BSL: no visible global function definition for 'read.asciigrid'
BSL: no visible global function definition for 'quantile'
PIF: no visible global function definition for 'read.asciigrid'
PIF: no visible global function definition for 'quantile'
RCS: no visible global function definition for 'quantile'
clouds: no visible global function definition for 'read.asciigrid'
geoshift: no visible global function definition for 'bbox'
histmatch: no visible global function definition for 'hist'
minnaert: no visible global function definition for 'coefficients'
minnaert: no visible global function definition for 'lm'
minnaert: no visible global function definition for 'predict'
topocorr: no visible global function definition for 'lm'
topocorr: no visible global function definition for 'coefficients'
Undefined global functions or variables:
  bbox coefficients hist lm predict quantile read.asciigrid
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "coefficients", "lm", "predict", "quantile")
to your NAMESPACE file.
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
betabreaker: no visible global function definition for 'predict'
coef.lars: no visible global function definition for 'predict'
cv.lars: no visible global function definition for 'predict'
cv.lars: no visible binding for global variable 'var'
error.bars: no visible global function definition for 'segments'
plot.lars: no visible global function definition for 'plot'
plot.lars: no visible global function definition for 'matplot'
plot.lars: no visible global function definition for 'title'
plot.lars: no visible global function definition for 'abline'
plot.lars: no visible global function definition for 'axis'
plotCVLars: no visible global function definition for 'plot'
predict.lars: no visible global function definition for 'approx'
Undefined global functions or variables:
  abline approx axis matplot plot predict segments title var
Consider adding
  importFrom("graphics", "abline", "axis", "matplot", "plot", "segments",
             "title")
  importFrom("stats", "approx", "predict", "var")
to your NAMESPACE file.
glassoscore: no visible global function definition for 'var'
glassoscore: no visible global function definition for 'pchisq'
lassoscore: no visible global function definition for 'txtProgressBar'
lassoscore: no visible global function definition for
  'setTxtProgressBar'
lassoscore: no visible global function definition for 'pchisq'
plot.glassoscore: no visible global function definition for 'legend'
plot.lassoscore: no visible global function definition for 'legend'
plot.mbscore: no visible global function definition for 'legend'
qqpval: no visible global function definition for 'ppoints'
qqpval: no visible global function definition for 'qbeta'
qqpval: no visible global function definition for 'points'
qqpval: no visible global function definition for 'plot'
qqpval: no visible global function definition for 'abline'
qqpval: no visible global function definition for 'polygon'
Undefined global functions or variables:
  abline legend pchisq plot points polygon ppoints qbeta
  setTxtProgressBar txtProgressBar var
Consider adding
  importFrom("graphics", "abline", "legend", "plot", "points", "polygon")
  importFrom("stats", "pchisq", "ppoints", "qbeta", "var")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
lbfgs: no visible global function definition for 'hasArg'
Undefined global functions or variables:
  hasArg
Consider adding
  importFrom("methods", "hasArg")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
LCA: no visible global function definition for 'dist'
LCA: no visible global function definition for 'combn'
LCA: no visible global function definition for 'p.adjust'
LCA: no visible global function definition for 'pchisq'
LCA : <anonymous>: no visible global function definition for 'pchisq'
LCD: no visible global function definition for 'ecdf'
estimateB: no visible global function definition for 'median'
evaluateDiffSignificance: no visible global function definition for
  'ecdf'
fitPTLmodel: no visible global function definition for 'lm'
getPTLparams: no visible global function definition for 'nls'
getPTLparams: no visible global function definition for 'coef'
predictPTLparams: no visible global function definition for
  'predict.lm'
Undefined global functions or variables:
  coef combn dist ecdf lm median nls p.adjust pchisq predict.lm
Consider adding
  importFrom("stats", "coef", "dist", "ecdf", "lm", "median", "nls",
             "p.adjust", "pchisq", "predict.lm")
  importFrom("utils", "combn")
to your NAMESPACE file.
cclcda.default: no visible global function definition for 'as.formula'
cclcda.default: no visible global function definition for 'chisq.test'
cclcda.formula: no visible global function definition for 'model.frame'
cclcda2.default: no visible global function definition for 'runif'
cclcda2.default: no visible global function definition for 'chisq.test'
cclcda2.formula: no visible global function definition for
  'model.frame'
lcda.default: no visible global function definition for 'as.formula'
lcda.formula: no visible global function definition for 'model.frame'
Undefined global functions or variables:
  as.formula chisq.test model.frame runif
Consider adding
  importFrom("stats", "as.formula", "chisq.test", "model.frame", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.6/ldatuning.Rcheck/00install.out' for details.
multistart : <anonymous>: no visible global function definition for
  'runif'
plot.FreD.x: no visible global function definition for 'modifyList'
plot.FreD.x: no visible global function definition for 'abline'
plot.FreD.x: no visible global function definition for 'points'
Undefined global functions or variables:
  abline modifyList points runif
Consider adding
  importFrom("graphics", "abline", "points")
  importFrom("stats", "runif")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
ARConfIntEst: no visible global function definition for 'sd'
PTLinkFunc: no visible global function definition for 'pnorm'
PTLinkFunc: no visible global function definition for 'qnorm'
PTMultiPeriodPD: no visible global function definition for 'uniroot'
PTOnePeriodPD : f: no visible global function definition for 'pbinom'
PTOnePeriodPD: no visible global function definition for 'uniroot'
QMMGetRLogitPD: no visible global function definition for 'ecdf'
QMMPDlinkFunc: no visible global function definition for 'qnorm'
QMMPlot: no visible global function definition for 'plot'
QMMPlot: no visible global function definition for 'lines'
QMMPlot: no visible global function definition for 'legend'
VDBCalibratePD: no visible global function definition for 'ecdf'
VDBGetK: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  ecdf legend lines pbinom plot pnorm qnorm sd uniroot
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "ecdf", "pbinom", "pnorm", "qnorm", "sd",
             "uniroot")
to your NAMESPACE file.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    geojson  11.9Mb
BEAPFrOG: no visible global function definition for 'jags.model'
BEAPFrOG: no visible global function definition for 'coda.samples'
LEAPFrOG_EM: no visible global function definition for 'write.table'
LEAPFrOG_EM: no visible global function definition for 'constrOptim'
LEAPFrOG_plot: no visible global function definition for 'par'
LEAPFrOG_plot: no visible global function definition for 'barplot'
LEAPFrOG_plot: no visible global function definition for 'legend'
constrOptim2: no visible global function definition for 'optim'
Undefined global functions or variables:
  barplot coda.samples constrOptim jags.model legend optim par
  write.table
Consider adding
  importFrom("graphics", "barplot", "legend", "par")
  importFrom("stats", "constrOptim", "optim")
  importFrom("utils", "write.table")
to your NAMESPACE file.
AlternateSVD: no visible binding for global variable 'sd'
IPOD: no visible global function definition for 'mad'
IPOD: no visible global function definition for 'pnorm'
Pvalue: no visible global function definition for 'pf'
ROCplot: no visible global function definition for 'png'
ROCplot: no visible global function definition for 'matplot'
ROCplot: no visible global function definition for 'legend'
ROCplot: no visible global function definition for 'dev.off'
leapp: no visible global function definition for 'png'
leapp: no visible global function definition for 'plot'
leapp: no visible global function definition for 'dev.off'
ridge: no visible global function definition for 'sd'
ridge: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dev.off legend mad matplot pf plot png pnorm sd
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "matplot", "plot")
  importFrom("stats", "mad", "pf", "pnorm", "sd")
to your NAMESPACE file.
Fmntd.a : Fmntd.a.sub: no visible global function definition for
  'weighted.mean'
Fmpd : Fmpd.sub: no visible global function definition for 'as.dist'
Fmpd.a : Fmpd.a.sub: no visible global function definition for
  'weighted.mean'
Fsntd : Fsntd.sub: no visible global function definition for 'sd'
com.trait.moments : skewness: no visible global function definition for
  'var'
com.trait.moments : kurtosis: no visible global function definition for
  'var'
com.trait.moments : sd.funk: no visible global function definition for
  'sd'
com.trait.weighted : weight.mean.funk: no visible global function
  definition for 'weighted.mean'
Undefined global functions or variables:
  as.dist sd var weighted.mean
Consider adding
  importFrom("stats", "as.dist", "sd", "var", "weighted.mean")
to your NAMESPACE file.
'library' or 'require' call to 'snow' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Running examples in 'liayson-Ex.R' failed
The error most likely occurred in:

> ### Name: clusterCells
> ### Title: Grouping cells into clones.
> ### Aliases: clusterCells
> 
> ### ** Examples
> 
> data(cnps)
> set.seed(2)
> rcells = sample(colnames(cnps), 120)
> outc = clusterCells(cnps[apply(cnps, 1, var)>0, rcells])
[1] "Neither k nor h is set."
[1] "Using Akaike information criterion to decide number of clusters..."
Error in kmeans(t(cnps), centers = x) : 
  more cluster centers than distinct data points.
Calls: clusterCells ... sapply -> lapply -> FUN -> .kmeansAIC -> ncol -> kmeans
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      3.9Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   2.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
    libs   1.5Mb
Packages in Depends field not imported from:
  'BB' 'Bolstad2' 'Rmpfr' 'moments' 'optimx' 'sn'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plotBox: no visible global function definition for 'sd'
plotBox: no visible global function definition for 'rect'
plotBox: no visible global function definition for 'qnorm'
plotBox: no visible global function definition for 'segments'
plotInit: no visible global function definition for 'plot'
plotInit: no visible global function definition for 'runif'
plotInit: no visible global function definition for 'mtext'
plotInit: no visible global function definition for 'segments'
plotStack: no visible global function definition for 'points'
Undefined global functions or variables:
  mtext plot points qnorm rect runif sd segments
Consider adding
  importFrom("graphics", "mtext", "plot", "points", "rect", "segments")
  importFrom("stats", "qnorm", "runif", "sd")
to your NAMESPACE file.
Plotranges.double: no visible global function definition for 'strwidth'
Plotranges.double: no visible global function definition for
  'strheight'
Plotranges.double: no visible global function definition for 'plot.new'
Plotranges.double: no visible global function definition for 'par'
Plotranges.double: no visible global function definition for
  'plot.window'
Plotranges.double: no visible global function definition for 'mtext'
Plotranges.double: no visible global function definition for 'abline'
Plotranges.double: no visible global function definition for 'points'
Plotranges.double: no visible global function definition for 'segments'
Plotranges.double: no visible global function definition for 'text'
Plotranges.double: no visible global function definition for 'axis'
Plotranges.double: no visible global function definition for 'box'
Plotranges.double: no visible global function definition for 'title'
Undefined global functions or variables:
  abline axis box mtext par plot.new plot.window points segments
  strheight strwidth text title
Consider adding
  importFrom("graphics", "abline", "axis", "box", "mtext", "par",
             "plot.new", "plot.window", "points", "segments",
             "strheight", "strwidth", "text", "title")
to your NAMESPACE file.
class.calib: no visible global function definition for 'lm'
class.calib: no visible global function definition for 'coef'
class.calib: no visible global function definition for 'qt'
hoad.calib: no visible global function definition for 'lm'
hoad.calib: no visible global function definition for 'anova'
hoad.calib: no visible global function definition for 'qt'
hoad.calib: no visible global function definition for 'rnorm'
huntlam.calib: no visible global function definition for 'lm'
huntlam.calib: no visible global function definition for 'anova'
huntlam.calib: no visible global function definition for 'rnorm'
huntlam.calib: no visible global function definition for 'qnorm'
inver.calib: no visible global function definition for 'lm'
inver.calib: no visible global function definition for 'coef'
inver.calib: no visible global function definition for 'anova'
inver.calib: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  anova coef lm qnorm qt rnorm
Consider adding
  importFrom("stats", "anova", "coef", "lm", "qnorm", "qt", "rnorm")
to your NAMESPACE file.
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("lineup")
  Loading required package: lineup
  -- 1. Failure: corbetw2mat works in the other cases (@test-corbetw2mat.R#45)  --
  `result1` not equal to `expected1`.
  Component "yindex": Mean relative difference: 0.3125
  Component "ycol": Attributes: < Component "levels": 2 string mismatches >
  Component "ycol": 3 string mismatches
  
  -- 2. Failure: corbetw2mat works in the other cases (@test-corbetw2mat.R#55)  --
  `result2` not equal to `expected2`.
  Component "cor": Mean relative difference: 0.3670566
  Component "yindex": Mean relative difference: 0.2083333
  Component "ycol": Attributes: < Component "levels": 4 string mismatches >
  Component "ycol": 4 string mismatches
  
  == testthat results  ===========================================================
  OK: 3 SKIPPED: 0 FAILED: 2
  1. Failure: corbetw2mat works in the other cases (@test-corbetw2mat.R#45) 
  2. Failure: corbetw2mat works in the other cases (@test-corbetw2mat.R#55) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("lineup")
  Loading required package: lineup
  -- 1. Failure: corbetw2mat works in the other cases (@test-corbetw2mat.R#45)  --
  `result1` not equal to `expected1`.
  Component "yindex": Mean relative difference: 0.3125
  Component "ycol": Attributes: < Component "levels": 2 string mismatches >
  Component "ycol": 3 string mismatches
  
  -- 2. Failure: corbetw2mat works in the other cases (@test-corbetw2mat.R#55)  --
  `result2` not equal to `expected2`.
  Component "cor": Mean relative difference: 0.8494099
  Component "yindex": Mean relative difference: 0.2083333
  Component "ycol": Attributes: < Component "levels": 4 string mismatches >
  Component "ycol": 4 string mismatches
  
  == testthat results  ===========================================================
  OK: 3 SKIPPED: 0 FAILED: 2
  1. Failure: corbetw2mat works in the other cases (@test-corbetw2mat.R#45) 
  2. Failure: corbetw2mat works in the other cases (@test-corbetw2mat.R#55) 
  
  Error: testthat unit tests failed
  Execution halted
gcomb: no visible global function definition for 'complete.cases'
linkim: no visible global function definition for 'runif'
missing.dist: no visible global function definition for
  'complete.cases'
pgdata1: no visible global function definition for 'barplot'
pgdata1: no visible global function definition for 'layout'
pgdata1: no visible global function definition for 'par'
pgdata1: no visible global function definition for 'rainbow'
singim: no visible global function definition for 'complete.cases'
singim: no visible global function definition for 'runif'
Undefined global functions or variables:
  barplot complete.cases layout par rainbow runif
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "barplot", "layout", "par")
  importFrom("stats", "complete.cases", "runif")
to your NAMESPACE file.
gen.lms: no visible global function definition for 'na.omit'
plot.idf: no visible global function definition for 'plot'
plot.idf: no visible global function definition for 'mtext'
plot.idf: no visible global function definition for 'points'
plot.idf: no visible global function definition for 'segments'
plot.idf: no visible global function definition for 'ftable'
plot.idf: no visible global function definition for 'image'
plot.idf: no visible global function definition for 'gray'
plot.idf: no visible global function definition for 'abline'
plot.s.linlir: no visible global function definition for 'plot'
plot.s.linlir: no visible global function definition for 'mtext'
plot.s.linlir: no visible global function definition for 'polygon'
plot.s.linlir: no visible global function definition for 'points'
plot.s.linlir: no visible global function definition for 'curve'
s.linlir: no visible global function definition for 'na.omit'
s.linlir: no visible global function definition for 'dbinom'
s.linlir: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  abline curve dbinom ftable gray image mtext na.omit pchisq plot
  points polygon segments
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "curve", "image", "mtext", "plot",
             "points", "polygon", "segments")
  importFrom("stats", "dbinom", "ftable", "na.omit", "pchisq")
to your NAMESPACE file.
'library' or 'require' call to 'lpSolve' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'lpSolve'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
solveLP: no visible global function definition for 'lp'
Undefined global functions or variables:
  lp
Found the following significant warnings:
  Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
See 'd:/Rcompile/CRANpkg/local/3.6/LipidMS.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.0Mb
last: no visible global function definition for 'tail'
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
getMatrix : <anonymous>: 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.
'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.
lm.beta: no visible global function definition for 'coef'
lm.beta: no visible global function definition for 'model.matrix'
lm.beta: no visible global function definition for 'model.frame'
Undefined global functions or variables:
  coef model.frame model.matrix
Consider adding
  importFrom("stats", "coef", "model.frame", "model.matrix")
to your NAMESPACE file.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    doc        2.4Mb
    libs       2.1Mb
    testdata   1.6Mb
lmec: warning in qr.Q(qrZ, compl = TRUE): partial argument match of
  'compl' to 'complete'
lmec: warning in qr.Q(qra, compl = TRUE): partial argument match of
  'compl' to 'complete'
lmec: no visible global function definition for 'lm'
lmec: no visible global function definition for 'pnorm'
lmec: no visible global function definition for 'dnorm'
lmec : vtrnorm2: no visible global function definition for 'runif'
lmec : vtrnorm2: no visible global function definition for 'qnorm'
lmec : vtrnorm2: no visible global function definition for 'pnorm'
lmec: no visible global function definition for 'rnorm'
lmec: no visible global function definition for 'ar'
Undefined global functions or variables:
  ar dnorm lm pnorm qnorm rnorm runif
Consider adding
  importFrom("stats", "ar", "dnorm", "lm", "pnorm", "qnorm", "rnorm",
             "runif")
to your NAMESPACE file.
mq.diagnostics : mq_missinggenotype_plot: no visible global function
  definition for 'plot.missing'
Undefined global functions or variables:
  plot.missing
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(lmeresampler)
  > 
  > test_check("lmeresampler")
  -- 1. Failure: two-level additive random intercept model (@test-case-lme4.R#30) 
  nrow(cr1) >= 48 * min(grouped$count) isn't true.
  
  -- 2. Failure: two-level additive random intercept model (@test-case-lme4.R#32) 
  nrow(cr3) >= 48 * min(grouped$count) isn't true.
  
  == testthat results  ===========================================================
  OK: 15 SKIPPED: 58 FAILED: 2
  1. Failure: two-level additive random intercept model (@test-case-lme4.R#30) 
  2. Failure: two-level additive random intercept model (@test-case-lme4.R#32) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.6/lmerTest.Rcheck/00install.out' for details.
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.
approx.Z : <anonymous>: no visible global function definition for
  'approx'
smspline: no visible global function definition for 'model.frame'
Undefined global functions or variables:
  approx model.frame
Consider adding
  importFrom("stats", "approx", "model.frame")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'emulator' 'methods' 'miscTools' 'penalized'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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' call to 'akima' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Missing or unexported objects:
  'lattice::render.3d.trellis' 'lattice::render.contour.trellis'
available.loglevels: no visible global function definition for
  'setNames'
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
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.
EstimateProbability: no visible global function definition for
  'predict'
LOGICOIL: no visible binding for global variable 'pssm'
LOGICOIL: no visible binding for global variable 'LOGICOILfit'
LOGICOIL: no visible binding for global variable 'Model_Parameters'
plot_LOGICOIL: no visible global function definition for 'png'
plot_LOGICOIL: no visible global function definition for 'par'
plot_LOGICOIL: no visible global function definition for 'plot'
plot_LOGICOIL: no visible global function definition for 'lines'
plot_LOGICOIL: no visible global function definition for 'axis'
plot_LOGICOIL: no visible global function definition for 'mtext'
plot_LOGICOIL: no visible global function definition for 'legend'
plot_LOGICOIL: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  LOGICOILfit Model_Parameters axis dev.off legend lines mtext par plot
  png predict pssm
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "axis", "legend", "lines", "mtext", "par",
             "plot")
  importFrom("stats", "predict")
to your NAMESPACE file.
test_compute_gradient: no visible global function definition for
  'rnorm'
test_compute_probabilities: no visible global function definition for
  'rnorm'
test_logitchoice: no visible global function definition for 'rnorm'
test_solver: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
LogitNet.weight: no visible global function definition for 'lowess'
LogitNet.weight: no visible global function definition for 'median'
Undefined global functions or variables:
  lowess median
Consider adding
  importFrom("stats", "lowess", "median")
to your NAMESPACE file.
rloglognorm: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
LogrankA: no visible global function definition for 'is.Surv'
LogrankA: no visible global function definition for 'na.omit'
LogrankA: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  is.Surv na.omit pchisq
Consider adding
  importFrom("stats", "na.omit", "pchisq")
to your NAMESPACE file.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(lolR)
  > 
  > test_check("lolR")
  -- 1. Failure: Optimal Embedding Dimensions (@test-xval.R#45)  -----------------
  result.rs$optimal.lhat not equal to result.rs.noset$optimal.lhat.
  Lengths differ: 2 is not 1
  
  == testthat results  ===========================================================
  OK: 446 SKIPPED: 0 FAILED: 1
  1. Failure: Optimal Embedding Dimensions (@test-xval.R#45) 
  
  Error: testthat unit tests failed
  Execution halted
fplot: no visible global function definition for 'rnorm'
fplot: no visible global function definition for 'plot'
fplot: no visible global function definition for 'segments'
fplot: no visible global function definition for 'points'
fplot: no visible global function definition for 'text'
fplot.foodweb: no visible global function definition for 'plot'
fplot.foodweb: no visible global function definition for 'segments'
fplot.foodweb: no visible global function definition for 'points'
fplot.foodweb: no visible global function definition for 'text'
gplot: no visible global function definition for 'runif'
groupplot: no visible global function definition for 'rnorm'
groupplot: no visible global function definition for 'plot'
groupplot: no visible global function definition for 'segments'
groupplot: no visible global function definition for 'points'
groupplot: no visible global function definition for 'text'
groupplot.foodweb: no visible global function definition for 'rnorm'
groupplot.foodweb: no visible global function definition for 'plot'
groupplot.foodweb: no visible global function definition for 'segments'
groupplot.foodweb: no visible global function definition for 'points'
groupplot.foodweb: no visible global function definition for 'text'
Undefined global functions or variables:
  plot points rnorm runif segments text
Consider adding
  importFrom("graphics", "plot", "points", "segments", "text")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
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.
Running 'testthat.R' [27s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(loo)
  This is loo version 2.0.0.
  **NOTE: As of version 2.0.0 loo defaults to 1 core but we recommend using as many as possible. Use the 'cores' argument or set options(mc.cores = NUM_CORES) for an entire session. Visit mc-stan.org/loo/news for details on other changes.
  
  Attaching package: 'loo'
  
  The following object is masked from 'package:testthat':
  
      compare
  
  > Sys.setenv("R_TESTS" = "")
  > test_check("loo")
  -- 1. Failure: weighted quantiles work (@test_E_loo.R#155)  --------------------
  .wquant(x1, w1, pr) not equal to .wquant_sim(x1, w1, pr, n_sim = 2e+06).
  35/39 mismatches (average diff: 0.012)
  [1]  -2.005 - -1.987 == -0.01808
  [2]  -1.688 - -1.647 == -0.04073
  [3]  -1.472 - -1.440 == -0.03245
  [4]  -1.269 - -1.280 ==  0.01101
  [5]  -1.143 - -1.152 ==  0.00863
  [6]  -1.040 - -1.042 ==  0.00202
  [7]  -0.946 - -0.943 == -0.00287
  [8]  -0.831 - -0.837 ==  0.00630
  [10] -0.658 - -0.667 ==  0.00869
  ...
  
  == testthat results  ===========================================================
  OK: 378 SKIPPED: 0 FAILED: 1
  1. Failure: weighted quantiles work (@test_E_loo.R#155) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      1.5Mb
lpint : <anonymous>: no visible global function definition for
  'integrate'
lpint: no visible global function definition for 'integrate'
lpint : lpint : <anonymous>: no visible global function definition for
  'integrate'
lplikint : lplikint.fun : <anonymous>: no visible global function
  definition for 'integrate'
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
'library' or 'require' call to 'Rsymphony' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
mipSolve.Rsymphony: no visible global function definition for
  'Rsymphony_solve_LP'
Undefined global functions or variables:
  Rsymphony_solve_LP
learnPattern.default: no visible global function definition for 'runif'
plot.learnPattern: no visible global function definition for 'matplot'
plotMDS: no visible global function definition for 'par'
plotMDS: no visible global function definition for 'rainbow'
plotMDS: no visible global function definition for 'plot'
plotMDS: no visible global function definition for 'pairs'
visualizePattern: no visible global function definition for 'par'
visualizePattern: no visible global function definition for 'plot'
visualizePattern: no visible global function definition for 'points'
visualizePattern: no visible global function definition for 'legend'
Undefined global functions or variables:
  legend matplot pairs par plot points rainbow runif
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend", "matplot", "pairs", "par", "plot",
             "points")
  importFrom("stats", "runif")
to your NAMESPACE file.
LP.comoment: no visible global function definition for 'cor'
LP.comoment: no visible global function definition for 'cov'
LP.moment: no visible global function definition for 'cor'
LPTrans: no visible global function definition for 'ecdf'
VAR: no visible global function definition for 'embed'
VAR: no visible global function definition for 'lm'
Undefined global functions or variables:
  cor cov ecdf embed lm
Consider adding
  importFrom("stats", "cor", "cov", "ecdf", "embed", "lm")
to your NAMESPACE file.
associate: no visible global function definition for 'cor'
textmatrix: no visible global function definition for 'xtabs'
textvector: no visible global function definition for 'data'
Undefined global functions or variables:
  cor data xtabs
Consider adding
  importFrom("stats", "cor", "xtabs")
  importFrom("utils", "data")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.6/lsbclust.Rcheck/00install.out' for details.
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(lsbclust)
  Loading required package: ggplot2
  > 
  > test_check("lsbclust")
  K-means on overall means...	DONE
  -- 1. Failure: cluster vector (@test_orc.R#29)  --------------------------------
  ovl$cluster not identical to ovltest$cluster.
  24/220 mismatches (average diff: 1.33)
  [1]    8 - 10 == -2
  [14]  10 -  9 ==  1
  [31]   9 -  8 ==  1
  [57]   9 -  8 ==  1
  [61]   8 - 10 == -2
  [64]   8 - 10 == -2
  [77]  10 -  9 ==  1
  [84]  10 -  9 ==  1
  [112]  9 -  8 ==  1
  ...
  
  -- 2. Failure: cluster means (@test_orc.R#33)  ---------------------------------
  ovl$centers not equal to ovltest$centers.
  3/12 mismatches (average diff: 3.68)
  [8]  7.22 - 2.70 ==  4.52
  [9]  2.70 - 1.70 ==  1.00
  [10] 1.70 - 7.22 == -5.52
  
  K-means on row margins...	DONE
  K-means on column margins...	DONE
  == testthat results  ===========================================================
  OK: 34 SKIPPED: 0 FAILED: 2
  1. Failure: cluster vector (@test_orc.R#29) 
  2. Failure: cluster means (@test_orc.R#33) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(lsbclust)
  Loading required package: ggplot2
  > 
  > test_check("lsbclust")
  K-means on overall means...	DONE
  -- 1. Failure: cluster vector (@test_orc.R#29)  --------------------------------
  ovl$cluster not identical to ovltest$cluster.
  24/220 mismatches (average diff: 1.33)
  [1]    8 - 10 == -2
  [14]  10 -  9 ==  1
  [31]   9 -  8 ==  1
  [57]   9 -  8 ==  1
  [61]   8 - 10 == -2
  [64]   8 - 10 == -2
  [77]  10 -  9 ==  1
  [84]  10 -  9 ==  1
  [112]  9 -  8 ==  1
  ...
  
  -- 2. Failure: cluster means (@test_orc.R#33)  ---------------------------------
  ovl$centers not equal to ovltest$centers.
  3/12 mismatches (average diff: 3.68)
  [8]  7.22 - 2.70 ==  4.52
  [9]  2.70 - 1.70 ==  1.00
  [10] 1.70 - 7.22 == -5.52
  
  K-means on row margins...	DONE
  K-means on column margins...	DONE
  == testthat results  ===========================================================
  OK: 34 SKIPPED: 0 FAILED: 2
  1. Failure: cluster vector (@test_orc.R#29) 
  2. Failure: cluster means (@test_orc.R#33) 
  
  Error: testthat unit tests failed
  Execution halted
Lsdv.formula: no visible global function definition for 'model.frame'
Lsdv.formula: no visible global function definition for 'model.matrix'
Lsdv.formula: no visible global function definition for
  'model.response'
lsdv: no visible global function definition for 'pf'
summary.Lsdv: no visible global function definition for 'coef'
summary.Lsdv: no visible global function definition for 'pt'
Undefined global functions or variables:
  coef model.frame model.matrix model.response pf pt
Consider adding
  importFrom("stats", "coef", "model.frame", "model.matrix",
             "model.response", "pf", "pt")
to your NAMESPACE file.
legend.lshorth: no visible global function definition for 'legend'
legend.lshorth: no visible global function definition for 'strwidth'
legend.lshorth: no visible global function definition for 'text'
plot.lshorth: no visible global function definition for 'plot.new'
plot.lshorth: no visible global function definition for 'plot.window'
plot.lshorth: no visible global function definition for 'axis'
plot.lshorth: no visible global function definition for 'title'
plot.lshorth: no visible global function definition for 'box'
plot.lshorth: no visible global function definition for 'lines'
plot.lshorth: no visible global function definition for 'legend'
plot.lshorth: no visible global function definition for 'strwidth'
plot.lshorth: no visible global function definition for 'text'
Undefined global functions or variables:
  axis box legend lines plot.new plot.window strwidth text title
Consider adding
  importFrom("graphics", "axis", "box", "legend", "lines", "plot.new",
             "plot.window", "strwidth", "text", "title")
to your NAMESPACE file.
OC : Lnapprox: no visible global function definition for 'pnorm'
OC : Lnapprox: no visible global function definition for 'qnorm'
OC : Lt: no visible global function definition for 'pt'
OC : Lt: no visible global function definition for 'qnorm'
OC : OC_emwa2: no visible global function definition for 'pnorm'
OC : OC_emwa2: no visible global function definition for 'qnorm'
OC: no visible global function definition for 'pnorm'
OC: no visible global function definition for 'qnorm'
cmBE : LAtHy: no visible global function definition for 'phyper'
cmBE: no visible global function definition for 'uniroot'
planAOQL : Gderivacex: no visible global function definition for
  'pnorm'
planAOQL : Mnk: no visible global function definition for 'uniroot'
planAOQL : k0AOQL : delta: no visible global function definition for
  'pnorm'
planAOQL : alpha0: no visible global function definition for 'pnorm'
planAOQL : alpha0: no visible global function definition for 'qnorm'
planAOQL : fMSmodq2: no visible global function definition for
  'optimize'
planAOQL : kAOQL: no visible global function definition for 'uniroot'
planLTPD : nAPPROXL : k0L : g: no visible global function definition
  for 'qnorm'
planLTPD : nAPPROXL : k0L : h: no visible global function definition
  for 'qnorm'
planLTPD : nAPPROXL : k0L: no visible global function definition for
  'qnorm'
planLTPD : nAPPROXL : alpha0: no visible global function definition for
  'pnorm'
planLTPD : nAPPROXL : alpha0: no visible global function definition for
  'qnorm'
planLTPD : nAPPROXL: no visible global function definition for
  'uniroot'
planLTPD : kEWMA: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  optimize phyper pnorm pt qnorm uniroot
Consider adding
  importFrom("stats", "optimize", "phyper", "pnorm", "pt", "qnorm",
             "uniroot")
to your NAMESPACE file.
fit.LTR: no visible global function definition for 'lm'
Undefined global functions or variables:
  lm
Consider adding
  importFrom("stats", "lm")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'robustbase'
  Please remove these calls from your code.
ltsbase: no visible global function definition for 'lm'
ltsbase: no visible global function definition for 'lines'
ltsbase: no visible global function definition for 'legend'
Undefined global functions or variables:
  legend lines lm
Consider adding
  importFrom("graphics", "legend", "lines")
  importFrom("stats", "lm")
to your NAMESPACE file.
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(lucr)
  > 
  > test_check("lucr")
  -- 1. Failure: Simple amounts can be converted (@test_conversion.R#4)  ---------
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "Â£12.00"
  y[1]: "£12.00"
  
  -- 2. Failure: Complex amounts can be converted (@test_conversion.R#8)  --------
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "Â£12,000.00"
  y[1]: "£12,000.00"
  
  == testthat results  ===========================================================
  OK: 6 SKIPPED: 0 FAILED: 2
  1. Failure: Simple amounts can be converted (@test_conversion.R#4) 
  2. Failure: Complex amounts can be converted (@test_conversion.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   1.6Mb
terrestrial.season: 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').
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
    proj   5.0Mb
generate.clonal.data : pcr.rpareto.func: no visible global function
  definition for 'runif'
generate.clonal.data : get.readcount.given.cellcount: no visible global
  function definition for 'rlnorm'
generate.clonal.data: no visible global function definition for
  'rmultinom'
generate.clonal.data: no visible global function definition for 'rpois'
infer.clonality: no visible global function definition for 'cov'
infer.clonality: no visible global function definition for
  'capture.output'
Undefined global functions or variables:
  capture.output cov rlnorm rmultinom rpois runif
Consider adding
  importFrom("stats", "cov", "rlnorm", "rmultinom", "rpois", "runif")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
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'
Undefined global functions or variables:
  CRS coordinates coordinates<- proj4string<- spTransform
maboost.default: no visible global function definition for
  'flush.console'
maboost.default: no visible binding for global variable 'na.pass'
maboost.default : predict.type: no visible global function definition
  for 'predict'
maboost.formula: no visible global function definition for
  'model.extract'
maboost.machine.bin: no visible global function definition for 'runif'
maboost.machine.bin: no visible binding for global variable 'na.pass'
maboost.machine.multi: no visible global function definition for
  'runif'
maboost.machine.multi: no visible binding for global variable 'na.pass'
projsplx_k: no visible global function definition for 'tail'
varplot.maboost: no visible global function definition for 'dotchart'
Undefined global functions or variables:
  dotchart flush.console model.extract na.pass predict runif tail
Consider adding
  importFrom("graphics", "dotchart")
  importFrom("stats", "model.extract", "na.pass", "predict", "runif")
  importFrom("utils", "flush.console", "tail")
to your NAMESPACE file.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    TS_files     5.8Mb
    base_files   6.3Mb
logistic_z: no visible global function definition for 'glm'
logistic_z: no visible binding for global variable 'binomial'
logistic_z: no visible global function definition for 'predict'
plsrf_x: no visible global function definition for 'qnorm'
plsrf_x: no visible global function definition for 'predict'
plsrf_x_pv: no visible global function definition for 'qnorm'
plsrf_x_pv: no visible global function definition for 'predict'
plsrf_xz: no visible global function definition for 'qnorm'
plsrf_xz: no visible global function definition for 'predict'
plsrf_xz_pv: no visible global function definition for 'qnorm'
plsrf_xz_pv: no visible global function definition for 'predict'
rf_z: no visible global function definition for 'qnorm'
rf_z: no visible global function definition for 'predict'
simuldata_list: no visible global function definition for 'rnorm'
simuldatacluster_list: no visible global function definition for
  'rnorm'
svm_x: no visible global function definition for 'predict'
Undefined global functions or variables:
  binomial glm predict qnorm rnorm
Consider adding
  importFrom("stats", "binomial", "glm", "predict", "qnorm", "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    6.8Mb
    libs  34.2Mb
Package in Depends field not imported from: 'rJava'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.hclust: no visible global function definition for 'hclust'
mallet.topic.hclust: no visible global function definition for 'dist'
mallet.topic.words: no visible global function definition for
  '.jevalArray'
mallet.word.freqs: no visible global function definition for
  '.jevalArray'
Undefined global functions or variables:
  .jcast .jevalArray .jnew J dist hclust
Consider adding
  importFrom("stats", "dist", "hclust")
to your NAMESPACE file.
mp_corpus: no visible binding for global variable 'annotations'
print.ManifestoAvailability: no visible binding for global variable
  'annotations'
Undefined global functions or variables:
  annotations
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc           1.2Mb
    htmlwidgets   1.4Mb
    libs          7.6Mb
cf1.sample: no visible global function definition for 'rexp'
cf1.sample: no visible global function definition for 'rmultinom'
dherlang : <anonymous> : <anonymous>: no visible global function
  definition for 'dgamma'
erhmm.param.kmeans: no visible global function definition for 'kmeans'
erhmm.param.kmeans: no visible global function definition for 'var'
erhmm.param.kmeans: no visible global function definition for 'runif'
gmmpp.param.kmeans: no visible global function definition for 'kmeans'
gmmpp.param.kmeans: no visible global function definition for 'runif'
herlang.param.kmeans: no visible global function definition for
  'kmeans'
herlang.param.kmeans: no visible global function definition for 'var'
map.param.kmeans: no visible global function definition for 'kmeans'
map.param.kmeans: no visible global function definition for 'runif'
ph.param.random: no visible global function definition for 'runif'
ph.sample: no visible global function definition for 'rmultinom'
ph.sample: no visible global function definition for 'rexp'
pherlang : <anonymous> : <anonymous>: no visible global function
  definition for 'pgamma'
rherlang: no visible global function definition for 'rmultinom'
rherlang : <anonymous>: no visible global function definition for
  'rgamma'
Undefined global functions or variables:
  dgamma kmeans pgamma rexp rgamma rmultinom runif var
Consider adding
  importFrom("stats", "dgamma", "kmeans", "pgamma", "rexp", "rgamma",
             "rmultinom", "runif", "var")
to your NAMESPACE file.
'library' or 'require' call to 'mgcv' which was already attached by Depends.
  Please remove these calls from your code.
ageprofile: no visible global function definition for 'model.frame'
ageprofile: no visible binding for global variable 'poisson'
ageprofile: no visible global function definition for 'predict.gam'
ageprofile: no visible global function definition for 'as.formula'
ageprofile: no visible global function definition for 'summary.gam'
ageprofile: no visible global function definition for 'contrasts<-'
ageprofile: no visible global function definition for 'anova.gam'
plotap: no visible global function definition for 'dev.new'
plotap: no visible global function definition for 'plot'
plotap: no visible global function definition for 'lines'
plotap: no visible global function definition for 'points'
plotap: no visible global function definition for 'legend'
splitter: no visible global function definition for 'reshape'
tabm: no visible global function definition for 'coef'
tabm: no visible global function definition for 'AIC'
Undefined global functions or variables:
  AIC anova.gam as.formula coef contrasts<- dev.new legend lines
  model.frame plot points poisson predict.gam reshape summary.gam
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "legend", "lines", "plot", "points")
  importFrom("stats", "AIC", "as.formula", "coef", "contrasts<-",
             "model.frame", "poisson", "reshape")
to your NAMESPACE file.
calcStats: no visible global function definition for 'as.formula'
calcStats: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  as.formula na.omit
Consider adding
  importFrom("stats", "as.formula", "na.omit")
to your NAMESPACE file.
plot.topics: no visible global function definition for 'hist'
plot.topics: no visible global function definition for 'grey'
plot.topics: no visible global function definition for 'plot'
plot.topics: no visible global function definition for 'par'
plot.topics: no visible global function definition for 'image'
plot.topics: no visible global function definition for 'axis'
plot.topics: no visible global function definition for 'points'
plot.topics: no visible global function definition for 'text'
rdir: no visible global function definition for 'rgamma'
summary.topics: no visible global function definition for 'pchisq'
tpxResids: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  axis grey hist image par pchisq plot points rgamma text
Consider adding
  importFrom("grDevices", "grey")
  importFrom("graphics", "axis", "hist", "image", "par", "plot",
             "points", "text")
  importFrom("stats", "pchisq", "rgamma")
to your NAMESPACE file.
Running examples in 'markmyassignment-Ex.R' failed
The error most likely occurred in:

> ### Name: mark_my_file
> ### Title: Mark assignment file
> ### Aliases: mark_my_file
> 
> ### ** Examples
> 
> assignment_path <- 
+   paste0(system.file(package = "markmyassignment"), "/extdata/example_assignment01.yml")
> file_path <- paste0(system.file(package = "markmyassignment"), "/extdata/example_lab_file.R")
> mark_my_file(mark_file = file_path, assignment_path = assignment_path)
v | OK F W S | Context

/ |  0       | task1
- |  1       | task1
\ |  2       | task1
| |  3       | task1
v |  3       | task1

/ |  0       | task2a
- |  1       | task2a
\ |  2       | task2a
| |  3       | task2a
v |  3       | task2a

/ |  0       | task2b
- |  1       | task2b
\ |  2       | task2b
| |  3       | task2b
/ |  4       | task2b
v |  4       | task2b

/ |  0       | Mandatory tests
- |  1       | Mandatory tests
v |  1       | Mandatory tests

== Results =====================================================================
OK:       11
Failed:   0
Warnings: 0
Skipped:  0
Keep up the good work!> 
> 
> 
> 
> cleanEx()
Error: connections left open:
	lines (textConnection)
Execution halted
Error(s) in re-building vignettes:
--- re-building 'GSoC-2017_additions.Rmd' using rmarkdown
Package:  markovchain
Version:  0.6.9.14
Date:     2019-01-20
BugReport: http://github.com/spedygiorgio/markovchain/issues

--- finished re-building 'GSoC-2017_additions.Rmd'

--- re-building 'an_introduction_to_markovchain_package.Rmd' using rmarkdown
Error: processing vignette 'an_introduction_to_markovchain_package.Rmd' failed with diagnostics:
pandoc version 2.2 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
--- failed re-building 'an_introduction_to_markovchain_package.Rmd'

--- re-building 'complicateSteadyStates.Rmd' using rmarkdown
Package:  markovchain
Version:  0.6.9.14
Date:     2019-01-20
BugReport: http://github.com/spedygiorgio/markovchain/issues

--- finished re-building 'complicateSteadyStates.Rmd'

--- re-building 'higher_order_markov_chains.Rmd' using rmarkdown
Error: processing vignette 'higher_order_markov_chains.Rmd' failed with diagnostics:
pandoc version 2.2 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
--- failed re-building 'higher_order_markov_chains.Rmd'

--- re-building 'markovchainCrashIntro.Rmd' using rmarkdown
--- finished re-building 'markovchainCrashIntro.Rmd'

SUMMARY: processing the following files failed:
  'an_introduction_to_markovchain_package.Rmd'
  'higher_order_markov_chains.Rmd'

Error: Vignette re-building failed.
Execution halted
negbin.rel.clust: no visible global function definition for 'kmeans'
negbin.rel.clust: no visible global function definition for 'matplot'
negbin.rel.pca: no visible global function definition for 'princomp'
negbin.rel.pca: no visible global function definition for 'biplot'
pois.rel.clust: no visible global function definition for 'kmeans'
pois.rel.clust: no visible global function definition for 'matplot'
pois.rel.pca: no visible global function definition for 'princomp'
pois.rel.pca: no visible global function definition for 'biplot'
sim.negbin: no visible global function definition for 'rnbinom'
sim.pois: no visible global function definition for 'rpois'
wt.rel.negbin: no visible global function definition for 'var'
wt.rel.negbin: no visible global function definition for 'optimize'
wt.rel.negbin: no visible global function definition for 'integrate'
wt.rel.pois: no visible global function definition for 'optimize'
wt.rel.pois: no visible global function definition for 'integrate'
Undefined global functions or variables:
  biplot integrate kmeans matplot optimize princomp rnbinom rpois var
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "biplot", "integrate", "kmeans", "optimize",
             "princomp", "rnbinom", "rpois", "var")
to your NAMESPACE file.
marqLevAlg: no visible global function definition for 'flush.console'
print.marqLevAlg: no visible global function definition for 'qnorm'
print.marqLevAlg: no visible global function definition for 'pchisq'
summary.marqLevAlg: no visible global function definition for 'qnorm'
summary.marqLevAlg: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  flush.console pchisq qnorm
Consider adding
  importFrom("stats", "pchisq", "qnorm")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
mAr.pca: no visible binding for global variable 'sd'
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   2.5Mb
Found the following possibly unsafe calls:
File 'matlab/R/zzz.R':
  unlockBinding("savedTime", .MatlabNamespaceEnv)

colorbar : colorbar.EO: no visible global function definition for 'par'
colorbar : colorbar.EO: no visible global function definition for
  'axis'
colorbar : colorbar.EO: no visible global function definition for
  'axTicks'
colorbar : colorbar.EO: no visible global function definition for 'box'
colorbar : colorbar.NO: no visible global function definition for
  'axis'
colorbar : colorbar.NO: no visible global function definition for
  'axTicks'
colorbar : colorbar.NO: no visible global function definition for 'box'
imagesc : pretty.axp: no visible global function definition for 'par'
imagesc: no visible global function definition for 'axis'
imagesc: no visible global function definition for 'box'
jet.colors: no visible global function definition for 'rgb'
multiline.plot.colors : get.gca.colororder: no visible global function
  definition for 'rgb'
std: no visible global function definition for 'sd'
Undefined global functions or variables:
  axTicks axis box par rgb sd
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axTicks", "axis", "box", "par")
  importFrom("stats", "sd")
to your NAMESPACE file.
Package suggested but not available for checking: 'gputools'
'library' or 'require' call to 'bigmemory' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
MAT: no visible global function definition for 'dev.new'
MAT: no visible global function definition for 'plot'
MAT: no visible global function definition for 'points'
MAT: no visible global function definition for 'abline'
MAT: no visible global function definition for 'text'
MAT: no visible global function definition for 'legend'
MAT: no visible global function definition for 'lines'
MAT: no visible global function definition for 'par'
MAT: no visible global function definition for 'barplot'
MAT: no visible global function definition for 'cor'
print.MAT: no visible global function definition for 'sd'
print.MAT: no visible global function definition for 'cor'
simM3PL: no visible global function definition for 'rnorm'
simM3PL: no visible global function definition for 'runif'
Undefined global functions or variables:
  abline barplot cor dev.new legend lines par plot points rnorm runif
  sd text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "barplot", "legend", "lines", "par",
             "plot", "points", "text")
  importFrom("stats", "cor", "rnorm", "runif", "sd")
to your NAMESPACE file.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Running 'testthat.R' [26s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(matrixTests)
  > 
  > test_check("matrixTests")
  -- 1. Failure: monte-carlo random testing gives equal results (@test-correct-cor
  `t1` not equal to `t2`.
  Component "conf.level": Mean absolute difference: 0.2742743
  
  == testthat results  ===========================================================
  OK: 836 SKIPPED: 0 FAILED: 1
  1. Failure: monte-carlo random testing gives equal results (@test-correct-cor_pearson.R#58) 
  
  Error: testthat unit tests failed
  Execution halted
GSTplot : <anonymous>: no visible global function definition for
  't.test'
GSTplot: no visible global function definition for 'rt'
GSTplot: no visible global function definition for 'layout'
GSTplot: no visible global function definition for 'par'
GSTplot: no visible global function definition for 'plot'
GSTplot: no visible global function definition for 'text'
GSTplot: no visible global function definition for 'lines'
GSTplot: no visible global function definition for 'polygon'
GSTplot: no visible global function definition for 'abline'
GSTplot: no visible global function definition for 'ecdf'
GSTplot: no visible global function definition for 'knots'
GSTplot : <anonymous>: no visible global function definition for 'aov'
GSTplot: no visible global function definition for 'qf'
MAVTn : <anonymous>: no visible global function definition for 'aov'
MAVTn: no visible global function definition for 'p.adjust'
MAVTn: no visible global function definition for 'plot'
MAVTn: no visible global function definition for 'par'
MAVTn: no visible global function definition for 'abline'
MAVTn: no visible global function definition for 'legend'
MAVTn: no visible global function definition for 'locator'
Tols : olsf: no visible global function definition for 't.test'
Tols: no visible global function definition for 'cor'
Undefined global functions or variables:
  abline aov cor ecdf knots layout legend lines locator p.adjust par
  plot polygon qf rt t.test text
Consider adding
  importFrom("graphics", "abline", "layout", "legend", "lines",
             "locator", "par", "plot", "polygon", "text")
  importFrom("stats", "aov", "cor", "ecdf", "knots", "p.adjust", "qf",
             "rt", "t.test")
to your NAMESPACE file.
Package in Depends field not imported from: 'mnormt'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
catt.test: no visible global function definition for 'pnorm'
fnorm2: no visible global function definition for 'sadmvn'
fnorm3: no visible global function definition for 'sadmvn'
Undefined global functions or variables:
  pnorm sadmvn
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
tune.maxent: no visible global function definition for 'predict'
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
File 'maxent/libs/i386/maxent.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'sgd.o'
File 'maxent/libs/x64/maxent.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'sgd.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
MI.2: no visible global function definition for 'xtabs'
RNASeq.Data: no visible binding for global variable 'quantile'
loc.node: no visible global function definition for 'head'
loc.node: no visible global function definition for 'tail'
plotHybrid.Tree: no visible global function definition for 'par'
plotHybrid.Tree: no visible global function definition for 'plot'
plotHybrid.Tree: no visible global function definition for 'text'
plotHybrid.Tree: no visible global function definition for 'image'
plotHybrid.Tree: no visible global function definition for 'grey'
plotHybrid.Tree: no visible global function definition for
  'heat.colors'
plotHybrid.Tree: no visible global function definition for 'head'
plotHybrid.Tree: no visible global function definition for 'segments'
plotbr: no visible global function definition for 'segments'
Undefined global functions or variables:
  grey head heat.colors image par plot quantile segments tail text
  xtabs
Consider adding
  importFrom("grDevices", "grey", "heat.colors")
  importFrom("graphics", "image", "par", "plot", "segments", "text")
  importFrom("stats", "quantile", "xtabs")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
cfull: no visible global function definition for 'combn'
cl: no visible global function definition for 'combn'
cn: no visible global function definition for 'combn'
crep: no visible global function definition for 'combn'
crich: no visible global function definition for 'combn'
ct: no visible global function definition for 'combn'
mjaccard: no visible global function definition for 'combn'
ml: no visible global function definition for 'combn'
mn: no visible global function definition for 'combn'
mrep: no visible global function definition for 'combn'
mrich: no visible global function definition for 'combn'
msorensen: no visible global function definition for 'combn'
mt: no visible global function definition for 'combn'
wnodf: no visible global function definition for 'combn'
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
Package in Depends field not imported from: 'logistf'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
mbmdr : NextModel: no visible global function definition for
  'read.table'
mbmdr : OffsetFit: no visible global function definition for 'glm'
mbmdr : Regresion: no visible global function definition for 'logistf'
mbmdr : Regresion: no visible global function definition for 'glm'
mbmdr: no visible global function definition for 'write.table'
mbmdr.PermTest: no visible global function definition for 'read.table'
mbmdr.PermTest: no visible global function definition for 'qnorm'
print.mbmdr: no visible global function definition for 'read.table'
summary.mbmdr: no visible global function definition for 'read.table'
Undefined global functions or variables:
  glm logistf qnorm read.table write.table
Consider adding
  importFrom("stats", "glm", "qnorm")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Package in Depends field not imported from: 'lpSolve'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
laugreen: no visible global function definition for 'combn'
laugreen: no visible global function definition for 'lp'
maxpear: no visible global function definition for 'hclust'
maxpear: no visible global function definition for 'as.dist'
maxpear : <anonymous>: no visible global function definition for
  'cutree'
medv: no visible global function definition for 'cutree'
medv: no visible global function definition for 'hclust'
medv: no visible global function definition for 'as.dist'
minbinder: no visible global function definition for 'hclust'
minbinder: no visible global function definition for 'as.dist'
minbinder : <anonymous>: no visible global function definition for
  'cutree'
relabel : min.perm.labels: no visible global function definition for
  'lp.transport'
Undefined global functions or variables:
  as.dist combn cutree hclust lp lp.transport
Consider adding
  importFrom("stats", "as.dist", "cutree", "hclust")
  importFrom("utils", "combn")
to your NAMESPACE file.
getbetap.A: no visible global function definition for 'pbeta'
getbetap.A: no visible global function definition for 'cor.test'
Undefined global functions or variables:
  cor.test pbeta
Consider adding
  importFrom("stats", "cor.test", "pbeta")
to your NAMESPACE file.
mcgibbsit: no visible global function definition for 'is.mcmc.list'
mcgibbsit: no visible global function definition for 'start'
mcgibbsit: no visible global function definition for 'end'
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 'qnorm'
mcgibbsit: no visible global function definition for 'niter'
mcgibbsit: no visible global function definition for 'quantile'
mcgibbsit : to.table: no visible global function definition for
  'window'
mcgibbsit: no visible global function definition for 'var'
read.mcmc: no visible global function definition for 'mcmc.list'
read.mcmc: no visible global function definition for 'mcmc'
Undefined global functions or variables:
  end is.mcmc.list mcmc mcmc.list niter nvar qnorm quantile start thin
  var varnames window
Consider adding
  importFrom("stats", "end", "qnorm", "quantile", "start", "var",
             "window")
to your NAMESPACE file.
call_localoptim: no visible global function definition for 'optim'
call_localoptim: no visible global function definition for 'nlminb'
call_localoptim: no visible global function definition for
  'txtProgressBar'
call_localoptim: no visible global function definition for
  'setTxtProgressBar'
call_localoptim : <anonymous>: no visible global function definition
  for 'optim'
call_localoptim : <anonymous>: no visible global function definition
  for 'nlminb'
multiStartoptim: no visible global function definition for 'median'
Undefined global functions or variables:
  median nlminb optim setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "median", "nlminb", "optim")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
mcheatmaps : coscolorFun: no visible global function definition for
  'rgb'
mcheatmaps : halfcmat: no visible global function definition for
  'order.dendrogram'
mcheatmaps : fullcmat: no visible global function definition for
  'order.dendrogram'
mcheatmaps : calculateDendrogram: no visible global function definition
  for 'hclust'
mcheatmaps : calculateDendrogram: no visible global function definition
  for 'as.dist'
mcheatmaps : calculateDendrogram: no visible global function definition
  for 'sd'
mcheatmaps : calculateDendrogram: no visible global function definition
  for 'cophenetic'
mcheatmaps : printDiag: no visible global function definition for
  'order.dendrogram'
mcheatmaps: no visible global function definition for 'strwidth'
mcheatmaps: no visible global function definition for 'pdf'
mcheatmaps: no visible global function definition for 'plot.new'
mcheatmaps: no visible global function definition for 'as.dendrogram'
mcheatmaps: no visible global function definition for 'reorder'
mcheatmaps: no visible global function definition for 'par'
mcheatmaps: no visible global function definition for 'plot'
mcheatmaps: no visible global function definition for
  'order.dendrogram'
mcheatmaps: no visible global function definition for 'heat.colors'
mcheatmaps: no visible global function definition for 'terrain.colors'
mcheatmaps: no visible global function definition for 'as.dist'
mcheatmaps: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  as.dendrogram as.dist cophenetic dev.off hclust heat.colors
  order.dendrogram par pdf plot plot.new reorder rgb sd strwidth
  terrain.colors
Consider adding
  importFrom("grDevices", "dev.off", "heat.colors", "pdf", "rgb",
             "terrain.colors")
  importFrom("graphics", "par", "plot", "plot.new", "strwidth")
  importFrom("stats", "as.dendrogram", "as.dist", "cophenetic", "hclust",
             "order.dendrogram", "reorder", "sd")
to your NAMESPACE file.
lik_locfit: no visible global function definition for 'predict'
mcll_coeff: no visible global function definition for 'optim'
mcll_est: no visible global function definition for 'cov'
mcll_est: no visible global function definition for 'optim'
mcll_se: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov optim predict
Consider adding
  importFrom("stats", "cov", "optim", "predict")
to your NAMESPACE file.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   1.6Mb
do.linear.conjoint: no visible global function definition for
  'as.formula'
do.linear.conjoint: no visible global function definition for 'lm'
do.linear.conjoint: no visible global function definition for
  'coefficients'
is.close.to.orthogonal: no visible global function definition for 'cor'
mc.add.to.design: no visible global function definition for 'combn'
mc.good.designs: no visible global function definition for 'combn'
Undefined global functions or variables:
  as.formula coefficients combn cor lm
Consider adding
  importFrom("stats", "as.formula", "coefficients", "cor", "lm")
  importFrom("utils", "combn")
to your NAMESPACE file.
'library' or 'require' call to 'scatterplot3d' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.nsga2: no visible global function definition for 'plot'
plot.nsga2: no visible global function definition for 'lines'
plot.nsga2: no visible global function definition for 'pairs'
plot.nsga2.collection: no visible global function definition for
  'devAskNewPage'
plot.nsga2.collection: no visible binding for global variable 'plot'
Undefined global functions or variables:
  devAskNewPage lines pairs plot
Consider adding
  importFrom("grDevices", "devAskNewPage")
  importFrom("graphics", "lines", "pairs", "plot")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'coda'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'MASS' 'coda'
  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 '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.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.2Mb
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.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   2.6Mb
    libs      1.5Mb
conf.interval: no visible global function definition for 'pbinom'
conf.statement: no visible global function definition for 'pbinom'
Undefined global functions or variables:
  pbinom
Consider adding
  importFrom("stats", "pbinom")
to your NAMESPACE file.
'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.
.df: no visible global function definition for 'logLik'
coef_simple: no visible global function definition for 'coef'
fitall: no visible binding for global variable 'as.formula'
fitbest: no visible binding for global variable 'as.formula'
lmboot: no visible global function definition for 'lm'
residuals.ensemble : <anonymous>: no visible global function definition
  for 'resid'
residuals.ensemble : <anonymous>: no visible global function definition
  for 'rstudent'
residuals.ensemble : <anonymous>: no visible global function definition
  for 'fitted'
residuals.ensemble : <anonymous>: no visible global function definition
  for 'influence.measures'
stdcoef: no visible global function definition for 'coef'
stdcoef: no visible global function definition for 'update'
summary.ensemble : <anonymous>: no visible global function definition
  for 'logLik'
summary.ensemble : <anonymous>: no visible global function definition
  for 'AIC'
summary.ensemble : <anonymous>: no visible global function definition
  for 'fitted'
summary.resid_ensemble: no visible binding for global variable
  'rstudent'
summary.resid_ensemble: no visible global function definition for 'sd'
summary.variable_ensemble: no visible global function definition for
  'sd'
Undefined global functions or variables:
  AIC as.formula coef fitted influence.measures lm logLik resid
  rstudent sd update
Consider adding
  importFrom("stats", "AIC", "as.formula", "coef", "fitted",
             "influence.measures", "lm", "logLik", "resid", "rstudent",
             "sd", "update")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'adegenet' 'geosphere'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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'
Undefined global functions or variables:
  SpatialPoints df2genind distMeeus distm propShared
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.5Mb
workspace_management : tellme: no visible global function definition
  for 'file.edit'
workspace_management: no visible global function definition for
  'object.size'
Undefined global functions or variables:
  file.edit object.size
Consider adding
  importFrom("utils", "file.edit", "object.size")
to your NAMESPACE file.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   2.0Mb
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.
Error(s) in re-building vignettes:
--- re-building 'metaBMA.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
INFORMATION: Es konnten keine Dateien mit dem angegebenen
Muster gefunden werden.
Quitting from lines 63-72 (metaBMA.Rmd) 
Error: processing vignette 'metaBMA.Rmd' failed with diagnostics:
Unable to call JAGS
--- failed re-building 'metaBMA.Rmd'

