom_text'
FFieldPtRepDemo: no visible global function definition for 'ggtitle'
FFieldPtRepDemo: no visible global function definition for
  'geom_segment'
FFieldPtRepDemo: no visible global function definition for
  'grid.arrange'
Namespace in Imports field not imported from: 'MASS'
  All declared Imports should be used.
garchFit: no visible binding for global variable 'dem2gbp'
fitted,fGARCH : .local: no visible binding for global variable 'fit'
dmymvnorm: no visible global function definition for 'dmvnorm'
dmymvt: no visible global function definition for 'dmvt'
gof.test : ecdf: no visible global function definition for 'mecdf'
gof.test: no visible global function definition for 'jacobian'
gradCdfT: no visible global function definition for 'pmvt'
influFun: no visible global function definition for 'jacobian'
plackettFormula: no visible global function definition for 'pmvt'
pmymvnorm: no visible global function definition for 'GenzBretz'
pmymvnorm: no visible global function definition for 'TVPACK'
pmymvnorm : <anonymous>: no visible global function definition for
  'pmvnorm'
pmymvt: no visible global function definition for 'GenzBretz'
pmymvt: no visible global function definition for 'TVPACK'
pmymvt : <anonymous>: no visible global function definition for 'pmvt'
rmymvnorm: no visible global function definition for 'rmvnorm'
rmymvt: no visible global function definition for 'rmvt'
Running examples in 'fheatmap-Ex.R' failed
The error most likely occurred in:

> ### Name:  Column Annotations 
> ### Title: Annotations of columns in "fheatmap_data"
> ### Aliases: ' annotation_col '
> ### Keywords: annotation_col
> 
> ### ** Examples
> 
> data(annotation_col)
> fheatmap(fheatmap_data,annotation_col=annotation_col)
Error in theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),  : 
  formal argument "plot.margin" matched by multiple actual arguments
Calls: fheatmap -> draw_tree -> theme_blank -> theme
Execution halted
createSQLite: no visible global function definition for 'dbDriver'
createSQLite: no visible global function definition for 'dbConnect'
createSQLite: no visible global function definition for
  'dbUnloadDriver'
createSQLite: no visible global function definition for 'dbGetQuery'
initializeSQLite: no visible global function definition for 'dbDriver'
initializeSQLite: no visible global function definition for 'dbConnect'
dbDelete,filehashSQLite-character: no visible global function
  definition for 'dbGetQuery'
dbDisconnect,filehashSQLite: no visible global function definition for
  'dbUnloadDriver'
dbFetch,filehashSQLite-character: no visible global function definition
  for 'dbGetQuery'
dbInsert,filehashSQLite-character: no visible global function
  definition for 'dbGetQuery'
dbList,filehashSQLite: no visible global function definition for
  'dbGetQuery'
dbMultiFetch,filehashSQLite-character: no visible global function
  definition for 'dbGetQuery'
Error in re-building vignettes:
  ...
Loading required package: RSQLite
Error: processing vignette 'Best_Prectices.Rmd' failed with diagnostics:
unused arguments (self_contained, lib_dir, output_dir)
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/filesstrings.Rcheck/00install.out' for details.
FinTS.stats: no visible global function definition for 'skewness'
FinTS.stats: no visible global function definition for 'kurtosis'
Unitroot: no visible global function definition for 'adfTest'
Unitroot: no visible global function definition for 'unitrootTest'
plotArmaTrueacf: no visible global function definition for 'polynomial'
summary.fHTEST: no visible global function definition for 'padf'
fem.estep: no visible global function definition for 'ginv'
fem.loglik: no visible global function definition for 'ginv'
fstep.GramSc: no visible global function definition for 'ginv'
fstep.fisher: no visible global function definition for 'ginv'
fstep.qiao: no visible global function definition for 'ginv'
fstep.sparse: no visible global function definition for 'ginv'
fstep.sparse: no visible global function definition for 'enet'
fstep.sparse: no visible global function definition for 'predict.enet'
FitARMA: no visible global function definition for 'PacfDL'
FitARMA: no visible global function definition for 'GetARMeanMLE'
FitARMA: no visible global function definition for
  'BackcastResidualsAR'
FitARMA: no visible global function definition for 'LjungBoxTest'
GetFitARMA: no visible global function definition for 'LoglikelihoodAR'
GetFitARMA: no visible global function definition for 'ChampernowneD'
GetFitARMA : EntropyARMA: no visible global function definition for
  'PacfToAR'
GetFitARMA : EntropyARMA: no visible global function definition for
  'PacfDL'
GetFitARMA : EntropyARMA: no visible global function definition for
  'FastLoglikelihoodAR'
GetFitARMA: no visible global function definition for 'PacfToAR'
InformationMatrixARMA: no visible global function definition for
  'InvertibleQ'
TacvfARMA: no visible global function definition for 'InvertibleQ'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/FIT.Rcheck/00install.out' for details.
saveMarkerModels: no visible global function definition for
  'registerDoMC'
saveMarkerModels: no visible global function definition for '%dopar%'
saveMarkerModels: no visible global function definition for 'foreach'
start.plot: no visible global function definition for 'emf'
getDifferentCluster: no visible global function definition for
  'solve_LSAP'
plot,FLXboot-missing : .local: no visible global function definition
  for 'rmvnorm'
plot,flexmix-missing : .local: no visible binding for global variable
  'cluster'
Namespace in Imports field not imported from: 'rgdal'
  All declared Imports should be used.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
     estimating kappas
     estimating mean dists
     estimating probs of migration
     estimating median dists
     creating output DONE!
  DONE!
  bird likely did not move, exiting without result
  testthat results ================================================================
  OK: 29 SKIPPED: 0 FAILED: 1
  1. Error: map_flightr_ggmap_works (@test_data_result_summary_and_plotting.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
flip.adjust : <anonymous>: no visible global function definition for
  'adjusted'
mf.flux: no visible global function definition for 'runsd'
Namespaces in Imports field not imported from:
  'stats' 'utils'
  All declared Imports should be used.
fmt.default: no visible global function definition for 'loessFit'
fmt.default: no visible global function definition for
  'trigammaInverse'
analyse.list: no visible binding for '<<-' assignment to 'files'
analyse.list: no visible binding for global variable 'files'
analyse.list: no visible binding for '<<-' assignment to 'foodweb'
analyse.list: no visible binding for '<<-' assignment to 'name'
analyse.list: no visible binding for global variable 'foodweb'
analyse.list: no visible binding for global variable 'name'
analyse.list: no visible binding for global variable 'indices'
analyse.seq: no visible binding for global variable 'indices'
analyse.single: no visible binding for global variable 'foodweb'
analyse.single: no visible binding for '<<-' assignment to 'foodweb'
analyse.single: no visible binding for '<<-' assignment to 'name'
analyse.single: no visible binding for global variable 'name'
analyse.single: no visible binding for global variable 'indices'
analyse.single: no visible binding for global variable 'levels.l'
analyse.single: no visible binding for global variable 'S'
analyse.single: no visible binding for global variable 'omn.l'
calculate.metrics: no visible binding for '<<-' assignment to 'S'
calculate.metrics: no visible binding for global variable 'S'
calculate.metrics: no visible binding for '<<-' assignment to 'indices'
calculate.metrics: no visible binding for global variable 'indices'
plotweb: no visible binding for global variable 'foodweb'
plotweb: no visible binding for global variable 'S'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Cross validating the tbats model
  Fitting the auto.arima model
  Fitting the nnetar model
  Fitting the stlm model
  Fitting the tbats model
  Fitting the ets model
  Fitting the thetam model
  testthat results ================================================================
  OK: 110 SKIPPED: 0 FAILED: 1
  1. Failure: Testing is.hybridModel(), fitted.hybridModel(), residuals.hybridModel(), and accuracy.hybridModel() (@test-hybridModel.R#73) 
  
  Error: testthat unit tests failed
  Execution halted
INFCvpe: no visible binding for global variable 'INFCstats'
INFCvpe: no visible binding for global variable 'INFCdomain'
fwdglm: warning in glm.fit(x = x[bsb, ], y = y[bsb], w = weights[bsb],
  offset = obsb, family = family, control = glm.control(epsilon =
  epsilon, maxit = maxit)): partial argument match of 'w' to 'weights'
lmsglm : subset.median: warning in glm.fit(x[bsb, ], ybsb, family =
  family, w = weights[bsb], offset = obsb, control =
  glm.control(epsilon = epsilon, maxit = maxit)): partial argument
  match of 'w' to 'weights'
lmsglm: warning in glm.fit(x[bsb, ], y[bsb], family = family, w =
  weights[bsb], offset = obsb, control = glm.control(epsilon = epsilon,
  maxit = maxit)): partial argument match of 'w' to 'weights'
WaveVarFD: no visible global function definition for 'modwt'
do.fd.estimate: no visible global function definition for
  'performParallel'
fd.Genton: no visible global function definition for 'qn'
fd.estimate.matrix: no visible global function definition for
  'performParallel'
fractal.random: no visible global function definition for 'flog.debug'
fractal.random: no visible global function definition for 'xts'
fractal.uniform: no visible global function definition for 'flog.debug'
fractal.uniform: no visible global function definition for 'xts'
getPortfolioPrices: no visible binding for global variable
  'holidayNYSE'
getPortfolioPrices: no visible binding for global variable
  'sampleInitiators'
getPortfolioPrices: no visible global function definition for
  'anylength'
getPortfolioPrices: no visible binding for global variable
  'sampleGenerators'
getPortfolioPrices: no visible global function definition for 'index<-'
getPortfolioPrices: no visible global function definition for
  'anynames<-'
getTradingDates: no visible binding for global variable 'holidayNYSE'
getTradingDates: no visible global function definition for
  'timeSequence'
getTradingDates: no visible global function definition for 'isBizday'
getTradingDates: no visible global function definition for 'anylength'
next.seeds: no visible global function definition for 'flog.debug'
ou.process: no visible global function definition for 'xts'
plotReturns: no visible global function definition for 'Delt'
em_fit: possible error in findInterval(Y[, 2], tev, left.open = FALSE,
  rightmost.closed = FALSE): unused argument (left.open = FALSE)
emfrail: possible error in findInterval(time, etime, left.open = TRUE):
  unused argument (left.open = TRUE)
Running examples in 'frailtyEM-Ex.R' failed
The error most likely occurred in:

> ### Name: emfrail
> ### Title: Fitting shared frailty models with the EM algorithm
> ### Aliases: emfrail
> 
> ### ** Examples
> 
> dat <- survival::rats
> 
> 
> m1 <- emfrail(.data =  dat,
+               .formula = Surv(time, status) ~  rx + sex + cluster(litter))
Error in findInterval(time, etime, left.open = TRUE) : 
  unused argument (left.open = TRUE)
Calls: emfrail -> findInterval
Execution halted
Errors in running code in vignettes:
when running code in 'frailtyEM_manual.Rnw'
  ...
Loading required package: survival

> bladder2$rx <- as.factor(bladder2$rx)

> m1 <- emfrail(.data = bladder2, .formula = Surv(start, 
+     stop, event) ~ rx + number + size + cluster(id))

  When sourcing 'frailtyEM_manual.R':
Error: unused argument (left.open = TRUE)
Execution halted
Error in re-building vignettes:
  ...
Loading required package: survival

Error: processing vignette 'frailtyEM_manual.Rnw' failed with diagnostics:
 chunk 3 (label = bladder2) 
Error in findInterval(time, etime, left.open = TRUE) : 
  unused argument (left.open = TRUE)
Execution halted
expandSlash : <anonymous>: no visible global function definition for
  'makeInteraction'
predict.FRBmultireg: no visible global function definition for
  'predict.mlm'
frcc: no visible global function definition for 'cor.shrink'
frcc: no visible global function definition for 'p.asym'
generate_multivariate_normal_sample: no visible global function
  definition for 'mvrnorm'
plot_units: no visible global function definition for 'textxy'
plot_variables: no visible global function definition for 'textxy'
chgbasismat: no visible global function definition for 'splineDesign'
coef.freekt: no visible global function definition for 'splineDesign'
fitted.freekt: no visible global function definition for 'splineDesign'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/FREGAT.Rcheck/00install.out' for details.
Package which this enhances but not available for checking: 'dggrids'
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    1.6Mb
    libs   1.2Mb
Bell : nways: no visible global function definition for 'setparts'
Bell: no visible global function definition for 'restrictedparts'
CalIncLapInt: no visible global function definition for 'is.whole'
CalIncLapInt: no visible global function definition for 'mpfr'
CalIncLapInt: no visible global function definition for 'chooseMpfr'
Namespaces in Imports field not imported from:
  'R.utils' 'grDevices' 'graphics' 'matrixStats' 'stats'
  All declared Imports should be used.
.alignment: warning in lm(Y ~ X, dat = fr): partial argument match of
  'dat' to 'data'
.alignment: warning in lm(as.formula(form), dat = fr): partial argument
  match of 'dat' to 'data'
display.tests: no visible binding for global variable 'parameter.list'
display.tests: no visible binding for global variable 'sigs'
display.tests: no visible binding for global variable 'clust.mat'
display.tests : <anonymous>: no visible binding for global variable
  'clust.mat'
display.tests : <anonymous>: no visible binding for global variable
  'parameter.list'
run.analysis: no visible binding for global variable 'centers'
run.cluster.matrix: no visible binding for global variable 'amps'
run.cluster.matrix: no visible binding for global variable
  'clust.constant'
run.cluster.matrix: no visible binding for global variable 'spect.base'
run.lrg.peaks: no visible binding for global variable 'spect.base'
fugeR.sfRun: no visible global function definition for 'sfInit'
fugeR.sfRun: no visible global function definition for 'sfLibrary'
fugeR.sfRun: no visible global function definition for 'sfExport'
fugeR.sfRun: no visible global function definition for 'sfLapply'
fugeR.sfRun: no visible global function definition for 'sfStop'
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'FunCluster/R/FunCluster.R':
  .First.lib calls:
    cat(paste("\nThis is FunCluster package version ", f.version,     " maintained by Corneliu Henegar.\n\n", "FunCluster(wd='', org='HS', go.direct=FALSE, clusterm='cc', compare='common.correl.genes',\n",     "\tcorr.met='greedy', corr.th=0.85, two.lists=TRUE, restrict=FALSE, alpha=0.05,\n",     "\tlocation=FALSE, details=FALSE)\n\n", sep = ""))

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

MiseEnFormeKegg: warning in gl(1, NbKmap, label = LL): partial argument
  match of 'label' to 'labels'
MiseEnFormeKeggSC: warning in gl(1, NbKmap, label = LL): partial
  argument match of 'label' to 'labels'
prop.alt: warning in matrix(seq(from = adjustment.args$edf.lower, by =
  stepsize, len = adjustment.args$num.steps), nr =
  adjustment.args$num.steps, nc = 1): partial argument match of 'nr' to
  'nrow'
prop.alt: warning in matrix(seq(from = adjustment.args$edf.lower, by =
  stepsize, len = adjustment.args$num.steps), nr =
  adjustment.args$num.steps, nc = 1): partial argument match of 'nc' to
  'ncol'
dualpathFusedX.mod: no visible global function definition for
  'graph.adjacency'
dualpathFusedX.mod: no visible global function definition for
  'clusters'
dualpathFusedX.mod: no visible global function definition for 'ginv'
dualpathFusedX.mod: no visible global function definition for
  'subcomponent'
dualpathFusedX.mod: no visible global function definition for 'rBind'
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'
plotMF: no visible global function definition for 'interpSpline'
fxreturns: no visible binding for global variable 'FXRatesCHF'
gbreakpoints: no visible global function definition for '%dopar%'
gbreakpoints: no visible global function definition for 'foreach'
DBNScoreStep1: no visible global function definition for 'rlm'
DBNScoreStep2: no visible global function definition for 'rlm'
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.
GAMBoost: no visible global function definition for 'Matrix'
cv.GAMBoost: no visible global function definition for 'mclapply'
estimPVal: no visible global function definition for 'mclapply'
nlgamlss: no visible global function definition for 'NO'
nlgamlss: no visible global function definition for 'as.gamlss.family'
gen.likelihood: no visible global function definition for 'startsWith'
getPEF: no visible global function definition for 'startsWith'
Running examples in 'gamlss-Ex.R' failed
The error most likely occurred in:

> ### Name: gen.likelihood
> ### Title: A function to generate the likelihood function from a GAMLSS
> ###   object
> ### Aliases: gen.likelihood
> ### Keywords: regression
> 
> ### ** Examples
> 
> data(aids)
> m1 <- gamlss(y~x+qrt, data=aids, family=NBI)
GAMLSS-RS iteration 1: Global Deviance = 492.7119 
GAMLSS-RS iteration 2: Global Deviance = 492.6375 
GAMLSS-RS iteration 3: Global Deviance = 492.6373 
> logL<-gen.likelihood(m1)
Error in gen.likelihood(m1) : could not find function "startsWith"
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/gamsel.Rcheck/00install.out' for details.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    data    3.7Mb
    doc     2.9Mb
    tests   2.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    1.0Mb
    libs   2.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      3.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.7Mb
gboot: no visible global function definition for 'boot'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/gbs2ploidy.Rcheck/00install.out' for details.
IsValidGDELT: no visible global function definition for 'md5sum'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   3.0Mb
    libs      1.2Mb
Running examples in 'gemtc-Ex.R' failed
The error most likely occurred in:

> ### Name: mtc.hy.prior
> ### Title: Set priors for the heterogeneity parameter
> ### Aliases: mtc.hy.prior mtc.hy.empirical.lor
> 
> ### ** Examples
> 
> # NOTE: the mtc.run commands below are for illustrative purposes, such a small
> # number of iterations should obviously not be used in practice.
> 
> # set a uniform prior standard deviation
> model1 <- mtc.model(smoking, hy.prior=mtc.hy.prior("std.dev", "dunif", 0, 2))
> result <- mtc.run(model1, n.adapt=10, n.iter=10)
Error: .onLoad failed in loadNamespace() for 'rjags', details:
  call: fun(libname, pkgname)
  error: The environment variable JAGS_HOME is set to
c:/Program Files/JAGS/JAGS-4.0.0
but no JAGS installation can be found there
Execution halted
arrange_probabel_phe: no visible global function definition for
  'databel'
as.genotype.snp.data: no visible global function definition for
  'genotype'
check.marker.internal: no visible global function definition for
  'qvalue'
extract.annotation.impute: no visible global function definition for
  'extract_text_file_columns'
extract.annotation.mach: no visible global function definition for
  'extract_text_file_columns'
impute2databel: no visible global function definition for
  'get_temporary_file_name'
impute2databel: no visible global function definition for
  'text2databel'
impute2databel: no visible global function definition for
  'get_dimnames'
impute2databel: no visible global function definition for 'apply2dfo'
impute2databel: no visible global function definition for 'databel'
impute2databel: no visible global function definition for
  'set_dimnames<-'
impute2databel: no visible global function definition for 'disconnect'
impute2mach: no visible global function definition for 'get_dimnames'
impute2mach: no visible global function definition for 'disconnect'
mach2databel: no visible global function definition for
  'get_temporary_file_name'
mach2databel: no visible global function definition for 'text2databel'
mach2databel: no visible global function definition for 'get_dimnames'
minimac2databel: no visible global function definition for
  'get_temporary_file_name'
minimac2databel: no visible global function definition for
  'text2databel'
minimac2databel: no visible global function definition for
  'get_dimnames'
polygenic: no visible global function definition for 'ginv'
polygenic_hglm: no visible global function definition for 'hglm'
polygenic_hglm: no visible global function definition for 'ginv'
scan.haplo: no visible global function definition for
  'haplo.score.slide'
scan.haplo.2D: no visible global function definition for
  'haplo.score.slide'
scan.haplo.2D: no visible global function definition for
  'score.sim.control'
header.info: no visible global function definition for 'mmap'
header.info: no visible global function definition for 'char'
header.info: no visible global function definition for 'is.mmap'
header.info: no visible global function definition for 'munmap'
read.bin: no visible global function definition for 'mmap'
read.bin: no visible global function definition for 'char'
read.bin: no visible global function definition for 'is.mmap'
read.bin: no visible global function definition for 'munmap'
read.bin: no visible global function definition for 'uint8'
GeneFeST: no visible global function definition for 'as.mcmc'
Missing or unexported objects:
  'DiagrammeR::create_edges' 'DiagrammeR::create_nodes'
Missing link or links in documentation object 'generate_grViz.Rd':
  '[DiagrammeR]{create_nodes}'

See section 'Cross-references' in the 'Writing R Extensions' manual.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  5: generate_grViz(x, ...)
  6: do.call(DiagrammeR::create_nodes, create_nodes_call)
  7: DiagrammeR::create_nodes
  8: getExportedValue(pkg, name)
  9: stop(gettextf("'%s' is not an exported object from 'namespace:%s'", name, getNamespaceName(ns)), 
         call. = FALSE, domain = NA)
  
  testthat results ================================================================
  OK: 118 SKIPPED: 0 FAILED: 1
  1. Error: plotting a tree works (@test_plot.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 102-103 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
'create_nodes' is not an exported object from 'namespace:DiagrammeR'
Execution halted
NCPUS: no visible global function definition for 'detectCores'
NCPUS: no visible global function definition for 'makeCluster'
importance: no visible global function definition for 'clusterExport'
importance: no visible global function definition for 'clusterEvalQ'
importance: no visible global function definition for 'parApply'
importance: no visible global function definition for 'stopCluster'
parallelFindBest: no visible global function definition for 'parApply'
parallelSignatureFinder: no visible global function definition for
  'parApply'
puttingAllTogether: no visible global function definition for
  'makeCluster'
puttingAllTogether: no visible global function definition for
  'stopCluster'
seedsFinder: no visible global function definition for 'clusterExport'
seedsFinder: no visible global function definition for 'clusterEvalQ'
seedsFinder: no visible global function definition for 'parApply'
seedsFinder: no visible global function definition for 'stopCluster'
signatureFinder: no visible global function definition for
  'clusterExport'
signatureFinder: no visible global function definition for
  'clusterEvalQ'
signatureFinder: no visible global function definition for
  'stopCluster'
testGE: no visible global function definition for 'clusterExport'
testGE: no visible global function definition for 'parApply'
testGE: no visible global function definition for 'stopCluster'
groupGenotype: no visible global function definition for 'mapLevels<-'
groupGenotype: no visible global function definition for 'as.levelsMap'
bandwidthselect: no visible global function definition for 'dpik'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.0Mb
Package suggested but not available for checking: 'sf'
Namespaces in Imports field not imported from:
  'DT' 'shinydashboard'
  All declared Imports should be used.
gTree: no visible global function definition for 'ctree'
gTree: no visible global function definition for 'ctree_control'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/gets.Rcheck/00install.out' for details.
gexmap : gexgraph: warning in axis(side = 2, at = min:max, tick = TRUE,
  lab = c(rep(min:max, 1)), cex.axis = 1): partial argument match of
  'lab' to 'labels'
gexmap : gexgraph: warning in axis(side = 1, at = seq(1, (may + 1), by
  = 5), tick = TRUE, lab = c(seq(0, may, by = 5)), cex.axis = 1):
  partial argument match of 'lab' to 'labels'
Namespace in Imports field not imported from: 'plotly'
  All declared Imports should be used.
macros/aesthetics.Rd: Sections \title, and \name must exist and be unique in Rd files
problem found in 'aesthetics.Rd'
Namespaces in Imports field not imported from:
  'dplyr' 'ggmap' 'gridExtra' 'scales' 'tnet'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/ggdmc.Rcheck/00install.out' for details.
Running examples in 'ggforce-Ex.R' failed
The error most likely occurred in:

> ### Name: facet_zoom
> ### Title: Facet data for zoom with context
> ### Aliases: facet_zoom
> 
> ### ** Examples
> 
> # Zoom in on the versicolor species on the x-axis
> ggplot(iris, aes(Petal.Length, Petal.Width, colour = Species)) +
+     geom_point() +
+     facet_zoom(x = Species == "versicolor")
Error in grid.Call.graphics(L_setviewport, vp, TRUE) : 
  INTEGER() can only be applied to a 'integer', not a 'NULL'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 336-339 (Visual_Guide.Rmd) 
Error: processing vignette 'Visual_Guide.Rmd' failed with diagnostics:
INTEGER() can only be applied to a 'integer', not a 'NULL'
Execution halted
Namespaces in Imports field not imported from:
  'gridExtra' 'lazyeval' 'readr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'XML' 'mapproj' 'moonBook'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'NHANES' 'gridExtra'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'reshape2'
  All declared Imports should be used.
prepare_Rd: geom_bar.Rd:94: unknown macro '\aesthetics'
prepare_Rd: geom_bin2d.Rd:76: unknown macro '\aesthetics'
prepare_Rd: geom_boxplot.Rd:110: unknown macro '\aesthetics'
prepare_Rd: geom_contour.Rd:78: unknown macro '\aesthetics'
prepare_Rd: geom_count.Rd:66: unknown macro '\aesthetics'
prepare_Rd: geom_density.Rd:89: unknown macro '\aesthetics'
prepare_Rd: geom_density_2d.Rd:82: unknown macro '\aesthetics'
prepare_Rd: geom_dotplot.Rd:110: unknown macro '\aesthetics'
prepare_Rd: geom_errorbarh.Rd:59: unknown macro '\aesthetics'
prepare_Rd: geom_hex.Rd:74: unknown macro '\aesthetics'
prepare_Rd: geom_jitter.Rd:80: unknown macro '\aesthetics'
prepare_Rd: geom_linerange.Rd:80: unknown macro '\aesthetics'
prepare_Rd: geom_map.Rd:60: unknown macro '\aesthetics'
prepare_Rd: geom_path.Rd:89: unknown macro '\aesthetics'
prepare_Rd: geom_point.Rd:90: unknown macro '\aesthetics'
prepare_Rd: geom_polygon.Rd:62: unknown macro '\aesthetics'
prepare_Rd: geom_qq.Rd:68: unknown macro '\aesthetics'
prepare_Rd: geom_quantile.Rd:82: unknown macro '\aesthetics'
prepare_Rd: geom_ribbon.Rd:74: unknown macro '\aesthetics'
prepare_Rd: geom_rug.Rd:70: unknown macro '\aesthetics'
prepare_Rd: geom_segment.Rd:89: unknown macro '\aesthetics'
prepare_Rd: geom_smooth.Rd:107: unknown macro '\aesthetics'
prepare_Rd: geom_spoke.Rd:61: unknown macro '\aesthetics'
prepare_Rd: geom_text.Rd:91: unknown macro '\aesthetics'
prepare_Rd: geom_tile.Rd:82: unknown macro '\aesthetics'
prepare_Rd: geom_violin.Rd:89: unknown macro '\aesthetics'
prepare_Rd: stat_function.Rd:68: unknown macro '\aesthetics'
prepare_Rd: stat_summary.Rd:78: unknown macro '\aesthetics'
prepare_Rd: stat_unique.Rd:58: unknown macro '\aesthetics'
macros/aesthetics.Rd: Sections \title, and \name must exist and be unique in Rd files
problem found in 'aesthetics.Rd'
Namespace in Imports field not imported from: 'randomForest'
  All declared Imports should be used.
ggroc: no visible global function definition for 'ggplot'
ggroc: no visible global function definition for 'aes'
ggroc: no visible global function definition for 'geom_point'
ggroc: no visible global function definition for 'geom_line'
ggroc: no visible global function definition for 'theme'
ggroc: no visible global function definition for 'element_text'
ggroc: no visible global function definition for 'labs'
ggroc: no visible global function definition for 'ggsave'
Namespace in Imports field not imported from: 'lazyeval'
  All declared Imports should be used.
Package required and available but unsuitable version: 'methods'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'gibbs.met/R/firstlib.R':
  .First.lib calls:
    cat("Naive Gibbs Sampling with Metropolis steps(gibbs.met) loaded\n",     "COPYRIGHT 2008 (c) Longhai Li (http://math.usask.ca/~longhai)\n",     "Type ?begin.gibbs.met for help to this package\n", sep = "")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
panel.pyramid: no visible global function definition for
  'trellis.par.get'
panel.pyramid: no visible global function definition for
  'current.panel.limits'
panel.pyramid: no visible global function definition for 'panel.abline'
panel.pyramid: no visible global function definition for 'panel.rect'
pyramid2.formula: no visible global function definition for
  'lattice.getOption'
pyramid2.formula: no visible global function definition for
  'is.shingle'
pyramid2.formula: no visible global function definition for
  'as.factorOrShingle'
useOuterStrips2 : new.strip: no visible global function definition for
  'strip.default'
useOuterStrips2 : new.strip.left: no visible global function definition
  for 'strip.default'
glm.fit2: no visible binding for global variable 'n'
el.CSW: no visible global function definition for 'logelr'
el.owen: no visible global function definition for 'logelr'
el.owen: no visible global function definition for 'llogp'
el.owen: no visible global function definition for 'llogpp'
el.owen: no visible global function definition for 'llog'
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  21.2Mb
glmnet.cr: no visible global function definition for 'glmnet'
glmpath.cr: no visible global function definition for 'glmpath'
predict.coxpath: no visible global function definition for 'coxph'
glmulti,character-character-ANY-ANY: no visible global function
  definition for 'regsubsets'
installed size is 45.6Mb
  sub-directories of 1Mb or more:
    libs  44.7Mb
predict.gnm: no visible binding for global variable 'eliminate'
cumres.lvmfit : myres: no visible global function definition for 'vars'
cumres.lvmfit: no visible global function definition for 'iid'
GOGANPA: no visible global function definition for 'GSE.Test.Main'
selectRho: no visible global function definition for
  'scaleFreeFitIndex'
goest,Goestica : .local: no visible global function definition for
  'fastICA'
Namespace in Imports field not imported from: 'googleCloudStorageR'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'readr'
  All declared Imports should be used.
Resdata : prepdata: no visible global function definition for 'sqldf'
gpca : Build3d: no visible global function definition for
  'scatterplot3d'
gpca: no visible global function definition for 'scatterplot3d'
gpCovGrads: no visible global function definition for 'diag.spam'
gpUpdateAD: no visible global function definition for 'diag.spam'
gpUpdateKernels: no visible global function definition for 'diag.spam'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/gpuR.Rcheck/00install.out' for details.
Errors in running code in vignettes:
when running code in 'GRAN-Overview.Rnw'
  ...
Building 0 packages
starting migrateToFinalRepo 2017-02-11 18:28:19
Built 0 packages