SUMMARY: processing the following file failed:
  'metaBMA.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/MetabolomicsBasics.Rcheck/00install.out' for details.
Running examples in 'metacart-Ex.R' failed
The error most likely occurred in:

> ### Name: FEmrt
> ### Title: Fixed effect meta-tree
> ### Aliases: FEmrt
> 
> ### ** Examples
> 
> data(dat.BCT2009)
> FEtree <- FEmrt(g ~ T1 + T2+ T4 + T25, vi = vi, data = dat.BCT2009, c = 0.5)
Warning in FEmrt(g ~ T1 + T2 + T4 + T25, vi = vi, data = dat.BCT2009, c = 0.5) :
  no moderator effect was detected
> print(FEtree)

Fixed Effects Meta-Tree (K = 106 studies); 
FEmrt(formula = g ~ T1 + T2 + T4 + T25, data = dat.BCT2009, vi = vi, 
    c = 0.5)

No moderator effect was detected
use summary() to see the meta-analysis results> summary(FEtree)

Fixed Effects meta-tree (K = 106 studies); 
FEmrt(formula = g ~ T1 + T2 + T4 + T25, data = dat.BCT2009, vi = vi, 
    c = 0.5)

No moderator effect was detected

Test for Heterogeneity under FE assumption:
Q = 253.0357 (df = 105), p-value < 1e-04;

Fixed Effect Meta-analysis Results:
   no.      g     se   zval   pval  ci.lb  ci.ub        
   106  0.229  0.012 18.803  0.000  0.206  0.253    *** 
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

> plot(FEtree)
Error in `rownames<-`(`*tmp*`, value = rank(as.numeric(rownames(frame)))) : 
  attempt to set 'rownames' on an object with no dimensions
Calls: plot -> plot.FEmrt -> rownames<-
Execution halted
Packages in Depends field not imported from:
  'gsl' 'rmeta'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
metacor.DSL: no visible global function definition for 'qnorm'
metacor.DSL: no visible global function definition for 'pnorm'
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 'qnorm'
metacor.OP: no visible global function definition for 'pnorm'
metacor.OP: no visible global function definition for 'metaplot'
Undefined global functions or variables:
  hyperg_2F1 metaplot pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
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.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   9.1Mb
EScombination: no visible global function definition for 'model.matrix'
EScombination: no visible global function definition for 'p.adjust'
EScombination: no visible global function definition for 'pt'
EScombination.paired: no visible global function definition for
  'p.adjust'
EScombination.paired: no visible global function definition for 'pt'
calcfit2Diffrep: no visible global function definition for
  'model.matrix'
directEScombi: no visible global function definition for 'pnorm'
directEScombi: no visible global function definition for 'p.adjust'
directpvalcombi : fstatmeta: no visible global function definition for
  'qnorm'
directpvalcombi: no visible global function definition for 'pnorm'
directpvalcombi: no visible global function definition for 'p.adjust'
pvalcombination: no visible global function definition for
  'model.matrix'
pvalcombination: no visible global function definition for 'p.adjust'
pvalcombination: no visible global function definition for 'pt'
pvalcombination.paired: no visible global function definition for
  'p.adjust'
pvalcombination.paired: no visible global function definition for 'pt'
Undefined global functions or variables:
  model.matrix p.adjust pnorm pt qnorm
Consider adding
  importFrom("stats", "model.matrix", "p.adjust", "pnorm", "pt", "qnorm")
to your NAMESPACE file.
MAPE: no visible global function definition for 'is'
MAPE: no visible global function definition for 'new'
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').
Packages suggested but not available for checking: 'doMC', 'doSMP'
Package in Depends field not imported from: 'foreach'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' calls which should be '::':
  'pcaPP:::l1median_HoCr' 'pcaPP:::l1median_VaZh'
  See the note in ?`:::` about the use of this operator.
fishercomb: no visible global function definition for 'pchisq'
fishercomb: no visible global function definition for 'p.adjust'
invnorm : <anonymous>: no visible global function definition for
  'qnorm'
invnorm: no visible global function definition for 'pnorm'
invnorm: no visible global function definition for 'p.adjust'
sim.function : <anonymous>: no visible global function definition for
  'rnorm'
sim.function : <anonymous>: no visible global function definition for
  'rnbinom'
Undefined global functions or variables:
  p.adjust pchisq pnorm qnorm rnbinom rnorm
Consider adding
  importFrom("stats", "p.adjust", "pchisq", "pnorm", "qnorm", "rnbinom",
             "rnorm")
to your NAMESPACE file.
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.
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.
RUVRand: no visible global function definition for 'barplot'
RUVRand: no visible global function definition for 'prcomp'
RuvRandIter: no visible global function definition for 'kmeans'
RuvRandIter: no visible global function definition for 'barplot'
RuvRandIter: no visible global function definition for 'prcomp'
opt: no visible global function definition for 'optim'
printdata: no visible global function definition for 'head'
Undefined global functions or variables:
  barplot head kmeans optim prcomp
Consider adding
  importFrom("graphics", "barplot")
  importFrom("stats", "kmeans", "optim", "prcomp")
  importFrom("utils", "head")
to your NAMESPACE file.
Running 'testthat.R' [31s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(metR)
  > library(vdiffr)
  > 
  > test_check("metR")
  -- 1. Failure: EOF changes probs (@test_eof.R#21)  -----------------------------
  {
      ...
  } not identical to 1524903.
  1/1 mismatches
  [1] 1523828 - 1524903 == -1075
  
  == testthat results  ===========================================================
  OK: 62 SKIPPED: 16 FAILED: 1
  1. Failure: EOF changes probs (@test_eof.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.1Mb
    libs   4.4Mb
    misc   1.1Mb
Packages in Depends field not imported from:
  'MASS' 'abind' 'pls'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
show,mewTyp: no visible global function definition for 'head'
Undefined global functions or variables:
  head
Consider adding
  importFrom("utils", "head")
to your NAMESPACE file.
maglm: no visible global function definition for 'combn'
maglm: no visible global function definition for 'glm'
maglm: no visible global function definition for 'logLik'
mamglm: no visible global function definition for 'combn'
mamglm: no visible global function definition for 'logLik'
ses.maglm: no visible global function definition for 'rnorm'
ses.maglm: no visible binding for global variable 'sd'
ses.mamglm: no visible global function definition for 'rnorm'
ses.mamglm: no visible binding for global variable 'sd'
Undefined global functions or variables:
  combn glm logLik rnorm sd
Consider adding
  importFrom("stats", "glm", "logLik", "rnorm", "sd")
  importFrom("utils", "combn")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'corpcor' 'evd' 'fields' 'numDeriv'
  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 'RJSONIO' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.onAttach: no visible global function definition for 'packageVersion'
.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 'download.file'
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'
doc.MGRAST: no visible global function definition for 'str'
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'
Undefined global functions or variables:
  .MGRAST download.file fromJSON isValidJSON packageVersion str
Consider adding
  importFrom("utils", "download.file", "packageVersion", "str")
to your NAMESPACE file.
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(mgsub)
  > 
  > test_check("mgsub")
  -- 1. Failure: multicharacter censor works (@test_mgsub_censor.R#53)  ----------
  mgsub_censor("What the flip?", "flip", "?#!*", seed = 10) not equal to "What the !##!?".
  1/1 mismatches
  x[1]: "What the !?#*?"
  y[1]: "What the !##!?"
  
  -- 2. Failure: multicharacter censor works (@test_mgsub_censor.R#54)  ----------
  mgsub_censor(...) not equal to "What the !##!?".
  1/1 mismatches
  x[1]: "What the !?#*?"
  y[1]: "What the !##!?"
  
  -- 3. Failure: multicharacter censor works (@test_mgsub_censor.R#55)  ----------
  mgsub_censor("What the flip?", "flip", c("?#", "!*"), seed = 10) not equal to "What the !##!?".
  1/1 mismatches
  x[1]: "What the !?#*?"
  y[1]: "What the !##!?"
  
  -- 4. Failure: multicharacter censor can be used badly (@test_mgsub_censor.R#61)
  mgsub_censor(...) not equal to "What the !*?#?#!*?".
  1/1 mismatches
  x[1]: "What the ?#?#!*!*?"
  y[1]: "What the !*?#?#!*?"
  
  == testthat results  ===========================================================
  OK: 56 SKIPPED: 0 FAILED: 4
  1. Failure: multicharacter censor works (@test_mgsub_censor.R#53) 
  2. Failure: multicharacter censor works (@test_mgsub_censor.R#54) 
  3. Failure: multicharacter censor works (@test_mgsub_censor.R#55) 
  4. Failure: multicharacter censor can be used badly (@test_mgsub_censor.R#61) 
  
  Error: testthat unit tests failed
  Execution halted
calc_z_var: no visible binding for global variable 'median'
diffScore: no visible global function definition for 'new'
diffScore: no visible global function definition for 'model.matrix'
logNORMcdf: no visible global function definition for 'pnorm'
mGSZ.adj.mean.std: no visible binding for global variable 'sd'
pick.data.cols: no visible binding for global variable 'var'
plotProfile: no visible binding for global variable 'quantile'
plotProfile: no visible global function definition for 'plot'
plotProfile: no visible global function definition for 'lines'
plotProfile: no visible global function definition for 'legend'
Undefined global functions or variables:
  legend lines median model.matrix new plot pnorm quantile sd var
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("methods", "new")
  importFrom("stats", "median", "model.matrix", "pnorm", "quantile",
             "sd", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
BCI: no visible global function definition for 'quantile'
Metro_Hastings: no visible global function definition for 'optim'
Metro_Hastings: no visible global function definition for 'runif'
Metro_Hastings: no visible global function definition for 'var'
plotMH: no visible global function definition for 'hist'
plotMH: no visible global function definition for 'plot'
plotMH: no visible global function definition for 'frame'
plotMH: no visible global function definition for 'text'
Undefined global functions or variables:
  frame hist optim plot quantile runif text var
Consider adding
  importFrom("graphics", "frame", "hist", "plot", "text")
  importFrom("stats", "optim", "quantile", "runif", "var")
to your NAMESPACE file.
.snqProfitImposeConvexityStEr: no visible global function definition
  for 'runif'
predict.snqProfitEst: no visible global function definition for
  'model.matrix'
predict.snqProfitEst: no visible global function definition for 'qt'
predict.snqProfitEst: no visible global function definition for
  'df.residual'
predict.snqProfitEst: no visible global function definition for
  'residuals'
snqProfitCoef: no visible global function definition for 'pt'
snqProfitEla: no visible global function definition for 'pt'
snqProfitEst: no visible global function definition for 'as.formula'
snqProfitEst: no visible global function definition for 'coef'
snqProfitEst: no visible global function definition for 'vcov'
snqProfitEst: no visible global function definition for 'fitted'
snqProfitEst: no visible global function definition for 'df.residual'
snqProfitImposeConvexity: no visible global function definition for
  'optim'
snqProfitSystem: no visible global function definition for 'as.formula'
Undefined global functions or variables:
  as.formula coef df.residual fitted model.matrix optim pt qt residuals
  runif vcov
Consider adding
  importFrom("stats", "as.formula", "coef", "df.residual", "fitted",
             "model.matrix", "optim", "pt", "qt", "residuals", "runif",
             "vcov")
to your NAMESPACE file.
Running 'testthat.R' [68s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(mice)
  Loading required package: lattice
  
  Attaching package: 'mice'
  
  The following objects are masked from 'package:base':
  
      cbind, rbind
  
  > 
  > test_check("mice")
  -- 1. Failure: retains same numerical result (@test-pool.R#13)  ----------------
  unname(getqbar(est)) not equal to `mn`.
  5/5 mismatches (average diff: 0.895)
  [1] 19.7878 - 18.7617 ==  1.02603
  [2]  0.0513 -  0.0536 == -0.00229
  [3] -6.1563 - -4.5737 == -1.58260
  [4] -7.7136 - -6.6360 == -1.07766
  [5]  2.9521 -  2.1636 ==  0.78847
  
  -- 2. Failure: retains same numerical result (@test-pool.R#14)  ----------------
  unname(summary(est)[, "std.error"]) not equal to `se`.
  5/5 mismatches (average diff: 0.329)
  [1] 3.4259 - 4.0028 == -0.57694
  [2] 0.0187 - 0.0224 == -0.00363
  [3] 1.6195 - 2.0340 == -0.41452
  [4] 1.9746 - 2.4598 == -0.48513
  [5] 1.8642 - 2.0290 == -0.16475
  
  == testthat results  ===========================================================
  OK: 274 SKIPPED: 0 FAILED: 2
  1. Failure: retains same numerical result (@test-pool.R#13) 
  2. Failure: retains same numerical result (@test-pool.R#14) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [69s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(mice)
  Loading required package: lattice
  
  Attaching package: 'mice'
  
  The following objects are masked from 'package:base':
  
      cbind, rbind
  
  > 
  > test_check("mice")
  -- 1. Failure: retains same numerical result (@test-pool.R#13)  ----------------
  unname(getqbar(est)) not equal to `mn`.
  5/5 mismatches (average diff: 0.895)
  [1] 19.7878 - 18.7617 ==  1.02603
  [2]  0.0513 -  0.0536 == -0.00229
  [3] -6.1563 - -4.5737 == -1.58260
  [4] -7.7136 - -6.6360 == -1.07766
  [5]  2.9521 -  2.1636 ==  0.78847
  
  -- 2. Failure: retains same numerical result (@test-pool.R#14)  ----------------
  unname(summary(est)[, "std.error"]) not equal to `se`.
  5/5 mismatches (average diff: 0.329)
  [1] 3.4259 - 4.0028 == -0.57694
  [2] 0.0187 - 0.0224 == -0.00363
  [3] 1.6195 - 2.0340 == -0.41452
  [4] 1.9746 - 2.4598 == -0.48513
  [5] 1.8642 - 2.0290 == -0.16475
  
  == testthat results  ===========================================================
  OK: 274 SKIPPED: 0 FAILED: 2
  1. Failure: retains same numerical result (@test-pool.R#13) 
  2. Failure: retains same numerical result (@test-pool.R#14) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: 'microcontax.data'
Package unavailable to check Rd xrefs: 'microcontax.data'
Running 'testthat.R' [18s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > #library(microsamplingDesign)
  > 
  > #source("generateTestData.R")
  > 
  > #test_check("microsamplingDesign")
  > 
  > testthat::test_check("microsamplingDesign")
  Loading required package: microsamplingDesign
  start Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 cores-- 1. Failure: Equal ranking timePoints (@testRankTimePoints.R#43)  ------------
  rankTimePointsOrig@ranking not equal to rankedTimePointsNew@ranking.
  Component "name": 7 string mismatches
  Component "criterion": Mean relative difference: 0.04047401
  
  == testthat results  ===========================================================
  OK: 20 SKIPPED: 4 FAILED: 1
  1. Failure: Equal ranking timePoints (@testRankTimePoints.R#43) 
  
  Error: testthat unit tests failed
  Execution halted
'library' or 'require' call to 'gWidgetsRGtk2' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'gWidgetsRGtk2'
  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:
  '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 use Fortran I/O
nor system RNGs.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
migration.cv.in : <anonymous>: no visible global function definition
  for 'sd'
migration.cv.out : <anonymous>: no visible global function definition
  for 'sd'
migration.field.diagram: no visible global function definition for
  'plot'
migration.field.diagram: no visible global function definition for
  'lines'
migration.field.diagram: no visible global function definition for
  'text'
migration.field.diagram: no visible global function definition for
  'polygon'
migration.field.diagram: no visible global function definition for 'lm'
migration.field.diagram: no visible global function definition for
  'predict'
migration.field.diagram: no visible global function definition for
  'points'
migration.field.diagram: no visible global function definition for
  'resid'
migration.field.diagram: no visible global function definition for
  'coef'
migration.field.diagram: no visible global function definition for
  'mtext'
migration.field.diagram: no visible global function definition for
  'density'
migration.field.diagram: no visible global function definition for
  'rug'
migration.gini.col : <anonymous>: no visible global function definition
  for 'dist'
migration.gini.in : <anonymous>: no visible global function definition
  for 'dist'
migration.gini.out : <anonymous>: no visible global function definition
  for 'dist'
migration.gini.row : <anonymous>: no visible global function definition
  for 'dist'
migration.gini.total: no visible global function definition for 'dist'
Undefined global functions or variables:
  coef density dist lines lm mtext plot points polygon predict resid
  rug sd text
Consider adding
  importFrom("graphics", "lines", "mtext", "plot", "points", "polygon",
             "rug", "text")
  importFrom("stats", "coef", "density", "dist", "lm", "predict",
             "resid", "sd")
to your NAMESPACE file.
.default_model: no visible global function definition for 'is'
.guess_type: no visible global function definition for 'is.ts'
.parse_trans: no visible binding for global variable 'qnorm'
do_get_data_from_disk: no visible global function definition for
  'read.csv'
do_get_data_from_mi: no visible global function definition for 'data'
do_get_data_from_r : <anonymous>: no visible global function definition
  for 'is'
do_parametric_eval : <anonymous>: no visible global function definition
  for 'dev.off'
do_parametric_eval : <anonymous>: no visible global function definition
  for 'title'
do_var_options : varHandler2: no visible global function definition for
  'is'
do_var_options : varHandler3: no visible global function definition for
  'getClass'
do_var_options : varHandler3: no visible global function definition for
  'is'
do_var_options : changeHandler: no visible global function definition
  for 'is'
do_var_options : <anonymous>: no visible global function definition for
  'title'
do_var_options: no visible global function definition for 'getClass'
do_var_options: no visible global function definition for 'is'
helpHandler: no visible global function definition for 'browseURL'
is.method_in_mi: no visible global function definition for
  'selectMethod'
is.method_in_mi: no visible global function definition for 'signature'
Undefined global functions or variables:
  browseURL data dev.off getClass is is.ts qnorm read.csv selectMethod
  signature title
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("graphics", "title")
  importFrom("methods", "getClass", "is", "selectMethod", "signature")
  importFrom("stats", "is.ts", "qnorm")
  importFrom("utils", "browseURL", "data", "read.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
nat_hist: no visible global function definition for 'data'
nat_hist: no visible binding for global variable 'current.other'
t_mal: no visible global function definition for 'uniroot'
t_prog: no visible global function definition for 'rlnorm'
tdeath_lung: no visible global function definition for 'data'
tdeath_lung: no visible binding for global variable 'ci.lung'
tdeath_lung: no visible binding for global variable 'current.other'
tdeath_lung: no visible binding for global variable 'former.other'
tdeath_lung: no visible binding for global variable 'never.other'
tdeath_other: no visible global function definition for 'data'
tdeath_other: no visible binding for global variable 'ci.lung'
tdeath_other: no visible binding for global variable 'current.other'
tdeath_other: no visible binding for global variable 'former.other'
tdeath_other: no visible binding for global variable 'never.other'
Undefined global functions or variables:
  ci.lung current.other data former.other never.other rlnorm uniroot
Consider adding
  importFrom("stats", "rlnorm", "uniroot")
  importFrom("utils", "data")
to your NAMESPACE file.
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.
miney : plot.initial.matrix: no visible global function definition for
  'plot'
miney : plot.initial.matrix: no visible global function definition for
  'rect'
miney : plot.known.matrix: no visible global function definition for
  'plot'
miney : plot.known.matrix: no visible global function definition for
  'rect'
miney : plot.known.matrix: no visible global function definition for
  'text'
miney: no visible global function definition for 'locator'
miney: no visible global function definition for 'rect'
miney: no visible global function definition for 'title'
Undefined global functions or variables:
  locator plot rect text title
Consider adding
  importFrom("graphics", "locator", "plot", "rect", "text", "title")
to your NAMESPACE file.
rminimax: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
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.
minxent.multiple: no visible global function definition for 'cov.wt'
minxent.single: no visible global function definition for 'optimize'
Undefined global functions or variables:
  cov.wt optimize
Consider adding
  importFrom("stats", "cov.wt", "optimize")
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.
.FCLoess: no visible global function definition for 'loess'
.FCLoessM: no visible global function definition for 'loess'
.FCLoessM: no visible global function definition for 'median'
.Import.Luminex: no visible global function definition for 'read.csv'
.Intra.Me: no visible global function definition for 'sd'
.Intra.Me: no visible global function definition for 'quantile'
.Intra.Me: no visible global function definition for 'qchisq'
.Intra.Median: no visible global function definition for 'median'
.boxplot.rtprofile: no visible global function definition for 'boxplot'
.denplot: no visible global function definition for 'plot'
.denplot: no visible global function definition for 'density'
.denplot: no visible global function definition for 'abline'
.normalize.Luminex: no visible global function definition for 'sd'
.normalize.qrtpcr: no visible global function definition for 'density'
.validate.default: no visible global function definition for 't.test'
Undefined global functions or variables:
  abline boxplot density loess median plot qchisq quantile read.csv sd
  t.test
Consider adding
  importFrom("graphics", "abline", "boxplot", "plot")
  importFrom("stats", "density", "loess", "median", "qchisq", "quantile",
             "sd", "t.test")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
fisher.combination: no visible global function definition for 'pchisq'
gs.test: no visible global function definition for 'ks.test'
gs.test: no visible global function definition for 'wilcox.test'
gs.test: no visible global function definition for 'fisher.test'
inverse.normal.combination: no visible global function definition for
  'qnorm'
inverse.normal.combination: no visible global function definition for
  'pnorm'
limma.one.sided: no visible global function definition for 'pt'
Undefined global functions or variables:
  fisher.test ks.test pchisq pnorm pt qnorm wilcox.test
Consider adding
  importFrom("stats", "fisher.test", "ks.test", "pchisq", "pnorm", "pt",
             "qnorm", "wilcox.test")
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'
missForest: no visible global function definition for 'predict'
missForest: no visible global function definition for 'idiv'
missForest: no visible global function definition for 'var'
nrmse: no visible global function definition for 'var'
Undefined global functions or variables:
  idiv predict var
Consider adding
  importFrom("stats", "predict", "var")
to your NAMESPACE file.
AndersonDarling: no visible global function definition for 'spline'
Hawkins: no visible global function definition for 'cov'
Hawkins: no visible global function definition for 'pf'
Impute: no visible global function definition for 'cov'
Mimpute: no visible global function definition for 'rnorm'
SimNey: no visible global function definition for 'runif'
TestMCARNormality: no visible global function definition for 'cov'
TestMCARNormality: no visible global function definition for 'pchisq'
TestUNey: no visible global function definition for 'pchisq'
boxplot.testhomosc: no visible global function definition for 'par'
boxplot.testhomosc: no visible global function definition for 'title'
boxplot.testhomosc: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline cov par pchisq pf rnorm runif spline title
Consider adding
  importFrom("graphics", "abline", "par", "title")
  importFrom("stats", "cov", "pchisq", "pf", "rnorm", "runif", "spline")
to your NAMESPACE file.
'library' or 'require' call to 'CompQuadForm' which was already attached by Depends.
  Please remove these calls from your code.
linear.test: no visible global function definition for 'lm'
linear.test: no visible global function definition for 'pchisq'
linear.weight.test: no visible global function definition for 'lm'
linear.weight.test: no visible global function definition for 'dbeta'
linear.weight.test: no visible global function definition for 'pchisq'
logit.test: no visible global function definition for 'glm'
logit.test: no visible global function definition for 'binomial'
logit.test: no visible binding for global variable 'logit'
logit.test: no visible global function definition for 'pchisq'
logit.weight.test: no visible global function definition for 'glm'
logit.weight.test: no visible global function definition for 'binomial'
logit.weight.test: no visible binding for global variable 'logit'
logit.weight.test: no visible global function definition for 'dbeta'
logit.weight.test: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  binomial dbeta glm lm logit pchisq
Consider adding
  importFrom("stats", "binomial", "dbeta", "glm", "lm", "pchisq")
to your NAMESPACE file.
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').
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/math/special_functions/detail/bernoulli_details.hpp:72:36: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/math/special_functions/detail/bernoulli_details.hpp:96:9: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.6/mixedMem.Rcheck/00install.out' for details.
Packages in Depends field not imported from:
  'MASS' 'RODBC' 'tcltk' 'tcltk2'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages suggested but not available for checking: 'REBayes', 'Rmosek'
Packages unavailable to check Rd xrefs: 'REBayes', 'Rmosek'
fit.mixtNB: no visible global function definition for 'dnbinom'
fit.mixtNB: no visible global function definition for 'nlminb'
wald.test: no visible global function definition for 'pnorm'
wald.test: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  dnbinom nlminb p.adjust pnorm
Consider adding
  importFrom("stats", "dnbinom", "nlminb", "p.adjust", "pnorm")
to your NAMESPACE file.
computeContourValues: no visible global function definition for
  'na.omit'
deselectNonMovementSteps : coOccurProb: no visible global function
  definition for 'dnorm'
deselectNonMovementSteps: no visible global function definition for
  'pnorm'
estVarMKDE: no visible global function definition for 'na.omit'
estVarMKDE: no visible global function definition for 'qnorm'
estVarMKDE: no visible global function definition for 'optimize'
plotMKDE: no visible global function definition for 'rainbow'
Undefined global functions or variables:
  dnorm na.omit optimize pnorm qnorm rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("stats", "dnorm", "na.omit", "optimize", "pnorm", "qnorm")
to your NAMESPACE file.
mkle: no visible global function definition for 'sd'
mkle: no visible global function definition for 'density'
mkle: no visible global function definition for 'optimize'
mkle.ci: no visible global function definition for 'sd'
mkle.ci: no visible binding for global variable 'var'
mkle.ci: no visible global function definition for 'quantile'
mkle.ci: no visible global function definition for 'qnorm'
opt.bw: no visible global function definition for 'sd'
opt.bw : mse: no visible global function definition for 'var'
opt.bw: no visible global function definition for 'optimize'
opt.bw: no visible global function definition for 'var'
Undefined global functions or variables:
  density optimize qnorm quantile sd var
Consider adding
  importFrom("stats", "density", "optimize", "qnorm", "quantile", "sd",
             "var")
to your NAMESPACE file.
mkssd: no visible global function definition for 'txtProgressBar'
mkssd: no visible global function definition for 'setTxtProgressBar'
Undefined global functions or variables:
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'cairoDevice' 'gplots'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  'MASS:::lda.default' 'MASS:::qda.default'
  'e1071:::naiveBayes.default' 'e1071:::svm.default'
  'randomForest:::randomForest.default'
  See the note in ?`:::` about the use of this operator.
confusionBarplot: no visible global function definition for 'par'
confusionBarplot: no visible global function definition for 'barplot'
confusionBarplot: no visible global function definition for 'lines'
confusionBarplot: no visible global function definition for 'text'
confusionBarplot: no visible global function definition for 'legend'
confusionBarplot: no visible global function definition for 'axis'
confusionDendrogram: no visible global function definition for 'plot'
confusionImage: no visible global function definition for 'par'
confusionImage: no visible global function definition for 'image'
confusionImage: no visible global function definition for 'text'
confusionImage: no visible global function definition for 'abline'
confusionImage: no visible global function definition for 'axis'
confusionImage: no visible global function definition for 'plot'
confusionImage: no visible global function definition for 'mtext'
confusionStars: no visible global function definition for 'par'
confusionStars: no visible global function definition for 'stars'
confusionStars: no visible global function definition for 'rect'
plot.mlearning: no visible global function definition for 'plot'
Undefined global functions or variables:
  abline axis barplot image legend lines mtext par plot rect stars text
Consider adding
  importFrom("graphics", "abline", "axis", "barplot", "image", "legend",
             "lines", "mtext", "par", "plot", "rect", "stars", "text")
to your NAMESPACE file.
dftest: no visible global function definition for 'slot'
mctest: no visible global function definition for 'rnorm'
mleurDiag: no visible global function definition for 'acf'
mleurDiag: no visible global function definition for 'pchisq'
mleurDiag: no visible global function definition for 'par'
mleurDiag: no visible global function definition for 'boxplot'
mleurDiag: no visible global function definition for 'shapiroTest'
mleurDiag: no visible global function definition for 'title'
mleurDiag: no visible global function definition for 'abline'
mleurDiag: no visible global function definition for 'lines'
simar1: no visible global function definition for 'rnorm'
simar1: no visible global function definition for 'rt'
simar1: no visible global function definition for 'convolve'
Undefined global functions or variables:
  abline acf boxplot convolve lines par pchisq rnorm rt shapiroTest
  slot title
Consider adding
  importFrom("graphics", "abline", "boxplot", "lines", "par", "title")
  importFrom("methods", "slot")
  importFrom("stats", "acf", "convolve", "pchisq", "rnorm", "rt")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
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.
CheckStability: no visible global function definition for 'cor'
CheckStability: no visible global function definition for 'var'
PriorNormPCA: no visible global function definition for 'barplot'
SortModes: no visible global function definition for 'rnorm'
mlicaMAIN: no visible global function definition for 'runif'
Undefined global functions or variables:
  barplot cor rnorm runif var
Consider adding
  importFrom("graphics", "barplot")
  importFrom("stats", "cor", "rnorm", "runif", "var")
to your NAMESPACE file.
Running examples in 'ML.MSBD-Ex.R' failed
The error most likely occurred in:

> ### Name: likelihood_MSBD_unresolved
> ### Title: Likelihood calculation for unresolved trees
> ### Aliases: likelihood_MSBD_unresolved
> 
> ### ** Examples
> 
> # Simulate a random phylogeny
> set.seed(24)
> tree <- ape::rcoal(10)
> 
> # Calculate the log likelihood under a constant birth-death model (i.e, no shifts) 
> # with unresolved tips
> likelihood_MSBD_unresolved(tree, shifts = c(), gamma = 0, lambdas = 10, mus = 1, 
+                            lineage_counts = c(2,5,1,3,1,1,1,1,2,6), tcut = 0.05)
Error in likelihood_MSBD_unresolved(tree, shifts = c(), gamma = 0, lambdas = 10,  : 
  Invalid cut-off time for tip t7
Execution halted
Error(s) in re-building vignettes:
--- re-building 'Using_ML.MSBD.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 57-58 (Using_ML.MSBD.Rmd) 
Error: processing vignette 'Using_ML.MSBD.Rmd' failed with diagnostics:
Tree edge 2 has negative length
--- failed re-building 'Using_ML.MSBD.Rmd'

SUMMARY: processing the following file failed:
  'Using_ML.MSBD.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages in Depends field not imported from:
  'BMA' 'abind' 'maxLik'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
listGenoToTable: no visible binding for global variable 'dummy'
Undefined global functions or variables:
  dummy
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
File which contains pragma(s) suppressing diagnostics:
  'src/lemon/core.h'
mmm2: no visible global function definition for 'model.frame'
mmm2: no visible global function definition for 'model.matrix'
mmm2: no visible global function definition for 'model.response'
mmm2: no visible global function definition for 'as.formula'
Undefined global functions or variables:
  as.formula model.frame model.matrix model.response
Consider adding
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response")
to your NAMESPACE file.
mmm: no visible global function definition for 'model.frame'
mmm: no visible global function definition for 'model.matrix'
mmm: no visible global function definition for 'model.response'
mmm: no visible global function definition for 'as.formula'
mmm: no visible global function definition for 'gee'
Undefined global functions or variables:
  as.formula gee model.frame model.matrix model.response
Consider adding
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response")
to your NAMESPACE file.
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').
sadmvng: no visible global function definition for 'cov2cor'
sadmvng: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  cov2cor pnorm
Consider adding
  importFrom("stats", "cov2cor", "pnorm")
to your NAMESPACE file.
'library' or 'require' call to 'SparseM' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to 'glmnet' in package code.
  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:
  'date' 'raster' 'rgdal' 'sfsmisc'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'date' 'raster' 'rgdal' 'sfsmisc' 'sp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.clustOrder: no visible global function definition for 'hclust'
.clustOrder: no visible global function definition for 'as.dist'
consensusMEDissimilarity: no visible global function definition for
  'cor'
mergeCloseModules: no visible global function definition for 'cor'
mergeCloseModules: no visible global function definition for 'hclust'
mergeCloseModules: no visible global function definition for 'as.dist'
moduleEigengenes: no visible global function definition for 'cor'
moduleEigengenes: no visible global function definition for 'cov'
moduleNumber: no visible global function definition for 'cutree'
orderMEs: no visible global function definition for 'cor'
orderMEs: no visible global function definition for 'as.dist'
plotHclustColors: no visible global function definition for 'barplot'
plotHclustColors: no visible global function definition for 'strwidth'
plotHclustColors: no visible global function definition for 'rect'
plotHclustColors: no visible global function definition for 'text'
plotHclustColors: no visible global function definition for 'lines'
Undefined global functions or variables:
  as.dist barplot cor cov cutree hclust lines rect strwidth text
Consider adding
  importFrom("graphics", "barplot", "lines", "rect", "strwidth", "text")
  importFrom("stats", "as.dist", "cor", "cov", "cutree", "hclust")
to your NAMESPACE file.
agostino.test: no visible global function definition for
  'complete.cases'
agostino.test: no visible global function definition for 'pnorm'
anscombe.test: no visible global function definition for
  'complete.cases'
anscombe.test: no visible global function definition for 'pnorm'
bonett.test: no visible global function definition for 'complete.cases'
bonett.test: no visible global function definition for 'pnorm'
jarque.test: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  complete.cases pchisq pnorm
Consider adding
  importFrom("stats", "complete.cases", "pchisq", "pnorm")
to your NAMESPACE file.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    1.8Mb
    libs   1.9Mb
Warning: no function found corresponding to methods exports from 'mondate' 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.
.date.to.mondate: no visible global function definition for 'new'
as.character.mondate: no visible global function definition for 'slot'
Arith,array-mondate: no visible global function definition for
  'callGeneric'
Arith,mondate-array: no visible global function definition for
  'callGeneric'
Arith,mondate-mondate: no visible global function definition for
  'callGeneric'
Arith,mondate-numeric: no visible global function definition for
  'callGeneric'
Arith,numeric-mondate: no visible global function definition for
  'callGeneric'
Compare,mondate-ANY: no visible global function definition for
  'callGeneric'
Compare,mondate-ANY: no visible global function definition for
  'getDataPart'
Summary,mondate: no visible global function definition for
  'callGeneric'
[,mondate: no visible global function definition for 'callNextMethod'
[,mondate: no visible global function definition for 'new'
array,mondate: no visible global function definition for
  'callNextMethod'
as.numeric,mondate: no visible global function definition for 'slot'
c,mondate: no visible global function definition for 'new'
c,mondate: no visible binding for global variable 'getDataPart'
c,mondate: no visible global function definition for 'getDataPart'
matrix,mondate: no visible global function definition for
  'callNextMethod'
mondate,Date: no visible global function definition for 'new'
mondate,POSIXt: no visible global function definition for 'new'
mondate,missing: no visible global function definition for 'new'
mondate,mondate: no visible global function definition for 'new'
mondate,numeric: no visible global function definition for 'new'
Undefined global functions or variables:
  callGeneric callNextMethod getDataPart new slot
Consider adding
  importFrom("methods", "callGeneric", "callNextMethod", "getDataPart",
             "new", "slot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running 'testthat.R' [166s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > # Sys.setenv("MONETDBLITE_INMEMORY" = "yes")
  > # test_check("MonetDBLite")
  > Sys.setenv("MONETDBLITE_INMEMORY" = "no")
  > test_check("MonetDBLite")
  Loading required package: MonetDBLite
  -- 1. Failure: db allows svyby commands (@test_05_survey.R#60)  ----------------
  round(...) not equal to 0.022.
  1/1 mismatches
  [1] 0.019 - 0.022 == -0.003
  
  -- 2. Failure: db allows svyby commands (@test_05_survey.R#62)  ----------------
  ...[] not equal to 10.11.
  1/1 mismatches
  [1] 10.3 - 10.1 == 0.23
  
  [1] "E"
  [1] "H"
  [1] "M"
  -- 3. Failure: db allows svyby commands (@test_05_survey.R#66)  ----------------
  round(SE(a)[2], 2) not equal to 4708.41.
  1/1 mismatches
  [1] 5476 - 4708 == 768
  
  -- 4. Failure: db allows svyby commands (@test_05_survey.R#67)  ----------------
  as.numeric(round(cv(a)[2], 4)) not equal to 0.2975.
  1/1 mismatches
  [1] 0.346 - 0.297 == 0.0486
  
  -- 5. Failure: db allows svyby commands (@test_05_survey.R#69)  ----------------
  round(confint(a, df = degf(rclus1))[2, 2], 2) not equal to 30808.26.
  1/1 mismatches
  [1] 33252 - 30808 == 2443
  
  == testthat results  ===========================================================
  OK: 296 SKIPPED: 13 FAILED: 5
  1. Failure: db allows svyby commands (@test_05_survey.R#60) 
  2. Failure: db allows svyby commands (@test_05_survey.R#62) 
  3. Failure: db allows svyby commands (@test_05_survey.R#66) 
  4. Failure: db allows svyby commands (@test_05_survey.R#67) 
  5. Failure: db allows svyby commands (@test_05_survey.R#69) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [152s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > # Sys.setenv("MONETDBLITE_INMEMORY" = "yes")
  > # test_check("MonetDBLite")
  > Sys.setenv("MONETDBLITE_INMEMORY" = "no")
  > test_check("MonetDBLite")
  Loading required package: MonetDBLite
  -- 1. Failure: db allows svyby commands (@test_05_survey.R#60)  ----------------
  round(...) not equal to 0.022.
  1/1 mismatches
  [1] 0.019 - 0.022 == -0.003
  
  -- 2. Failure: db allows svyby commands (@test_05_survey.R#62)  ----------------
  ...[] not equal to 10.11.
  1/1 mismatches
  [1] 10.3 - 10.1 == 0.23
  
  [1] "E"
  [1] "H"
  [1] "M"
  -- 3. Failure: db allows svyby commands (@test_05_survey.R#66)  ----------------
  round(SE(a)[2], 2) not equal to 4708.41.
  1/1 mismatches
  [1] 5476 - 4708 == 768
  
  -- 4. Failure: db allows svyby commands (@test_05_survey.R#67)  ----------------
  as.numeric(round(cv(a)[2], 4)) not equal to 0.2975.
  1/1 mismatches
  [1] 0.346 - 0.297 == 0.0486
  
  -- 5. Failure: db allows svyby commands (@test_05_survey.R#69)  ----------------
  round(confint(a, df = degf(rclus1))[2, 2], 2) not equal to 30808.26.
  1/1 mismatches
  [1] 33252 - 30808 == 2443
  
  == testthat results  ===========================================================
  OK: 296 SKIPPED: 16 FAILED: 5
  1. Failure: db allows svyby commands (@test_05_survey.R#60) 
  2. Failure: db allows svyby commands (@test_05_survey.R#62) 
  3. Failure: db allows svyby commands (@test_05_survey.R#66) 
  4. Failure: db allows svyby commands (@test_05_survey.R#67) 
  5. Failure: db allows svyby commands (@test_05_survey.R#69) 
  
  Error: testthat unit tests failed
  Execution halted
Missing or unexported objects:
  'dplyr::base_agg' 'dplyr::base_scalar' 'dplyr::build_sql'
  'dplyr::is.ident' 'dplyr::sql_infix' 'dplyr::sql_prefix'
  'dplyr::sql_translator' 'dplyr::sql_variant' 'dplyr::src_sql'
  'dplyr::tbl_sql'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
mopsocd : initialize_pop: no visible global function definition for
  'runif'
mopsocd : compute_velocity: no visible global function definition for
  'runif'
mopsocd : mutate: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
checkTH: no visible global function definition for 'pchisq'
getOrderPval: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
ametrine : <anonymous>: no visible global function definition for
  'approx'
ametrine: no visible global function definition for 'rgb'
isolum : <anonymous>: no visible global function definition for
  'approx'
isolum: no visible global function definition for 'rgb'
morgenstemning : <anonymous>: no visible global function definition for
  'approx'
morgenstemning: no visible global function definition for 'rgb'
Undefined global functions or variables:
  approx rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "approx")
to your NAMESPACE file.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.5Mb
cor.gen: no visible global function definition for 'rnorm'
cor.gen: no visible global function definition for 'resid'
cor.gen: no visible global function definition for 'lm'
cor.gen: no visible binding for global variable 'sd'
cor.gen: no visible global function definition for 'cor'
cor.gen: no visible global function definition for 'write.table'
stat.gen: no visible global function definition for 'rexp'
stat.gen: no visible global function definition for 'rnorm'
stat.gen: no visible binding for global variable 'sd'
stat.gen: no visible global function definition for 'write.table'
Undefined global functions or variables:
  cor lm resid rexp rnorm sd write.table
Consider adding
  importFrom("stats", "cor", "lm", "resid", "rexp", "rnorm", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Mort1Dsmooth: no visible global function definition for 'time'
Mort1Dsmooth: no visible global function definition for 'glm'
Mort1Dsmooth: no visible binding for global variable 'poisson'
Mort1Dsmooth_optimize: no visible global function definition for
  'median'
Mort2Dsmooth: no visible global function definition for 'glm'
Mort2Dsmooth: no visible binding for global variable 'poisson'
Mort2Dsmooth: no visible global function definition for 'median'
Mort2Dsmooth_optimize: no visible global function definition for
  'median'
plot.HMDdata: no visible global function definition for 'plot'
plot.Mort1Dsmooth: no visible global function definition for 'matplot'
plot.Mort2Dsmooth: no visible global function definition for 'quantile'
predict.Mort1Dsmooth: no visible global function definition for 'glm'
predict.Mort1Dsmooth: no visible binding for global variable 'poisson'
predict.Mort2Dsmooth: no visible global function definition for 'glm'
predict.Mort2Dsmooth: no visible binding for global variable 'poisson'
print.summary.Mort1Dsmooth: no visible global function definition for
  'quantile'
print.summary.Mort2Dsmooth: no visible global function definition for
  'quantile'
Undefined global functions or variables:
  glm matplot median plot poisson quantile time
Consider adding
  importFrom("graphics", "matplot", "plot")
  importFrom("stats", "glm", "median", "poisson", "quantile", "time")
to your NAMESPACE file.
getmouseDV: no visible global function definition for 'tail'
interpltraj: no visible global function definition for 'approx'
trim1: no visible global function definition for 'tail'
Undefined global functions or variables:
  approx tail
Consider adding
  importFrom("stats", "approx")
  importFrom("utils", "tail")
to your NAMESPACE file.
Error(s) in re-building vignettes:
--- re-building 'estimatingWindSpeed.Rmd' using rmarkdown
--- finished re-building 'estimatingWindSpeed.Rmd'

--- re-building 'windEstimationParameters.Rmd' using rmarkdown
Quitting from lines 92-93 (windEstimationParameters.Rmd) 
Error: processing vignette 'windEstimationParameters.Rmd' failed with diagnostics:
some 'x' not counted; maybe 'breaks' do not span range of 'x'
--- failed re-building 'windEstimationParameters.Rmd'

SUMMARY: processing the following file failed:
  'windEstimationParameters.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'corpus.useR.2008.abstracts'
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'mpa/R/zzz.R':
  .First.lib calls:
    cat("\n mpa: CoWords Method")
    cat("\n ")
    cat("\n Universidad Nacional de Colombia")
    cat("\n ")
    cat("\n Elaborado por: Daniel Rodriguez <dhrodriguezt@unal.edu.co>")
    cat("\n                Campo Elias Pardo <cepardot@unal.edu.co>")
    cat("\n For help: ?mpa   \n\n")

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

diagram.mpa: no visible global function definition for 'plot'
diagram.mpa: no visible global function definition for 'abline'
diagram.mpa: no visible global function definition for 'text'
plotmpa: no visible global function definition for 'plot'
Undefined global functions or variables:
  abline plot text
Consider adding
  importFrom("graphics", "abline", "plot", "text")
to your NAMESPACE file.
mpcv: no visible binding for global variable 'median'
mpcv: no visible global function definition for 'cov'
mpcv: no visible global function definition for 'dist'
plot.mpcv: no visible binding for global variable 'median'
plot.mpcv: no visible global function definition for 'par'
plot.mpcv: no visible global function definition for 'plot'
plot.mpcv: no visible global function definition for 'rect'
plot.mpcv: no visible global function definition for 'lines'
plot.mpcv: no visible global function definition for 'points'
plot.mpcv: no visible global function definition for 'legend'
Undefined global functions or variables:
  cov dist legend lines median par plot points rect
Consider adding
  importFrom("graphics", "legend", "lines", "par", "plot", "points",
             "rect")
  importFrom("stats", "cov", "dist", "median")
to your NAMESPACE file.
GetExampleData: no visible binding for global variable 'MPINetData'
Getenvir: no visible binding for global variable 'MPINetData'
getPSS: no visible global function definition for 'lines'
performpcls: no visible global function definition for 'binomial'
Undefined global functions or variables:
  MPINetData binomial lines
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "binomial")
to your NAMESPACE file.
'library' or 'require' call to 'MASS' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'KernSmooth' 'MASS'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
export.summary.mpm: warning in complex(real = x$Rows[, FdimsR[1]], imag
  = x$Rows[, FdimsR[2]]): partial argument match of 'imag' to
  'imaginary'
export.summary.mpm: warning in complex(real = x$Columns[, FdimsC[1]],
  imag = x$Columns[, FdimsC[2]]): partial argument match of 'imag' to
  'imaginary'
.onAttach: no visible global function definition for
  'packageDescription'
export.summary.mpm: no visible global function definition for
  'write.table'
mpm: no visible binding for global variable 'median'
plot.mpm: no visible global function definition for 'rainbow'
plot.mpm: no visible global function definition for 'quantile'
plot.mpm: no visible global function definition for 'par'
plot.mpm: no visible global function definition for 'points'
plot.mpm: no visible global function definition for 'smoothScatter'
plot.mpm: no visible global function definition for 'colorRampPalette'
plot.mpm: no visible global function definition for 'symbols'
plot.mpm: no visible global function definition for 'text'
plot.mpm: no visible global function definition for 'lines'
plot.mpm: no visible global function definition for 'box'
Undefined global functions or variables:
  box colorRampPalette lines median packageDescription par points
  quantile rainbow smoothScatter symbols text write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "rainbow")
  importFrom("graphics", "box", "lines", "par", "points",
             "smoothScatter", "symbols", "text")
  importFrom("stats", "median", "quantile")
  importFrom("utils", "packageDescription", "write.table")
to your NAMESPACE file.
place: no visible global function definition for 'points'
plot,mproc: no visible binding for global variable 'rainbow'
plot,mproc: no visible global function definition for 'plot.default'
plot,mproc: no visible global function definition for 'axis'
plot,mproc: no visible global function definition for 'points'
Undefined global functions or variables:
  axis plot.default points rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "plot.default", "points")
to your NAMESPACE file.
Running examples in 'mptools-Ex.R' failed
The error most likely occurred in:

> ### Name: kch
> ### Title: Extract Metapop KCH
> ### Aliases: kch
> 
> ### ** Examples
> 
> mp <- system.file('example.mp', package='mptools')
> k <- kch(meta=meta(mp), path=dirname(mp))
Extracting population metadata from file:
D:/temp/RtmpcT8mgq/RLIBS_2f2583a8c113e/mptools/example.mp
> 
> 
> 
> cleanEx()
Error: connections left open:
	pops[1] (textConnection)
Execution halted
ppersp: no visible global function definition for 'colorRampPalette'
Undefined global functions or variables:
  colorRampPalette
Consider adding
  importFrom("grDevices", "colorRampPalette")
to your NAMESPACE file.
densityfn: no visible global function definition for 'dnbinom'
densityfn: no visible global function definition for 'dpois'
densityfn: no visible global function definition for 'dgeom'
form.add: no visible global function definition for 'formula'
mreg: no visible global function definition for 'model.frame'
mreg: no visible global function definition for 'model.response'
mreg: no visible global function definition for 'model.matrix'
mreg: no visible global function definition for 'model.offset'
mreg: no visible global function definition for 'nlm'
paper: no visible global function definition for 'model.matrix'
randfn: no visible global function definition for 'rnbinom'
randfn: no visible global function definition for 'rpois'
randfn: no visible global function definition for 'rgeom'
randfn: no visible global function definition for 'rbinom'
summary.mreg: no visible global function definition for 'pnorm'
summary.mreg: no visible global function definition for 'printCoefmat'
Undefined global functions or variables:
  dgeom dnbinom dpois formula model.frame model.matrix model.offset
  model.response nlm pnorm printCoefmat rbinom rgeom rnbinom rpois
Consider adding
  importFrom("stats", "dgeom", "dnbinom", "dpois", "formula",
             "model.frame", "model.matrix", "model.offset",
             "model.response", "nlm", "pnorm", "printCoefmat", "rbinom",
             "rgeom", "rnbinom", "rpois")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'mvtnorm' 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
MRsurvival: no visible global function definition for 'rmvnorm'
MRsurvival: no visible global function definition for 'optim'
MRsurvival : <anonymous>: no visible global function definition for
  'quantile'
Undefined global functions or variables:
  optim quantile rmvnorm
Consider adding
  importFrom("stats", "optim", "quantile")
to your NAMESPACE file.
MRwarp: no visible global function definition for 'dev.new'
MRwarp: no visible global function definition for 'plot'
MRwarp: no visible global function definition for 'lines'
MRwarp: no visible global function definition for 'points'
MRwarp: no visible global function definition for 'hist'
Undefined global functions or variables:
  dev.new hist lines plot points
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "hist", "lines", "plot", "points")
to your NAMESPACE file.
File 'MRwarping/libs/i386/MRwarping.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'interfaceRC_warp.o'
File 'MRwarping/libs/x64/MRwarping.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'interfaceRC_warp.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
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.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.6/MSCMT.Rcheck/00install.out' for details.
cv.msda: no visible global function definition for 'predict'
formatoutput: no visible global function definition for 'new'
msda.prep: no visible global function definition for 'cov'
plot.msda: no visible global function definition for 'par'
plot.msda: no visible global function definition for 'matplot'
plot.msda: no visible global function definition for 'rainbow'
plot.msda: no visible global function definition for 'approx'
plot.msda: no visible global function definition for 'axis'
predict.msda: no visible binding for global variable 'sd'
predict.msda: no visible global function definition for 'predict'
zeromat: no visible global function definition for 'new'
Undefined global functions or variables:
  approx axis cov matplot new par predict rainbow sd
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "matplot", "par")
  importFrom("methods", "new")
  importFrom("stats", "approx", "cov", "predict", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
csv2list: no visible global function definition for 'read.csv'
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'
msea_ora: no visible global function definition for 'fisher.test'
msea_ora: no visible global function definition for 'p.adjust'
msea_sub: no visible global function definition for 'sd'
msea_sub: no visible global function definition for 'cor.test'
pathway_class: no visible global function definition for 'untar'
pca_scaled: no visible binding for global variable 'sd'
pca_scaled: no visible global function definition for 'cor.test'
pca_scaled: no visible global function definition for 'p.adjust'
pca_scaled: no visible binding for global variable 'var'
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'
Undefined global functions or variables:
  append.xmlNode cor.test fisher.test p.adjust read.csv sd untar var
  xmlAttrs xmlNode xmlRoot xmlToList xmlTreeParse
Consider adding
  importFrom("stats", "cor.test", "fisher.test", "p.adjust", "sd", "var")
  importFrom("utils", "read.csv", "untar")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
See 'd:/Rcompile/CRANpkg/local/3.6/MSeasy.Rcheck/00install.out' for details.
'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.
Found the following significant warnings:
  Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
See 'd:/Rcompile/CRANpkg/local/3.6/MSeasyTkGUI.Rcheck/00install.out' for details.
'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 21.2Mb
  sub-directories of 1Mb or more:
    libs  19.8Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Running examples in 'msgpack-Ex.R' failed
The error most likely occurred in:

> ### Name: msgConnection
> ### Title: Read and write msgpack formatted messages over R connections.
> ### Aliases: msgConnection close.msgConnection partial
> ###   partial.msgConnection readMsgs status status.msgConnection
> ###   seek.msgConnection readMsg writeMsg writeMsgs
> 
> ### ** Examples
> 
> out <- rawConnection(raw(0), open="wb")
> apply(quakes, 1, function(x) writeMsg(x, out))
NULL
> length(rawConnectionValue(out))
[1] 57300
> inn <- msgConnection(rawConnection(rawConnectionValue(out), open="rb"))
> readMsg(inn)
     lat     long    depth      mag stations 
  -20.42   181.62   562.00     4.80    41.00 
> readMsgs(inn, 3)
[[1]]
     lat     long    depth      mag stations 
  -20.62   181.03   650.00     4.20    15.00 

[[2]]
     lat     long    depth      mag stations 
   -26.0    184.1     42.0      5.4     43.0 

[[3]]
     lat     long    depth      mag stations 
  -17.97   181.66   626.00     4.10    19.00 

> 
> 
> 
> cleanEx()
Error: connections left open:
	raw(0) (rawConnection)
	rawConnectionValue(out) (rawConnection)
Execution halted
Found the following significant warnings:
  Warning: unable to re-encode 'dfgps.R' line 51
  Warning: unable to re-encode 'msgps.R' line 98
  Warning: unable to re-encode 'plot.msgps.R' line 60
  Warning: unable to re-encode 'print.msgps.R' line 36
  Warning: unable to re-encode 'summary.msgps.R' line 45
See 'd:/Rcompile/CRANpkg/local/3.6/msgps.Rcheck/00install.out' for details.
MSIseq.classify: no visible global function definition for 'predict'
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
Running 'test_base.R' [44s]
Running the tests in 'tests/test_base.R' failed.
Complete output:
  > library(testthat)
  > test_check("msm")
  Loading required package: msm
  -- 1. Failure: Information matrix (@test_deriv.r#138)  -------------------------
  c(0.88475550512612, 0.202501688704573, -0.474183198550202) not equal to tm$paramdata$info[1:3].
  3/3 mismatches (average diff: 0.284)
  [1]  0.885 -  1.0455 == -0.161
  [2]  0.203 -  0.0872 ==  0.115
  [3] -0.474 - -1.0490 ==  0.575
  
  -- 2. Failure: piecewise constant intensities with pci, with other covariates (@
  448.1228 not equal to cav5cov.msm$minus2loglik.
  1/1 mismatches
  [1] 448 - 456 == -7.79
  
  -- 3. Failure: piecewise constant intensities with pci, with other covariates (@
  448.1228 not equal to cav5cov.msm$minus2loglik.
  1/1 mismatches
  [1] 448 - 456 == -7.79
  
  -- 4. Failure: piecewise constant intensities with pci, with uncentered covariat
  449.692 not equal to cav5cov.msm$minus2loglik.
  1/1 mismatches
  [1] 450 - 458 == -7.82
  
  -- 5. Failure: piecewise constant intensities with pci, with uncentered covariat
  449.692 not equal to cav5cov.msm$minus2loglik.
  1/1 mismatches
  [1] 450 - 458 == -7.82
  
  == testthat results  ===========================================================
  OK: 462 SKIPPED: 2 FAILED: 5
  1. Failure: Information matrix (@test_deriv.r#138) 
  2. Failure: piecewise constant intensities with pci, with other covariates (@test_models.r#202) 
  3. Failure: piecewise constant intensities with pci, with other covariates (@test_models.r#210) 
  4. Failure: piecewise constant intensities with pci, with uncentered covariates (@test_models.r#218) 
  5. Failure: piecewise constant intensities with pci, with uncentered covariates (@test_models.r#226) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'test_base.R' [49s]
Running the tests in 'tests/test_base.R' failed.
Complete output:
  > library(testthat)
  > test_check("msm")
  Loading required package: msm
  -- 1. Failure: Information matrix (@test_deriv.r#138)  -------------------------
  c(0.88475550512612, 0.202501688704573, -0.474183198550202) not equal to tm$paramdata$info[1:3].
  3/3 mismatches (average diff: 0.284)
  [1]  0.885 -  1.0455 == -0.161
  [2]  0.203 -  0.0872 ==  0.115
  [3] -0.474 - -1.0490 ==  0.575
  
  -- 2. Failure: piecewise constant intensities with pci, with other covariates (@
  448.1228 not equal to cav5cov.msm$minus2loglik.
  1/1 mismatches
  [1] 448 - 456 == -7.79
  
  -- 3. Failure: piecewise constant intensities with pci, with other covariates (@
  448.1228 not equal to cav5cov.msm$minus2loglik.
  1/1 mismatches
  [1] 448 - 456 == -7.79
  
  -- 4. Failure: piecewise constant intensities with pci, with uncentered covariat
  449.692 not equal to cav5cov.msm$minus2loglik.
  1/1 mismatches
  [1] 450 - 458 == -7.82
  
  -- 5. Failure: piecewise constant intensities with pci, with uncentered covariat
  449.692 not equal to cav5cov.msm$minus2loglik.
  1/1 mismatches
  [1] 450 - 458 == -7.82
  
  == testthat results  ===========================================================
  OK: 462 SKIPPED: 2 FAILED: 5
  1. Failure: Information matrix (@test_deriv.r#138) 
  2. Failure: piecewise constant intensities with pci, with other covariates (@test_models.r#202) 
  3. Failure: piecewise constant intensities with pci, with other covariates (@test_models.r#210) 
  4. Failure: piecewise constant intensities with pci, with uncentered covariates (@test_models.r#218) 
  5. Failure: piecewise constant intensities with pci, with uncentered covariates (@test_models.r#226) 
  
  Error: testthat unit tests failed
  Execution halted
BS.var: no visible binding for global variable 'var'
BS.var: no visible global function definition for 'cov'
Dist.CIs: no visible global function definition for 'qnorm'
MSM.CIs: no visible global function definition for 'qnorm'
plot,msSurv-missing: no visible global function definition for 'update'
summary,msSurv: no visible global function definition for 'quantile'
Undefined global functions or variables:
  cov qnorm quantile update var
Consider adding
  importFrom("stats", "cov", "qnorm", "quantile", "update", "var")
to your NAMESPACE file.
'library' or 'require' call to 'MASS' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
Packages in Depends field not imported from:
  'DiceKriging' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CrossValidationMuFicokm: no visible global function definition for
  'covMatrix'
CrossValidationMuFicokmAll: no visible global function definition for
  'covMatrix'
MuFicokm: no visible global function definition for 'km'
compute.beta.hat: no visible global function definition for 'lm'
computeAuxVariables: no visible global function definition for
  'covMatrix'
kmCok: no visible global function definition for 'new'
kmCok: no visible global function definition for 'drop.response'
kmCok: no visible global function definition for 'model.matrix'
kmCok: no visible global function definition for 'covStruct.create'
kmCok: no visible global function definition for 'validObject'
kmCok: no visible global function definition for 'covParametersBounds'
kmCok: no visible binding for global variable 'kmEstimate'
kmCok : cv: no visible global function definition for 'leaveOneOut.km'
kmCok: no visible global function definition for 'plot'
predict.kmCok: no visible global function definition for 'model.matrix'
predict.kmCok: no visible global function definition for 'covMat1Mat2'
predict.kmCok: no visible global function definition for 'qnorm'
predict.kmCok: no visible global function definition for 'qt'
predict.kmCok: no visible global function definition for 'covMatrix'
summary.MuFicokm: no visible global function definition for
  'covparam2vect'
Undefined global functions or variables:
  covMat1Mat2 covMatrix covParametersBounds covStruct.create
  covparam2vect drop.response km kmEstimate leaveOneOut.km lm
  model.matrix new plot qnorm qt validObject
Consider adding
  importFrom("graphics", "plot")
  importFrom("methods", "new", "validObject")
  importFrom("stats", "lm", "model.matrix", "qnorm", "qt")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
multeq.diff: no visible global function definition for 'cov'
multeq.diff: no visible global function definition for 'pt'
multeq.diff: no visible global function definition for 'qt'
multeq.rat: no visible global function definition for 'cov'
multeq.rat: no visible global function definition for 'pt'
multeq.rat: no visible global function definition for 'qt'
Undefined global functions or variables:
  cov pt qt
Consider adding
  importFrom("stats", "cov", "pt", "qt")
to your NAMESPACE file.
plotOptionValues: no visible global function definition for 'plot'
plotOptionValues: no visible global function definition for 'persp'
Undefined global functions or variables:
  persp plot
Consider adding
  importFrom("graphics", "persp", "plot")
to your NAMESPACE file.
synthetic_multiband: no visible global function definition for 'runif'
synthetic_multiband: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
calculate_direction: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
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.
multinb.fit: no visible global function definition for 'nlminb'
multinbmod: no visible global function definition for 'is.empty.model'
multinbmod: no visible global function definition for 'model.matrix'
multinbmod: no visible binding for global variable 'contrasts'
multinbmod: no visible global function definition for 'model.response'
multinbmod: no visible global function definition for 'model.offset'
Undefined global functions or variables:
  contrasts is.empty.model model.matrix model.offset model.response
  nlminb
Consider adding
  importFrom("stats", "contrasts", "is.empty.model", "model.matrix",
             "model.offset", "model.response", "nlminb")
to your NAMESPACE file.
.moments: no visible global function definition for 'ppois'
.truncpoi: no visible global function definition for 'ppois'
Undefined global functions or variables:
  ppois
Consider adding
  importFrom("stats", "ppois")
to your NAMESPACE file.
Package in Depends field not imported from: 'rgenoud'
  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
  'packageDescription'
genoudRob: no visible global function definition for 'genoud'
get.XYdata: no visible global function definition for 'terms'
get.xdata: no visible global function definition for 'terms'
get.xdata: no visible global function definition for 'model.matrix'
get.xy: no visible global function definition for 'terms'
get.xynames: no visible global function definition for 'terms'
get.ydata: no visible global function definition for 'terms'
get.ydata: no visible global function definition for 'model.response'
get.ydata: no visible global function definition for 'model.frame'
mt.dev: no visible global function definition for 'pt'
mt.dev.grad: no visible global function definition for 'pt'
mt.dev.grad: no visible global function definition for 'dt'
mt.mle: no visible global function definition for 'optim'
multinomRob: no visible global function definition for 'var'
plot.multinomRob: no visible global function definition for 'par'
plot.multinomRob: no visible global function definition for 'plot'
plot.multinomRob: no visible global function definition for 'title'
rdirich: no visible global function definition for 'rgamma'
residual.generator: no visible global function definition for 'median'
rmultinomial: no visible global function definition for 'runif'
rmultinomial: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  dt genoud median model.frame model.matrix model.response optim
  packageDescription par plot pt rbinom rgamma runif terms title var
Consider adding
  importFrom("graphics", "par", "plot", "title")
  importFrom("stats", "dt", "median", "model.frame", "model.matrix",
             "model.response", "optim", "pt", "rbinom", "rgamma",
             "runif", "terms", "var")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
multiPIM : expand.factors: no visible global function definition for
  'formula'
multiPIM : expand.factors: no visible global function definition for
  'model.matrix'
multiPIM : <anonymous>: no visible global function definition for 'glm'
multiPIM : <anonymous>: no visible binding for global variable
  'binomial'
multiPIM : <anonymous>: no visible global function definition for
  'qlogis'
multiPIM : <anonymous>: no visible global function definition for
  'as.formula'
multiPIM : <anonymous>: no visible global function definition for 'lm'
multiPIM: no visible global function definition for 'glm'
multiPIM: no visible global function definition for 'qlogis'
multiPIM: no visible binding for global variable 'binomial'
multiPIM: no visible global function definition for 'plogis'
multiPIM: no visible global function definition for 'sd'
multiPIM: no visible global function definition for 'lm'
summary.multiPIM: no visible binding for global variable 'sd'
summary.multiPIM: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  as.formula binomial formula glm lm model.matrix plogis pnorm qlogis
  sd
Consider adding
  importFrom("stats", "as.formula", "binomial", "formula", "glm", "lm",
             "model.matrix", "plogis", "pnorm", "qlogis", "sd")
to your NAMESPACE file.
CCM_boot : <anonymous>: no visible global function definition for 'sd'
SSR_check_signal: no visible global function definition for 'cor'
SSR_check_signal: no visible global function definition for 'cor.test'
SSR_check_signal: no visible global function definition for 'lm'
SSR_pred_boot: no visible global function definition for 'cor'
make_ccm_data: no visible global function definition for 'rnorm'
make_ccm_data: no visible global function definition for 'runif'
make_ccm_data: no visible global function definition for 'rlnorm'
Undefined global functions or variables:
  cor cor.test lm rlnorm rnorm runif sd
Consider adding
  importFrom("stats", "cor", "cor.test", "lm", "rlnorm", "rnorm",
             "runif", "sd")
to your NAMESPACE file.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
PrbMlt.default: no visible binding for global variable 'na.omit'
PrbMlt.default: no visible global function definition for 'anova'
Undefined global functions or variables:
  anova na.omit
Consider adding
  importFrom("stats", "anova", "na.omit")
to your NAMESPACE file.
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'.

paradjp: no visible global function definition for 'pt'
parci: no visible global function definition for 'qt'
pdunnett: no visible global function definition for 'GenzBretz'
pvalci: no visible global function definition for 'qnorm'
qdunnett: no visible global function definition for 'GenzBretz'
Undefined global functions or variables:
  GenzBretz pt qnorm qt
Consider adding
  importFrom("stats", "pt", "qnorm", "qt")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'car' 'gplots' 'pdist' 'pls' 'rrcov'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'bitops' 'caTools' 'car' 'gplots' 'gtools' 'mvtnorm' 'pcaPP' 'pdist'
  'pls' 'robustbase' 'rrcov'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
plotFID: no visible global function definition for 'plot'
plotFID: no visible global function definition for 'points'
Undefined global functions or variables:
  plot points
Consider adding
  importFrom("graphics", "plot", "points")
to your NAMESPACE file.
prentice.test: 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').
mvb.simu: no visible global function definition for 'runif'
plot.lps: no visible global function definition for 'matplot'
unifit: no visible global function definition for 'model.frame'
unifit: no visible global function definition for 'model.matrix'
unifit: no visible global function definition for 'model.response'
unilps: no visible global function definition for 'model.frame'
unilps: no visible global function definition for 'model.matrix'
unilps: no visible global function definition for 'model.response'
Undefined global functions or variables:
  matplot model.frame model.matrix model.response runif
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "model.frame", "model.matrix", "model.response",
             "runif")
to your NAMESPACE file.
conceptIndicesSkm: no visible global function definition for
  'txtProgressBar'
conceptIndicesSkm: no visible global function definition for
  'setTxtProgressBar'
conceptVectorsSkm: no visible global function definition for
  'txtProgressBar'
conceptVectorsSkm: no visible global function definition for
  'setTxtProgressBar'
mvcmb: no visible global function definition for 'runif'
mvcmb: no visible global function definition for 'str'
mvcsph: no visible global function definition for 'pdf'
mvcsph: no visible global function definition for 'heatmap'
mvcsph: no visible global function definition for 'dev.off'
mvcsph: no visible global function definition for 'hclust'
mvcsph: no visible global function definition for 'dist'
mvcsph: no visible global function definition for 'str'
Undefined global functions or variables:
  dev.off dist hclust heatmap pdf runif setTxtProgressBar str
  txtProgressBar
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("stats", "dist", "hclust", "heatmap", "runif")
  importFrom("utils", "setTxtProgressBar", "str", "txtProgressBar")
to your NAMESPACE file.
mvnpermute: no visible global function definition for 'lm'
mvnpermute: no visible global function definition for 'coef'
mvnpermute: no visible global function definition for 'resid'
Undefined global functions or variables:
  coef lm resid
Consider adding
  importFrom("stats", "coef", "lm", "resid")
to your NAMESPACE file.
mvorpb: no visible global function definition for 'pnorm'
mvorpb: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm pnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm")
to your NAMESPACE file.
rtn: no visible global function definition for 'runif'
rtn: no visible global function definition for 'qnorm'
rtn: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm qnorm runif
Consider adding
  importFrom("stats", "pnorm", "qnorm", "runif")
to your NAMESPACE file.
mvtmeta_fe: no visible global function definition for 'combinations'
Undefined global functions or variables:
  combinations
'library' or 'require' call to 'RColorBrewer' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'RColorBrewer'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plot.matchedwake: no visible global function definition for
  'filled.contour'
plot.matchedwake: no visible binding for global variable 'gray.colors'
plot.matchedwake: no visible global function definition for 'axis'
plot.matchedwake: no visible global function definition for 'rect'
slideWakeMatch: no visible binding for global variable 'lm'
slideWakeMatch: no visible global function definition for 'as.formula'
slideWakeMatch: no visible global function definition for 'summary.glm'
Undefined global functions or variables:
  as.formula axis filled.contour gray.colors lm rect summary.glm
Consider adding
  importFrom("grDevices", "gray.colors")
  importFrom("graphics", "axis", "filled.contour", "rect")
  importFrom("stats", "as.formula", "lm", "summary.glm")
to your NAMESPACE file.
mxkssd: no visible global function definition for 'txtProgressBar'
mxkssd: no visible global function definition for 'setTxtProgressBar'
Undefined global functions or variables:
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
abcpred_nmer: no visible global function definition for 'write.table'
algpred: no visible global function definition for 'read.table'
algpred: no visible global function definition for 'write.table'
allermatch: no visible global function definition for 'read.table'
allermatch: no visible global function definition for 'write.table'
bcepred_nmer: no visible global function definition for 'write.table'
bimas_nmer: no visible global function definition for 'write.table'
filter.firstlayer: no visible global function definition for
  'read.table'
filter.firstlayer: no visible global function definition for
  'write.table'
iedb_arb_mhci_nmer: no visible global function definition for
  'write.table'
iedb_arb_mhcii_nmer: no visible global function definition for
  'write.table'
iedb_consensus_mhci_nmer: no visible global function definition for
  'write.table'
iedb_consensus_mhcii_nmer: no visible global function definition for
  'write.table'
netmhcNN_nmer: no visible global function definition for 'write.table'
netmhcWT_nmer: no visible global function definition for 'write.table'
propred_nmer: no visible global function definition for 'write.table'
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
update_episode: no visible global function definition for 'browseURL'
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.4Mb
    libs   1.5Mb
Running 'testthat.R' [66s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(myTAI)
  > 
  > test_check("myTAI")
  
  
  
  -- 1. Failure: PlotEnrichment() computes correct values... (@test-PlotEnrichment
  round(...) not equal to round(c(1, 1, 0.2406024, 1, 1, 0.4215795, 1), 5).
  5/7 mismatches (average diff: 0.519)
  [1] 0.525 - 1.000 == -0.475
  [3] 0.553 - 0.241 ==  0.313
  [5] 0.350 - 1.000 == -0.650
  [6] 1.000 - 0.422 ==  0.578
  [7] 0.422 - 1.000 == -0.578
  
  == testthat results  ===========================================================
  OK: 265 SKIPPED: 1 FAILED: 1
  1. Failure: PlotEnrichment() computes correct values... (@test-PlotEnrichment.R#271) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [50s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(myTAI)
  > 
  > test_check("myTAI")
  
  
  
  -- 1. Failure: PlotEnrichment() computes correct values... (@test-PlotEnrichment
  round(...) not equal to round(c(1, 1, 0.2406024, 1, 1, 0.4215795, 1), 5).
  5/7 mismatches (average diff: 0.519)
  [1] 0.525 - 1.000 == -0.475
  [3] 0.553 - 0.241 ==  0.313
  [5] 0.350 - 1.000 == -0.650
  [6] 1.000 - 0.422 ==  0.578
  [7] 0.422 - 1.000 == -0.578
  
  == testthat results  ===========================================================
  OK: 265 SKIPPED: 1 FAILED: 1
  1. Failure: PlotEnrichment() computes correct values... (@test-PlotEnrichment.R#271) 
  
  Error: testthat unit tests failed
  Execution halted
abs_dif: no visible global function definition for 'as.formula'
env_dif: no visible global function definition for 'lm'
env_dif: no visible global function definition for 'as.formula'
env_dif_logistic: no visible global function definition for
  'as.formula'
fam_env: no visible global function definition for 'as.formula'
log_dif: no visible global function definition for 'as.formula'
Undefined global functions or variables:
  as.formula lm
Consider adding
  importFrom("stats", "as.formula", "lm")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
See 'd:/Rcompile/CRANpkg/local/3.6/NanoStringNorm.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
See 'd:/Rcompile/CRANpkg/local/3.6/NAPPA.Rcheck/00install.out' for details.
NAPPA: no visible binding for global variable 'sd'
NAPPA: no visible global function definition for 'sd'
calibrate.sigmoid.curve : <anonymous> : <anonymous>: no visible global
  function definition for 'coef'
calibrate.sigmoid.curve : <anonymous> : <anonymous>: no visible global
  function definition for 'lm'
calibrate.sigmoid.curve: no visible global function definition for
  'nls'
calibrate.sigmoid.curve: no visible binding for global variable
  'weights'
calibrate.sigmoid.curve: no visible global function definition for
  'coef'
calibrate.sigmoid.curve: no visible global function definition for
  'plot'
calibrate.sigmoid.curve: no visible global function definition for
  'rgb'
calibrate.sigmoid.curve: no visible global function definition for
  'box'
calibrate.sigmoid.curve: no visible global function definition for
  'axis'
calibrate.sigmoid.curve: no visible global function definition for
  'abline'
calibrate.sigmoid.curve: no visible global function definition for
  'lines'
calibrate.sigmoid.curve: no visible global function definition for
  'predict'
calibrate.sigmoid.curve: no visible global function definition for
  'smooth.spline'
calibrate.sigmoid.curve : <anonymous>: no visible global function
  definition for 'nls'
calibrate.sigmoid.curve : <anonymous>: no visible binding for global
  variable 'weights'
calibrate.sigmoid.curve: no visible binding for global variable 'coef'
calibrate.sigmoid.curve: no visible global function definition for 'pf'
calibrate.sigmoid.curve: no visible global function definition for
  'legend'
Undefined global functions or variables:
  abline axis box coef legend lines lm nls pf plot predict rgb sd
  smooth.spline weights
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "abline", "axis", "box", "legend", "lines",
             "plot")
  importFrom("stats", "coef", "lm", "nls", "pf", "predict", "sd",
             "smooth.spline", "weights")
to your NAMESPACE file.
NB.estimator: no visible global function definition for 'optimize'
NB.estimator: no visible global function definition for 'uniroot'
NB.example.dataset: no visible global function definition for
  'write.table'
NB.plot.likelihood: no visible global function definition for 'plot'
Undefined global functions or variables:
  optimize plot uniroot write.table
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "optimize", "uniroot")
  importFrom("utils", "write.table")
to your NAMESPACE file.
ncbit : FUN: no visible global function definition for 'read.table'
ncbit : FUN: no visible global function definition for 'head'
Undefined global functions or variables:
  head read.table
Consider adding
  importFrom("utils", "head", "read.table")
to your NAMESPACE file.
get.split.filename.cmip5: no visible global function definition for
  'tail'
nc.conform.data : <anonymous>: no visible global function definition
  for 'na.omit'
nc.get.subset.recursive: no visible global function definition for
  'head'
nc.get.subset.recursive: no visible global function definition for
  'tail'
nc.put.subset.recursive: no visible global function definition for
  'head'
nc.put.subset.recursive: no visible global function definition for
  'tail'
Undefined global functions or variables:
  head na.omit tail
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
infoNcdfVars: no visible global function definition for 'na.omit'
modifyNcdfDefAtts: no visible global function definition for 'na.omit'
plotDatacube: no visible global function definition for 'runif'
plotDatacube: no visible global function definition for
  'colorRampPalette'
plotDatacube: no visible global function definition for 'dev.cur'
plotDatacube: no visible global function definition for 'dev.new'
plotDatacube: no visible global function definition for 'layout'
plotDatacube: no visible global function definition for 'par'
plotDatacube: no visible global function definition for 'points'
plotDatacube: no visible global function definition for 'text'
plotDatacube: no visible global function definition for 'plot.new'
plotDatacube: no visible global function definition for 'mtext'
plotDatacube: no visible global function definition for 'rgb'
plotDatacube: no visible global function definition for 'legend'
transNcdfRotate: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  colorRampPalette dev.cur dev.new layout legend mtext na.omit par
  plot.new points rgb runif text
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.cur", "dev.new",
             "rgb")
  importFrom("graphics", "layout", "legend", "mtext", "par", "plot.new",
             "points", "text")
  importFrom("stats", "na.omit", "runif")
to your NAMESPACE file.
d0: no visible global function definition for 'qnorm'
dncgamma: no visible global function definition for 'dpois'
indncgamma: no visible global function definition for 'pgamma'
indncgamma: no visible global function definition for 'dpois'
inxncgamma: no visible global function definition for 'qnorm'
inxncgamma: no visible global function definition for 'pgamma'
inxncgamma: no visible global function definition for 'dpois'
pncgamma: no visible global function definition for 'pgamma'
pncgamma: no visible global function definition for 'dpois'
Undefined global functions or variables:
  dpois pgamma qnorm
Consider adding
  importFrom("stats", "dpois", "pgamma", "qnorm")
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 use Fortran I/O
nor system RNGs.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
population: no visible global function definition for 'weighted.mean'
population: no visible global function definition for 'rpois'
population: no visible global function definition for 'lm'
population: no visible global function definition for 'coefficients'
population: no visible global function definition for 'sd'
population: no visible global function definition for 'par'
population: no visible global function definition for 'plot'
population: no visible global function definition for 'lines'
Undefined global functions or variables:
  coefficients lines lm par plot rpois sd weighted.mean
Consider adding
  importFrom("graphics", "lines", "par", "plot")
  importFrom("stats", "coefficients", "lm", "rpois", "sd",
             "weighted.mean")
to your NAMESPACE file.
Running examples in 'neonUtilities-Ex.R' failed
The error most likely occurred in:

> ### Name: getDatatable
> ### Title: Get NEON data table
> ### Aliases: getDatatable
> 
> ### ** Examples
> 
> sls_soilCoreCollection <- getDatatable(
+   sample_location_list = c('CPER','TALL'),
+   sample_date_min = '2014-01-01',
+   sample_date_max = '2014-06-01',
+   dpid = "DP1.10086.001",
+   data_table_name = 'sls_soilCoreCollection')
Loading required namespace: dplyr
Note: method with signature 'Timespan#Timespan' chosen for function '%/%',
 target signature 'Interval#Period'.
 "Interval#ANY", "ANY#Period" would also be valid
Warning: Expected 3 pieces. Additional pieces discarded in 534 rows [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].
Error in mapply(FUN = fn_get_available_data, data_table_name = data_table_name,  : 
  zero-length inputs cannot be mixed with those of non-zero length
Calls: getDatatable -> mapply
Execution halted
The following files look like leftovers/mistakes:
  'Rplots.pdf', 'Rplots.ps'
Please remove them from your package.
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.
netVal: no visible global function definition for 'cutree'
netVal: no visible global function definition for 'hclust'
netVal: no visible global function definition for 'as.dist'
Undefined global functions or variables:
  as.dist cutree hclust
Consider adding
  importFrom("stats", "as.dist", "cutree", "hclust")
to your NAMESPACE file.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.2Mb
EnvInd: no visible global function definition for 'sd'
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Package suggested but not available for checking: 'fastshp'
simulate.sisnetwork: no visible global function definition for 'var'
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
balloon: no visible global function definition for 'convolve'
physnoise: no visible global function definition for 'sd'
physnoise: no visible global function definition for 'rnorm'
rrice: no visible global function definition for 'rnorm'
simTSrestingstate: no visible global function definition for 'runif'
simTSrestingstate: no visible global function definition for 'fft'
spatialnoise: no visible global function definition for 'rnorm'
spatialnoise: no visible global function definition for 'qgamma'
spatialnoise: no visible global function definition for 'pnorm'
specifydesign: no visible global function definition for 'convolve'
systemnoise: no visible global function definition for 'rnorm'
tasknoise: no visible global function definition for 'rnorm'
tasknoise: no visible global function definition for 'sd'
temporalnoise: no visible global function definition for 'arima.sim'
Undefined global functions or variables:
  arima.sim convolve fft pnorm qgamma rnorm runif sd
Consider adding
  importFrom("stats", "arima.sim", "convolve", "fft", "pnorm", "qgamma",
             "rnorm", "runif", "sd")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'MASS' 'boot' 'lattice' 'psych'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
nfca : nFCAmain: no visible global function definition for 'hist'
nfca : nFCAmain: no visible global function definition for
  'flush.console'
nfca : nFCAmain: no visible global function definition for 'qnorm'
nfca : nFCAmain: no visible global function definition for 'read.csv'
nfca : nFCAmain: no visible global function definition for 'cor'
nfca : nFCAmain: no visible global function definition for 'as.dist'
nfca : nFCAmain: no visible global function definition for 'cophenetic'
nfca : nFCAmain: no visible global function definition for 'hclust'
nfca : thresholdTEST: no visible global function definition for
  'read.csv'
nfca : gScript: no visible global function definition for 'read.csv'
nfca : gScript0: no visible global function definition for 'read.csv'
nfca : gMatrix: no visible global function definition for 'read.csv'
nfca: no visible global function definition for 'cor'
Undefined global functions or variables:
  as.dist cophenetic cor flush.console hclust hist qnorm read.csv
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "as.dist", "cophenetic", "cor", "hclust", "qnorm")
  importFrom("utils", "flush.console", "read.csv")
to your NAMESPACE file.
Package suggested but not available for checking: 'NFPdata'
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
compare.CDF: no visible global function definition for 'quantile'
download.single.game: no visible global function definition for
  'download.file'
fit.shot.probs.simple: no visible global function definition for
  'predict'
integrate.old.pieces: no visible global function definition for
  'na.omit'
prob.score.simple.objects: no visible global function definition for
  'binomial'
prob.score.simple.objects: no visible binding for global variable
  'logit'
prob.score.simple.objects: no visible global function definition for
  'predict'
process.pl.new: no visible global function definition for 'na.omit'
read.gif: no visible global function definition for 'download.file'
read.gif: no visible global function definition for 'rgb'
solver.with.nlm: no visible global function definition for 'nlm'
team.table : thisplot: no visible global function definition for 'par'
team.table : thisplot: no visible global function definition for 'plot'
team.table : thisplot: no visible global function definition for 'text'
team.table : thisplot: no visible global function definition for
  'abline'
Undefined global functions or variables:
  abline binomial download.file logit na.omit nlm par plot predict
  quantile rgb text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "abline", "par", "plot", "text")
  importFrom("stats", "binomial", "na.omit", "nlm", "predict",
             "quantile")
  importFrom("utils", "download.file")
to your NAMESPACE file.
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    CppCode   2.5Mb
    R         5.7Mb
    include   5.6Mb
    libs      1.8Mb
    tests     1.5Mb
nlmeODE: no visible global function definition for 'deriv'
Undefined global functions or variables:
  deriv
Consider adding
  importFrom("stats", "deriv")
to your NAMESPACE file.
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.
Package in Depends field not imported from: 'proto'
  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:
  'stats:::nlsModel' 'stats:::nlsModel.plinear'
  See the note in ?`:::` about the use of this operator.
nls2: no visible global function definition for 'nls.control'
nls2: no visible global function definition for 'as.formula'
nls2: no visible global function definition for 'coef'
nls2: no visible global function definition for 'runif'
nls2 : <anonymous>: no visible global function definition for
  'deviance'
Undefined global functions or variables:
  as.formula coef deviance nls.control runif
Consider adding
  importFrom("stats", "as.formula", "coef", "deviance", "nls.control",
             "runif")
to your NAMESPACE file.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.2Mb
nnmf_als: no visible global function definition for 'rnorm'
nnmf_mm: no visible global function definition for 'rnorm'
nnmf_prob: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.6/NMF.Rcheck/00install.out' for details.
makeRules: no visible global function definition for 'sd'
makeRules: no visible global function definition for 'rnorm'
nodeHarvest: no visible global function definition for 'capture.output'
nodeHarvest: no visible global function definition for 'lm'
nodeHarvest: no visible global function definition for 'coef'
plot.nodeHarvest: no visible global function definition for 'rgb'
Undefined global functions or variables:
  capture.output coef lm rgb rnorm sd
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "coef", "lm", "rnorm", "sd")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'Hmisc' 'gdata' 'geometry' 'lpSolve' 'psych' 'rms'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'Hmisc' 'gdata' 'geometry' 'lpSolve' 'psych' 'pwt' 'rms'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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'
faremalm2: no visible global function definition for 'na.omit'
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'
Undefined global functions or variables:
  Lag convhulln lp na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'histogram' 'optimx'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dnormgam: no visible global function definition for 'qgamma'
dnormgam: no visible global function definition for 'fft'
dnormgam: no visible global function definition for 'dgamma'
dnormgam: no visible global function definition for 'approx'
normgam.fit : mkdfftNormalGammaOptim : <anonymous>: no visible global
  function definition for 'dnorm'
normgam.fit : estimation_param_normexp_RMA : max.density: no visible
  global function definition for 'density'
normgam.fit: no visible global function definition for 'sd'
normgam.fit: no visible global function definition for 'median'
normgam.fit: no visible global function definition for 'IQR'
normgam.fit: no visible global function definition for 'optimx'
normgam.fit: no visible global function definition for 'coef'
normgam.signal: no visible global function definition for 'approx'
normgam.signal: no visible global function definition for 'hist'
Undefined global functions or variables:
  IQR approx coef density dgamma dnorm fft hist median optimx qgamma sd
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "IQR", "approx", "coef", "density", "dgamma",
             "dnorm", "fft", "median", "qgamma", "sd")
to your NAMESPACE file.
ajb.norm.test: no visible global function definition for 'rnorm'
frosini.norm.test: no visible global function definition for 'var'
frosini.norm.test: no visible global function definition for 'pnorm'
frosini.norm.test: no visible global function definition for 'rnorm'
geary.norm.test: no visible global function definition for 'rnorm'
hegazy1.norm.test: no visible global function definition for 'var'
hegazy1.norm.test: no visible global function definition for 'qnorm'
hegazy1.norm.test: no visible global function definition for 'rnorm'
hegazy2.norm.test: no visible global function definition for 'var'
hegazy2.norm.test: no visible global function definition for 'qnorm'
hegazy2.norm.test: no visible global function definition for 'rnorm'
jb.norm.test: no visible global function definition for 'rnorm'
kurtosis.norm.test: no visible global function definition for 'rnorm'
skewness.norm.test: no visible global function definition for 'rnorm'
spiegelhalter.norm.test: no visible global function definition for
  'rnorm'
wb.norm.test: no visible global function definition for 'qnorm'
wb.norm.test: no visible global function definition for 'var'
wb.norm.test: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  pnorm qnorm rnorm var
Consider adding
  importFrom("stats", "pnorm", "qnorm", "rnorm", "var")
to your NAMESPACE file.
normality.test1: no visible global function definition for 'cov.wt'
normality.test1: no visible global function definition for 'cor'
normality.test1: no visible global function definition for 'pnorm'
normality.test1: no visible global function definition for 'pchisq'
normality.test2: no visible global function definition for 'cov.wt'
normality.test2: no visible global function definition for 'cor'
normality.test2: no visible global function definition for 'acf'
normality.test2: no visible global function definition for 'pnorm'
normality.test2: no visible global function definition for 'pchisq'
whitenoise.test: no visible global function definition for 'acf'
whitenoise.test: no visible global function definition for 'spec.pgram'
whitenoise.test: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  acf cor cov.wt pchisq pnorm spec.pgram
Consider adding
  importFrom("stats", "acf", "cor", "cov.wt", "pchisq", "pnorm",
             "spec.pgram")
to your NAMESPACE file.
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.
.newReportId : <anonymous>: no visible global function definition for
  'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'smcure' 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
NPHMC: no visible global function definition for 'integrate'
NPHMC: no visible global function definition for 'qnorm'
NPHMC: no visible global function definition for 'pnorm'
NPHMC: no visible global function definition for 'plot'
NPHMC: no visible global function definition for 'lines'
NPHMC: no visible global function definition for 'smcure'
NPHMC: no visible global function definition for 'coxph'
Undefined global functions or variables:
  coxph integrate lines plot pnorm qnorm smcure
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "integrate", "pnorm", "qnorm")
to your NAMESPACE file.
nppbib: no visible global function definition for 'read.table'
nppbib: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  pchisq read.table
Consider adding
  importFrom("stats", "pchisq")
  importFrom("utils", "read.table")
to your NAMESPACE file.
File 'NPsimex/R/onload.R':
  .onLoad calls:
    packageStartupMessage("NPsimex 0.2-1 loaded")

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

lambda.select: no visible global function definition for 'bw.nrd0'
lambda.select: no visible global function definition for 'bw.nrd'
lambda.select: no visible global function definition for 'bw.ucv'
lambda.select: no visible global function definition for 'bw.bcv'
lambda.select: no visible global function definition for 'bw.SJ'
plot.NPsimex: no visible global function definition for 'plot.default'
simex.H.density : simex1.est: no visible global function definition for
  'lm'
simex.density : simex1.est: no visible global function definition for
  'lm'
span.H.select: no visible global function definition for 'density'
span.H.select : conden : <anonymous>: no visible global function
  definition for 'dnorm'
span.select: no visible global function definition for 'density'
span.select : conden : <anonymous>: no visible global function
  definition for 'dnorm'
Undefined global functions or variables:
  bw.SJ bw.bcv bw.nrd bw.nrd0 bw.ucv density dnorm lm plot.default
Consider adding
  importFrom("graphics", "plot.default")
  importFrom("stats", "bw.SJ", "bw.bcv", "bw.nrd", "bw.nrd0", "bw.ucv",
             "density", "dnorm", "lm")
to your NAMESPACE file.
nps.test: no visible global function definition for 'qnorm'
nps.test: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
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.
npst: no visible global function definition for 'mclapply'
Undefined global functions or variables:
  mclapply
Package in Depends field not imported from: 'mco'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
boundedPolyMutation: no visible global function definition for 'runif'
boundedSBXover: no visible global function definition for 'runif'
nsga2R : <anonymous>: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
.mcmc.bar: no visible global function definition for 'rnorm'
.mcmc.bar: no visible global function definition for 'runif'
.mcmc.comb: no visible global function definition for 'rnorm'
.mcmc.comb: no visible global function definition for 'runif'
.mcmc.rd: no visible global function definition for 'rnorm'
.mcmc.rd: no visible global function definition for 'runif'
.mcmc.trans: no visible global function definition for 'rnorm'
.mcmc.trans: no visible global function definition for 'runif'
.simulate.bar: no visible global function definition for 'rlnorm'
.simulate.bar: no visible global function definition for 'rbeta'
.simulate.bar: no visible global function definition for 'rbinom'
.simulate.comb: no visible global function definition for 'rlnorm'
.simulate.comb: no visible global function definition for 'rbeta'
.simulate.comb: no visible global function definition for 'rbinom'
.simulate.rd: no visible global function definition for 'rlnorm'
.simulate.rd: no visible global function definition for 'rbinom'
.simulate.trans: no visible global function definition for 'rlnorm'
.simulate.trans: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  rbeta rbinom rlnorm rnorm runif
Consider adding
  importFrom("stats", "rbeta", "rbinom", "rlnorm", "rnorm", "runif")
to your NAMESPACE file.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs   2.5Mb
installed size is 38.9Mb
  sub-directories of 1Mb or more:
    extdata  38.9Mb
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.
'library' or 'require' call to 'methods' which was already attached by Depends.
  Please remove these calls from your code.
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.
File 'nws/R/zzz.R':
  .onLoad calls:
    require(methods)

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

blendOptions: warning in assign(names[i], new[[i]], env = options):
  partial argument match of 'env' to 'envir'
docall: warning in get(as.character(fun), env = .GlobalEnv, mode =
  "function"): partial argument match of 'env' to 'envir'
logMsg: no visible global function definition for 'flush.console'
nwsPkgInfo: no visible global function definition for
  'packageDescription'
initialize,nwsServer: no visible global function definition for
  'make.socket'
initialize,nwsServer: no visible global function definition for
  'close.socket'
Undefined global functions or variables:
  close.socket flush.console make.socket packageDescription
Consider adding
  importFrom("utils", "close.socket", "flush.console", "make.socket",
             "packageDescription")
to your NAMESPACE file.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
Malformed Title field: should not end in a period.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods' 'objectSignals'
A package should be listed in only one of these fields.
Color: no visible global function definition for 'new'
NegativeInteger: no visible global function definition for 'new'
NonnegativeInteger: no visible global function definition for 'new'
NonpositiveInteger: no visible global function definition for 'new'
PositiveInteger: no visible global function definition for 'new'
setMultipleEnum: no visible global function definition for 'setClass'
setMultipleEnum: no visible global function definition for 'prototype'
setNumericWithRange: no visible global function definition for
  'setClass'
setNumericWithRange: no visible global function definition for
  'prototype'
setPropertySet: no visible binding for global variable 'extends'
setPropertySet: no visible global function definition for 'setRefClass'
setSingleEnum: no visible global function definition for 'setClass'
setSingleEnum: no visible global function definition for 'prototype'
as.list,PropertySet: no visible global function definition for 'as'
initialize,SingleEnum: no visible global function definition for
  'callNextMethod'
initialize,SingleEnum: no visible global function definition for 'head'
Undefined global functions or variables:
  as callNextMethod extends head new prototype setClass setRefClass
Consider adding
  importFrom("methods", "as", "callNextMethod", "extends", "new",
             "prototype", "setClass", "setRefClass")
  importFrom("utils", "head")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods'
A package should be listed in only one of these fields.
Signal.gen: 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').
obliclus: no visible global function definition for 'rnorm'
obliclus: no visible global function definition for 'kmeans'
Undefined global functions or variables:
  kmeans rnorm
Consider adding
  importFrom("stats", "kmeans", "rnorm")
to your NAMESPACE file.
File 'obliclus/libs/i386/obliclus.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'random_cluster_C.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'random_cluster_C.o'
File 'obliclus/libs/x64/obliclus.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'random_cluster_C.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'random_cluster_C.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'ROCR' 'e1071' 'mda' 'pls'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
log_wrapper: no visible global function definition for 'glm'
log_wrapper: no visible global function definition for 'binomial'
log_wrapper: no visible global function definition for 'coef'
log_wrapper: no visible global function definition for 'anova'
obliqueRF.default: no visible binding for global variable 'predict'
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'
pls_wrapper: no visible global function definition for 'coef'
ridge_slow_wrapper: no visible global function definition for
  'gen.ridge'
ridge_slow_wrapper: no visible global function definition for 'predict'
ridge_svd_wrapper: no visible global function definition for
  'gen.ridge'
rnd_wrapper: no visible global function definition for 'rnorm'
svm_wrapper: no visible global function definition for 'svm'
svm_wrapper: no visible global function definition for 'predict'
Undefined global functions or variables:
  anova binomial coef gen.ridge glm kernelpls.fit performance predict
  prediction rnorm svm
Consider adding
  importFrom("stats", "anova", "binomial", "coef", "glm", "predict",
             "rnorm")
to your NAMESPACE file.
IBMD: no visible global function definition for 'runif'
IBMD: no visible global function definition for 'quantile'
RAI: no visible global function definition for 'runif'
RAI: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile runif
Consider adding
  importFrom("stats", "quantile", "runif")
to your NAMESPACE file.
obsSensCCC: no visible global function definition for 'coef'
obsSensCCC: no visible global function definition for 'confint'
obsSensCCN: no visible global function definition for 'coef'
obsSensCCN: no visible global function definition for 'confint'
obsSensCNN: no visible global function definition for 'coef'
obsSensCNN: no visible global function definition for 'confint'
obsSensCNN: no visible global function definition for 'sd'
obsSensCNN: no visible global function definition for 'model.matrix'
obsSensNNN: no visible global function definition for 'coef'
obsSensNNN: no visible global function definition for 'confint'
obsSensNNN: no visible global function definition for 'sd'
obsSensNNN: no visible global function definition for 'model.matrix'
Undefined global functions or variables:
  coef confint model.matrix sd
Consider adding
  importFrom("stats", "coef", "confint", "model.matrix", "sd")
to your NAMESPACE file.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    1.5Mb
    help   2.5Mb
    libs   2.3Mb
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.
Found the following significant warnings:
  Warning: replacing previous import 'zip::unzip' by 'utils::unzip' when loading 'officer'
See 'd:/Rcompile/CRANpkg/local/3.6/officer.Rcheck/00install.out' for details.
Running 'testthat.R' [19s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > suppressPackageStartupMessages({
  +   library(testthat)
  +   library(officer)
  +   library(magrittr)
  +   library(xml2)
  + })
  Warning message:
  replacing previous import 'zip::unzip' by 'utils::unzip' when loading 'officer' 
  > 
  > test_check("officer")
  -- 1. Failure: test filename with accent (@test-zip.R#31)  ---------------------
  "filenameäüöß.pptx" %in% list.files(tempdir(), pattern = "^filename.*\\.pptx$") isn't true.
  
  == testthat results  ===========================================================
  OK: 453 SKIPPED: 3 FAILED: 1
  1. Failure: test filename with accent (@test-zip.R#31) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following hidden files and directories:
  .Rapp.history
  data/.Rapp.history
  data/.Rhistory
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'RCurl' 'maps'
A package should be listed in only one of these fields.
mapvar: no visible global function definition for 'data'
mapvar: no visible binding for global variable 'state.fips'
mapvar: no visible global function definition for 'rgb'
mapvar: no visible global function definition for 'rect'
mapvar: no visible global function definition for 'text'
rowScrape: no visible global function definition for 'tail'
rowScrape: no visible global function definition for 'head'
scrapeTable: no visible binding for global variable 'tail'
Undefined global functions or variables:
  data head rect rgb state.fips tail text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "rect", "text")
  importFrom("utils", "data", "head", "tail")
to your NAMESPACE file.
avgokmts: no visible global function definition for 'aggregate'
downloadstn: no visible global function definition for 'read.csv'
nearstn: no visible binding for global variable 'okstations'
nearstn: no visible binding for global variable 'Commissioned'
nearstn: no visible binding for global variable 'Decommissioned'
okcurobs: no visible global function definition for 'read.csv'
okmts: no visible binding for global variable 'okstations'
okmts: no visible binding for global variable 'TIME'
retrievemts: no visible global function definition for 'read.csv'
totalprecip: no visible binding for global variable 'TIME'
totalprecip: no visible global function definition for 'aggregate'
vincenty: no visible global function definition for 'runif'
Undefined global functions or variables:
  Commissioned Decommissioned TIME aggregate okstations read.csv runif
Consider adding
  importFrom("stats", "aggregate", "runif")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
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.
fhcor: no visible global function definition for 'cor'
Undefined global functions or variables:
  cor
Consider adding
  importFrom("stats", "cor")
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.
generate.data: no visible global function definition for 'rbinom'
least.common.ancestor: no visible global function definition for
  'na.omit'
oncotree.fit : estimate.error.rates: no visible global function
  definition for 'optim'
plot.boottree: no visible global function definition for 'par'
plot.boottree: no visible global function definition for
  'dev.interactive'
plot.boottree: no visible global function definition for 'mtext'
plot.oncotree: no visible global function definition for 'par'
plot.oncotree: no visible global function definition for 'xinch'
plot.oncotree: no visible global function definition for 'yinch'
plot.oncotree: no visible global function definition for 'lines'
plot.oncotree: no visible global function definition for 'rect'
plot.oncotree: no visible global function definition for 'strwidth'
plot.oncotree: no visible global function definition for 'strheight'
plot.oncotree: no visible global function definition for 'text'
Undefined global functions or variables:
  dev.interactive lines mtext na.omit optim par rbinom rect strheight
  strwidth text xinch yinch
Consider adding
  importFrom("grDevices", "dev.interactive")
  importFrom("graphics", "lines", "mtext", "par", "rect", "strheight",
             "strwidth", "text", "xinch", "yinch")
  importFrom("stats", "na.omit", "optim", "rbinom")
to your NAMESPACE file.
ci.prop: no visible global function definition for 'qf'
ci.prop: no visible global function definition for 'qnorm'
ePCP: no visible global function definition for 'qnorm'
sevennum: no visible global function definition for 'na.omit'
sevennum: no visible global function definition for 'quantile'
Undefined global functions or variables:
  na.omit qf qnorm quantile
Consider adding
  importFrom("stats", "na.omit", "qf", "qnorm", "quantile")
to your NAMESPACE file.
Package suggested but not available for checking: 'unix'
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    R        2.5Mb
    libs     7.1Mb
    models   4.9Mb
Package suggested but not available for checking: 'openNLPmodels.en'
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   5.6Mb
Df2SpLinesDf: no visible global function definition for 'slot'
PlotTraj: no visible global function definition for 'par'
PlotTraj: no visible global function definition for 'grid'
PlotTraj: no visible global function definition for 'box'
PlotTrajFreq: no visible global function definition for 'par'
PlotTrajFreq: no visible global function definition for 'grid'
PlotTrajFreq: no visible global function definition for
  'colorRampPalette'
PlotTrajFreq: no visible global function definition for 'legend'
PlotTrajFreq: no visible binding for global variable 'title'
PlotTrajFreq: no visible global function definition for 'dev.off'
ReadFiles: no visible global function definition for 'read.table'
Undefined global functions or variables:
  box colorRampPalette dev.off grid legend par read.table slot title
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off")
  importFrom("graphics", "box", "grid", "legend", "par", "title")
  importFrom("methods", "slot")
  importFrom("utils", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
nlsolve: no visible global function definition for 'optim'
nlsolve: no visible global function definition for 'runif'
optAUC: no visible global function definition for 'var'
Undefined global functions or variables:
  optim runif var
Consider adding
  importFrom("stats", "optim", "runif", "var")
to your NAMESPACE file.
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.
calculate.empirical.AUC: no visible global function definition for
  'qnorm'
ci.AgrestiCoull: no visible global function definition for 'qnorm'
ci.GartNam: no visible global function definition for 'qnorm'
ci.NotTransformed: no visible global function definition for 'qnorm'
ci.RubinSchenker: no visible global function definition for 'qnorm'
ci.RubinSchenker: no visible global function definition for 'plogis'
ci.RubinSchenker: no visible global function definition for 'qlogis'
ci.exact: no visible global function definition for 'qf'
ci.quadratic: no visible global function definition for 'qnorm'
ci.transformed: no visible global function definition for 'qnorm'
ci.wald: no visible global function definition for 'qnorm'
function.MinPvalue: no visible global function definition for
  'chisq.test'
function.MinPvalue : PADJMS: no visible global function definition for
  'qnorm'
function.MinPvalue : PADJMS: no visible global function definition for
  'dnorm'
optimal.cutpoints.default: no visible global function definition for
  'na.omit'
optimal.cutpoints.formula: no visible global function definition for
  'terms'
plot.optimal.cutpoints: no visible global function definition for 'par'
plot.optimal.cutpoints: no visible global function definition for
  'plot'
plot.optimal.cutpoints: no visible global function definition for
  'abline'
plot.optimal.cutpoints: no visible global function definition for
  'lines'
plot.optimal.cutpoints: no visible global function definition for
  'points'
Undefined global functions or variables:
  abline chisq.test dnorm lines na.omit par plogis plot points qf
  qlogis qnorm terms
Consider adding
  importFrom("graphics", "abline", "lines", "par", "plot", "points")
  importFrom("stats", "chisq.test", "dnorm", "na.omit", "plogis", "qf",
             "qlogis", "qnorm", "terms")
to your NAMESPACE file.
Package which this enhances but not available for checking: 'gurobi'
print.optimbase: no visible global function definition for 'str'
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
to your NAMESPACE file.
calc.stress: no visible global function definition for 'sd'
opscale: no visible global function definition for 'sd'
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
getMinimumArborescence: no visible global function definition for
  'capture.output'
getMinimumCutTree: no visible global function definition for
  'capture.output'
getMinimumCutTree: no visible global function definition for 'par'
getMinimumSpanningTree: no visible global function definition for
  'capture.output'
getShortestPathTree: no visible global function definition for
  'capture.output'
Undefined global functions or variables:
  capture.output par
Consider adding
  importFrom("graphics", "par")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Agrestiind.CI: no visible global function definition for 'qnorm'
BPexact.CI: no visible global function definition for 'uniroot'
BPmidp.CI: no visible global function definition for 'uniroot'
Cornfieldexact.CI: no visible global function definition for 'uniroot'
Cornfieldmidp.CI: no visible global function definition for 'uniroot'
Gart.CI: no visible global function definition for 'qnorm'
Invsinh.CI: no visible global function definition for 'qnorm'
Woolf.CI: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  qnorm uniroot
Consider adding
  importFrom("stats", "qnorm", "uniroot")
to your NAMESPACE file.
BTLboost: no visible global function definition for 'as.formula'
design: no visible global function definition for 'as.formula'
wide2long: no visible global function definition for 'reshape'
Undefined global functions or variables:
  as.formula reshape
Consider adding
  importFrom("stats", "as.formula", "reshape")
to your NAMESPACE file.
'library' or 'require' call to 'psych' which was already attached by Depends.
  Please remove these calls from your code.
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of 'nr' to 'nrow'
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of 'nc' to 'ncol'
bgmm: no visible global function definition for 'ecdf'
bgmm : SplineGMM: no visible global function definition for
  'constrOptim'
blr: no visible global function definition for 'ecdf'
blr: no visible global function definition for 'constrOptim'
blr: no visible global function definition for 'lm'
parentcdf : combinations: no visible global function definition for
  'combn'
parentcdf : solver: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  combn constrOptim ecdf lm uniroot
Consider adding
  importFrom("stats", "constrOptim", "ecdf", "lm", "uniroot")
  importFrom("utils", "combn")
to your NAMESPACE file.
'library' or 'require' call to 'methods' which was already attached by Depends.
  Please remove these calls from your code.
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.
Running 'anova.R' [3s]
  Running 'clm.fit.R' [3s]
  Running 'clm.formula.R' [4s]
  Running 'clmm.R' [10s]
  Running 'clmm.control.R' [3s]
  Running 'clmm.formula.R' [5s]
  Running 'confint.R' [5s]
  Running 'nominal.test.R' [8s]
  Running 'test-all.R' [25s]
  Running 'test.clm.Theta.R' [5s]
  Running 'test.clm.convergence.R' [3s]
  Running 'test.clm.flex.link.R' [4s]
  Running 'test.clm.model.matrix.R' [3s]
  Running 'test.clm.predict.R' [3s]
  Running 'test.clm.profile.R' [3s]
  Running 'test.clm.single.anova.R' [4s]
  Running 'test.general.R' [1s]
  Running 'test.makeThresholds.R' [3s]
  Running 'test.sign.R' [4s]
  Running 'test0weights.R' [5s]
  Running 'testAnova.clm2.R' [4s]
  Running 'testCLM.R' [5s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > 
  > if(require(testthat) && require(ordinal)) {
  +     test_check("ordinal")
  + }
  Loading required package: testthat
  Loading required package: ordinal
  -- 1. Failure: clm gives contrast warnings when it should (@test-contrasts.R#11)
  givesWarnings(...) isn't false.
  
  -- 2. Failure: clm gives contrast warnings when it should (@test-contrasts.R#15)
  givesWarnings(...) isn't false.
  
  -- 3. Failure: clm gives contrast warnings when it should (@test-contrasts.R#19)
  givesWarnings(...) isn't false.
  
  -- 4. Failure: clm gives contrast warnings when it should (@test-contrasts.R#23)
  givesWarnings(...) isn't false.
  
  == testthat results  ===========================================================
  OK: 80 SKIPPED: 0 FAILED: 4
  1. Failure: clm gives contrast warnings when it should (@test-contrasts.R#11) 
  2. Failure: clm gives contrast warnings when it should (@test-contrasts.R#15) 
  3. Failure: clm gives contrast warnings when it should (@test-contrasts.R#19) 
  4. Failure: clm gives contrast warnings when it should (@test-contrasts.R#23) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'anova.R' [4s]
  Running 'clm.fit.R' [4s]
  Running 'clm.formula.R' [4s]
  Running 'clmm.R' [10s]
  Running 'clmm.control.R' [3s]
  Running 'clmm.formula.R' [5s]
  Running 'confint.R' [6s]
  Running 'nominal.test.R' [7s]
  Running 'test-all.R' [27s]
  Running 'test.clm.Theta.R' [5s]
  Running 'test.clm.convergence.R' [3s]
  Running 'test.clm.flex.link.R' [4s]
  Running 'test.clm.model.matrix.R' [4s]
  Running 'test.clm.predict.R' [4s]
  Running 'test.clm.profile.R' [4s]
  Running 'test.clm.single.anova.R' [4s]
  Running 'test.general.R' [1s]
  Running 'test.makeThresholds.R' [3s]
  Running 'test.sign.R' [4s]
  Running 'test0weights.R' [5s]
  Running 'testAnova.clm2.R' [4s]
  Running 'testCLM.R' [5s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > 
  > if(require(testthat) && require(ordinal)) {
  +     test_check("ordinal")
  + }
  Loading required package: testthat
  Loading required package: ordinal
  -- 1. Failure: clm gives contrast warnings when it should (@test-contrasts.R#11)
  givesWarnings(...) isn't false.
  
  -- 2. Failure: clm gives contrast warnings when it should (@test-contrasts.R#15)
  givesWarnings(...) isn't false.
  
  -- 3. Failure: clm gives contrast warnings when it should (@test-contrasts.R#19)
  givesWarnings(...) isn't false.
  
  -- 4. Failure: clm gives contrast warnings when it should (@test-contrasts.R#23)
  givesWarnings(...) isn't false.
  