  When sourcing 'GRAN-Overview.R':
Error: dims [product 0] do not match the length of object [1]
No traceback available 
> proc.time()
   user  system elapsed 
   1.13    0.43   22.86
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/graphql.Rcheck/00install.out' for details.
GrassmannOptim : <anonymous>: no visible global function definition for
  'expm'
GrassmannOptim : <anonymous>: no visible global function definition for
  'Matrix'
Namespace in Imports field not imported from: 'rgeos'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'BiasedUrn'
  All declared Imports should be used.
GriegSmith: no visible global function definition for 'is.ppp'
grouped: no visible binding for global variable 'n'
lL.gaussian: no visible binding for global variable 'p'
lL.gaussian: no visible binding for global variable 'X'
lL.gaussian: no visible binding for global variable 'qb'
lL.gaussian: no visible binding for global variable 'qa'
lL.logistic: no visible binding for global variable 'p'
lL.logistic: no visible binding for global variable 'X'
lL.logistic: no visible binding for global variable 'qb'
lL.logistic: no visible binding for global variable 'qa'
lL.t: no visible binding for global variable 'p'
lL.t: no visible binding for global variable 'X'
lL.t: no visible binding for global variable 'qb'
lL.t: no visible binding for global variable 'df.'
lL.t: no visible binding for global variable 'qa'
sc.gaussian: no visible binding for global variable 'p'
sc.gaussian: no visible binding for global variable 'X'
sc.gaussian: no visible binding for global variable 'qb'
sc.gaussian: no visible binding for global variable 'qa'
sc.gaussian: no visible binding for global variable 'qb.'
sc.gaussian: no visible binding for global variable 'qa.'
sc.logistic: no visible binding for global variable 'p'
sc.logistic: no visible binding for global variable 'X'
sc.logistic: no visible binding for global variable 'qb'
sc.logistic: no visible binding for global variable 'qa'
sc.logistic: no visible binding for global variable 'qb.'
sc.logistic: no visible binding for global variable 'qa.'
sc.t: no visible binding for global variable 'p'
sc.t: no visible binding for global variable 'X'
sc.t: no visible binding for global variable 'qb'
sc.t: no visible binding for global variable 'df.'
sc.t: no visible binding for global variable 'qa'
sc.t: no visible binding for global variable 'qb.'
sc.t: no visible binding for global variable 'qa.'
GSA: no visible global function definition for 'impute.knn'
plotgsCP: no visible global function definition for 'opts'
plotgsPower: no visible global function definition for 'opts'
qplotit: no visible global function definition for 'opts'
Namespace in Imports field not imported from: 'rrcov'
  All declared Imports should be used.
gee_wrap: no visible global function definition for 'gee'
geeglm_wrap: no visible global function definition for 'geeglm'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  2. Failure: segm returns correct output (@test_segm.R#17) ----------------------
  dim(dat$cna) not equal to c(104, 6).
  1/2 mismatches
  [1] 103 - 104 == -1
  
  
  testthat results ================================================================
  OK: 29 SKIPPED: 0 FAILED: 2
  1. Failure: cnv returns correct output (@test_cnv.R#18) 
  2. Failure: segm returns correct output (@test_segm.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following possibly unsafe calls:
File 'gtools/R/unByteCode.R':
  unlockBinding(name, env = env)
Error in re-building vignettes:
  ...
Loading required package: survival
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "ashg2012.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.2.5/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.2.5/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'ashg2012.tex' failed

LaTeX errors:
! LaTeX Error: File `D:/RCompile/recent/R-32\unhbox\voidb@x \penalty \@M \ {}1.
5/share/texmf/tex/latex/Sweave.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
Execution halted
Namespace in Imports field not imported from: 'rvest'
  All declared Imports should be used.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  1. Error: gutenberg_get_mirror works (@test-download.R#13) 
  2. Failure: Can download Charles Dickens' Christmas Carol and Jane Austen's Persuasion (@test-download.R#22) 
  3. Failure: Can download Charles Dickens' Christmas Carol and Jane Austen's Persuasion (@test-download.R#23) 
  4. Failure: Can download Charles Dickens' Christmas Carol and Jane Austen's Persuasion (@test-download.R#31) 
  5. Failure: Can download Charles Dickens' Christmas Carol and Jane Austen's Persuasion (@test-download.R#32) 
  6. Failure: Can download books from a data frame with gutenberg_id column (@test-download.R#43) 
  7. Failure: We can download a file that only has a -8 version (@test-download.R#50) 
  8. Failure: read_zip_url can download and read a zip file (@test-utils.R#7) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  closing unused connection 3 (http://www.gutenberg.lib.md.us) 
  Execution halted
normalweight: no visible binding for global variable 'NW_above'
normalweight: no visible binding for global variable 'NW_below'
obese: no visible binding for global variable 'OB_above'
obese: no visible binding for global variable 'OB_below'
overweight: no visible binding for global variable 'OW_above'
overweight: no visible binding for global variable 'OW_below'
gwl.beta: no visible global function definition for 'lars'
gwl.cv.err: no visible global function definition for 'lars'
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
AIC: no visible global function definition for 'hash'
AIC: no visible global function definition for 'values'
AIC: no visible global function definition for 'values<-'
ODS.ror: no visible global function definition for 'hash'
ODS.ror: no visible global function definition for 'values<-'
ODS.ror: no visible global function definition for 'keys'
ODS.ror: no visible global function definition for 'values'
ODS.ror: no visible global function definition for 'read.tree'
ODS.ror: no visible global function definition for 'nodelabels'
cc.sim: no visible global function definition for 'hash'
cc.sim: no visible global function definition for 'values<-'
cc.sim: no visible global function definition for 'values'
collapse: no visible global function definition for 'hash'
collapse: no visible global function definition for 'values<-'
collapse: no visible global function definition for 'keys'
collapse: no visible global function definition for 'values'
deletion: no visible global function definition for 'hash'
deletion: no visible global function definition for 'values<-'
deletion: no visible global function definition for 'keys'
deletion: no visible global function definition for 'values'
grp.list: no visible global function definition for 'hash'
grp.list: no visible global function definition for 'values'
Found the following significant warnings:
  readstat/stata/readstat_dta_read.c:181:25: warning: too many arguments for format [-Wformat-extra-args]
  readstat/stata/readstat_dta_read.c:366:21: warning: too many arguments for format [-Wformat-extra-args]
  readstat/stata/readstat_dta_read.c:584:21: warning: too many arguments for format [-Wformat-extra-args]
  readstat/stata/readstat_dta_read.c:831:21: warning: too many arguments for format [-Wformat-extra-args]
See 'd:/Rcompile/CRANpkg/local/3.2/haven.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'hms'
  All declared Imports should be used.
The following directory looks like a leftover from 'knitr':
  'cache'
Please remove from your package.
Namespaces in Imports field not imported from:
  'RColorBrewer' 'grDevices' 'magrittr'
  All declared Imports should be used.
print.tsum: warning in print.default(x$resid, digits = digits, na = "",
  print.gap = 2): partial argument match of 'na' to 'na.print'
print.tsum: warning in symnum(correl, abbr.col = NULL): partial
  argument match of 'abbr.col' to 'abbr.colnames'
tlm: no visible binding for global variable 'response'
tlm: no visible binding for global variable 'dofse'
tscore: no visible binding for global variable 'response'
Btilde: no visible global function definition for 'bs'
hgam: no visible global function definition for 'LinReg'
hgam.fit: no visible global function definition for 'LinReg'
hgam.fit: no visible global function definition for 'grplasso'
hgam.fit: no visible global function definition for 'grpl.control'
hrisk: no visible binding for global variable 'mclapply'
hrisk : <anonymous>: no visible global function definition for
  'lambdamax'
plot.hrisk: no visible global function definition for 'plot3d'
plot.hrisk: no visible global function definition for 'levelplot'
gcline.fn: no visible global function definition for 'multinom'
Namespace in Imports field not imported from: 'quantmod'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'colorspace'
  All declared Imports should be used.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > test_check("hms")
  1. Failure: coercion in (@test-coercion.R#6) -----------------------------------
  as.numeric(x) not equal to as.numeric(y).
  1/1 mismatches
  [1] 41696 - 45296 == -3600
  
  
  testthat results ================================================================
  OK: 98 SKIPPED: 0 FAILED: 1
  1. Failure: coercion in (@test-coercion.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
hand1: no visible binding for global variable 'name1'
hotelling.stat: no visible global function definition for 'cov.shrink'
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'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.1Mb
get.pdf: no visible global function definition for 'dmvnorm'
hsmm.sim: no visible global function definition for 'rmvnorm'
Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'phyloseq'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Namespaces in Imports field not imported from:
  'EnvStats' 'MASS' 'RColorBrewer' 'TeachingDemos' 'classInt' 'ks'
  'reshape2'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'jsonlite'
  All declared Imports should be used.
humarray version 1.1

See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
humarray version 1.1

The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
humarray version 1.1

See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
humarray version 1.1

All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
humarray version 1.1

humarray version 1.1

humarray version 1.1
humarray version 1.1

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Error in re-building vignettes:
  ...
trying URL 'https://arxiv.org/e-print/1406.4806v1'
Content type 'application/x-eprint-tar' length 29273 bytes (28 KB)
==================================================
downloaded 28 KB

Quitting from lines 153-159 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
replacement has 0 rows, data has 4973
Execution halted
Warning in .doLoadActions(where, attach) :
  trying to execute load actions without 'methods' package
See sections 'The INDEX file' and 'Package subdirectories' in the
'Writing R Extensions' manual.
Warning in .doLoadActions(where, attach) :
  trying to execute load actions without 'methods' package
hybridMC: no visible global function definition for 'mcmc'
Running examples in 'HydeNet-Ex.R' failed
The error most likely occurred in:

> ### Name: HydePosterior
> ### Title: Posterior Distributions of a Decision Network
> ### Aliases: HydePosterior
> 
> ### ** Examples
> 
> data(PE, package="HydeNet")
> Net <- HydeNetwork(~ wells + 
+                      pe | wells + 
+                      d.dimer | pregnant*pe + 
+                      angio | pe + 
+                      treat | d.dimer*angio + 
+                      death | pe*treat,
+                      data = PE) 
>   
>                  
> compiledNet <- compileJagsModel(Net, n.chains=5)
Error: .onLoad failed in loadNamespace() for 'rjags', details:
  call: fun(libname, pkgname)
  error: The environment variable JAGS_HOME is set to
c:/Program Files/JAGS/JAGS-4.0.0
but no JAGS installation can be found there
Execution halted
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library("testthat")
  > library("HydeNet")
  Loading required package: nnet
  > 
  > test_check("HydeNet")
  Error: .onLoad failed in loadNamespace() for 'rjags', details:
    call: fun(libname, pkgname)
    error: The environment variable JAGS_HOME is set to
  c:/Program Files/JAGS/JAGS-4.0.0
  but no JAGS installation can be found there
  testthat results ================================================================
  OK: 3 SKIPPED: 0 FAILED: 0
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: nnet
Quitting from lines 314-325 (DecisionNetworks.Rmd) 
Error: processing vignette 'DecisionNetworks.Rmd' failed with diagnostics:
.onLoad failed in loadNamespace() for 'rjags', details:
  call: fun(libname, pkgname)
  error: The environment variable JAGS_HOME is set to
c:/Program Files/JAGS/JAGS-4.0.0
but no JAGS installation can be found there
Execution halted
hydromod: no visible global function definition for 'ggof'
plot_out: no visible global function definition for 'zoo'
plot_out: no visible global function definition for 'ggof'
plot_params.default: no visible global function definition for
  'vioplot'
plot_params.default: no visible global function definition for
  'hydropairs'
hyperbCvMTestPValue: no visible binding for global variable
  'hyperbWSqTable'
momIntegrated : ddist: no visible global function definition for 'dvg'
requiprobable: no visible global function definition for 'extract'
requiprobable : make.tree: no visible global function definition for
  'extract'
fitter.gen.rParam.uniform: no visible global function definition for
  '%do%'
fitter.gen.rParam.uniform: no visible global function definition for
  'foreach'
hzar.chain.doSeq: no visible global function definition for 'mcmc'
hzar.chain.doSeq: no visible global function definition for 'thin'
hzar.dataGroup.null: no visible global function definition for 'mcmc'
hzar.doChain.multi: no visible global function definition for '%dopar%'
hzar.doChain.multi: no visible global function definition for 'foreach'
hzar.doChain.multi: no visible global function definition for '%do%'
hzar.doFit: no visible global function definition for 'MCMCmetrop1R'
hzar.doFit.multi: no visible global function definition for '%dopar%'
hzar.doFit.multi: no visible global function definition for 'foreach'
hzar.doFit.multi: no visible global function definition for '%do%'
hzar.eval.clineLL: no visible global function definition for '%dopar%'
hzar.eval.clineLL: no visible global function definition for 'foreach'
hzar.eval.clineLL: no visible global function definition for '%do%'
hzar.fit2DataGroup: no visible global function definition for 'mcmc'
hzar.mcmc.bindLL: no visible global function definition for 'mcmc'
hzar.mcmc.bindLL: no visible global function definition for 'as.mcmc'
hzar.mcmc.bindLL: no visible global function definition for 'thin'
hzar.profile.dataGroup: no visible global function definition for
  'equal.count'
hzar.profile.dataGroup: no visible global function definition for
  'foreach'
hzar.profile.dataGroup: no visible global function definition for
  '%dopar%'
hzar.profile.dataGroup: no visible global function definition for
  '%do%'
optimizeTrace: no visible global function definition for 'as.mcmc'
Namespaces in Imports field not imported from:
  'Rcpp' 'ggplot2' 'pander'
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   1.9Mb
TrainIBHM: no visible global function definition for 'enableJIT'
Found the following significant warnings:
  Warning: failed to assign NativeSymbolInfo for lhs since lhs is already defined in the 'lazyeval' namespace
  Warning: failed to assign NativeSymbolInfo for rhs since rhs is already defined in the 'lazyeval' namespace
See 'd:/Rcompile/CRANpkg/local/3.2/ibmdbR.Rcheck/00install.out' for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.1Mb
    libs   1.2Mb
NB: this package is only installed for sub-architecture 'x64'
str_match_all: possible error in regexec(pattern, x, perl = perl,
  useBytes = useBytes): unused argument (perl = perl)
str_pair_match : <anonymous>: possible error in regexec(pattern =
  pattern, text = x, perl = perl, useBytes = useBytes): unused argument
  (perl = perl)
Running the tests in 'tests/test-current-no-comorbid.R' failed.
Last 13 lines of output:
  unused argument (perl = perl)
  1: expect_identical(chapter_to_desc_range.icd10("jack (A10-A20)"), list(Jack = c(start = "A10", 
         end = "A20"))) at testthat/test-current-util.R:135
  2: identical(object, expected)
  3: chapter_to_desc_range.icd10("jack (A10-A20)")
  4: .chapter_to_desc_range(x, re_major = re_icd10_major_bare)
  5: str_match_all(x, re_code_range)
  6: regmatches(x, regexec(pattern, x, perl = perl, useBytes = useBytes))
  7: regexec(pattern, x, perl = perl, useBytes = useBytes)
  
  DONE ===========================================================================
  Error: Test failures
  Execution halted
plot.ICEepmap: no visible global function definition for 'contourplot'
plotHeatmap: no visible global function definition for 'bluered'
plotHeatmap : my.panel.levelplot: no visible global function definition
  for 'panel.levelplot'
plotHeatmap : my.panel.levelplot: no visible global function definition
  for 'panel.abline'
plotHeatmap : my.panel.levelplot.2: no visible global function
  definition for 'panel.levelplot'
plotHeatmap : my.panel.levelplot.2: no visible global function
  definition for 'panel.abline'
plotHeatmap: no visible global function definition for 'levelplot'
tune.iCluster2: no visible binding for global variable 'glp'
tune.iCluster2: no visible global function definition for 'mclapply'
agent_returnGridResolution: no visible global function definition for
  'xmlAttrs'
agent_returnIVoxels: no visible global function definition for
  'xmlAttrs'
agent_returnJVoxels: no visible global function definition for
  'xmlAttrs'
agent_returnKVoxels: no visible global function definition for
  'xmlAttrs'
agent_returnSimIteration: no visible global function definition for
  'xmlAttrs'
agent_returnSimTime: no visible global function definition for
  'xmlAttrs'
agent_returnSpeciesResultData: no visible global function definition
  for 'xmlSize'
agent_returnSpeciesResultData: no visible global function definition
  for 'xmlAttrs'
env_returnConcentrationAndRateChange: no visible global function
  definition for 'xmlSize'
env_returnConcentrationAndRateChange: no visible global function
  definition for 'xmlName'
env_returnConcentrationAndRateChange: no visible global function
  definition for 'xmlAttrs'
env_returnGlobalProductionRates: no visible global function definition
  for 'xmlSize'
env_returnGlobalProductionRates: no visible global function definition
  for 'xmlAttrs'
env_returnSimIteration: no visible global function definition for
  'xmlAttrs'
env_returnSimTime: no visible global function definition for 'xmlAttrs'
env_returnSoluteGridIVoxels: no visible global function definition for
  'xmlAttrs'
env_returnSoluteGridJVoxels: no visible global function definition for
  'xmlAttrs'
env_returnSoluteGridKVoxels: no visible global function definition for
  'xmlAttrs'
env_returnSoluteGridRes: no visible global function definition for
  'xmlAttrs'
env_returnSpecifiedSoluteData: no visible global function definition
  for 'xmlSize'
env_soluteProductionRateOverTime: no visible global function definition
  for 'xmlValue'
readSimResultFile: no visible global function definition for
  'xmlTreeParse'
readSimResultFile: no visible global function definition for 'xmlRoot'
simpsonIndex: no visible global function definition for 'diversity'
Package suggested but not available for checking: 'states2k'
Error in re-building vignettes:
  ...
Error in (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  : 
  there is no package called 'states2k'
Quitting from lines 24-109 (US-Engineering-Weather-Map.Rmd) 
Error: processing vignette 'US-Engineering-Weather-Map.Rmd' failed with diagnostics:
object 'states2k_map' not found
Execution halted
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    help   1.2Mb
    libs  12.8Mb
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       4.2Mb
    extdata   1.0Mb
    include   2.8Mb
    libs     12.2Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R  10.7Mb
select.lines: warning in symbols(long[segment[1:2]], lat[segment[1:2]],
  cir = c(1, 0.1), add = TRUE, col = 8): partial argument match of
  'cir' to 'circles'
IMIS: no visible global function definition for 'sample.prior'
IMIS: no visible global function definition for 'prior'
IMIS: no visible global function definition for 'likelihood'
IMIS : posterior: no visible global function definition for 'prior'
IMIS : posterior: no visible global function definition for
  'likelihood'
Package suggested but not available for checking: 'odbc'
Package unavailable to check Rd xrefs: 'odbc'
Found the following significant warnings:
  Warning: failed to assign NativeSymbolInfo for env since env is already defined in the 'lazyeval' namespace
See 'd:/Rcompile/CRANpkg/local/3.2/ImportExport.Rcheck/00install.out' for details.
FctReducedNodevalues: no visible global function definition for
  'cfunction'
TotalVar: no visible global function definition for 'lp'
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'
heal_data: no visible global function definition for 'optimum_k'
heal_data: no visible global function definition for 'optimum_w'
heal_data: no visible global function definition for 'pred_for_w'
initialize,Image : .local: no visible global function definition for
  'readJPEG'
initialize,Image : .local: no visible global function definition for
  'readPNG'
initialize,Image : .local: no visible global function definition for
  'read.bmp'
initialize,OrthIm : .local: no visible binding for global variable
  'obj'
dependogram: no visible global function definition for 'makeCluster'
dependogram: no visible global function definition for
  'clusterSetupSPRNG'
dependogram: no visible global function definition for 'clusterCall'
dependogram: no visible global function definition for 'stopCluster'
infer,coxph : .local: no visible global function definition for
  'sandwich'
infer,glm : .local: no visible global function definition for
  'sandwich'
infer,lm : .local: no visible global function definition for 'sandwich'
infer,lme : .local: no visible global function definition for
  'fixed.effects'
infer,mer : .local: no visible binding for global variable 'fm1'
est.expDeath : surv_p: no visible global function definition for
  'survfit'
function1: no visible global function definition for 'coxph.detail'
var.expDeath : surv_p: no visible global function definition for
  'survfit'
Package required and available but unsuitable version: 'Rmixmod'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
boot.compute.fj: no visible global function definition for
  'supplementaryCols'
epCA.inference.battery : permute.components.ca: no visible global
  function definition for 'epCA'
epCA.inference.battery: no visible global function definition for
  'epCA'
epGPCA.inference.battery : permute.components.pca: no visible global
  function definition for 'epGPCA'
epGPCA.inference.battery: no visible global function definition for
  'epGPCA'
epMCA.inference.battery : permute.components.mca: no visible global
  function definition for 'epMCA'
epMCA.inference.battery: no visible global function definition for
  'makeNominalData'
epMCA.inference.battery: no visible global function definition for
  'epMCA'
epPCA.inference.battery : permute.components.pca: no visible global
  function definition for 'epPCA'
epPCA.inference.battery: no visible global function definition for
  'epPCA'
inGraphs: no visible global function definition for
  'createColorVectorsByDesign'
inGraphs: no visible global function definition for
  'calculateConstraints'
inGraphs: no visible global function definition for 'prettyPlot'
inGraphs: no visible global function definition for 'prettyBars'
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'insideRODE/R/zzz.r':
  .First.lib calls:
    require(nlme)
    require(lattice)
    require(deSolve)
    require(compiler)

Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.
cgrad: no visible global function definition for 'res'
doshade: no visible global function definition for 'projection'
doshade: no visible global function definition for 'extent'
doshade: no visible global function definition for 'res'
doshade: no visible global function definition for 'raster'
doshade: no visible global function definition for 'extent<-'
Namespace in Imports field not imported from: 'prodlim'
  All declared Imports should be used.
date.time: no visible global function definition for 'chron'
date.time: no visible global function definition for 'years'
date.time: no visible global function definition for 'days'
date.time: no visible global function definition for 'hours'
par_calibration: no visible global function definition for 'date.mdy'
par_calibration: no visible global function definition for 'as.date'
plot_meas_sim: no visible global function definition for 'as.date'
plot_meas_sim: no visible global function definition for 'date.mdy'
shape_calibration: no visible global function definition for 'date.mdy'
shape_calibration: no visible global function definition for 'as.date'
ILik: no visible global function definition for 'maxLik'
ILik: no visible global function definition for 'hessian'
f.grovest3 : f.est: no visible global function definition for 'survfit'
Namespace in Imports field not imported from: 'png'
  All declared Imports should be used.
summary,ipdlme: warning in pt(abs(stat), df = object@df, lower =
  FALSE): partial argument match of 'lower' to 'lower.tail'
.getListRegObjects: no visible global function definition for 'rmvnorm'
.getListRegObjectsFec: no visible global function definition for
  'rmvnorm'
diagnosticsPmatrix: no visible global function definition for
  'dtruncnorm'
sampleVitalRateObj: no visible global function definition for
  'rdirichlet'
sampleVitalRateObj: no visible global function definition for 'rmvnorm'
simulateCarlina: no visible global function definition for 'rmvnorm'
growth,numeric-numeric-data.frame-growthObjTruncIncr: no visible global
  function definition for 'dtruncnorm'
growthCum,numeric-numeric-data.frame-growthObjTruncIncr: no visible
  global function definition for 'ptruncnorm'
plot.htest: no visible global function definition for
  'normal.and.t.dist'
Namespaces in Imports field not imported from:
  'coda' 'lattice'
  All declared Imports should be used.
convert_edgeList_to_graph: no visible global function definition for
  'ftM2graphNEL'
convert_edgeList_to_graph: no visible global function definition for
  'graph.data.frame'
convert_graph_to_edgeList: no visible global function definition for
  'edgeWeights'
convert_graph_to_edgeList: no visible global function definition for
  'get.edgelist'
convert_graph_to_edgeList: no visible global function definition for
  'E'
summary_graph: no visible global function definition for
  'connectedComp'
summary_graph: no visible global function definition for 'subGraph'
summary_graph: no visible global function definition for 'clusters'
summary_graph: no visible global function definition for 'subgraph'
summary_graph: no visible binding for global variable
  'layout.fruchterman.reingold'
dendrify: no visible binding for global variable 'item'
dendrify: no visible binding for global variable 'node'
dendrify: no visible binding for global variable 'value'
exogenize: no visible binding for global variable 'item'
Namespaces in Imports field not imported from:
  'colorRamps' 'virtualspecies'
  All declared Imports should be used.
IS: no visible global function definition for 'mclapply'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/IUPS.Rcheck/00install.out' for details.
clusterVCV: no visible global function definition for 'estfun'
covc: no visible global function definition for 'sandwich'
ftest: no visible global function definition for 'vcovHC'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/jagsUI.Rcheck/00install.out' for details.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

make_template: no visible global function definition for 'invalid'
.getJavaGDObject: no visible global function definition for '.jmkref'
JavaGD: no visible global function definition for '.jinit'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/jmotif.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'BayesFactor' 'GGally' 'GPArotation' 'PMCMR' 'afex' 'car' 'lsmeans'
  'lsr' 'multcomp' 'psych' 'vcd' 'vcdExtra'
  All declared Imports should be used.
Found the following significant warnings:
  Warning: replacing previous import 'lme4::sigma' by 'nlme::sigma' when loading 'joineRML'
See 'd:/Rcompile/CRANpkg/local/3.2/joineRML.Rcheck/00install.out' for details.
JointRegBC.default: no visible global function definition for 'fdHess'
JointRegBC.default: no visible global function definition for 'ginv'
JOP: no visible global function definition for 'dglm'
JOP: no visible global function definition for 'gosolnp'
JOP: no visible global function definition for 'solnp'
File 'jsonlite/libs/i386/jsonlite.dll':
  Found non-API call to R: 'getConnection'
File 'jsonlite/libs/x64/jsonlite.dll':
  Found non-API call to R: 'getConnection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Error in re-building vignettes:
  ...
Quitting from lines 126-127 (interactions.Rmd) 
Error: processing vignette 'interactions.Rmd' failed with diagnostics:
'data' must be of a vector type, was 'NULL'
Execution halted
Found the following significant warnings:
  Warning: `legend.margin` must be specified using `margin()`. For the old behavior use legend.spacing
See 'd:/Rcompile/CRANpkg/local/3.2/JWileymisc.Rcheck/00install.out' for details.
KappaV: no visible global function definition for 'over'
plot,kaps-missing : .local: no visible global function definition for
  'locfit.censor'
kcirt.fitMSS: no visible global function definition for 'sfInit'
kcirt.fitMSS: no visible global function definition for 'sfExport'
kcirt.fitMSS: no visible global function definition for 'sfIsRunning'
kcirt.fitMSS: no visible global function definition for 'sfStop'
Namespace in Imports field not imported from: 'kirby21.t1'
  All declared Imports should be used.
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 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'
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.
dataFiller: no visible global function definition for 'daisy'
theme_ms: possible error in theme(axis.text = element_text(size =
  rel(0.8)), axis.ticks = element_line(colour = "black"), legend.key =
  element_rect(colour = "grey80"), panel.background = element_rect(fill
  = "white", colour = NA), panel.border = element_rect(fill = NA,
  colour = "grey50"), panel.grid.major = element_line(colour =
  "grey90", size = 0.2), panel.grid.minor = element_line(colour =
  "grey98", size = 0.5), strip.background = element_rect(fill =
  "grey80", colour = "grey50"), strip.background = element_rect(fill =
  "grey80", : formal argument "strip.background" matched by multiple
  actual arguments
theme_ms: possible error in colour = "grey50")): formal argument
  "strip.background" matched by multiple actual arguments
kobe2sm,data.frame : .local: no visible global function definition for
  'kobe2smFn'
kobe,data.frame-missing : .local : <anonymous>: no visible global
  function definition for 'kobeFn'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   2.0Mb
Package in Depends field not imported from: 'Sejong'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'rJava:::.jniInitialized'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.KoNLPEnv'
Namespaces in Imports field not imported from:
  'dplyr' 'tibble'
  All declared Imports should be used.
plot.krls: no visible global function definition for 'histogram'
readSelexFile: no visible global function definition for 'startsWith'
ROC.offset: no visible global function definition for 'pData'
ROC.offset: no visible global function definition for 'exprs'
ROC.voting: no visible global function definition for 'pData'
ROC.voting: no visible global function definition for 'exprs'
bootstrap.ktsp: no visible global function definition for 'exprs'
bootstrap.ktsp: no visible global function definition for
  'featureNames'
bootstrap.ktsp: no visible global function definition for 'pData'
ktspcalc: no visible global function definition for 'exprs'
ktspcalc: no visible global function definition for 'featureNames'
ktspcalc: no visible global function definition for 'pData'
ktspcalc2: no visible global function definition for 'exprs'
ktspcalc2: no visible global function definition for 'featureNames'
ktspcalc2: no visible global function definition for 'pData'
predict.ktsp: no visible global function definition for 'featureNames'
predict.ktsp: no visible global function definition for 'exprs'
updatePackages: possible error in available.packages(repos = repos):
  unused argument (repos = repos)
Errors in running code in vignettes:
when running code in 'variablekey.Rnw'
  ...
Warning in file(outfile, "w") :
  cannot open file 'plots/t-Roptions.R': No such file or directory

  When tangling 'variablekey.Rnw':
Error: cannot open the connection
Execution halted
cv.l2boost: no visible global function definition for 'detectCores'
impute.cov: no visible global function definition for 'complete'
impute.cov: no visible global function definition for 'mice'
BSL: no visible global function definition for 'read.asciigrid'
PIF: no visible global function definition for 'read.asciigrid'
clouds: no visible global function definition for 'read.asciigrid'
geoshift: no visible global function definition for 'bbox'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/largeList.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/largeVis.Rcheck/00install.out' for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    dataset   1.4Mb
    include   4.3Mb
    libs      2.0Mb
Tkp: no visible global function definition for 'is.spam'
addObservations: no visible global function definition for 'bbox'
addObservations: no visible global function definition for 'as.ppp'
addObservations: no visible global function definition for 'nncross'
addQuantVar: no visible global function definition for 'bbox'
addQuantVar: no visible global function definition for 'as.ppp'
addQuantVar: no visible global function definition for 'nncross'
areaRegion: no visible global function definition for 'areapl'
editLattice: no visible global function definition for 'card'
formLattice: no visible global function definition for 'dnearneigh'
makeTmatrix: no visible global function definition for 'as.spam.listw'
makeTmatrix: no visible global function definition for 'nb2listw'
makeTmatrix: no visible global function definition for 'diag.spam'
makeTmatrix: no visible global function definition for 'nb2mat'
nodeFilling: no visible global function definition for 'inout'
nodeFilling: no visible global function definition for 'as.points'
plot.formLatticeOutput: no visible global function definition for
  'card'
predict.NparRegOut: no visible global function definition for 'bbox'
predict.NparRegOut: no visible global function definition for 'as.ppp'
predict.NparRegOut: no visible global function definition for 'nncross'
removeHole: no visible global function definition for 'inout'
lbfit.par : loglogistic.fit.optim : loglik.lb.loglogis: no visible
  global function definition for 'pllogis'
optim.const.ordi: no visible binding for global variable 'k'
LD.Measures: no visible global function definition for 'mclapply'
Fisher1sided: warning in round(dp, d = 9): partial argument match of
  'd' to 'digits'
HWE2sided.table: warning in round(xtable, d = 4): partial argument
  match of 'd' to 'digits'
LD2sided.pvals: warning in round(dp, d = 9): partial argument match of
  'd' to 'digits'
LD2sided.pvals: warning in round(LR, d = 9): partial argument match of
  'd' to 'digits'
LD2sided.pvals: warning in round(rr, d = 9): partial argument match of
  'd' to 'digits'
LD2sided.pvals: warning in round(dprime, d = 9): partial argument match
  of 'd' to 'digits'
LD2sided.pvals: warning in round(delta2, d = 9): partial argument match
  of 'd' to 'digits'
LD2sided.pvals: warning in round(yuleQ, d = 9): partial argument match
  of 'd' to 'digits'
LD2sided.tables: warning in round(dp, d = 9): partial argument match of
  'd' to 'digits'
LD2sided.tables: warning in round(LR, d = 9): partial argument match of
  'd' to 'digits'
LD2sided.tables: warning in round(rr, d = 9): partial argument match of
  'd' to 'digits'
LD2sided.tables: warning in round(dprime, d = 9): partial argument
  match of 'd' to 'digits'
LD2sided.tables: warning in round(delta2, d = 9): partial argument
  match of 'd' to 'digits'
LD2sided.tables: warning in round(yuleQ, d = 9): partial argument match
  of 'd' to 'digits'
LD2sided.tables: warning in round(xtable, d = 3): partial argument
  match of 'd' to 'digits'
LD2sided.tables: warning in round(ztable, d = 3): partial argument
  match of 'd' to 'digits'
leafletProxy: no visible global function definition for 'startsWith'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Type 'demo()' for some demos, 'help()' for on-line help, or
  'help.start()' for an HTML browser interface to help.
  Type 'q()' to quit R.
  