  == testthat results  ===========================================================
  OK: 80 SKIPPED: 0 FAILED: 4
  1. Failure: clm gives contrast warnings when it should (@test-contrasts.R#11) 
  2. Failure: clm gives contrast warnings when it should (@test-contrasts.R#15) 
  3. Failure: clm gives contrast warnings when it should (@test-contrasts.R#19) 
  4. Failure: clm gives contrast warnings when it should (@test-contrasts.R#23) 
  
  Error: testthat unit tests failed
  Execution halted
genRidge: no visible global function definition for 'plogis'
ordGene: no visible global function definition for 'anova'
ordGene: no visible global function definition for 'lm'
ordSelect: no visible binding for global variable 'sd'
ordSmooth: no visible binding for global variable 'sd'
plot.ordPen: no visible global function definition for 'grey'
plot.ordPen: no visible global function definition for 'devAskNewPage'
plot.ordPen: no visible global function definition for 'plot'
plot.ordPen: no visible global function definition for 'lines'
predict.ordPen: no visible global function definition for 'plogis'
Undefined global functions or variables:
  anova devAskNewPage grey lines lm plogis plot sd
Consider adding
  importFrom("grDevices", "devAskNewPage", "grey")
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "anova", "lm", "plogis", "sd")
to your NAMESPACE file.
ORICC1: no visible binding for global variable 'sd'
ORICC1: no visible global function definition for 'write.table'
ORICC1: no visible global function definition for 'postscript'
ORICC1: no visible global function definition for 'jpeg'
ORICC1: no visible global function definition for 'plot'
ORICC1: no visible global function definition for 'points'
ORICC1: no visible global function definition for 'dev.off'
ORICC1: no visible global function definition for 'par'
ORICC2: no visible binding for global variable 'sd'
ORICC2: no visible global function definition for 'write.table'
ORICC2: no visible global function definition for 'postscript'
ORICC2: no visible global function definition for 'jpeg'
ORICC2: no visible global function definition for 'plot'
ORICC2: no visible global function definition for 'points'
ORICC2: no visible global function definition for 'dev.off'
ORICC2: no visible global function definition for 'par'
Undefined global functions or variables:
  dev.off jpeg par plot points postscript sd write.table
Consider adding
  importFrom("grDevices", "dev.off", "jpeg", "postscript")
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
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.
Running 'testthat.R' [28s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(origami)
  origami: Generalized Cross-Validation Framework
  Version: 1.0.0
  > library(data.table)
  > test_check("origami")
  -- 1. Failure: CV MSE matches previous value (@test-overall.R#36)  -------------
  `cv_MSE` not equal to 13.32.
  1/1 mismatches
  [1] 14.1 - 13.3 == 0.791
  
  == testthat results  ===========================================================
  OK: 33 SKIPPED: 1 FAILED: 1
  1. Failure: CV MSE matches previous value (@test-overall.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
File 'OriGen/libs/i386/OriGen.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'OriGen.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'OriGen.o'
File 'OriGen/libs/x64/OriGen.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'OriGen.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'OriGen.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
mdr.c: no visible global function definition for 'combn'
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
dicomTable: no visible global function definition for 'txtProgressBar'
dicomTable: no visible global function definition for
  'setTxtProgressBar'
readDICOM: no visible global function definition for 'txtProgressBar'
readDICOM: no visible global function definition for
  'setTxtProgressBar'
writeHeader: no visible global function definition for 'write.table'
Undefined global functions or variables:
  setTxtProgressBar txtProgressBar write.table
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar",
             "write.table")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'Rcpp' 'genefilter' 'gtools' 'nlme'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
est.lme : <anonymous>: warning in rank(iru, ties = "min"): partial
  argument match of 'ties' to 'ties.method'
est.lme : <anonymous>: no visible global function definition for 'lme'
est.lme : <anonymous>: no visible global function definition for
  'VarCorr'
guo: no visible global function definition for 'p.adjust'
guo: no visible global function definition for 'na.omit'
pttest : ptest: no visible global function definition for 'na.omit'
srt : <anonymous>: no visible global function definition for
  'rowttests'
Undefined global functions or variables:
  VarCorr lme na.omit p.adjust rowttests
Consider adding
  importFrom("stats", "na.omit", "p.adjust")
to your NAMESPACE file.
plot.SplineBasis: no visible global function definition for 'matplot'
plot,SplineBasis-matrix: no visible global function definition for
  'matplot'
plot,SplineBasis-missing: no visible global function definition for
  'matplot'
Undefined global functions or variables:
  matplot
Consider adding
  importFrom("graphics", "matplot")
to your NAMESPACE file.
'library' or 'require' call to 'polynom' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'polynom'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.derivatives: no visible global function definition for
  'deriv'
polynomial.integrals: no visible global function definition for
  'integral'
polynomial.values: no visible global function definition for 'predict'
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'
Undefined global functions or variables:
  deriv integral polynomial predict
Consider adding
  importFrom("stats", "deriv", "predict")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'igraph' 'sp'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
as_igraph : <anonymous>: no visible global function definition for
  'distHaversine'
as_igraph: no visible global function definition for 'graph.edgelist'
as_igraph: no visible global function definition for 'E'
as_igraph: no visible global function definition for 'E<-'
as_sp_lines: no visible global function definition for 'Lines'
as_sp_points: no visible global function definition for
  'SpatialPointsDataFrame'
as_sp_polygons: no visible global function definition for 'Polygons'
as_sp_polygons: no visible global function definition for
  'SpatialPolygons'
as_sp_polygons: no visible global function definition for
  'SpatialPolygonsDataFrame'
make_SLDF: no visible global function definition for 'SpatialLines'
make_SLDF: no visible global function definition for
  'SpatialLinesDataFrame'
osm_crs: no visible global function definition for 'CRS'
plot.osmar: no visible global function definition for 'gray'
plot_nodes: no visible global function definition for 'points'
plot_nodes: no visible global function definition for 'plot'
plot_ways: no visible global function definition for 'plot'
plot_ways: no visible global function definition for 'lines'
ways_nodes2Line: no visible global function definition for 'Line'
ways_nodes2Polygon: no visible global function definition for 'Polygon'
Undefined global functions or variables:
  CRS E E<- Line Lines Polygon Polygons SpatialLines
  SpatialLinesDataFrame SpatialPointsDataFrame SpatialPolygons
  SpatialPolygonsDataFrame distHaversine graph.edgelist gray lines plot
  points
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "lines", "plot", "points")
to your NAMESPACE file.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
Package suggested but not available for checking: 'Rcplex'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   1.8Mb
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/OutliersO3.Rcheck/00install.out' for details.
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.
loadCSVtoP2distance: no visible global function definition for
  'read.table'
p2distance : calcularDistancia: no visible binding for global variable
  'sd'
p2distance : ordenarVariables: no visible global function definition
  for 'cor'
p2distance : calculoFactoresPonderacion: no visible global function
  definition for 'lm'
p2distance: no visible global function definition for 'cor'
Undefined global functions or variables:
  cor lm read.table sd
Consider adding
  importFrom("stats", "cor", "lm", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'library' or 'require' call to 'survival' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
p3state: no visible global function definition for 'survfit'
p3state: no visible global function definition for 'terms'
p3state: no visible global function definition for 'as.formula'
p3state: no visible global function definition for 'coxph'
p3state: no visible binding for global variable 'na.exclude'
plot.p3state: no visible global function definition for 'matplot'
plot.p3state: no visible global function definition for 'devAskNewPage'
plot.p3state: no visible global function definition for 'persp'
plot.p3state: no visible global function definition for 'colours'
plot.p3state: no visible global function definition for
  'filled.contour'
Undefined global functions or variables:
  as.formula colours coxph devAskNewPage filled.contour matplot
  na.exclude persp survfit terms
Consider adding
  importFrom("grDevices", "colours", "devAskNewPage")
  importFrom("graphics", "filled.contour", "matplot", "persp")
  importFrom("stats", "as.formula", "na.exclude", "terms")
to your NAMESPACE file.
pacbpred : thetaFunc: no visible global function definition for 'lsfit'
pacbpred : thetaFunc: no visible global function definition for 'rnorm'
pacbpred: no visible global function definition for 'var'
pacbpred: no visible global function definition for 'runif'
pacbpred: no visible global function definition for 'rnorm'
pacbpred: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  lsfit rbinom rnorm runif var
Consider adding
  importFrom("stats", "lsfit", "rbinom", "rnorm", "runif", "var")
to your NAMESPACE file.
Running 'testthat_chi2.R' [5s]
  Running 'testthat_extractSubTree.R' [21s]
  Running 'testthat_pacotestRegressionTests.R' [6s]
  Running 'testthat_pacotestRvineSeqRegressionTests.R' [59s]
  Running 'testthat_pacotestRvineSingleCopulaRegressionTests.R' [187s]
Running the tests in 'tests/testthat_pacotestRvineSeqRegressionTests.R' failed.
Complete output:
  > 
  > library("testthat")
  > library("pacotest")
  > 
  > test_check("pacotest", filter = "pacotestRvineSeqRegressionTests")
  -- 1. Failure: pacotestRvineSeq7 (@test-pacotestRvineSeqRegressionTests.R#194)  
  resPacotestComputed[iTest, 1:3] not equal to hardCodedResPacotestRvineSeq[iTest, 1:3].
  1/3 mismatches
  [2] 0.768 - 0.755 == 0.013
  
  == testthat results  ===========================================================
  OK: 4 SKIPPED: 5 FAILED: 1
  1. Failure: pacotestRvineSeq7 (@test-pacotestRvineSeqRegressionTests.R#194) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat_chi2.R' [5s]
  Running 'testthat_extractSubTree.R' [20s]
  Running 'testthat_pacotestRegressionTests.R' [6s]
  Running 'testthat_pacotestRvineSeqRegressionTests.R' [60s]
  Running 'testthat_pacotestRvineSingleCopulaRegressionTests.R' [184s]
Running the tests in 'tests/testthat_pacotestRvineSeqRegressionTests.R' failed.
Complete output:
  > 
  > library("testthat")
  > library("pacotest")
  > 
  > test_check("pacotest", filter = "pacotestRvineSeqRegressionTests")
  -- 1. Failure: pacotestRvineSeq7 (@test-pacotestRvineSeqRegressionTests.R#194)  
  resPacotestComputed[iTest, 1:3] not equal to hardCodedResPacotestRvineSeq[iTest, 1:3].
  1/3 mismatches
  [2] 0.768 - 0.755 == 0.013
  
  == testthat results  ===========================================================
  OK: 4 SKIPPED: 5 FAILED: 1
  1. Failure: pacotestRvineSeq7 (@test-pacotestRvineSeqRegressionTests.R#194) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(padr)
  > 
  > test_check("padr")
  -- 1. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#
  fill_by_function(x_df, y1)$y1 %>% median not equal to 14.77.
  1/1 mismatches
  [1] 14.8 - 14.8 == 0.04
  
  -- 2. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#
  fill_by_function(x_df, y1, y2)$y1 %>% median not equal to 14.77.
  1/1 mismatches
  [1] 14.8 - 14.8 == 0.04
  
  -- 3. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#
  fill_by_function(x_df, y1, y2)$y2 %>% median not equal to 22.765.
  1/1 mismatches
  [1] 25.3 - 22.8 == 2.5
  
  -- 4. Failure: fill_by_prevalent gives expected outcomes (@test_fill_functions.R
  `fill_by_prevalent(x_df, y1)` did not throw an error.
  
  == testthat results  ===========================================================
  OK: 584 SKIPPED: 1 FAILED: 4
  1. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#36) 
  2. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#37) 
  3. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#38) 
  4. Failure: fill_by_prevalent gives expected outcomes (@test_fill_functions.R#48) 
  
  Error: testthat unit tests failed
  Execution halted
paf: no visible global function definition for 'as.formula'
paf: no visible global function definition for 'model.response'
paf: no visible global function definition for 'model.frame'
paf: no visible global function definition for 'model.matrix'
plot.paf: no visible global function definition for 'plot'
plot.paf: no visible global function definition for 'lines'
Undefined global functions or variables:
  as.formula lines model.frame model.matrix model.response plot
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response")
to your NAMESPACE file.
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.
paired.Loc: no visible global function definition for 'qt'
paired.Loc: no visible global function definition for 'median'
paired.Loc: no visible global function definition for 'qsignrank'
paired.Loc: no visible global function definition for 'qnorm'
paired.Scale: no visible global function definition for 'var'
paired.Scale: no visible global function definition for 'cor'
paired.Scale: no visible global function definition for 'qt'
paired.Scale: no visible global function definition for 'median'
paired.Scale: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  cor median qnorm qsignrank qt var
Consider adding
  importFrom("stats", "cor", "median", "qnorm", "qsignrank", "qt", "var")
to your NAMESPACE file.
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 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(palasso)
  > 
  > testthat::test_check("palasso")
  -- 1. Failure: deviance stats (@test.R#146)  -----------------------------------
  `x` isn't true.
  
  -- 2. Error: coef stats (@test.R#126)  -----------------------------------------
  attempt to select less than one element in get1index
  1: coef(fit, model = "standard_xz", s = 0) at testthat/test.R:126
  2: coef.palasso(fit, model = "standard_xz", s = 0)
  3: subset.palasso(x = object, model = model, max = max)
  
  -- 3. Error: deviance stats (@test.R#142)  -------------------------------------
  attempt to select less than one element in get1index
  1: deviance(fit, model = "standard_xz") at testthat/test.R:142
  2: deviance.palasso(fit, model = "standard_xz")
  3: subset.palasso(x = object, model = model, max = max)
  
  -- 4. Error: logLik stats (@test.R#150)  ---------------------------------------
  attempt to select less than one element in get1index
  1: logLik(fit, model = "standard_xz") at testthat/test.R:150
  2: logLik.palasso(fit, model = "standard_xz")
  3: subset.palasso(x = object, model = model, max = max)
  
  == testthat results  ===========================================================
  OK: 2107 SKIPPED: 2 FAILED: 4
  1. Failure: deviance stats (@test.R#146) 
  2. Error: coef stats (@test.R#126) 
  3. Error: deviance stats (@test.R#142) 
  4. Error: logLik stats (@test.R#150) 
  
  Error: testthat unit tests failed
  Execution halted
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'lattice' 'vegan'
  Please remove these calls from your code.
EAMM: no visible global function definition for 'anova'
PAMM: no visible global function definition for 'anova'
SSF: no visible global function definition for 'anova'
Undefined global functions or variables:
  anova
Consider adding
  importFrom("stats", "anova")
to your NAMESPACE file.
GOpredict: no visible global function definition for 'fisher.test'
KEGGpredict: no visible global function definition for 'fisher.test'
ProteinCluster: no visible global function definition for 'ecdf'
ProteinCluster: no visible global function definition for 'as.hclust'
ProteinCluster: no visible global function definition for
  'as.dendrogram'
ProteinCluster : addE: no visible global function definition for
  'is.leaf'
ProteinCluster: no visible global function definition for 'plot'
SignificantSubcluster: no visible global function definition for
  'order.dendrogram'
SignificantSubcluster: no visible global function definition for
  'fisher.test'
SignificantSubcluster: no visible global function definition for 'plot'
Undefined global functions or variables:
  as.dendrogram as.hclust ecdf fisher.test is.leaf order.dendrogram
  plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "as.dendrogram", "as.hclust", "ecdf",
             "fisher.test", "is.leaf", "order.dendrogram")
to your NAMESPACE file.
Paneldata.formula: no visible global function definition for
  'model.frame'
Paneldata.formula: no visible global function definition for
  'model.matrix'
Paneldata.formula: no visible global function definition for
  'model.response'
summary.Paneldata: no visible global function definition for 'coef'
summary.Paneldata: no visible global function definition for 'pt'
Undefined global functions or variables:
  coef model.frame model.matrix model.response pt
Consider adding
  importFrom("stats", "coef", "model.frame", "model.matrix",
             "model.response", "pt")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from 'parallelize.dynamic' for: 'initialize'

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

Probably some imports need to be declared in the NAMESPACE file.
'library' or 'require' call to 'package' 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:
  'methods' 'parallel' 'tools'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
consensusMCcov: no visible global function definition for 'var'
consensusMCcov: no visible global function definition for 'cov'
consensusMCindep: no visible global function definition for 'var'
semiparamDPE: no visible binding for global variable 'var'
semiparamDPE: no visible global function definition for 'cov'
semiparamDPE: no visible global function definition for 'runif'
Undefined global functions or variables:
  cov runif var
Consider adding
  importFrom("stats", "cov", "runif", "var")
to your NAMESPACE file.
parallelSVM.default: no visible binding for global variable 'na.omit'
parallelSVM.formula: no visible binding for global variable 'na.omit'
predict.parallelSVM: no visible binding for global variable 'predict'
Undefined global functions or variables:
  na.omit predict
Consider adding
  importFrom("stats", "na.omit", "predict")
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.
adalasso: no visible global function definition for 'predict'
lm.ridge.univariate: no visible global function definition for 'sd'
mylars: no visible global function definition for 'predict'
mylars: no visible binding for global variable 'var'
performance.pcor: no visible global function definition for
  'ggm.test.edges'
performance.pcor: no visible global function definition for 'var'
ridge.cv: no visible global function definition for 'coef'
ridge.cv: no visible global function definition for 'plot'
Undefined global functions or variables:
  coef ggm.test.edges plot predict sd var
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "coef", "predict", "sd", "var")
to your NAMESPACE file.
ParentOffspring: no visible global function definition for 'axis'
ParentOffspring: no visible global function definition for 'abline'
ParentOffspring: no visible global function definition for 'title'
ParentOffspring: no visible global function definition for 'box'
Undefined global functions or variables:
  abline axis box title
Consider adding
  importFrom("graphics", "abline", "axis", "box", "title")
to your NAMESPACE file.
par.nmds : nmdscalc: no visible global function definition for 'runif'
par.nmds : nmdscalc: no visible global function definition for 'dist'
par.nmds: no visible binding for global variable 'j'
par.nmds: no visible global function definition for 'cor'
par.nmds: no visible global function definition for 'dist'
par.spp.est: no visible binding for global variable 'i'
par.spp.est: no visible global function definition for 'sd'
Undefined global functions or variables:
  cor dist i j runif sd
Consider adding
  importFrom("stats", "cor", "dist", "runif", "sd")
to your NAMESPACE file.
Package in Depends field not imported from: 'nnet'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fitOR: no visible global function definition for 'multinom'
fitOR: no visible global function definition for 'formula'
fitOR: no visible global function definition for 'coef'
fitOR: no visible global function definition for 'optim'
reportOR: no visible global function definition for 'qnorm'
reportOR: no visible global function definition for 'pchisq'
reportOR: no visible global function definition for 'coef'
simData: no visible global function definition for 'rnorm'
simData: no visible global function definition for 'runif'
Undefined global functions or variables:
  coef formula multinom optim pchisq qnorm rnorm runif
Consider adding
  importFrom("stats", "coef", "formula", "optim", "pchisq", "qnorm",
             "rnorm", "runif")
to your NAMESPACE file.
partitionMap: no visible global function definition for 'predict'
partitionMap: no visible global function definition for 'rnorm'
partitionMap: no visible binding for global variable 'sd'
partitionMap: no visible global function definition for 'sd'
partitionMap: no visible global function definition for 'quantile'
Undefined global functions or variables:
  predict quantile rnorm sd
Consider adding
  importFrom("stats", "predict", "quantile", "rnorm", "sd")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from 'partsm' 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.
parviol: no visible global function definition for 'plot.new'
parviol: no visible global function definition for 'plot.window'
parviol: no visible global function definition for 'title'
parviol: no visible global function definition for 'lines'
parviol: no visible global function definition for 'text'
parviol: no visible global function definition for 'rgb'
selecto: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines plot.new plot.window rgb text title
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "plot.new", "plot.window", "text",
             "title")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'ape' 'caper'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
conch: no visible global function definition for 'read.tree'
conch: no visible global function definition for 'reorder'
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'
pastis_main: no visible global function definition for 'combn'
read_input: no visible global function definition for 'read.tree'
read_input: no visible global function definition for 'reorder'
read_input: no visible global function definition for 'read.csv'
read_input: no visible global function definition for 'read.dna'
Undefined global functions or variables:
  .compressTipLabel combn drop.tip extract.clade read.csv read.dna
  read.nexus read.tree reorder which.edge write.tree
Consider adding
  importFrom("stats", "reorder")
  importFrom("utils", "combn", "read.csv")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'e1071'
  Please remove these calls from your code.
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: 'datautils'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
animatePatches: no visible global function definition for
  'getTimestamp'
animatePatches: no visible global function definition for 'getElapsed'
colorPlot: no visible global function definition for 'layout'
colorPlot: no visible global function definition for 'par'
colorPlot: no visible global function definition for 'image'
colorPlot: no visible global function definition for 'axis'
drawPatches: no visible global function definition for 'rgb'
getInterRGB: no visible global function definition for 'col2rgb'
getInterRGB: no visible global function definition for 'rgb'
plotGmmOverlay: no visible global function definition for 'rgb'
plotGreyPatches : squarepatch: no visible global function definition
  for 'rgb'
plotGreyPatches : trianglepatch: no visible global function definition
  for 'rgb'
Undefined global functions or variables:
  axis col2rgb getElapsed getTimestamp image layout par rgb
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
  importFrom("graphics", "axis", "image", "layout", "par")
to your NAMESPACE file.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
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.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    data      2.5Mb
    doc       1.3Mb
    extdata   9.5Mb
Packages in Depends field not imported from:
  'plspm' 'tester'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > std_getwd <- function() 
  + {
  +   pwd <- getwd()
  +   # Enforce upper case Windows drive letters
  +   substring(pwd, 1, 1) <- toupper(substring(pwd, 1, 1))
  +   pwd
  + }
  > 
  > test_check("pathological")
  Loading required package: pathological
  -- 1. Failure: decompose_path handles paths with a unicode directory name. (@tes
  actual$dirname not equal to expected$dirname.
  1/1 mismatches
  x[1]: "D:/Rcompile/CRANpkg/local/3.6/pathological.Rcheck/tests/testthat/CRAN"
  y[1]: "D:/Rcompile/CRANpkg/local/3.6/pathological.Rcheck/tests/testthat/CRAN"
  
  -- 2. Failure: standardize_path works with missing files with ./ prefix (@test_s
  standardize_path(x) not equal to `expected`.
  1/2 mismatches
  x[1]: "D:/RCompile/CRANpkg/local/3.6/pathological.Rcheck/tests/testthat/test_dec
  x[1]: ompose_path.R"
  y[1]: "D:/Rcompile/CRANpkg/local/3.6/pathological.Rcheck/tests/testthat/test_dec
  y[1]: ompose_path.R"
  
  == testthat results  ===========================================================
  OK: 186 SKIPPED: 18 FAILED: 2
  1. Failure: decompose_path handles paths with a unicode directory name. (@test_decompose_path.R#466) 
  2. 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.
Not exits: C:/Program Files/netCDF 4.3.2
Not exits: C:/Program Files/netCDF 4.3.2/bin
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/msvcp100.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/msvcr100.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/zlib.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/hdf5.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/hdf5_hl.dll
Not exits: C:/Program Files/netCDF 4.3.2/bin/netcdf.dll
===== WARNING =====
- netCDF 4.3.2 may not install at compile time.
- Environment variables may not be correct at compile and run time.
- pbdNCDF4 binary may not link with netCDF.
- Please consider to rebuild from source.
===================
Not exits: C:/Program Files/netCDF 4.3.2
Not exits: C:/Program Files/netCDF 4.3.2/bin
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/msvcp100.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/msvcr100.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/zlib.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/hdf5.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/hdf5_hl.dll
Not exits: C:/Program Files/netCDF 4.3.2/bin/netcdf.dll
===== WARNING =====
- netCDF 4.3.2 may not install at compile time.
- Environment variables may not be correct at compile and run time.
- pbdNCDF4 binary may not link with netCDF.
- Please consider to rebuild from source.
===================
get.sysenv: no visible global function definition for 'shortPathName'
Undefined global functions or variables:
  shortPathName
Consider adding
  importFrom("utils", "shortPathName")
to your NAMESPACE file.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    lib    6.6Mb
    libs   5.3Mb
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.
a_get_native: no visible global function definition for 'par'
a_get_relative: no visible global function definition for 'par'
brackets: no visible global function definition for 'par'
brackets: no visible global function definition for 'dist'
brackets: no visible global function definition for 'lines'
Undefined global functions or variables:
  dist lines par
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "dist")
to your NAMESPACE file.
.win.appendLog: no visible binding for global variable 'lines'
plotMC : panel: no visible global function definition for 'points'
plotMC: no visible global function definition for 'pairs'
plotMC: no visible global function definition for 'mtext'
plotMC: no visible global function definition for 'axis'
plotMC: no visible global function definition for 'par'
readADpaths: no visible global function definition for 'read.table'
readRep: no visible global function definition for 'read.table'
saveADpaths: no visible global function definition for 'write.table'
Undefined global functions or variables:
  axis lines mtext pairs par points read.table write.table
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "pairs", "par",
             "points")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.4Mb
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  7.1Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   2.7Mb
    libs      1.8Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.1Mb
    libs   2.3Mb
Running examples in 'pcalg-Ex.R' failed
The error most likely occurred in:

> ### Name: backdoor
> ### Title: Find Set Satisfying the Generalized Backdoor Criterion (GBC)
> ### Aliases: backdoor
> ### Keywords: multivariate models graphs
> 
> ### ** Examples
> 
> #####################################################################
> ##DAG
> #####################################################################
> ## Simulate the true DAG
> set.seed(123)
> p <- 7
> myDAG <- randomDAG(p, prob = 0.2) ## true DAG
> 
> ## Extract the adjacency matrix of the true DAG
> true.amat <- (amat <- as(myDAG, "matrix")) != 0 # TRUE/FALSE <==> 1/0
> print.table(1*true.amat, zero.=".") # "visualization"
  1 2 3 4 5 6 7
1 . . . 1 . . .
2 . . . 1 . . 1
3 . . . . . . 1
4 . . . . 1 . .
5 . . . . . . 1
6 . . . . . . .
7 . . . . . . .
> 
> ## Compute set satisfying the GBC:
> backdoor(true.amat, 5, 7, type="dag")
[1] 4
> ## Don't show: 
> stopifnot(backdoor(true.amat, 5, 7, type="dag") == 3)
Error: backdoor(true.amat, 5, 7, type = "dag") == 3 is not TRUE
Execution halted
PCDReg.wf: no visible global function definition for 'optimize'
Undefined global functions or variables:
  optimize
Consider adding
  importFrom("stats", "optimize")
to your NAMESPACE file.
defineTasks: no visible global function definition for 'par'
defineTasks: no visible global function definition for 'abline'
plotCorCoeff: no visible global function definition for 'hist'
plotCorCoeff: no visible global function definition for 'plot.new'
plotCorCoeff: no visible global function definition for 'plot.window'
plotCorCoeff: no visible global function definition for 'rect'
plotCorCoeff: no visible global function definition for 'axis'
plotCorCoeff: no visible global function definition for 'title'
plotCorCoeff: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline axis hist legend par plot.new plot.window rect title
Consider adding
  importFrom("graphics", "abline", "axis", "hist", "legend", "par",
             "plot.new", "plot.window", "rect", "title")
to your NAMESPACE file.
Running examples in 'pcnetmeta-Ex.R' failed
The error most likely occurred in:

> ### Name: absolute.plot
> ### Title: Plotting Treatment-Specific 95% Credible Intervals
> ### Aliases: absolute.plot
> 
> ### ** Examples
> 
> data(smoke)
> # increase n.iter to reach convergence
> # increase n.adapt to enhance efficiency
> set.seed(1234)
> nma.out <- nma.ab.bin(s.id, t.id, r, n, data = smoke,
+   trtname = c("NC", "SH", "IC", "GC"), param= "AR",
+   model = "het_cor", n.adapt = 400, n.iter = 100, n.chains = 1)
Start running MCMC...
Compiling model graph
   Resolving undeclared variables
   Allocating nodes
Graph information:
   Observed stochastic nodes: 50
   Unobserved stochastic nodes: 29
   Total graph size: 611

Initializing model

> absolute.plot(nma.out)
The absolute plot is saved in your working directory:
d:/Rcompile/CRANpkg/local/3.6/pcnetmeta.Rcheck
> absolute.plot(nma.out, alphabetic = FALSE)
The absolute plot is saved in your working directory:
d:/Rcompile/CRANpkg/local/3.6/pcnetmeta.Rcheck
> 
> 
> 
> cleanEx()
Error: connections left open:
	modelstring (textConnection)
Execution halted
PdofCSGt.bootstrap5: no visible global function definition for 'rnorm'
PdofCSGt.bootstrap5: no visible global function definition for 'rt'
PdofCSt.T1or2: no visible global function definition for 'combn'
PofCSGt: no visible global function definition for 'combn'
PofCSLt.bootstrap5: no visible global function definition for 'rnorm'
PofCSLt.bootstrap5: no visible global function definition for 'rt'
PofCSt: no visible global function definition for 'pnorm'
tindep: no visible binding for global variable 'var'
tindep: no visible global function definition for 'pt'
Undefined global functions or variables:
  combn pnorm pt rnorm rt var
Consider adding
  importFrom("stats", "pnorm", "pt", "rnorm", "rt", "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    libs   13.3Mb
    share  11.9Mb
pdist: no visible global function definition for 'dist'
pdist: no visible global function definition for 'new'
Undefined global functions or variables:
  dist new
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "dist")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
band.chol.cv: no visible global function definition for 'cov'
pdsoft.cv: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
Package suggested but not available for checking: 'faahKO'
peacf: no visible global function definition for 'is.ts'
peacf: no visible global function definition for 'cycle'
peacf: no visible global function definition for 'ts.intersect'
peacf: no visible global function definition for 'lag'
peacf: no visible global function definition for 'ts'
peacf: no visible global function definition for 'pchisq'
peacf.plot: no visible global function definition for 'plot'
peacf.plot: no visible global function definition for 'segments'
peacf.plot: no visible global function definition for 'title'
pear: no visible global function definition for 'cycle'
pear: no visible global function definition for 'pchisq'
peboxplot: no visible global function definition for 'cycle'
peboxplot: no visible global function definition for 'boxplot'
peboxplot: no visible global function definition for 'title'
peplot: no visible global function definition for 'par'
peplot: no visible global function definition for 'cycle'
peplot: no visible global function definition for 'plot'
peplot: no visible global function definition for 'identify'
peplot: no visible global function definition for 'mtext'
Undefined global functions or variables:
  boxplot cycle identify is.ts lag mtext par pchisq plot segments title
  ts ts.intersect
Consider adding
  importFrom("graphics", "boxplot", "identify", "mtext", "par", "plot",
             "segments", "title")
  importFrom("stats", "cycle", "is.ts", "lag", "pchisq", "ts",
             "ts.intersect")
to your NAMESPACE file.
The following files should probably not be installed:
  'addendum.tex', 'slplot.tex', 'table1.tex', 'table3.tex'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
PearsonICA: no visible global function definition for 'rnorm'
PearsonICAdemo: no visible global function definition for 'rnorm'
PearsonICAdemo: no visible global function definition for 'dev.new'
PearsonICAdemo: no visible global function definition for 'par'
PearsonICAdemo: no visible global function definition for 'plot'
PearsonICAdemo: no visible global function definition for 'axis'
PearsonICAdemo: no visible global function definition for 'title'
PearsonICAdemo: no visible global function definition for 'lines'
Undefined global functions or variables:
  axis dev.new lines par plot rnorm title
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "axis", "lines", "par", "plot", "title")
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.6/PedCNV.Rcheck/00install.out' for details.
Malformed Title field: should not end in a period.
'LinkingTo' for 'ggplot2' is unused as it has no 'include' directory
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.
Package in Depends field not imported from: 'reshape'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
blup: no visible global function definition for 'model.matrix'
blup: no visible global function definition for 'model.frame'
blup: no visible global function definition for 'read.table'
calcG: no visible global function definition for 'as'
gblup: no visible global function definition for 'model.matrix'
gblup: no visible global function definition for 'model.frame'
Undefined global functions or variables:
  as model.frame model.matrix read.table
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "model.frame", "model.matrix")
  importFrom("utils", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
PEMM_fun : find.lambda: no visible global function definition for
  'optimize'
PEMM_fun: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov optimize
Consider adding
  importFrom("stats", "cov", "optimize")
to your NAMESPACE file.
Running examples in 'penDvine-Ex.R' failed
The error most likely occurred in:

> ### Name: penDvine-package
> ### Title: The package 'penDvine' offers routines for estimating densities
> ###   and copula distribution of D-vines.
> ### Aliases: penDvine-package
> 
> ### ** Examples
> 
> #This examples describes the estimation of a D-vine to winddata,
> #available in this package. After the margins are prepared, we estimate a
> #D-vine using B-splines with 9 (K+1) marginal knots and penalizing second (m=2)
> #order differences (pen=1) of the basis coefficients.
> 
> data(Winddata)
> ex.data<-Winddata[c(1:100),c(1:4)] #examplary subdata for fast calculation
> wind.example<-Dvine(ex.data,K=7,pen=1,lambda=100,order.Dvine=FALSE,base="B-spline",m=2,cores=2)
>   
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11023 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11023 (sockconn)
Execution halted
create.data: no visible global function definition for 'rexp'
create.data: no visible global function definition for 'runif'
create.data: no visible global function definition for 'rbinom'
opt.splitval: no visible global function definition for 'na.omit'
opt2D : opt.both: no visible global function definition for 'optim'
Undefined global functions or variables:
  na.omit optim rbinom rexp runif
Consider adding
  importFrom("stats", "na.omit", "optim", "rbinom", "rexp", "runif")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'CoxBoost' 'codetools' 'locfit' 'penalized'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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'
Undefined global functions or variables:
  CoxBoost cv.CoxBoost findGlobals locfit penalized profL1
performance.curves.plot: no visible global function definition for
  'postscript'
performance.curves.plot: no visible global function definition for
  'axis'
performance.curves.plot: no visible global function definition for
  'lines'
performance.curves.plot: no visible global function definition for
  'legend'
performance.curves.plot: no visible global function definition for
  'grid'
performance.curves.plot: no visible global function definition for
  'dev.off'
precision.recall.curves.plot: no visible global function definition for
  'postscript'
precision.recall.curves.plot: no visible global function definition for
  'axis'
precision.recall.curves.plot: no visible global function definition for
  'lines'
precision.recall.curves.plot: no visible global function definition for
  'legend'
precision.recall.curves.plot: no visible global function definition for
  'grid'
precision.recall.curves.plot: no visible global function definition for
  'dev.off'
Undefined global functions or variables:
  axis dev.off grid legend lines postscript
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "axis", "grid", "legend", "lines")
to your NAMESPACE file.
Package suggested but not available for checking: 'dendextendRcpp'
permalgorithm: 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').
ksample.pclt: no visible global function definition for 'pchisq'
pCI: no visible global function definition for 'qbeta'
permKS.formula: no visible global function definition for 'terms'
permTREND.default: no visible global function definition for 'cor'
permTREND.formula: no visible global function definition for 'terms'
permTS.formula: no visible global function definition for 'terms'
trend.pclt: no visible global function definition for 'pnorm'
twosample.pclt: no visible global function definition for 'pnorm'
twosample.pclt: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  cor pchisq pnorm qbeta terms
Consider adding
  importFrom("stats", "cor", "pchisq", "pnorm", "qbeta", "terms")
to your NAMESPACE file.
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > ## Test `permute` using the `testthat` package
  > 
  > ## Setup
  > library("testthat")
  > library("permute")
  > 
  > ## Runs the tests in inst/tests
  > test_check("permute")
  -- 1. Failure: shuffle() works for non-contigous blocks of samples (@test-shuffl
  `x` not identical to `expected`.
  10/20 mismatches (average diff: 3)
  [3]   4 -  1 ==  3
  [4]   1 -  4 == -3
  [7]   8 -  5 ==  3
  [8]   5 -  8 == -3
  [11] 12 -  9 ==  3
  [12]  9 - 12 == -3
  [15] 16 - 13 ==  3
  [16] 13 - 16 == -3
  [19] 20 - 17 ==  3
  ...
  
  -- 2. Failure: shuffle() works for non-contigous blocks of samples (@test-shuffl
  `x` not identical to `expected`.
  10 string mismatches
  
  == testthat results  ===========================================================
  OK: 298 SKIPPED: 0 FAILED: 2
  1. Failure: shuffle() works for non-contigous blocks of samples (@test-shuffle.R#40) 
  2. Failure: shuffle() works for non-contigous blocks of samples (@test-shuffle.R#42) 
  
  Error: testthat unit tests failed
  Execution halted
hasMethod: no visible global function definition for 'getS3method'
Undefined global functions or variables:
  getS3method
Consider adding
  importFrom("utils", "getS3method")
to your NAMESPACE file.
pGLS: no visible global function definition for 'model.response'
pGLS: no visible global function definition for 'model.matrix'
pGLS: no visible global function definition for 'pt'
Undefined global functions or variables:
  model.matrix model.response pt
Consider adding
  importFrom("stats", "model.matrix", "model.response", "pt")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.6/PGRdup.Rcheck/00install.out' for details.
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > suppressPackageStartupMessages(library(phangorn))
  > 
  > test_check("phangorn")
  loglik: -11409.87 --> -11409.87 
  -- 1. Failure: SPR distance (@test_treedist.R#100)  ----------------------------
  SPR.dist(tree1, trees) not equal to 1:5.
  1/5 mismatches
  [2] 1 - 2 == -1
  
  == testthat results  ===========================================================
  OK: 120 SKIPPED: 28 FAILED: 1
  1. Failure: SPR distance (@test_treedist.R#100) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [14s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > suppressPackageStartupMessages(library(phangorn))
  > 
  > test_check("phangorn")
  loglik: -11409.87 --> -11409.87 
  -- 1. Failure: SPR distance (@test_treedist.R#100)  ----------------------------
  SPR.dist(tree1, trees) not equal to 1:5.
  1/5 mismatches
  [2] 1 - 2 == -1
  
  == testthat results  ===========================================================
  OK: 120 SKIPPED: 28 FAILED: 1
  1. Failure: SPR distance (@test_treedist.R#100) 
  
  Error: testthat unit tests failed
  Execution halted
PharmPow_crossover: no visible global function definition for
  'read.table'
PharmPow_crossover: no visible global function definition for
  'write.csv'
PharmPow_crossover: no visible global function definition for 'pdf'
PharmPow_crossover: no visible global function definition for 'dev.off'
PharmPow_parallel: no visible global function definition for
  'read.table'
PharmPow_parallel: no visible global function definition for
  'write.csv'
PharmPow_parallel: no visible global function definition for 'pdf'
PharmPow_parallel: no visible global function definition for 'dev.off'
fig_PharmPow_crossover: no visible global function definition for
  'read.csv'
fig_PharmPow_parallel: no visible global function definition for
  'read.csv'
Undefined global functions or variables:
  dev.off pdf read.csv read.table write.csv
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("utils", "read.csv", "read.table", "write.csv")
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 use Fortran I/O
nor system RNGs.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
fox: no visible binding for global variable 'sd'
fox: no visible global function definition for 'cor'
fox: no visible global function definition for 'interaction.plot'
fox: no visible global function definition for 'reorder'
fox: no visible global function definition for 'plot'
kang: no visible global function definition for 'var'
kang: no visible binding for global variable 'sd'
kang: no visible global function definition for 'cor'
kang: no visible global function definition for 'interaction.plot'
kang: no visible global function definition for 'reorder'
kang: no visible global function definition for 'plot'
nahu: no visible global function definition for 'interaction.plot'
nahu: no visible global function definition for 'reorder'
nahu: no visible global function definition for 'plot'
thsu: no visible global function definition for 'median'
thsu: no visible binding for global variable 'sd'
thsu: no visible global function definition for 'cor'
thsu: no visible global function definition for 'interaction.plot'
thsu: no visible global function definition for 'reorder'
thsu: no visible global function definition for 'plot'
Undefined global functions or variables:
  cor interaction.plot median plot reorder sd var
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "cor", "interaction.plot", "median", "reorder",
             "sd", "var")
to your NAMESPACE file.
pheno.ddm: no visible global function definition for 'new'
pheno.flm.fit: no visible binding for global variable 'na.exclude'
pheno.flm.fit: no visible global function definition for 'terms'
pheno.flm.fit: no visible global function definition for 'residuals'
pheno.flm.fit: no visible global function definition for 'qt'
pheno.lad.fit: no visible binding for global variable 'na.exclude'
pheno.mlm.fit: no visible binding for global variable 'na.exclude'
pheno.mlm.fit: no visible global function definition for 'residuals'
Undefined global functions or variables:
  na.exclude new qt residuals terms
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "na.exclude", "qt", "residuals", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Running examples in 'phylosim-Ex.R' failed
The error most likely occurred in:

> ### Name: getLogLevel.PhyloSim
> ### Title: Get the log level from a PhyloSim object
> ### Aliases: getLogLevel.PhyloSim PhyloSim.getLogLevel
> ###   getLogLevel,PhyloSim-method
> 
> ### ** Examples
> 
> 	# Create a PhyloSim object
> 	sim<-PhyloSim();
> 	# get/set log level
> 	getLogLevel(sim)
[1] -1
> 	setLogLevel(sim,0)
[1] 0
> 	# set/get log level via virtual field
> 	sim$logLevel<- -1
> 	sim$logLevel
[1] -1
> 	# clean up
> 	unlink(sim$logFile)
>  
> 
> 
> cleanEx()
Error: connections left open:
	PhyloSim_Anonymous_287514720.log (file)
Execution halted
incident: no visible global function definition for 'splinefun'
incident: no visible global function definition for 'integrate'
phytoprod: no visible global function definition for 'approx'
phytoprod: no visible global function definition for 'splinefun'
phytoprod: no visible global function definition for 'integrate'
reflectance: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx integrate splinefun
Consider adding
  importFrom("stats", "approx", "integrate", "splinefun")
to your NAMESPACE file.
File which contains pragma(s) suppressing diagnostics:
  'src/pijavski.cpp'
plot.pred.int: no visible global function definition for 'plot.default'
plot.pred.int: no visible global function definition for 'axis'
plot.pred.int: no visible global function definition for 'box'
plot.pred.int : cidist: no visible global function definition for
  'ecdf'
plot.pred.int : negcidist: no visible global function definition for
  'ecdf'
plot.pred.int : pi.col.fun: no visible global function definition for
  'gray'
plot.pred.int: no visible global function definition for 'segments'
plot.pred.int: no visible global function definition for 'points'
plot.pred.int: no visible global function definition for 'abline'
pred.int: no visible binding for global variable 'sd'
prop.test.mult: no visible global function definition for 'qnorm'
sim.basic: no visible global function definition for 'rbinom'
sim.basic: no visible global function definition for 'rnorm'
t.test.mult: no visible global function definition for 'qt'
Undefined global functions or variables:
  abline axis box ecdf gray plot.default points qnorm qt rbinom rnorm
  sd segments
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "box", "plot.default",
             "points", "segments")
  importFrom("stats", "ecdf", "qnorm", "qt", "rbinom", "rnorm", "sd")
to your NAMESPACE file.
Package suggested but not available for checking: 'ggsubplot'
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.
Running 'testthat.R' [32s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(PKNCA)
  > 
  > test_check("PKNCA")
  -- 1. Failure: provenance (@test-provenance.R#7)  ------------------------------
  <... isn't true.
  A correct time is set in provenance
  
  -- 2. Failure: provenance (@test-provenance.R#11)  -----------------------------
  attr(a, "provenance", exact = TRUE)$sessionInfo not equal to sessionInfo().
  Component "loadedOnly": Names: 8 string mismatches
  Component "loadedOnly": Length mismatch: comparison on first 21 components
  Component "loadedOnly": Component 14: Names: 18 string mismatches
  Component "loadedOnly": Component 14: Attributes: < Component "file": 1 string mismatch >
  Component "loadedOnly": Component 14: Length mismatch: comparison on first 21 components
  Component "loadedOnly": Component 14: Component "Package": 1 string mismatch
  Component "loadedOnly": Component 14: Component 2: 1 string mismatch
  Component "loadedOnly": Component 14: Component 3: 1 string mismatch
  Component "loadedOnly": Component 14: Component 4: 1 string mismatch
  ...
  Correct session information is set in provenance
  
  Provenance hash a generated on b with c.
  == testthat results  ===========================================================
  OK: 1218 SKIPPED: 2 FAILED: 2
  1. Failure: provenance (@test-provenance.R#7) 
  2. Failure: provenance (@test-provenance.R#11) 
  
  Error: testthat unit tests failed
  Execution halted
PKmod: no visible global function definition for 'deriv'
Undefined global functions or variables:
  deriv
Consider adding
  importFrom("stats", "deriv")
to your NAMESPACE file.
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.
Running examples in 'plater-Ex.R' failed
The error most likely occurred in:

> ### Name: add_plate
> ### Title: Read a plater-formatted file and combine it with an existing
> ###   data frame.
> ### Aliases: add_plate
> 
> ### ** Examples
> 
> # Part of the data is tidy
> file <- system.file("extdata", "example-2-part-A.csv", package = "plater")
> data <- read.csv(file)
> 
> # Part of the data is plate-shaped
> plate_shaped <- system.file("extdata", "example-2-part-B.csv", package = "plater")
> 
> # Combine the two
> data <- add_plate(
+    data = data, 
+    file = plate_shaped,
+    well_ids_column = "Wells")
> 
> # Now data are tidy
> head(data)
  Wells Killing Drug Concentration Bacteria
1   A01      98    A       100.000  E. coli
2   A02      95    A        20.000  E. coli
3   A03      92    A         4.000  E. coli
4   A04      41    A         0.800  E. coli
5   A05      17    A         0.160  E. coli
6   A06       2    A         0.032  E. coli
> 
> 
> 
> cleanEx()
Error: connections left open:
	plate (textConnection)
	plate (textConnection)
	plate (textConnection)
Execution halted
bwfw.hmm: no visible global function definition for 'dnorm'
bwfw1.hmm: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'Formula' 'sm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
nrmlepln: no visible global function definition for 'pchisq'
nrmlerasch: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.0Mb
plotAuto: no visible global function definition for 'window'
plotAuto: no visible global function definition for 'title'
plotAuto: no visible global function definition for 'axis'
plotAuto: no visible global function definition for 'box'
plotCumu: no visible global function definition for 'title'
plotCumu: no visible global function definition for 'axis'
plotCumu: no visible global function definition for 'box'
plotDens : panel.dens: no visible global function definition for 'var'
plotDens : panel.dens: no visible global function definition for
  'quantile'
plotDens : panel.dens: no visible global function definition for
  'median'
plotDens: no visible global function definition for 'tail'
plotQuant: no visible global function definition for 'par'
plotQuant: no visible binding for global variable 'quantile'
plotQuant: no visible global function definition for 'plot'
plotQuant: no visible global function definition for 'lines'
plotQuant: no visible global function definition for 'bxp'
plotQuant: no visible global function definition for 'matplot'
plotQuant: no visible global function definition for 'axis'
plotQuant: no visible global function definition for 'box'
plotQuant: no visible global function definition for 'title'
plotSplom: no visible global function definition for 'pairs'
plotTrace : panel.trace: no visible global function definition for
  'var'
plotTrace : panel.trace: no visible global function definition for
  'median'
plotTrace: no visible global function definition for 'tail'
Undefined global functions or variables:
  axis box bxp lines matplot median pairs par plot quantile tail title
  var window
Consider adding
  importFrom("graphics", "axis", "box", "bxp", "lines", "matplot",
             "pairs", "par", "plot", "title")
  importFrom("stats", "median", "quantile", "var", "window")
  importFrom("utils", "tail")
to your NAMESPACE file.
generateEnvelope: no visible global function definition for 'tail'
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
llla.bi: no visible global function definition for 'as.formula'
llla.bi: no visible global function definition for 'glm'
llla.bi: no visible global function definition for 'binomial'
llla.bi: no visible binding for global variable 'logit'
llla.bi: no visible global function definition for 'vcov'
llla.bi: no visible global function definition for 'coef'
llla.mc: no visible global function definition for 'model.matrix'
llla.mc: no visible global function definition for 'as.formula'
llla.mc: no visible global function definition for 'coxph'
llla.mc: no visible global function definition for 'vcov'
llla.mc: no visible global function definition for 'coef'
llla.mle: no visible global function definition for 'as.formula'
llla.mle: no visible global function definition for 'glm'
llla.mle: no visible global function definition for 'poisson'
llla.mle: no visible global function definition for 'coef'
llla.mle: no visible global function definition for 'vcov'
mclgen: no visible global function definition for 'reshape'
simRasch.1D: no visible global function definition for 'rnorm'
simRasch.1D: no visible global function definition for 'runif'
vcov.sandwich.glm: no visible global function definition for
  'model.matrix'
vcov.sandwich.glm: no visible global function definition for 'weights'
vcov.sandwich.glm: no visible global function definition for
  'residuals'
vcov.sandwich.glm: no visible global function definition for 'vcov'
Undefined global functions or variables:
  as.formula binomial coef coxph glm logit model.matrix poisson reshape
  residuals rnorm runif vcov weights
Consider adding
  importFrom("stats", "as.formula", "binomial", "coef", "glm",
             "model.matrix", "poisson", "reshape", "residuals", "rnorm",
             "runif", "vcov", "weights")
to your NAMESPACE file.
print.densityEHpi: no visible global function definition for 'str'
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
to your NAMESPACE file.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   1.6Mb
.MCM: no visible global function definition for 'runif'
.MCM: no visible global function definition for 'rmultinom'
.MCM: no visible global function definition for 'mahalanobis'
.MCM: no visible global function definition for 'optimize'
.MCM : f: no visible global function definition for 'mahalanobis'
.MCM: no visible global function definition for 'alarm'
.igpark: no visible global function definition for 'kmeans'
.loglik: no visible global function definition for 'mahalanobis'
.plot.gpcm: no visible global function definition for 'plot'
.plot.gpcm: no visible global function definition for 'lines'
.plot.gpcm: no visible global function definition for 'legend'
.rwgpar: no visible global function definition for 'rexp'
.weights: no visible global function definition for 'mahalanobis'
Undefined global functions or variables:
  alarm kmeans legend lines mahalanobis optimize plot rexp rmultinom
  runif
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "kmeans", "mahalanobis", "optimize", "rexp",
             "rmultinom", "runif")
  importFrom("utils", "alarm")
to your NAMESPACE file.
dbm: no visible global function definition for 'optim'
dbm: no visible global function definition for 'new'
destat: no visible global function definition for 'weighted.mean'
local.knn: no visible global function definition for 'sd'
local.knn: no visible global function definition for 'optim'
mdpref: no visible global function definition for 'sd'
mdpref: no visible global function definition for 'text'
mdpref: no visible global function definition for 'lines'
phicom: no visible global function definition for 'optim'
phicom: no visible global function definition for 'new'
pl: no visible global function definition for 'optim'
pl: no visible global function definition for 'new'
rol: no visible global function definition for 'nlm'
rol: no visible global function definition for 'new'
wdbm: no visible global function definition for 'optim'
wdbm: no visible global function definition for 'new'
Undefined global functions or variables:
  lines new nlm optim sd text weighted.mean
Consider adding
  importFrom("graphics", "lines", "text")
  importFrom("methods", "new")
  importFrom("stats", "nlm", "optim", "sd", "weighted.mean")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' call to 'MASS' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'MASS'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
pnmtrem1: no visible global function definition for 'pnorm'
pnmtrem1: no visible global function definition for 'dnorm'
pnmtrem1: no visible global function definition for 'ginv'
pnmtrem1 : fun: no visible global function definition for 'pnorm'
pnmtrem1 : derf: no visible global function definition for 'dnorm'
pnmtrem1 : derf: no visible global function definition for 'pnorm'
pnmtrem1 : fun: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm ginv pnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm")
to your NAMESPACE file.
'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.
bipoilogMLE: no visible global function definition for 'optim'
bipoilogMLE: no visible global function definition for 'write.table'
poilogMLE: no visible global function definition for 'optim'
rbipoilog : sim: no visible global function definition for 'rnorm'
rbipoilog : sim: no visible global function definition for 'rpois'
rpoilog : sim: no visible global function definition for 'rnorm'
rpoilog : sim: no visible global function definition for 'rpois'
Undefined global functions or variables:
  optim rnorm rpois write.table
Consider adding
  importFrom("stats", "optim", "rnorm", "rpois")
  importFrom("utils", "write.table")
to your NAMESPACE file.
approxMargMLE: no visible global function definition for 'optim'
approxMargMLECI : ciFunction: no visible global function definition for
  'qchisq'
approxMargMLECI: no visible global function definition for 'uniroot'
margMLE: no visible global function definition for 'optim'
margMLECI: no visible global function definition for 'optim'
margMLECI : unNormLikeMinusVal: no visible global function definition
  for 'qchisq'
margMLECI: no visible global function definition for 'uniroot'
profMLECI : ciFunction: no visible global function definition for
  'qchisq'
profMLECI: no visible global function definition for 'uniroot'
rtbinom: no visible global function definition for 'rbinom'
rtpois: no visible global function definition for 'rpois'
waldCI: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  optim qchisq qnorm rbinom rpois uniroot
Consider adding
  importFrom("stats", "optim", "qchisq", "qnorm", "rbinom", "rpois",
             "uniroot")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'combinat' 'splines'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Est.Depth: no visible global function definition for 'quantile'
PS.FDR: no visible global function definition for 'quantile'
Permu.Ind: no visible global function definition for 'permn'
Permu.Ind: no visible global function definition for 'hcube'
Trans.Data: no visible global function definition for 'write.table'
Trans.Data: no visible global function definition for 'predict'
Trans.Data: no visible global function definition for 'lm'
Undefined global functions or variables:
  hcube lm permn predict quantile write.table
Consider adding
  importFrom("stats", "lm", "predict", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
rpoistweedie: no visible global function definition for 'runif'
testOmegaPT: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'MASS' 'scatterplot3d'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plot.poLCA: no visible global function definition for 'layout'
plot.poLCA: no visible global function definition for 'par'
poLCA: no visible global function definition for 'model.frame'
poLCA: no visible global function definition for 'model.response'
poLCA: no visible global function definition for 'model.matrix'
poLCA: no visible global function definition for 'runif'
poLCA: no visible global function definition for 'ginv'
poLCA: no visible global function definition for 'flush.console'
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'
poLCA.simdata: no visible global function definition for 'runif'
poLCA.simdata: no visible global function definition for 'rnorm'
poLCA.table: no visible global function definition for 'model.frame'
print.poLCA: no visible global function definition for 'pt'
print.poLCA: no visible global function definition for 'flush.console'
rmulti: no visible global function definition for 'runif'
Undefined global functions or variables:
  flush.console ginv layout model.frame model.matrix model.response par
  pt rnorm runif scatterplot3d
Consider adding
  importFrom("graphics", "layout", "par")
  importFrom("stats", "model.frame", "model.matrix", "model.response",
             "pt", "rnorm", "runif")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Package suggested but not available for checking: 'pollimetrydata'
qPolyaAeppliSingle: no visible global function definition for 'qgamma'
rPolyaAeppli: no visible global function definition for 'rpois'
rPolyaAeppli: no visible global function definition for 'rgeom'
Undefined global functions or variables:
  qgamma rgeom rpois
Consider adding
  importFrom("stats", "qgamma", "rgeom", "rpois")
to your NAMESPACE file.
'library' or 'require' call to 'matrixcalc' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'matrixcalc'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
print.mixed.pom: no visible global function definition for 'pnorm'
print.pom: no visible global function definition for 'pnorm'
siteocc : get.mod.matrix: no visible binding for global variable
  'na.pass'
siteocc : get.mod.matrix: no visible global function definition for
  'formula'
siteocc : get.mod.matrix: no visible global function definition for
  'model.matrix'
siteocc: no visible global function definition for 'nlminb'
siteocc: no visible global function definition for
  'is.positive.definite'
Undefined global functions or variables:
  formula is.positive.definite model.matrix na.pass nlminb pnorm
Consider adding
  importFrom("stats", "formula", "model.matrix", "na.pass", "nlminb",
             "pnorm")
to your NAMESPACE file.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
asymmetricIntervals: no visible global function definition for 'stack'
bonferroniIntervals: no visible global function definition for 'stack'
bonferroniIntervals: no visible global function definition for 'lm'
bonferroniIntervals: no visible global function definition for
  'predict'
bootstrapIntervals: no visible global function definition for 'stack'
component1a: no visible global function definition for 'pnorm'
component1b: no visible global function definition for 'pnorm'
component2: no visible global function definition for 'dgamma'
eqnForMin: no visible global function definition for 'pnorm'
eqnForMin: no visible global function definition for 'integrate'
integrand : <anonymous>: no visible global function definition for
  'pnorm'
integrand: no visible global function definition for 'dnorm'
integrate2: no visible global function definition for 'integrate'
integrate2a: no visible global function definition for 'integrate'
integrate2b: no visible global function definition for 'integrate'
integrate4a: no visible global function definition for 'integrate'
integrate4b: no visible global function definition for 'integrate'
optimalCScalar2: no visible global function definition for 'uniroot'
optimalLambda: no visible global function definition for 'optimise'
optimalLambdaC: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dgamma dnorm integrate lm optimise pnorm predict stack uniroot
Consider adding
  importFrom("stats", "dgamma", "dnorm", "integrate", "lm", "optimise",
             "pnorm", "predict", "uniroot")
  importFrom("utils", "stack")
to your NAMESPACE file.
Running 'test-all.R' [12s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > options(poppr.debug = TRUE)
  > test_check("poppr")
  Loading required package: poppr
  Loading required package: adegenet
  Loading required package: ade4
  
     /// adegenet 2.1.1 is loaded ////////////
  
     > overview: '?adegenet'
     > tutorials/doc/questions: 'adegenetWeb()' 
     > bug reports/feature requests: adegenetIssues()
  
  
  This is poppr version 2.8.1. To get started, type package?poppr
  OMP parallel support: available
  -- 1. Failure: rrmlg produces the correct mlgs (@test-round-robin.R#24)  -------
  `rrx_m` not equivalent to `mlg_truth`.
  11/15 mismatches (average diff: 1.73)
  [2]  3 - 2 ==  1
  [3]  2 - 3 == -1
  [5]  4 - 1 ==  3
  [6]  1 - 2 == -1
  [7]  3 - 4 == -1
  [9]  1 - 3 == -2
  [10] 4 - 1 ==  3
  [12] 4 - 3 ==  1
  [13] 3 - 2 ==  1
  ...
  