  > library(testthat)
  > library(leaflet)
  > 
  > test_check("leaflet")
  Error in library(sf) : there is no package called 'sf'
  Calls: test_check ... with_reporter -> force -> source_file -> eval -> eval -> library
  testthat results ================================================================
  OK: 41 SKIPPED: 0 FAILED: 0
  Execution halted
BEAPFrOG: no visible global function definition for 'jags.model'
BEAPFrOG: no visible global function definition for 'coda.samples'
Namespaces in Imports field not imported from:
  'gridExtra' 'scales' 'tidyverse'
  All declared Imports should be used.
File 'LeLogicielR/R/zzz.R':
  .onLoad calls:
    packageStartupMessage(utils::packageDescription("LeLogicielR",     lib.loc = libname), appendLF = TRUE)

See section 'Good practice' in '?.onAttach'.
Namespace in Imports field not imported from: 'syuzhet'
  All declared Imports should be used.
gap.default: no visible global function definition for 'makeCluster'
gap.default: no visible global function definition for 'clusterEvalQ'
gap.default: no visible global function definition for 'clusterApply'
gap.default: no visible global function definition for 'clusterCall'
gap.default: no visible global function definition for 'stopCluster'
lga.default: no visible global function definition for 'makeCluster'
lga.default: no visible global function definition for 'clusterEvalQ'
lga.default: no visible global function definition for 'clusterApplyLB'
lga.default: no visible global function definition for 'stopCluster'
rlga.default: no visible global function definition for 'makeCluster'
rlga.default: no visible global function definition for 'clusterEvalQ'
rlga.default: no visible global function definition for
  'clusterApplyLB'
rlga.default: no visible global function definition for 'stopCluster'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      3.3Mb
estimate_LC_pdf_state: no visible global function definition for
  'huge.select'
estimate_LC_pdf_state: no visible global function definition for 'huge'
search_knn: no visible global function definition for 'ann'
LICurvature.default: no visible global function definition for 'ginv'
Namespaces in Imports field not imported from:
  'Rcpp' 'rgeos'
  All declared Imports should be used.
Running examples in 'lidR-Ex.R' failed
The error most likely occurred in:

> ### Name: lastrees
> ### Title: Individual tree segmentation
> ### Aliases: lastrees
> 
> ### ** Examples
> 
> LASfile <- system.file("extdata", "Tree.laz", package="lidR")
> las = readLAS(LASfile, XYZonly = TRUE, filter = "-drop_z_below 0")
> 
> # compute a canopy image
> chm = grid_canopy(las, res = 0.5, subcircle = 0.1, na.fill = "knnidw", k = 4)
[using inverse distance weighting]
> chm = as.raster(chm)
> 
> # smoothing post-process (e.g. 2x mean)
> kernel = matrix(1,3,3)
> chm = raster::focal(chm, w = kernel, fun = mean)
> chm = raster::focal(chm, w = kernel, fun = mean)
> raster::plot(chm, col = height.colors(50)) # check the image
> 
> # segmentation (default parameters but th = 4 + extra output)
> extra = lastrees(las, "dalponte2016", chm, th = 4, extra = TRUE)
Error in as.vector(data) : 
  no method for coercing this S4 class to a vector
Calls: lastrees -> dalponte2012 -> matrix -> as.vector
Execution halted
.N: no visible global function definition for 'mpfr'
LIHNPSD_prepare_data: no visible global function definition for
  'skewness'
LIHNPSD_prepare_data: no visible global function definition for
  'kurtosis'
LIHNPSD_standardfit_test: no visible global function definition for
  'skewness'
LIHNPSD_standardfit_test: no visible global function definition for
  'kurtosis'
LihnBetaPoly: no visible global function definition for 'Const'
LihnBetaPoly: no visible global function definition for 'getPrec'
LihnTildeFunction: no visible global function definition for 'Const'
LihnTildeFunction: no visible global function definition for 'getPrec'
prepare.LIHNPSD : D: no visible global function definition for 'mpfr'
prepare.LIHNPSD: no visible global function definition for 'Const'
psdunittest.LIHNPSD: no visible global function definition for
  'sintegral'
rawcdf.LIHNPSD : cdf: no visible global function definition for 'erf'
rawcdf.LIHNPSD : cdf: no visible global function definition for
  'T.Owen'
rawsn.LIHNPSD: no visible global function definition for 'erf'
standardfit.LIHNPSD: no visible global function definition for
  'skewness'
standardfit.LIHNPSD: no visible global function definition for
  'kurtosis'
standardfit.LIHNPSD: no visible global function definition for 'optimx'
Package required but not available: 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
solveLP: no visible global function definition for 'lp'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/lira.Rcheck/00install.out' for details.
ave.sorted: warning in matrix(y[lens == i], nr = i): partial argument
  match of 'nr' to 'nrow'
ave.sorted: warning in matrix(weights[lens == i], nr = i): partial
  argument match of 'nr' to 'nrow'
liso.adaptive: warning in multistep(coefc = rep(0, (nrow(x) - 1) *
  ncol(x)), x = x, intercept = sum(weights * y)/sum(weights), residual
  = y - sum(weights * y)/sum(weights), sorter = getSort(x)): partial
  argument match of 'coefc' to 'coefchain'
liso.backfit: warning in multistep(coefc = rep(0, (nrow(x) - 1) *
  ncol(x)), x = x, intercept = sum(weights * y)/sum(weights), residual
  = y - sum(weights * y)/sum(weights), sorter = getSort(x)): partial
  argument match of 'coefc' to 'coefchain'
liso.maxlamb: no visible global function definition for 'pava'
pavareg: no visible global function definition for 'pava'
pavaregorig: no visible global function definition for 'pava'
lle_sound: no visible binding for global variable 'lle_wave'
plot_lle: no visible global function definition for 'plot3d'
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc        1.8Mb
    libs       2.1Mb
    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'
Namespace in Imports field not imported from: 'boot'
  All declared Imports should be used.
File 'lmmlasso/R/zzz.R':
  .onAttach calls:
    cat("----------------------------------------------------------------------",     "This is a test release of the package 'lmmlasso'. If you have any questions or problems, do not hesitate to contact the author.",     "----------------------------------------------------------------------",     sep = "\n")

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

LambdaInv: no visible global function definition for 'quad.tform'
MLloglik: no visible global function definition for 'quad.form'
MLpdSym: no visible global function definition for 'triang'
MLpdSym: no visible global function definition for 'vecli'
MLpdSymLambda: no visible global function definition for 'quad.tform'
MLsigmaZPsiZt: no visible global function definition for 'quad.tform'
ObjFunction : tResLRes: no visible global function definition for
  'quad.form'
covStartingValues : optimize3: no visible global function definition
  for 'quad.form.inv'
lmmlasso.default: no visible global function definition for 'optL1'
lmmlasso.default: no visible global function definition for 'optL2'
lmmlasso.default: no visible global function definition for 'vecli'
lmmlasso.default: no visible global function definition for 'triang'
lfbas: no visible global function definition for 'basis'
EMmixlcd: no visible global function definition for 'hc'
EMmixlcd: no visible global function definition for 'hclass'
interactive2D: no visible global function definition for 'tktoplevel'
interactive2D: no visible global function definition for 'tclVar'
interactive2D : plotdens: no visible global function definition for
  'tclvalue'
interactive2D: no visible global function definition for 'tkrplot'
interactive2D : densplot: no visible global function definition for
  'tkrreplot'
interactive2D: no visible global function definition for 'tkscale'
interactive2D: no visible global function definition for 'tklabel'
interactive2D: no visible global function definition for 'tkpack'
plot.LogConcDEAD: no visible global function definition for 'open3d'
plot.LogConcDEAD: no visible global function definition for 'par3d'
plot.LogConcDEAD: no visible global function definition for 'surface3d'
plot.LogConcDEAD: no visible global function definition for
  'decorate3d'
plot.LogConcDEAD: no visible global function definition for
  'rgl.surface'
plot.LogConcDEAD: no visible global function definition for 'plot3d'
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.
LCLRCImode: no visible global function definition for 'preProcess'
Local_LL.mode: no visible global function definition for 'Local_LL'
MLE.mode: no visible global function definition for 'LocalNormalize'
MLE.mode: no visible global function definition for 'Local_LL'
MLE.mode: no visible global function definition for 'LocalF'
activeSetLogCon: no visible global function definition for 'preProcess'
activeSetLogCon: no visible global function definition for
  'LocalNormalize'
activeSetLogCon: no visible global function definition for 'LocalMLE'
activeSetLogCon: no visible global function definition for
  'LocalConvexity'
activeSetLogCon: no visible global function definition for 'LocalF'
activeSetLogCon : phi.f: no visible global function definition for
  'evaluateLogConDens'
activeSetLogCon : fhat.f: no visible global function definition for
  'evaluateLogConDens'
activeSetLogCon : Fhat.f: no visible global function definition for
  'evaluateLogConDens'
activeSetLogCon.mode: no visible global function definition for
  'preProcess'
activeSetLogCon.mode: no visible global function definition for
  'LocalNormalize'
activeSetLogCon.mode: no visible global function definition for
  'LocalF'
activeSetLogCon.mode : phi.f: no visible global function definition for
  'evaluateLogConDens'
activeSetLogCon.mode : fhat.f: no visible global function definition
  for 'evaluateLogConDens'
activeSetLogCon.mode : Fhat.f: no visible global function definition
  for 'evaluateLogConDens'
estimateLRdistn: no visible global function definition for 'preProcess'
intECDFfn : Y: no visible global function definition for 'intECDF'
intFfn: multiple local function definitions for 'H' with different
  formal arguments
logConDens: no visible global function definition for
  'evaluateLogConDens'
x2z: no visible global function definition for 'LocalNormalize'
LOGICOIL: no visible binding for global variable 'pssm'
LOGICOIL: no visible binding for global variable 'LOGICOILfit'
LOGICOIL: no visible binding for global variable 'Model_Parameters'
LogrankA: no visible global function definition for 'is.Surv'
predict.KernS: no visible global function definition for 'chkDots'
mipSolve.Rsymphony: no visible global function definition for
  'Rsymphony_solve_LP'
print.summary.lqa: warning in printCoefmat(coefs, P.value = FALSE,
  has.Pvalue = FALSE): partial argument match of 'P.value' to
  'P.values'
example.ls2w: no visible global function definition for 'lda'
Namespace in Imports field not imported from: 'tcltk2'
  All declared Imports should be used.
lsplsCv: no visible global function definition for 'cvsegments'
orthlspls.fit: no visible binding for global variable 'oscorespls.fit'
orthlsplsCv: no visible binding for global variable 'oscorespls.fit'
lss: no visible binding for global variable 'response'
lss.betag: no visible global function definition for 'l1fit'
gauher: no visible binding for global variable 'gh'
vcov.gpcm: no visible global function definition for 'ginv'
vcov.grm: no visible global function definition for 'ginv'
get.Z.HWP: no visible global function definition for 'is.genotype'
get.Z.HWP: no visible global function definition for 'allele.count'
get.lambda: no visible global function definition for 'is.genotype'
get.lambda: no visible global function definition for 'heterozygote'
luca: no visible global function definition for 'is.genotype'
luca: no visible global function definition for 'genotype'
luca: no visible global function definition for 'Surv'
luca: no visible global function definition for 'coxph.fit'
luca: no visible global function definition for 'coxph.control'
Error in re-building vignettes:
  ...
Loading required package: lucid
Loading required package: lattice
Loading required package: rjags
Loading required package: coda
Error : .onLoad failed in loadNamespace() for 'rjags', details:
  call: fun(libname, pkgname)
  error: The environment variable JAGS_HOME is set to
c:/Program Files/JAGS/JAGS-4.0.0
but no JAGS installation can be found there

Quitting from lines 269-293 (lucid_printing.Rmd) 
Error: processing vignette 'lucid_printing.Rmd' failed with diagnostics:
could not find function "jags.model"
Execution halted
LVMMCOR.default: no visible global function definition for 'fdHess'
LVMMCOR.default: no visible global function definition for 'ginv'
project.M3.1.to.M3.2: no visible global function definition for
  'coordinates<-'
project.M3.1.to.M3.2: no visible global function definition for
  'proj4string<-'
project.M3.1.to.M3.2: no visible global function definition for 'CRS'
project.M3.1.to.M3.2: no visible global function definition for
  'spTransform'
project.M3.1.to.M3.2: no visible global function definition for
  'coordinates'
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 41.0Mb
  sub-directories of 1Mb or more:
    doc    6.9Mb
    libs  34.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/maGUI.Rcheck/00install.out' for details.
MalletLDA: no visible global function definition for '.jnew'
mallet.doc.topics: no visible global function definition for
  '.jevalArray'
mallet.import: no visible global function definition for 'J'
mallet.import: no visible global function definition for '.jnew'
mallet.import: no visible global function definition for '.jcast'
mallet.subset.topic.words: no visible global function definition for
  '.jevalArray'
mallet.topic.words: no visible global function definition for
  '.jevalArray'
mallet.word.freqs: no visible global function definition for
  '.jevalArray'
Depends: includes the non-default packages:
  'genefilter' 'metaMA' 'xtable' 'multtest' 'gtools' 'grid' 'GeneMeta'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'GeneMeta' 'xtable' 'methods'
A package should be listed in only one of these fields.
'library' or 'require' calls to packages already attached by Depends:
  'gtools' 'xtable'
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'RankProd' 'gplots'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'grid' 'metaMA' 'multtest'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ageprofile: no visible global function definition for 'predict.gam'
ageprofile: no visible global function definition for 'summary.gam'
ageprofile: no visible global function definition for 'anova.gam'
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.2/maps/libs/i386/maps.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.2/maps/libs/x64/maps.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: 'spatstat.utils'

Package which this enhances but not available for checking: 'gpclib'
aa.account: no visible binding for global variable 'last'
cashflow.portfolio.bond: no visible global function definition for
  'sort.data.frame'
connectTheDots: no visible global function definition for
  'sort.data.frame'
connectTheDots: no visible global function definition for 'last'
connectTheDots: no visible global function definition for 'first'
current.market: no visible global function definition for 'last'
findMaxMat: no visible global function definition for 'lambert_W0'
market.rate: no visible global function definition for 'last'
plot.history.market: no visible global function definition for
  'sort.data.frame'
print.account: no visible binding for global variable 'last'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  testthat results ================================================================
  OK: 97 SKIPPED: 0 FAILED: 1
  1. Failure: Check steadyStates (@testSteadyStates.R#39) 
  
  Error: testthat unit tests failed
  In addition: Warning messages:
  1: In markovchainFit(mix_seq, "map", sanitize = TRUE, possibleStates = c("d")) :
    
  'estimate' is the MAP set of parameters where as 'expectedValue' 
  is the expectation of the parameters with respect to the posterior.
  The confidence intervals are given for 'estimate'.
  2: In data(cav) : data set 'cav' not found
  Execution halted
build.eqn.tex: no visible global function definition for 'str_detect'
build.eqn.tex: no visible global function definition for 'str_trim'
get.mat.tex : tmp.fun: no visible global function definition for
  'latexTranslate'
get.mat.tex : tmp.fun.2: no visible global function definition for
  'str_replace_all'
get.mat.tex: no visible global function definition for 'latexTabular'
get.mat.tex: no visible global function definition for
  'str_replace_all'
parameters.time.varying: no visible global function definition for
  'str_detect'
parameters.time.varying: no visible global function definition for
  'str_trim'
toLatex.marssMODEL: no visible global function definition for
  'str_detect'
toLatex.marssMODEL: no visible global function definition for
  'str_trim'
toLatex.marssMODEL: no visible global function definition for 'str_sub'
toLatex.marssMODEL: no visible global function definition for 'sys'
toLatex.marssMODEL: no visible global function definition for
  'str_replace'
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   1.8Mb
Found the following possibly unsafe calls:
File 'matlab/R/zzz.R':
  unlockBinding("savedTime", .MatlabNamespaceEnv)
fnorm2: no visible global function definition for 'sadmvn'
fnorm3: no visible global function definition for 'sadmvn'
mbmdr : Regresion: no visible global function definition for 'logistf'
laugreen: no visible global function definition for 'lp'
relabel : min.perm.labels: no visible global function definition for
  'lp.transport'
mcgibbsit: no visible global function definition for 'is.mcmc.list'
mcgibbsit: no visible global function definition for 'thin'
mcgibbsit: no visible global function definition for 'nvar'
mcgibbsit: no visible global function definition for 'mcmc'
mcgibbsit: no visible global function definition for 'mcmc.list'
mcgibbsit: no visible global function definition for 'varnames'
mcgibbsit: no visible global function definition for 'niter'
read.mcmc: no visible global function definition for 'mcmc.list'
read.mcmc: no visible global function definition for 'mcmc'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.1Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/mcPAFit.Rcheck/00install.out' for details.
I2.MCPerm: no visible global function definition for 'rma'
I2.MCPerm: no visible global function definition for 'rma.mh'
I2.MCPerm: no visible global function definition for 'rma.peto'
I2.TradPerm: no visible global function definition for 'rma'
I2.TradPerm: no visible global function definition for 'rma.mh'
I2.TradPerm: no visible global function definition for 'rma.peto'
Q.MCPerm: no visible global function definition for 'rma'
Q.MCPerm: no visible global function definition for 'rma.mh'
Q.MCPerm: no visible global function definition for 'rma.peto'
Q.TradPerm: no visible global function definition for 'rma'
Q.TradPerm: no visible global function definition for 'rma.mh'
Q.TradPerm: no visible global function definition for 'rma.peto'
meta: no visible global function definition for 'rma'
meta: no visible global function definition for 'rma.mh'
meta: no visible global function definition for 'rma.peto'
meta.MCPerm: no visible global function definition for 'rma'
meta.MCPerm: no visible global function definition for 'rma.mh'
meta.MCPerm: no visible global function definition for 'rma.peto'
meta.TradPerm: no visible global function definition for 'rma'
meta.TradPerm: no visible global function definition for 'rma.mh'
meta.TradPerm: no visible global function definition for 'rma.peto'
geoshape: no visible global function definition for 'coordinates'
geoshape: no visible global function definition for 'ppp'
geoshape: no visible global function definition for 'nncross'
gmmlogit: no visible global function definition for 'poly2nb'
gmmlogit: no visible global function definition for 'nb2mat'
gmmprobit: no visible global function definition for 'poly2nb'
gmmprobit: no visible global function definition for 'nb2mat'
makew: no visible global function definition for 'coordinates'
makew: no visible global function definition for 'poly2nb'
makew: no visible global function definition for 'nb2mat'
makew: no visible global function definition for 'knearneigh'
makew: no visible global function definition for 'knn2nb'
qregsim1: no visible global function definition for 'brewer.pal'
qregspiv: no visible global function definition for 'poly2nb'
qregspiv: no visible global function definition for 'nb2mat'
sarml: no visible global function definition for 'poly2nb'
sarml: no visible global function definition for 'nb2mat'
sarml: no visible global function definition for 'nb2listw'
sarml: no visible global function definition for 'eigenw'
smooth12: no visible global function definition for 'nn2'
splogit: no visible global function definition for 'poly2nb'
splogit: no visible global function definition for 'nb2mat'
splogit: no visible global function definition for 'hccm'
spprobit: no visible global function definition for 'poly2nb'
spprobit: no visible global function definition for 'nb2mat'
spprobit: no visible global function definition for 'hccm'
spprobitml : makevar: no visible global function definition for
  'poly2nb'
spprobitml : makevar: no visible global function definition for
  'nb2mat'
File 'medSTC/libs/i386/medSTC.dll':
  Found 'rand', possibly from 'rand' (C)
    Objects: 'medstc/medstc.o', 'medstc/corpus.o',
      'svmlight/svm_common.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'medstc/corpus.o'
File 'medSTC/libs/x64/medSTC.dll':
  Found 'rand', possibly from 'rand' (C)
    Objects: 'medstc/medstc.o', 'medstc/corpus.o',
      'svmlight/svm_common.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'medstc/corpus.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Error in re-building vignettes:
  ...
Quitting from lines 101-107 (Getting-started.rnw) 
Error: processing vignette 'Getting-started.rnw' failed with diagnostics:
1: Unknown IO error2: failed to load external entity "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nucleotide&term=cytB%20%5Ball%5D%20OR%20Cytb%20%5Ball%5D%20OR%20CYTB%20%5Ball%5D%20OR%20cytb%20%5Ball%5D%20OR%20CytB%20%5Ball%5D&rettype=gb&retmode=xml"
Execution halted
Namespaces in Imports field not imported from:
  'RColorBrewer' 'RGtk2' 'RNifti' 'cairoDevice' 'gtools' 'jsonlite'
  All declared Imports should be used.
codomToPropShared: no visible global function definition for
  'df2genind'
codomToPropShared: no visible global function definition for
  'propShared'
mgLandscape: no visible global function definition for 'SpatialPoints'
mgQuick: no visible global function definition for 'distm'
mgQuick: no visible binding for global variable 'distMeeus'
metacor.DSL: no visible global function definition for 'metaplot'
metacor.OP: no visible global function definition for 'hyperg_2F1'
metacor.OP: no visible global function definition for 'metaplot'
CDF.rop : <anonymous> : <anonymous>: no visible global function
  definition for 'dmnom'
MetaDE.impute: no visible global function definition for 'impute.knn'
cal.logrank : get.stat: no visible global function definition for
  'coxph'
cal.p.logrank : get.p: no visible global function definition for
  'coxph'
get.RP: no visible binding for global variable 'na.rm'
get.RP: no visible global function definition for 'NaReplace2'
Error in re-building vignettes:
  ...
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Error: processing vignette 'MetaIntegrator.Rmd' failed with diagnostics:
unused arguments (self_contained, lib_dir, output_dir)
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/MetaLandSim.Rcheck/00install.out' for details.
.MetaSparsePCA: no visible global function definition for '%do%'
.MetaSparsePCA: no visible global function definition for 'foreach'
.MetaSparsePCA: no visible global function definition for 'iter'
DropDupGenes: no visible global function definition for 'registerDoMC'
DropDupGenes: no visible global function definition for 'startWorkers'
DropDupGenes: no visible global function definition for 'registerDoSMP'
DropDupGenes: no visible global function definition for '%dopar%'
DropDupGenes: no visible global function definition for 'foreach'
DropDupGenes: no visible global function definition for 'iter'
DropDupGenes: no visible global function definition for 'stopWorkers'
MetaPCA: no visible global function definition for 'PCAgrid'
PlotPC2D: no visible global function definition for 'cov.mve'
PlotPC2D: no visible global function definition for 'ellipse'
PreprocessMetaAnalysis: no visible global function definition for
  '%do%'
PreprocessMetaAnalysis: no visible global function definition for
  'foreach'
PreprocessMetaAnalysis: no visible global function definition for
  'iter'
PreprocessMetaAnalysis: no visible binding for global variable 'dat'
PreprocessMetaAnalysis: no visible global function definition for
  'impute.knn'
requireAll: no visible global function definition for 'biocLite'
downloadAEMETcurrentday: no visible global function definition for
  'startsWith'
downloadAEMETcurrentday: no visible global function definition for
  'endsWith'
QCRep: warning in axis(1, at = 0:axislen, lab = 0:axislen, cex.axis =
  0.7, tcl = -0.2): partial argument match of 'lab' to 'labels'
QCplot: warning in axis(1, at = 1:lenRow, lab = 1:lenRow, cex.axis =
  0.7): partial argument match of 'lab' to 'labels'
AltReg: no visible global function definition for 'lme'
BA.est: no visible global function definition for 'lmeControl'
MCmcmc: no visible global function definition for 'jags.model'
MCmcmc: no visible global function definition for 'bugs'
MCmcmc: no visible global function definition for 'read.bugs'
VC.est: no visible global function definition for 'lmeControl'
VC.est.fixed: no visible global function definition for 'lmeControl'
VC.est.fixed: no visible global function definition for 'lme'
VC.est.fixed: no visible global function definition for 'pdIdent'
VC.est.fixed: no visible global function definition for 'varIdent'
VC.est.fixed: no visible global function definition for 'pdDiag'
VC.est.fixed: no visible global function definition for 'pdSymm'
VC.est.random: no visible global function definition for 'lmeControl'
VC.est.random: no visible global function definition for 'lme'
VC.est.random: no visible global function definition for 'pdBlocked'
VC.est.random: no visible global function definition for 'pdIdent'
VC.est.random: no visible global function definition for 'varIdent'
VC.est.random: no visible global function definition for 'ranef'
VC.est.random: no visible global function definition for 'pdDiag'
find.mean: no visible global function definition for 'varnames'
find.vars: no visible global function definition for 'varnames'
pairs.MCmcmc: no visible global function definition for 'varnames'
subset.MCmcmc : char.2.num: no visible global function definition for
  'varnames'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   2.8Mb
eventpois: no visible global function definition for 'dsort'
FoM.FitBinnedSampleRepeatErrors : local.fit.function: no visible global
  function definition for 'rlm'
RevNet.JacobianMethod : RevNet.FirstEstimate: no visible global
  function definition for 'lm.ridge'
dbgpd_bilog: no visible global function definition for 'pbvevd'
dbgpd_negbilog: no visible global function definition for 'pbvevd'
dtgpd_psilog : conv: no visible global function definition for
  'is.positive.definite'
dtgpd_psilog: no visible global function definition for 'image.plot'
dtgpd_psineglog : conv: no visible global function definition for
  'is.positive.definite'
dtgpd_psineglog: no visible global function definition for 'image.plot'
mgpd_init: no visible global function definition for 'fgev'
ml_bilog: no visible global function definition for 'pbvevd'
ml_negbilog: no visible global function definition for 'pbvevd'
pbgpd_bilog: no visible global function definition for 'pbvevd'
pbgpd_ct: no visible global function definition for 'pbvevd'
pbgpd_negbilog: no visible global function definition for 'pbvevd'
ptgpd_psilog : conv: no visible global function definition for
  'is.positive.definite'
ptgpd_psilog: no visible global function definition for 'image.plot'
ptgpd_psineglog : conv: no visible global function definition for
  'is.positive.definite'
ptgpd_psineglog: no visible global function definition for 'image.plot'
inbar: no visible global function definition for 'spplot'
inbox: no visible global function definition for 'spplot'
indot: no visible global function definition for
  'SpatialPointsDataFrame'
indot: no visible global function definition for 'coordinates'
indot: no visible global function definition for 'CRS'
indot: no visible global function definition for 'bubble'
inhist: no visible global function definition for 'spplot'
inline: no visible global function definition for 'spplot'
inmap: no visible global function definition for
  'SpatialPointsDataFrame'
inmap: no visible global function definition for 'coordinates'
inmap: no visible global function definition for 'CRS'
inmap: no visible global function definition for 'bubble'
inmap: no visible global function definition for 'spplot'
inpie: no visible global function definition for 'spplot'
inscatter: no visible global function definition for 'spplot'
.onAttach: no visible binding for global variable '.MGRAST'
build.MGRAST: no visible binding for global variable '.MGRAST'
build.MGRAST: no visible global function definition for 'fromJSON'
call.MGRAST: no visible binding for global variable '.MGRAST'
call.MGRAST: no visible global function definition for 'isValidJSON'
call.MGRAST: no visible global function definition for 'fromJSON'
doc.MGRAST: no visible binding for global variable '.MGRAST'
load.MGRAST: no visible binding for global variable '.MGRAST'
parse.MGRAST: no visible binding for global variable '.MGRAST'
this.package: no visible binding for global variable '.MGRAST'
Running examples in 'micropan-Ex.R' failed
The error most likely occurred in:

> ### Name: entrezDownload
> ### Title: Downloading genome data
> ### Aliases: entrezDownload
> 
> ### ** Examples
> 
> # Accession numbers for the chromosome and plasmid of Buchnera aphidicola, strain APS
> entrezDownload( accession="BA000003.2,AP001071.1", out.file="Buchnera_aphidicola_APS.fsa" )
Downloading genome...Warning in url(adr, open = "rt") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in url(adr, open = "rt") : cannot open the connection
Calls: entrezDownload -> url
Execution halted
MigClim.genClust: no visible global function definition for 'raster'
MigClim.migrate: no visible global function definition for 'raster'
MigClim.migrate: no visible global function definition for
  'dataframe2asc'
MigClim.migrate: no visible global function definition for
  'writeRaster'
MigClim.migrate: no visible global function definition for 'cellStats'
MigClim.plot: no visible global function definition for 'raster'
MigClim.plot: no visible global function definition for 'ymax'
MigClim.plot: no visible global function definition for 'ymin'
MigClim.plot: no visible global function definition for 'xmax'
MigClim.plot: no visible global function definition for 'xmin'
summary.MImixresult: warning in qt(alpha/2, object$df, lower = FALSE):
  partial argument match of 'lower' to 'lower.tail'
Namespaces in Imports field not imported from:
  'DiceDesign' 'MaxPro' 'doSNOW'
  All declared Imports should be used.
minPtest: no visible global function definition for 'sfIsRunning'
minPtest: no visible global function definition for 'sfInit'
minPtest: no visible global function definition for 'sfLibrary'
minPtest: no visible global function definition for 'sfExport'
minPtest: no visible global function definition for 'sfClusterApplyLB'
minPtest: no visible global function definition for 'mclapply'
minPtest: no visible global function definition for 'sfStop'
Namespaces in Imports field not imported from:
  'MASS' 'cluster' 'dendextend' 'npmv' 'utils'
  All declared Imports should be used.
change_family,missing-proportion-family : .local: no visible binding
  for global variable '.identity_transformation'
fit_model,missing-multilevel_missing_data.frame : .local: no visible
  binding for global variable 'X'
image,mi : .local: no visible global function definition for 'Matrix'
image,missing_data.frame : .local: no visible global function
  definition for 'Matrix'
mi,grouped-binary-clogit : .local: no visible global function
  definition for 'untangle.specials'
drawScene.rgl: no visible global function definition for 'rgl.cur'
drawScene.rgl: no visible global function definition for 'open3d'
drawScene.rgl: no visible global function definition for 'clear3d'
drawScene.rgl: no visible global function definition for 'triangles3d'
image3d: no visible global function definition for 'clear3d'
image3d: no visible global function definition for 'sprites3d'
image3d: no visible global function definition for 'points3d'
slices3d : mkimg: no visible global function definition for 'tkrplot'
slices3d : mkscale : f: no visible global function definition for
  'tclvalue'
slices3d : mkscale : f: no visible global function definition for
  'tkrreplot'
slices3d : mkscale : f: no visible global function definition for
  'tkconfigure'
slices3d : mkscale: no visible global function definition for 'tkframe'
slices3d : mkscale: no visible global function definition for 'tkscale'
slices3d : mkscale: no visible global function definition for 'tklabel'
slices3d : mkscale: no visible global function definition for 'tkgrid'
slices3d : move: no visible global function definition for 'tkbind'
slices3d : move : <anonymous>: no visible global function definition
  for 'tkwinfo'
slices3d : move : <anonymous>: no visible global function definition
  for 'tkrreplot'
slices3d : move : <anonymous>: no visible global function definition
  for 'tclvalue<-'
slices3d: no visible global function definition for 'tktoplevel'
slices3d: no visible global function definition for 'tktitle<-'
slices3d: no visible binding for global variable 'tclVar'
slices3d: no visible global function definition for 'tkgrid'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/miscF.Rcheck/00install.out' for details.
missForest: no visible global function definition for 'idiv'
dmvgt: no visible global function definition for 'dmvt'
rmvgt: no visible global function definition for 'rmvt'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
anova.mix: warning in pchisq(dchisq, ddf, low = FALSE): partial
  argument match of 'low' to 'lower.tail'
Namespace in Imports field not imported from: 'rjags'
  All declared Imports should be used.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  OK: 26 SKIPPED: 0 FAILED: 9
  1. Error: Wolves ex works (@test_ex1_wolves.R#33) 
  2. Error: Geese ex works (@test_ex2_geese.R#27) 
  3. Error: Lake ex works (@test_ex3_lake.R#27) 
  4. Error: Palmyra ex works (@test_ex4_palmyra.R#27) 
  5. Error: Killer whale ex works (@test_ex5_killerwhale.R#28) 
  6. Error: Snail ex works (@test_ex6_snail.R#27) 
  7. Error: Storm-petrel ex works (@test_ex7_stormpetrel.R#27) 
  8. Error: Cladocera ex works (@test_ex8_cladocera.R#31) 
  9. Error: Isopod ex works (@test_ex9_isopod.R#27) 
  
  Error: testthat unit tests failed
  Execution halted
.DNA.connectivitylist : .fun_conn_idx: no visible global function
  definition for 'attach.big.matrix'
.DNA.distance: no visible global function definition for
  'as.big.matrix'
.checkadjmatrix: no visible global function definition for
  'is.big.matrix'
.filterLowCorrelation: no visible global function definition for
  'is.big.matrix'
.network.differences : .fun_distance: no visible global function
  definition for 'attach.big.matrix'
.uniqueTissues: no visible global function definition for 'str_sub'
geneRanker: no visible global function definition for 'RankingTstat'
geneRanker: no visible global function definition for 'RankingFC'
geneRanker: no visible global function definition for 'RankingWilcoxon'
geneRanker: no visible global function definition for
  'RankingBaldiLong'
geneRanker: no visible global function definition for
  'RankingShrinkageT'
geneRanker: no visible global function definition for 'RankingSam'
geneRanker: no visible global function definition for
  'RankingSoftthresholdT'
geneRanker: no visible global function definition for 'RankingLimma'
geneRanker: no visible global function definition for 'toplist'
mlegp: no visible global function definition for 'sfLapply'
mleurDiag: no visible global function definition for 'shapiroTest'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/MLID.Rcheck/00install.out' for details.
do.estimate.mlogit: no visible global function definition for 'maxLik'
get.mnl.data: no visible global function definition for 'abind'
imageplot.mlogit: no visible global function definition for
  'imageplot.bma'
listGenoToTable: no visible binding for global variable 'dummy'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/mlVAR.Rcheck/00install.out' for details.
Found the following significant warnings:
  mmap.c:223:48: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  mmap.c:226:46: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.2/mmap.Rcheck/00install.out' for details.
mmm: no visible global function definition for 'gee'
.Oarray_to_MB: no visible global function definition for 'is.Oarray'
.gunter: no visible global function definition for 'minmax'
.gunter: no visible global function definition for 'compositions'
MM: no visible global function definition for 'minmax'
MM_allsamesum: no visible global function definition for 'quad.tform'
MM_allsamesum_A: no visible global function definition for 'minmax'
MM_allsamesum_A: no visible global function definition for 'tr'
MM_allsamesum_A: no visible global function definition for 'quad.tform'
MM_differsums: no visible global function definition for 'quad.tform'
MM_single: no visible global function definition for 'quad.form'
NormC: no visible global function definition for 'compositions'
as.array.gunter_MB: no visible global function definition for 'Oarray'
expected_suffstats: no visible global function definition for
  'compositions'
optimizer: no visible global function definition for 'minmax'
optimizer_allsamesum: no visible global function definition for
  'minmax'
suffstats: no visible global function definition for 'minmax'
gunter,data.frame: no visible global function definition for 'minmax'
gunter,data.frame: no visible global function definition for
  'compositions'
gunter,matrix: no visible global function definition for 'minmax'
gunter,matrix: no visible global function definition for 'compositions'
biplot.character: no visible global function definition for 'opts'
biplot.character: no visible global function definition for
  'theme_blank'
distributionplot.factor: no visible global function definition for
  'opts'
distributionplot.factor: no visible global function definition for
  'theme_text'
scatterplot: no visible global function definition for 'opts'
scatterplot: no visible global function definition for 'theme_text'
timeplot: no visible global function definition for 'opts'
clusval: no visible global function definition for 'std.ext'
clusval: no visible global function definition for 'confusion.matrix'
clusval: no visible global function definition for 'similarity.index'
clusval: no visible global function definition for 'clv.Jaccard'
clusval: no visible global function definition for 'clv.Folkes.Mallows'
predict_baseline: no visible global function definition for 'knn1'
predict_cclust: no visible global function definition for 'cclust'
predict_kmeans: no visible global function definition for 'knn1'
predict_single: no visible global function definition for 'agnes'
predict_single: no visible global function definition for 'knn1'
contour.hmac: no visible global function definition for 'kde2d'
modalclust: no visible global function definition for 'mclapply'
phmac: no visible global function definition for 'mclapply'
File 'modeest/R/zzz.R':
  .onLoad calls:
    packageStartupMessage("\nThis is package 'modeest' written by P. PONCET.\nFor a complete list of functions, use 'library(help = \"modeest\")' or 'help.start()'.\n")

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

.mlv.fisk: no visible global function definition for 'pfisk'
.mlv.frechet: no visible global function definition for 'pfrechet'
.mlv.gev: no visible global function definition for 'pgev'
.mlv.gh: no visible global function definition for 'pgh'
.mlv.gompertz: no visible global function definition for 'pgompertz'
.mlv.gpd: no visible global function definition for 'pgpd'
.mlv.gumbel: no visible global function definition for 'pgumbel'
.mlv.hyp: no visible global function definition for 'phyp'
.mlv.koenker: no visible global function definition for 'pkoenker'
.mlv.kumar: no visible global function definition for 'pkumar'
.mlv.laplace: no visible global function definition for 'plaplace'
.mlv.nig: no visible global function definition for 'pnig'
.mlv.paralogistic: no visible global function definition for
  'pparalogistic'
.mlv.pareto: no visible global function definition for 'ppareto'
.mlv.rayleigh: no visible global function definition for 'prayleigh'
.mlv.rweibull: no visible global function definition for 'prweibull'
.mlv.stable: no visible global function definition for 'pstable'
ghMode: no visible global function definition for 'qgh'
ghMode: no visible binding for global variable 'dgh'
nigMode: no visible global function definition for 'qnig'
nigMode: no visible binding for global variable 'dnig'
stableMode: no visible binding for global variable 'dstable'
Namespace in Imports field not imported from: 'broom'
  All declared Imports should be used.
byteint2bit: no visible global function definition for 'digitsBase'
extract_bit: no visible global function definition for 'digitsBase'
get_bitgrid: no visible global function definition for 'raster'
get_bitgrid: no visible global function definition for 'coordinates'
get_bitgrid: no visible global function definition for 'extract'
get_bitgrid_2bits: no visible global function definition for 'raster'
get_bitgrid_2bits: no visible global function definition for
  'coordinates'
get_bitgrid_2bits: no visible global function definition for 'extract'
make_cloudcount_product: no visible global function definition for
  'CRS'
make_cloudcount_product: no visible global function definition for
  'proj4string'
make_cloudcount_product: no visible global function definition for
  'extent'
make_cloudcount_product: no visible global function definition for
  'coordinates<-'
make_cloudcount_product: no visible global function definition for
  'SpatialPixelsDataFrame'
make_cloudcount_product: no visible global function definition for
  'coordinates'
numslist_to_grd: no visible global function definition for 'CRS'
numslist_to_grd: no visible global function definition for
  'proj4string'
numslist_to_grd: no visible global function definition for 'extent'
numslist_to_grd: no visible global function definition for
  'coordinates<-'
numslist_to_grd: no visible global function definition for
  'SpatialPixelsDataFrame'
numslist_to_grd: no visible global function definition for
  'coordinates'
yearday_to_date: no visible global function definition for 'mdy.date'
yearday_to_date: no visible global function definition for 'date.mdy'
yearmonthday_to_julianday: no visible global function definition for
  'mdy.date'
Package required and available but unsuitable version: 'graphics'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
Namespaces in Imports field not imported from:
  'rlecuyer' 'snow'
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/morse.Rcheck/00install.out' for details.
mMap: no visible binding for global variable 'facet'
mScatter: no visible binding for global variable 'facet'
mUniplot: no visible binding for global variable 'facet'
Package required and available but unsuitable version: 'slam'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'mpa/R/zzz.R':
  .First.lib calls:
    cat("\n mpa: CoWords Method")
    cat("\n ")
    cat("\n Universidad Nacional de Colombia")
    cat("\n ")
    cat("\n Elaborado por: Daniel Rodriguez <dhrodriguezt@unal.edu.co>")
    cat("\n                Campo Elias Pardo <cepardot@unal.edu.co>")
    cat("\n For help: ?mpa   \n\n")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
GetExampleData: no visible binding for global variable 'MPINetData'
Getenvir: no visible binding for global variable 'MPINetData'
Found the following significant warnings:
  Warning: failed to assign NativeSymbolInfo for env since env is already defined in the 'lazyeval' namespace
See 'd:/Rcompile/CRANpkg/local/3.2/mpMap.Rcheck/00install.out' for details.
CR_calcLD: no visible global function definition for 'lowerTriangle'
fill: no visible global function definition for 'upperTriangle<-'
fill: no visible global function definition for 'lowerTriangle<-'
fill: no visible global function definition for 'lowerTriangle'
fill: no visible global function definition for 'upperTriangle'
findqtl2: no visible global function definition for 'dilation'
fit.mpqtl: no visible global function definition for 'wald.test'
mpIM: no visible global function definition for 'stepAIC'
mpIM: no visible global function definition for 'wald.test'
mpcalcld: no visible global function definition for 'lowerTriangle<-'
mpcalcld: no visible global function definition for 'upperTriangle<-'
mpcalcld: no visible global function definition for 'upperTriangle'
mpestrf: no visible global function definition for 'lowerTriangle<-'
mpestrf: no visible global function definition for 'upperTriangle<-'
mpestrf: no visible global function definition for 'upperTriangle'
mporder : <anonymous>: no visible global function definition for
  'seriate'
mporder: no visible binding for global variable 'get_order'
mpprob: no visible global function definition for 'happy'
mpprob: no visible global function definition for 'hdesign'
plot.mapcomp: no visible global function definition for 'xyplot'
plot.mpcross: no visible global function definition for
  'upperTriangle<-'
plot.mpcross: no visible global function definition for 'upperTriangle'
plot.mpcross: no visible global function definition for
  'lowerTriangle<-'
plot.mpcross: no visible global function definition for 'lowerTriangle'
plot.mpcross: no visible global function definition for 'heatmap_2'
mpmcorrelogram: no visible global function definition for
  'mantel.partial'
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'
plot.mpm: warning in symbols(ss[isel, 1], ss[isel, 2], circle =
  sqs[isel], inches = FALSE, lwd = 3, add = TRUE, fg = colors[2]):
  partial argument match of 'circle' to 'circles'
plot.mpm: warning in symbols(ll[ii, 1], ll[ii, 2], square = sqs, inches
  = FALSE, lwd = 3, add = TRUE, fg = colors[2 + iGroup[i]]): partial
  argument match of 'square' to 'squares'
Note: significantly better compression could be obtained
        by using R CMD build --resave-data
           old_size new_size compress
  cgps.rda    1.5Mb    1.4Mb       xz
MRsurvival: no visible global function definition for 'rmvnorm'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/msBP.Rcheck/00install.out' for details.
kgml_i: no visible global function definition for 'xmlTreeParse'
kgml_i: no visible global function definition for 'xmlRoot'
kgml_i: no visible global function definition for 'xmlAttrs'
list2xml: no visible global function definition for 'xmlNode'
list2xml: no visible global function definition for 'append.xmlNode'
read_pathway: no visible global function definition for 'xmlTreeParse'
read_pathway: no visible global function definition for 'xmlRoot'
read_pathway: no visible global function definition for 'xmlToList'
read_pathway: no visible global function definition for 'xmlAttrs'
Found the following significant warnings:
  Warning: 'loadRcppModules' is deprecated.
See 'd:/Rcompile/CRANpkg/local/3.2/MSeasy.Rcheck/00install.out' for details.
MS.DataCreation: no visible global function definition for 'tclvalue'
MS.DataCreation: no visible global function definition for
  'tkchooseDirectory'
MS.clust: no visible global function definition for 'tk_choose.files'
MS.test.clust: no visible global function definition for
  'tk_choose.files'
MSeasyToARISTO: no visible global function definition for
  'tk_choose.files'
MSeasyToMSP: no visible global function definition for
  'tk_choose.files'
SearchNIST: no visible global function definition for 'tclvalue'
SearchNIST: no visible global function definition for
  'tkchooseDirectory'
SearchNIST: no visible global function definition for 'tk_choose.files'
trans.ASCII: no visible global function definition for 'tclvalue'
trans.ASCII: no visible global function definition for
  'tkchooseDirectory'
Found the following significant warnings:
  Warning: 'loadRcppModules' is deprecated.
See 'd:/Rcompile/CRANpkg/local/3.2/MSeasyTkGUI.Rcheck/00install.out' for details.
dialog.MS.clust: no visible binding for global variable
  'Agilent_quantF_MSclust'
dialog.MS.test.clust: no visible binding for global variable
  'Data_testclust'
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
[,MSM.fitted-character-missing-missing : .local: warning in switch(EXP
  = i, CondMean = return(x@CondMean), error = return(x@error), Likel =
  return(x@Likel), margLik = return(x@margLik), filtProb =
  return(x@filtProb), smoProb = return(x@smoProb), states =
  return(apply(x@smoProb, 1, which.max)), smoTransMat =
  return(x@smoTransMat), logLikel = return(x@logLikel), stop("Error:",
  i, "is not a MSM.fitted slot")): partial argument match of 'EXP' to
  'EXPR'
[,MSM.glm-character-missing-missing : .local: warning in switch(EXP =
  i, call = return(x@call), model = return(x@model), k = return(x@k),
  switch = return(x@switch), Coef = return(x@Coef), seCoef =
  return(x@seCoef), transMat = return(x@transMat), iniProb =
  return(x@iniProb), Fit = return(x@Fit), states =
  return(x@Fit["states"]), family = return(x@family), stop("Error:", i,
  "is not a MSM slot")): partial argument match of 'EXP' to 'EXPR'
[,MSM.lm-character-missing-missing : .local: warning in switch(EXP = i,
  call = return(x@call), model = return(x@model), k = return(x@k),
  switch = return(x@switch), Coef = return(x@Coef), seCoef =
  return(x@seCoef), std = return(x@std), transMat = return(x@transMat),
  iniProb = return(x@iniProb), Fit = return(x@Fit), states =
  return(x@Fit["states"]), stop("Error:", i, "is not a MSM slot")):
  partial argument match of 'EXP' to 'EXPR'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Error: `mapped_plot` not equal to lazyLoadDBfetch(c(36516L, 321L), datafile, compressed, envhook).
  Component "layers": Component 1: Component 3: Component 2: Modes of target, current: function, environment
  Component "layers": Component 1: Component 3: Component 2: target, current do not match when deparsed
  Component "layers": Component 1: Component 7: Component 2: Modes of target, current: function, environment
  Component "layers": Component 1: Component 7: Component 2: target, current do not match when deparsed
  Component "layers": Component 1: Component 9: Component 2: Modes of target, current: function, environment
  Component "layers": Component 1: Component 9: Component 2: target, current do not match when deparsed
  Component "layers": Component 1: Component 12: Modes of target, current: function, environment
  Component "layers": Component 1: Component 12: target, current do not match when deparsed
  Component "layers": Component 2: Component 3: Component 2: Modes of target, current: fun
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
plmm.mtk: no visible global function definition for 'stepAIC'
File 'mtsdi/R/zzz.R':
  .onLoad calls:
    packageStartupMessage(paste("This is 'mtsdi' library", ver, sep = " "))

See section 'Good practice' in '?.onAttach'.
getFlights: no visible binding for global variable 'htmlTreeParse'
getFlights: no visible binding for global variable 'xpathSApply'
getFlights: no visible binding for global variable 'xmlAttrs'
getFlights: no visible binding for global variable 'free'
plot.routes : a: no visible global function definition for
  'gcIntermediate'
routes: no visible global function definition for 'distHaversine'
routes: no visible global function definition for 'gcIntermediate'
CrossValidationMuFicokm: no visible global function definition for
  'covMatrix'
CrossValidationMuFicokmAll: no visible global function definition for
  'covMatrix'
MuFicokm: no visible global function definition for 'km'
computeAuxVariables: no visible global function definition for
  'covMatrix'
kmCok: no visible global function definition for 'drop.response'
kmCok: no visible global function definition for 'covStruct.create'
kmCok: no visible global function definition for 'covParametersBounds'
kmCok: no visible binding for global variable 'kmEstimate'
kmCok : cv: no visible global function definition for 'leaveOneOut.km'
predict.kmCok: no visible global function definition for 'covMat1Mat2'
predict.kmCok: no visible global function definition for 'covMatrix'
summary.MuFicokm: no visible global function definition for
  'covparam2vect'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/multinet.Rcheck/00install.out' for details.
genoudRob: no visible global function definition for 'genoud'
Found the following significant warnings:
  Warning: replacing previous import 'class::somgrid' by 'kohonen::somgrid' when loading 'multisom'
See 'd:/Rcompile/CRANpkg/local/3.2/multisom.Rcheck/00install.out' for details.
showmap: no visible binding for global variable 'landmask'
File 'multxpert/R/zzz.R':
  .onLoad calls:
    cat("multxpert: Implementation of commonly used p-value based and parametric\n",     "multiple testing procedures and parallel gatekeeping procedures.\n",     "For more information visit http://multxpert.com/wiki/MultXpert_package\n",     sep = "")

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

pdunnett: no visible global function definition for 'GenzBretz'
qdunnett: no visible global function definition for 'GenzBretz'
Plot.pca.score: no visible global function definition for 'dataEllipse'
Plot.plsda: no visible global function definition for 'dataEllipse'
explore.data: no visible global function definition for 'T2.test'
oplsda: no visible global function definition for 'dataEllipse'
ostocsy: no visible global function definition for 'colorpanel'
outlier: no visible global function definition for 'pdist'
plsda: no visible global function definition for 'plsr'
stocsy: no visible global function definition for 'colorpanel'
stocsy.1d: no visible global function definition for 'rich.colors'
mvtmeta_fe: no visible global function definition for 'combinations'
mvtsplot: no visible global function definition for 'brewer.pal'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.3Mb
    libs   1.3Mb
quantile,cenmle-lognormal : .local: warning in formatC(100 * q, format
  = "fg", wid = 1): partial argument match of 'wid' to 'width'
summary,ros : .local: no visible global function definition for
  'plot.lm'
Found the following significant warnings:
  Warning: failed to assign NativeSymbolInfo for env since env is already defined in the 'lazyeval' namespace
See 'd:/Rcompile/CRANpkg/local/3.2/NanoStringNorm.Rcheck/00install.out' for details.
Package required but not available: 'RcppCCTZ'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  Warning: failed to assign NativeSymbolInfo for env since env is already defined in the 'lazyeval' namespace
See 'd:/Rcompile/CRANpkg/local/3.2/NAPPA.Rcheck/00install.out' for details.
bcrm: no visible global function definition for 'startsWith'
getVarComponent.bcrm: no visible global function definition for
  'endsWith'
ncal.formula: no visible global function definition for 'startsWith'
plot.marginals: no visible global function definition for 'startsWith'
read.luminex.xls: no visible global function definition for
  'startsWith'
Running the tests in 'tests/doRUnit.R' failed.
Last 13 lines of output:
  Number of test functions: 3 
  Number of errors: 1 
  Number of failures: 0 
  
   
  1 Test Suite : 
  nCal unit testing - 3 test functions, 1 error, 0 failures
  ERROR in test.ncal: Error in getVarComponent.bcrm(fit) : could not find function "endsWith"
  Error: 
  
  unit testing failed (#test failures: 0, #R errors: 1)
  
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 100-102 (nCal-vignette.Rnw) 
Error: processing vignette 'nCal-vignette.Rnw' failed with diagnostics:
could not find function "endsWith"
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/ndjson.Rcheck/00install.out' for details.
XH: no visible binding for global variable 'exprs'
XIs: no visible binding for global variable 'exprs'
cv.aep: no visible global function definition for 'mclapply'
cv.frsvm: no visible global function definition for 'mclapply'
cv.hubc: no visible global function definition for 'mclapply'
cv.pac: no visible global function definition for 'mclapply'
cv.stsvm: no visible global function definition for 'mclapply'
probeset2pathway: no visible binding for global variable
  'KEGGEXTID2PATHID'
probeset2pathwayTrain: no visible binding for global variable
  'KEGGEXTID2PATHID'
spanbound: no visible global function definition for 'param'
spanbound: no visible global function definition for 'error'
spanbound: no visible global function definition for 'kernelf'
spanbound: no visible global function definition for 'b'
svm.predict: no visible global function definition for 'b'
macros/struct_test.Rd: Sections \title, and \name must exist and be unique in Rd files
problem found in 'struct_test.Rd'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/NetRep.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'htmlTable' 'lme4' 'stringi'
  All declared Imports should be used.
nMreg: warning in pt(tmreg[i], (length(xa) - 1) + (length(xb) - 1) - 4,
  lower = FALSE, log = TRUE): partial argument match of 'lower' to
  'lower.tail'
nMreg: warning in pt(tmreg[i], (length(xa) - 1) + (length(xb) - 1) - 4,
  lower = FALSE, log = TRUE): partial argument match of 'log' to
  'log.p'
bentlerParameters: no visible global function definition for
  'wireframe'
bentlerParameters: no visible global function definition for
  'contourplot'
bentlerParameters: no visible global function definition for
  'levelplot'
corFA: no visible global function definition for 'ginv'
iterativePrincipalAxis: no visible global function definition for
  'ginv'
parallel: no visible global function definition for 'mvrnorm'
parallel: no visible global function definition for 'ginv'
principalAxis: no visible global function definition for 'ginv'
structureSim: no visible global function definition for 'sim.structure'
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    CppCode   1.7Mb
    R         2.4Mb
    include   3.7Mb
    libs      1.3Mb
Error in re-building vignettes:
  ...
Error in deriv.default(firstd, "x") : 
  invalid expression in 'FindSubexprs'
Error : object 'x' not found
Error : object 'x' not found
Loading required package: Ryacas
d:\RCompile\CRANpkg\lib\3.2\Ryacas\yacdir\yacas.exe and/or d:\RCompile\CRANpkg\lib\3.2\Ryacas\yacdir\scripts.dat not found
run yacasInstall() without arguments to installation yacas.

Attaching package: 'Ryacas'

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

    Simplify

Quitting from lines 428-442 (nlsr-derivs.Rmd) 
Error: processing vignette 'nlsr-derivs.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
denoiseperm: no visible global function definition for 'ebayesthresh'
add.test: no visible global function definition for 'ace'
ll.order: no visible global function definition for 'locfit.raw'
ll.order: no visible global function definition for 'dat'
predict.ll.order: no visible global function definition for
  'locfit.raw'
algorithm,NMFStrategyOctave : .local: no visible global function
  definition for 'fstop'
evar,ANY : .local: no visible binding for global variable 'Biobase'
nmf,matrix-numeric-NMFStrategy : .local : run.all: no visible binding
  for global variable 'n'
nmf,matrix-numeric-NMFStrategy : .local : run.all: no visible binding
  for global variable 'RNGobj'
rss,matrix : .local: no visible binding for global variable 'Biobase'
NNS.M.reg: possible error in findInterval(original.IVs[, j],
  sort(na.omit(reg.points.matrix[, j])), left.open = T): unused
  argument (left.open = T)
NNS.M.reg: possible error in findInterval(original.IVs[, j],
  sort(na.omit(reg.points.matrix[, j])), left.open = F): unused
  argument (left.open = F)
NNS.reg: possible error in findInterval(x, Regression.Coefficients[,
  (X.Lower.Range)], left.open = F): unused argument (left.open = F)
NNS.reg: possible error in findInterval(x, regression.points[, x],
  left.open = F): unused argument (left.open = F)
NNS.reg: possible error in findInterval(point.est,
  Regression.Coefficients[, (X.Lower.Range)], left.open = F): unused
  argument (left.open = F)
NNS.reg: possible error in findInterval(point.est, regression.points[,
  x], left.open = F): unused argument (left.open = F)
Running examples in 'NNS-Ex.R' failed
The error most likely occurred in:

> ### Name: NNS.ARMA
> ### Title: NNS ARMA
> ### Aliases: NNS.ARMA
> ### Keywords: Autoregressive model
> 
> ### ** Examples
> 
> ## Nonlinear NNS.ARMA using AirPassengers monthly data and 12 period lag
> NNS.ARMA(AirPassengers,h=45,Training_set=100,Seasonal_Factor=12,Method='nonlin')
Error in findInterval(x, Regression.Coefficients[, (X.Lower.Range)], left.open = F) : 
  unused argument (left.open = F)
Calls: NNS.ARMA -> sapply -> lapply -> FUN -> NNS.reg -> findInterval
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 39-40 (NNSvignette_clustreg.Rmd) 
Error: processing vignette 'NNSvignette_clustreg.Rmd' failed with diagnostics:
unused argument (left.open = F)
Execution halted
Found the following significant warnings:
  Warning: failed to assign NativeSymbolInfo for env since env is already defined in the 'lazyeval' namespace
See 'd:/Rcompile/CRANpkg/local/3.2/nonparaeff.Rcheck/00install.out' for details.
additive: no visible global function definition for 'lp'
ar.dual.dea: no visible global function definition for 'lp'
cost.dea: no visible global function definition for 'lp'
ddf: no visible global function definition for 'lp'
dea: no visible global function definition for 'lp'
direc.dea: no visible global function definition for 'lp'
dual.dea: no visible global function definition for 'lp'
effdea.b.f: no visible global function definition for 'convhulln'
effdea.b.f: no visible global function definition for 'lp'
faremalm2: no visible binding for global variable 'Lag'
int.dea: no visible global function definition for 'lp'
lp2: no visible global function definition for 'lp'
revenue.dea: no visible global function definition for 'lp'
sbm.tone: no visible global function definition for 'lp'
sbm.vrs: no visible global function definition for 'lp'
dist.plot.bar.plot: no visible global function definition for
  'rainbow_hcl'
dist.plot.hist.plot: no visible global function definition for
  'rainbow_hcl'
plot.stdf: no visible global function definition for 'rainbow_hcl'
Error in re-building vignettes:
  ...
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "nonrandom.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.2.5/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.2.5/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'nonrandom.tex' failed

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

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

Execution halted
normgam.fit: no visible global function definition for 'optimx'
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.
File 'npde/R/zzz.R':
  .onLoad calls:
    packageStartupMessage("     Loading library npde, version 2.0, August 2012\n         please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr\n")

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

npde.binning: no visible global function definition for 'Mclust'
NPHMC: no visible global function definition for 'smcure'
NPHMC: no visible global function definition for 'coxph'
allsomv: no visible binding for global variable 'raw_data'
apsomv: no visible binding for global variable 'raw_data'
apsomv: no visible binding for '<<-' assignment to 'NAwarning'
cfuinterpolation: no visible binding for global variable
  'measured_values'
disconestep: no visible binding for global variable 'measured_values'
disconestep: no visible binding for global variable 'psteps'
makepdfoutput: no visible binding for '<<-' assignment to 'textt'
npmpm: no visible binding for '<<-' assignment to 'inputsettings'
npmpm: no visible binding for global variable 'psteps'
npmpm: no visible binding for '<<-' assignment to 'cfu'
npmpm: no visible binding for '<<-' assignment to 'countwarnings'
npmpm: no visible binding for global variable 'cfu'
onestep: no visible binding for global variable 'measured_values'
onestep: no visible binding for global variable 'psteps'
simpleinterpolation: no visible binding for global variable
  'measured_values'
npqcmstest : boot.wild: no visible global function definition for 'rq'
npqcmstest : boot.wild.rademacher: no visible global function
  definition for 'rq'
npqcmstest : boot.iid: no visible global function definition for 'rq'
File 'NPsimex/R/onload.R':
  .onLoad calls:
    packageStartupMessage("NPsimex 0.2-1 loaded")

See section 'Good practice' in '?.onAttach'.
npst: no visible global function definition for 'mclapply'
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'
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ### Aliases: weight_polls
> 
> ### ** Examples
> 
> polldates <- tail(unique(polls$MidDate), 20)
> weight_polls(polldates, method = "curia")
 [1] NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
[20] NaN
> weight_polls(polldates, method = "pundit")
 [1] 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
 [7] 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
[13] 0.00000000 0.00000000 0.00000000 0.03960526 0.06044955 0.15833013
[19] 0.33013825 0.41147682
> 
> 
> 
> ### * <FOOTER>
> ###
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  5.07 0.14 5.21 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
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.
obliqueRF.default: no visible global function definition for
  'prediction'
obliqueRF.default: no visible global function definition for
  'performance'
pls_wrapper: no visible global function definition for 'kernelpls.fit'
ridge_slow_wrapper: no visible global function definition for
  'gen.ridge'
ridge_svd_wrapper: no visible global function definition for
  'gen.ridge'
svm_wrapper: no visible global function definition for 'svm'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/odbc.Rcheck/00install.out' for details.
isClosed: no visible global function definition for 'dbSendUpdate'
odb.close: no visible global function definition for 'dbSendUpdate'
odb.close: no visible global function definition for 'dbDisconnect'
odb.insert: no visible global function definition for 'dbSendQuery'
odb.insert: no visible global function definition for 'dbColumnInfo'
odb.open: no visible global function definition for 'JDBC'
odb.open: no visible global function definition for 'dbConnect'
odb.read: no visible global function definition for 'dbSendQuery'
odb.read: no visible global function definition for 'fetch'
odb.read: no visible global function definition for 'dbColumnInfo'
odb.tables: no visible global function definition for 'dbListTables'
odb.tables: no visible global function definition for 'dbSendQuery'
odb.tables: no visible global function definition for 'dbColumnInfo'
odb.write: no visible global function definition for 'dbSendUpdate'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
         e$call <- sys.calls()[(frame + 11):(sys.nframe() - 2)]
         register_expectation(e, frame + 11, sys.nframe() - 2)
         signalCondition(e)
     }, "could not find function \"logi\"", quote(eval(expr, envir, enclos))) at testthat/test_odeintr.R:33
  2: eval(expr, envir, enclos)
  
  testthat results ================================================================
  OK: 3 SKIPPED: 0 FAILED: 2
  1. Error: compile_sys works (@test_odeintr.R#25) 
  2. Error: compile_implicit works (@test_odeintr.R#33) 
  
  Error: testthat unit tests failed
  Execution halted
mapvar: no visible binding for global variable 'state.fips'
nearstn: no visible binding for global variable 'okstations'
nearstn: no visible binding for global variable 'Commissioned'
nearstn: no visible binding for global variable 'Decommissioned'
okmts: no visible binding for global variable 'okstations'
okmts: no visible binding for global variable 'TIME'
totalprecip: no visible binding for global variable 'TIME'
Running examples in 'onlineCPD-Ex.R' failed
The error most likely occurred in:

> ### Name: findCP
> ### Title: Wisely Pick Changepoints
> ### Aliases: findCP
> 
> ### ** Examples
> 
> ## Two changepoints within \code{buffer} points:
> set.seed(5)
> y <- c(rnorm(15,0.5,0.01),0.505,0.51,0.015,0.52,rnorm(15,0.6,0.05))
> res <- offlineCPD(y)
> plot(res,buffer=10)     ## Will replace the two changepoints
Error: Aesthetics must be either length 1 or the same as the data (1): x, y, xend, yend, alpha
Execution halted
Namespaces in Imports field not imported from:
  'randomForest' 'ranger'
  All declared Imports should be used.
Packages suggested but not available for checking: 'RAppArmor' 'feather'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/OpenImageR.Rcheck/00install.out' for details.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs     5.9Mb
    models   4.7Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   4.8Mb
Package required and available but unsuitable version: 'utils'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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'
File 'orderbook/R/AllGenerics.R':
  .onLoad calls:
    require(methods)

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

.animate.plot : new.yscale.components: no visible global function
  definition for 'yscale.components.default'
.animate.plot: no visible global function definition for 'barchart'
.plot.ob : new.yscale.components: no visible global function definition
  for 'yscale.components.default'
.plot.ob: no visible global function definition for 'xyplot'
.plot.ob : <anonymous>: no visible global function definition for
  'panel.xyplot'
.plot.ob : <anonymous>: no visible global function definition for
  'panel.lines'
.plot.orders.ob : new.yscale.components: no visible global function
  definition for 'yscale.components.default'
.plot.orders.ob: no visible global function definition for 'xyplot'
.plot.orders.ob : <anonymous>: no visible global function definition
  for 'panel.xyplot'
.plot.orders.ob : <anonymous>: no visible global function definition
  for 'panel.lines'
.plot.side.ob : new.yscale.components: no visible global function
  definition for 'yscale.components.default'
.plot.side.ob: no visible global function definition for 'barchart'
.plot.side.ob: no visible global function definition for
  'trellis.focus'
.plot.side.ob: no visible global function definition for 'grid.text'
.plot.side.ob: no visible global function definition for
  'trellis.unfocus'
.supply.demand.plot: no visible global function definition for 'xyplot'
.supply.demand.plot : <anonymous>: no visible global function
  definition for 'panel.xyplot'
.supply.demand.plot : <anonymous>: no visible global function
  definition for 'panel.abline'
copy,orderbook : .local: no visible global function definition for
  'hash'
reset,orderbook: no visible global function definition for 'clear'
Attaching package: 'BiocGenerics'

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

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

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

    IQR, mad, xtabs

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

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

Welcome to Bioconductor

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

All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
boat3d: no visible global function definition for 'rgl.cur'
boat3d: no visible global function definition for 'open3d'
boat3d: no visible global function definition for 'clear3d'
boat3d: no visible global function definition for 'bg3d'
boat3d: no visible global function definition for 'rgl.set'
boat3d: no visible global function definition for 'triangles3d'
boat3d: no visible global function definition for 'quads3d'
boat3d: no visible global function definition for 'decorate3d'
boat3d: no visible global function definition for 'scatterplot3d'
zsuml2minucminf.loca.p: no visible global function definition for
  'ucminf'
zsumlpminucminf.loca.p: no visible global function definition for
  'ucminf'
est.lme : <anonymous>: warning in rank(iru, ties = "min"): partial
  argument match of 'ties' to 'ties.method'
est.lme : <anonymous>: no visible global function definition for 'lme'
est.lme : <anonymous>: no visible global function definition for
  'VarCorr'
srt : <anonymous>: no visible global function definition for
  'rowttests'
chebyshev.c.polynomials: no visible global function definition for
  'polynomial'
chebyshev.s.polynomials: no visible global function definition for
  'polynomial'
chebyshev.t.polynomials: no visible global function definition for
  'polynomial'
chebyshev.u.polynomials: no visible global function definition for
  'polynomial'
gegenbauer.polynomials: no visible global function definition for
  'polynomial'
ghermite.h.polynomials: no visible global function definition for
  'polynomial'
glaguerre.polynomials: no visible global function definition for
  'polynomial'
hermite.h.polynomials: no visible global function definition for
  'polynomial'
hermite.he.polynomials: no visible global function definition for
  'polynomial'
jacobi.g.polynomials: no visible global function definition for
  'polynomial'
jacobi.p.polynomials: no visible global function definition for
  'polynomial'
legendre.polynomials: no visible global function definition for
  'polynomial'
monic.polynomials: no visible global function definition for
  'polynomial'
orthogonal.polynomials: no visible global function definition for
  'polynomial'
orthonormal.polynomials: no visible global function definition for
  'polynomial'
polynomial.integrals: no visible global function definition for
  'integral'
schebyshev.t.polynomials: no visible global function definition for
  'polynomial'
schebyshev.u.polynomials: no visible global function definition for
  'polynomial'
slegendre.polynomials: no visible global function definition for
  'polynomial'
as_igraph : <anonymous>: no visible global function definition for
  'distHaversine'
as_igraph: no visible global function definition for 'graph.edgelist'
as_igraph: no visible global function definition for 'E'
as_igraph: no visible global function definition for 'E<-'
as_sp_lines: no visible global function definition for 'Lines'
as_sp_points: no visible global function definition for
  'SpatialPointsDataFrame'
as_sp_polygons: no visible global function definition for 'Polygons'
as_sp_polygons: no visible global function definition for
  'SpatialPolygons'
as_sp_polygons: no visible global function definition for
  'SpatialPolygonsDataFrame'
make_SLDF: no visible global function definition for 'SpatialLines'
make_SLDF: no visible global function definition for
  'SpatialLinesDataFrame'
osm_crs: no visible global function definition for 'CRS'
ways_nodes2Line: no visible global function definition for 'Line'
ways_nodes2Polygon: no visible global function definition for 'Polygon'
Namespace in Imports field not imported from: 'bitops'
  All declared Imports should be used.
plot,OutlierDM-missing : .local: no visible binding for global variable
  'pch'
p3state: no visible global function definition for 'survfit'
p3state: no visible global function definition for 'coxph'
[,ClassW : .local: warning in switch(EXP = i, u1 = {: partial argument
  match of 'EXP' to 'EXPR'
[,ClassW : .local: warning in return(x@u1): partial argument match of
  'EXP' to 'EXPR'
[,ClassW : .local: warning in }, u2 = {: partial argument match of
  'EXP' to 'EXPR'
[,ClassW : .local: warning in return(x@u2): partial argument match of
  'EXP' to 'EXPR'
[,ClassW : .local: warning in }, w1 = {: partial argument match of
  'EXP' to 'EXPR'
[,ClassW : .local: warning in return(x@w1): partial argument match of
  'EXP' to 'EXPR'
[,ClassW : .local: warning in }): partial argument match of 'EXP' to
  'EXPR'
[<-,ClassW : .local: warning in switch(EXP = i, u1 = {: partial
  argument match of 'EXP' to 'EXPR'
[<-,ClassW : .local: warning in x@u1 <- value: partial argument match
  of 'EXP' to 'EXPR'
[<-,ClassW : .local: warning in }, u2 = {: partial argument match of
  'EXP' to 'EXPR'
[<-,ClassW : .local: warning in x@u2 <- value: partial argument match
  of 'EXP' to 'EXPR'
[<-,ClassW : .local: warning in }, w1 = {: partial argument match of
  'EXP' to 'EXPR'
[<-,ClassW : .local: warning in x@w1 <- value: partial argument match
  of 'EXP' to 'EXPR'
[<-,ClassW : .local: warning in }): partial argument match of 'EXP' to
  'EXPR'
CalGIF: no visible binding for global variable 'PAGIData'
CalGIF2: no visible binding for global variable 'PAGIData'
PAGI.Main: no visible binding for global variable 'PAGIData'
getclass.labels: no visible binding for global variable 'ExampleData'
getdataset: no visible binding for global variable 'ExampleData'
Errors in running code in vignettes:
when running code in 'paleofire-paper.Rnw'
  ...

> download.file(url = "http://blarquez.com/public/data/data_cageo.zip", 
+     destfile = "data_cageo.zip")
trying URL 'http://blarquez.com/public/data/data_cageo.zip'
Warning in download.file(url = "http://blarquez.com/public/data/data_cageo.zip",  :
  cannot open URL 'http://blarquez.com/public/data/data_cageo.zip': HTTP status was '404 Not Found'

  When sourcing 'paleofire-paper.R':
Error: cannot open URL 'http://blarquez.com/public/data/data_cageo.zip'
Execution halted
clapply_cluster: no visible global function definition for
  'makeCluster'
clapply_cluster: no visible global function definition for
  'clusterSetRNGStream'
clapply_cluster: no visible global function definition for
  'clusterExport'
clapply_cluster: no visible global function definition for
  'clusterApply'
clapply_cluster: no visible global function definition for
  'clusterApplyLB'
clapply_cluster: no visible global function definition for
  'stopCluster'
md5sumString: no visible global function definition for 'md5sum'
writeRdocumentationToDir: no visible global function definition for
  'list_files_with_exts'
performance.pcor: no visible global function definition for
  'ggm.test.edges'
par.nmds: no visible binding for global variable 'j'
par.spp.est: no visible binding for global variable 'i'
Namespace in Imports field not imported from: 'RSQLite'
  All declared Imports should be used.
fitOR: no visible global function definition for 'multinom'
parpdist: no visible binding for global variable 'tmpx'
Running examples in 'partools-Ex.R' failed
cv_nfold: no visible global function definition for 'cv.glmnet'
glmcvbeta: no visible global function definition for 'cv.glmnet'
Errors in running code in vignettes:
when running code in 'pasta_intro.Rmd'
  ...

  When running vignette 'pasta_intro.Rmd':
Error: No such vignette 'pasta_intro.Rmd'
Execution halted
conch: no visible global function definition for 'read.tree'
conch: no visible global function definition for 'read.nexus'
conch: no visible global function definition for '.compressTipLabel'
conch: no visible global function definition for 'drop.tip'
conch: no visible global function definition for 'extract.clade'
conch: no visible global function definition for 'which.edge'
conch: no visible global function definition for 'write.tree'
read_input: no visible global function definition for 'read.tree'
read_input: no visible global function definition for 'read.dna'
oneway.plots: warning in dotchart(x = Y, groups = fac1, col = COL[2],
  pch = 1, xlab = deparse(substitute(Y)), xlim = YL, gdata = tapply(Y,
  fac1, mean), gpch = 17): partial argument match of 'col' to 'color'
animatePatches: no visible global function definition for
  'getTimestamp'
animatePatches: no visible global function definition for 'getElapsed'
Loading required package: ROCR
Loading required package: gplots

Attaching package: 'gplots'

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

    lowess

Loading required package: igraph

Attaching package: 'igraph'

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

    normalize, union

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

    decompose, spectrum

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

    union

Loading required package: lpSolve
'library' or 'require' call to 'ROCR' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'Biobase' 'ROCR' 'affy' 'igraph' 'kernlab' 'lpSolve' 'svmpath'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'parallel:::detectCores'
  See the note in ?`:::` about the use of this operator.
Loading required package: ROCR
Loading required package: gplots

Attaching package: 'gplots'

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

    lowess

Loading required package: igraph

Attaching package: 'igraph'

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

    normalize, union

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

    decompose, spectrum

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

    union

Loading required package: lpSolve
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
Loading required package: ROCR
Loading required package: gplots

Attaching package: 'gplots'

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

    lowess

Loading required package: igraph

Attaching package: 'igraph'

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

    normalize, union

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

    decompose, spectrum

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

    union

Loading required package: lpSolve
The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
Loading required package: ROCR
Loading required package: gplots

Attaching package: 'gplots'

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

    lowess

Loading required package: igraph

Attaching package: 'igraph'

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

    normalize, union

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

    decompose, spectrum

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

    union

Loading required package: lpSolve
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
Attaching package: 'gplots'

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

    lowess


Attaching package: 'igraph'

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

    normalize, union

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

    decompose, spectrum

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

    union

All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Loading required package: ROCR
Loading required package: gplots

Attaching package: 'gplots'

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

    lowess

Loading required package: igraph

Attaching package: 'igraph'

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

    normalize, union

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

    decompose, spectrum

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

    union

Loading required package: lpSolve
Loading required package: ROCR
Loading required package: gplots

Attaching package: 'gplots'

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

    lowess

Loading required package: igraph

Attaching package: 'igraph'

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

    normalize, union

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

    decompose, spectrum

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

    union

Loading required package: lpSolve
Loading required package: ROCR
Loading required package: gplots

Attaching package: 'gplots'

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

    lowess

Loading required package: igraph

Attaching package: 'igraph'

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

    normalize, union

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

    decompose, spectrum

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

    union

Loading required package: lpSolve
Loading required package: ROCR
Loading required package: gplots

Attaching package: 'gplots'

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

    lowess

Loading required package: igraph

Attaching package: 'igraph'

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

    normalize, union

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

    decompose, spectrum

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

    union

Loading required package: lpSolve
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.
draw: no visible global function definition for 'plotellipse'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  1/2 mismatches
  x[1]: "D:/RCompile/CRANpkg/local/3.2/pathological.Rcheck/tests/testthat/test_dec
  x[1]: ompose_path.R"
  y[1]: "D:/Rcompile/CRANpkg/local/3.2/pathological.Rcheck/tests/testthat/test_dec
  y[1]: ompose_path.R"
  
  
  testthat results ================================================================
  OK: 187 SKIPPED: 15 FAILED: 1
  1. Failure: standardize_path works with missing files with ./ prefix (@test_standardize_path.R#198) 
  
  Error: testthat unit tests failed
  Execution halted
pen_or1: no visible global function definition for 'multiroot'
plot.pedigree: no visible global function definition for
  'align.pedigree'
plotPed: no visible global function definition for 'pedigree'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/pbdBASE.Rcheck/00install.out' for details.
Package which this enhances but not available for checking: 'pmclust'
Package required and available but unsuitable version: 'pbdBASE'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/pbdMPI.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/pbdSLAP.Rcheck/00install.out' for details.
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
pbo: no visible global function definition for '%dopar%'
pbo: no visible global function definition for 'foreach'
xyplot.pbo: no visible global function definition for 'doubleYScale'
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    data   2.1Mb
    libs   2.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/pcnetmeta.Rcheck/00install.out' for details.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
Namespaces in Imports field not imported from:
  'car' 'sandwich'
  All declared Imports should be used.
genomesim : extractA: no visible global function definition for
  'is.genotype'
genomesim : extractA : <anonymous>: no visible global function
  definition for 'nallele'
phensim: no visible global function definition for 'rmvnorm'
Malformed Title field: should not end in a period.
'LinkingTo' for 'ggplot2' is unused as it has no 'include' directory
plot.clust: no visible global function definition for 'qplot'
plot.clust: no visible global function definition for 'geom_histogram'
plot.clust: no visible global function definition for 'aes_string'
.replaceinf: no visible global function definition for 'fcn_values<-'
complexity.LASSO: no visible global function definition for 'profL1'
complexity.ipec.CoxBoost: no visible global function definition for
  'CoxBoost'
complexity.ipec.CoxBoost: no visible global function definition for
  'locfit'
complexity.mincv.CoxBoost: no visible global function definition for
  'cv.CoxBoost'
complexity.ripec.CoxBoost: no visible global function definition for
  'CoxBoost'
complexity.ripec.CoxBoost: no visible global function definition for
  'locfit'
extract: no visible global function definition for 'findGlobals'
fit.CoxBoost: no visible global function definition for 'CoxBoost'
fit.LASSO: no visible global function definition for 'penalized'
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

phantom : model: missing arguments not allowed in calls to 'c'
readData: no visible global function definition for 'read.image'
writeData: no visible global function definition for 'make.image'
writeData: no visible global function definition for 'write.image'
File 'pgam/R/zzz.r':
  .onLoad calls:
    require("stats", character.only = TRUE, quietly = TRUE, warn.conflicts = FALSE)
    require("utils", character.only = TRUE, quietly = TRUE, warn.conflicts = FALSE)
    cat("This is pgam library version", ver, "\n", sep = " ")

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

This is pgam library version 0.4.12 
pgam: warning in assign("loglik", NULL, env = pgam.env): partial
  argument match of 'env' to 'envir'
pgam: warning in get("loglik", env = pgam.env): partial argument match
  of 'env' to 'envir'
pgam.likelihood: warning in assign("loglik", loglik, env = env):
  partial argument match of 'env' to 'envir'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/phase1RMD.Rcheck/00install.out' for details.
plot.phtMCMC: no visible global function definition for 'ggplot'
plot.phtMCMC: no visible global function definition for 'melt'
plot.phtMCMC: no visible global function definition for 'geom_line'
plot.phtMCMC: no visible global function definition for 'aes_string'
plot.phtMCMC: no visible global function definition for 'geom_smooth'
plot.phtMCMC: no visible global function definition for 'facet_wrap'
plot.phtMCMC: no visible global function definition for 'ggtitle'
plot.phtMCMC: no visible global function definition for 'xlab'
plot.phtMCMC: no visible global function definition for 'ylab'
plot.phtMCMC: no visible global function definition for 'geom_density'
Namespace in Imports field not imported from: 'quanteda'
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
bg.similarity.test: no visible global function definition for
  'sampleRandom'
bg.similarity.test: no visible global function definition for
  'coordinates'
bg.similarity.test: no visible global function definition for 'extract'
bg.similarity.test: no visible global function definition for
  'SpatialPoints'
bg.similarity.test : random.presence: no visible global function
  definition for 'sampleRandom'
bg.similarity.test : random.presence: no visible global function
  definition for 'coordinates'
bg.similarity.test: no visible global function definition for
  'writeRaster'
bg.similarity.test: no visible global function definition for
  'read.asciigrid'
di.enm: no visible global function definition for 'read.asciigrid'
niche.equivalency.test: no visible global function definition for
  'extract'
niche.equivalency.test: no visible global function definition for
  'SpatialPoints'
niche.equivalency.test: no visible global function definition for
  'sampleRandom'
niche.equivalency.test: no visible global function definition for
  'coordinates'
niche.equivalency.test: no visible global function definition for
  'writeRaster'
niche.equivalency.test: no visible global function definition for
  'read.asciigrid'
niche.overlap: no visible global function definition for
  'read.asciigrid'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/PhyloMeasures.Rcheck/00install.out' for details.
comm.phylo.qr: no visible global function definition for 'rq'
sppregs: no visible global function definition for 'brglm'
ARTP.GE: no visible global function definition for 'ARTP_pathway'
LR.cont.surv: no visible global function definition for 'coxph'
LR.inter.cat.surv: no visible global function definition for 'coxph'
LR.inter.cont.surv: no visible global function definition for 'coxph'
permutation.snp: no visible global function definition for 'sfInit'
permutation.snp: no visible global function definition for 'sfLibrary'
permutation.snp: no visible global function definition for
  'sfExportAll'
permutation.snp: no visible global function definition for 'sfLapply'
permutation.snp: no visible global function definition for 'sfStop'
fitaci: no visible global function definition for 'chkDots'
.var.ij: no visible global function definition for 'hcv'
.var.ij: no visible global function definition for 'h.select'
.var.ij: no visible global function definition for 'sm.regression'
LiStengos: no visible global function definition for 'h.select'
LiStengos: no visible global function definition for 'hcv'
LiStengos: no visible global function definition for 'sm.regression'
cal_df_gamma1: no visible global function definition for 'binning'
cal_df_gamma2: no visible global function definition for 'binning'
iteration: no visible global function definition for 'h.select'
iteration: no visible global function definition for 'hcv'
iteration: no visible global function definition for 'sm.regression'
iteration0: no visible global function definition for 'sm.regression'
iteration0: no visible global function definition for 'h.select'
plmm: no visible global function definition for 'Formula'
plmm.bs: no visible global function definition for 'Formula'
plot.plmm: no visible global function definition for 'Formula'
plot.plmm: no visible global function definition for 'sm.regression'
predict.plmm: no visible global function definition for 'Formula'
predict.plmm: no visible global function definition for 'sm.regression'
print.summary.plmm: no visible global function definition for 'Formula'
ranef.plmm: no visible global function definition for 'Formula'
select.h0: no visible global function definition for 'Formula'
select.h0: no visible global function definition for 'h.select'
select.h0: no visible global function definition for 'hcv'
var.plot: no visible global function definition for 'Formula'
var.plot: no visible global function definition for 'sm.regression'
wplmm: no visible global function definition for 'Formula'
Namespaces in Imports field not imported from:
  'hexbin' 'quantreg'
  All declared Imports should be used.
llla.mc: no visible global function definition for 'coxph'
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   1.4Mb
cor.xl.ImputeData: no visible global function definition for
  'impute.knn'
Package suggested but not available for checking: 'neighbr'
Running examples in 'pmml-Ex.R' failed
The error most likely occurred in:

> ### Name: pmml.neighbr
> ### Title: Generate PMML for a neighbr object from the *neighbr* package.
> ### Aliases: pmml.neighbr
> 
> ### ** Examples
> 
> # continuous features with continuous target, categorical target,
> # and neighbor ranking
> 
> library(neighbr)
Error in library(neighbr) : there is no package called 'neighbr'
Execution halted
pnmtrem1: no visible global function definition for 'ginv'
smooth: no visible global function definition for 'genoud'
Permu.Ind: no visible global function definition for 'permn'
Permu.Ind: no visible global function definition for 'hcube'
poLCA: no visible global function definition for 'ginv'
poLCA.makeplot.dich: no visible global function definition for
  'scatterplot3d'
poLCA.makeplot.poly: no visible global function definition for
  'scatterplot3d'
poLCA.se: no visible global function definition for 'ginv'
Packages in Depends field not imported from:
  'mvtnorm' 'sfsmisc'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
binBvn: no visible global function definition for 'pmvnorm'
hetcor.data.frame: no visible global function definition for 'nearcor'
Package unavailable to check Rd xrefs: 'gpclib'
plot.preplot.polywog: no visible global function definition for
  'persp3d'
siteocc: no visible global function definition for
  'is.positive.definite'
outputBottleSim: no visible binding for global variable 'final.vec'
outputBottleSim: no visible binding for global variable 'kvec'
portest : OneMonteCarlo: no visible global function definition for
  'garchFit'
portest: no visible global function definition for 'makeCluster'
portest: no visible global function definition for
  'clusterSetRNGStream'
portest: no visible global function definition for 'clusterEvalQ'
portest: no visible global function definition for 'clusterExport'
portest: no visible global function definition for 'clusterCall'
portest: no visible global function definition for 'parSapply'
portest: no visible global function definition for 'stopCluster'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/PortfolioEffectEstim.Rcheck/00install.out' for details.
File 'portfolioSim/R/AllClasses.R':
  .onLoad calls:
    require(methods)

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

getSimTrades,stiFromSignal-orderable-portfolio-simData-logical :
  .local: no visible binding for global variable 'shares'
loadIn,simResult-character-missing : .local: no visible binding for
  global variable 'master.freq'
loadIn,simResult-character-missing : .local: no visible binding for
  global variable 'master.errors'
loadIn,simResult-character-missing : .local: no visible binding for
  global variable 'master.type'
loadIn,simResult-character-missing : .local: no visible binding for
  global variable 'master.summary.interface'
loadIn,simResultSinglePeriod-character-missing : .local: no visible
  binding for global variable 'x'
plot,simResult-missing: no visible global function definition for
  'xyplot'
runSim,portfolioSim-logical : .local: no visible binding for global
  variable 'id'
runSim,portfolioSim-logical : .local: no visible global function
  definition for 'updateSummary'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/PottsUtils.Rcheck/00install.out' for details.
ExampleModels: no visible binding for global variable 'ExampleData'
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'predmixcor/R/firstlib.r':
  .First.lib calls:
    cat("predmixcor loaded\n", "COPY RIGHT: Longhai Li\n", "http://math.usask.ca/~longhai\n",     "Type ?begin.predmixcor for help\n", sep = "")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
Namespace in Imports field not imported from: 'e1071'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/prevalence.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'graphics' 'stats'
  All declared Imports should be used.
getCandidates: no visible binding for global variable 'envData'
getGraph: no visible binding for global variable 'envData'
getProvidedDiseaseName: no visible binding for global variable
  'envData'
getSeed: no visible binding for global variable 'envData'
getTopDiseaseMetabolites: no visible binding for global variable
  'envData'
LR.pvalue: warning in matrix(c(y1, y2, (n1 - y1), (n2 - y2)), nr = 2,
  dimnames = list(c("treat", "control"), c("Success", "No success"))):
  partial argument match of 'nr' to 'nrow'
profilelike.gls: no visible global function definition for 'gls'
profilelike.lme: no visible global function definition for 'lme'
profilelike.polr: no visible global function definition for 'polr'
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    extdata  10.9Mb
    libs      1.4Mb
ggplot.profr: no visible global function definition for 'ggplot'
ggplot.profr: no visible global function definition for 'geom_rect'
ggplot.profr: no visible global function definition for 'aes'
ggplot.profr: no visible global function definition for 'geom_text'
ggplot.profr: no visible global function definition for
  'scale_y_continuous'
ggplot.profr: no visible global function definition for
  'scale_x_continuous'
IndividualPROC: no visible global function definition for 'survfit'
optim.two.stage.appr: no visible global function definition for
  'mvrnorm'
optim.two.stage.group: no visible global function definition for
  'mvrnorm'
optim.two.stage.single: no visible global function definition for
  'mvrnorm'
power.group.cost: no visible global function definition for 'mvrnorm'
power.single.cost: no visible global function definition for 'mvrnorm'
predict.protoclass: no visible global function definition for 'knn1'
Missing or unexported object: 'tools::nonS3methods'
Namespaces in Imports field not imported from:
  'forecast' 'knitr'
  All declared Imports should be used.
learnParameters: no visible global function definition for
  'coordinates'
makePrediction: no visible global function definition for 'coordinates'
spatialPredict.psgp: no visible global function definition for
  'coordinates'
spatialPredict.psgp: no visible global function definition for
  'makeCluster'
spatialPredict.psgp: no visible global function definition for
  'registerDoParallel'
spatialPredict.psgp: no visible global function definition for
  'clusterEvalQ'
spatialPredict.psgp: no visible global function definition for
  '%dopar%'
spatialPredict.psgp: no visible global function definition for
  'foreach'
spatialPredict.psgp: no visible global function definition for
  'stopCluster'
spatialPredict.psgp: no visible global function definition for
  'SpatialPointsDataFrame'
spatialPredict.psgp: no visible global function definition for 'bbox'
spatialPredict.psgp: no visible global function definition for
  'proj4string<-'
spatialPredict.psgp: no visible global function definition for
  'proj4string'
test.problem : g: no visible global function definition for 'grad'
catEffectBootAdaptor: no visible binding for global variable 'sumSqCat'
compPowerCatSelectivity: no visible binding for global variable
  'fRatioStat'
compPowerGeneralRespDetection: no visible binding for global variable
  'sumSqCat'
compPowerRespDetection: no visible binding for global variable
  'sumSqCat'
testCatEffectBoot: no visible global function definition for 'boot'
Errors in running code in vignettes:
when running code in 'intro.Rnw'
  ...