  == testthat results  ===========================================================
  OK: 308 SKIPPED: 186 FAILED: 1
  1. Failure: rrmlg produces the correct mlgs (@test-round-robin.R#24) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'test-all.R' [14s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > options(poppr.debug = TRUE)
  > test_check("poppr")
  Loading required package: poppr
  Loading required package: adegenet
  Loading required package: ade4
  
     /// adegenet 2.1.1 is loaded ////////////
  
     > overview: '?adegenet'
     > tutorials/doc/questions: 'adegenetWeb()' 
     > bug reports/feature requests: adegenetIssues()
  
  
  This is poppr version 2.8.1. To get started, type package?poppr
  OMP parallel support: available
  -- 1. Failure: rrmlg produces the correct mlgs (@test-round-robin.R#24)  -------
  `rrx_m` not equivalent to `mlg_truth`.
  11/15 mismatches (average diff: 1.73)
  [2]  3 - 2 ==  1
  [3]  2 - 3 == -1
  [5]  4 - 1 ==  3
  [6]  1 - 2 == -1
  [7]  3 - 4 == -1
  [9]  1 - 3 == -2
  [10] 4 - 1 ==  3
  [12] 4 - 3 ==  1
  [13] 3 - 2 ==  1
  ...
  
  == testthat results  ===========================================================
  OK: 308 SKIPPED: 186 FAILED: 1
  1. Failure: rrmlg produces the correct mlgs (@test-round-robin.R#24) 
  
  Error: testthat unit tests failed
  Execution halted
popRangeSim: no visible global function definition for 'write.table'
Undefined global functions or variables:
  write.table
Consider adding
  importFrom("utils", "write.table")
to your NAMESPACE file.
Running examples in 'popRange-Ex.R' failed
The error most likely occurred in:

> ### Name: popRangeSim
> ### Title: popRangeSim
> ### Aliases: popRangeSim
> 
> ### ** Examples
>  
> ## Example: In this scenario, we are simulating a 3x3 grid of populations for 50 
> ## generations. Each population starts with 100 diploid individuals. Each individual 
> ## has a 0.01 probability of migrating away from their populations. There are 100 
> ## SNPs that all have a starting frequency of 0.5, and the program outputs the standard 
> ## "results" file, as well as a PLINK file. 
> 
> ## Commands
> 
> mat = matrix(1,nrow=3,ncol=3) 
> popRangeSim(world = mat, popSize = 100, diploid = TRUE, nGens = 50,
+               mig = 0.01, SNP_model = 0, nSNPs = 100, SNPs_starting_freq = 0.5, 
+               outfile= "outFile1", PLINK=TRUE)
Error in find_python_cmd(minimum_version = minimum_version, maximum_version = maximum_version,  : 
  Couldn't find a sufficient Python binary. If you haven't installed the Python dependency yet please do so. If you have but it isn't on the system path (as is default on Windows) please add it to path or set options('python_cmd'='/path/to/binary')  or set the PYTHON, PYTHON2, or PYTHON3 environmental variables. Python must be at least version 2.7 Python must be at most version 3.4 Python must have access to the modules: numpy
[1] "Could not find an acceptable version of python with numpy installed. This should be able to locate python \n      anywhere on your computer, but perhaps try adding python to your PATH if you think this message is an error."
Error in popRangeSim(world = mat, popSize = 100, diploid = TRUE, nGens = 50,  : 
  
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
'library' or 'require' call to 'methods' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'lattice' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File 'portfolioSim/R/AllClasses.R':
  .onLoad calls:
    require(methods)

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

contributionSummaryDf,simResult : <anonymous>: no visible global
  function definition for 'aggregate'
getSimTrades,stiFromSignal-orderable-portfolio-simData-logical: no
  visible binding for global variable 'shares'
loadIn,simResult-character-missing: no visible binding for global
  variable 'master.freq'
loadIn,simResult-character-missing: no visible binding for global
  variable 'master.errors'
loadIn,simResult-character-missing: no visible binding for global
  variable 'master.type'
loadIn,simResult-character-missing: no visible binding for global
  variable 'master.summary.interface'
loadIn,simResultSinglePeriod-character-missing: no visible binding for
  global variable 'x'
plot,simResult-missing: no visible global function definition for
  'xyplot'
runSim,portfolioSim-logical: no visible binding for global variable
  'id'
runSim,portfolioSim-logical: no visible global function definition for
  'updateSummary'
securityPerfSummaryDf,simResult: no visible global function definition
  for 'aggregate'
summary,simResult: no visible global function definition for 'sd'
summary,simResult: no visible global function definition for 'head'
summary,simResult: no visible global function definition for 'tail'
Undefined global functions or variables:
  aggregate head id master.errors master.freq master.summary.interface
  master.type sd shares tail updateSummary x xyplot
Consider adding
  importFrom("stats", "aggregate", "sd")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

powell: no visible global function definition for 'Quote'
Undefined global functions or variables:
  Quote
Consider adding
  importFrom("methods", "Quote")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File 'powell/libs/i386/powell.dll':
  Found 'printf', possibly from 'printf' (C)
    Object: 'powell.o'
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
    Object: 'powell.o'
File 'powell/libs/x64/powell.dll':
  Found 'printf', possibly from 'printf' (C)
    Object: 'powell.o'
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
    Object: 'powell.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
fnfam: no visible global function definition for 'qnorm'
fx: no visible global function definition for 'qnorm'
normplot : <local> : replot: no visible global function definition for
  'qnorm'
normplot : <local> : replot: no visible global function definition for
  'pnorm'
normplot : <local> : replot: no visible global function definition for
  'plot'
normplot : <local> : replot: no visible global function definition for
  'dnorm'
normplot : <local> : replot: no visible global function definition for
  'points'
normplot : <local> : replot: no visible global function definition for
  'lines'
normplot : <local> : regen: no visible global function definition for
  'rnorm'
normplot : <local> : regen: no visible global function definition for
  'rexp'
nsibs: no visible global function definition for 'qnorm'
ntdt: no visible global function definition for 'uniroot'
plotDom: no visible global function definition for 'plot'
plotNsibs: no visible global function definition for 'plot'
plotNtdt: no visible global function definition for 'plot'
plotNtdt: no visible global function definition for 'lines'
plotNtdt: no visible global function definition for 'legend'
ptdt: no visible global function definition for 'optimize'
ptdt: no visible global function definition for 'uniroot'
ptdt: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dnorm legend lines optimize plot pnorm points qnorm rexp rnorm
  uniroot
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points")
  importFrom("stats", "dnorm", "optimize", "pnorm", "qnorm", "rexp",
             "rnorm", "uniroot")
to your NAMESPACE file.
Error(s) in re-building vignettes:
--- re-building 'intro_pfit.Rmd' using rmarkdown
PP package calling ...
Follow this project on github: https://github.com/manuelreif/PP.git
Quitting from lines 131-155 (intro_pfit.Rmd) 
Error: processing vignette 'intro_pfit.Rmd' failed with diagnostics:
'x' contains missing values
--- failed re-building 'intro_pfit.Rmd'

--- re-building 'intro_pp.Rmd' using rmarkdown
--- finished re-building 'intro_pp.Rmd'

--- re-building 'ppass_par_and_fit.Rmd' using rmarkdown
--- finished re-building 'ppass_par_and_fit.Rmd'

SUMMARY: processing the following file failed:
  'intro_pfit.Rmd'

Error: Vignette re-building failed.
Execution halted
pps1: no visible global function definition for 'runif'
ppss: no visible global function definition for 'runif'
ppswr: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
LDA.Tree : Find.proj: no visible binding for global variable 'var'
LDA.Tree : Find.proj: no visible binding for global variable 'IQR'
LDA.Tree : Find.proj: no visible binding for global variable 'median'
PDA.Tree : Find.proj: no visible binding for global variable 'var'
PDA.Tree : Find.proj: no visible binding for global variable 'median'
PDA.Tree : Find.proj: no visible binding for global variable 'IQR'
PP.Tree : Find.proj: no visible binding for global variable 'var'
PP.Tree : Find.proj: no visible binding for global variable 'median'
PP.Tree : Find.proj: no visible binding for global variable 'IQR'
PP.optimize.Huber: no visible binding for global variable 'sd'
PP.optimize.anneal: no visible binding for global variable 'sd'
PP.optimize.plot: no visible binding for global variable 'sd'
PP.optimize.plot: no visible global function definition for 'hist'
PP.optimize.plot: no visible global function definition for 'text'
PP.optimize.plot: no visible global function definition for 'par'
PP.optimize.plot: no visible global function definition for 'plot'
PP.optimize.plot: no visible global function definition for 'colors'
PP.optimize.plot: no visible global function definition for 'pairs'
PP.optimize.random: no visible binding for global variable 'sd'
Undefined global functions or variables:
  IQR colors hist median pairs par plot sd text var
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "hist", "pairs", "par", "plot", "text")
  importFrom("stats", "IQR", "median", "sd", "var")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.6/PPtreeViz.Rcheck/00install.out' for details.
TT.test : <anonymous>: no visible global function definition for
  't.test'
TT.test: no visible binding for global variable 'sd'
TT.test: no visible global function definition for 'setNames'
kirjelda : combo: no visible binding for global variable 'sd'
kor.tabel: no visible binding for global variable 'cor.test'
Undefined global functions or variables:
  cor.test sd setNames t.test
Consider adding
  importFrom("stats", "cor.test", "sd", "setNames", "t.test")
to your NAMESPACE file.
Package suggested but not available for checking: 'Rmosek'
gausspred: no visible global function definition for 'qt'
mvapred: no visible global function definition for 'qt'
Undefined global functions or variables:
  qt
Consider adding
  importFrom("stats", "qt")
to your NAMESPACE file.
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'.

Predict.mix: no visible global function definition for 'dbinom'
abs_cor: no visible global function definition for 'cor'
gen.alpha.IGamma: no visible global function definition for 'qgamma'
gendata.mix: no visible global function definition for 'runif'
gendata.mix: no visible global function definition for 'rbeta'
mh1.unif: no visible global function definition for 'runif'
train_predict_mix: no visible global function definition for 'dbinom'
training: no visible global function definition for 'runif'
training: no visible global function definition for 'dbinom'
Undefined global functions or variables:
  cor dbinom qgamma rbeta runif
Consider adding
  importFrom("stats", "cor", "dbinom", "qgamma", "rbeta", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.6/preText.Rcheck/00install.out' for details.
Found the following hidden files and directories:
  data/.Rapp.history
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
'library' or 'require' call to 'deSolve' which was already attached by Depends.
  Please remove these calls from your code.
LVCompGames: no visible global function definition for 'runif'
LVCompGames: no visible global function definition for 'plot'
LVCompGames: no visible global function definition for 'axis'
LVCompGames: no visible global function definition for 'box'
LVCompGames: no visible global function definition for 'lines'
LVCompGames: no visible global function definition for 'points'
MetaSim: no visible global function definition for 'runif'
chesson: no visible global function definition for 'rbeta'
chesson: no visible global function definition for 'dbeta'
chesson : rhof: no visible global function definition for 'dbeta'
chesson: no visible global function definition for 'integrate'
pimmlawton: no visible global function definition for 'runif'
Undefined global functions or variables:
  axis box dbeta integrate lines plot points rbeta runif
Consider adding
  importFrom("graphics", "axis", "box", "lines", "plot", "points")
  importFrom("stats", "dbeta", "integrate", "rbeta", "runif")
to your NAMESPACE file.
basisplot: no visible global function definition for 'plot'
basisplot: no visible global function definition for 'abline'
basisplot: no visible global function definition for 'text'
basisplot: no visible global function definition for 'par'
plot.prinsimp: no visible global function definition for 'screeplot'
plot.simpart: no visible global function definition for 'par'
position_text: no visible global function definition for 'par'
position_text: no visible global function definition for 'strwidth'
simpart.formula: no visible global function definition for 'terms'
simpart.formula: no visible global function definition for
  'model.matrix'
varperc: no visible global function definition for 'plot'
varperc: no visible global function definition for 'lines'
varperc: no visible global function definition for 'text'
varsimp: no visible global function definition for 'plot'
varsimp: no visible global function definition for 'points'
varsimp: no visible global function definition for 'text'
varsimp: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline lines model.matrix par plot points screeplot strwidth terms
  text
Consider adding
  importFrom("graphics", "abline", "lines", "par", "plot", "points",
             "strwidth", "text")
  importFrom("stats", "model.matrix", "screeplot", "terms")
to your NAMESPACE file.
Package suggested but not available for checking: 'gurobi'
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   2.6Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.6/PRISMA.Rcheck/00install.out' for details.
pr.conditional: no visible global function definition for 'qnorm'
pr.marginal: no visible global function definition for 'qnorm'
prLogisticDelta: no visible global function definition for 'glm'
prLogisticDelta: no visible binding for global variable 'binomial'
Undefined global functions or variables:
  binomial glm qnorm
Consider adding
  importFrom("stats", "binomial", "glm", "qnorm")
to your NAMESPACE file.
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(probably)
  
  Attaching package: 'probably'
  
  The following objects are masked from 'package:base':
  
      as.factor, as.ordered
  
  > 
  > test_check("probably")
  -- 1. Failure: class_pred printing (@test-class-pred.R#408)  -------------------
  `cat_levels\(cp\)` does not match "10 Levels: dkkjddgmgwbludofdtxj grkuclzxxedqirieucmn \\.\\.\\. xsqzrsophdzxruamtfig".
  Actual value: "10 Levels: dahtypxvkpthcdtlvqjt hzgjisdnqkgulojmgiij \.\.\. zptfkhvvgpqvrqbdmevs"
  
  == testthat results  ===========================================================
  OK: 116 SKIPPED: 0 FAILED: 1
  1. Failure: class_pred printing (@test-class-pred.R#408) 
  
  Error: testthat unit tests failed
  Execution halted
.pfda.fstep: no visible global function definition for 'dist'
.pfda.main: no visible global function definition for 'plot'
.pfda.mstep: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov dist plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "cov", "dist")
to your NAMESPACE file.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc           6.5Mb
    help          2.1Mb
    htmlwidgets   2.5Mb
GPois: no visible global function definition for 'dnorm'
GPois: no visible binding for global variable 'poisson'
GPois: no visible global function definition for 'predict'
GPois: no visible global function definition for 'fitted'
GPois: no visible global function definition for 'residuals'
GPois: no visible global function definition for 'smooth.spline'
ProDenICA: no visible global function definition for 'rnorm'
d.gaussmix: no visible global function definition for 'dnorm'
djordan: no visible global function definition for 'dt'
djordan: no visible global function definition for 'dunif'
mixmat: no visible global function definition for 'rnorm'
mixmat: no visible global function definition for 'runif'
plot.ProDenICA: no visible global function definition for 'plot'
r.gaussmix: no visible global function definition for 'rmultinom'
r.gaussmix: no visible global function definition for 'rnorm'
rjordan: no visible global function definition for 'rt'
rjordan: no visible global function definition for 'runif'
rmix.dexp: no visible global function definition for 'runif'
Undefined global functions or variables:
  dnorm dt dunif fitted plot poisson predict residuals rmultinom rnorm
  rt runif smooth.spline
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dnorm", "dt", "dunif", "fitted", "poisson",
             "predict", "residuals", "rmultinom", "rnorm", "rt", "runif",
             "smooth.spline")
to your NAMESPACE file.
profBinary: no visible global function definition for 'model.frame'
profBinary: no visible global function definition for 'model.matrix'
profLinear: no visible global function definition for 'model.frame'
profLinear: no visible global function definition for 'model.matrix'
profLinear: no visible global function definition for 'model.response'
profLinear: no visible global function definition for 'model.extract'
summary.profBinary: no visible global function definition for 'terms'
summary.profBinary: no visible global function definition for 'qbeta'
summary.profLinear: no visible global function definition for 'terms'
Undefined global functions or variables:
  model.extract model.frame model.matrix model.response qbeta terms
Consider adding
  importFrom("stats", "model.extract", "model.frame", "model.matrix",
             "model.response", "qbeta", "terms")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'MASS' 'nlme'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    extdata   6.4Mb
    libs      1.6Mb
Package suggested but not available for checking: 'qtbase'
Packages in Depends field not imported from:
  'splines' 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
IndividualPROC: no visible global function definition for 'survfit'
IndividualPROC: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile survfit
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
addpi: no visible global function definition for 'lines'
genPerms: no visible global function definition for 'combn'
getVar: no visible global function definition for 'glm'
getVar: no visible global function definition for 'binomial'
getVar: no visible global function definition for 'var'
pba: no visible global function definition for 'glm'
pba: no visible global function definition for 'binomial'
pba: no visible global function definition for 'predict'
pba: no visible global function definition for 'rbinom'
pcr: no visible global function definition for 'quantile'
plotpi: no visible global function definition for 'plot'
plotpi: no visible global function definition for 'axis'
plotpi: no visible global function definition for 'abline'
plotpi: no visible global function definition for 'lines'
Undefined global functions or variables:
  abline axis binomial combn glm lines plot predict quantile rbinom var
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "plot")
  importFrom("stats", "binomial", "glm", "predict", "quantile", "rbinom",
             "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
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.
estimateLSEparam: no visible global function definition for 'lm'
estimateMLEparam: no visible global function definition for 'optim'
getCCnlL: no visible global function definition for 'dnorm'
iterateScampi: no visible global function definition for 'quantile'
plot.scampi: no visible global function definition for 'hist'
plot.scampiVal: no visible global function definition for 'par'
plot.scampiVal: no visible global function definition for 'hist'
plot.scampiVal: no visible global function definition for 'abline'
plot.scampiVal: no visible global function definition for 'qqnorm'
plot.scampiVal: no visible global function definition for 'qqline'
sampleInitialVector: no visible global function definition for 'runif'
Undefined global functions or variables:
  abline dnorm hist lm optim par qqline qqnorm quantile runif
Consider adding
  importFrom("graphics", "abline", "hist", "par")
  importFrom("stats", "dnorm", "lm", "optim", "qqline", "qqnorm",
             "quantile", "runif")
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.
Extract_plant_grapevine_function: 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.
Package suggested but not available for checking: 'rdt'
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.3Mb
Package in Depends field not imported from: 'rpart'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
candidate.overlap: no visible global function definition for
  'write.table'
fisher: no visible global function definition for 'fisher.test'
fisher.iteration: no visible global function definition for
  'download.file'
fisher.iteration: no visible global function definition for
  'read.table'
pSI.list: no visible global function definition for 'write.table'
specificity.index: no visible global function definition for 'png'
specificity.index: no visible global function definition for 'par'
specificity.index: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  dev.off download.file fisher.test par png read.table write.table
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "par")
  importFrom("stats", "fisher.test")
  importFrom("utils", "download.file", "read.table", "write.table")
to your NAMESPACE file.
'library' or 'require' call to 'numDeriv' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
test.problem : g: no visible global function definition for 'grad'
test.problem: no visible global function definition for 'new'
psoptim,test.problem-missing-missing-missing-missing: no visible global
  function definition for 'new'
show,test.result: no visible global function definition for 'show'
show,test.result: no visible global function definition for 'sd'
Undefined global functions or variables:
  grad new sd show
Consider adding
  importFrom("methods", "new", "show")
  importFrom("stats", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
pspearman: no visible global function definition for 'pt'
spearman.test: no visible global function definition for
  'complete.cases'
spearman.test: no visible global function definition for 'cor'
Undefined global functions or variables:
  complete.cases cor pt
Consider adding
  importFrom("stats", "complete.cases", "cor", "pt")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'EffectsRelBaseline' 'boot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
catEffectBootAdaptor: no visible binding for global variable 'sumSqCat'
compExclusionFraction: no visible global function definition for
  'rpois'
compExclusionFraction: no visible global function definition for
  't.test'
compExclusionFraction: no visible global function definition for 'glm'
compExclusionFraction: no visible global function definition for
  'anova'
compPowerCatSelectivity: no visible binding for global variable
  'fRatioStat'
compPowerGeneralRespDetection: no visible binding for global variable
  'sumSqCat'
compPowerRespDetection: no visible binding for global variable
  'sumSqCat'
compRejectionFraction: no visible global function definition for
  'rpois'
compRejectionFraction: no visible global function definition for
  't.test'
compRejectionFraction: no visible global function definition for 'glm'
compRejectionFraction: no visible global function definition for
  'anova'
simCatResp: no visible global function definition for 'rpois'
simNormCatResp: no visible global function definition for 'rnorm'
testCatEffectBoot: no visible global function definition for 'boot'
Undefined global functions or variables:
  anova boot fRatioStat glm rnorm rpois sumSqCat t.test
Consider adding
  importFrom("stats", "anova", "glm", "rnorm", "rpois", "t.test")
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:
  'multilevel' 'nlme'
A package should be listed in only one of these fields.
'library' or 'require' calls to packages already attached by Depends:
  'multilevel' 'nlme'
  Please remove these calls from your code.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     1.7Mb
    doc   2.4Mb
Running examples in 'psymonitor-Ex.R' failed
The error most likely occurred in:

> ### Name: disp
> ### Title: Generate a table with identified bubble/crisis periods
> ### Aliases: disp
> 
> ### ** Examples
> 
> data(spread)
> 
> y        <- spread$value[150:200]
> obs      <- length(y)
> swindow0 <- floor(obs*(0.01 + 1.8/sqrt(obs)))
> dim      <- obs - swindow0 + 1
> Tb       <- 24 + swindow0 - 1
> 
> # Estimate PSY statistics and CVs
> bsadf          <- PSY(y, swindow0)
> quantilesBsadf <- cvPSYwmboot(y, swindow0, Tb=Tb, nboot = 49, nCores = 2)
> quantile95     <- quantilesBsadf %*% matrix(1, nrow = 1, ncol = dim)
> 
> # locate bubble/crisis dates
> ind95        <- (bsadf > t(quantile95[2, ])) * 1
> monitorDates <- spread$date[swindow0:obs]
> OT           <- locate(ind95, monitorDates)
Warning: No bubble or crisis periods found
> 
> # Show bubble/crisis periods
> disp(OT, obs)
Error: No bubble or crisis periods found.
Execution halted
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.
PurBayes: no visible global function definition for 'update'
PurBayes: no visible global function definition for 'sd'
plot.PurBayes: no visible global function definition for 'plot'
plot.PurBayes: no visible global function definition for 'quantile'
plot.PurBayes: no visible global function definition for 'lines'
summary.PurBayes : <anonymous>: no visible global function definition
  for 'quantile'
Undefined global functions or variables:
  lines plot quantile sd update
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "quantile", "sd", "update")
to your NAMESPACE file.
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.
.grid.matrix: no visible global function definition for 'slot'
.matrix2grid: no visible global function definition for 'as'
.poly2grid: no visible global function definition for 'is'
.poly2grid: no visible global function definition for 'slot'
.poly2grid: no visible global function definition for 'as'
.pycno.core : smooth2D : s1d: no visible global function definition for
  'filter'
.pycno.core: no visible global function definition for 'flush.console'
.pycno2matrix: no visible global function definition for 'slot'
Undefined global functions or variables:
  as filter flush.console is slot
Consider adding
  importFrom("methods", "as", "is", "slot")
  importFrom("stats", "filter")
  importFrom("utils", "flush.console")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
pyramid: no visible global function definition for 'plot'
pyramid: no visible global function definition for 'segments'
pyramid: no visible global function definition for 'lines'
pyramid: no visible global function definition for 'text'
pyramid: no visible global function definition for 'rect'
pyramidf: no visible global function definition for 'segments'
pyramidf: no visible global function definition for 'lines'
pyramidf: no visible global function definition for 'text'
pyramidf: no visible global function definition for 'rect'
Undefined global functions or variables:
  lines plot rect segments text
Consider adding
  importFrom("graphics", "lines", "plot", "rect", "segments", "text")
to your NAMESPACE file.
csQCAbinTest: no visible global function definition for 'p.adjust'
fsQCApermTest: no visible global function definition for 'p.adjust'
mvQCAbinTest: no visible global function definition for 'p.adjust'
p.threshold.adjust: no visible global function definition for
  'p.adjust'
plot.fsQCApt: no visible global function definition for 'dev.cur'
plot.fsQCApt: no visible global function definition for 'dev.new'
plot.fsQCApt: no visible global function definition for 'par'
plot.fsQCApt: no visible global function definition for 'plot'
plot.fsQCApt: no visible global function definition for 'density'
plot.fsQCApt: no visible global function definition for 'axis'
plot.fsQCApt: no visible global function definition for 'polygon'
plot.fsQCApt: no visible global function definition for 'points'
plot.fsQCApt: no visible global function definition for 'hist'
summary.csQCAbt: no visible global function definition for
  'printCoefmat'
summary.fsQCApt: no visible global function definition for
  'printCoefmat'
summary.mvQCAbt: no visible global function definition for
  'printCoefmat'
Undefined global functions or variables:
  axis density dev.cur dev.new hist p.adjust par plot points polygon
  printCoefmat
Consider adding
  importFrom("grDevices", "dev.cur", "dev.new")
  importFrom("graphics", "axis", "hist", "par", "plot", "points",
             "polygon")
  importFrom("stats", "density", "p.adjust", "printCoefmat")
to your NAMESPACE file.
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.
Package suggested but not available for checking: 'biom'
chooseMDoubleBootstrap: no visible global function definition for
  'model.matrix'
chooseMDoubleBootstrap: no visible global function definition for
  'as.formula'
chooseMDoubleBootstrap: no visible global function definition for
  'model.frame'
chooseMDoubleBootstrap: no visible global function definition for 'lm'
chooseMDoubleBootstrap: no visible global function definition for
  'coef'
chooseMDoubleBootstrap: no visible global function definition for
  'quantile'
chooseMDoubleBootstrap: no visible global function definition for
  'qnorm'
getModel: no visible global function definition for 'lm'
getModel: no visible global function definition for 'model.matrix'
getModel: no visible global function definition for 'as.formula'
getModel: no visible global function definition for 'model.frame'
getModel: no visible global function definition for 'model.response'
getModel: no visible global function definition for 'coef'
getModel: no visible global function definition for 'qnorm'
qLearn: no visible global function definition for 'model.matrix'
qLearn: no visible global function definition for 'as.formula'
qLearn: no visible global function definition for 'model.frame'
qLearn: no visible global function definition for 'coef'
qLearn: no visible global function definition for 'lm'
qLearn: no visible global function definition for 'quantile'
Undefined global functions or variables:
  as.formula coef lm model.frame model.matrix model.response qnorm
  quantile
Consider adding
  importFrom("stats", "as.formula", "coef", "lm", "model.frame",
             "model.matrix", "model.response", "qnorm", "quantile")
to your NAMESPACE file.
pcAxisCubeMake: no visible global function definition for 'aggregate'
pcAxisCubeToCSV: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  aggregate write.csv
Consider adding
  importFrom("stats", "aggregate")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    data  11.8Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
ci.length: no visible global function definition for 'qexp'
detectable.bc: no visible global function definition for 'uniroot'
detectable.f2: no visible global function definition for 'uniroot'
detectable.ri: no visible global function definition for 'uniroot'
nu: no visible global function definition for 'pnorm'
nullinfo: no visible global function definition for 'qnorm'
nullinfo: no visible global function definition for 'dnorm'
optselection.bc: no visible global function definition for 'optimize'
optselection.f2: no visible global function definition for 'optimize'
optspacing.bc: no visible global function definition for 'optim'
optspacing.bc: no visible global function definition for 'optimize'
optspacing.f2: no visible global function definition for 'optim'
optspacing.f2: no visible global function definition for 'optimize'
powercalc.bc: no visible global function definition for 'pchisq'
powercalc.f2: no visible global function definition for 'pchisq'
samplesize.bc: no visible global function definition for 'uniroot'
samplesize.f2: no visible global function definition for 'uniroot'
samplesize.ri: no visible global function definition for 'uniroot'
tailprob: no visible global function definition for 'pchisq'
thresh: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  dnorm optim optimize pchisq pnorm qexp qnorm uniroot
Consider adding
  importFrom("stats", "dnorm", "optim", "optimize", "pchisq", "pnorm",
             "qexp", "qnorm", "uniroot")
to your NAMESPACE file.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.6Mb
    doc       2.9Mb
'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').
quadp: no visible global function definition for 'var'
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
alphaf: no visible global function definition for 'pchisq'
alphaf: no visible global function definition for 'dbinom'
conout: no visible global function definition for 'sd'
ibgaout: no visible global function definition for 'qnorm'
ibgaout: no visible global function definition for 'pnorm'
plot.qualint: no visible global function definition for 'qnorm'
powerval: no visible global function definition for 'rnorm'
powerval: no visible global function definition for 'qnorm'
powerval: no visible global function definition for 'pnorm'
print.expplot: no visible global function definition for 'gray'
print.expplot: no visible binding for global variable 'coef'
print.outplot: no visible global function definition for 'gray'
print.outplot: no visible binding for global variable 'coef'
qualint: no visible global function definition for 'qnorm'
qualint: no visible global function definition for 'plot'
qualval: no visible global function definition for 'qnorm'
qualval: no visible global function definition for 'plot'
surout: no visible global function definition for 'tail'
surout: no visible global function definition for 'coef'
Undefined global functions or variables:
  coef dbinom gray pchisq plot pnorm qnorm rnorm sd tail
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "plot")
  importFrom("stats", "coef", "dbinom", "pchisq", "pnorm", "qnorm",
             "rnorm", "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   1.3Mb
    libs   3.3Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   2.1Mb
Running 'testthat.R' [55s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(Quartet)
  > 
  > test_check("Quartet")
  -- 1. Failure: CompareSplits works (@test-PartitionDistance.R#27)  -------------
  c(N = 6, P1 = 3L, P2 = 3L, s = 3, d1 = 0, d2 = 0, r1 = 0, r2 = 0) not equal to CompareSplits(splits9Fewer, splits9).
  4/8 mismatches (average diff: 3)
  [1] 6 -  9 == -3
  [2] 3 -  6 == -3
  [4] 3 -  6 == -3
  [6] 0 - -3 ==  3
  
  == testthat results  ===========================================================
  OK: 146 SKIPPED: 0 FAILED: 1
  1. Failure: CompareSplits works (@test-PartitionDistance.R#27) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [35s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(Quartet)
  > 
  > test_check("Quartet")
  -- 1. Failure: CompareSplits works (@test-PartitionDistance.R#27)  -------------
  c(N = 6, P1 = 3L, P2 = 3L, s = 3, d1 = 0, d2 = 0, r1 = 0, r2 = 0) not equal to CompareSplits(splits9Fewer, splits9).
  4/8 mismatches (average diff: 3)
  [1] 6 -  9 == -3
  [2] 3 -  6 == -3
  [4] 3 -  6 == -3
  [6] 0 - -3 ==  3
  
  == testthat results  ===========================================================
  OK: 146 SKIPPED: 0 FAILED: 1
  1. Failure: CompareSplits works (@test-PartitionDistance.R#27) 
  
  Error: testthat unit tests failed
  Execution halted
File 'QUIC/libs/i386/QUIC.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'QUIC.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'QUIC.o'
File 'QUIC/libs/x64/QUIC.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'QUIC.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'QUIC.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
File 'qVarSel/libs/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 use Fortran I/O
nor system RNGs.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(qwraps2)
  > 
  > test_check("qwraps2")
  -- 1. Failure: Boot Strap (@test-confusion_matrix.R#15)  -----------------------
  round(con_mat_boot$stats[, "Boot Est"], 3) not equivalent to c(0.573, 0.669, 0.532, 0.382, 0.788).
  5/5 mismatches (average diff: 0.003)
  [1] 0.570 - 0.573 == -0.003
  [2] 0.670 - 0.669 ==  0.001
  [3] 0.527 - 0.532 == -0.005
  [4] 0.377 - 0.382 == -0.005
  [5] 0.789 - 0.788 ==  0.001
  
  == testthat results  ===========================================================
  OK: 49 SKIPPED: 0 FAILED: 1
  1. Failure: Boot Strap (@test-confusion_matrix.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(qwraps2)
  > 
  > test_check("qwraps2")
  -- 1. Failure: Boot Strap (@test-confusion_matrix.R#15)  -----------------------
  round(con_mat_boot$stats[, "Boot Est"], 3) not equivalent to c(0.573, 0.669, 0.532, 0.382, 0.788).
  5/5 mismatches (average diff: 0.003)
  [1] 0.570 - 0.573 == -0.003
  [2] 0.670 - 0.669 ==  0.001
  [3] 0.527 - 0.532 == -0.005
  [4] 0.377 - 0.382 == -0.005
  [5] 0.789 - 0.788 ==  0.001
  
  == testthat results  ===========================================================
  OK: 49 SKIPPED: 0 FAILED: 1
  1. Failure: Boot Strap (@test-confusion_matrix.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
mutualCoherence : .setOneMutualP: no visible global function definition
  for 'combn'
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
conf2d.default: no visible global function definition for 'polygon'
conf2d_int: no visible global function definition for 'contourLines'
Undefined global functions or variables:
  contourLines polygon
Consider adding
  importFrom("grDevices", "contourLines")
  importFrom("graphics", "polygon")
to your NAMESPACE file.
'library' or 'require' call to 'rgdal' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'matrixStats' 'rgdal' 'sp'
  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/3.6/R2GUESS.Rcheck/00install.out' for details.
Running examples in 'R2HTML-Ex.R' failed
The error most likely occurred in:

> ### Name: HTM2clip
> ### Title: Wrapper around HTML() to save output to the clipboard
> ### Aliases: HTML2clip
> ### Keywords: print IO file
> 
> ### ** Examples
> 
> if (.Platform$OS == "windows")
+ 	HTML2clip(summary(lm(rating ~., attitude)))
> 
> 
> 
> cleanEx()
Error: connections left open:
	clipboard (clipboard)
Execution halted
Packages suggested but not available for checking: 'rcom', 'RDCOMClient'
'library' or 'require' calls in package code:
  'RDCOMClient' 'rcom'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
PPT.AddBlankSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddDataFrame: no visible global function definition for
  'comIsValidHandle'
PPT.AddDataFrame: no visible global function definition for
  'write.table'
PPT.AddDataFrame: no visible global function definition for 'write.csv'
PPT.AddGraphicstoSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddGraphicstoSlide: no visible global function definition for
  'dev.cur'
PPT.AddGraphicstoSlide: no visible global function definition for
  'dev.list'
PPT.AddGraphicstoSlide: no visible global function definition for
  'savePlot'
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'
Undefined global functions or variables:
  COMCreate comCreateObject comIsValidHandle dev.cur dev.list
  readWindowsShortcut savePlot write.csv write.table
Consider adding
  importFrom("grDevices", "dev.cur", "dev.list", "savePlot")
  importFrom("utils", "write.csv", "write.table")
to your NAMESPACE file.
r2stl: no visible global function definition for 'persp'
Undefined global functions or variables:
  persp
Consider adding
  importFrom("graphics", "persp")
to your NAMESPACE file.
'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.
Package suggested but not available for checking: 'rpvm'
'library' or 'require' call to 'rpvm' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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'
race : aux2.friedman: no visible global function definition for
  'pchisq'
race : aux2.friedman: no visible global function definition for 'qt'
race : aux.friedman: no visible global function definition for
  'wilcox.test'
race : aux.ttest: no visible global function definition for 't.test'
race : aux.ttest: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  .PVM.bufinfo .PVM.exit .PVM.initsend .PVM.mytid .PVM.pkint
  .PVM.pkstrvec .PVM.recv .PVM.send .PVM.spawn .PVM.upkdblvec
  .PVM.upkint .PVM.upkstrvec p.adjust pchisq qt t.test wilcox.test
Consider adding
  importFrom("stats", "p.adjust", "pchisq", "qt", "t.test",
             "wilcox.test")
to your NAMESPACE file.
getsonde: no visible global function definition for 'read.table'
plotsonde: no visible global function definition for 'par'
plotwind: no visible global function definition for 'plot'
plotwind: no visible global function definition for 'mtext'
plotwind: no visible global function definition for 'abline'
skewt.axis: no visible global function definition for 'par'
skewt.axis: no visible global function definition for 'plot'
skewt.axis: no visible global function definition for 'axis'
skewt.axis: no visible global function definition for 'mtext'
skewt.axis: no visible global function definition for 'segments'
skewt.axis: no visible global function definition for 'text'
skewt.axis: no visible global function definition for 'lines'
skewt.lines: no visible global function definition for 'lines'
skewt.points: no visible global function definition for 'points'
station.symbol: no visible global function definition for 'sd'
station.symbol: no visible global function definition for 'par'
station.symbol: no visible global function definition for 'lines'
station.symbol: no visible global function definition for 'polygon'
station.symbol: no visible global function definition for 'text'
station.symbol: no visible global function definition for 'segments'
Undefined global functions or variables:
  abline axis lines mtext par plot points polygon read.table sd
  segments text
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "mtext", "par",
             "plot", "points", "polygon", "segments", "text")
  importFrom("stats", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
RnDif.het: no visible global function definition for 'runif'
RnDif.hom: no visible global function definition for 'runif'
RnDifAdv.hom: no visible global function definition for 'runif'
SoilAdv.hom: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Running 'testthat.R' [11s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rags2ridges)
  > 
  > test_check("rags2ridges")
  -- 1. Failure: armaRidgeP.fused agrees with the old R implmentation (@test-armaR
  isTRUE(...) isn't true.
  
  == testthat results  ===========================================================
  OK: 3893 SKIPPED: 0 FAILED: 1
  1. Failure: armaRidgeP.fused agrees with the old R implmentation (@test-armaRidgeP.fused.R#149) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rags2ridges)
  > 
  > test_check("rags2ridges")
  -- 1. Failure: armaRidgeP.fused agrees with the old R implmentation (@test-armaR
  isTRUE(...) isn't true.
  
  == testthat results  ===========================================================
  OK: 3893 SKIPPED: 0 FAILED: 1
  1. Failure: armaRidgeP.fused agrees with the old R implmentation (@test-armaRidgeP.fused.R#149) 
  
  Error: testthat unit tests failed
  Execution halted
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.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    api           3.1Mb
    htmlwidgets   8.9Mb
Found the following significant warnings:
  Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
See 'd:/Rcompile/CRANpkg/local/3.6/RAMClustR.Rcheck/00install.out' for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   1.2Mb
    libs   3.0Mb
.disableThreads: no visible global function definition for
  'stopCluster'
.enableThreads: no visible global function definition for 'detectCores'
.enableThreads: no visible global function definition for
  'makePSOCKcluster'
.enableThreads: no visible global function definition for
  'clusterExport'
.enableThreads: no visible global function definition for 'clusterCall'
.forwardSelection: no visible binding for global variable 'var'
.forwardSelection: no visible global function definition for 'glm'
.forwardSelection: no visible global function definition for 'formula'
.forwardSelection: no visible global function definition for 'binomial'
.forwardSelection: no visible global function definition for 'lm'
.forwardSelection: no visible global function definition for 'predict'
.predict.internal: no visible global function definition for 'predict'
randomGLM: no visible binding for global variable 'cor'
randomGLM: no visible binding for global variable 'sd'
randomGLM: no visible global function definition for 'var'
thinRandomGLM: no visible global function definition for 'glm'
thinRandomGLM: no visible global function definition for 'binomial'
thinRandomGLM: no visible global function definition for 'lm'
Undefined global functions or variables:
  binomial clusterCall clusterExport cor detectCores formula glm lm
  makePSOCKcluster predict sd stopCluster var
Consider adding
  importFrom("stats", "binomial", "cor", "formula", "glm", "lm",
             "predict", "sd", "var")
to your NAMESPACE file.
anovaF: no visible global function definition for 'anova'
anovaF: no visible global function definition for 'lm'
randInterval: no visible global function definition for 'quantile'
randInterval : <anonymous>: no visible global function definition for
  'quantile'
randPlot: no visible global function definition for 'par'
randPlot: no visible global function definition for 'hist'
randPlot: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline anova hist lm par quantile
Consider adding
  importFrom("graphics", "abline", "hist", "par")
  importFrom("stats", "anova", "lm", "quantile")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/randstr.Rcheck/00install.out' for details.
bartels.rank.test: no visible global function definition for 'na.omit'
bartels.rank.test: no visible global function definition for 'pbeta'
bartels.rank.test: no visible global function definition for 'pnorm'
cox.stuart.test: no visible global function definition for 'pbinom'
difference.sign.test: no visible global function definition for
  'na.omit'
difference.sign.test: no visible global function definition for 'pnorm'
rank.test: no visible global function definition for 'na.omit'
rank.test: no visible global function definition for 'pnorm'
rruns: no visible global function definition for 'runif'
runs.test: no visible global function definition for 'median'
runs.test: no visible global function definition for 'na.omit'
runs.test: no visible global function definition for 'points'
runs.test: no visible global function definition for 'abline'
runs.test: no visible global function definition for 'gray'
runs.test: no visible global function definition for 'pnorm'
turning.point.test: no visible global function definition for 'embed'
turning.point.test: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  abline embed gray median na.omit pbeta pbinom pnorm points runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "points")
  importFrom("stats", "embed", "median", "na.omit", "pbeta", "pbinom",
             "pnorm", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  congruRand.c:180:3: warning: ISO C does not support the 'I64' ms_scanf length modifier [-Wformat=]
  congruRand.c:187:2: warning: ISO C does not support the 'I64' ms_scanf length modifier [-Wformat=]
  congruRand.c:188:2: warning: ISO C does not support the 'I64' ms_scanf length modifier [-Wformat=]
  congruRand.c:189:2: warning: ISO C does not support the 'I64' ms_scanf length modifier [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/3.6/randtoolbox.Rcheck/00install.out' for details.
rank.L2R: no visible global function definition for 'kmeans'
rank.L2R: no visible global function definition for 'pnorm'
rank.LN: no visible global function definition for 'kmeans'
rank.LN: no visible global function definition for 'pnorm'
rank.gs: no visible global function definition for 'qnorm'
rank.wald: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  kmeans pnorm qnorm
Consider adding
  importFrom("stats", "kmeans", "pnorm", "qnorm")
to your NAMESPACE file.
'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.
freq: no visible global function definition for 'xtabs'
freq: no visible binding for global variable 'na.pass'
freq: no visible global function definition for 'melt'
freq: no visible global function definition for 'complete.cases'
freq: no visible global function definition for 'tail'
kurtosis: no visible global function definition for 'na.omit'
label: no visible global function definition for 'tail'
name: no visible global function definition for 'tail'
nvalid : <anonymous>: no visible global function definition for
  'na.omit'
rp.desc: no visible global function definition for 'melt.data.frame'
rp.desc: no visible global function definition for 'cast'
rp.desc: no visible global function definition for 'na.omit'
rp.desc : <anonymous>: no visible global function definition for 'tail'
rp.desc : <anonymous>: no visible global function definition for 'head'
rp.freq: no visible global function definition for 'xtabs'
rp.freq: no visible binding for global variable 'na.pass'
rp.freq: no visible global function definition for 'melt'
rp.freq: no visible global function definition for 'complete.cases'
rp.freq: no visible global function definition for 'tail'
rp.label: no visible global function definition for 'tail'
rp.name: no visible global function definition for 'tail'
rp.outlier : lundcrit: no visible global function definition for 'qf'
rp.outlier: no visible global function definition for 'lm'
rp.outlier: no visible global function definition for 'rstandard'
rp.valid : <anonymous>: no visible global function definition for
  'na.omit'
skewness: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  cast complete.cases head lm melt melt.data.frame na.omit na.pass qf
  rstandard tail xtabs
Consider adding
  importFrom("stats", "complete.cases", "lm", "na.omit", "na.pass", "qf",
             "rstandard", "xtabs")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
fnRAP: no visible global function definition for 'chisq.test'
fnRAP: no visible global function definition for 'combn'
Undefined global functions or variables:
  chisq.test combn
Consider adding
  importFrom("stats", "chisq.test")
  importFrom("utils", "combn")
to your NAMESPACE file.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs   2.3Mb
plotarc: no visible global function definition for 'par'
plotarc: no visible global function definition for 'plot'
plotarc: no visible global function definition for 'lines'
plotpoly: no visible global function definition for 'par'
plotpoly: no visible global function definition for 'plot'
plotpoly: no visible global function definition for 'polygon'
Undefined global functions or variables:
  lines par plot polygon
Consider adding
  importFrom("graphics", "lines", "par", "plot", "polygon")
to your NAMESPACE file.
INT_FIX: no visible global function definition for 'rbinom'
INT_FIX: no visible global function definition for 'glm'
INT_FIX: no visible global function definition for 'as.formula'
INT_FIX: no visible global function definition for 'residuals'
INT_FIX: no visible global function definition for 'var'
INT_RAN: no visible global function definition for 'rbinom'
INT_RAN: no visible global function definition for 'as.formula'
INT_RAN: no visible global function definition for 'predict'
JOINT: no visible global function definition for 'rbinom'
JOINT: no visible global function definition for 'glm'
JOINT: no visible global function definition for 'as.formula'
JOINT: no visible global function definition for 'var'
JOINT: no visible global function definition for 'residuals'
pKuonen: no visible global function definition for 'pchisq'
pKuonen: no visible global function definition for 'uniroot'
pKuonen: no visible global function definition for 'pnorm'
rareGE: no visible global function definition for 'rbinom'
rareGE: no visible global function definition for 'as.formula'
rareGE: no visible global function definition for 'predict'
rareGE: no visible global function definition for 'glm'
rareGE: no visible global function definition for 'residuals'
rareGE: no visible global function definition for 'var'
rareGE_joint_mc: no visible global function definition for 'pchisq'
rareGE_joint_mc: no visible global function definition for 'qchisq'
wuweights: no visible global function definition for 'dbeta'
Undefined global functions or variables:
  as.formula dbeta glm pchisq pnorm predict qchisq rbinom residuals
  uniroot var
Consider adding
  importFrom("stats", "as.formula", "dbeta", "glm", "pchisq", "pnorm",
             "predict", "qchisq", "rbinom", "residuals", "uniroot",
             "var")
to your NAMESPACE file.
BiogTest.individual: no visible global function definition for 'combn'
BiogTest.individual: no visible global function definition for 'runif'
BiogTest.individual: no visible global function definition for 'rlnorm'
BiogTest.individual: no visible global function definition for
  'rnbinom'
BiogTest.sample: no visible global function definition for 'combn'
BiogTest.sample: no visible global function definition for 'runif'
BiogTest.sample: no visible global function definition for 'rlnorm'
BiogTest.sample: no visible global function definition for 'rnbinom'
BiogTest.sample: no visible global function definition for 'aggregate'
EcoTest.individual: no visible global function definition for 'xtabs'
plot.BiogTest: no visible global function definition for 'quantile'
plot.BiogTest: no visible global function definition for 'combn'
plot.EcoTest: no visible global function definition for 'quantile'
Undefined global functions or variables:
  aggregate combn quantile rlnorm rnbinom runif xtabs
Consider adding
  importFrom("stats", "aggregate", "quantile", "rlnorm", "rnbinom",
             "runif", "xtabs")
  importFrom("utils", "combn")
to your NAMESPACE file.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    libs   2.3Mb
rateratio.test: no visible global function definition for
  'complete.cases'
rateratio.test: no visible global function definition for 'pbinom'
rateratio.test : p.L: no visible global function definition for 'qbeta'
rateratio.test : p.U: no visible global function definition for 'qbeta'
Undefined global functions or variables:
  complete.cases pbinom qbeta
Consider adding
  importFrom("stats", "complete.cases", "pbinom", "qbeta")
to your NAMESPACE file.
concordance: no visible global function definition for 'quantile'
concordance : Normal: no visible global function definition for 'qnorm'
concordance : Normal: no visible global function definition for 'pnorm'
concordance : MC: no visible global function definition for 'rmultinom'
concordance : MC: no visible global function definition for 'quantile'
concordance: no visible global function definition for 'qnorm'
concordance: no visible global function definition for 'pnorm'
concordance : Chisq: no visible global function definition for 'qchisq'
concordance : Chisq: no visible global function definition for 'pchisq'
concordance : Normal2: no visible global function definition for
  'qnorm'
concordance : Normal2: no visible global function definition for
  'pnorm'
concordance : MC2: no visible global function definition for
  'rmultinom'
concordance : MC2: no visible global function definition for 'quantile'
wlin.conc: no visible global function definition for 'quantile'
wlin.conc : MC: no visible global function definition for 'rmultinom'
wlin.conc : MC: no visible global function definition for 'quantile'
wquad.conc: no visible global function definition for 'quantile'
wquad.conc : MC: no visible global function definition for 'rmultinom'
wquad.conc : MC: no visible global function definition for 'quantile'
Undefined global functions or variables:
  pchisq pnorm qchisq qnorm quantile rmultinom
Consider adding
  importFrom("stats", "pchisq", "pnorm", "qchisq", "qnorm", "quantile",
             "rmultinom")
to your NAMESPACE file.
.GCD: no visible global function definition for 'as.polynomial'
.LCM: no visible global function definition for 'as.polynomial'
.is_zero_polynomial: no visible global function definition for 'coef'
.poly2expr: no visible global function definition for 'coef'
integral.rationalfun: no visible global function definition for 'coef'
integraterf.transcendent: no visible global function definition for
  'coef'
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 'coef'
simplify: no visible global function definition for 'polynomial'
Undefined global functions or variables:
  as.polynomial coef is.polynomial polynomial
Consider adding
  importFrom("stats", "coef")
to your NAMESPACE file.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    etc    1.9Mb
    po     1.2Mb
.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.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.7Mb
Error(s) in re-building vignettes:
--- re-building 'PoS_codata.Rmd' using rmarkdown
--- finished re-building 'PoS_codata.Rmd'

--- re-building 'PoS_interim.Rmd' using rmarkdown
--- finished re-building 'PoS_interim.Rmd'

--- re-building 'customizing_plots.Rmd' using rmarkdown
Loading required package: Rcpp
This is RBesT version 1.3.7
This is bayesplot version 1.6.0
- Online documentation and vignettes at mc-stan.org/bayesplot
- bayesplot theme set to bayesplot::theme_default()
   * Does _not_ affect other ggplot2 plots
   * See ?bayesplot_theme_set for details on theme setting
Final MCMC sample equivalent to less than 1000 independent draws.
Please consider increasing the MCMC simulation size.
--- finished re-building 'customizing_plots.Rmd'

--- re-building 'introduction.Rmd' using rmarkdown
--- finished re-building 'introduction.Rmd'

--- re-building 'introduction_normal.Rmd' using rmarkdown
--- finished re-building 'introduction_normal.Rmd'

--- re-building 'robustMAP.Rmd' using rmarkdown
--- finished re-building 'robustMAP.Rmd'

--- re-building 'variances_MAP.Rmd' using rmarkdown
Quitting from lines 137-148 (variances_MAP.Rmd) 
Error: processing vignette 'variances_MAP.Rmd' failed with diagnostics:
dims [product 2] do not match the length of object [3]
--- failed re-building 'variances_MAP.Rmd'

SUMMARY: processing the following file failed:
  'variances_MAP.Rmd'

Error: Vignette re-building failed.
Execution halted
GetHistoricTradeData: 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.
bn2nbn: no visible binding for global variable 'bn.fit'
chain4chain: no visible binding for global variable 'head'
chain4chain: no visible binding for global variable 'tail'
estimate8arcs: no visible global function definition for 'lm'
estimate8arcs: no visible global function definition for 'coefficients'
estimate8nbn: no visible global function definition for 'lm'
estimate8nbn: no visible global function definition for 'as.formula'
estimate8nbn: no visible global function definition for 'anova'
estimate8nbn: no visible global function definition for 'coefficients'
generate8chain: no visible global function definition for 'runif'
generate8chain: no visible global function definition for 'rbinom'
generate8nbn: no visible global function definition for 'runif'
generate8nbn: no visible global function definition for 'rbinom'
nbn2bnfit: no visible global function definition for 'model2network'
nbn2bnfit: no visible global function definition for 'custom.fit'
simulate8gema: no visible global function definition for 'rnorm'
simulate8mn: no visible global function definition for 'mvrnorm'
simulate8nbn: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  anova as.formula bn.fit coefficients custom.fit head lm model2network
  mvrnorm rbinom rnorm runif tail
Consider adding
  importFrom("stats", "anova", "as.formula", "coefficients", "lm",
             "rbinom", "rnorm", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
SumTestSens: no visible global function definition for 'pnorm'
binarysens: no visible global function definition for 'dbinom'
hlsens: no visible global function definition for 'wilcox.test'
iv_sens: no visible global function definition for 'pnorm'
mcontrol: no visible global function definition for 'pnorm'
psens: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dbinom pnorm wilcox.test
Consider adding
  importFrom("stats", "dbinom", "pnorm", "wilcox.test")
to your NAMESPACE file.
Running examples in 'rbtc-Ex.R' failed
The error most likely occurred in:

> ### Name: Wif2PrivKey
> ### Title: Create private key from WIF
> ### Aliases: Wif2PrivKey
> 
> ### ** Examples
> 
> pk1 <- createPrivateKey()
Warning in createPrivateKey() :
  
For exemplary purposes, only.
Use at your own risk!

> wif <- PrivKey2Wif(pk1)
Warning in PrivKey2Wif(pk1) :
  
For exemplary purposes, only.
Use at your own risk!

Warning in base58CheckEncode(privkeyextcs) :
  out-of-range values treated as 0 in coercion to raw
> pk2 <- Wif2PrivKey(wif)
Warning in Wif2PrivKey(wif) :
  
For exemplary purposes, only.
Use at your own risk!