> scores <- scoreItems(keys, msq[, 1:75])

> png("msq.png")

> pairs.panels(scores$scores, smoother = TRUE, main = "Density distributions of four measures of affect")

  When sourcing 'intro.R':
Error: there is no package called 'KernSmooth'
Execution halted
bootstrap_inference: no visible global function definition for
  'makeCluster'
bootstrap_inference: no visible global function definition for
  '%dopar%'
bootstrap_inference: no visible global function definition for
  'foreach'
bootstrap_inference: no visible global function definition for
  'stopCluster'
plot_chase_observed_expected: no visible global function definition for
  'meta.MH'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/PurBayes.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/PVAClone.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/QCAGUI.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'RSVGTipsDevice'
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

Calc.Expr: no visible binding for global variable 'Type'
Calc.Expr: no visible binding for global variable 'Identifier'
Calc.Expr: no visible binding for global variable 'Fluor'
GroupPlot: no visible binding for global variable 'Type'
plot.CT: no visible binding for global variable 'tr_gene_name'
plot.qrfactor : sp.label: no visible global function definition for
  'coordinates'
plot.qrfactor: no visible global function definition for 'spplot'
plot.qrfactor: no visible global function definition for 'bpy.colors'
plot.qrfactor: no visible global function definition for 'readOGR'
rq: no visible global function definition for 'readOGR'
Namespace in Imports field not imported from: 'xts'
  All declared Imports should be used.
tailprob: warning in pchisq(t, df, low = FALSE): partial argument match
  of 'low' to 'lower.tail'
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    contrib   3.7Mb
    doc       2.9Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    2.3Mb
    libs   2.0Mb
Namespace in Imports field not imported from: 'Rdpack'
  All declared Imports should be used.
prepare_Rd: DR_Qopt.Rd:225: unknown macro '\insertRef'
prepare_Rd: IPWE_MADopt.Rd:159: unknown macro '\insertRef'
prepare_Rd: IPWE_Mopt.Rd:133: unknown macro '\insertRef'
prepare_Rd: IPWE_Qopt.Rd:165: unknown macro '\insertRef'
prepare_Rd: TwoStg_Mopt.Rd:180: unknown macro '\insertRef'
prepare_Rd: TwoStg_Qopt.Rd:174: unknown macro '\insertRef'
prepare_Rd: abso_diff_est.Rd:76: unknown macro '\insertRef'
prepare_Rd: augX.Rd:137: unknown macro '\insertRef'
prepare_Rd: mestimate.Rd:52: unknown macro '\insertRef'
prepare_Rd: qestimate.Rd:54: unknown macro '\insertRef'
prepare_Rd: quantoptr-package.Rd:47: unknown macro '\insertRef'
prepare_Rd: quantoptr-package.Rd:49: unknown macro '\insertRef'
prepare_Rd: quantoptr-package.Rd:51: unknown macro '\insertRef'
prepare_Rd: quantoptr-package.Rd:53: unknown macro '\insertRef'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/QuantTools.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'afex' 'data.table' 'dplyr' 'lmerTest'
  All declared Imports should be used.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    Output   2.2Mb
    bin      4.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/R2jags.Rcheck/00install.out' for details.
PPT.AddBlankSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddDataFrame: no visible global function definition for
  'comIsValidHandle'
PPT.AddGraphicstoSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTextSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTitleOnlySlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTitleSlide: no visible global function definition for
  'comIsValidHandle'
PPT.ApplyTemplate: no visible global function definition for
  'comIsValidHandle'
PPT.Close: no visible global function definition for 'comIsValidHandle'
PPT.Init: no visible global function definition for 'comCreateObject'
PPT.Init: no visible global function definition for 'comIsValidHandle'
PPT.Init: no visible global function definition for 'COMCreate'
PPT.Present: no visible global function definition for
  'comIsValidHandle'
PPT.SaveAs: no visible global function definition for
  'comIsValidHandle'
PPT.getAbsolutePath : PPT.filePath: no visible global function
  definition for 'readWindowsShortcut'
allpossregs.formula: no visible global function definition for
  'regsubsets'
allpossregs.lm: no visible global function definition for 'regsubsets'
reg3d: no visible global function definition for 'rgl.open'
reg3d: no visible global function definition for 'rgl.bg'
reg3d: no visible global function definition for 'rgl.material'
reg3d: no visible global function definition for 'rgl.lines'
reg3d: no visible global function definition for 'rgl.spheres'
reg3d: no visible global function definition for 'rgl.surface'
reg3d: no visible global function definition for 'rgl.texts'
race : killSlaves.exit: no visible global function definition for
  '.PVM.initsend'
race : killSlaves.exit: no visible global function definition for
  '.PVM.send'
race : killSlaves.exit: no visible global function definition for
  '.PVM.exit'
race: no visible global function definition for '.PVM.mytid'
race: no visible global function definition for '.PVM.spawn'
race: no visible global function definition for '.PVM.initsend'
race: no visible global function definition for '.PVM.pkstrvec'
race: no visible global function definition for '.PVM.send'
race: no visible global function definition for '.PVM.recv'
race: no visible global function definition for '.PVM.bufinfo'
race: no visible global function definition for '.PVM.upkstrvec'
race : job.start: no visible global function definition for
  '.PVM.initsend'
race : job.start: no visible global function definition for
  '.PVM.pkint'
race : job.start: no visible global function definition for '.PVM.send'
race : job.wait: no visible global function definition for '.PVM.recv'
race : job.wait: no visible global function definition for
  '.PVM.bufinfo'
race : job.wait: no visible global function definition for
  '.PVM.upkint'
race : job.wait: no visible global function definition for
  '.PVM.upkdblvec'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/RandomFieldsUtils.Rcheck/00install.out' for details.
.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'
Errors in running code in vignettes:
when running code in 'RankAggreg.Rnw'
  ...
The following object is masked from 'package:kohonen':

    map

Warning in fanny(DistDel, nc, ...) :
  FANNY algorithm has not converged in 'maxit' = 500 iterations

  When sourcing 'RankAggreg.R':
Error: invalid argument type
Execution halted
CropSpatialPolygonsDataFrame: no visible global function definition for
  'bbox'
CropSpatialPolygonsDataFrame: no visible global function definition for
  'clipPolys'
BinBam: no visible binding for global variable
  'BSgenome.Hsapiens.UCSC.hg19'
BinBam: no visible global function definition for 'seqlengths'
makeGCContentData: no visible binding for global variable
  'BSgenome.Hsapiens.UCSC.hg19'
makeGCContentData: no visible global function definition for
  'seqlengths'
makeGCContentPerPos: no visible binding for global variable
  'BSgenome.Hsapiens.UCSC.hg19'
freq: no visible global function definition for 'melt'
rp.desc: no visible global function definition for 'melt.data.frame'
rp.desc: no visible global function definition for 'cast'
rp.freq: no visible global function definition for 'melt'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   1.5Mb
.GCD: no visible global function definition for 'as.polynomial'
.LCM: no visible global function definition for 'as.polynomial'
rationalfun: no visible global function definition for 'polynomial'
rationalfun.poly: no visible global function definition for
  'polynomial'
rationalfun.poly: no visible global function definition for
  'is.polynomial'
rfun: no visible global function definition for 'polynomial'
rfun.poly: no visible global function definition for 'polynomial'
rfun.poly: no visible global function definition for 'is.polynomial'
simplify: no visible global function definition for 'polynomial'
bef.get.categories_for: no visible binding for global variable 'id'
bef.portal.get.categories_for: no visible binding for global variable
  'id'
bn2nbn: no visible binding for global variable 'bn.fit'
nbn2bnfit: no visible global function definition for 'model2network'
nbn2bnfit: no visible global function definition for 'custom.fit'
simulate8mn: no visible global function definition for 'mvrnorm'
rbugs2coda: no visible global function definition for 'as.mcmc'
rbugs2coda: no visible global function definition for 'mcmc'
rbugs2coda: no visible global function definition for 'as.mcmc.list'
install_version: no visible global function definition for
  'install_url'
circlesSize: no visible global function definition for 'bbox'
discretVar: no visible global function definition for 'classIntervals'
discretVar: no visible global function definition for 'brewer.pal'
frameAutoSize: no visible global function definition for 'bbox'
mapChoroTypo: no visible global function definition for
  'readShapeSpatial'
mapChoropleth: no visible global function definition for
  'readShapeSpatial'
mapCircles: no visible global function definition for
  'readShapeSpatial'
mapCircles: no visible global function definition for 'coordinates'
mapCirclesChoro: no visible global function definition for
  'readShapeSpatial'
mapCirclesChoro: no visible global function definition for
  'coordinates'
mapCirclesTypo: no visible global function definition for
  'readShapeSpatial'
mapCirclesTypo: no visible global function definition for 'coordinates'
northArrowDisplay: no visible global function definition for
  'SpatialPolygonsRescale'
northArrowDisplay: no visible global function definition for
  'layout.north.arrow'
scalebarDisplay: no visible global function definition for
  'SpatialPolygonsRescale'
scalebarDisplay: no visible global function definition for
  'layout.scale.bar'
typo: no visible global function definition for 'brewer.pal'
Namespace in Imports field not imported from: 'dplyr'
  All declared Imports should be used.
climdex.data.frame: no visible global function definition for
  'as.PCICt'
computeMBD : OnOutput: no visible global function definition for
  'tkbutton'
computeMBD: no visible global function definition for 'tkbutton'
computeMBD : OnPlot: no visible global function definition for
  'tkcanvas'
computeMBD : OnPlot: no visible global function definition for
  'tkbutton'
computeTmean: no visible global function definition for 'tkcanvas'
computeTmean: no visible global function definition for 'tkbutton'
plotCentralCurves: no visible global function definition for 'tkcanvas'
plotCentralCurves: no visible global function definition for 'tkbutton'
.onAttach: no visible global function definition for 'getRcmdr'
.onAttach: no visible global function definition for 'closeCommander'
.onAttach: no visible global function definition for 'Commander'
mosaicMenuItem: no visible global function definition for
  'mosaicSelectDialog'
mosaicMenuItem: no visible global function definition for 'Message'
Rcmdr.new.loca.p: no visible binding for global variable 'top'
Rcmdr.new.loca.p: no visible binding for global variable 'buttonsFrame'
Rcmdr.orloca.norm: no visible binding for global variable 'top'
Rcmdr.orloca.norm : onOK: no visible binding for global variable
  'normaVariable'
Rcmdr.orloca.norm: no visible binding for global variable 'normaFrame'
Rcmdr.orloca.norm: no visible binding for global variable
  'buttonsFrame'
Rcmdr.rloca.p: no visible binding for global variable 'top'
Rcmdr.rloca.p: no visible binding for global variable 'buttonsFrame'
Rcmdr.zsum: no visible binding for global variable 'top'
Rcmdr.zsum: no visible binding for global variable 'buttonsFrame'
Rcmdr.zsummin: no visible binding for global variable 'top'
Rcmdr.zsummin : onOK: no visible binding for global variable
  'algorithmVariable'
Rcmdr.zsummin : onOK: no visible binding for global variable '.sol'
Rcmdr.zsummin: no visible binding for global variable 'algorithmFrame'
Rcmdr.zsummin: no visible binding for global variable 'buttonsFrame'
BOXWP: no visible binding for global variable 'top'
BOXWP: no visible binding for global variable 'buttonsFrame'
HIST: no visible binding for global variable 'top'
HIST: no visible binding for global variable 'buttonsFrame'
QQN: no visible binding for global variable 'top'
QQN: no visible binding for global variable 'buttonsFrame'
bigraphe0: no visible global function definition for 'qgraph'
bisummarize0: no visible global function definition for 'dudi.coa'
chalandise.DEP0: no visible global function definition for 'map'
histbackback0: no visible global function definition for 'mgp.axis'
mapAFC: no visible global function definition for 'scatter'
mapAFC: no visible global function definition for 'dudi.coa'
multivariate0: no visible global function definition for 'dudi.mix'
plotCat2: no visible global function definition for 's.class'
plotLikert1: no visible global function definition for 'trellis.device'
plotLikert1: no visible global function definition for 'dotplot'
plotLikert1: no visible global function definition for 'simpleKey'
plotMissing: no visible global function definition for 'whatis'
plotNum: no visible global function definition for 's.corcircle'
plotTabCont0: no visible global function definition for 'assoc'
plotTabCont0: no visible binding for global variable 'shading_hcl'
plotTabCont0: no visible global function definition for 'corresp'
sortAnova: no visible global function definition for 'Anova'
statMissing: no visible global function definition for 'whatis'
vpAFC: no visible global function definition for 'dudi.coa'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/RcmdrPlugin.RMTCJags.Rcheck/00install.out' for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    include   4.9Mb
    libs      1.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/RcppBlaze.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/RcppCCTZ.Rcheck/00install.out' for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    include   4.5Mb
    libs      1.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/RcppHMM.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/RcppOctave.Rcheck/00install.out' for details.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib       6.4Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    include   6.3Mb
    libs      1.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/RcppShark.Rcheck/00install.out' for details.
sumry_categorical: no visible global function definition for 'freq'
prepare_Rd: Rdpack-package.Rd:154: unknown macro '\insertRef'
prepare_Rd: Rdpack-package.Rd:156: unknown macro '\insertRef'
prepare_Rd: insert_ref.Rd:89: unknown macro '\insertRef'
prepare_Rd: insert_ref.Rd:91: unknown macro '\insertRef'
macros/refmacros.Rd: Sections \title, and \name must exist and be unique in Rd files
problem found in 'refmacros.Rd'
Package suggested but not available for checking: 'RSelenium'
File 'readr/libs/i386/readr.dll':
  Found non-API call to R: 'getConnection'
File 'readr/libs/x64/readr.dll':
  Found non-API call to R: 'getConnection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
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'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   1.6Mb
Namespaces in Imports field not imported from:
  'devtools' 'dplyr' 'magrittr' 'plyr' 'reshape2'
  All declared Imports should be used.
Error in re-building vignettes:
  ...

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

    intersect, setdiff, setequal, union

Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Quitting from lines 47-64 (recexcavAAR-vignette-1.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-1.Rmd' failed with diagnostics:
object 'x' not found
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 76-93 (BasicREDCapROperations.Rmd) 
Error: processing vignette 'BasicREDCapROperations.Rmd' failed with diagnostics:
object 'ds' not found
Execution halted
mergeNamespace_roclet: no visible global function definition for
  'new_roclet'
Namespaces in Imports field not imported from:
  'igraph' 'rJava'
  All declared Imports should be used.
REEMtree: no visible binding for global variable 'SubsetVector'
Namespace in Imports field not imported from: 'curl'
  All declared Imports should be used.
macros/macros.Rd: Sections \title, and \name must exist and be unique in Rd files
problem found in 'macros.Rd'
wcr: no visible global function definition for 'ginv'
cv.alpha.relaxnet: no visible global function definition for
  'mc.reset.stream'
cv.alpha.relaxnet: no visible global function definition for 'mclapply'
cv.relaxnet: no visible global function definition for
  'mc.reset.stream'
cv.relaxnet: no visible global function definition for 'mclapply'
relaxo: no visible global function definition for 'lars'
cross: no visible binding for global variable 'is.Surv'
is.numeric.and.not.surv: no visible global function definition for
  'is.Surv'
remix: no visible global function definition for 'is.formula'
remix : <anonymous>: no visible global function definition for
  'is.Surv'
remix: no visible binding for global variable 'is.Surv'
remix: no visible global function definition for 'llply'
summarize.by: no visible global function definition for 'dlply'
summarize.by: no visible global function definition for '.'
summarize.data.frame.by: no visible global function definition for
  'dlply'
survival: no visible global function definition for 'survfit'
survival: no visible global function definition for 'daply'
survival: no visible global function definition for '.'
test.survival.logrank: no visible global function definition for
  'survdiff'
Running examples in 'rentrez-Ex.R' failed
The error most likely occurred in:

> ### Name: entrez_db_summary
> ### Title: Retrieve summary information about an NCBI database
> ### Aliases: entrez_db_summary
> 
> ### ** Examples
> 
> entrez_db_summary("pubmed")
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached
Calls: entrez_db_summary ... request_fetch -> request_fetch.write_memory -> <Anonymous> -> .Call
Execution halted
GlobTestMissing: no visible global function definition for 'lme'
TestStatSimple: no visible global function definition for 'ginv'
reshapeGUI: no visible global function definition for 'gwindow'
reshapeGUI: no visible global function definition for 'gnotebook'
reshapeGUI: no visible global function definition for 'size<-'
reshapeGUI: no visible global function definition for 'ggroup'
reshapeGUI: no visible global function definition for 'gtable'
reshapeGUI: no visible global function definition for 'addSpring'
reshapeGUI: no visible global function definition for 'gbutton'
reshapeGUI: no visible global function definition for 'glabel'
reshapeGUI: no visible global function definition for 'gedit'
reshapeGUI: no visible global function definition for 'gcheckbox'
reshapeGUI: no visible global function definition for 'gdf'
reshapeGUI: no visible global function definition for 'visible<-'
reshapeGUI: no visible global function definition for
  'addHandlerClicked'
reshapeGUI : <anonymous>: no visible global function definition for
  'gmessage'
reshapeGUI : <anonymous>: no visible global function definition for
  'svalue'
reshapeGUI : <anonymous>: no visible global function definition for
  'svalue<-'
reshapeGUI : <anonymous>: no visible global function definition for
  'delete'
reshapeGUI : <anonymous>: no visible global function definition for
  'add'
reshapeGUI : <anonymous>: no visible global function definition for
  'gdf'
reshapeGUI : <anonymous>: no visible global function definition for
  'visible<-'
reshapeGUI: no visible global function definition for
  'addHandlerChanged'
updateMeltCodeBox: no visible global function definition for 'svalue<-'
findCredentials: no visible global function definition for 'startsWith'
Running examples in 'restfulr-Ex.R' failed
The error most likely occurred in:

> ### Name: RestContainer-class
> ### Title: RestContainer
> ### Aliases: class:RestContainer RestContainer-class RestContainer
> ###   [,RestContainer-method [<-,RestContainer-method
> ###   $,RestContainer-method [[,RestContainer-method
> ###   $<-,RestContainer-method [[<-,RestContainer-method
> ###   show,RestContainer-method
> ### Keywords: methods classes
> 
> ### ** Examples
> 
> apache <- RestContainer("http://wiki.apache.org")
Error in which(startsWith(uri, as.character(names(config)))) : 
  could not find function "startsWith"
Calls: RestContainer -> container -> RestUri -> findCredentials -> which
Execution halted
normalize_python_path: no visible global function definition for
  'endsWith'
mat2coo: no visible global function definition for 'as.matrix.coo'
quoteFXTsData : function.fx: no visible global function definition for
  'xmlValue'
quoteFundTsData : function.fund: no visible global function definition
  for 'xmlValue'
quoteStockTsData : function.stock: no visible global function
  definition for 'xmlSize'
quoteStockTsData : function.stock: no visible global function
  definition for 'xmlValue'
quoteTsData: no visible global function definition for 'xmlRoot'
quoteTsData: no visible global function definition for 'htmlTreeParse'
quoteTsData: no visible global function definition for
  'xmlErrorCumulator'
quoteTsData: no visible global function definition for 'xmlSize'
toXts: no visible global function definition for 'as.xts'
Namespace in Imports field not imported from: 'RcppProgress'
  All declared Imports should be used.
gammaIntegral : <anonymous>: no visible global function definition for
  'hyperg_1F1'
installed size is 34.1Mb
  sub-directories of 1Mb or more:
    gdal       3.0Mb
    libs      23.7Mb
    pictures   1.3Mb
    proj       4.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.5Mb
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  1. Failure: add_flags works properly guessing names for rvertnet dataset (@test_multiple_records.R#38) 
  2. Failure: add_flags works properly with a 1-row data.frame (@test_multiple_records.R#51) 
  3. Failure: add_flags works properly with a 1-row data.frame (@test_multiple_records.R#52) 
  4. Failure: add_flags works properly with a 1-row data.frame (@test_multiple_records.R#53) 
  5. Failure: add_flags works properly with a 1-row data.frame (@test_multiple_records.R#54) 
  6. Failure: add_flags works properly with a 1-row data.frame (@test_multiple_records.R#55) 
  7. Failure: add_flags works properly with a 1-row data.frame (@test_multiple_records.R#56) 
  8. Failure: add_flags works properly with a 1-row data.frame (@test_multiple_records.R#57) 
  9. Failure: add_flags works properly with a 1-row data.frame (@test_multiple_records.R#58) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc     2.6Mb
    fonts   1.5Mb
    libs    1.2Mb
exprToIgraph: no visible global function definition for 'graph'
exprToIgraph: no visible global function definition for 'V'
exprToIgraph: no visible global function definition for 'V<-'
multiNicheGeneticProgramming: no visible binding for global variable
  'sfClusterApplyLB'
multiNicheGeneticProgramming: no visible binding for global variable
  'sfExport'
multiNicheSymbolicRegression: no visible binding for global variable
  'sfClusterApplyLB'
multiNicheSymbolicRegression: no visible binding for global variable
  'sfExport'
Error in re-building vignettes:
  ...
mpiler/texmf/fonts/type1/public/amsfonts/cm/cmr8.pfb><D:/Compiler/texmf/fonts/t
ype1/public/amsfonts/cm/cmr9.pfb><D:/Compiler/texmf/fonts/type1/public/amsfonts
/cm/cmsltt10.pfb><D:/Compiler/texmf/fonts/type1/public/amsfonts/cm/cmss10.pfb><
D:/Compiler/texmf/fonts/type1/public/amsfonts/cm/cmss8.pfb><D:/Compiler/texmf/f
onts/type1/public/amsfonts/cm/cmss9.pfb><D:/Compiler/texmf/fonts/type1/public/a
msfonts/cm/cmsy10.pfb><D:/Compiler/texmf/fonts/type1/public/amsfonts/cm/cmti10.
pfb><D:/Compiler/texmf/fonts/type1/public/amsfonts/cm/cmti12.pfb><D:/Compiler/t
exmf/fonts/type1/public/amsfonts/cm/cmtt10.pfb><D:/Compiler/texmf/fonts/type1/p
ublic/amsfonts/cm/cmtt8.pfb><D:/Compiler/texmf/fonts/type1/public/mathpazo/fplm
ri.pfb><D:/Compiler/texmf/fonts/type1/public/cm-super/sfrm0900.pfb><D:/Compiler
/texmf/fonts/type1/public/cm-super/sfrm1000.pfb><D:/Compiler/texmf/fonts/type1/
urw/palatino/uplr8a.pfb><D:/Compiler/texmf/fonts/type1/urw/palatino/uplri8a.pfb
>
Output written on rgp_introduction.pdf (16 pages, 430970 bytes).
Transcript written on rgp_introduction.log.
"D:/RCompile/recent/R-32~1.5/bin/Rscript" -e "tools::compactPDF('rgp_introduction.pdf', gs_quality='ebook')"
  compacted 'rgp_introduction.pdf' from 421Kb to 205Kb
rm -f Rplots.pdf
rm: cannot remove 'Rplots.pdf': Device or resource busy
make[1]: *** [pdf] Error 1
make[1]: Leaving directory `/cygdrive/d/RCompile/CRANpkg/local/3.2/rgp.Rcheck/vign_test/rgp/vignettes'
Warning: running command 'make' had status 2
Error in buildVignettes(dir = "d:/Rcompile/CRANpkg/local/3.2/rgp.Rcheck/vign_test/rgp") : 
  running 'make' failed
Execution halted
server: no visible global function definition for 'mcparallel'
Found the following significant warnings:
  gdkFuncs.c:1466:3: warning: passing argument 1 of 'gdk_drag_get_protocol' makes pointer from integer without a cast [enabled by default]
  gdkFuncs.c:1510:3: warning: passing argument 2 of 'gdk_drag_get_protocol_for_display' makes pointer from integer without a cast [enabled by default]
See 'd:/Rcompile/CRANpkg/local/3.2/RGtk2.Rcheck/00install.out' for details.
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    help  10.6Mb
    libs   4.6Mb
dbConnect,H2Driver : .local: no visible global function definition for
  '.jgetEx'
dbSendQuery,H2Connection-character : .local: no visible global function
  definition for '.jfield'
.quick_fetch: no visible global function definition for 'POST'
.quick_fetch: no visible global function definition for 'add_headers'
.quick_fetch: no visible global function definition for
  'stop_for_status'
.quick_fetch: no visible global function definition for 'content'
fetch_healthdata: no visible binding for global variable 'resources'
fetch_healthdata : <anonymous>: no visible binding for global variable
  'filters'
eclDirectCall: no visible global function definition for 'postForm'
parseResults: no visible global function definition for 'xmlRoot'
parseResults: no visible global function definition for 'xmlTreeParse'
parseResults: no visible global function definition for 'getNodeSet'
parseResults: no visible global function definition for 'xmlGetAttr'
parseResults: no visible global function definition for 'xmlValue'
Namespace in Imports field not imported from: 'httr'
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    lib    3.2Mb
    libs   4.3Mb
Package required but not available: 'feather'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
NumConv: no visible global function definition for 'pchip'
NumConv: no visible global function definition for 'cmpfun'
NumDeconv: no visible global function definition for 'pchip'
NumDeconv : error_function: no visible global function definition for
  'pchip'
NumDeconv: no visible global function definition for 'cmpfun'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/rjags.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.2/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.2/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'rJava/libs/i386/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'
File 'rJava/libs/x64/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/rjmcmc.Rcheck/00install.out' for details.
getStatsData: no visible global function definition for 'xmlRoot'
getStatsData: no visible global function definition for 'xmlTreeParse'
getStatsData: no visible global function definition for 'xmlValue'
getStatsData: no visible global function definition for 'getNodeSet'
getStatsData: no visible global function definition for 'xmlSApply'
getStatsData: no visible binding for global variable 'xmlGetAttr'
getStatsData: no visible binding for global variable 'xmlValue'
getStatsList: no visible global function definition for 'xmlRoot'
getStatsList: no visible global function definition for 'xmlTreeParse'
getStatsList: no visible global function definition for 'xmlValue'
getStatsList: no visible binding for global variable 'xmlGetAttr'
getStatsList : <anonymous>: no visible global function definition for
  'xmlValue'
getStatsList : <anonymous>: no visible global function definition for
  'xmlGetAttr'
Namespace in Imports field not imported from: 'crul'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Matrix' 'arules' 'pmml' 'rJava'
  All declared Imports should be used.
Package required and available but unsuitable version: 'Luminescence'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
parse_grammar : <anonymous>: no visible global function definition for
  'startsWith'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  
  Generating LALR tables 
  testthat results ================================================================
  OK: 153 SKIPPED: 0 FAILED: 5
  1. Failure: rule (@test.yacc_badrule.R#181) 
  2. Failure: rule (@test.yacc_badrule.R#183) 
  3. Failure: rule (@test.yacc_badrule.R#185) 
  4. Failure: rule (@test.yacc_badrule.R#187) 
  5. Failure: misplaced (@test.yacc_misplaced.R#52) 
  
  Error: testthat unit tests failed
  Execution halted
PD_internal: no visible global function definition for 'qtnorm'
Namespaces in Imports field not imported from:
  'mnormt' 'pwr'
  All declared Imports should be used.
.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'
plot.meta.cum: warning in qnorm((1 - conf.level)/2, s = ses[m]):
  partial argument match of 's' to 'sd'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/Rmixmod.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/Rmpi.Rcheck/00install.out' for details.
CoeffYWeq: no visible global function definition for 'index'
fitdistrForPrecipitation: no visible global function definition for
  'fitdistr'
DESeqWrapper: no visible global function definition for
  'newCountDataSet'
DESeqWrapper: no visible global function definition for
  'estimateSizeFactors'
DESeqWrapper: no visible global function definition for 'counts'
DESeqWrapper: no visible global function definition for
  'estimateDispersions'
DESeqWrapper: no visible global function definition for 'nbinomTest'
DESeqWrapper: no visible global function definition for
  'getVarianceStabilizedData'
DESeqWrapper: no visible global function definition for 'pData'
kaksFromVariants : <anonymous>: no visible global function definition
  for 'as.alignment'
kaksFromVariants : <anonymous>: no visible global function definition
  for 'kaks'
nSynNonSites : <anonymous>: no visible global function definition for
  'as.alignment'
nSynNonSites : <anonymous>: no visible global function definition for
  'kaks'
plotDispEsts: no visible global function definition for 'counts'
plotDispEsts: no visible global function definition for 'fitInfo'
runGOAnalysis: no visible binding for global variable 'annFUN.gene2GO'
runGOAnalysis: no visible global function definition for 'runTest'
runGOAnalysis: no visible global function definition for 'score'
runGOAnalysis: no visible global function definition for 'termStat'
runGOAnalysis: no visible global function definition for 'Term'
runGOAnalysis: no visible binding for global variable 'GOTERM'
runGOAnalysis: no visible global function definition for
  'showSigOfNodes'
Package required but not available: 'sf'

Package suggested but not available for checking: 'rnaturalearthhires'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
RNGseq : <anonymous>: no visible global function definition for
  'nextRNGStream'
RNGseq: no visible global function definition for 'nextRNGStream'
RNGseq_seed: no visible global function definition for 'nextRNGStream'
checkRNG: no visible global function definition for 'checkTrue'
psdcor: no visible global function definition for 'posdefify'
psdcor: no visible global function definition for 'nearcor'
robcor: no visible global function definition for 'covMcd'
robloxbioc,beadLevelData : .local: warning in
  packageDescription(annoPkg, field = "Version"): partial argument
  match of 'field' to 'fields'
AffySimStudy: no visible global function definition for 'estimate'
IlluminaSimStudy: no visible global function definition for 'estimate'
KolmogorovMinDist,BeadLevelList-AbscontDistribution : .local: no
  visible global function definition for 'arrayNames'
KolmogorovMinDist,BeadLevelList-AbscontDistribution : .local: no
  visible global function definition for 'getArrayData'
robloxbioc,beadLevelData : .local: no visible global function
  definition for 'mappedkeys'
robloxbioc,beadLevelData : .local: no visible global function
  definition for 'revmap'
robloxbioc,beadLevelData : .local: no visible global function
  definition for 'featureData<-'
robloxbioc,beadLevelData : .local: no visible global function
  definition for 'phenoData<-'
FaClassic.default: no visible global function definition for 'Cov'
FaClassic.default: no visible global function definition for 'getCov'
FaCov.default: no visible global function definition for
  'CovControlMcd'
FaCov.default: no visible global function definition for 'restimate'
FaCov.default: no visible global function definition for 'Cov'
FaCov.default: no visible global function definition for 'getCov'
compute_cov_cor: no visible global function definition for 'CovRobust'
compute_cov_cor: no visible global function definition for 'getCov'
compute_cov_cor: no visible global function definition for 'getCorr'
myplotDD: no visible global function definition for 'getData'
myplotDD: no visible global function definition for 'getCov'
myplotDD: no visible global function definition for 'CovClassic'
myplotDD: no visible global function definition for 'getDistance'
pred.robustgam: no visible global function definition for
  'Predict.matrix'
robustgam: no visible global function definition for 's'
robustgam: no visible global function definition for
  'smooth.construct.tp.smooth.spec'
robustgam: no visible global function definition for
  'smooth.construct.cr.smooth.spec'
robustgam: no visible global function definition for
  'smooth.construct.ps.smooth.spec'
robustgam : w.fun: no visible global function definition for 'covMcd'
robustgam.crossval : w.fun: no visible global function definition for
  'covMcd'
boot.ROC: no visible global function definition for 'penalized'
boot.ROC: no visible global function definition for 'optL1'
boot.ROCt: no visible global function definition for 'penalized'
boot.ROCt: no visible global function definition for 'Surv'
boot.ROCt: no visible global function definition for 'survivalROC'
boot.ROCt: no visible global function definition for 'optL1'
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'
tr.rocc: no visible global function definition for 'prediction'
tr.rocc: no visible global function definition for 'performance'
Namespace in Imports field not imported from: 'matrixcalc'
  All declared Imports should be used.
api: no visible global function definition for 'endsWith'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.1Mb
P: no visible global function definition for 'has.key'
rand_partitions: no visible global function definition for 'hash'
rpart.rules.push: no visible global function definition for 'sqlSave'
GenerateData: no visible global function definition for 'mvrnorm'
GetVarImp : FitPenalizedModel: no visible global function definition
  for 'clogit'
cell.density.default: no visible binding for global variable
  'universalConstants'
conect.pdb: no visible binding for global variable 'elements'
masses.default: no visible binding for global variable 'elements'
toSymbols.character: no visible binding for global variable 'elements'
toSymbols.integer: no visible binding for global variable 'elements'
visualize.coords: no visible binding for global variable 'elements'
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   2.6Mb
read.multi.dna: no visible binding for global variable 'read.dna'
read.phylip.data: no visible global function definition for 'read.dna'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is 24.2Mb
  sub-directories of 1Mb or more:
    libs  23.8Mb
rrest: no visible binding for global variable 'glasso'
rrest: no visible global function definition for 'pcout'
rrlda : centerObservations: no visible global function definition for
  'l1median_NLM'
rrlda : df.L2glasso: no visible global function definition for
  'duplication.matrix'
rrlda : alt.df.L2glasso: no visible global function definition for
  'lower.triangle'
Package required but not available: 'wdman'

Package suggested but not available for checking: 'Rcompression'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  d:\compiler\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/winsock2.h:15:2: warning: #warning Please include winsock2.h before windows.h [-Wcpp]
  qap_decode.c:200:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:200:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:55: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:60: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.2/Rserve.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.2/Rserve/libs/i386/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'd:/Rcompile/CRANpkg/lib/3.2/Rserve/libs/x64/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'Rserve/libs/i386/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
rsig: no visible binding for global variable 'mclapply'
rsig.all: no visible binding for global variable 'mclapply'
Namespace in Imports field not imported from: 'parallel'
  All declared Imports should be used.
Found the following significant warnings:
  Warning: replacing previous import 'kohonen::somgrid' by 'class::somgrid' when loading 'Rsomoclu'
See 'd:/Rcompile/CRANpkg/local/3.2/Rsomoclu.Rcheck/00install.out' for details.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  10.3Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
RStorm: no visible global function definition for 'alply'
Namespace in Imports field not imported from: 'mc2d'
  All declared Imports should be used.
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    libs  17.3Mb
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'
Namespaces in Imports field not imported from:
  'RSQLite' 'stats'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/rtk.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/runjags.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
rvgt.ftable : myrdist: no visible global function definition for 'ur'
uerror: no visible global function definition for 'unuran.is.inversion'
uerror : myaqdist: no visible global function definition for 'uq'
unuran.distr.class: no visible global function definition for
  'unuran.details'
xerror: no visible global function definition for 'unuran.is.inversion'
xerror : myaqdist: no visible global function definition for 'uq'
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'
check_ISO_code: no visible binding for global variable 'NoAm_country'
check_ISO_code: no visible binding for global variable 'SoAm_country'
check_ISO_code: no visible binding for global variable 'Oceana_country'
check_ISO_code: no visible binding for global variable 'Africa_country'
check_ISO_code: no visible binding for global variable 'Asia_country'
check_ISO_code: no visible binding for global variable 'Eur_country'
Running examples in 'rwty-Ex.R' failed
The error most likely occurred in:

> ### Name: makeplot.splitfreq.matrix
> ### Title: Plots a matrix of split frequency comparisons between multiple
> ###   MCMC chains.
> ### Aliases: makeplot.splitfreq.matrix
> ### Keywords: ASDSF MCMC, clade consensus, convergence, frequency,
> ###   phylogenetics,
> 
> ### ** Examples
> 
> data(salamanders)
> makeplot.splitfreq.matrix(salamanders[1:4], burnin = 20)
[1] "Creating split frequency matrix and ASDSF clustering plots"
$splitfreq.matrix

$asdsf.tree
Error in .Call.graphics(C_palette2, .Call(C_palette2, NULL)) : 
  invalid graphics state
Calls: print -> print.ggplot -> grid.newpage -> <Anonymous>
Execution halted
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 in `[.data.frame`(countrycode::countrycode_data, , c("country.name",  : 
  undefined columns selected
Calls: set_location ... is_valid_territory -> list_countries -> [ -> [.data.frame
Execution halted
Analyze: no visible global function definition for 'mcmc'
Analyze: no visible global function definition for 'varnames<-'
AnalyzeWithExitPoll: no visible global function definition for 'mcmc'
AnalyzeWithExitPoll: no visible global function definition for
  'varnames<-'
form.mcmc.object: no visible global function definition for
  'varnames<-'
gq.summary: no visible global function definition for 'mcmc.list'
gq.summary: no visible global function definition for 'mcmc'
gq_diagnostics: no visible global function definition for 'mcmc.list'
gq_diagnostics: no visible global function definition for 'mcmc'
gq_diagnostics: no visible global function definition for 'gelman.diag'
gq_diagnostics: no visible global function definition for 'geweke.diag'
gq_diagnostics: no visible global function definition for 'heidel.diag'
gq_diagnostics: no visible global function definition for
  'autocorr.diag'
RXlarlso: no visible global function definition for 'lars'
RXuclars: no visible global function definition for 'lars'
gtkFileChooserDialogFilteredActivate: no visible binding for global
  variable 'theme_grey'
summary.CrossTable: no visible global function definition for
  'assocstats'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/s2.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'spanel'
  All declared Imports should be used.
Plot.ll: warning in axis(1, chpt - n * 2.5/100, tick = F, lab =
  expression(hat(k)), cex.axis = 1, col.axis = "red"): partial argument
  match of 'lab' to 'labels'
plot,SaemixSimData : .local: no visible binding for global variable
  'name.group'
separator: no visible global function definition for 'make.lp'
separator: no visible global function definition for 'set.column'
separator: no visible global function definition for 'set.rhs'
separator: no visible global function definition for 'set.constr.type'
separator: no visible global function definition for 'set.objfn'
separator: no visible global function definition for 'set.bounds'
separator: no visible global function definition for 'lp.control'
separator: no visible global function definition for 'get.variables'
separator: no visible global function definition for 'set.basis'
separator: no visible global function definition for
  'get.dual.solution'
distanceLimitedPDSIZ,downLog-perpendicularDistance-dlsNumeric : .local:
  warning in matrix(c(os.len, 0, 1), nr = 1): partial argument match of
  'nr' to 'nrow'
downLogs,numeric-missing : .local: warning in matrix(c(xlim, ylim), nr
  = 2, byrow = TRUE, dimnames = list(c("x", "y"), c("min", "max"))):
  partial argument match of 'nr' to 'nrow'
standingTrees,numeric-missing : .local: warning in matrix(c(xlim,
  ylim), nr = 2, byrow = TRUE, dimnames = list(c("x", "y"), c("min",
  "max"))): partial argument match of 'nr' to 'nrow'
clipStemsToTract,downLogs-SpatialPolygons : .local: no visible global
  function definition for 'gIntersects'
clipStemsToTract,downLogs-SpatialPolygons : .local: no visible global
  function definition for 'gIntersection'
izGrid,matrix-Tract : .local: no visible global function definition for
  'intersectExtent'
izGridMirage,InclusionZone-mirageTract : .local: no visible global
  function definition for 'gIntersects'
izGridMirage,InclusionZone-mirageTract : .local : mirageSection: no
  visible global function definition for 'gIntersection'
predict.samEL: no visible global function definition for 'ns'
predict.samHL: no visible global function definition for 'ns'
predict.samLL: no visible global function definition for 'ns'
predict.samQL: no visible global function definition for 'ns'
samEL: no visible global function definition for 'ns'
samHL: no visible global function definition for 'ns'
samLL: no visible global function definition for 'ns'
samQL: no visible global function definition for 'ns'
foldchange.seq.twoclass.paired: no visible global function definition
  for 'rowMedians'
foldchange.seq.twoclass.unpaired: no visible global function definition
  for 'rowMedians'
samr: no visible global function definition for 'impute.knn'
samr.xl.impute.data: no visible global function definition for
  'impute.knn'
samr.xl.impute.data: no visible binding for global variable
  'samr.xl.var.knn.neighbors'
my.SOnePro: missing arguments not allowed in calls to 'c'
slassoEst: no visible global function definition for 'lars'
slassoEst: no visible global function definition for 'predict.lars'
convert.infusion: no visible global function definition for 'size'
create.intervals: no visible global function definition for 'size'
create.intervals: no visible global function definition for 'transpose'
dde.model: no visible global function definition for 'size'
dde.model: no visible global function definition for 'transpose'
de.output: no visible global function definition for 'size'
explicit.model: no visible global function definition for 'size'
finalize.report: no visible global function definition for 'transpose'
finalize.report: no visible global function definition for 'size'
fitmle : obj.fun: no visible global function definition for 'size'
fitmle.cov: no visible global function definition for 'transpose'
get.cov.matrix: no visible global function definition for 'size'
get.parms.data: no visible global function definition for 'size'
get.secondary: no visible global function definition for 'transpose'
init.cond: no visible global function definition for 'size'
init.update: no visible global function definition for 'size'
input.scaling: no visible global function definition for 'size'
make.dosing: no visible global function definition for 'size'
ode.model: no visible global function definition for 'size'
ode.model: no visible global function definition for 'transpose'
problem.eval: no visible global function definition for 'size'
residual.report: no visible global function definition for 'size'
scarabee.check.model: no visible global function definition for 'size'
scarabee.gridsearch : grid.obj.fun: no visible global function
  definition for 'size'
scarabee.read.data: no visible global function definition for 'size'
scarabee.read.parms: no visible global function definition for 'size'
simulation.report: no visible global function definition for 'size'
weighting: no visible global function definition for 'size'
prime.factor: no visible binding for global variable 'primlist'
c,scidbdf : .local: warning in build_dim_schema(x, newname = j):
  partial argument match of 'newname' to 'newnames'
scio.refit: no visible global function definition for 'QUIC'
CreatePssm: no visible binding for global variable 'training'
scrape: no visible global function definition for 'getURLAsynchronous'
scrape: no visible binding for global variable 'xmlParse'
scrape: no visible binding for global variable 'htmlParse'
buildSNPannotation: no visible global function definition for 'db'
buildSNPannotation: no visible global function definition for
  'dbListFields'
buildSNPannotation: no visible global function definition for
  'dbGetQuery'
fblr: no visible global function definition for 'mvrnorm'
fblr.weight: no visible global function definition for 'mvrnorm'
extractLabels: no visible global function definition for 'validUTF8'
Namespaces in Imports field not imported from:
  'gbm' 'graphics' 'ncdf4' 'rgdal' 'sp'
  All declared Imports should be used.
ConnCompLabel: no visible global function definition for 'setValues'
SigDiff: no visible global function definition for 'setValues'
asc.from.raster: no visible global function definition for 'getValues'
aspect: no visible global function definition for 'setValues'
grid.area: no visible global function definition for 'setValues'
grid.perimeter: no visible global function definition for 'setValues'
lcmw: no visible global function definition for 'setValues'
raster.from.asc: no visible global function definition for 'raster'
raster.from.asc: no visible global function definition for
  'projection<-'
raster.from.asc: no visible global function definition for 'setValues'
slope: no visible global function definition for 'setValues'
sp.from.asc: no visible global function definition for 'CRS'
sp.from.asc: no visible global function definition for 'GridTopology'
sp.from.asc: no visible global function definition for
  'SpatialGridDataFrame'
sealasso: no visible global function definition for 'lars'
weight.calc: no visible global function definition for 'lars'
dathomog: no visible global function definition for 'kde2d'
fitMod: no visible global function definition for 'survreg'
fitswavecav: no visible global function definition for 'year'
prepData: no visible global function definition for 'year'
prepData: no visible global function definition for 'month'
prepData: no visible global function definition for 'day'
rosBoxPlot: no visible global function definition for 'ros'
GKhat.env: no visible global function definition for 'Gest'
GKhat.env: no visible global function definition for 'rpoispp'
GKhat.env: no visible global function definition for 'Kest'
GKhat.env: no visible global function definition for 'runifpoint'
Okriging: no visible global function definition for 'point'
Okriging: no visible global function definition for 'krige'
eda6: no visible global function definition for 'qqPlot'
makeppp: no visible global function definition for 'ppp'
nnGK.ppp: no visible global function definition for 'Gest'
nnGK.ppp: no visible global function definition for 'Kest'
nnGKenv.ppp: no visible global function definition for 'Gest'
nnGKenv.ppp: no visible global function definition for 'Kest'
plotkriged: no visible global function definition for 'point'
quad.chisq.ppp: no visible global function definition for 'ppp'
quad.poisson.ppp: no visible global function definition for 'ppp'
vario: no visible global function definition for 'point'
vario: no visible global function definition for 'pair'
vario: no visible global function definition for 'est.variogram'
vario: no visible global function definition for 'plot.point'
vario: no visible global function definition for 'spacecloud'
vario: no visible global function definition for 'spacebox'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.4Mb
.use.spgrass6: no visible global function definition for 'listw2mat'
.use.spgrass6: no visible global function definition for 'sn2listw'
Found the following significant warnings:
  Warning: S3 methods '[.xml_missing', '[.xml_nodeset', '[[.xml_missing', 'xml_attr<-.xml_missing', 'xml_attr<-.xml_node', 'xml_attr<-.xml_nodeset', 'xml_attrs<-.xml_missing', 'xml_attrs<-.xml_node', 'xml_attrs<-.xml_nodeset', 'xml_name<-.xml_missing', 'xml_name<-.xml_node', 'xml_name<-.xml_nodeset', 'xml_text<-.xml_missing', 'xml_text<-.xml_node', 'xml_text<-.xml_nodeset', 'as.character.xml_document', 'as.character.xml_missing', 'as.character.xml_node', 'as.character.xml_nodeset', 'as_list.xml_missing', 'as_list.xml_node', 'as_list.xml_nodeset', 'as_xml_document.character', 'as_xml_document.connection', 'as_xml_document.list', 'as_xml_document.raw', 'as_xml_document.response', 'as_xml_document.xml_document', 'as_xml_document.xml_node', 'as_xml_document.xml_nodeset', 'format.xml_node', 'is.na.xml_missing', 'is.na.xml_node', 'is.na.xml_nodeset', 'nodeset_apply.xml_document', 'nodeset_apply.xml_missing', 'nodeset_apply.xml_node', 'nodeset_apply.xml_nodeset', 'print.xml_document', 'print.xml_missing [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.2/selectr.Rcheck/00install.out' for details.
predict.SEL: warning in splineDesign(newdata, knots = knts, ord =
  object$nord, deriv = rep(deriv, length(newdata)), outer.ok = TRUE):
  partial argument match of 'deriv' to 'derivs'
semdiag: no visible global function definition for 'sem'
semdiag.robfit.r: no visible global function definition for 'sem'
semdiag.robfit1.r: no visible global function definition for 'sem'
computeProjectionFromKernel : <anonymous>: no visible global function
  definition for 'irlba'
ChiSquaredLRTest: no visible global function definition for 'dmvnorm'
NormalTheoryLRTest: no visible global function definition for 'dmvnorm'
semPlotModel.mplus.model: no visible global function definition for
  'readModels'
plot.sempls: no visible global function definition for
  'trellis.par.get'
plot.sempls: no visible global function definition for
  'trellis.par.set'
plot.sempls: no visible global function definition for 'xyplot'
plsm2sem.plsm: no visible global function definition for 'specifyModel'
plsm2sem.plsm: no visible global function definition for
  'specify.model'
read.splsm: no visible global function definition for
  'xmlInternalTreeParse'
read.splsm: no visible global function definition for 'xpathApply'
read.splsm: no visible binding for global variable 'xmlGetAttr'
summary.bootsempls: no visible global function definition for 'boot.ci'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/semver.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'sp'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'lexicon' 'syuzhet'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/SeqFeatR.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/seqminer.Rcheck/00install.out' for details.
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 binding for '<<-' assignment to
  '.save.session.search'
save.session: no visible binding for '<<-' assignment to
  '.save.session.packages'
Malformed Title field: should not end in a period.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'lattice' 'betareg'
A package should be listed in only one of these fields.
Namespaces in Imports field not imported from:
  'betareg' 'lattice'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'betareg' 'lattice'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
indirectCalibration: no visible global function definition for
  'betareg'
xy.plot.lat: no visible global function definition for 'xyplot'
xy.plot.lat: no visible global function definition for 'strip.custom'
xy.plot.lat : <anonymous>: no visible global function definition for
  'panel.abline'
xy.plot.lat : <anonymous>: no visible global function definition for
  'panel.xyplot'
xy.plot.lat : <anonymous>: no visible global function definition for
  'panel.text'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/sf.Rcheck/00install.out' for details.
plotBoundary: no visible global function definition for
  'scale_y_continuous'
distLaplacian: no visible global function definition for 'sparseMatrix'
laplacian: no visible global function definition for 'sparseMatrix'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/sharx.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'DT' 'gridExtra' 'latticeExtra' 'msm'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'shinyBS' 'shinythemes'
  All declared Imports should be used.
Package required and available but unsuitable version: 'CompQuadForm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
footpoint.nodes: no visible global function definition for
  'coordinates'
nt.connect: no visible global function definition for 'bbox'
nt.connect: no visible global function definition for
  'as.SpatialLines.SLDF'
nt.connect: no visible global function definition for
  'SpatialLinesDataFrame'
ptsinnt.view: no visible global function definition for 'bbox'
readshpnw: no visible global function definition for 'coordinates'
Undocumented S4 methods:
  generic '[' and siglist 'Prob0,ANY,missing,ANY'
  generic '[' and siglist 'bFdr,ANY,missing,ANY'
  generic '[' and siglist 'basicFdr,ANY,missing,ANY'
  generic '[' and siglist 'eFdr,ANY,missing,ANY'
  generic '[' and siglist 'estimate,ANY,missing,ANY'
  generic '[' and siglist 'loss,ANY,missing,ANY'
  generic '[' and siglist 'pseudoFdr,ANY,missing,ANY'
  generic '[' and siglist 'sFdr,ANY,missing,ANY'
  generic '[' and siglist 'sortableEstimate,ANY,missing,ANY'
  generic '[' and siglist 'unsortableEstimate,ANY,missing,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
bayesMVN: no visible global function definition for 'rmultireg'
bayestwoNorm: no visible global function definition for 'runireg'
overlap: no visible global function definition for 'overlap.xypolygon'
panelcontour: no visible global function definition for 'kde2d'
siardensityplot: no visible global function definition for 'hdr'
siarhdrs: no visible global function definition for 'hdr'
siarhdrs: no visible global function definition for 'geweke.diag'
siarproportionbygroupplot: no visible global function definition for
  'hdr'
siarproportionbysourceplot: no visible global function definition for
  'hdr'
Namespace in Imports field not imported from: 'viridis'
  All declared Imports should be used.
Running examples in 'SIBER-Ex.R' failed
The error most likely occurred in:

> ### Name: fitEllipse
> ### Title: Fit a multivariate normal distribution to x and y data using
> ###   jags
> ### Aliases: fitEllipse
> 
> ### ** Examples
> 
> x <- stats::rnorm(50)
> y <- stats::rnorm(50)
> parms <- list()
> parms$n.iter <- 2 * 10^3
> parms$n.burnin <- 500
> parms$n.thin <- 2     
> parms$n.chains <- 2    
> priors <- list()
> priors$R <- 1 * diag(2)
> priors$k <- 2
> priors$tau.mu <- 1.0E-3
> fitEllipse(x, y, parms, priors)
Error: .onLoad failed in loadNamespace() for 'rjags', details:
  call: fun(libname, pkgname)
  error: The environment variable JAGS_HOME is set to
c:/Program Files/JAGS/JAGS-4.0.0
but no JAGS installation can be found there
Execution halted
Error in re-building vignettes:
  ...
Warning in buildVignettes(dir = "d:/Rcompile/CRANpkg/local/3.2/SIBER.Rcheck/vign_test/SIBER") :
  Files named as vignettes but with no recognized vignette engine:
   'vignettes/test-nonnumeric-community-labels.Rmd'
   'vignettes/test-nonnumeric-group-labels.Rmd'
(Is a VignetteBuilder field missing?)
Quitting from lines 120-155 (Ellipse-Overlap.Rmd) 
Error: processing vignette 'Ellipse-Overlap.Rmd' failed with diagnostics:
.onLoad failed in loadNamespace() for 'rjags', details:
  call: fun(libname, pkgname)
  error: The environment variable JAGS_HOME is set to
c:/Program Files/JAGS/JAGS-4.0.0
but no JAGS installation can be found there
Execution halted
filter.mRMR.default: no visible global function definition for
  'discretize'
gaussian.default: no visible global function definition for
  'cov.shrink'
predict.filter.RegressionTreeFilter: no visible global function
  definition for 'is.struct'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/SigTree.Rcheck/00install.out' for details.
clusterSetup,ANY-data.frame-SampleControl : .local: no visible binding
  for global variable 'cnam'
clusterSetup,ANY-data.frame-TwoStageControl : .local: no visible
  binding for global variable 'cnam'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/simmr.Rcheck/00install.out' for details.
Simpsons: no visible global function definition for 'Mclust'
simSummary: no visible global function definition for 'abind'
simSummary_unitTests: no visible global function definition for
  'clearLog'
simSummary_unitTests: no visible global function definition for
  'runTest'
simSummary_unitTests: no visible global function definition for
  'svSuite'
simSummary_unitTests: no visible global function definition for 'Log'
simSummary_unitTests: no visible global function definition for 'stats'
simSummary_unitTests: no visible global function definition for
  'metadata'
simSummary_unitTests: no visible global function definition for
  'errorLog'
Namespace in Imports field not imported from: 'pracma'
  All declared Imports should be used.
Running examples in 'sisus-Ex.R' failed
The error most likely occurred in:

> ### Name: sisus.run
> ### Title: driver program for SISUS
> ### Aliases: sisus.run
> 
> ### ** Examples
> 
> # set working directory for many output files with setwd()
> # see http://statacumen.com/sisus for workbook
> filename = "http://statacumen.com/sw/sisus/examples/SISUS_v0_09_template.xls";
> sisus.run(filename)
trying URL 'http://statacumen.com/sw/sisus/examples/SISUS_v0_09_template.xls'
Warning in download.file(xls, tf, mode = "wb") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in download.file(xls, tf, mode = "wb") : 
  cannot open URL 'http://statacumen.com/sw/sisus/examples/SISUS_v0_09_template.xls'
Calls: sisus.run ... as.matrix -> <Anonymous> -> xls2sep -> download.file
Error in file.exists(tfn) : invalid 'file' argument
Calls: sisus.run ... <Anonymous> -> xls2sep -> download.file -> file.exists
Execution halted
Namespace in Imports field not imported from: 'mcmc'
  All declared Imports should be used.
cvskda: no visible global function definition for 'detectCores'
cvskda: no visible global function definition for 'makeCluster'
cvskda: no visible global function definition for 'clusterApplyLB'
cvskda: no visible global function definition for 'mclapply'
cvskda: no visible global function definition for 'stopCluster'
qskewhyp: multiple local function definitions for 'zeroFn' with
  different formal arguments
Namespaces in Imports field not imported from:
  'rgdal' 'utils'
  All declared Imports should be used.
fitted.sma: no visible global function definition for 'join'
File 'smco/R/smco.R':
  .onAttach calls:
    cat(paste("This is smco package", version, "\n"))

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
File 'SMC/R/zzz.R':
  .onLoad calls:
    packageStartupMessage("##\n", "## Sequential Monte Carlo Package (SMC)\n",     "##\n", "## Functionality: sequential Monte Carlo (SMC) or sequential importance\n",     "## sampling (SIS) or hidden Markov models (HMM), particle filter (PF)\n",     "## and auxiliary particle filter (APF)\n", "##\n", "## Use: \"help(package = SMC)\" at the R prompt for more info\n",     "##\n", "## Copyright (C) 2006-", this.year, " Gopi Goswami\n",     "##\n", "##    Created by: Gopi Goswami <goswami@stat.harvard.edu>\n",     "## Maintained by: Gopi Goswami <grgoswami@gmail.com>\n",     "##\n")

See section 'Good practice' in '?.onAttach'.
em: no visible global function definition for 'coxph'
smcure: no visible global function definition for 'coxph'
smcure: no visible global function definition for 'survreg'
simDic: no visible global function definition for 'simil'
simDoc: no visible global function definition for 'simil'
getRoughnessMatrix: no visible global function definition for 'ns'
plotSmeRaw: no visible global function definition for 'xyplot'
plotSmeRaw : <anonymous>: no visible global function definition for
  'panel.xyplot'
plotSmeRaw : <anonymous>: no visible global function definition for
  'panel.lines'
sme.default: no visible global function definition for 'ns'
sme.list: no visible binding for global variable 'ns'
sme.list : <anonymous>: no visible global function definition for 'ns'
vcov.sme: no visible global function definition for 'ns'
coxph.disparity: no visible global function definition for 'basehaz'
disparity.glm : <anonymous>: no visible global function definition for
  'gamma.shape'
Running examples in 'smnet-Ex.R' failed
The error most likely occurred in:

> ### Name: m
> ### Title: Specify Smooth Terms in Formulae
> ### Aliases: m
> 
> ### ** Examples
> 
> 
> # Set up an SSN object - this part taken 
> # from the SSN:::SimulateOnSSN help file
> example_network<- createSSN(
+                      n          = 50,
+                      obsDesign  = binomialDesign(200), 
+                      predDesign = binomialDesign(50),
+                      importToR  = TRUE, 
+                      path = paste(tempdir(),"/example_network",sep = ""),
+                      treeFunction = iterativeTreeLayout
+                      )
Error in writeOGR(sldf, ".", "edges", verbose = FALSE, driver = "ESRI Shapefile") : 
  layer exists, use a new layer name
Calls: createSSN -> writeOGR
Execution halted
Namespaces in Imports field not imported from:
  'compiler' 'lmtest'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'MASS' 'nlme' 'survival'
  All declared Imports should be used.
sfApply: no visible global function definition for 'parApply'
sfClusterApply: no visible global function definition for
  'clusterApply'
sfClusterApplyLB: no visible global function definition for
  'clusterApplyLB'
sfClusterCall: no visible global function definition for 'clusterCall'
sfClusterSetupRNG: no visible global function definition for
  'clusterSetupRNG'
sfClusterSetupRNGstream: no visible global function definition for
  'clusterSetupRNGstream'
sfClusterSetupSPRNG: no visible global function definition for
  'clusterSetupSPRNG'
sfClusterSplit: no visible global function definition for
  'clusterSplit'
sfInit: no visible global function definition for
  'setDefaultClusterOptions'
sfInit: no visible global function definition for 'makeCluster'
sfInit: no visible global function definition for 'makeNWScluster'
sfInit: no visible global function definition for 'makeMPIcluster'
sfLapply: no visible global function definition for 'parLapply'
sfMM: no visible global function definition for 'parMM'
sfSapply: no visible global function definition for 'parSapply'
sfStop: no visible global function definition for 'stopCluster'
WGassociation: no visible global function definition for 'mclapply'
interleave: no visible global function definition for 'mclapply'
setupSNP: no visible global function definition for 'mclapply'
summary.setupSNP: no visible global function definition for 'mclapply'
tableHWE: no visible global function definition for 'mclapply'
convert.genes.to.GRanges: no visible global function definition for
  'GRanges'
convert.genes.to.GRanges: no visible global function definition for
  'IRanges'
convert.genes.to.GRanges: no visible global function definition for
  'metadata<-'
convert.pos.to.GRanges: no visible global function definition for
  'GRanges'
convert.pos.to.GRanges: no visible global function definition for
  'IRanges'
convert.variants.to.GRanges: no visible global function definition for
  'GRanges'
convert.variants.to.GRanges: no visible global function definition for
  'IRanges'
convert.variants.to.GRanges: no visible global function definition for
  'metadata<-'
find.overlapping.genes: no visible global function definition for
  'findOverlaps'
find.overlapping.genes: no visible global function definition for
  'subjectHits'
get.mgi.features: no visible global function definition for 'TabixFile'
get.mgi.features: no visible global function definition for
  'headerTabix'
get.mgi.features: no visible global function definition for 'scanTabix'
get.strains: no visible global function definition for 'TabixFile'
get.strains: no visible global function definition for 'headerTabix'
get.variants: no visible global function definition for 'TabixFile'
get.variants: no visible global function definition for 'headerTabix'
get.variants: no visible global function definition for 'scanTabix'
get.hnx.B.initialW: no visible global function definition for
  'normalize.vector'
get.hnx.B.initialW: no visible global function definition for 'adiag'
my.normdata.gen: no visible global function definition for 'mvrnorm'
odc.cv: no visible global function definition for 'ginv'
odc.optimallambda2: no visible global function definition for 'tr'
odc.optimallambda2: no visible global function definition for 'ginv'
eplot: no visible global function definition for 'trellis.par.get'
eplot: no visible global function definition for 'trellis.par.set'
eplot: no visible global function definition for 'xyplot'
munsell_to_rgb: no visible global function definition for 'munsell2rgb'
roots: no visible global function definition for 'areapl'
roots: no visible global function definition for 'point.in.polygon'
skeletal: no visible global function definition for 'areapl'
skeletal: no visible global function definition for 'point.in.polygon'
turnoverFit: no visible binding for global variable 'IntCal13'
turnoverFit: no visible binding for global variable 'Hua2013'
initialize,NlModel : .local: no visible global function definition for
  'TransportDecompositionOperator.new'
Running the tests in 'tests/prediction-test.R' failed.
Last 13 lines of output:
  > stopifnot(predict(nsom, iris[1,1:4])==nsom$clustering[1])
  > stopifnot(identical(predict(nsom), nsom$clustering))
  > 
  > rsom <- trainSOM(dissim.lesmis, type="relational", maxit=10, scaling= "none")
  > stopifnot(identical(predict(rsom, dissim.lesmis), rsom$clustering))
  > stopifnot(predict(rsom, dissim.lesmis[1,])==rsom$clustering[1])
  > stopifnot(identical(predict(rsom), rsom$clustering))
  > 
  > rsom <- trainSOM(dissim.lesmis, type="relational", maxit=10, 
  +                  radius.type="letremy")
  > stopifnot(identical(predict(rsom, dissim.lesmis), rsom$clustering))
  Error: identical(predict(rsom, dissim.lesmis), rsom$clustering) is not TRUE
  Execution halted
plot3d: no visible global function definition for 'persp3d'
SOS: no visible global function definition for 'getCurlHandle'
Namespaces in Imports field not imported from:
  'gtools' 'hashmap' 'uuid'
  All declared Imports should be used.
mHP.b : crossingProbDiff: no visible global function definition for
  'Miwa'
mHP.c : crossingProbDiff: no visible global function definition for
  'Miwa'
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'
SJ: no visible binding for global variable 'bs'
SJ: no visible global function definition for 'get.adjacency'
SJ : <anonymous>: no visible global function definition for
  'graph.adjacency'
SJ: no visible binding for global variable 'ecount'
SJ.dag: no visible binding for global variable 'bs'
SJ.dag : <anonymous>: no visible global function definition for
  'graph.adjacency'
SJ.dag: no visible binding for global variable 'ecount'
SJpath: no visible global function definition for 'get.adjacency'
SJpath : <anonymous>: no visible global function definition for
  'graph.adjacency'
generate.dag.data: no visible global function definition for 'vcount'
generate.dag.data: no visible global function definition for
  'topological.sort'
generate.dag.data: no visible global function definition for
  'neighbors'
grpsel: no visible global function definition for 'Matrix'
moralize: no visible global function definition for 'vcount'
moralize: no visible global function definition for 'as.undirected'
moralize: no visible global function definition for 'get.adjacency'
moralize: no visible global function definition for 'add.edges'
moralize: no visible global function definition for 'simplify'
plot.SJ: no visible global function definition for
  'layout.fruchterman.reingold'
plot.SJ.dag: no visible global function definition for
  'layout.fruchterman.reingold'
print.SJ: no visible binding for global variable 'ecount'
print.SJ: no visible global function definition for 'ecount'
print.SJ.dag: no visible binding for global variable 'ecount'
print.SJ.dag: no visible global function definition for 'ecount'
rdag: no visible global function definition for 'graph.adjacency'
cophen: no visible global function definition for 'Ntip'
get.descendants.of.node: no visible global function definition for
  'Ntip'
phy.deresolve: no visible global function definition for
  'branching.times'
phy.deresolve: no visible global function definition for 'Ntip'
phy.dotplot: no visible global function definition for 'tiplabels'
phy.nodetimes: no visible global function definition for 'Ntip'
phy.nodetimes: no visible global function definition for
  'branching.times'
reorderspacodiobj: no visible global function definition for 'drop.tip'
resamp.phy: no visible global function definition for 'Ntip'
resamp.phy: no visible global function definition for 'branching.times'
spacodi.all.nodes: no visible global function definition for 'subtrees'
spacodi.all.nodes: no visible global function definition for
  'branching.times'
spacodi.exp.nodes: no visible global function definition for 'subtrees'
spacodi.treeplot: no visible global function definition for
  'diverge_hcl'
spacodi.treeplot: no visible global function definition for
  'nodelabels'
Namespace in Imports field not imported from: 'rstudioapi'
  All declared Imports should be used.
livy_statement_parse_response : scalaTypeOfArray: possible error in
  regexec("^\\[L(.*);", scalaType, perl = TRUE): unused argument (perl
  = TRUE)
SPARQL: no visible binding for global variable 'getURL'
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'
getcoef_list: no visible global function definition for 'drop0'
sparsepredict: no visible global function definition for
  'lambda.interp'
sparsepredict: no visible global function definition for 'nonzeroCoef'
Namespaces in Imports field not imported from:
  'RColorBrewer' 'SpatialEpi' 'dplyr' 'dygraphs' 'ggplot2'
  'htmlwidgets' 'knitr' 'leaflet' 'mapproj' 'maptools' 'rgeos'
  'rmarkdown' 'shinyjs' 'spdep' 'xts'
  All declared Imports should be used.
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'
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'
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    data   3.4Mb
    doc    5.0Mb
    help   4.8Mb
    libs   1.2Mb
Found the following significant warnings:
  Warning: replacing previous import 'Matrix::expm' by 'expm::expm' when loading 'spdep'
See 'd:/Rcompile/CRANpkg/local/3.2/spdep.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    1.5Mb
    etc    1.7Mb
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'
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'
cv.spikeslab: no visible global function definition for 'mclapply'
gnet.get: no visible global function definition for 'lars'
gnet.get: no visible global function definition for 'predict.lars'
plot.spikeslab: no visible global function definition for 'plot.lars'
sparsePC.spikeslab : get.pc : <anonymous>: no visible global function
  definition for 'randomForest'
sparsePC.spikeslab: no visible global function definition for
  'randomForest'
spikeslab: no visible global function definition for 'randomForest'
SPIn: no visible global function definition for 'solve.QP'
Ell.Theta: no visible global function definition for 'ell.theta'
Namespace in Imports field not imported from: 'geoR'
  All declared Imports should be used.
Errors in running code in vignettes:
when running code in 'SQUAREM.Rnw'
  ...
+     Ap <- pvec * tA
+     pnew <- colMeans(t(Ap)/colSums(Ap))
+     pnew * (pnew > 0)
+ }