Error in Wif2PrivKey(wif) : First character in WIF does neither
correspond to mainnet nor testnet.
Execution halted
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.
'library' or 'require' calls to packages already attached by Depends:
  'RColorBrewer' 'classInt' 'maptools'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'RColorBrewer' 'classInt' 'maptools'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
RC.read.table: no visible global function definition for 'type.convert'
Undefined global functions or variables:
  type.convert
Consider adding
  importFrom("utils", "type.convert")
to your NAMESPACE file.
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    cont  23.3Mb
.onAttach: no visible global function definition for
  'packageDescription'
rselect.list: no visible global function definition for 'select.list'
Undefined global functions or variables:
  packageDescription select.list
Consider adding
  importFrom("utils", "packageDescription", "select.list")
to your NAMESPACE file.
climdex.data.frame: no visible global function definition for
  'as.PCICt'
Undefined global functions or variables:
  as.PCICt
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.
cmaOptimDP: no visible global function definition for 'flush.console'
Undefined global functions or variables:
  flush.console
Consider adding
  importFrom("utils", "flush.console")
to your NAMESPACE file.
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.
'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
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.
'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.
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'
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.0Mb
    po    2.1Mb
brewer.pal: no visible global function definition for 'rgb'
display.brewer.all: no visible global function definition for 'par'
display.brewer.all: no visible global function definition for 'plot'
display.brewer.all: no visible global function definition for 'rect'
display.brewer.all: no visible global function definition for 'text'
display.brewer.pal: no visible global function definition for 'image'
Undefined global functions or variables:
  image par plot rect rgb text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "image", "par", "plot", "rect", "text")
to your NAMESPACE file.
Running examples in 'rcongresso-Ex.R' failed
The error most likely occurred in:

> ### Name: fetch_despesas_deputado
> ### Title: Fetches expenditures from deputy
> ### Aliases: fetch_despesas_deputado
> 
> ### ** Examples
> 
> gastos_abel_mesquita <- fetch_despesas_deputado(id = 178957)
Error: Falha na requisicao a API dos Dados Abertos. Erro 400 ao tentar acessar: https://dadosabertos.camara.leg.br/api/v2/deputados/178957/despesas?id=178957
Execution halted
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rcongresso)
  > 
  > test_check("rcongresso")
  -- 1. Error: (unknown) (@test_deputados.R#81)  ---------------------------------
  argument "message" is missing, with no default
  1: skip() at testthat/test_deputados.R:81
  2: structure(list(message = message), class = c("skip", "condition"))
  
  -- 2. Error: (unknown) (@test_proposicoes.R#91)  -------------------------------
  could not find function "FUN1"
  1: check_api() at testthat/test_proposicoes.R:91
  2: tryCatch(setup(), error = function(e) {
         message(e)
         return(FALSE)
     }) at testthat/test_proposicoes.R:15
  3: tryCatchList(expr, classes, parentenv, handlers)
  4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  5: value[[3L]](cond)
  6: message(e) at testthat/test_proposicoes.R:16
  7: withRestarts({
         signalCondition(cond)
         defaultHandler(cond)
     }, muffleMessage = function() NULL)
  8: withOneRestart(expr, restarts[[1L]])
  9: doWithOneRestart(return(expr), restart)
  
  -- 3. Error: (unknown) (@test_votacoes.R#70)  ----------------------------------
  argument "message" is missing, with no default
  1: skip() at testthat/test_votacoes.R:70
  2: structure(list(message = message), class = c("skip", "condition"))
  
  == testthat results  ===========================================================
  OK: 13 SKIPPED: 0 FAILED: 3
  1. Error: (unknown) (@test_deputados.R#81) 
  2. Error: (unknown) (@test_proposicoes.R#91) 
  3. Error: (unknown) (@test_votacoes.R#70) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'introducao-rcongresso.Rmd' using rmarkdown

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 36-38 (introducao-rcongresso.Rmd) 
Error: processing vignette 'introducao-rcongresso.Rmd' failed with diagnostics:
could not find function "FUN1"
--- failed re-building 'introducao-rcongresso.Rmd'

--- re-building 'utilizando-fetch-proposicao.Rmd' using rmarkdown

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 57-63 (utilizando-fetch-proposicao.Rmd) 
Error: processing vignette 'utilizando-fetch-proposicao.Rmd' failed with diagnostics:
could not find function "FUN1"
--- failed re-building 'utilizando-fetch-proposicao.Rmd'

SUMMARY: processing the following files failed:
  'introducao-rcongresso.Rmd' 'utilizando-fetch-proposicao.Rmd'

Error: Vignette re-building failed.
Execution halted
addLine: no visible global function definition for 'abline'
ellipse: no visible global function definition for 'approx'
ellipse: no visible global function definition for 'tail'
Undefined global functions or variables:
  abline approx tail
Consider adding
  importFrom("graphics", "abline")
  importFrom("stats", "approx")
  importFrom("utils", "tail")
to your NAMESPACE file.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    corpora   7.4Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    include   5.7Mb
    libs      1.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    include   7.7Mb
    libs      1.8Mb
Gauss: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    include   1.8Mb
    lib       3.9Mb
    libs      2.8Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      1.7Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib       8.9Mb
    libs      1.0Mb
installed size is 35.0Mb
  sub-directories of 1Mb or more:
    include   8.8Mb
    libs     26.1Mb
Files which contain pragma(s) suppressing diagnostics:
  'inst/include/ql/math/distributions/normaldistribution.hpp'
  'inst/include/ql/math/matrix.hpp'
  'inst/include/ql/math/optimization/levenbergmarquardt.hpp'
  'inst/include/ql/math/statistics/incrementalstatistics.hpp'
  'inst/include/ql/time/date.hpp' 'inst/include/ql/time/imm.hpp'
  'inst/include/ql/utilities/dataparsers.hpp'
  'inst/include/ql/utilities/null.hpp'
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    doc       2.6Mb
    include   6.3Mb
    libs      2.0Mb
Package suggested but not available for checking: 'Rcompression'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Packages in Depends field not imported from:
  'MASS' 'Matrix' 'lattice' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CUR: no visible global function definition for 'runif'
CUR: no visible global function definition for 'new'
plotLeverage,CURobj: no visible global function definition for 'plot'
plotLeverage,CURobj: no visible global function definition for 'points'
plotLeverage,CURobj: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline new plot points runif
Consider adding
  importFrom("graphics", "abline", "plot", "points")
  importFrom("methods", "new")
  importFrom("stats", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
get.datamarket.csv: no visible global function definition for
  'read.csv'
getUserAgent: no visible global function definition for 'sessionInfo'
Undefined global functions or variables:
  read.csv sessionInfo
Consider adding
  importFrom("utils", "read.csv", "sessionInfo")
to your NAMESPACE file.
Running 'testthat.R' [31s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("rdefra")
  > 
  > test_check("rdefra")
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  -- 1. Failure: Metadata should be in the right format (@test-data.R#44)  -------
  `x` not equal to `expected`.
  1 element mismatch
  
  Error in file(file, "rt") : cannot open the connection
  -- 2. Failure: Data should be in the right format (@test-data.R#55)  -----------
  `x` not equal to `expected`.
  'is.NA' value mismatch: 0 in current 1 in target
  
  == testthat results  ===========================================================
  OK: 39 SKIPPED: 1 FAILED: 2
  1. Failure: Metadata should be in the right format (@test-data.R#44) 
  2. Failure: Data should be in the right format (@test-data.R#55) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'rdefra_vignette.Rmd' using knitr
Warning in file(file, "rt") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine sichere in eine nicht sichere Verbindung.'
No data available for station MY1
Warning: Unknown or uninitialised column: 'unit'.
Warning: Unknown or uninitialised column: 'unit'.

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Warning: Unknown or uninitialised column: 'datetime'.
Quitting from lines 117-123 (rdefra_vignette.Rmd) 
Error: processing vignette 'rdefra_vignette.Rmd' failed with diagnostics:
do not know how to convert 'df$datetime' to class "POSIXlt"
--- failed re-building 'rdefra_vignette.Rmd'

SUMMARY: processing the following file failed:
  'rdefra_vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
distimage: no visible binding for global variable 'terrain.colors'
distimage: no visible global function definition for 'filled.contour'
distimage: no visible global function definition for 'title'
distimage: no visible global function definition for 'axis'
distimage: no visible global function definition for 'lines'
drawkpc: no visible global function definition for 'plot'
drawkpc: no visible global function definition for 'segments'
drawkpc: no visible global function definition for 'lines'
modelimage: no visible binding for global variable 'topo.colors'
modelimage: no visible global function definition for 'filled.contour'
modelimage: no visible global function definition for 'title'
modelimage: no visible global function definition for 'axis'
modelimage: no visible global function definition for 'lines'
sincdata: no visible global function definition for 'runif'
sincdata: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  axis filled.contour lines plot rnorm runif segments terrain.colors
  title topo.colors
Consider adding
  importFrom("grDevices", "terrain.colors", "topo.colors")
  importFrom("graphics", "axis", "filled.contour", "lines", "plot",
             "segments", "title")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Running 'testthat.R' [16s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rdhs)
  > 
  > Sys.setenv("rdhs_RENVIRON_PERMISSION" = 1)
  > test_check("rdhs")
  -- 1. Error: update_rdhs_config (@test_miscellaneous.R#97)  --------------------
  cannot open the connection
  1: dhs_data_updates() at testthat/test_miscellaneous.R:97
  2: handle_api_request(endpoint, query, all_results, client, force)
  3: check_for_client()
  4: rdhs_setup()
  5: client_dhs(config = config, root = config$cache_path)
  6: R6_client_dhs$new(config, api_key, root)
  7: .subset2(public_bind_env, "initialize")(...)
  8: saveRDS(self, file.path(root, client_file_name()))
  9: gzfile(file, mode)
  
  trying URL 'https://dhsprogram.com/customcf/legacy/data/sample_download_dataset.cfm?Filename=ZZMR61FL.ZIP&Tp=1&Ctry_Code=zz&survey_id=0&doctype=dhs'
  Content type 'application/x-zip-compressed' length 597481 bytes (583 KB)
  ==================================================
  downloaded 583 KB
  
    adding: temp/RtmpmIOlVP/fileb9e0cbb63d8/ZZMR61FL.DAT (deflated 85%)
  trying URL 'https://dhsprogram.com/customcf/legacy/data/sample_download_dataset.cfm?Filename=ZZAR61FL.ZIP&Tp=4&Ctry_Code=zz&survey_id=0&doctype=hiv'
  Content type 'application/x-zip-compressed' length 81939 bytes (80 KB)
  ==================================================
  downloaded 80 KB
  
  == testthat results  ===========================================================
  OK: 31 SKIPPED: 42 FAILED: 1
  1. Error: update_rdhs_config (@test_miscellaneous.R#97) 
  
  Error: testthat unit tests failed
  Execution halted
sumry_categorical: no visible global function definition for 'freq'
sumry_continous: no visible global function definition for 'quantile'
Undefined global functions or variables:
  freq quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
Found the following significant warnings:
  skein_block64.c:226:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.6/RDieHarder.Rcheck/00install.out' for details.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
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.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   2.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   2.6Mb
Files which contain pragma(s) suppressing diagnostics:
  'inst/include/re2/prog.h' 'inst/include/re2/re2.h'
  'inst/include/re2/regexp.h' 'src/dfa.cc' 'src/onepass.cc'
'library' or 'require' calls to packages already attached by Depends:
  'leaps' 'mgcv'
  Please remove these calls from your code.
xy: warning in assign(xname, X, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
xy: warning in assign(yname, y, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
bestmods: no visible global function definition for 'abline'
bestmods: no visible global function definition for 'axis'
bestmods: no visible global function definition for 'lines'
cic: no visible global function definition for 'lsfit'
cic: no visible global function definition for 'var'
cvic: no visible global function definition for 'lsfit'
cvic: no visible global function definition for 'lm'
eic: no visible global function definition for 'lsfit'
eic: no visible global function definition for 'lm'
ic.min: no visible global function definition for 'lsfit'
scoremods: no visible global function definition for 'lsfit'
scoremods: no visible global function definition for 'var'
xy: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  abline axis lines lm lsfit rnorm var
Consider adding
  importFrom("graphics", "abline", "axis", "lines")
  importFrom("stats", "lm", "lsfit", "rnorm", "var")
to your NAMESPACE file.
ReCiPa: no visible global function definition for 'count.fields'
ReCiPa: 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.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
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.
cook.outliers: no visible global function definition for 'lm'
cook.outliers: no visible global function definition for
  'cooks.distance'
nonparRI: no visible global function definition for 'quantile'
plot.interval: no visible global function definition for 'par'
plot.interval: no visible global function definition for 'plot.new'
plot.interval: no visible global function definition for 'plot.window'
plot.interval: no visible global function definition for 'segments'
plot.interval: no visible global function definition for 'axis'
plot.interval: no visible global function definition for 'title'
plot.interval: no visible global function definition for 'legend'
plot.interval: no visible global function definition for 'box'
plot.interval: no visible global function definition for 'text'
robust: no visible global function definition for 'qt'
singleRefLimit: no visible global function definition for 'qnorm'
singleRefLimit: no visible global function definition for
  'shapiro.test'
singleRefLimit: no visible global function definition for 'ks.test'
Undefined global functions or variables:
  axis box cooks.distance ks.test legend lm par plot.new plot.window
  qnorm qt quantile segments shapiro.test text title
Consider adding
  importFrom("graphics", "axis", "box", "legend", "par", "plot.new",
             "plot.window", "segments", "text", "title")
  importFrom("stats", "cooks.distance", "ks.test", "lm", "qnorm", "qt",
             "quantile", "shapiro.test")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.6/refund.Rcheck/00install.out' for details.
cluster.reg: no visible global function definition for 'rnorm'
cluster.reg: no visible global function definition for 'runif'
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
.area.my: no visible global function definition for 'density'
optimalGT : <anonymous>: no visible global function definition for
  'median'
optimalGT: no visible global function definition for 'png'
optimalGT: no visible global function definition for 'dev.off'
permutation: no visible global function definition for 'flush.console'
plot.wls: no visible global function definition for 'par'
plot.wls: no visible global function definition for 'plot'
plot.wls: no visible global function definition for 'text'
plot.wls: no visible global function definition for 'abline'
reGenotyper: no visible global function definition for 'flush.console'
reGenotyper: no visible binding for global variable 'var'
reGenotyper: no visible global function definition for 'plot'
Undefined global functions or variables:
  abline density dev.off flush.console median par plot png text var
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "abline", "par", "plot", "text")
  importFrom("stats", "density", "median", "var")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
binregtest: no visible global function definition for 'str'
binregtest: no visible binding for global variable 'str'
binregtest: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif str
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "str")
to your NAMESPACE file.
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(reinforcelearn)
  > 
  > test_check("reinforcelearn")
  -- 1. Failure: getReplayMemory returns list (@test_accessor_functions.R#22)  ---
  getReplayMemory(agent) not equal to list(...).
  Component 1: Component 2: Mean absolute difference: 1
  Component 1: Component 4: Mean relative difference: 0.03333333
  Component 2: Component 1: Mean relative difference: 0.03333333
  Component 2: Component 4: Mean relative difference: 0.05
  
  == testthat results  ===========================================================
  OK: 20 SKIPPED: 0 FAILED: 1
  1. Failure: getReplayMemory returns list (@test_accessor_functions.R#22) 
  
  Error: testthat unit tests failed
  Execution halted
Package which this enhances but not available for checking: 'Rcplex'
.onAttach: no visible global function definition for
  'packageDescription'
.relax.cv.elnet: no visible global function definition for 'predict'
.relax.cv.elnet: no visible binding for global variable 'weighted.mean'
.relax.cv.lognet: no visible global function definition for 'predict'
.relax.cv.lognet: no visible binding for global variable
  'weighted.mean'
.relax.cvcompute: no visible binding for global variable
  'weighted.mean'
.single.column: no visible global function definition for 'glm'
.single.column: no visible global function definition for 'coef'
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 'predict'
cv.relaxnet: no visible global function definition for
  'mc.reset.stream'
cv.relaxnet: no visible global function definition for 'mclapply'
predict.cv.alpha.relaxnet: no visible global function definition for
  'predict'
predict.cv.relaxnet: no visible global function definition for
  'predict'
predict.relaxnet: no visible global function definition for 'predict'
Undefined global functions or variables:
  coef glm mc.reset.stream mclapply packageDescription predict
  weighted.mean
Consider adding
  importFrom("stats", "coef", "glm", "predict", "weighted.mean")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
'library' or 'require' call to 'lars' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'lars'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
relaxo: no visible global function definition for 'lars'
Undefined global functions or variables:
  lars
print.summary.rem: no visible global function definition for
  'printCoefmat'
print.summary.rem: no visible global function definition for 'pnorm'
print.summary.rem: no visible binding for global variable 'quantile'
print.summary.rem: no visible global function definition for 'pchisq'
print.summary.rem.dyad: no visible global function definition for
  'printCoefmat'
print.summary.rem.dyad: no visible global function definition for
  'pnorm'
print.summary.rem.dyad: no visible global function definition for
  'pchisq'
rem: no visible global function definition for 'rnorm'
rem: no visible global function definition for 'dnorm'
rem: no visible global function definition for 'runif'
rem: no visible global function definition for 'rchisq'
rem: no visible global function definition for 'cov'
rem.dyad: no visible global function definition for 'rnorm'
rem.dyad: no visible global function definition for 'optim'
rem.dyad: no visible global function definition for 'rchisq'
rem.dyad: no visible global function definition for 'quantile'
rem.dyad: no visible global function definition for 'sd'
rem.dyad: no visible global function definition for 'var'
rem.dyad.lprior: no visible global function definition for 'dnorm'
rem.dyad.lprior: no visible global function definition for 'dt'
Undefined global functions or variables:
  cov dnorm dt optim pchisq pnorm printCoefmat quantile rchisq rnorm
  runif sd var
Consider adding
  importFrom("stats", "cov", "dnorm", "dt", "optim", "pchisq", "pnorm",
             "printCoefmat", "quantile", "rchisq", "rnorm", "runif",
             "sd", "var")
to your NAMESPACE file.
CapDistSlope: no visible global function definition for 'coef'
CapDistSlope: no visible global function definition for 'lm'
EnergyEntropyDecomp: no visible global function definition for 'legend'
FernholzDecomp: no visible global function definition for 'legend'
Invest: no visible global function definition for 'par'
Invest: no visible global function definition for 'legend'
SimMarketModel: no visible global function definition for 'rnorm'
plot.capdist: no visible global function definition for 'plot'
plot.capdist: no visible global function definition for 'abline'
plot.capdist: no visible global function definition for 'lm'
plot.toymkt: no visible global function definition for 'par'
plot.toymkt: no visible global function definition for 'plot'
plot.toymkt: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline coef legend lm par plot rnorm
Consider adding
  importFrom("graphics", "abline", "legend", "par", "plot")
  importFrom("stats", "coef", "lm", "rnorm")
to your NAMESPACE file.
RearrangeData: no visible global function definition for 'rainbow'
RearrangeData: no visible global function definition for 'hclust'
RearrangeData: no visible global function definition for
  'as.dendrogram'
RearrangeData: no visible global function definition for 'heatmap'
RearrangeData: no visible global function definition for 'pdf'
RearrangeData: no visible global function definition for
  'colorRampPalette'
RearrangeData: no visible global function definition for 'legend'
RearrangeData: no visible global function definition for 'dev.off'
RearrangeJoseph: no visible global function definition for
  'write.table'
RearrangeJoseph: no visible global function definition for
  'as.dendrogram'
RearrangeJoseph: no visible global function definition for
  'order.dendrogram'
colorDendClass : colLab: no visible global function definition for
  'is.leaf'
colorDendClass: no visible global function definition for 'dendrapply'
colorDendClass: no visible global function definition for 'plot'
testData1: no visible global function definition for 'runif'
testData1: no visible global function definition for 'image'
testData2: no visible global function definition for 'runif'
testData2: no visible global function definition for 'image'
Undefined global functions or variables:
  as.dendrogram colorRampPalette dendrapply dev.off hclust heatmap
  image is.leaf legend order.dendrogram pdf plot rainbow runif
  write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf",
             "rainbow")
  importFrom("graphics", "image", "legend", "plot")
  importFrom("stats", "as.dendrogram", "dendrapply", "hclust", "heatmap",
             "is.leaf", "order.dendrogram", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file.
GlobTestMissing: no visible global function definition for 'lme'
GlobTestMissing: no visible global function definition for 'anova'
TestStatSP: no visible global function definition for 'pf'
TestStatSimple: no visible global function definition for 'ginv'
TestStatSimple: no visible global function definition for 'pf'
Undefined global functions or variables:
  anova ginv lme pf
Consider adding
  importFrom("stats", "anova", "pf")
to your NAMESPACE file.
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.
MBoxtest: no visible global function definition for 'var'
jrparams: no visible global function definition for 'prcomp'
jrparams: no visible global function definition for 'predict'
jrparams: no visible global function definition for 'qchisq'
jrparams: no visible global function definition for 'qf'
Undefined global functions or variables:
  prcomp predict qchisq qf var
Consider adding
  importFrom("stats", "prcomp", "predict", "qchisq", "qf", "var")
to your NAMESPACE file.
call.eqs: no visible global function definition for 'write.table'
read.eqs: no visible global function definition for 'read.fwf'
Undefined global functions or variables:
  read.fwf write.table
Consider adding
  importFrom("utils", "read.fwf", "write.table")
to your NAMESPACE file.
.resampleMakeFunction: no visible global function definition for 'is'
.resampleSetSeed: no visible global function definition for 'runif'
CI.bca: no visible global function definition for 'is'
CI.bca: no visible global function definition for 'qnorm'
CI.bca: no visible global function definition for 'pnorm'
CI.t: no visible global function definition for 'qt'
ExpandProbs: no visible global function definition for 'pnorm'
ExpandProbs: no visible global function definition for 'qt'
colVars : f: no visible global function definition for 'var'
colVars: no visible global function definition for 'var'
hist.resample: no visible global function definition for 'density'
hist.resample: no visible global function definition for 'lines'
hist.resample: no visible global function definition for 'points'
hist.resample: no visible global function definition for 'approx'
hist.resample: no visible global function definition for 'segments'
resample: no visible global function definition for 'is'
samp.bootknife: no visible global function definition for 'runif'
samp.bootstrap: no visible global function definition for 'runif'
Undefined global functions or variables:
  approx density is lines pnorm points qnorm qt runif segments var
Consider adding
  importFrom("graphics", "lines", "points", "segments")
  importFrom("methods", "is")
  importFrom("stats", "approx", "density", "pnorm", "qnorm", "qt",
             "runif", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages in Depends field not imported from:
  'gWidgets' 'gWidgetsRGtk2' 'plyr' 'reshape2'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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<-'
Undefined global functions or variables:
  add addHandlerChanged addHandlerClicked addSpring delete gbutton
  gcheckbox gdf gedit ggroup glabel gmessage gnotebook gtable gwindow
  size<- svalue svalue<- visible<-
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.
Warning: no function found corresponding to methods exports from 'retimes' 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.
dexgauss: no visible global function definition for 'pnorm'
loglik: no visible global function definition for 'pnorm'
mexgauss: no visible global function definition for 'sd'
rexgauss: no visible global function definition for 'rnorm'
rexgauss: no visible global function definition for 'rexp'
timefit: no visible global function definition for 'optim'
timefit: no visible global function definition for 'sd'
timefit: no visible global function definition for 'par'
timefit: no visible global function definition for 'hist'
timefit: no visible global function definition for 'density'
timefit: no visible global function definition for 'curve'
timefit: no visible global function definition for 'new'
plot,timefit: no visible global function definition for 'density'
plot,timefit: no visible global function definition for 'par'
plot,timefit: no visible global function definition for 'curve'
Undefined global functions or variables:
  curve density hist new optim par pnorm rexp rnorm sd
Consider adding
  importFrom("graphics", "curve", "hist", "par")
  importFrom("methods", "new")
  importFrom("stats", "density", "optim", "pnorm", "rexp", "rnorm", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
plot.reweight: no visible global function definition for 'par'
plot.reweight: no visible global function definition for 'plot'
plot.reweight: no visible global function definition for 'density'
plot.reweight: no visible global function definition for 'rug'
reweight: no visible global function definition for 'aggregate'
search.best.h: no visible global function definition for 'quantile'
Undefined global functions or variables:
  aggregate density par plot quantile rug
Consider adding
  importFrom("graphics", "par", "plot", "rug")
  importFrom("stats", "aggregate", "density", "quantile")
to your NAMESPACE file.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
FDSNGetTimeSeries: 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.
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.
Packages in Depends field not imported from:
  'XML' 'xts'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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'
Undefined global functions or variables:
  as.xts htmlTreeParse xmlErrorCumulator xmlRoot xmlSize xmlValue
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    java   5.2Mb
.testLTS: no visible binding for global variable 'stackloss'
Undefined global functions or variables:
  stackloss
Consider adding
  importFrom("datasets", "stackloss")
to your NAMESPACE file.
gabriel.plot: no visible global function definition for 'barplot'
gabriel.plot: no visible global function definition for 'arrows'
rgabriel: no visible binding for global variable 'sd'
rgabriel : psmm_x: no visible global function definition for 'pnorm'
rgabriel : psmm: no visible global function definition for 'integrate'
rgabriel : qsmm: no visible global function definition for 'qnorm'
rgabriel : qsmm: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  arrows barplot integrate pnorm qnorm sd uniroot
Consider adding
  importFrom("graphics", "arrows", "barplot")
  importFrom("stats", "integrate", "pnorm", "qnorm", "sd", "uniroot")
to your NAMESPACE file.
Package in Depends field not imported from: 'gsl'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
gammaIntegral: no visible global function definition for 'integrate'
gammaIntegral : <anonymous>: no visible global function definition for
  'hyperg_1F1'
gammaMLE: no visible global function definition for 'weighted.mean'
gammaMME: no visible binding for global variable 'sd'
gammaMME: no visible binding for global variable 'var'
Undefined global functions or variables:
  hyperg_1F1 integrate sd var weighted.mean
Consider adding
  importFrom("stats", "integrate", "sd", "var", "weighted.mean")
to your NAMESPACE file.
installed size is 80.3Mb
  sub-directories of 1Mb or more:
    gdal       3.9Mb
    libs      68.7Mb
    pictures   1.3Mb
    proj       5.0Mb
genoud: multiple local function definitions for 'fn1.bfgs' with
  different formal arguments
genoud: multiple local function definitions for 'gr1' with different
  formal arguments
genoud: multiple local function definitions for 'hess.fn' with
  different formal arguments
genoud_transform: multiple local function definitions for 'fn1.bfgs'
  with different formal arguments
genoud_transform: multiple local function definitions for 'gr1' with
  different formal arguments
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.8Mb
gexf.to.igraph: no visible global function definition for 'rgb'
igraph.to.gexf: no visible global function definition for 'col2rgb'
Undefined global functions or variables:
  col2rgb rgb
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
to your NAMESPACE file.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc     3.9Mb
    fonts   1.5Mb
    libs    2.0Mb
Packages suggested but not available for checking: 'pmg', 'SVGAnnotation'
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extra   9.3Mb
'library' or 'require' call to 'gWidgetsRGtk2' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'RGtk2' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    help  10.7Mb
    libs   5.1Mb
File 'RGtk2/libs/i386/RGtk2.dll':
  Found non-API calls to R: 'R_new_custom_connection',
    'Rf_EncodeInteger', 'Rf_EncodeLogical', 'Rf_EncodeReal',
    'Rf_formatInteger', 'Rf_formatLogical', 'Rf_formatReal'
File 'RGtk2/libs/x64/RGtk2.dll':
  Found non-API calls to R: 'R_new_custom_connection',
    'Rf_EncodeInteger', 'Rf_EncodeLogical', 'Rf_EncodeReal',
    'Rf_formatInteger', 'Rf_formatLogical', 'Rf_formatReal'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
.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
Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd' using rmarkdown
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-1'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Quitting from lines 40-46 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
package or namespace load failed for 'ggtree':
 object 'as_data_frame' is not exported by 'namespace:tidytree'
--- failed re-building 'introduction.Rmd'

SUMMARY: processing the following file failed:
  'introduction.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages in Depends field not imported from:
  'RCurl' 'XML' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ECL: no visible global function definition for 'new'
ECLDataset: no visible global function definition for 'new'
ECLDedUp: no visible global function definition for 'new'
ECLDistribute: no visible global function definition for 'new'
ECLIterate: no visible global function definition for 'new'
ECLJoin: no visible global function definition for 'new'
ECLOutput: no visible global function definition for 'new'
ECLProject: no visible global function definition for 'new'
ECLRecord: no visible global function definition for 'new'
ECLRollUp: no visible global function definition for 'new'
ECLSort: no visible global function definition for 'new'
ECLTOPN: no visible global function definition for 'new'
ECLTable: no visible global function definition for 'new'
ECLTransform: no visible global function definition for 'new'
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'
parseResults: no visible global function definition for 'write.table'
Undefined global functions or variables:
  getNodeSet new postForm write.table xmlGetAttr xmlRoot xmlTreeParse
  xmlValue
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
RHT.2samp : my.HotellingT2 : my.InvCov2: no visible global function
  definition for 'cov'
RHT.2samp : get.lambda : get.para: no visible global function
  definition for 'optimize'
RHT.2samp : get.lambda : gg: no visible global function definition for
  'qchisq'
RHT.2samp : get.lambda : ggl: no visible global function definition for
  'qnorm'
RHT.2samp : <anonymous>: no visible global function definition for
  'cov'
RHT.fun : my.HotellingT : my.InvCov: no visible global function
  definition for 'cov'
RHT.fun : get.lambda : get.para: no visible global function definition
  for 'optimize'
RHT.fun : get.lambda : gg: no visible global function definition for
  'qchisq'
RHT.fun : get.lambda : ggl: no visible global function definition for
  'qnorm'
RHT.fun : <anonymous>: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov optimize qchisq qnorm
Consider adding
  importFrom("stats", "cov", "optimize", "qchisq", "qnorm")
to your NAMESPACE file.
FusedQDA : <anonymous>: no visible global function definition for 'cov'
RidgeFused: no visible binding for global variable 'cov2cor'
RidgeFusedCV : <anonymous>: no visible global function definition for
  'cov'
SSRidgeFused : <anonymous>: no visible global function definition for
  'cov'
Undefined global functions or variables:
  cov cov2cor
Consider adding
  importFrom("stats", "cov", "cov2cor")
to your NAMESPACE file.
ridit.raw: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
R2ngon: no visible global function definition for 'approx'
plotR2pre: no visible global function definition for 'plot'
plotR2pre: no visible global function definition for 'points'
plotR2pre: no visible global function definition for 'gray'
plotR2pre: no visible global function definition for 'legend'
plotR2pre: no visible global function definition for 'rainbow'
Undefined global functions or variables:
  approx gray legend plot points rainbow
Consider adding
  importFrom("grDevices", "gray", "rainbow")
  importFrom("graphics", "legend", "plot", "points")
  importFrom("stats", "approx")
to your NAMESPACE file.
plot.ijzip: no visible global function definition for 'plot'
plot.ijzip : <anonymous>: no visible global function definition for
  'plot'
plot.ijzip: no visible global function definition for 'axis'
read.ijzip: no visible global function definition for 'unzip'
Undefined global functions or variables:
  axis plot unzip
Consider adding
  importFrom("graphics", "axis", "plot")
  importFrom("utils", "unzip")
to your NAMESPACE file.
File 'rindex/R/zzz.R':
  .onLoad calls:
    packageStartupMessage("package rindex is under development and still may change considerably")

See section 'Good practice' in '?.onAttach'.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    lib    3.5Mb
    libs   4.8Mb
File 'RInside/libs/i386/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/i386/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/i386/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/x64/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/i386/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/x64/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
desmat.sanitize: no visible global function definition for 'aggregate'
dispdist: no visible global function definition for 'quantile'
dispdist: no visible global function definition for 'hist'
dispdist: no visible global function definition for 'lines'
estate: no visible global function definition for 'weighted.mean'
estate: no visible global function definition for 'lm'
genperms: no visible global function definition for 'combn'
genprobexact: no visible global function definition for 'ave'
invert.ci: no visible global function definition for 'quantile'
invert.ci: no visible global function definition for 'uniroot'
omni.ate: no visible global function definition for 'hist'
omni.ate: no visible global function definition for 'lines'
omni.ate: no visible global function definition for 'quantile'
resresplot: no visible global function definition for 'lm'
resresplot: no visible global function definition for 'symbols'
resresplot: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline aggregate ave combn hist lines lm quantile symbols uniroot
  weighted.mean
Consider adding
  importFrom("graphics", "abline", "hist", "lines", "symbols")
  importFrom("stats", "aggregate", "ave", "lm", "quantile", "uniroot",
             "weighted.mean")
  importFrom("utils", "combn")
to your NAMESPACE file.
KM.plot: no visible global function definition for 'plot'
KM.plot: no visible global function definition for 'lines'
SchoenSmooth: no visible global function definition for 'lm'
llCoxReg: no visible binding for global variable 'time'
risksetAUC: no visible global function definition for 'abline'
risksetROC: no visible global function definition for 'abline'
weightedKM: no visible binding for global variable 'time'
Undefined global functions or variables:
  abline lines lm plot time
Consider adding
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "lm", "time")
to your NAMESPACE file.
Alg2: no visible global function definition for 'uniroot'
Alg3: no visible global function definition for 'optim'
NVCopula: no visible global function definition for 'rnorm'
NVCopula: no visible global function definition for 'rgamma'
NVCopula: no visible global function definition for 'var'
NVCopula: no visible global function definition for 'cov'
NVCopula: no visible global function definition for 'qnorm'
NVCopulaMT: no visible global function definition for 'rnorm'
NVCopulaMT: no visible global function definition for 'rgamma'
NVCopulaMT: no visible global function definition for 'var'
NVCopulaMT: no visible global function definition for 'cov'
NVCopulaMT: no visible global function definition for 'qnorm'
R2X: no visible global function definition for 'write.table'
ReturnCopula: no visible global function definition for 'qt'
ReturnCopula: no visible global function definition for 'pt'
SISCopula: no visible global function definition for 'runif'
SISCopula: no visible global function definition for 'qnorm'
SISCopula: no visible global function definition for 'rnorm'
SISCopula: no visible global function definition for 'qgamma'
SISCopula: no visible global function definition for 'var'
SISCopula: no visible global function definition for 'cov'
SISCopulaMT: no visible global function definition for 'runif'
SISCopulaMT: no visible global function definition for 'qnorm'
SISCopulaMT: no visible global function definition for 'rnorm'
SISCopulaMT: no visible global function definition for 'qgamma'
SISCopulaMT: no visible global function definition for 'var'
SISCopulaMT: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov optim pt qgamma qnorm qt rgamma rnorm runif uniroot var
  write.table
Consider adding
  importFrom("stats", "cov", "optim", "pt", "qgamma", "qnorm", "qt",
             "rgamma", "rnorm", "runif", "uniroot", "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'compiler' 'signal'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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'
NumDeconv: no visible global function definition for 'optim'
RivivcA: no visible global function definition for 'lm'
Undefined global functions or variables:
  cmpfun lm optim pchip
Consider adding
  importFrom("stats", "lm", "optim")
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/3.6/rJava.Rcheck/00install.out' for details.
Found the following possibly unsafe calls:
File 'rJava/R/import.R':
  unlockBinding(IMPORTER, env = env)
  assignInNamespace(IMPORTER, importer, envir = env)
File 'rJava/R/jinit.R':
  unlockBinding(x, .env)
  unlockBinding(x, pe)
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.6/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.6/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'rJava/libs/i386/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'
File 'rJava/libs/x64/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
cubeHelix : <anonymous>: no visible global function definition for
  'rgb'
rdirichlet: no visible global function definition for 'rgamma'
Undefined global functions or variables:
  rgamma rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "rgamma")
to your NAMESPACE file.
'library' or 'require' call to 'rJava' which was already attached by Depends.
  Please remove these calls from your code.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
cv.coef: no visible global function definition for 'sd'
normalize.softmax: no visible global function definition for 'plogis'
plot.rknnBeg: no visible global function definition for 'plot'
plot.rknnBel: no visible global function definition for 'plot'
plot.rknnSupport: no visible global function definition for 'dotchart'
predicted: no visible global function definition for 'influence'
predicted: no visible global function definition for 'fitted'
predicted: no visible global function definition for 'resid'
pressresid: no visible global function definition for 'influence'
pressresid: no visible global function definition for 'resid'
Undefined global functions or variables:
  dotchart fitted influence plogis plot resid sd
Consider adding
  importFrom("graphics", "dotchart", "plot")
  importFrom("stats", "fitted", "influence", "plogis", "resid", "sd")
to your NAMESPACE file.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
':::' calls which should be '::':
  'stats:::dexp' 'stats:::dgamma' 'stats:::dweibull' 'stats:::pexp'
  'stats:::pgamma' 'stats:::pweibull' 'stats:::qexp' 'stats:::qgamma'
  'stats:::qweibull' 'stats:::rexp' 'stats:::rgamma' 'stats:::rweibull'
  See the note in ?`:::` about the use of this operator.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Found the following Makefile(s) without a final LF:
  src/Makevars.in
Some 'make' programs ignore lines not ending in LF.
Package in Depends field not imported from: 'msm'
  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:
  'EMSRb_internal' 'EM_internal' 'PD_internal'
EMSRb_internal: no visible global function definition for 'qnorm'
EM_internal: no visible global function definition for 'dnorm'
EM_internal: no visible global function definition for 'pnorm'
PD_internal: no visible global function definition for 'qtnorm'
PD_internal: no visible global function definition for 'sd'
Undefined global functions or variables:
  dnorm pnorm qnorm qtnorm sd
Consider adding
  importFrom("stats", "dnorm", "pnorm", "qnorm", "sd")
to your NAMESPACE file.
ma.filter: no visible global function definition for 'par'
ma.filter: no visible global function definition for 'lines'
ma.filter: no visible global function definition for 'abline'
qn: no visible global function definition for 'lm'
qn: no visible global function definition for 'var'
qn: no visible global function definition for 'resid'
ss.filter: no visible global function definition for 'smooth.spline'
ss.filter: no visible global function definition for 'par'
ss.filter: no visible global function definition for 'lines'
ss.filter: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline lines lm par resid smooth.spline var
Consider adding
  importFrom("graphics", "abline", "lines", "par")
  importFrom("stats", "lm", "resid", "smooth.spline", "var")
to your NAMESPACE file.
Mallows: no visible global function definition for 'runif'
Mallows: no visible global function definition for 'x11'
Mallows: no visible global function definition for 'plot'
Mallows: no visible global function definition for 'dev.off'
UpdateLambda: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  dev.off plot runif uniroot x11
Consider adding
  importFrom("grDevices", "dev.off", "x11")
  importFrom("graphics", "plot")
  importFrom("stats", "runif", "uniroot")
to your NAMESPACE file.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    rmd   8.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   2.1Mb
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.
Combi: no visible global function definition for 'new'
barplotMixCluster: no visible global function definition for 'is'
barplotMixCluster: no visible global function definition for 'par'
barplotMixCluster: no visible global function definition for 'lines'
barplotMixCluster: no visible global function definition for 'text'
barplotMixCluster: no visible global function definition for 'title'
barplotMixCluster: no visible global function definition for 'mtext'
histMixCluster: no visible global function definition for 'is'
histMixCluster: no visible global function definition for 'par'
histMixCluster: no visible global function definition for 'dnorm'
histMixCluster: no visible global function definition for 'lines'
mixmodEntPlot: no visible global function definition for 'par'
mixmodEntPlot: no visible global function definition for 'lines'
mixmodEntPlot: no visible global function definition for 'axis'
mixmodEntPlot: no visible global function definition for 'title'
mixmodEntPlot: no visible binding for global variable 'par'
plot,MixmodCombi: no visible global function definition for 'par'
plot,MixmodCombi: no visible global function definition for 'plot.new'
plot,MixmodCombi: no visible global function definition for 'title'
Undefined global functions or variables:
  axis dnorm is lines mtext new par plot.new text title
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "par", "plot.new",
             "text", "title")
  importFrom("methods", "is", "new")
  importFrom("stats", "dnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
.pLGP_qvec: no visible global function definition for 'ppois'
.qLGP_pvec: no visible global function definition for 'qpois'
.rLGP.failsafe: no visible global function definition for 'runif'
.subdmg: no visible global function definition for 'dbinom'
dnegbin: no visible global function definition for 'dnbinom'
pLGP: no visible global function definition for 'ppois'
qLGP: no visible global function definition for 'qpois'
rLGP: no visible global function definition for 'rpois'
rLGP: no visible global function definition for 'rnorm'
rLGP: no visible global function definition for 'runif'
rbinegbin: no visible global function definition for 'rnbinom'
rmanaclash: no visible global function definition for 'rbinom'
rmanaclash: no visible global function definition for 'runif'
Undefined global functions or variables:
  dbinom dnbinom ppois qpois rbinom rnbinom rnorm rpois runif
Consider adding
  importFrom("stats", "dbinom", "dnbinom", "ppois", "qpois", "rbinom",
             "rnbinom", "rnorm", "rpois", "runif")
to your NAMESPACE file.
CoeffYWeq: no visible global function definition for 'index'
fitdistrForPrecipitation: no visible global function definition for
  'fitdistr'
generate.CCGammaObject: no visible binding for global variable 'rnorm'
generate.CCGammaObject: no visible global function definition for
  'pnorm'
generate.YuleWalkerCoefficientBlockmatrices: no visible binding for
  global variable 'rnorm'
generate.YuleWalkerCoefficientBlockmatricesPerEachMonth: no visible
  binding for global variable 'rnorm'
generatePrecipitationAmount: no visible global function definition for
  'str'
omega_inv: no visible global function definition for 'uniroot'
qqfit: no visible binding for global variable 'qexp'
qqfit: no visible global function definition for 'ecdf'
Undefined global functions or variables:
  ecdf fitdistr index pnorm qexp rnorm str uniroot
Consider adding
  importFrom("stats", "ecdf", "pnorm", "qexp", "rnorm", "uniroot")
  importFrom("utils", "str")
to your NAMESPACE file.
rms.pval: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Running examples in 'rms-Ex.R' failed
The error most likely occurred in:

> ### Name: Function
> ### Title: Compose an S Function to Compute X beta from a Fit
> ### Aliases: Function.rms Function.cph sascode perlcode
> ### Keywords: regression methods interface models survival math
> 
> ### ** Examples
> 
> set.seed(1331)
> x1 <- exp(rnorm(100))
> x2 <- factor(sample(c('a','b'),100,rep=TRUE))
> dd <- datadist(x1, x2)
> options(datadist='dd')
> y  <- log(x1)^2+log(x1)*(x2=='b')+rnorm(100)/4
> f  <- ols(y ~ pol(log(x1),2)*x2)
> f$coef
   Intercept           x1         x1^2         x2=b    x1 * x2=b  x1^2 * x2=b 
-0.001885864 -0.019198566  1.017432226  0.047810769  1.037259829 -0.032005994 
> g  <- Function(f, digits=5)
> g
function (x1 = 1.0906, x2 = "b") 
{
    x1 <- log(x1)
    -0.0018859 - 0.019199 * x1 + 1.0174 * x1^2 + 0.047811 * (x2 == 
        "b") + (x2 == "b") * (1.0373 * x1 - 0.032006 * x1^2)
}
<environment: 0x08729d78>
> sascode(g)
    x1 = log(x1)
    -0.0018859 - 0.019199 * x1 + 1.0174 * x1**2 + 0.047811 * (x2 = 
        "b") + (x2 = "b") * (1.0373 * x1 - 0.032006 * x1**2);
> cat(perlcode(g), '\n')
Error in expr[[3]] : subscript out of bounds
Calls: cat ... convert -> f -> paste -> convert -> f -> paste -> convert
Execution halted
Running examples in 'rms-Ex.R' failed
The error most likely occurred in:

> ### Name: Function
> ### Title: Compose an S Function to Compute X beta from a Fit
> ### Aliases: Function.rms Function.cph sascode perlcode
> ### Keywords: regression methods interface models survival math
> 
> ### ** Examples
> 
> set.seed(1331)
> x1 <- exp(rnorm(100))
> x2 <- factor(sample(c('a','b'),100,rep=TRUE))
> dd <- datadist(x1, x2)
> options(datadist='dd')
> y  <- log(x1)^2+log(x1)*(x2=='b')+rnorm(100)/4
> f  <- ols(y ~ pol(log(x1),2)*x2)
> f$coef
   Intercept           x1         x1^2         x2=b    x1 * x2=b  x1^2 * x2=b 
-0.001885864 -0.019198566  1.017432226  0.047810769  1.037259829 -0.032005994 
> g  <- Function(f, digits=5)
> g
function (x1 = 1.0906, x2 = "b") 
{
    x1 <- log(x1)
    -0.0018859 - 0.019199 * x1 + 1.0174 * x1^2 + 0.047811 * (x2 == 
        "b") + (x2 == "b") * (1.0373 * x1 - 0.032006 * x1^2)
}
<environment: 0x000000001145a360>
> sascode(g)
    x1 = log(x1)
    -0.0018859 - 0.019199 * x1 + 1.0174 * x1**2 + 0.047811 * (x2 = 
        "b") + (x2 = "b") * (1.0373 * x1 - 0.032006 * x1**2);
> cat(perlcode(g), '\n')
Error in expr[[3]] : subscript out of bounds
Calls: cat ... convert -> f -> paste -> convert -> f -> paste -> convert
Execution halted
dWishartSpike: no visible global function definition for 'dnorm'
pWishartSpike: no visible global function definition for 'pnorm'
qWishartSpike: no visible global function definition for 'qnorm'
rWishartSpike: no visible global function definition for 'qnorm'
rmp: no visible global function definition for 'runif'
rtw: no visible global function definition for 'runif'
Undefined global functions or variables:
  dnorm pnorm qnorm runif
Consider adding
  importFrom("stats", "dnorm", "pnorm", "qnorm", "runif")
to your NAMESPACE file.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
'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'
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Package suggested but not available for checking: 'taxadb'
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rngtools)
  Loading required package: pkgmaker
  Loading required package: registry
  
  Attaching package: 'pkgmaker'
  
  The following object is masked from 'package:base':
  
      isFALSE
  
  > 
  > test_check("rngtools")
  -- 1. Failure: RNGtype (@test-format.R#100)  -----------------------------------
  length(d) not identical to `expL`.
  1/1 mismatches
  [1] 3 - 2 == 1
  MISSING : result has correct length ( [ 2 ) ]
  
  -- 2. Failure: RNGtype (@test-format.R#101)  -----------------------------------
  length(d) not identical to `expL`.
  1/1 mismatches
  [1] 3 - 2 == 1
  numeric(1) : result has correct length ( [ 2 ) Valid single numeric seed ]
  
  -- 3. Failure: RNGtype (@test-format.R#102)  -----------------------------------
  length(d) not identical to `expL`.
  1/1 mismatches
  [1] 3 - 2 == 1
  integer(3) : result has correct length ( [ 2 ) Valid seed ]
  
  -- 4. Failure: RNGtype (@test-format.R#103)  -----------------------------------
  length(d) not identical to `expL`.
  1/1 mismatches
  [1] 3 - 2 == 1
  integer(1) : result has correct length ( [ 2 ) Valid encoded kind ]
  
  -- 5. Failure: RNGtype (@test-format.R#106)  -----------------------------------
  length(d) not identical to `expL`.
  1/1 mismatches
  [1] 3 - 2 == 1
  list(2) : result has correct length ( [ 2 ) list with rng slot ]
  
  == testthat results  ===========================================================
  OK: 225 SKIPPED: 0 FAILED: 5
  1. Failure: RNGtype (@test-format.R#100) 
  2. Failure: RNGtype (@test-format.R#101) 
  3. Failure: RNGtype (@test-format.R#102) 
  4. Failure: RNGtype (@test-format.R#103) 
  5. Failure: RNGtype (@test-format.R#106) 
  
  Error: testthat unit tests failed
  Execution halted
well19937.validate: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      5.5Mb
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.
Running 'testthat.R' [15s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rnn)
  > 
  > test_check("rnn")
  -- 1. Failure: (unknown) (@test_rnn.R#66)  -------------------------------------
  sum(bin2int(B)) not equal to 888626.
  1/1 mismatches
  [1] 209284 - 888626 == -679342
  
  == testthat results  ===========================================================
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Failure: (unknown) (@test_rnn.R#66) 
  
  Error: testthat unit tests failed
  Execution halted
'library' or 'require' calls in package code:
  'robustbase' 'sfsmisc'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.BuildPartial: no visible global function definition for 'as.formula'
.BuildPartial: no visible global function definition for 'residuals'
.PairwiseCorrelation : .Standardize : <anonymous>: no visible global
  function definition for 'na.omit'
.PairwiseCorrelation : .Standardize: no visible binding for global
  variable 'median'
.PairwiseCorrelation: no visible global function definition for
  'complete.cases'
.yw: no visible global function definition for 'toeplitz'
FastQn: no visible global function definition for 'median'
FastQn: no visible global function definition for 'mad'
fqn: no visible global function definition for 'median'
fqn: no visible global function definition for 'mad'
psdcor: no visible global function definition for 'posdefify'
psdcor: no visible global function definition for 'nearcor'
robar: no visible global function definition for 'frequency'
robcor: no visible global function definition for 'covMcd'
s_FastQn: no visible global function definition for 'median'
Undefined global functions or variables:
  as.formula complete.cases covMcd frequency mad median na.omit nearcor
  posdefify residuals toeplitz
Consider adding
  importFrom("stats", "as.formula", "complete.cases", "frequency", "mad",
             "median", "na.omit", "residuals", "toeplitz")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
See 'd:/Rcompile/CRANpkg/local/3.6/RobLoxBioC.Rcheck/00install.out' for details.
RobRSVD: no visible global function definition for 'median'
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
'LinkingTo' for 'mgcv' is unused as it has no 'include' directory
Packages in Depends field not imported from:
  'Rcpp' 'RcppArmadillo' 'mgcv' 'robustbase'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GIC: no visible global function definition for 'integrate'
QM.poisson: no visible global function definition for 'ppois'
QM.poisson: no visible global function definition for 'dpois'
cplot.robustgam: no visible global function definition for 'plot'
expect.poisson: no visible global function definition for 'dpois'
expect.poisson: no visible global function definition for 'ppois'
pred.robustgam: no visible global function definition for
  'Predict.matrix'
robust.sigma: no visible global function definition for 'median'
robustgam: no visible global function definition for 's'
robustgam: no visible global function definition for
  'smooth.construct.tp.smooth.spec'
robustgam: no visible global function definition for
  'smooth.construct.cr.smooth.spec'
robustgam: no visible global function definition for
  'smooth.construct.ps.smooth.spec'
robustgam : w.fun: no visible global function definition for 'covMcd'
robustgam.GIC.optim: no visible global function definition for 'optim'
robustgam.crossval : w.fun: no visible global function definition for
  'covMcd'
robustgam.crossval: no visible global function definition for
  'integrate'
smooth.construct.tr.smooth.spec: no visible global function definition
  for 'quantile'
w.binomial: no visible global function definition for 'pbinom'
w.poisson: no visible global function definition for 'ppois'
Undefined global functions or variables:
  Predict.matrix covMcd dpois integrate median optim pbinom plot ppois
  quantile s smooth.construct.cr.smooth.spec
  smooth.construct.ps.smooth.spec smooth.construct.tp.smooth.spec
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dpois", "integrate", "median", "optim", "pbinom",
             "ppois", "quantile")
to your NAMESPACE file.
aggregateRanks: no visible binding for global variable 'median'
aggregateRanks: no visible global function definition for 'pnorm'
betaScores: no visible global function definition for 'pbeta'
correctBetaPvaluesExact: no visible binding for global variable 'qbeta'
thresholdBetaScore: no visible global function definition for 'pbeta'
Undefined global functions or variables:
  median pbeta pnorm qbeta
Consider adding
  importFrom("stats", "median", "pbeta", "pnorm", "qbeta")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'penalized' 'splines' 'survival' 'survivalROC'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
boot.ROC: no visible global function definition for 'qnorm'
boot.ROC: no visible global function definition for 'penalized'
boot.ROC: no visible global function definition for 'coefficients'
boot.ROC: no visible global function definition for 'sd'
boot.ROC: no visible global function definition for 'optL1'
boot.ROCt: no visible global function definition for 'qnorm'
boot.ROCt: no visible global function definition for 'penalized'
boot.ROCt: no visible global function definition for 'Surv'
boot.ROCt: no visible global function definition for 'coefficients'
boot.ROCt: no visible global function definition for 'sd'
boot.ROCt: no visible global function definition for 'survivalROC'
boot.ROCt: no visible global function definition for 'optL1'
Undefined global functions or variables:
  Surv coefficients optL1 penalized qnorm sd survivalROC
Consider adding
  importFrom("stats", "coefficients", "qnorm", "sd")
to your NAMESPACE file.
'library' or 'require' call to 'ROCR' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'ROCR'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
o.rocc: warning in factor(pr, level = c(0, 1)): partial argument match
  of 'level' to 'levels'
p.rocc: warning in factor(pr, level = c(0, 1)): partial argument match
  of 'level' to 'levels'
o.rocc: no visible global function definition for 'prediction'
o.rocc: no visible global function definition for 'performance'
o.rocc: no visible global function definition for 'binom.test'
tr.rocc: no visible global function definition for 'prediction'
tr.rocc: no visible global function definition for 'performance'
Undefined global functions or variables:
  binom.test performance prediction
Consider adding
  importFrom("stats", "binom.test")
to your NAMESPACE file.
NPROCwoGS: no visible global function definition for 'quantile'
NPROCwoGS : rdirichlet: no visible global function definition for
  'rgamma'
NPROCwoGS: no visible global function definition for 'rbinom'
NPROCwoGS: no visible global function definition for 'rbeta'
NPROCwoGS: no visible binding for global variable 'quantile'
Undefined global functions or variables:
  quantile rbeta rbinom rgamma
Consider adding
  importFrom("stats", "quantile", "rbeta", "rbinom", "rgamma")
to your NAMESPACE file.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'RODBC'
A package should be listed in only one of these fields.
'library' or 'require' call to 'RODBC' which was already attached by Depends.
  Please remove these calls from your code.
ROSE.eval: no visible global function definition for 'methods'
ROSE.eval: no visible binding for global variable 'model.frame'
ROSE.eval: no visible binding for global variable 'predict'
adj.formula: no visible global function definition for 'terms'
adj.formula: no visible global function definition for 'as.formula'
omnibus.balancing: no visible binding for global variable 'model.frame'
ou.sampl: no visible global function definition for 'rbinom'
over.sampl: no visible global function definition for 'rbinom'
plot.roc.inner: no visible global function definition for 'plot'
roc.curve: no visible global function definition for 'lines'
roc.curve: no visible global function definition for 'abline'
rose.real: no visible binding for global variable 'sd'
rose.real: no visible global function definition for 'sd'
rose.real: no visible global function definition for 'rnorm'
rose.sampl: no visible global function definition for 'rbinom'
under.sampl: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  abline as.formula lines methods model.frame plot predict rbinom rnorm
  sd terms
Consider adding
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "as.formula", "model.frame", "predict", "rbinom",
             "rnorm", "sd", "terms")
  importFrom("utils", "methods")
to your NAMESPACE file.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.3Mb
    libs   2.2Mb
bestFM: no visible global function definition for 'data'
gaRoth: no visible global function definition for 'data'
ros: no visible global function definition for 'na.omit'
rosunc: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  data na.omit rnorm
Consider adding
  importFrom("stats", "na.omit", "rnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
mfix : m4m: no visible global function definition for 'median'
rrfa: no visible global function definition for 'predict'
rrfb: no visible global function definition for 'predict'
rrfc1: no visible global function definition for 'predict'
rrfc2: no visible global function definition for 'predict'
rrfc3: no visible global function definition for 'predict'
rrfc4: no visible global function definition for 'predict'
rrfc5 : regdat: no visible global function definition for 'predict'
rrfc5 : regdat: no visible global function definition for 'glm'
rrfc5: no visible global function definition for 'predict'
rrfc6: no visible global function definition for 'predict'
rrfc7: no visible global function definition for 'predict'
rrfd: no visible global function definition for 'predict'
rrfe : rdms: no visible global function definition for 'rbinom'
rrfe: no visible global function definition for 'predict'
Undefined global functions or variables:
  glm median predict rbinom
Consider adding
  importFrom("stats", "glm", "median", "predict", "rbinom")
to your NAMESPACE file.
.computeValueReduct: no visible global function definition for 'combn'
.findAllReductsFromCore: no visible global function definition for
  'combn'
.findFirstReductsFromCore: no visible global function definition for
  'combn'
.findSmallestReductFamilyFromCore: no visible global function
  definition for 'combn'
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
royston.test: no visible global function definition for 'shapiro.test'
royston.test: no visible global function definition for 'cor'
royston.test: no visible global function definition for 'qnorm'
royston.test: no visible global function definition for 'pnorm'
royston.test: no visible global function definition for 'cov'
royston.test: no visible global function definition for 'mahalanobis'
royston.test: no visible global function definition for 'qqplot'
royston.test: no visible global function definition for 'qchisq'
royston.test: no visible global function definition for 'ppoints'
royston.test: no visible global function definition for 'abline'
royston.test: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  abline cor cov mahalanobis pchisq pnorm ppoints qchisq qnorm qqplot
  shapiro.test
Consider adding
  importFrom("graphics", "abline")
  importFrom("stats", "cor", "cov", "mahalanobis", "pchisq", "pnorm",
             "ppoints", "qchisq", "qnorm", "qqplot", "shapiro.test")
to your NAMESPACE file.
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rPackedBar)
  > 
  > test_check("rPackedBar")
  -- 1. Failure: object value (@test-gen_gray_bars.R#277)  -----------------------
  `test` not equivalent to `expected`.
  Component "bar_list": Component 1: Component 2: 1 string mismatch
  Component "bar_list": Component 1: Component 3: Component 1: 1 string mismatch
  Component "bar_list": Component 2: Component 2: 1 string mismatch
  Component "bar_list": Component 2: Component 3: Component 1: 1 string mismatch
  Component "bar_list": Component 3: Component 2: 1 string mismatch
  Component "bar_list": Component 3: Component 3: Component 1: 1 string mismatch
  Component "bar_list": Component 4: Component 2: 1 string mismatch
  Component "bar_list": Component 4: Component 3: Component 1: 1 string mismatch
  Component "bar_list": Component 5: Component 2: 1 string mismatch
  ...
  