> library(interval)

  When sourcing 'SQUAREM.R':
Error: there is no package called 'interval'
Execution halted
File 'sROC/R/onload.R':
  .onLoad calls:
    packageStartupMessage("sROC 0.1-2 loaded")

See section 'Good practice' in '?.onAttach'.
Namespace in Imports field not imported from: 'shinyFiles'
  All declared Imports should be used.
fit.model: no visible global function definition for 'hadamard'
Namespaces in Imports field not imported from:
  'filematrix' 'foreach'
  All declared Imports should be used.
station: no visible binding for global variable 'WTdiff'
stkde: no visible global function definition for 'npudensbw'
stkde: no visible global function definition for 'npudens'
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'
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    include   8.2Mb
as.spikeTrain: no visible global function definition for 'spikeTimes'
gamObj.gampsth: no visible binding for global variable 'PoissonF'
gammaMLE: multiple local function definitions for 'rFct' with different
  formal arguments
gssObj.gsspsth: no visible binding for global variable 'gfit'
gssObj.gsspsth0: no visible binding for global variable 'gfit'
gsslockedTrain: no visible global function definition for 'gssanova'
gsslockedTrain0: no visible global function definition for 'gssanova0'
gsspsth: no visible global function definition for 'gssanova'
gsspsth0: no visible global function definition for 'gssanova0'
invgaussMLE: multiple local function definitions for 'rFct' with
  different formal arguments
lines.CountingProcessSamplePath: no visible binding for global variable
  'st'
mkAR: no visible binding for global variable 'lN.1'
mkM2U: no visible global function definition for 'ssden'
mkM2U : <anonymous>: no visible global function definition for 'dssden'
mkM2U : dFct: no visible global function definition for 'dssden'
mkPostSimAnalysis: no visible global function definition for
  'findGlobals'
qqDuration: no visible binding for global variable 'yi'
qqDuration: no visible binding for global variable 'si'
thinProcess: no visible binding for global variable 'targetFct'
thinProcess: no visible binding for global variable 'posMax'
rg.robmva: no visible global function definition for 'cov.mve'
Namespaces in Imports field not imported from:
  'magrittr' 'rpart'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/StatMethRank.Rcheck/00install.out' for details.
getHb: no visible binding for global variable 'masshb'
getHbgrid: no visible binding for global variable 'masshbgrid'
showComposition: no visible binding for global variable 'compositions'
testComposition: no visible binding for global variable 'compositions'
Namespaces in Imports field not imported from:
  'SnowballC' 'tm'
  All declared Imports should be used.
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'
Error in re-building vignettes:
  ...
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "VignetteforSTPGA.ltx" --max-iterations=20 -I "D:/RCompile/recent/R-3.2.5/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.2.5/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'VignetteforSTPGA.ltx' failed with diagnostics:
running 'texi2dvi' on 'VignetteforSTPGA.ltx' failed

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

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

Execution halted
.rp.stan3d: no visible global function definition for 'rp.control'
.rp.stan3d: no visible global function definition for 'rp.slider'
.rp.stan3d: no visible global function definition for 'rp.button'
.rp.stan3d : <anonymous>: no visible global function definition for
  'par3d'
.rp.stan3d : <anonymous>: no visible global function definition for
  'rotationMatrix'
.rp.stan3d: no visible global function definition for 'rp.do'
.rp.stan3d: no visible global function definition for 'rp.block'
.setBG: no visible global function definition for 'surface3d'
.setPlot: no visible global function definition for 'plot3d'
.setPlot: no visible global function definition for 'axis3d'
.setPlot: no visible global function definition for 'par3d'
.setPlot: no visible global function definition for 'aspect3d'
.setPlot: no visible global function definition for 'rotationMatrix'
.stan3d.redraw: no visible global function definition for 'par3d'
.stan3d.redraw: no visible global function definition for 'rgl.pop'
.stan3d.redraw: no visible binding for global variable 'spheres3d'
rlgcp: no visible global function definition for 'bbox'
stan: no visible global function definition for 'lines3d'
stan: no visible global function definition for 'segments3d'
stan: no visible global function definition for 'points3d'
bin.info.cubature : compute.fun: no visible global function definition
  for 'adaptIntegrate'
tess.info : new.points: no visible global function definition for
  'as.points'
tess.info : new.points: no visible global function definition for 'csr'
tess.info.MISER : int.fun: no visible global function definition for
  'as.points'
tess.info.MISER : int.fun: no visible global function definition for
  'inpip'
tessdev: no visible global function definition for 'deldir'
tessdev: no visible global function definition for 'tile.list'
tessdev : sum.l: no visible global function definition for 'as.points'
tessdev : sum.l: no visible global function definition for 'inpip'
tessdev.info : all: no visible global function definition for
  'as.points'
tessdev.info : all: no visible global function definition for 'inpip'
tessresid: no visible global function definition for 'deldir'
tessresid: no visible global function definition for 'tile.list'
tessresid : num: no visible global function definition for 'as.points'
tessresid : num: no visible global function definition for 'inpip'
Namespace in Imports field not imported from: 'sna'
  All declared Imports should be used.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  
  testthat results ================================================================
  OK: 4 SKIPPED: 0 FAILED: 6
  1. Failure: basic (@test-strip.R#13) 
  2. Failure: big (@test-strip.R#20) 
  3. Failure: libre (@test-strip.R#29) 
  4. Failure: abiword (@test-strip.R#39) 
  5. Failure: Japanese (cp932) (@test-strip.R#49) 
  6. Failure: Chinese and Korean (@test-strip.R#59) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  'broom' 'car' 'lmerTest' 'pbkrtest'
  All declared Imports should be used.
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
plot,GBH-ANY : .local: no visible binding for global variable
  'sorted.hyp'
plot,GBH-ANY : .local: no visible binding for global variable 'pval'
plot,GBH-ANY : .local: no visible binding for global variable 'group'
plot,GBH-ANY : .local: no visible binding for global variable 'type'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/subprocess.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'ISwR' 'MASS' 'corpcor'
  All declared Imports should be used.
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'
test_subtype_only: no visible global function definition for 'survdiff'
test_subtype_only: no visible global function definition for 'survfit'
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 'tkbind'
playSudoku: no visible global function definition for 'tkwait.window'
.p.1gen: warning in formatC(id, wid = 6): partial argument match of
  'wid' to 'width'
.p.1gen: warning in formatC(s, wid = 4): partial argument match of
  'wid' to 'width'
.p.1gen: warning in formatC(format(c(round(m, digits = digits),
  0.735))[1], wid = 7, dig = 3): partial argument match of 'dig' to
  'digits'
.p.1gen: warning in formatC(format(c(round(m, digits = digits),
  0.735))[1], wid = 7, dig = 3): partial argument match of 'wid' to
  'width'
predict.pelora: warning in matrix(c((1/(1 + exp(-(X[, 1:(noc[i] + 1)]
  %*% koeff))))), nc = 1): partial argument match of 'nc' to 'ncol'
ridge.coef: warning in diag(apply(X, 2, var) * lambda * nrow(X), nr =
  ncol(X)): partial argument match of 'nr' to 'nrow'
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 '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'
gen.y.mat2: no visible global function definition for 'survfit'
superpc.cv: no visible global function definition for 'coxph'
superpc.cv: no visible global function definition for 'coxph.control'
superpc.fit.to.outcome: no visible global function definition for
  'coxph'
superpc.fit.to.outcome: no visible global function definition for
  'coxph.control'
superpc.lrtest.curv: no visible global function definition for 'coxph'
superpc.predictionplot: no visible binding for global variable
  'shrinkages'
superpc.predictionplot: no visible global function definition for
  'survfit'
surv.to.class2: no visible global function definition for 'survfit'
pbc.sample: no visible binding for global variable 'pbc'
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

schemper: no visible global function definition for 'survfit'
Est.PH: no visible global function definition for 'coxph'
cvC: no visible global function definition for 'coxph'
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   1.5Mb
AER: no visible binding for global variable 'survexp.fr'
AER: no visible global function definition for 'survexp'
LR: no visible binding for global variable 'survexp.fr'
LR: no visible global function definition for 'survexp'
SMR: no visible binding for global variable 'survexp.fr'
SMR: no visible global function definition for 'survexp'
survexp_plot: no visible binding for global variable 'survexp.fr'
survexp_plot: no visible global function definition for 'survfit'
survexp_plot: no visible global function definition for 'survexp'
Est.HR.FUN: no visible global function definition for 'coxph'
Est.HR.FUN: no visible global function definition for 'basehaz'
Ghat.FUN: no visible global function definition for 'survfit'
IDI.INF: no visible global function definition for 'kmcens'
svd3dplot: no visible global function definition for 'wireframe'
svd3dplot: no visible global function definition for 'levelplot'
Namespaces in Imports field not imported from:
  'MASS' 'graphics' 'methods' 'stats'
  All declared Imports should be used.
Package in Depends field not imported from: 'kernlab'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
roccurve: warning in formatC(sum(c1 * cumsum(c2)), digit = 4): partial
  argument match of 'digit' to 'digits'
svmmajtuning: warning in .svmmaj(Z[groups != i, ], y[groups != i],
  lambda = lambda[l], w = w[groups != i], increase.step =
  increase.step, hinge = newHinge, theta = theta, check.positive =
  FALSE, convergence = convergence, ...): partial argument match of
  'hinge' to 'hingef'
auc: no visible global function definition for 'error'
getUpdate: no visible global function definition for 'vanilladot'
getUpdate: no visible global function definition for 'kernelMatrix'
qhat.theta: no visible global function definition for 'kernelMatrix'
roccurve: no visible global function definition for 'error'
svmmaj.default: no visible binding for global variable 'vanilladot'
svmmaj.default: no visible global function definition for 'kpar'
svmmaj2.default: no visible binding for global variable 'vanilladot'
svmmaj2.default: no visible global function definition for 'kpar'
svmmajtuning: no visible binding for global variable 'vanilladot'
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'
adjust.linearmodel: no visible global function definition for 'rlm'
confounding: no visible global function definition for 'heatmap.2'
hca.plot: no visible global function definition for 'colorpanel'
hca.plot: no visible global function definition for 'hcluster'
hca.test: no visible global function definition for 'hcluster'
kill.pc: no visible global function definition for 'impute.knn'
prince: no visible global function definition for 'impute.knn'
prince.plot: no visible global function definition for 'heatmap.2'
prince.var.plot: no visible global function definition for 'impute.knn'
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
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'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/sybilSBML.Rcheck/00install.out' for details.
integrate.polynomial : f: no visible global function definition for
  'dmvnorm'
Namespaces in Imports field not imported from:
  'doParallel' 'foreach' 'parallel'
  All declared Imports should be used.
cleavogram : savecleavogram : savefic: warning in jpeg(file =
  filename): partial argument match of 'file' to 'filename'
fn.V: no visible global function definition for 'LowRankQP'
synth: no visible global function definition for 'LowRankQP'
Namespace in Imports field not imported from: 'shiny'
  All declared Imports should be used.
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'
tableplot.colldiag: no visible global function definition for
  'colldiag'
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'
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.9Mb
    libs   1.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/TDA.Rcheck/00install.out' for details.
ConvDiffCoef: no visible global function definition for 'pascal'
DeconTrace: no visible global function definition for 'as.Zpg'
DeconTrace: no visible global function definition for 'butter'
MakeDPZ: no visible global function definition for 'bilinear'
MatchCoefDPZ: no visible global function definition for 'Zpg'
PZ2Coef: no visible global function definition for 'Poly'
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'
installed size is 44.0Mb
  sub-directories of 1Mb or more:
    libs      13.0Mb
    tessdata  30.9Mb
test_pkg : <anonymous>: no visible global function definition for
  '.traceback'
Dif.Surv.Rec: no visible global function definition for 'survfitr'
Plot.Event.Rec: no visible global function definition for 'survfitr'
Plot.Surv.Rec: no visible global function definition for 'survfitr'
Plot.Surv.Rec: no visible global function definition for 'q.search'
Print.Summary: no visible global function definition for 'survfitr'
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    3.5Mb
    libs   2.2Mb
Namespace in Imports field not imported from: 'irlba'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/textTinyR.Rcheck/00install.out' for details.
Package required and available but unsuitable version: 'stats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
determine_replications: no visible global function definition for
  'microbenchmark'
plot.timeit: no visible global function definition for 'ggplot'
plot.timeit: no visible global function definition for 'aes'
plot.timeit: no visible global function definition for 'geom_boxplot'
plot.timeit: no visible global function definition for 'geom_point'
plot.timeit: no visible global function definition for 'xlab'
plot.timeit: no visible global function definition for 'ylab'
plot.timeit: no visible global function definition for 'ggtitle'
plot.timeit: no visible global function definition for 'coord_flip'
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'
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'
boot_autocov: no visible global function definition for 'tsboot'
boot_spec: no visible global function definition for 'tsboot'
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.Estimate: no visible global function definition for 'flexmix'
flexmix.Estimate: no visible global function definition for 'FLXglm'
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 '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 'dmvt'
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    examples  19.2Mb
    include    2.9Mb
Namespace in Imports field not imported from: 'ape'
  All declared Imports should be used.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  2: eval(code, new_test_environment)
  3: eval(expr, envir, enclos)
  4: expect_is(trakt.user.watchlist(user = sample_user, type = "movies", extended = "min"), 
         "data.frame") at test_user.R:25
  5: expect_that(object, is_a(class), info, label)
  6: condition(object)
  7: paste0(class(x), collapse = ", ")
  8: trakt.user.watchlist(user = sample_user, type = "movies", extended = "min")
  9: convert_datetime(response)
  10: stop("Object type not supported")
  
  Error: Test failures
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/TreeBUGS.Rcheck/00install.out' for details.
mytree.asymmetric.age: no visible global function definition for
  'collapse.singles'
mytree.asymmetric.age: no visible global function definition for
  'drop.fossil'
mytree.asymmetric.taxa: no visible global function definition for
  'collapse.singles'
mytree.asymmetric.taxa: no visible global function definition for
  'drop.fossil'
mytree.symmetric.age: no visible global function definition for
  'collapse.singles'
mytree.symmetric.age: no visible global function definition for
  'drop.fossil'
mytree.symmetric.taxa: no visible global function definition for
  'collapse.singles'
mytree.symmetric.taxa: no visible global function definition for
  'drop.fossil'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.2Mb
plot.tkm: no visible global function definition for 'plotcluster'
plot.tkm: no visible global function definition for 'discrcoord'
HtoGp: no visible global function definition for 'odd'
HtoGp: no visible global function definition for 'even'
trioGxE: no visible global function definition for 'qtnorm'
trioplot: no visible global function definition for 'gam'
sim.cont: no visible global function definition for 'lsoda'
TSget,character-TSfameLocalConnection : .local: no visible global
  function definition for 'zoo'
TSget,character-TSfameServerConnection : .local: no visible global
  function definition for 'zoo'
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'
plotDominationGraph: no visible global function definition for
  'graph.adjacency'
plotDominationGraph: no visible global function definition for
  'layout.norm'
sampleCombinations: no visible global function definition for
  'qrng_alloc'
sampleCombinations: no visible global function definition for
  'qrng_get'
tunePareto: no visible global function definition for 'sfLibrary'
tunePareto : <anonymous>: no visible global function definition for
  'sfLibrary'
tunePareto: no visible global function definition for 'sfExport'
tunePareto: no visible global function definition for 'sfLapply'
tunePareto.NaiveBayes: no visible binding for global variable
  'NaiveBayes'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/uaparserjs.Rcheck/00install.out' for details.
Package required but not available: 'RSelenium'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
uniCoxCV: no visible global function definition for 'coxph'
Namespace in Imports field not imported from: 'mcmcplots'
  All declared Imports should be used.
Running examples in 'upmfit-Ex.R' failed
The error most likely occurred in:

> ### Name: upmrun
> ### Title: Bayesian Markov Chain Monte Carlo model building for
> ###   household-community tuberculosis transmission models
> ### Aliases: upmrun
> 
> ### ** Examples
> 
> upmrun(design.matrix=upmdata, n.iter=100, prior.alpha = c(-2.2, 1/sqrt(3)))
Error: .onLoad failed in loadNamespace() for 'rjags', details:
  call: fun(libname, pkgname)
  error: The environment variable JAGS_HOME is set to
c:/Program Files/JAGS/JAGS-4.0.0
but no JAGS installation can be found there
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 119-122 (upm-primer.Rmd) 
Error: processing vignette 'upm-primer.Rmd' failed with diagnostics:
.onLoad failed in loadNamespace() for 'rjags', details:
  call: fun(libname, pkgname)
  error: The environment variable JAGS_HOME is set to
c:/Program Files/JAGS/JAGS-4.0.0
but no JAGS installation can be found there
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/uroot.Rcheck/00install.out' for details.
File 'UScensus2010/R/zzz.R':
  .onLoad calls:
    packageStartupMessage("\n")
    packageStartupMessage(paste("Package ", dscr$Package, ": ", dscr$Title,     "\n", "Version ", dscr$Version, " created on ", dscr$Date,     ".\n", sep = ""))
    packageStartupMessage(paste("Zack Almquist, University of California-Irvine\nne\n",     sep = ""))
    packageStartupMessage("For citation information, type citation(\"UScensus2010\").")
    packageStartupMessage("Type help(package=UScensus2010) to get started.")

See section 'Good practice' in '?.onAttach'.
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
mcmc.estimate: no visible global function definition for '%dopar%'
mcmc.estimate: no visible global function definition for 'foreach'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/valr.Rcheck/00install.out' for details.
SVEC: no visible global function definition for 'Null'
causality: no visible global function definition for 'ginv'
stability: no visible global function definition for 'efp'
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   2.3Mb
Namespace in Imports field not imported from: 'nlme'
  All declared Imports should be used.
vioplot: warning in axis(1, at = at, label = label): partial argument
  match of 'label' to 'labels'
vioplot: warning in axis(2, at = at, label = label): partial argument
  match of 'label' to 'labels'
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc           3.6Mb
    htmlwidgets   3.5Mb
raster.proj: no visible global function definition for 'rasterFromXYZ'
.vdensecalc: no visible global function definition for 'contour3d'
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 65-67 (vtreatRareLevels.Rmd) 
Error: processing vignette 'vtreatRareLevels.Rmd' failed with diagnostics:
unused argument (left.open = TRUE)
Execution halted
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'
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'
Namespaces in Imports field not imported from:
  'DT' 'ENMeval' 'RColorBrewer' 'devtools' 'dismo' 'dplyr' 'maptools'
  'raster' 'rgdal' 'rgeos' 'rmarkdown' 'shinyBS' 'shinyjs'
  'shinythemes' 'spThin' 'spocc'
  All declared Imports should be used.
color.factor: warning in rgb(red = t.rgb[1, ], green = t.rgb[2, ], blue
  = t.rgb[3, ], max = 255): partial argument match of 'max' to
  'maxColorValue'
p.flow_comp: warning in line_sumrain(xdata = xdata, cum_sum =
  cumsum(data[crain, ])/10, theMax = rain.max, col = "grey"): partial
  argument match of 'cum_sum' to 'cum_sum_rain'
Errors in running code in vignettes:
when running code in 'vignette.Rnw'
  ...

> library(waterData)

> q05054000 <- importDVs("05054000", code = "00060", 
+     stat = "00003", sdate = "2000-01-01", edate = "2010-12-31")
Unknown IO errorfailed to load external entity "http://waterservices.usgs.gov/nwis/dv?site=05054000&parameterCd=00060&statCd=00003&startDt=2000-01-01&endDt=2010-12-31"

  When sourcing 'vignette.R':
Error: 1: Unknown IO error2: failed to load external entity "http://waterservices.usgs.gov/nwis/dv?site=05054000&parameterCd=00060&statCd=00003&startDt=2000-01-01&endDt=2010-12-31"
Execution halted
Error in re-building vignettes:
  ...

Error: processing vignette 'vignette.Rnw' failed with diagnostics:
 chunk 1 
Error : 1: Unknown IO error2: failed to load external entity "http://waterservices.usgs.gov/nwis/dv?site=05054000&parameterCd=00060&statCd=00003&startDt=2000-01-01&endDt=2010-12-31"

Execution halted
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'
Packages required but not available: 'subprocess' 'semver'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
getStationCode: no visible binding for global variable
  'USAirportWeatherStations'
getStationCode: no visible binding for global variable 'IntlWxStations'
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."
pairtest: no visible global function definition for 'p.value'
pairtest: no visible global function definition for 'single.snp.tests'
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'
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'
Bundesliga.Mannschaft: no visible binding for global variable
  'Bundesliga'
Bundesliga.Tabelle: no visible binding for global variable 'Bundesliga'
Bundesliga.XML: no visible binding for global variable 'Bundesliga'
Running examples in 'wiqid-Ex.R' failed
The error most likely occurred in:

> ### Name: dippers
> ### Title: Capture-recapture data for European dippers
> ### Aliases: dippers
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(dippers)
> 
> DH <- dippers[1:7]  # Extract the detection histories
> survCJS(DH)  # the phi(.) p(.) model
Call: survCJS(DH = DH)

Real values (duplicates omitted):
        est  lowCI  uppCI
phi1 0.5602 0.5105 0.6088
p1   0.9026 0.8305 0.9460

AIC: 670.8377 
> survCJS(DH, phi ~ .time)  # the phi(t) p(.) model
Call: survCJS(DH = DH, model = phi ~ .time)

Real values (duplicates omitted):
        est  lowCI  uppCI
phi1 0.6258 0.3965 0.8098
phi2 0.4542 0.3295 0.5849
phi3 0.4784 0.3669 0.5921
phi4 0.6244 0.5079 0.7281
phi5 0.6079 0.4970 0.7088
phi6 0.5833 0.4688 0.6895
p1   0.9021 0.8286 0.9461

AIC: 673.7301 
> 
> # Floods affected the 2nd and 3rd intervals
> df <- data.frame(flood = c(FALSE, TRUE, TRUE, FALSE, FALSE, FALSE))
> survCJS(DH, phi ~ flood, data=df)
Call: survCJS(DH = DH, model = phi ~ flood, data = df)

Real values (duplicates omitted):
        est  lowCI  uppCI
phi1 0.6071 0.5451 0.6658
phi2 0.4688 0.3858 0.5537
p1   0.8998 0.8262 0.9443

AIC: 666.1028 
> 
> # Including a grouping factor:
> survCJS(DH, phi ~ flood * group, data=df, group=dippers$sex)
Call: survCJS(DH = DH, model = phi ~ flood * group, data = df, group = dippers$sex)

Real values (duplicates omitted):
          est  lowCI  uppCI
F:phi1 0.6033 0.5163 0.6842
F:phi2 0.4568 0.3468 0.5712
M:phi1 0.6108 0.5246 0.6906
M:phi2 0.4833 0.3612 0.6073
F:p1   0.8999 0.8263 0.9444

AIC: 669.9911 
> 
> # Bayesian estimation:
> 
> Bdip <- BsurvCJS(DH, parallel=FALSE)
Error: The 'rjags' package and the JAGS program are needed to run this function.
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    5.0Mb
    libs   1.4Mb
Namespace in Imports field not imported from: 'RMySQL'
  All declared Imports should be used.
wordcloud: no visible global function definition for 'Corpus'
wordcloud: no visible global function definition for 'VectorSource'
wordcloud: no visible global function definition for 'tm_map'
wordcloud: no visible binding for global variable 'removePunctuation'
wordcloud : <anonymous>: no visible global function definition for
  'removeWords'
wordcloud : <anonymous>: no visible global function definition for
  'stopwords'
wordcloud: no visible global function definition for
  'TermDocumentMatrix'
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'
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.6Mb
simul.wsvm: no visible binding for global variable 'mixture.example'
plot,x12Batch : .local: no visible binding for global variable 'xb'
x12,ts : .local: no visible binding for global variable 'out'
x12,x12Batch : .local: no visible global function definition for
  'mclapply'
x12,x12Single : .local: no visible binding for global variable 'out'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/xgboost.Rcheck/00install.out' for details.
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'
File 'xml2/libs/i386/xml2.dll':
  Found non-API call to R: 'getConnection'
File 'xml2/libs/x64/xml2.dll':
  Found non-API call to R: 'getConnection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    exampleData   1.4Mb
    examples      4.5Mb
    libs          4.1Mb
newXMLDoc: no visible binding for global variable 'doc'
xmlFlatListTree : f: no visible binding for global variable 'nodeNames'
xmlFlatListTree : f: no visible binding for global variable 'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'nodeSet'
xmlFlatListTree : addNode: no visible binding for global variable
  'nodeSet'
xmlFlatListTree : addNode: no visible binding for global variable 'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'nodeNames'
xmlFlatListTree : addNode: no visible binding for global variable
  'nodeNames'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'parentCount'
xmlFlatListTree : addNode: no visible binding for global variable
  'parentCount'
xmlFlatListTree : <anonymous>: no visible binding for global variable
  'e'
xmlFlatTree : <anonymous>: no visible binding for global variable 'e'
[[,XMLCodeFile : .local: possible error in updateIds(doc, save = x):
  unused argument (save = x)
as.xts.ts: no visible global function definition for 'as.yearqtr'
as.xts.ts: no visible global function definition for 'as.yearmon'
rollapply.xts: no visible global function definition for 'na.fill'
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'yacca/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("Copyright (c) 2008, Carter T. Butts, University of California-Irvine\n")
    cat("For citation information, type citation(\"yacca\").\n")
    cat("Type help(\"yacca-package\") to get started.\n")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
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'
epirice.weather: no visible binding for global variable
  'weather_SouthAsia'
maize.multisy: no visible binding for global variable
  'weather_EuropeEU'
maize.multisy240 : <anonymous>: no visible binding for global variable
  'weather_EuropeEU'
maize.weather: no visible binding for global variable
  'weather_FranceWest'
param.rtriangle: no visible global function definition for 'rtriangle'
population.age.model.ode: no visible global function definition for
  'ode'
population.age.model.ode: no visible global function definition for
  'rkMethod'
predator.prey.model: no visible global function definition for 'ode'
predator.prey.model: no visible global function definition for
  'rkMethod'
watbal.weather: no visible binding for global variable
  'weather_FranceWest'
Namespaces in Imports field not imported from:
  'dplyr' 'ggplot2' 'lubridate'
  All declared Imports should be used.