  == testthat results  ===========================================================
  OK: 43 SKIPPED: 0 FAILED: 1
  1. Failure: object value (@test-gen_gray_bars.R#277) 
  
  Error: testthat unit tests failed
  Execution halted
Package in Depends field not imported from: 'hash'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
P: no visible global function definition for 'has.key'
get_rand_int: no visible global function definition for 'runif'
last: no visible global function definition for 'tail'
rand_partitions: no visible global function definition for 'hash'
Undefined global functions or variables:
  has.key hash runif tail
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "tail")
to your NAMESPACE file.
evalMedian: no visible global function definition for 'xtabs'
evalMode: no visible global function definition for 'xtabs'
rpartScore: no visible global function definition for 'model.extract'
rpartScore: no visible global function definition for 'var'
rpartScore: no visible binding for global variable 'var'
splitAbs: no visible global function definition for 'xtabs'
Undefined global functions or variables:
  model.extract var xtabs
Consider adding
  importFrom("stats", "model.extract", "var", "xtabs")
to your NAMESPACE file.
'library' or 'require' call to 'RODBC' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
rpart.rules.push: no visible global function definition for 'sqlSave'
rpart.rules.table : <anonymous>: no visible global function definition
  for 'setNames'
rpart.subrules.table : <anonymous>: no visible global function
  definition for 'setNames'
Undefined global functions or variables:
  setNames sqlSave
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'survival'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'MASS' 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GenerateData: no visible global function definition for 'mvrnorm'
GetVarImp : FitPenalizedModel: no visible global function definition
  for 'clogit'
Undefined global functions or variables:
  clogit mvrnorm
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      2.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
but_last: no visible global function definition for 'head'
first: no visible global function definition for 'head'
last: no visible global function definition for 'tail'
preview_frames: no visible global function definition for 'str'
print.EprimeFrame: no visible global function definition for 'str'
print.FrameList: no visible global function definition for 'str'
Undefined global functions or variables:
  head str tail
Consider adding
  importFrom("utils", "head", "str", "tail")
to your NAMESPACE file.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.7Mb
Package which this enhances but not available for checking: 'rjpod'
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    libs  27.0Mb
Found the following significant warnings:
  Warning: replacing previous import 'dplyr::group_rows' by 'kableExtra::group_rows' when loading 'Rraven'
See 'd:/Rcompile/CRANpkg/local/3.6/Rraven.Rcheck/00install.out' for details.
rrBlupM6: no visible global function definition for 'optimize'
Undefined global functions or variables:
  optimize
Consider adding
  importFrom("stats", "optimize")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'glasso' 'matrixcalc' 'mvoutlier' 'pcaPP'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
rrest: no visible binding for global variable 'glasso'
rrest: no visible global function definition for 'pcout'
rrest: no visible global function definition for 'var'
rrest: no visible global function definition for 'mahalanobis'
rrlda : centerObservations: no visible global function definition for
  'l1median_NLM'
rrlda : df.L2glasso: no visible global function definition for
  'duplication.matrix'
rrlda : alt.df.L2glasso: no visible global function definition for
  'lower.triangle'
Undefined global functions or variables:
  duplication.matrix glasso l1median_NLM lower.triangle mahalanobis
  pcout var
Consider adding
  importFrom("stats", "mahalanobis", "var")
to your NAMESPACE file.
'library' or 'require' call to 'robustbase' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.computekappa: no visible global function definition for 'pnorm'
.computekappa: no visible global function definition for 'dnorm'
.initmethod : <anonymous>: no visible global function definition for
  'median'
.initmethod: no visible global function definition for 'model.matrix'
.mspe: no visible global function definition for 'rnorm'
.mspe : <anonymous>: no visible global function definition for 'rnorm'
makedata: no visible global function definition for 'rnorm'
makedata : addraneff: no visible global function definition for 'rnorm'
plot.meanssaemodel: no visible global function definition for 'par'
plot.meanssaemodel: no visible global function definition for 'plot'
plot.meanssaemodel: no visible global function definition for 'lines'
plot.meanssaemodel: no visible global function definition for 'axis'
plot.meanssaemodel: no visible global function definition for 'grid'
plot.meanssaemodel: no visible global function definition for 'box'
plot.meanssaemodel: no visible global function definition for 'legend'
plot.meanssaemodel: no visible global function definition for 'arrows'
saemodel: no visible global function definition for 'model.frame'
saemodel: no visible global function definition for 'model.response'
saemodel: no visible global function definition for 'model.matrix'
summary.fitsaemodel: no visible global function definition for 'pt'
summary.fitsaemodel: no visible global function definition for
  'printCoefmat'
Undefined global functions or variables:
  arrows axis box dnorm grid legend lines median model.frame
  model.matrix model.response par plot pnorm printCoefmat pt rnorm
Consider adding
  importFrom("graphics", "arrows", "axis", "box", "grid", "legend",
             "lines", "par", "plot")
  importFrom("stats", "dnorm", "median", "model.frame", "model.matrix",
             "model.response", "pnorm", "printCoefmat", "pt", "rnorm")
to your NAMESPACE file.
stripslash: no visible global function definition for 'tail'
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
convexhull: no visible global function definition for 'chull'
convexhull: no visible global function definition for 'rnorm'
drawcompletegraph: no visible global function definition for 'plot'
drawcompletegraph: no visible global function definition for 'segments'
getbag: no visible global function definition for 'plot'
getbag: no visible global function definition for 'chull'
getbag: no visible global function definition for 'polygon'
getbag: no visible global function definition for 'points'
inflate: no visible global function definition for 'rnorm'
rsmed: no visible global function definition for 'runif'
rsplot: no visible global function definition for 'plot'
rsplot: no visible global function definition for 'chull'
rsplot: no visible global function definition for 'polygon'
rsplot: no visible global function definition for 'points'
rsrings: no visible global function definition for 'plot'
rsrings: no visible global function definition for 'chull'
rsrings: no visible global function definition for 'polygon'
rsrings: no visible global function definition for 'points'
rstinterval: no visible global function definition for 'plot'
rstinterval: no visible global function definition for 'runif'
rstinterval: no visible global function definition for 'rnorm'
rstinterval: no visible global function definition for 'chull'
rstinterval: no visible global function definition for 'polygon'
Undefined global functions or variables:
  chull plot points polygon rnorm runif segments
Consider adding
  importFrom("grDevices", "chull")
  importFrom("graphics", "plot", "points", "polygon", "segments")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
rsem: no visible global function definition for 'write.table'
rsem.Ascov: no visible global function definition for 'qchisq'
rsem.Ascov: no visible global function definition for 'pchisq'
rsem.emmusig: no visible global function definition for 'na.omit'
rsem.emmusig: no visible global function definition for 'qchisq'
rsem.emmusig: no visible global function definition for 'pchisq'
rsem.fit: no visible global function definition for 'pchisq'
rsem.fit: no visible global function definition for 'pf'
rsem.print : print.estimate: no visible global function definition for
  'pnorm'
rsem.weight: no visible global function definition for 'qchisq'
rsem.weight: no visible global function definition for 'pchisq'
semdiag.call.eqs: no visible global function definition for
  'write.table'
semdiag.read.eqs: no visible global function definition for 'read.fwf'
Undefined global functions or variables:
  na.omit pchisq pf pnorm qchisq read.fwf write.table
Consider adding
  importFrom("stats", "na.omit", "pchisq", "pf", "pnorm", "qchisq")
  importFrom("utils", "read.fwf", "write.table")
to your NAMESPACE file.
Found the following significant warnings:
   #warning Please include winsock2.h before windows.h
  qap_decode.c:200:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:200:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:55: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:60: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.6/Rserve.Rcheck/00install.out' for details.
Rserve: no visible global function definition for 'shortPathName'
Undefined global functions or variables:
  shortPathName
Consider adding
  importFrom("utils", "shortPathName")
to your NAMESPACE file.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.6/Rserve/libs/i386/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'd:/Rcompile/CRANpkg/lib/3.6/Rserve/libs/x64/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'Rserve/libs/i386/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
addNoisyCopies: no visible global function definition for 'rnorm'
eta: no visible global function definition for 'var'
gaussClassifier: no visible global function definition for 'runif'
getSigma: no visible global function definition for 'sd'
getSigma: no visible binding for global variable 'sd'
sfaClassify: no visible global function definition for 'rainbow'
sfaClassify: no visible global function definition for 'par'
sfaClassify: no visible global function definition for 'plot'
sfaClassify: no visible global function definition for 'points'
sfaClassify: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines par plot points rainbow rnorm runif sd var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "lines", "par", "plot", "points")
  importFrom("stats", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
'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.
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.
Running 'testthat.R' [34s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("RSSL")
  Loading required package: RSSL
  -- 1. Failure: Multi class gives an output (@test-ICLeastSquaresClassifier.R#53)
  sum(predict(g_sup, problem$X_test) == problem$y_test) not equal to 61.
  1/1 mismatches
  [1] 55 - 61 == -6
  
  -- 2. Failure: Multi class gives an output (@test-ICLeastSquaresClassifier.R#54)
  sum(predict(g_semi, problem$X_test) == problem$y_test) not equal to 61.
  1/1 mismatches
  [1] 55 - 61 == -6
  
  -- 3. Failure: Multi class gives an output (@test-ICLeastSquaresClassifier.R#55)
  sum(predict(g_euc, problem$X_test) == problem$y_test) not equal to 57.
  1/1 mismatches
  [1] 55 - 57 == -2
  
  -- 4. Failure: Multiclass gives an output (@test-LeastSquaresClassifier.R#46)  -
  sum(...) not equal to 61.
  1/1 mismatches
  [1] 60 - 61 == -1
  
  == testthat results  ===========================================================
  OK: 466 SKIPPED: 0 FAILED: 4
  1. Failure: Multi class gives an output (@test-ICLeastSquaresClassifier.R#53) 
  2. Failure: Multi class gives an output (@test-ICLeastSquaresClassifier.R#54) 
  3. Failure: Multi class gives an output (@test-ICLeastSquaresClassifier.R#55) 
  4. Failure: Multiclass gives an output (@test-LeastSquaresClassifier.R#46) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs  17.4Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    Lib  11.5Mb
Math.Sym: no visible binding for global variable 'transtab'
jythonStart: no visible global function definition for '.jinit'
jythonStart: no visible global function definition for '.jnew'
jythonStart: no visible binding for global variable '.Jython'
sympy: no visible binding for global variable '.Jython'
sympy: no visible global function definition for '.jstrVal'
sympyStart: no visible binding for global variable '.Jython'
Undefined global functions or variables:
  .Jython .jinit .jnew .jstrVal transtab
barplot.rtconnect: no visible global function definition for 'rainbow'
barplot.rtconnect: no visible global function definition for 'text'
plot.rtconnect: no visible global function definition for 'par'
plot.rtconnect: no visible global function definition for 'plot'
plot.rtconnect: no visible global function definition for 'axis.Date'
rtconnect: no visible global function definition for 'read.table'
Undefined global functions or variables:
  axis.Date par plot rainbow read.table text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis.Date", "par", "plot", "text")
  importFrom("utils", "read.table")
to your NAMESPACE file.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
classify_model: no visible global function definition for 'predict'
cross_validate: no visible global function definition for 'predict'
read_data: no visible global function definition for 'read.csv'
read_data: no visible global function definition for 'read.delim'
Undefined global functions or variables:
  predict read.csv read.delim
Consider adding
  importFrom("stats", "predict")
  importFrom("utils", "read.csv", "read.delim")
to your NAMESPACE file.
plotGLCM: no visible global function definition for 'plot'
plotGLCM: no visible global function definition for 'points'
Undefined global functions or variables:
  plot points
Consider adding
  importFrom("graphics", "plot", "points")
to your NAMESPACE file.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       1.8Mb
    projects   2.7Mb
Running examples in 'rtson-Ex.R' failed
The error most likely occurred in:

> ### Name: readTSON
> ### Title: Deserialize a connection
> ### Aliases: readTSON
> 
> ### ** Examples
> 
> ## Example
> 
> library(rtson)
> 
> list = list(integer=42L,
+             double=42,
+             bool=TRUE,
+             uint8=tson.uint8.vec(c(42,0)),
+             uint16=tson.uint16.vec(c(42,0)),
+             uint32=tson.uint32.vec(c(42,0)),
+             int8=tson.int8.vec(c(42,0)),
+             int16=tson.int16.vec(c(42,0)),
+             int32=as.integer(c(42,0)),
+             float32=tson.float32.vec(c(0.0, 42.0)),
+             float64=c(42.0,42.0),
+             map=list(x=42, y=42, label="42"),
+             list=list("42",42)
+ )
> 
> con = rawConnection(raw(0), "r+")
> writeTSON(list, con)
<Serializer>
  Public:
    addBool: function (object) 
    addDouble: function (object) 
    addDoubleList: function (object) 
    addFloat32List: function (object) 
    addFloat64List: function (object) 
    addInt16List: function (object) 
    addInt32List: function (object) 
    addInt8List: function (object) 
    addInteger: function (object) 
    addIntegerList: function (object) 
    addLength: function (len) 
    addList: function (object) 
    addListOrMap: function (object) 
    addMap: function (object) 
    addNull: function () 
    addObject: function (object) 
    addRootObject: function (object) 
    addString: function (object) 
    addStringList: function (object) 
    addType: function (type) 
    addUInt16List: function (object) 
    addUInt32List: function (object) 
    addUInt8List: function (object) 
    clone: function (deep = FALSE) 
    con: 3
    initialize: function (object, con) 
> bytes = rawConnectionValue(con)
> close(con)
> con = rawConnection(bytes, "r")
> object = readTSON(con)
> 
> 
> 
> cleanEx()
Error: connections left open:
	bytes (rawConnection)
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   2.2Mb
HapMendlianCheck: no visible global function definition for
  'write.table'
rvPDT.test.sub: no visible global function definition for 'pnorm'
whap.prehap: no visible global function definition for 'write.table'
whap.prehap: no visible global function definition for 'read.table'
Undefined global functions or variables:
  pnorm read.table write.table
Consider adding
  importFrom("stats", "pnorm")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
'library' or 'require' call to 'pixmap' which was already attached by Depends.
  Please remove these calls from your code.
rvideopoker: warning in rp.radiogroup(mypanel, var =
  state$penny.nickel.quarter.dollar, initval = 1, values = c(1, 5, 25,
  100), title = "Bet (in Cents)", action = setbet): partial argument
  match of 'var' to 'variable'
rvideopoker: warning in rp.slider(mypanel, var = state$no.of.credits,
  from = 1, to = 5, initval = 1, title = "How many Credits?",
  resolution = 1, action = creditset, showvalue = TRUE): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC1, action = card1check, title = "Keep Card 1?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC2, action = card2check, title = "Keep Card 2?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC3, action = card3check, title = "Keep Card 3?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC4, action = card4check, title = "Keep Card 4?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC5, action = card5check, title = "Keep Card 5?"): partial
  argument match of 'var' to 'variable'
rvideopoker : plotFrame: no visible global function definition for
  'par'
rvideopoker : showBack: no visible global function definition for
  'title'
rvideopoker : showCardsInitially: no visible global function definition
  for 'title'
Undefined global functions or variables:
  par title
Consider adding
  importFrom("graphics", "par", "title")
to your NAMESPACE file.
Package suggested but not available for checking: 'gpuR'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    include   5.2Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    include   2.5Mb
    libs      8.1Mb
lc_TDT: no visible global function definition for 'pchisq'
rvTDT: no visible global function definition for 'dbeta'
Undefined global functions or variables:
  dbeta pchisq
Consider adding
  importFrom("stats", "dbeta", "pchisq")
to your NAMESPACE file.
LASSO: no visible global function definition for 'lm'
LASSO: no visible global function definition for 'anova'
LASSO: no visible global function definition for 'glm'
LASSO: no visible global function definition for 'pchisq'
LASSO : <anonymous>: no visible global function definition for
  'extractAIC'
PCR : <anonymous>: no visible global function definition for 'cor'
PLS : <anonymous>: no visible global function definition for 'cor'
RR : RRscore: no visible binding for global variable 'sd'
SPLS: no visible global function definition for 'lm'
SPLS: no visible global function definition for 'anova'
SPLS : <anonymous>: no visible global function definition for
  'extractAIC'
VTWOD : getScores: no visible global function definition for 'sd'
VTWOD : getScores: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  anova cor extractAIC glm lm pchisq pnorm sd
Consider adding
  importFrom("stats", "anova", "cor", "extractAIC", "glm", "lm",
             "pchisq", "pnorm", "sd")
to your NAMESPACE file.
check_ISO_code: no visible binding for global variable 'NoAm_country'
check_ISO_code: no visible binding for global variable 'SoAm_country'
check_ISO_code: no visible binding for global variable 'Oceana_country'
check_ISO_code: no visible binding for global variable 'Africa_country'
check_ISO_code: no visible binding for global variable 'Asia_country'
check_ISO_code: no visible binding for global variable 'Eur_country'
climate_map: no visible binding for global variable 'data'
date_correct: no visible global function definition for 'tail'
Undefined global functions or variables:
  Africa_country Asia_country Eur_country NoAm_country Oceana_country
  SoAm_country data tail
Consider adding
  importFrom("utils", "data", "tail")
to your NAMESPACE file.
RWBP.default: no visible global function definition for 'na.omit'
RWBP.default: no visible global function definition for 'kmeans'
RWBP.formula: no visible global function definition for 'model.extract'
plot.RWBP: no visible global function definition for 'plot'
predict.RWBP: no visible global function definition for 'head'
Undefined global functions or variables:
  head kmeans model.extract na.omit plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "kmeans", "model.extract", "na.omit")
  importFrom("utils", "head")
to your NAMESPACE file.
weblogo: no visible global function definition for 'browseURL'
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
File 'RWinEdt/R/zzz.R':
  .onAttach calls:
    writeLines(edtFile, con = send2RedtLoc)
    writeLines(edtFile, con = send2RedtLoc)

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
.dwt: no visible global function definition for 'median'
.udwt: no visible global function definition for 'median'
plotSignalTransformation: no visible global function definition for
  'plot'
plotSignalTransformation: no visible global function definition for
  'box'
plotSignalTransformation: no visible global function definition for
  'axis'
plotSignalTransformation: no visible global function definition for
  'lines'
plotSignalTransformation: no visible global function definition for
  'legend'
Undefined global functions or variables:
  axis box legend lines median plot
Consider adding
  importFrom("graphics", "axis", "box", "legend", "lines", "plot")
  importFrom("stats", "median")
to your NAMESPACE file.
Analyze: no visible global function definition for 'runif'
Analyze: no visible global function definition for 'mcmc'
Analyze: no visible global function definition for 'varnames<-'
AnalyzeWithExitPoll: no visible global function definition for 'runif'
AnalyzeWithExitPoll: no visible global function definition for 'mcmc'
AnalyzeWithExitPoll: no visible global function definition for
  'varnames<-'
Tune: no visible global function definition for 'runif'
TuneWithExitPoll: no visible global function definition for 'runif'
form.mcmc.object: no visible global function definition for
  'varnames<-'
gendata.ep : rdirichlet: no visible global function definition for
  'rgamma'
gendata.ep : rwish: no visible global function definition for 'rchisq'
gendata.ep : rwish: no visible global function definition for 'rnorm'
gendata.ep: no visible global function definition for 'rpois'
gendata.ep: no visible global function definition for 'runif'
gendata.ep: no visible global function definition for 'rmultinom'
gendata.ep: no visible global function definition for 'cov2cor'
gq.summary: no visible global function definition for 'mcmc.list'
gq.summary: no visible global function definition for 'mcmc'
gq_diagnostics: no visible global function definition for 'mcmc.list'
gq_diagnostics: no visible global function definition for 'mcmc'
gq_diagnostics: no visible global function definition for 'gelman.diag'
gq_diagnostics: no visible global function definition for 'geweke.diag'
gq_diagnostics: no visible global function definition for 'heidel.diag'
gq_diagnostics: no visible global function definition for
  'autocorr.diag'
Undefined global functions or variables:
  autocorr.diag cov2cor gelman.diag geweke.diag heidel.diag mcmc
  mcmc.list rchisq rgamma rmultinom rnorm rpois runif varnames<-
Consider adding
  importFrom("stats", "cov2cor", "rchisq", "rgamma", "rmultinom",
             "rnorm", "rpois", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: 'SnakeCharmR'
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   5.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    sample_data   3.0Mb
calculate.summary: no visible global function definition for 'sd'
detect.saccades: no visible global function definition for 'median'
diagnostic.plot: no visible global function definition for 'dev.new'
diagnostic.plot: no visible global function definition for 'par'
diagnostic.plot: no visible global function definition for 'recordPlot'
diagnostic.plot: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  dev.new dev.off median par recordPlot sd
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "recordPlot")
  importFrom("graphics", "par")
  importFrom("stats", "median", "sd")
to your NAMESPACE file.
eblupDyn: no visible global function definition for 'model.frame'
eblupDyn: no visible global function definition for 'model.matrix'
eblupDyn: no visible global function definition for 'pnorm'
eblupRY: no visible global function definition for 'model.frame'
eblupRY: no visible global function definition for 'model.matrix'
eblupRY: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  model.frame model.matrix pnorm
Consider adding
  importFrom("stats", "model.frame", "model.matrix", "pnorm")
to your NAMESPACE file.
fit.saery.AR1: no visible global function definition for 'qnorm'
fit.saery.MA1: no visible global function definition for 'qnorm'
fit.saery.indep: no visible global function definition for 'qnorm'
mse.saery.boot.AR1.typeI: no visible global function definition for
  'rnorm'
mse.saery.boot.AR1.typeI: no visible global function definition for
  'write.table'
mse.saery.boot.AR1.typeII: no visible global function definition for
  'rnorm'
mse.saery.boot.AR1.typeII: no visible global function definition for
  'write.table'
mse.saery.boot.MA1.typeI: no visible global function definition for
  'rnorm'
mse.saery.boot.MA1.typeI: no visible global function definition for
  'write.table'
mse.saery.boot.MA1.typeII: no visible global function definition for
  'rnorm'
mse.saery.boot.MA1.typeII: no visible global function definition for
  'write.table'
plot.saery: no visible global function definition for 'devAskNewPage'
plot.saery: no visible global function definition for 'par'
plot.saery: no visible global function definition for 'plot'
plot.saery: no visible global function definition for 'abline'
plot.saery: no visible global function definition for 'title'
plot.saery: no visible global function definition for 'axis'
plot.saery: no visible global function definition for 'lines'
plot.saery: no visible global function definition for 'legend'
pvalue: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  abline axis devAskNewPage legend lines par plot pnorm qnorm rnorm
  title write.table
Consider adding
  importFrom("grDevices", "devAskNewPage")
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "plot", "title")
  importFrom("stats", "pnorm", "qnorm", "rnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Package in Depends field not imported from: 'lpSolveAPI'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
glm: no visible binding for global variable 'gaussian'
glm: no visible global function definition for 'glm.control'
glm: no visible global function definition for 'model.response'
glm: no visible global function definition for 'is.empty.model'
glm: no visible global function definition for 'model.matrix'
glm: no visible global function definition for 'model.weights'
glm: no visible global function definition for 'model.offset'
glm: no visible global function definition for 'model.extract'
glm: no visible global function definition for 'glm.fit'
glm: no visible global function definition for '.getXlevels'
separator: no visible global function definition for 'make.lp'
separator: no visible global function definition for 'set.column'
separator: no visible global function definition for 'set.rhs'
separator: no visible global function definition for 'set.constr.type'
separator: no visible global function definition for 'set.objfn'
separator: no visible global function definition for 'set.bounds'
separator: no visible global function definition for 'lp.control'
separator: no visible global function definition for 'get.variables'
separator: no visible global function definition for 'set.basis'
separator: no visible global function definition for
  'get.dual.solution'
Undefined global functions or variables:
  .getXlevels gaussian get.dual.solution get.variables glm.control
  glm.fit is.empty.model lp.control make.lp model.extract model.matrix
  model.offset model.response model.weights set.basis set.bounds
  set.column set.constr.type set.objfn set.rhs
Consider adding
  importFrom("stats", ".getXlevels", "gaussian", "glm.control",
             "glm.fit", "is.empty.model", "model.extract",
             "model.matrix", "model.offset", "model.response",
             "model.weights")
to your NAMESPACE file.
propdiff.acc: no visible global function definition for 'rbeta'
propdiff.acc: no visible global function definition for 'rbinom'
propdiff.acc: no visible global function definition for 'pbeta'
propdiff.alc: no visible global function definition for 'rbeta'
propdiff.alc: no visible global function definition for 'rbinom'
propdiff.alc: no visible global function definition for 'qbeta'
propdiff.freq: no visible global function definition for 'qnorm'
propdiff.mblacc: no visible global function definition for 'rbeta'
propdiff.mblacc: no visible global function definition for 'rbinom'
propdiff.mblacc: no visible global function definition for 'pbeta'
propdiff.mblalc: no visible global function definition for 'rbeta'
propdiff.mblalc: no visible global function definition for 'rbinom'
propdiff.mblalc: no visible global function definition for 'qbeta'
propdiff.mblmodwoc: no visible global function definition for 'qchisq'
propdiff.mblmodwoc: no visible global function definition for 'pbeta'
propdiff.mblwoc: no visible global function definition for 'pbeta'
propdiff.modwoc: no visible global function definition for 'qchisq'
propdiff.modwoc: no visible global function definition for 'pbeta'
propdiff.woc: no visible global function definition for 'pbeta'
Undefined global functions or variables:
  pbeta qbeta qchisq qnorm rbeta rbinom
Consider adding
  importFrom("stats", "pbeta", "qbeta", "qchisq", "qnorm", "rbeta",
             "rbinom")
to your NAMESPACE file.
GraphBinaryForestPlot: no visible global function definition for
  'abline'
GraphBinaryForestPlot: no visible global function definition for 'text'
GraphContinuousForestPlot: no visible global function definition for
  'abline'
GraphContinuousForestPlot: no visible global function definition for
  'text'
ImputeBinaryEvents: no visible global function definition for 'rbinom'
ImputeSMD: no visible global function definition for 'rnorm'
funnelplot: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline rbinom rnorm text
Consider adding
  importFrom("graphics", "abline", "text")
  importFrom("stats", "rbinom", "rnorm")
to your NAMESPACE file.
generate.sample.core: no visible global function definition for
  'predict'
mdh: no visible global function definition for 'model.frame'
mdh: no visible binding for global variable 'na.fail'
mdh: no visible global function definition for '.getXlevels'
mdh: no visible global function definition for 'quantile'
mdh: no visible global function definition for 'hist'
predict.mdh: no visible global function definition for 'model.frame'
samur: no visible global function definition for 'predict'
Undefined global functions or variables:
  .getXlevels hist model.frame na.fail predict quantile
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", ".getXlevels", "model.frame", "na.fail", "predict",
             "quantile")
to your NAMESPACE file.
download.sas7bdat.sources : <anonymous>: no visible global function
  definition for 'download.file'
generate.sas7bdat.source: no visible global function definition for
  'download.file'
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
parse.SAScii: no visible binding for global variable 'end'
parse.SAScii: no visible binding for global variable 'start'
read.SAScii: no visible global function definition for 'download.file'
read.SAScii: no visible global function definition for 'unzip'
read.SAScii: no visible global function definition for 'read.fwf'
read.SAScii: no visible global function definition for 'capture.output'
Undefined global functions or variables:
  capture.output download.file end read.fwf start unzip
Consider adding
  importFrom("stats", "end", "start")
  importFrom("utils", "capture.output", "download.file", "read.fwf",
             "unzip")
to your NAMESPACE file.
SASPECT: no visible global function definition for 'dbinom'
my.SOnePro: missing arguments not allowed in calls to 'c'
my.ttest: no visible global function definition for 'var'
Undefined global functions or variables:
  dbinom var
Consider adding
  importFrom("stats", "dbinom", "var")
to your NAMESPACE file.
loads: no visible global function definition for 'untar'
saves: no visible global function definition for 'tar'
Undefined global functions or variables:
  tar untar
Consider adding
  importFrom("utils", "tar", "untar")
to your NAMESPACE file.
clogistCalc: no visible global function definition for 'model.matrix'
clogistCalc: no visible global function definition for 'glm.fit'
clogistCalc: no visible global function definition for 'binomial'
clogistInfo : all.not.equal: no visible global function definition for
  'var'
geeUOmega: no visible global function definition for 'model.extract'
geeUOmega: no visible global function definition for 'model.matrix'
geeUOmega: no visible binding for global variable 'contrasts'
mgee: no visible binding for global variable 'gaussian'
sawsCalc: no visible global function definition for 'pf'
sawsCalc: no visible global function definition for 'qt'
Undefined global functions or variables:
  binomial contrasts gaussian glm.fit model.extract model.matrix pf qt
  var
Consider adding
  importFrom("stats", "binomial", "contrasts", "gaussian", "glm.fit",
             "model.extract", "model.matrix", "pf", "qt", "var")
to your NAMESPACE file.
K: no visible global function definition for 'dnorm'
sBF: no visible global function definition for 'density'
sBF: no visible global function definition for 'txtProgressBar'
sBF: no visible global function definition for 'setTxtProgressBar'
Undefined global functions or variables:
  density dnorm setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "density", "dnorm")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Found the following significant warnings:
  d:/Compiler/gcc-4.9.3/local330/include/gmp-x64.h:140:23: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/Compiler/gcc-4.9.3/local330/include/gmp-x64.h:141:14: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.6/sbrl.Rcheck/00install.out' for details.
fitSBSA: no visible binding for global variable 'var'
fitSBSA: no visible global function definition for 'var'
fitSBSA: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  qnorm var
Consider adding
  importFrom("stats", "qnorm", "var")
to your NAMESPACE file.
ChooseBest: no visible global function definition for 'head'
GetScores: no visible global function definition for 'write.table'
ReportTable: no visible binding for global variable 'sd'
ReportTable: no visible global function definition for 'write.table'
Undefined global functions or variables:
  head sd write.table
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "head", "write.table")
to your NAMESPACE file.
plot.scair: no visible global function definition for 'par'
plot.scair: no visible global function definition for 'plot'
plot.scair: no visible global function definition for 'points'
plot.scar: no visible global function definition for 'par'
plot.scar: no visible global function definition for 'plot'
plot.scar: no visible global function definition for 'points'
predict.scair: no visible global function definition for 'approx'
predict.scar: no visible global function definition for 'approx'
scair: no visible global function definition for 'gaussian'
scair: no visible global function definition for 'runif'
scair: no visible global function definition for 'rnorm'
scar: no visible global function definition for 'gaussian'
scar: no visible global function definition for 'glm.fit'
scar: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx gaussian glm.fit par plot points rnorm runif
Consider adding
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "approx", "gaussian", "glm.fit", "rnorm", "runif")
to your NAMESPACE file.
prime.factor: no visible global function definition for 'data'
prime.factor: no visible binding for global variable 'primlist'
Undefined global functions or variables:
  data primlist
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
'library' or 'require' call to 'QUIC' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
scio.cv: no visible global function definition for 'cov'
scio.refit: no visible global function definition for 'QUIC'
Undefined global functions or variables:
  QUIC cov
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
Running examples in 'scorecardModelUtils-Ex.R' failed
The error most likely occurred in:

> ### Name: scalling
> ### Title: Converting coefficients of logistic regression into scores for
> ###   scorecard building
> ### Aliases: scalling
> 
> ### ** Examples
> 
> data <- iris
> set.seed(11)
> data$Y <- sample(0:1,size=nrow(data),replace=TRUE)
> x <- c("Sepal.Length","Sepal.Width","Petal.Length","Petal.Width")
> iv_table_list <- iv_table(base = data,target = "Y",num_var_name = x,cat_var_name = "Species")
> num_cat <- num_to_cat(base = data,num_woe_table = iv_table_list$num_woe_table)
> log_model <- glm(Y ~ ., data = num_cat, family = "binomial")
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
  contrasts can be applied only to factors with 2 or more levels
Calls: glm ... model.matrix -> model.matrix.default -> contrasts<-
Execution halted
score.GGUM: no visible global function definition for 'dnorm'
score.GGUM: no visible global function definition for 'hist'
score.GGUM: no visible global function definition for 'write.table'
Undefined global functions or variables:
  dnorm hist write.table
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "dnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file.
CreatePssm: no visible binding for global variable 'training'
Undefined global functions or variables:
  training
'library' or 'require' calls to packages already attached by Depends:
  'RCurl' 'XML'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'RCurl' 'XML'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
scrape: no visible global function definition for 'getURLAsynchronous'
scrape: no visible global function definition for 'runif'
scrape: no visible global function definition for 'capture.output'
scrape: no visible binding for global variable 'xmlParse'
scrape: no visible binding for global variable 'htmlParse'
Undefined global functions or variables:
  capture.output getURLAsynchronous htmlParse runif xmlParse
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
lahiri.design: 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  5.1Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   3.5Mb
estimateTimeToComputeTargetDefinition: no visible global function
  definition for 'flush.console'
estimateTimeToComputeTargetDefinition: no visible global function
  definition for 'combn'
initialize,sdcTargetDefinitionClass: no visible global function
  definition for 'flush.console'
initialize,sdcTargetDefinitionClass: no visible global function
  definition for 'combn'
initialize,sdcTargetDefinitionClass: no visible global function
  definition for 'quantile'
initialize,sdcTargetMatrixClass: no visible global function definition
  for 'flush.console'
Undefined global functions or variables:
  combn flush.console quantile
Consider adding
  importFrom("stats", "quantile")
  importFrom("utils", "combn", "flush.console")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'raster' 'sp'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'lars'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
sealasso: no visible global function definition for 'lars'
weight.calc: no visible global function definition for 'lars'
Undefined global functions or variables:
  lars
adx: no visible global function definition for 'abline'
adx: no visible global function definition for 'legend'
dx: no visible global function definition for 'abline'
dx: no visible global function definition for 'legend'
maxd: no visible global function definition for 'abline'
maxd: no visible global function definition for 'legend'
pc: no visible global function definition for 'rainbow'
pc: no visible global function definition for 'plot'
pc: no visible global function definition for 'abline'
pc: no visible global function definition for 'legend'
pc: no visible global function definition for 'points'
pcu: no visible global function definition for 'rainbow'
pcu: no visible global function definition for 'plot'
pcu: no visible global function definition for 'abline'
pcu: no visible global function definition for 'legend'
pcu: no visible global function definition for 'points'
rmsd: no visible global function definition for 'abline'
rmsd: no visible global function definition for 'legend'
rsd: no visible global function definition for 'abline'
rsd: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline legend plot points rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "legend", "plot", "points")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'NADA' 'lubridate' 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package in Depends field not imported from: 'JM'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SEchart: no visible global function definition for 'plot'
SEchart: no visible global function definition for 'rect'
SEchart: no visible global function definition for 'par'
SEchart: no visible global function definition for 'grid'
SEchart: no visible global function definition for 'axis'
SEchart: no visible global function definition for 'text'
SEchart: no visible global function definition for 'lines'
SEchart: no visible global function definition for 'heat.colors'
SEchart: no visible global function definition for 'topo.colors'
SEchart: no visible global function definition for 'cm.colors'
SEchart: no visible global function definition for 'terrain.colors'
SEchart: no visible global function definition for 'gray.colors'
SEchart: no visible global function definition for 'rainbow'
SEchart: no visible global function definition for 'points'
SEchart: no visible global function definition for 'legend'
Undefined global functions or variables:
  axis cm.colors gray.colors grid heat.colors legend lines par plot
  points rainbow rect terrain.colors text topo.colors
Consider adding
  importFrom("grDevices", "cm.colors", "gray.colors", "heat.colors",
             "rainbow", "terrain.colors", "topo.colors")
  importFrom("graphics", "axis", "grid", "legend", "lines", "par",
             "plot", "points", "rect", "text")
to your NAMESPACE file.
fdc2s: no visible global function definition for 'lm'
fdc3s: no visible global function definition for 'lm'
fds2s: no visible global function definition for 'lm'
fds3s: no visible global function definition for 'lm'
Undefined global functions or variables:
  lm
Consider adding
  importFrom("stats", "lm")
to your NAMESPACE file.
Running examples in 'secret-Ex.R' failed
The error most likely occurred in:

> ### Name: add_github_user
> ### Title: Add a user via their GitHub username.
> ### Aliases: add_github_user
> 
> ### ** Examples
> 
> vault <- file.path(tempdir(), ".vault")
> create_vault(vault)
> 
> add_github_user("hadley", vault = vault)
> list_users(vault = vault)
[1] "github-hadley"
> delete_user("github-hadley", vault = vault)
> 
> 
> 
> cleanEx()
Error: connections left open:
	file (textConnection)
Execution halted
.read.SeerStatTXT: no visible global function definition for
  'read.table'
.write.SeerStatTXT: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.5Mb
get.infectiousness: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  qchisq
Consider adding
  importFrom("stats", "qchisq")
to your NAMESPACE file.
get_statistics_from_file: no visible global function definition for
  'read.csv'
glm_anova: no visible global function definition for 'aov'
glm_anova: no visible global function definition for 'glm'
glm_anova: no visible global function definition for 'gaussian'
glm_anova: no visible global function definition for 'anova'
glm_anova: no visible global function definition for 'quasipoisson'
glm_anova: no visible global function definition for 'sd'
glm_anova: no visible global function definition for 'p.adjust'
ttest_cohens_d: no visible global function definition for 't.test'
ttest_cohens_d: no visible global function definition for 'sd'
Undefined global functions or variables:
  anova aov gaussian glm p.adjust quasipoisson read.csv sd t.test
Consider adding
  importFrom("stats", "anova", "aov", "gaussian", "glm", "p.adjust",
             "quasipoisson", "sd", "t.test")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
predict.SEL: warning in splineDesign(newdata, knots = knts, ord =
  object$nord, deriv = rep(deriv, length(newdata)), outer.ok = TRUE):
  partial argument match of 'deriv' to 'derivs'
getbinPost: no visible binding for global variable 'dbeta'
getbinPost: no visible binding for global variable 'pbeta'
getbinPost : fu: no visible global function definition for 'dbinom'
getbinPost : fu: no visible global function definition for 'predict'
getbinPost: no visible global function definition for 'integrate'
getbinPost: no visible global function definition for 'splinefun'
int.funct: no visible global function definition for 'integrate'
int.funct2: no visible global function definition for 'integrate'
min.abs: no visible global function definition for 'uniroot'
plot.SEL: no visible global function definition for 'plot'
print.SEL: no visible global function definition for 'integrate'
print.summary.SEL : foo1: no visible global function definition for
  'predict'
print.summary.SEL : foo2: no visible global function definition for
  'predict'
print.summary.SEL: no visible global function definition for
  'integrate'
quantSEL: no visible global function definition for 'predict'
quantSEL: no visible global function definition for 'splinefun'
rvSEL: no visible global function definition for 'runif'
Undefined global functions or variables:
  dbeta dbinom integrate pbeta plot predict runif splinefun uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dbeta", "dbinom", "integrate", "pbeta", "predict",
             "runif", "splinefun", "uniroot")
to your NAMESPACE file.
Package in Depends field not imported from: 'sem'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ChiSquaredLRTest: no visible global function definition for 'na.omit'
ChiSquaredLRTest: no visible global function definition for 'cov'
ChiSquaredLRTest: no visible global function definition for 'dmvnorm'
ChiSquaredLRTest: no visible global function definition for 'pchisq'
NormalTheoryLRTest: no visible global function definition for 'na.omit'
NormalTheoryLRTest: no visible global function definition for 'cov'
NormalTheoryLRTest: no visible global function definition for 'dmvnorm'
NormalTheoryLRTest: no visible global function definition for 'sd'
NormalTheoryLRTest: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  cov dmvnorm na.omit pchisq pnorm sd
Consider adding
  importFrom("stats", "cov", "na.omit", "pchisq", "pnorm", "sd")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'XML' 'boot' 'sem'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  'boot:::const' 'stats:::AIC.logLik' 'stats:::BIC.logLik'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'addPath.plsm' 'endogenous' 'predecessors' 'qSquared' 'reorder'
  'resempls' 'residuals.sempls'
.plot_attachment: no visible global function definition for 'dev.off'
.update_list: no visible global function definition for 'modifyList'
mime_part.data.frame: no visible global function definition for
  'write.table'
mime_part.ggplot: no visible binding for global variable 'pdf'
mime_part.matrix: no visible global function definition for
  'write.table'
mime_part.trellis: no visible binding for global variable 'pdf'
Undefined global functions or variables:
  dev.off modifyList pdf write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("utils", "modifyList", "write.table")
to your NAMESPACE file.
'library' or 'require' call to 'rtiff' which was already attached by Depends.
  Please remove these calls from your code.
gconv: no visible global function definition for 'convolve'
sens.analysis.aberrant.rank: no visible global function definition for
  'pnorm'
sens.analysis.mh: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  convolve pnorm
Consider adding
  importFrom("stats", "convolve", "pnorm")
to your NAMESPACE file.
mscorev: no visible global function definition for 'quantile'
senmwCI : funcCI: no visible global function definition for 'qnorm'
senmwCI : funcCI2: no visible global function definition for 'qnorm'
separable1k: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm qnorm quantile
Consider adding
  importFrom("stats", "pnorm", "qnorm", "quantile")
to your NAMESPACE file.
plot.sensitivity.2.0d: no visible global function definition for 'gray'
sensitivitySGD: no visible global function definition for 'tail'
sensitivitySGL: no visible global function definition for 'tail'
Undefined global functions or variables:
  gray tail
Consider adding
  importFrom("grDevices", "gray")
  importFrom("utils", "tail")
to your NAMESPACE file.
Running 'testthat.R' [8s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("sentimentr")
  > 
  > test_check("sentimentr")
  -- 1. Failure: extract_sentiment_terms extracts the terms (@test-extract_sentime
  pol_words$negative[1:3] not equal to list(character(0), c("wait", "restless", "fire"), character(0)).
  Component 2: Lengths (0, 3) differ (string compare on first 0)
  
  == testthat results  ===========================================================
  OK: 32 SKIPPED: 0 FAILED: 1
  1. Failure: extract_sentiment_terms extracts the terms (@test-extract_sentiment_terms.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
separationplot: no visible global function definition for 'dev.new'
separationplot: no visible global function definition for 'pdf'
separationplot: no visible global function definition for 'par'
separationplot: no visible global function definition for 'plot'
separationplot: no visible global function definition for 'title'
separationplot: no visible global function definition for 'segments'
separationplot: no visible global function definition for 'rect'
separationplot: no visible global function definition for 'points'
separationplot: no visible global function definition for 'lines'
separationplot: no visible global function definition for
  'colorRampPalette'
separationplot: no visible global function definition for 'layout'
separationplot: no visible global function definition for 'plot.new'
separationplot: no visible global function definition for 'legend'
separationplot: no visible global function definition for 'dev.off'
separationplot: no visible global function definition for 'locator'
sp.categorical: no visible global function definition for 'dev.new'
sp.categorical: no visible global function definition for 'pdf'
sp.categorical: no visible global function definition for 'par'
sp.categorical: no visible global function definition for 'layout'
sp.categorical: no visible global function definition for 'plot'
sp.categorical: no visible global function definition for 'text'
sp.categorical: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  colorRampPalette dev.new dev.off layout legend lines locator par pdf
  plot plot.new points rect segments text title
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.new", "dev.off",
             "pdf")
  importFrom("graphics", "layout", "legend", "lines", "locator", "par",
             "plot", "plot.new", "points", "rect", "segments", "text",
             "title")
to your NAMESPACE file.
GammaDist: no visible binding for global variable 'rgamma'
VEpowerPP: no visible global function definition for 'qnorm'
applyStopRules: no visible global function definition for 'qnorm'
finalLogRankTest: no visible global function definition for 'qnorm'
finalLogRankTest: no visible global function definition for 'pchisq'
generateDropout: no visible global function definition for 'rexp'
generateEnrollment: no visible global function definition for 'rpois'
generateEnrollment: no visible global function definition for 'runif'
generateInfection: no visible global function definition for 'rexp'
generateInfection : <anonymous>: no visible global function definition
  for 'rexp'
getAlphaPerTest: no visible global function definition for 'uniroot'
getHarmBound: no visible global function definition for 'dbinom'
getHarmBound: no visible global function definition for 'write.csv'
getTreatmentAssignment : <anonymous>: no visible global function
  definition for 'runif'
getTreatmentAssignment: no visible global function definition for
  'runif'
simTrial: no visible global function definition for 'runif'
sumTrialOneTrtArm: no visible global function definition for 'quantile'
testVE: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  dbinom pchisq qnorm quantile rexp rgamma rpois runif uniroot
  write.csv
Consider adding
  importFrom("stats", "dbinom", "pchisq", "qnorm", "quantile", "rexp",
             "rgamma", "rpois", "runif", "uniroot")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs   3.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
plotenz : addmark: no visible global function definition for 'par'
plotenz : addmark: no visible global function definition for 'plot'
plotenz : addmark: no visible global function definition for 'text'
plotenz : addmark: no visible global function definition for 'segments'
plotenz : addband: no visible global function definition for 'segments'
plotenz : addband: no visible global function definition for 'text'
plotenz: no visible global function definition for 'layout'
plotenz: no visible global function definition for 'text'
plotenz: no visible global function definition for 'dev.new'
Undefined global functions or variables:
  dev.new layout par plot segments text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "layout", "par", "plot", "segments", "text")
to your NAMESPACE file.
Error(s) in re-building vignettes:
--- re-building 'Introduction.Rmd' using rmarkdown
trying URL 'https://pure.strath.ac.uk/portal/files/43595106/Figure_2.zip'
Quitting from lines 38-41 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
cannot open URL 'https://pure.strath.ac.uk/portal/files/43595106/Figure_2.zip'
--- failed re-building 'Introduction.Rmd'

SUMMARY: processing the following file failed:
  'Introduction.Rmd'

Error: Vignette re-building failed.
Execution halted
capture: no visible binding for global variable 'resultText'
restore.session: no visible binding for global variable
  '.save.session.packages'
restore.session: no visible binding for global variable
  '.save.session.search'
save.session: no visible global function definition for 'dev.list'
save.session: no visible binding for '<<-' assignment to
  '.save.session.search'
save.session: no visible binding for '<<-' assignment to
  '.save.session.packages'
Undefined global functions or variables:
  .save.session.packages .save.session.search dev.list resultText
Consider adding
  importFrom("grDevices", "dev.list")
to your NAMESPACE file.
setpath: no visible global function definition for 'cov'
setpath: no visible global function definition for 'median'
setpath: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  cov median pchisq
Consider adding
  importFrom("stats", "cov", "median", "pchisq")
to your NAMESPACE file.
random.number.test: no visible global function definition for 'runif'
random.number.test: no visible global function definition for 'rnorm'
setRNG: no visible global function definition for 'runif'
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: 'loomR'
'library' or 'require' call to 'graphics' which was already attached by Depends.
  Please remove these calls from your code.
severity: no visible global function definition for 'qnorm'
severity: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
L_exp: no visible global function definition for 'pnorm'
L_hNV: no visible global function definition for 'pnorm'
L_trunc: no visible global function definition for 'pnorm'
L_trunc_mufest: no visible global function definition for 'pnorm'
dgp: no visible global function definition for 'runif'
dgp: no visible global function definition for 'rnorm'
eff.sfa: no visible global function definition for 'predict'
fitted.sfa: no visible global function definition for 'predict'
predict.sfa: no visible global function definition for 'coef'
print.sfa: no visible global function definition for 'coef'
residuals.sfa: no visible global function definition for 'fitted'
sfa: no visible global function definition for 'model.frame'
sfa: no visible global function definition for 'model.response'
sfa.fit: no visible global function definition for 'lm'
sfa.fit: no visible global function definition for 'resid'
sfa.fit: no visible global function definition for 'var'
sfa.fit: no visible global function definition for 'optim'
summary.sfa: no visible global function definition for 'logLik'
summary.sfa: no visible global function definition for 'pchisq'
te.eff.sfa: no visible global function definition for 'residuals'
te.eff.sfa: no visible global function definition for 'pnorm'
u.sfa: no visible global function definition for 'residuals'
u.sfa: no visible global function definition for 'dnorm'
u.sfa: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  coef dnorm fitted lm logLik model.frame model.response optim pchisq
  pnorm predict resid residuals rnorm runif var
Consider adding
  importFrom("stats", "coef", "dnorm", "fitted", "lm", "logLik",
             "model.frame", "model.response", "optim", "pchisq", "pnorm",
             "predict", "resid", "residuals", "rnorm", "runif", "var")
to your NAMESPACE file.
installed size is 94.0Mb
  sub-directories of 1Mb or more:
    doc     11.2Mb
    gdal     3.9Mb
    libs    70.0Mb
    proj     5.0Mb
    sqlite   1.5Mb
.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  5.3Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.0Mb
amse: no visible global function definition for 'na.omit'
arb: no visible global function definition for 'na.omit'
rdatagen: no visible global function definition for 'qnorm'
rdatagen: no visible global function definition for 'pbinom'
rdatagen: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  na.omit pbinom pnorm qnorm
Consider adding
  importFrom("stats", "na.omit", "pbinom", "pnorm", "qnorm")
to your NAMESPACE file.
UQnormalize.count: no visible binding for global variable 'quantile'
plotNScores: no visible global function definition for 'par'
plotNScores: no visible global function definition for 'hist'
plotNScores: no visible global function definition for 'title'
plotScores: no visible global function definition for 'par'
plotScores: no visible global function definition for 'hist'
plotScores: no visible global function definition for 'title'
sgRSEA: no visible binding for global variable 'sd'
sgRSEA: no visible global function definition for 'p.adjust'
sgRSEA.mean: no visible binding for global variable 'sd'
sgRSEA.mean: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  hist p.adjust par quantile sd title
Consider adding
  importFrom("graphics", "hist", "par", "title")
  importFrom("stats", "p.adjust", "quantile", "sd")
to your NAMESPACE file.
'library' or 'require' call to 'foreign' which was already attached by Depends.
  Please remove these calls from your code.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    www   7.5Mb
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 10.1Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    www   7.8Mb
shrink.estim: no visible global function definition for 'cov'
shrink.estim: no visible global function definition for 'cor'
shrink.estim: no visible global function definition for 'cov2cor'
targetCor: no visible global function definition for 'cor.test'
targetCor: no visible global function definition for 'cor'
targetCor: no visible global function definition for 'sd'
targetCor: no visible global function definition for 'cov'
targetD: no visible binding for global variable 'var'
targetF: no visible global function definition for 'cov'
targetF: no visible global function definition for 'cor'
targetG: no visible global function definition for 'cor'
targetG: no visible global function definition for 'sd'
targetG: no visible global function definition for 'cov'
targetGpos: no visible global function definition for 'cor'
targetGpos: no visible global function definition for 'sd'
targetGpos: no visible global function definition for 'cov'
targetGstar: no visible global function definition for 'cor'
targetGstar: no visible global function definition for 'sd'
targetGstar: no visible global function definition for 'cov'
Undefined global functions or variables:
  cor cor.test cov cov2cor sd var
Consider adding
  importFrom("stats", "cor", "cor.test", "cov", "cov2cor", "sd", "var")
to your NAMESPACE file.
.params: no visible binding for global variable 'URLencode'
.params: no visible global function definition for 'URLencode'
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'MASS' 'bayesm' 'coda' 'hdrcde' 'mnormt' 'spatstat'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages in Depends field not imported from:
  'ade4' 'corpcor'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
filter.PCA.default: no visible global function definition for
  'princomp'
filter.mRMR.default: no visible global function definition for
  'discretize'
gaussian.default: no visible global function definition for 'cov'
gaussian.default: no visible global function definition for
  'cov.shrink'
plot.verify.cv: no visible global function definition for 'plot'
plot.verify.cv: no visible global function definition for 'points'
plot.verify.ho: no visible global function definition for 'plot'
plot.verify.ho: no visible global function definition for 'points'
plot.verify.loo: no visible global function definition for 'plot'
plot.verify.loo: no visible global function definition for 'points'
predict.dpa1: no visible global function definition for 'cor'
predict.filter.PCA: no visible global function definition for 'predict'
predict.filter.RegressionTreeFilter: no visible global function
  definition for 'is.struct'
predict.filter.RegressionTreeFilter: no visible global function
  definition for 'var'
simulator.Simple1: no visible global function definition for 'rnorm'
verify.ho.default: no visible global function definition for 'predict'
verify.loo.default: no visible global function definition for 'predict'
Undefined global functions or variables:
  cor cov cov.shrink discretize is.struct plot points predict princomp
  rnorm var
Consider adding
  importFrom("graphics", "plot", "points")
  importFrom("stats", "cor", "cov", "predict", "princomp", "rnorm",
             "var")
to your NAMESPACE file.
dSepAdji: no visible global function definition for 'as'
dag2cpdagAdj: no visible global function definition for 'as'
randomDAG: no visible global function definition for 'rbinom'
structIntervDist: no visible global function definition for 'as'
Undefined global functions or variables:
  as rbinom
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "rbinom")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
.cluster: no visible global function definition for 'kmeans'
.plot.sigclust: no visible global function definition for 'par'
.plot.sigclust: no visible global function definition for 'density'
.plot.sigclust: no visible global function definition for 'runif'
.plot.sigclust: no visible global function definition for 'dnorm'
.plot.sigclust: no visible global function definition for 'lines'
.plot.sigclust: no visible global function definition for 'points'
.plot.sigclust: no visible global function definition for 'title'
.plot.sigclust: no visible global function definition for 'text'
.plot.sigclust: no visible global function definition for 'qnorm'
.plot.sigclust: no visible global function definition for 'abline'
.plot.sigclust: no visible global function definition for 'quantile'
.plot.sigclust: no visible global function definition for 'legend'
.simnull: no visible global function definition for 'rnorm'
.vareigen: no visible global function definition for 'mad'
.vareigen: no visible global function definition for 'cov'
sigclust: no visible global function definition for 'sd'
sigclust: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  abline cov density dnorm kmeans legend lines mad par pnorm points
  qnorm quantile rnorm runif sd text title
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "points",
             "text", "title")
  importFrom("stats", "cov", "density", "dnorm", "kmeans", "mad",
             "pnorm", "qnorm", "quantile", "rnorm", "runif", "sd")
to your NAMESPACE file.
Sight.Est: no visible global function definition for 'glm'
Sight.Est: no visible global function definition for 'binomial'
Sight.Est: no visible global function definition for 'coef'
Sight.Est: no visible global function definition for 'terms'
Sight.Est: no visible binding for global variable 'binomial'
covtheta: no visible global function definition for 'cov'
print.sightest: no visible global function definition for 'qnorm'
summary.sightest: no visible global function definition for 'qnorm'
vardiff: no visible global function definition for 'vcov'
vardiff: no visible global function definition for 'coef'
vardiff: no visible global function definition for 'terms'
varlog.lam: no visible global function definition for 'vcov'
varlog.lam: no visible global function definition for 'coef'
varlog.lam: no visible global function definition for 'terms'
Undefined global functions or variables:
  binomial coef cov glm qnorm terms vcov
Consider adding
  importFrom("stats", "binomial", "coef", "cov", "glm", "qnorm", "terms",
             "vcov")
to your NAMESPACE file.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(sigmajs)
  Welcome to sigmajs
  
  Docs: sigmajs.john-coene.com
  > 
  > test_check("sigmajs")
  Found # 3 clusters
  -- 1. Failure: delay (@test-graph.R#50)  ---------------------------------------
  unlist(unname(sg$x$addNodesDelay[[1]][5])) not equal to " 566.004".
  1/1 mismatches
  x[1]: " 548.9736"
  y[1]: " 566.004"
  
  == testthat results  ===========================================================
  OK: 65 SKIPPED: 0 FAILED: 1
  1. Failure: delay (@test-graph.R#50) 
  
  Error: testthat unit tests failed
  Execution halted
signmedian.test: no visible global function definition for 'median'
signmedian.test: no visible global function definition for 'binom.test'
signmedian.test: no visible global function definition for 'pbinom'
signmedian.test: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  binom.test median pbinom pnorm
Consider adding
  importFrom("stats", "binom.test", "median", "pbinom", "pnorm")
to your NAMESPACE file.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
'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.
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(simcdm)
  > 
  > test_check("simcdm")
  -- 1. Failure: Simulation of attributes matches (@test-attributes.R#71)  -------
  `subject_alphas_func` not equal to `subject_alphas_base`.
  34/60 mismatches (average diff: 1)
  [1]  0 - 1 == -1
  [3]  0 - 1 == -1
  [4]  1 - 0 ==  1
  [5]  1 - 0 ==  1
  [6]  0 - 1 == -1
  [10] 1 - 0 ==  1
  [12] 0 - 1 == -1
  [14] 0 - 1 == -1
  [15] 1 - 0 ==  1
  ...
  Equivalent subject alpha Generation
  
  == testthat results  ===========================================================
  OK: 14 SKIPPED: 0 FAILED: 1
  1. Failure: Simulation of attributes matches (@test-attributes.R#71) 
  
  Error: testthat unit tests failed
  Execution halted
getFormula: no visible global function definition for 'as.formula'
internalSimXyplot : f: no visible global function definition for
  'median'
runSimulation: no visible global function definition for 'runif'
setup: no visible global function definition for 'runif'
clusterSetup,ANY-data.frame-SampleControl: no visible binding for
  global variable 'cnam'
clusterSetup,ANY-data.frame-TwoStageControl: no visible binding for
  global variable 'cnam'
initialize,DCARContControl: no visible binding for global variable
  'rnorm'
initialize,DataControl: no visible binding for global variable 'rnorm'
Undefined global functions or variables:
  as.formula cnam median rnorm runif
Consider adding
  importFrom("stats", "as.formula", "median", "rnorm", "runif")
to your NAMESPACE file.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   2.9Mb
cumallcausehr: no visible global function definition for 'integrate'
plotbe: no visible global function definition for 'plot'
plotbe: no visible global function definition for 'lines'
plotbe: no visible global function definition for 'legend'
plotcph: no visible global function definition for 'confint'
plotcph: no visible global function definition for 'plot'
plotcph: no visible global function definition for 'abline'
plotcph: no visible global function definition for 'axis'
plotcph: no visible global function definition for 'polygon'
plotcph: no visible global function definition for 'lines'
plotnae: no visible global function definition for 'plot'
simCR: no visible global function definition for 'rnorm'
simEBMT: no visible global function definition for 'model.matrix'
simexit: no visible global function definition for 'runif'
simexitinner: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  abline axis confint integrate legend lines model.matrix plot polygon
  rnorm runif uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "plot",
             "polygon")
  importFrom("stats", "confint", "integrate", "model.matrix", "rnorm",
             "runif", "uniroot")
to your NAMESPACE file.
randInitializeWeights: no visible global function definition for
  'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(SimplifyStats)
  > 
  > test_check("SimplifyStats")
  
  The Shapiro-Wilk test requires 3 < N < 5000.
  
  -- 1. Failure: valid input produce valid output (@test.group_summarize.R#34)  --
  {
      ...
  } isn't true.
  
  == testthat results  ===========================================================
  OK: 8 SKIPPED: 0 FAILED: 1
  1. Failure: valid input produce valid output (@test.group_summarize.R#34) 
  
  Error: testthat unit tests failed
  Execution halted
Package in Depends field not imported from: 'mclust'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Simpsons: no visible global function definition for 'Mclust'
Simpsons: no visible global function definition for 'lm'
Simpsons: no visible global function definition for 'plot'
Simpsons: no visible global function definition for 'abline'
Simpsons: no visible global function definition for 'par'
Simpsons: no visible global function definition for 'legend'
Simpsons: no visible global function definition for 'txtProgressBar'
Simpsons: no visible global function definition for 'setTxtProgressBar'
Simpsons: no visible global function definition for 'quantile'
plot.Simpson: no visible global function definition for 'plot'
plot.Simpson: no visible global function definition for 'lm'
plot.Simpson: no visible global function definition for 'abline'
plot.Simpson: no visible global function definition for 'par'
plot.Simpson: no visible global function definition for 'legend'
Undefined global functions or variables:
  Mclust abline legend lm par plot quantile setTxtProgressBar
  txtProgressBar
Consider adding
  importFrom("graphics", "abline", "legend", "par", "plot")
  importFrom("stats", "lm", "quantile")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
simrel: no visible global function definition for 'runif'
simrel: no visible global function definition for 'rnorm'
simrelplot: no visible global function definition for 'par'
simrelplot: no visible global function definition for 'layout'
simrelplot: no visible global function definition for 'devAskNewPage'
simrelplot: no visible global function definition for 'dev.hold'
simrelplot: no visible global function definition for 'plot'
simrelplot: no visible global function definition for 'abline'
simrelplot: no visible global function definition for 'dev.flush'
simrelplot: no visible global function definition for 'points'
simrelplot: no visible global function definition for 'axis'
simrelplot: no visible global function definition for 'mtext'
simrelplot: no visible global function definition for 'box'
simrelplot: no visible global function definition for 'cov'
Undefined global functions or variables:
  abline axis box cov dev.flush dev.hold devAskNewPage layout mtext par
  plot points rnorm runif
Consider adding
  importFrom("grDevices", "dev.flush", "dev.hold", "devAskNewPage")
  importFrom("graphics", "abline", "axis", "box", "layout", "mtext",
             "par", "plot", "points")
  importFrom("stats", "cov", "rnorm", "runif")
to your NAMESPACE file.
Found the following hidden files and directories:
  vignettes/.Rhistory
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'abind' 'svUnit'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
simSummary: no visible global function definition for 'abind'
simSummary_unitTests: no visible global function definition for
  'clearLog'
simSummary_unitTests: no visible global function definition for
  'runTest'
simSummary_unitTests: no visible global function definition for
  'svSuite'
simSummary_unitTests: no visible global function definition for 'Log'
simSummary_unitTests: no visible global function definition for 'stats'
simSummary_unitTests: no visible global function definition for
  'metadata'
simSummary_unitTests: no visible global function definition for
  'errorLog'
Undefined global functions or variables:
  Log abind clearLog errorLog metadata runTest stats svSuite
Running 'testthat.R' [18s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(simTool)
  > 
  > test_check("simTool")
  [1] "Estimated replications per hour:  NA"
  [1] "Estimated replications per hour:  NA"
  [1] "Estimated replications per hour:  769228"
  
    |                                                                            
    |                                                                      |   0%[1] "With fallback!"
  
    |                                                                            
    |==============                                                        |  20%
    |                                                                            
    |============================                                          |  40%
    |                                                                            
    |==========================================                            |  60%[1] "Estimated replications per hour:  NA"
  [1] "Estimated replications per hour:  NA"
  [1] "Estimated replications per hour:  230769"
  [1] "Estimated replications per hour:  2307838"
  [1] "Estimated replications per hour:  288464"
  [1] "Estimated replications per hour:  2307697"
  [1] "Estimated replications per hour:  384620"
  -- 1. Failure: Two groups for summary_fun. Results were created and stored in si
  eg$simulation[[col]] not identical to expected_df[[col]].
  Objects equal but not identical
  
  == testthat results  ===========================================================
  OK: 132 SKIPPED: 0 FAILED: 1
  1. Failure: Two groups for summary_fun. Results were created and stored in simulation (@test_eval_tibbles.R#847) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    libs   2.5Mb
cvskda: no visible global function definition for 'detectCores'
cvskda: no visible global function definition for 'makeCluster'
cvskda: no visible global function definition for 'clusterApplyLB'
cvskda: no visible global function definition for 'mclapply'
cvskda: no visible global function definition for 'stopCluster'
Undefined global functions or variables:
  clusterApplyLB detectCores makeCluster mclapply stopCluster
dskt: no visible global function definition for 'dt'
pskt: no visible global function definition for 'pt'
qskt: no visible global function definition for 'qt'
rskt: no visible global function definition for 'runif'
Undefined global functions or variables:
  dt pt qt runif
Consider adding
  importFrom("stats", "dt", "pt", "qt", "runif")
to your NAMESPACE file.
Package which this enhances but not available for checking: 'kmndirs'
Unavailable namespace imported from by a ':::' call: 'kmndirs'
  See the note in ?`:::` about the use of this operator.
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.6/RcppParallel/include/tthread/tinythread.h:632:14: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/RcppParallel/include/tbb/tbb_stddef.h:470:37: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/RcppParallel/include/tbb/atomic.h:29:30: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/RcppParallel/include/tbb/tick_count.h:42:14: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/RcppParallel/include/tbb/tick_count.h:43:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/RcppParallel/include/tbb/tick_count.h:75:21: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/RcppParallel/include/tbb/tick_count.h:102:10: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/RcppParallel/include/tbb/tick_count.h:80:37: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/RcppParallel/include/tbb/tick_count.h:127:30: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.6/skm.Rcheck/00install.out' for details.
slcestimates: no visible global function definition for 'par'
slcestimates: no visible global function definition for 'plot'
slcestimates: no visible global function definition for 'abline'
slcestimates: no visible global function definition for 'lines'
slcestimates: no visible global function definition for 'axis'
slcestimates: no visible global function definition for 'points'
slcestimates: no visible global function definition for 'title'
Undefined global functions or variables:
  abline axis lines par plot points title
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "par", "plot",
             "points", "title")
to your NAMESPACE file.
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(slouch)
  > 
  > # testsetup <- function(){
  > #   pars <- list(myfunc = myfunc, dummydata = dummydata, model.id.btk = model.id.btk)
  > #   return(pars)
  > # }
  > 
  > test_check("slouch")
  -- 1. Failure: No errors ANOVA (@test_anova.R#37)  -----------------------------
  structure(...) not equal to m1$beta_primary$coefficients.
  3/4 mismatches (average diff: 0.0444)
  [1] 0.4216 - 0.4893 == -0.06774
  [2] 0.4815 - 0.4220 ==  0.05951
  [4] 0.0504 - 0.0445 ==  0.00591
  
  == testthat results  ===========================================================
  OK: 9 SKIPPED: 0 FAILED: 1
  1. Failure: No errors ANOVA (@test_anova.R#37) 
  
  Error: testthat unit tests failed
  Execution halted
cvsmac: no visible global function definition for 'predict'
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(SmartEDA)
  > 
  > 
  > context("Summary statistics")
  > 
  > test_that("ExpKurtosis and ExpSkew are measures of shapes value", {
  +   expect_equal(ExpKurtosis(c(1:4),type="moment"), 1.64)
  +   set.seed(1234)
  +   expect_equal(ExpSkew(sample(1:100,10),type="moment"),-0.2131082)
  + })
  Error: Test failed: 'ExpKurtosis and ExpSkew are measures of shapes value'
  * ExpSkew(sample(1:100, 10), type = "moment") not equal to -0.2131082.
  1/1 mismatches
  [1] 0.618 - -0.213 == 0.831
  Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.6/SmarterPoland.Rcheck/00install.out' for details.
File 'smco/R/smco.R':
  .onAttach calls:
    cat(paste("This is smco package", version, "\n"))

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

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

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

.MHUpdateFuncGen.PF : MHUpdateFunc: no visible global function
  definition for 'runif'
MarkovSwitchingFuncGenerator : generateNextStreamsFunc: no visible
  global function definition for 'runif'
MarkovSwitchingFuncGenerator: no visible global function definition for
  'rnorm'
MarkovSwitchingFuncGenerator: no visible global function definition for
  'runif'
MarkovSwitchingFuncGenerator : logObsDensFunc: no visible global
  function definition for 'dnorm'
MarkovSwitchingFuncGenerator : propagateFunc: no visible global
  function definition for 'dnorm'
MarkovSwitchingFuncGenerator : propagateFunc: no visible global
  function definition for 'runif'
Undefined global functions or variables:
  dnorm rnorm runif
Consider adding
  importFrom("stats", "dnorm", "rnorm", "runif")
to your NAMESPACE file.
em: no visible global function definition for 'coxph'
em: no visible global function definition for 'optim'
plotpredictsmcure: no visible global function definition for 'plot'
plotpredictsmcure: no visible global function definition for 'matplot'
plotpredictsmcure: no visible global function definition for 'lines'
smcure: no visible binding for global variable 'na.omit'
smcure: no visible global function definition for 'model.frame'
smcure: no visible global function definition for 'model.extract'
smcure: no visible global function definition for 'model.matrix'
smcure: no visible global function definition for 'coxph'
smcure: no visible global function definition for 'survreg'
smcure: no visible binding for global variable 'var'
smcure: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  coxph lines matplot model.extract model.frame model.matrix na.omit
  optim plot pnorm survreg var
Consider adding
  importFrom("graphics", "lines", "matplot", "plot")
  importFrom("stats", "model.extract", "model.frame", "model.matrix",
             "na.omit", "optim", "pnorm", "var")
to your NAMESPACE file.
'library' or 'require' call to 'proxy' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'proxy' 'tm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
normalize: no visible binding for global variable 'sd'
simDic: no visible global function definition for 'simil'
simDoc: no visible global function definition for 'simil'
Undefined global functions or variables:
  sd simil
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Grad.sph: no visible global function definition for 'dist'
IMDS: no visible global function definition for 'cmdscale'
IMDS: no visible global function definition for 'as.dist'
IMDS: no visible global function definition for 'runif'
IMDS: no visible global function definition for 'optim'
idistSph: no visible global function definition for 'dist'
obj.sph: no visible global function definition for 'dist'
plot.imds: no visible binding for global variable 'lines'
plot.imds: no visible global function definition for 'plot'
plot.imds: no visible global function definition for 'text'
plot.imds: no visible global function definition for 'rect'
Undefined global functions or variables:
  as.dist cmdscale dist lines optim plot rect runif text
Consider adding
  importFrom("graphics", "lines", "plot", "rect", "text")
  importFrom("stats", "as.dist", "cmdscale", "dist", "optim", "runif")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  '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.
Running 'testthat.R' [15s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # setting R_TESTS to empty string because of
  > # https://github.com/hadley/testthat/issues/144
  > # https://github.com/hadley/testthat/issues/86
  > # revert this when that issue in R is fixed.
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(Smisc)
  > 
  > # There shouldn't be any files in the tmp folder
  > unlink("testthat/tmp", recursive = TRUE, force = TRUE)
  > dir.create("testthat/tmp")
  > 
  > test_check("Smisc")
  -- 1. Failure: parseJob() doesn't deviate from historical behavior (@test_parseJ
  `xout` not equal to `xin`.
  Component "x2": Component 1: Mean relative difference: 0.8461538
  Component "x2": Component 2: Mean relative difference: 0.7532468
  Component "x2": Component 3: Mean relative difference: 0.5416667
  Component "x2": Component 4: Mean relative difference: 0.34375
  Component "x2": Component 5: Mean relative difference: 0.5441176
  
  == testthat results  ===========================================================
  OK: 286 SKIPPED: 0 FAILED: 1
  1. Failure: parseJob() doesn't deviate from historical behavior (@test_parseJob.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [17s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # setting R_TESTS to empty string because of
  > # https://github.com/hadley/testthat/issues/144
  > # https://github.com/hadley/testthat/issues/86
  > # revert this when that issue in R is fixed.
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(Smisc)
  > 
  > # There shouldn't be any files in the tmp folder
  > unlink("testthat/tmp", recursive = TRUE, force = TRUE)
  > dir.create("testthat/tmp")
  > 
  > test_check("Smisc")
  -- 1. Failure: parseJob() doesn't deviate from historical behavior (@test_parseJ
  `xout` not equal to `xin`.
  Component "x2": Component 1: Mean relative difference: 0.8461538
  Component "x2": Component 2: Mean relative difference: 0.7532468
  Component "x2": Component 3: Mean relative difference: 0.5416667
  Component "x2": Component 4: Mean relative difference: 0.34375
  Component "x2": Component 5: Mean relative difference: 0.5441176
  
  == testthat results  ===========================================================
  OK: 286 SKIPPED: 0 FAILED: 1
  1. Failure: parseJob() doesn't deviate from historical behavior (@test_parseJob.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
lines.SmithWilsonYieldCurve: no visible global function definition for
  'lines'
plot.SmithWilsonYieldCurve: no visible global function definition for
  'plot'
points.SmithWilsonYieldCurve: no visible global function definition for
  'points'
Undefined global functions or variables:
  lines plot points
Consider adding
  importFrom("graphics", "lines", "plot", "points")
to your NAMESPACE file.
Fourier2d: no visible global function definition for 'fft'
kernel2dsmooth: no visible global function definition for 'fft'
Undefined global functions or variables:
  fft
Consider adding
  importFrom("stats", "fft")
to your NAMESPACE file.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.4Mb
dNMR: no visible global function definition for 'pnorm'
dNMR: no visible global function definition for 'dnorm'
pNMR: no visible global function definition for 'pnorm'
pNMR: no visible global function definition for 'dnorm'
rMR: no visible global function definition for 'rnorm'
rMR: no visible global function definition for 'rchisq'
Undefined global functions or variables:
  dnorm pnorm rchisq rnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm", "rchisq", "rnorm")
to your NAMESPACE file.
SMVar.paired : <anonymous>: no visible global function definition for
  'var'
SMVar.paired: no visible global function definition for 'var'
SMVar.paired: no visible global function definition for 'pt'
SMVar.paired: no visible global function definition for 'p.adjust'
SMVar.paired: no visible global function definition for 'write.table'
SMVar.unpaired : <anonymous>: no visible global function definition for
  'var'
SMVar.unpaired: no visible global function definition for 'var'
SMVar.unpaired: no visible global function definition for 'pt'
SMVar.unpaired: no visible global function definition for 'p.adjust'
SMVar.unpaired: no visible global function definition for 'write.table'
Undefined global functions or variables:
  p.adjust pt var write.table
Consider adding
  importFrom("stats", "p.adjust", "pt", "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
sclust: no visible global function definition for 'var'
snipEM: no visible global function definition for 'cov'
stEM: no visible global function definition for 'cov'
stEM: no visible global function definition for 'quantile'
Undefined global functions or variables:
  cov quantile var
Consider adding
  importFrom("stats", "cov", "quantile", "var")
to your NAMESPACE file.
Package in Depends field not imported from: 'snow'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
KS.test: no visible global function definition for 'quantile'
KS.test : Fgaus: no visible global function definition for 'pnorm'
KS.test: no visible global function definition for 'setNames'
cs.test: no visible global function definition for 'pbinom'
cs.test: no visible global function definition for 'pnorm'
cs.test: no visible global function definition for 'setNames'
kde: no visible global function definition for 'quantile'
kde : Fgaus: no visible global function definition for 'pnorm'
kde: no visible global function definition for 'par'
kre: no visible global function definition for 'quantile'
kre: no visible global function definition for 'lines'
ns.test: no visible global function definition for 'complete.cases'
ns.test: no visible global function definition for 'qnorm'
ns.test: no visible global function definition for 'pnorm'
ns.test: no visible global function definition for 'pchisq'
ns.test: no visible global function definition for 'setNames'
ns.test: no visible global function definition for 'qt'
quant.test: no visible global function definition for 'complete.cases'
quant.test: no visible global function definition for 'pbinom'
quant.test: no visible global function definition for 'pnorm'
quant.test: no visible global function definition for 'setNames'
quant.test: no visible global function definition for 'quantile'
quant.test: no visible global function definition for 'phyper'
runs.test: no visible global function definition for 'median'
runs.test: no visible global function definition for 'setNames'
runs.test: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  complete.cases lines median par pbinom pchisq phyper pnorm qnorm qt
  quantile setNames
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "complete.cases", "median", "pbinom", "pchisq",
             "phyper", "pnorm", "qnorm", "qt", "quantile", "setNames")
to your NAMESPACE file.
Running examples in 'SNPknock-Ex.R' failed
The error most likely occurred in:

> ### Name: SNPknock.fp.loadFit
> ### Title: Load the parameter estimates obtained by fastPHASE
> ### Aliases: SNPknock.fp.loadFit
> 
> ### ** Examples
> 
> # Specify the location of the fastPHASE output files containing the parameter estimates.
> # Example files can be found in the package installation directory.
> r_file = system.file("extdata", "genotypes_rhat.txt", package = "SNPknock")
> alpha_file = system.file("extdata", "genotypes_alphahat.txt", package = "SNPknock")
> theta_file = system.file("extdata", "genotypes_thetahat.txt", package = "SNPknock")
> char_file = system.file("extdata", "genotypes_origchars", package = "SNPknock")
> 
> # Read the parameter files and build the HMM
> hmm = SNPknock.fp.loadFit(r_file, alpha_file, theta_file, char_file)
> 
> 
> 
> 
> cleanEx()
Error: connections left open:
	lines (textConnection)
	lines (textConnection)
	lines (textConnection)
	lines (textConnection)
Execution halted
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'mvtnorm' 'combinat'
A package should be listed in only one of these fields.
chisq.test.a: no visible global function definition for 'chisq.test'
maxsel: no visible global function definition for 'complete.cases'
maxsel.asymp.test: no visible global function definition for
  'complete.cases'
Undefined global functions or variables:
  chisq.test complete.cases
Consider adding
  importFrom("stats", "chisq.test", "complete.cases")
to your NAMESPACE file.
MDSplot: no visible global function definition for 'par'
MDSplot: no visible global function definition for 'rainbow'
MDSplot: no visible global function definition for 'plot'
MDSplot: no visible global function definition for 'pairs'
classCenter : <anonymous>: no visible binding for global variable
  'median'
grow.snpRF: no visible global function definition for 'update'
na.roughfix.data.frame : roughfix: no visible global function
  definition for 'median'
na.roughfix.default: no visible global function definition for 'median'
outlier.default: no visible global function definition for 'median'
outlier.default: no visible global function definition for 'mad'
plot.margin: no visible global function definition for
  'installed.packages'
plot.margin: no visible global function definition for 'rainbow'
plot.margin: no visible global function definition for 'plot.default'
plot.snpRF: no visible global function definition for 'matplot'
tuneSnpRF: no visible global function definition for 'axis'
varImpPlot: no visible global function definition for 'par'
varImpPlot: no visible global function definition for 'dotchart'
varImpPlot: no visible global function definition for 'mtext'
Undefined global functions or variables:
  axis dotchart installed.packages mad matplot median mtext pairs par
  plot plot.default rainbow update
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "dotchart", "matplot", "mtext", "pairs",
             "par", "plot", "plot.default")
  importFrom("stats", "mad", "median", "update")
  importFrom("utils", "installed.packages")
to your NAMESPACE file.
calculate.areas: no visible global function definition for 'runif'
calculate.gradedareas: no visible global function definition for
  'rnorm'
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from 'SoDA' for: 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Missing or unexported object: 'base::WHAT'
Packages in Depends field not imported from:
  'MASS' 'magic' 'ppls' 'psych'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
get.hnx.B.initialW: no visible global function definition for
  'normalize.vector'
get.hnx.B.initialW: no visible global function definition for 'adiag'
hclust.wrap: no visible global function definition for 'hclust'
hclust.wrap: no visible global function definition for 'dist'
hclust.wrap: no visible global function definition for 'cutree'
my.normdata.gen: no visible global function definition for 'mvrnorm'
my.normdata.gen: no visible global function definition for 'rnorm'
odc.clust: no visible binding for global variable 'kmeans'
odc.cv: no visible global function definition for 'ginv'
odc.optimallambda2: no visible global function definition for 'tr'
odc.optimallambda2: no visible global function definition for 'ginv'
odc.optimallambda2: no visible binding for global variable 'sd'
sodc.clust: no visible binding for global variable 'kmeans'
Undefined global functions or variables:
  adiag cutree dist ginv hclust kmeans mvrnorm normalize.vector rnorm
  sd tr
Consider adding
  importFrom("stats", "cutree", "dist", "hclust", "kmeans", "rnorm",
             "sd")
to your NAMESPACE file.
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.soma: no visible global function definition for 'plot'
soma: no visible global function definition for 'runif'
Undefined global functions or variables:
  plot runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
to your NAMESPACE file.
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("SOMbrero")
  Loading required package: igraph
  
  Attaching package: 'igraph'
  
  The following object is masked from 'package:testthat':
  
      compare
  
  The following objects are masked from 'package:stats':
  
      decompose, spectrum
  
  The following object is masked from 'package:base':
  
      union
  
  
  ***********************************************************
  
        This is 'SOMbrero' package, v 1.2
  
  Citation details with citation('SOMbrero')
  
  Further information with help(SOMbrero)...
  
  Use sombreroGUI() to start the Graphical Interface.
  
  ***********************************************************
  > 
  > test_check("SOMbrero")
  -- 1. Failure: case relational - radius 'letremy' and affectation 'heskes' (@tes
  predict(rsom, dissim.lesmis) not equal to rsom$clustering.
  2/77 mismatches (average diff: 6)
  [44] 22 - 16 == 6
  [56] 22 - 16 == 6
  
  -- 2. Failure: case relational - radius 'letremy' and affectation 'heskes' (@tes
  predict(rsom) not equal to rsom$clustering.
  2/77 mismatches (average diff: 6)
  [44] 22 - 16 == 6
  [56] 22 - 16 == 6
  
  == testthat results  ===========================================================
  OK: 26 SKIPPED: 0 FAILED: 2
  1. Failure: case relational - radius 'letremy' and affectation 'heskes' (@test-prediction.R#61) 
  2. Failure: case relational - radius 'letremy' and affectation 'heskes' (@test-prediction.R#63) 
  
  Error: testthat unit tests failed
  Execution halted
bm: no visible global function definition for 'rnorm'
bm: no visible global function definition for 'ts'
fbm: no visible global function definition for 'fft'
fbm: no visible global function definition for 'rnorm'
fbm: no visible global function definition for 'ts'
gbm: no visible global function definition for 'rnorm'
gbm: no visible global function definition for 'ts'
Undefined global functions or variables:
  fft rnorm ts
Consider adding
  importFrom("stats", "fft", "rnorm", "ts")
to your NAMESPACE file.
getAlpha: no visible global function definition for 'pbinom'
kfweOrd: no visible global function definition for 'qnbinom'
Undefined global functions or variables:
  pbinom qnbinom
Consider adding
  importFrom("stats", "pbinom", "qnbinom")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from 'someMTP' for: 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   2.1Mb
'library' or 'require' call to 'hexbin' which was already attached by Depends.
  Please remove these calls from your code.
hexbinpie: no visible global function definition for 'quantile'
hexbinpie: no visible global function definition for 'polygon'
hexbinpie: no visible global function definition for 'text'
makehexbinplot: no visible global function definition for 'rainbow'
makehexbinplot: no visible global function definition for 'col2rgb'
makehexbinplot: no visible global function definition for 'edit'
makehexbinplot: no visible global function definition for 'dev.new'
makehexbinplot: no visible global function definition for 'plot.new'
makehexbinplot: no visible global function definition for 'plot.window'
makehexbinplot: no visible global function definition for 'box'
makehexbinplot: no visible global function definition for 'axis'
makehexbinplot: no visible global function definition for 'legend'
som.plot: no visible global function definition for 'read.table'
Undefined global functions or variables:
  axis box col2rgb dev.new edit legend plot.new plot.window polygon
  quantile rainbow read.table text
Consider adding
  importFrom("grDevices", "col2rgb", "dev.new", "rainbow")
  importFrom("graphics", "axis", "box", "legend", "plot.new",
             "plot.window", "polygon", "text")
  importFrom("stats", "quantile")
  importFrom("utils", "edit", "read.table")
to your NAMESPACE file.
dfrag: no visible global function definition for 'qgeom'
dfrag: no visible global function definition for 'plogis'
dfrag: no visible global function definition for 'dgeom'
estAbund: no visible global function definition for 'xtabs'
mmN : <anonymous>: no visible global function definition for 'uniroot'
pfrag: no visible global function definition for 'qgeom'
phi.deriv.default: no visible global function definition for
  'model.matrix'
phi.deriv.default: no visible binding for global variable 'sd'
phi.update.default: no visible global function definition for 'glm'
phi.update.default: no visible binding for global variable
  'quasipoisson'
phi.update.default: no visible global function definition for 'predict'
phi.update.lframe: no visible global function definition for 'glm'
phi.update.lframe: no visible binding for global variable
  'quasipoisson'
phi.update.lframe: no visible global function definition for 'predict'
pr.y.given.x : <anonymous>: no visible global function definition for
  'dpois'
pr.y.given.x : <anonymous> : <anonymous>: no visible global function
  definition for 'dpois'
pr.y.given.x : <anonymous>: no visible global function definition for
  'convolve'
qfrag: no visible global function definition for 'qgeom'
rfrag: no visible global function definition for 'qgeom'
simSonic: no visible global function definition for 'rpois'
Undefined global functions or variables:
  convolve dgeom dpois glm model.matrix plogis predict qgeom
  quasipoisson rpois sd uniroot xtabs
Consider adding
  importFrom("stats", "convolve", "dgeom", "dpois", "glm",
             "model.matrix", "plogis", "predict", "qgeom",
             "quasipoisson", "rpois", "sd", "uniroot", "xtabs")
to your NAMESPACE file.
plot.soo_function: no visible global function definition for
  'terrain.colors'
plot.soo_function: no visible binding for global variable 'image'
plot.soo_function: no visible binding for global variable 'contour'
plot3d: no visible global function definition for 'persp3d'
plot3d: no visible global function definition for 'terrain.colors'
random_parameters.soo_function: no visible global function definition
  for 'runif'
random_rotation_matrix: no visible global function definition for
  'runif'
Undefined global functions or variables:
  contour image persp3d runif terrain.colors
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "contour", "image")
  importFrom("stats", "runif")
to your NAMESPACE file.
simdata_contaminated : <anonymous>: no visible global function
  definition for 'rbinom'
simdata_uniform : multivariate_uniform : <anonymous>: no visible global
  function definition for 'runif'
which_min: no visible global function definition for 'head'
which_min: no visible global function definition for 'tail'
Undefined global functions or variables:
  head rbinom runif tail
Consider adding
  importFrom("stats", "rbinom", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
convert_municipality_names: no visible global function definition for
  'read.csv'
regression_plot: no visible binding for global variable 'loess'
regression_plot: no visible global function definition for
  'colorRampPalette'
regression_plot: no visible global function definition for
  'loess.control'
regression_plot: no visible global function definition for 'predict'
regression_plot : <anonymous>: no visible global function definition
  for 'quantile'
regression_plot : <anonymous>: no visible global function definition
  for 'pnorm'
regression_plot: no visible global function definition for
  'flush.console'
regression_plot: no visible global function definition for 'density'
Undefined global functions or variables:
  colorRampPalette density flush.console loess loess.control pnorm
  predict quantile read.csv
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "density", "loess", "loess.control", "pnorm",
             "predict", "quantile")
  importFrom("utils", "flush.console", "read.csv")
to your NAMESPACE file.
Package suggested but not available for checking: 'r2cytoscape'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
analyzeSP23Design: no visible global function definition for 'plot'
exploreSP23Design: no visible global function definition for
  'txtProgressBar'
exploreSP23Design: no visible global function definition for
  'setTxtProgressBar'
generateClinicalTrialData : <anonymous>: no visible global function
  definition for 'runif'
generateClinicalTrialData: no visible global function definition for
  'rbinom'
generateClinicalTrialData: no visible global function definition for
  'rexp'
mHP.b : crossingProbDiff: no visible global function definition for
  'pnorm'
mHP.b : crossingProbDiff: no visible global function definition for
  'Miwa'
mHP.b: no visible global function definition for 'qnorm'
mHP.b: no visible global function definition for 'uniroot'
mHP.c : crossingProbDiff: no visible global function definition for
  'Miwa'
mHP.c: no visible global function definition for 'uniroot'
mHP.c: no visible global function definition for 'qnorm'
performInterimLook: no visible global function definition for 'optim'
performInterimLook: no visible global function definition for
  'constrOptim'
performInterimLook: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  Miwa constrOptim optim plot pnorm qnorm rbinom rexp runif
  setTxtProgressBar txtProgressBar uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "constrOptim", "optim", "pnorm", "qnorm", "rbinom",
             "rexp", "runif", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
SPA: no visible global function definition for 'var'
Score.Test.Interact: no visible global function definition for 'pchisq'
Score.Test.Overall: no visible global function definition for 'var'
Score.Test.Overall: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  pchisq var
Consider adding
  importFrom("stats", "pchisq", "var")
to your NAMESPACE file.
'library' or 'require' call to 'Matrix' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'Matrix' 'igraph' 'splines'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GenPar: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'Rcpp' 'colorspace' 'picante'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running 'test-all.R' [70s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("SpaDES.tools")
  Loading required package: SpaDES.tools
  -- 1. Failure: spread produces legal RasterLayer (@test-spread.R#60)  ----------
  all(...) isn't true.
  
  -- 2. Failure: spread stopRule does not work correctly (@test-spread.R#163)  ---
  sum(getValues(circs) > 0) > sum(getValues(circs3) > 0) isn't true.
  
  -- 3. Failure: spreadProb with relative values does not work correctly (@test-sp
  sum(hab3[events1[] > 0]) > sum(hab3[events2[] > 0]) isn't true.
  
  -- 4. Failure: spread2 tests (@test-spread2.R#220)  ----------------------------
  cht$p.value > 0.05 isn't true.
  
  [1] "Scales with number of starts, not maxSize of raster"
  -- 5. Failure: spread2 tests -- asymmetry (@test-spread2.R#710)  ---------------
  circs[sams] == circs[ciCentre[] == 1] isn't true.
  
  == testthat results  ===========================================================
  OK: 1047 SKIPPED: 11 FAILED: 5
  1. Failure: spread produces legal RasterLayer (@test-spread.R#60) 
  2. Failure: spread stopRule does not work correctly (@test-spread.R#163) 
  3. Failure: spreadProb with relative values does not work correctly (@test-spread.R#1259) 
  4. Failure: spread2 tests (@test-spread2.R#220) 
  5. Failure: spread2 tests -- asymmetry (@test-spread2.R#710) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'test-all.R' [73s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("SpaDES.tools")
  Loading required package: SpaDES.tools
  -- 1. Failure: spread produces legal RasterLayer (@test-spread.R#60)  ----------
  all(...) isn't true.
  
  -- 2. Failure: spread stopRule does not work correctly (@test-spread.R#163)  ---
  sum(getValues(circs) > 0) > sum(getValues(circs3) > 0) isn't true.
  
  -- 3. Failure: spreadProb with relative values does not work correctly (@test-sp
  sum(hab3[events1[] > 0]) > sum(hab3[events2[] > 0]) isn't true.
  
  -- 4. Failure: spread2 tests (@test-spread2.R#220)  ----------------------------
  cht$p.value > 0.05 isn't true.
  
  [1] "Scales with number of starts, not maxSize of raster"
  -- 5. Failure: spread2 tests -- asymmetry (@test-spread2.R#710)  ---------------
  circs[sams] == circs[ciCentre[] == 1] isn't true.
  
  == testthat results  ===========================================================
  OK: 1047 SKIPPED: 11 FAILED: 5
  1. Failure: spread produces legal RasterLayer (@test-spread.R#60) 
  2. Failure: spread stopRule does not work correctly (@test-spread.R#163) 
  3. Failure: spreadProb with relative values does not work correctly (@test-spread.R#1259) 
  4. Failure: spread2 tests (@test-spread2.R#220) 
  5. Failure: spread2 tests -- asymmetry (@test-spread2.R#710) 
  
  Error: testthat unit tests failed
  Execution halted
hausman: no visible global function definition for 'pchisq'
span.formula: no visible global function definition for 'model.frame'
span.formula: no visible global function definition for 'model.matrix'
span.formula: no visible global function definition for
  'model.response'
spbe: no visible global function definition for 'cor'
spbe: no visible global function definition for 'pt'
spfe: no visible global function definition for 'cor'
spfe: no visible global function definition for 'pt'
sprandom: no visible global function definition for 'cor'
sprandom: no visible global function definition for 'pt'
summary.span: no visible global function definition for 'printCoefmat'
Undefined global functions or variables:
  cor model.frame model.matrix model.response pchisq printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.frame", "model.matrix",
             "model.response", "pchisq", "printCoefmat", "pt")
to your NAMESPACE file.
plot.spa: no visible global function definition for 'plot'
plot.spa: no visible global function definition for 'lines'
plot.spa: no visible global function definition for 'points'
plot.spa: no visible global function definition for 'gray'
plot.spa: no visible global function definition for 'box'
predict.spa: no visible global function definition for 'fitted'
predict.spa: no visible global function definition for 'coef'
spa.gcv: no visible global function definition for 'density'
spa.gcv: no visible global function definition for 'quantile'
spa.sim: no visible global function definition for 'runif'
spa.sim: no visible global function definition for 'rnorm'
spa.sim: no visible global function definition for 'rbinom'
update.spa: no visible global function definition for 'quantile'
Undefined global functions or variables:
  box coef density fitted gray lines plot points quantile rbinom rnorm
  runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "box", "lines", "plot", "points")
  importFrom("stats", "coef", "density", "fitted", "quantile", "rbinom",
             "rnorm", "runif")
to your NAMESPACE file.
Running examples in 'spa-Ex.R' failed
The error most likely occurred in:

> ### Name: predict.spa
> ### Title: Inductive Predict Procedure For SPA
> ### Aliases: predict.spa
> ### Keywords: classes models methods
> 
> ### ** Examples
> 
> ## Use simulated example (two moon) and generate a contour plot of the border
> set.seed(100)
> dat=spa.sim(type="moon") 
> 
> L=which(!is.na(dat$y))
> U=which(is.na(dat$y))
> Dij=as.matrix(daisy(dat[,-1]))
> 
> ##Use spa to train with a supervised/transductive kernel smoother
> gsup<-spa(dat$y[L],graph=Dij[L,L],control=spa.control(gcv="lGCV"))
Error in if (g1 < g2) { : missing value where TRUE/FALSE needed
Calls: spa -> spa.gcv
Execution halted
Packages in Depends field not imported from:
  'RCurl' 'XML'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SPARQL : <anonymous>: no visible global function definition for
  'URLencode'
SPARQL: no visible binding for global variable 'getURL'
SPARQL: no visible global function definition for 'URLencode'
SPARQL: no visible binding for global variable 'xmlParse'
SPARQL: no visible global function definition for 'getNodeSet'
SPARQL: no visible global function definition for 'xpathApply'
SPARQL: no visible binding for global variable 'postForm'
get_attr: no visible global function definition for 'getNodeSet'
get_attr : <anonymous> : <anonymous>: no visible global function
  definition for 'getNodeSet'
get_attr : <anonymous> : <anonymous>: no visible global function
  definition for 'xmlDoc'
get_value: no visible global function definition for 'xmlDoc'
get_value: no visible global function definition for 'xpathSApply'
get_value: no visible binding for global variable 'xmlValue'
get_value: no visible global function definition for 'xpathApply'
get_value: no visible binding for global variable 'xmlGetAttr'
readCSVstring: no visible global function definition for 'read.csv'
readTSVstring: no visible global function definition for 'read.delim'
Undefined global functions or variables:
  URLencode getNodeSet getURL postForm read.csv read.delim xmlDoc
  xmlGetAttr xmlParse xmlValue xpathApply xpathSApply
Consider adding
  importFrom("utils", "URLencode", "read.csv", "read.delim")
to your NAMESPACE file.
f.I2.cont: no visible global function definition for 'combn'
f.I2.dich: no visible global function definition for 'combn'
f.pstar.cont: no visible global function definition for 'combn'
f.pstar.dich: no visible global function definition for 'combn'
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
image.matrixBC: no visible global function definition for 'dev.new'
image.matrixBC: no visible global function definition for 'image'
image.matrixBC: no visible global function definition for 'heat.colors'
image.matrixBC: no visible global function definition for 'axis'
image.matrixBC: no visible global function definition for 'title'
image.sparseBC: no visible global function definition for 'dev.new'
image.sparseBC: no visible global function definition for 'image'
image.sparseBC: no visible global function definition for 'heat.colors'
image.sparseBC: no visible global function definition for 'axis'
image.sparseBC: no visible global function definition for 'tail'
image.sparseBC: no visible global function definition for 'title'
matrixBC: no visible global function definition for 'kmeans'
sparseBC: no visible global function definition for 'kmeans'
sparseBC.choosekr: no visible global function definition for 'kmeans'
sparseBC.choosekr: no visible binding for global variable 'sd'
Undefined global functions or variables:
  axis dev.new heat.colors image kmeans sd tail title
Consider adding
  importFrom("grDevices", "dev.new", "heat.colors")
  importFrom("graphics", "axis", "image", "title")
  importFrom("stats", "kmeans", "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
gev.impute: no visible global function definition for 'rnorm'
gev.init: no visible global function definition for 'rbinom'
gev.init: no visible global function definition for 'var'
gev.init: no visible global function definition for 'optimize'
gev.logscore: no visible global function definition for 'density'
gev.logscore: no visible global function definition for 'splinefun'
gev.update.M: no visible global function definition for 'runif'
gev.update.hyper: no visible global function definition for 'rgamma'
gev.update.lambda: no visible global function definition for 'rnorm'
gev.update.lambda: no visible global function definition for 'dgamma'
gev.update.lambda: no visible global function definition for 'dnorm'
gev.update.lambda: no visible global function definition for 'runif'
gev.update.tau.kappa: no visible global function definition for 'rnorm'
gev.update.tau.kappa: no visible global function definition for 'dnorm'
gev.update.tau.kappa: no visible global function definition for 'runif'
gev.update.tau.mu: no visible global function definition for 'rnorm'
gev.update.tau.mu: no visible global function definition for 'dnorm'
gev.update.tau.mu: no visible global function definition for 'runif'
gev.update.tau.xi: no visible global function definition for 'rnorm'
gev.update.tau.xi: no visible global function definition for 'dnorm'
gev.update.tau.xi: no visible global function definition for 'runif'
gev.update.theta: no visible global function definition for 'rnorm'
gp.like.lambda: no visible global function definition for 'dgamma'
Undefined global functions or variables:
  density dgamma dnorm optimize rbinom rgamma rnorm runif splinefun var
Consider adding
  importFrom("stats", "density", "dgamma", "dnorm", "optimize", "rbinom",
             "rgamma", "rnorm", "runif", "splinefun", "var")
to your NAMESPACE file.
I2BR: no visible global function definition for 'pnorm'
I2SmD2: no visible global function definition for 'pnorm'
IBR: no visible global function definition for 'pnorm'
ISmD2: no visible global function definition for 'pnorm'
MestimatorBR: no visible global function definition for 'optim'
MestimatorSmith: no visible global function definition for 'optim'
psidotBR: no visible global function definition for 'dnorm'
psidotBR: no visible global function definition for 'pnorm'
psidotSmD2: no visible global function definition for 'dnorm'
psidotSmD2: no visible global function definition for 'pnorm'
tailBRInt: no visible global function definition for 'pnorm'
tailSmithInt: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dnorm optim pnorm
Consider adding
  importFrom("stats", "dnorm", "optim", "pnorm")
to your NAMESPACE file.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.7Mb
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    R      5.1Mb
    doc    4.8Mb
    help   5.1Mb
    libs   1.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
GenerateCliquesCovariance: no visible global function definition for
  'rnorm'
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Package suggested but not available for checking: 'spDataLarge'
bartlett: no visible global function definition for 'pchisq'
local.rbfdot: no visible binding for global variable 'sd'
local.rbfdot: no visible global function definition for 'dist'
local.rbfdot : <anonymous>: no visible global function definition for
  'median'
speccalt: no visible global function definition for 'kmeans'
Undefined global functions or variables:
  dist kmeans median pchisq sd
Consider adding
  importFrom("stats", "dist", "kmeans", "median", "pchisq", "sd")
to your NAMESPACE file.
ChaoBunge: no visible global function definition for 'qnorm'
ChaoLee1992: no visible global function definition for 'qnorm'
Pmix: no visible global function definition for 'dpois'
PmixSCon: no visible global function definition for 'dbeta'
bootPCG: no visible global function definition for 'flush.console'
bootPCG: no visible global function definition for 'quantile'
bootPnpmle: no visible global function definition for 'flush.console'
bootPnpmle: no visible global function definition for 'quantile'
bootUnpmle: no visible global function definition for 'flush.console'
bootUnpmle: no visible global function definition for 'quantile'
chao1984: no visible global function definition for 'qnorm'
jackknife: no visible global function definition for 'dbinom'
jackknife: no visible global function definition for 'qnorm'
pcg: no visible global function definition for 'flush.console'
unpmle: no visible global function definition for 'flush.console'
untrunPmix: no visible global function definition for 'dpois'
Undefined global functions or variables:
  dbeta dbinom dpois flush.console qnorm quantile
Consider adding
  importFrom("stats", "dbeta", "dbinom", "dpois", "qnorm", "quantile")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Output for data("spinalCord", package = "specmine"):
  Warning messages:
  1: In fun(libname, pkgname) :
    mzR has been built against a different Rcpp version (0.12.17)
  than is installed on your system (1.0.0). This might lead to errors
  when loading mzR. If you encounter such issues, please send a report,
  including the output of sessionInfo() to the Bioc support forum at 
  https://support.bioconductor.org/. For details see also
  https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
  2: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
    package instead.
'library' or 'require' call to 'leaps' which was already attached by Depends.
  Please remove these calls from your code.
modSearch: no visible global function definition for 'glm'
modSearch: no visible binding for global variable 'binomial'
modSearch: no visible global function definition for 'na.omit'
modSearch: no visible global function definition for 'as.formula'
speff: no visible binding for global variable 'na.pass'
speff: no visible global function definition for 'model.matrix'
speff: no visible global function definition for 'terms'
speff: no visible global function definition for 'model.response'
speff: no visible global function definition for 'as.formula'
speff: no visible global function definition for 'predict'
speff: no visible global function definition for 'na.omit'
speff: no visible global function definition for 'glm'
speff: no visible binding for global variable 'na.omit'
speffSurv: no visible global function definition for 'model.matrix'
speffSurv: no visible global function definition for 'terms'
speffSurv: no visible global function definition for 'model.response'
speffSurv: no visible global function definition for 'as.formula'
speffSurv: no visible global function definition for 'uniroot'
summary.speff: no visible global function definition for 'qnorm'
summary.speff: no visible global function definition for 'pnorm'
summary.speffSurv: no visible global function definition for 'qnorm'
summary.speffSurv: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  as.formula binomial glm model.matrix model.response na.omit na.pass
  pnorm predict qnorm terms uniroot
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "model.matrix",
             "model.response", "na.omit", "na.pass", "pnorm", "predict",
             "qnorm", "terms", "uniroot")
to your NAMESPACE file.
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nr' to 'nrow'
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nc' to 'ncol'
spe: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Running 'testthat.R' [25s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(spew)
  > 
  > test_check("spew")
  -- 1. Error: Moment Matching (@test-sampling.R#32)  ----------------------------
  abs(2.8 - mean(pums[inds, ]$NP)) < 0.05 is not TRUE
  1: stopifnot(abs(2.8 - mean(pums[inds, ]$NP)) < 0.05) at testthat/test-sampling.R:32
  
  [1] "Place has 0 Households!"
  == testthat results  ===========================================================
  OK: 101 SKIPPED: 7 FAILED: 1
  1. Error: Moment Matching (@test-sampling.R#32) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Packages in Depends field not imported from:
  'lars' 'parallel' 'randomForest'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' call to 'quadprog' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'quadprog'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SPIn: no visible global function definition for 'density'
SPIn: no visible global function definition for 'quantile'
SPIn: no visible global function definition for 'solve.QP'
bootSPIn: no visible global function definition for 'runif'
plot.SPIn: no visible global function definition for 'hist'
plot.SPIn: no visible global function definition for 'lines'
plot.SPIn: no visible global function definition for 'text'
plot.SPIn: no visible global function definition for 'quantile'
plot.SPIn: no visible global function definition for 'legend'
Undefined global functions or variables:
  density hist legend lines quantile runif solve.QP text
Consider adding
  importFrom("graphics", "hist", "legend", "lines", "text")
  importFrom("stats", "density", "quantile", "runif")
to your NAMESPACE file.
spi: no visible global function definition for 'read.table'
spi: no visible global function definition for 'ecdf'
spi: no visible global function definition for 'qnorm'
spi: no visible global function definition for 'colorRampPalette'
spi: no visible global function definition for 'filled.contour'
spi: no visible global function definition for 'axis'
Undefined global functions or variables:
  axis colorRampPalette ecdf filled.contour qnorm read.table
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "filled.contour")
  importFrom("stats", "ecdf", "qnorm")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(splitstackshape)
  > 
  > test_check("splitstackshape")
  -- 1. Failure: stratified returns the expected number of rows (@test_stratified.
  nrow(stratified(DF, "A", 0.1, select = list(A = c("AA", "BB")))) not equal to 3.
  1/1 mismatches
  [1] 4 - 3 == 1
  
  == testthat results  ===========================================================
  OK: 51 SKIPPED: 0 FAILED: 1
  1. Failure: stratified returns the expected number of rows (@test_stratified.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
R2.global: no visible global function definition for 'var'
calculer.var.exp: no visible global function definition for 'var'
creer.noeud: no visible global function definition for 'var'
ponderer.classe: no visible global function definition for 'var'
ponderer.classe: no visible global function definition for 'cov'
spodt: no visible global function definition for 'model.frame'
spodt.tree: no visible global function definition for 'plot.new'
spodt.tree: no visible global function definition for 'par'
spodt.tree: no visible global function definition for 'plot.window'
spodt.tree: no visible global function definition for 'text'
spodt.tree: no visible global function definition for 'segments'
test.spodt: no visible global function definition for 'model.frame'
test.spodt: no visible global function definition for 'hist'
test.spodt: no visible global function definition for 'abline'
tracer.noeud: no visible global function definition for 'text'
tracer.noeud: no visible global function definition for 'segments'
Undefined global functions or variables:
  abline cov hist model.frame par plot.new plot.window segments text
  var
Consider adding
  importFrom("graphics", "abline", "hist", "par", "plot.new",
             "plot.window", "segments", "text")
  importFrom("stats", "cov", "model.frame", "var")
to your NAMESPACE file.
Ell.Theta: no visible global function definition for 'ell.theta'
confid.int.theta: no visible global function definition for 'qchisq'
confid.int.theta : sim.c: no visible global function definition for
  'runif'
confid.int.theta: no visible global function definition for 'quantile'
dd.est: no visible global function definition for 'ecdf'
ks.sporm : Simul: no visible global function definition for 'runif'
ks.stat: no visible global function definition for 'ecdf'
plotor: no visible global function definition for 'ecdf'
plotor: no visible global function definition for 'plot'
test.theta: no visible global function definition for 'ecdf'
test.theta : sim: no visible global function definition for 'runif'
Undefined global functions or variables:
  ecdf ell.theta plot qchisq quantile runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "ecdf", "qchisq", "quantile", "runif")
to your NAMESPACE file.
fetch_NBAPlayerStatistics: no visible global function definition for
  'read.table'
Undefined global functions or variables:
  read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   2.7Mb
plot.SPRT: no visible global function definition for 'par'
plot.SPRT: no visible global function definition for 'plot'
plot.SPRT: no visible global function definition for 'abline'
print.SPRT: no visible global function definition for 'head'
Undefined global functions or variables:
  abline head par plot
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("utils", "head")
to your NAMESPACE file.
fssa20: no visible global function definition for 'runif'
fssa2d: no visible global function definition for 'runif'
fssa30: no visible global function definition for 'runif'
fssa3d: no visible global function definition for 'runif'
ssa20: no visible global function definition for 'runif'
ssa2d: no visible global function definition for 'runif'
ssa30: no visible global function definition for 'runif'
ssa3d: no visible global function definition for 'runif'
ssi20: no visible global function definition for 'runif'
ssi2d: no visible global function definition for 'runif'
ssi30: no visible global function definition for 'runif'
ssi3d: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs   2.0Mb
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.
sGda : <anonymous>: no visible global function definition for 'cov'
sortgene: no visible global function definition for 'model.matrix'
Undefined global functions or variables:
  cov model.matrix
Consider adding
  importFrom("stats", "cov", "model.matrix")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'RJDBC' 'RMySQL' 'RODBC' 'RPostgreSQL' 'RSQLite' 'tcltk'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
cacheQuery: no visible global function definition for 'read.csv'
cacheQuery: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  read.csv write.csv
Consider adding
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
SQN: no visible binding for global variable 'median'
SQN: no visible global function definition for 'quantile'
SQN.demo.data: no visible global function definition for 'rnorm'
mix.qn: no visible global function definition for 'ecdf'
mix.qn: no visible global function definition for 'quantile'
Undefined global functions or variables:
  ecdf median quantile rnorm
Consider adding
  importFrom("stats", "ecdf", "median", "quantile", "rnorm")
to your NAMESPACE file.
plot.srafit: no visible global function definition for 'layout'
plot.srafit: no visible global function definition for 'par'
sraData : vartruncGauss : ff: no visible global function definition for
  'dnorm'
sraData : vartruncGauss : ff: no visible global function definition for
  'pnorm'
sraData : vartruncGauss: no visible global function definition for
  'uniroot'
sraPlotMean: no visible global function definition for 'axis'
sraPlotMean: no visible global function definition for 'points'
sraPlotMean: no visible global function definition for 'lines'
sraPlotMeanResid: no visible global function definition for 'axis'
sraPlotMeanResid: no visible global function definition for 'abline'
sraPlotMeanResid: no visible global function definition for 'points'
sraPlotVar: no visible global function definition for 'axis'
sraPlotVar: no visible global function definition for 'points'
sraPlotVar: no visible global function definition for 'lines'
sraPlotVarResid: no visible global function definition for 'axis'
sraPlotVarResid: no visible global function definition for 'abline'
sraPlotVarResid: no visible global function definition for 'points'
sraPlotlegend: no visible global function definition for 'legend'
sraStartingvalues : sraStartingvalues.mu0: no visible global function
  definition for 'rnorm'
sraStartingvalues : sraStartingvalues.logvarA0: no visible global
  function definition for 'rnorm'
sraStartingvalues : sraStartingvalues.logvarE0: no visible global
  function definition for 'rnorm'
sraStartingvalues: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  abline axis dnorm layout legend lines par pnorm points rnorm uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "layout", "legend", "lines",
             "par", "points")
  importFrom("stats", "dnorm", "pnorm", "rnorm", "uniroot")
to your NAMESPACE file.
Found the following hidden files and directories:
  .Rapp.history
  inst/script/.Rapp.history
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
File 'sROC/R/onload.R':
  .onLoad calls:
    packageStartupMessage("sROC 0.1-2 loaded")

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

AUC : TrapezInt: no visible global function definition for 'approx'
AUC : SimpsonInt: no visible global function definition for 'approx'
CI.CDF: no visible global function definition for 'qnorm'
bw.CDF: no visible global function definition for 'sd'
bw.CDF: no visible global function definition for 'IQR'
bw.CDF.pi: no visible global function definition for 'sd'
bw.CDF.pi: no visible global function definition for 'bw.nrd0'
bw.CDF.pi: no visible global function definition for 'bw.nrd'
bw.CDF.pi: no visible global function definition for 'bw.ucv'
bw.CDF.pi: no visible global function definition for 'bw.bcv'
bw.CDF.pi: no visible global function definition for 'bw.SJ'
bw.CDF.pi: no visible global function definition for 'IQR'
plot.CDF: no visible global function definition for 'plot.default'
plot.CDF: no visible global function definition for 'lines'
plot.CDF: no visible global function definition for 'polygon'
plot.ROC: no visible global function definition for 'plot.default'
plot.ROC: no visible global function definition for 'abline'
Undefined global functions or variables:
  IQR abline approx bw.SJ bw.bcv bw.nrd bw.nrd0 bw.ucv lines
  plot.default polygon qnorm sd
Consider adding
  importFrom("graphics", "abline", "lines", "plot.default", "polygon")
  importFrom("stats", "IQR", "approx", "bw.SJ", "bw.bcv", "bw.nrd",
             "bw.nrd0", "bw.ucv", "qnorm", "sd")
to your NAMESPACE file.
ssd : correction_method_D: no visible global function definition for
  'rnorm'
ssd : generate_bootstrap: no visible global function definition for
  'rmultinom'
ssd : bootstrap_method: no visible global function definition for
  'median'
ssd : bootstrap_method: no visible global function definition for
  'quantile'
ssd : unbalanced_generate_bootstrap: no visible global function
  definition for 'rmultinom'
ssd : unbalanced_bootstrap_method: no visible global function
  definition for 'median'
ssd : unbalanced_bootstrap_method: no visible global function
  definition for 'quantile'
ssd: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  median qchisq quantile rmultinom rnorm
Consider adding
  importFrom("stats", "median", "qchisq", "quantile", "rmultinom",
             "rnorm")
to your NAMESPACE file.
L_hNV: no visible global function definition for 'pnorm'
L_hNV_rho: no visible global function definition for 'pnorm'
eff.ssfa: no visible global function definition for 'pnorm'
plot_fitted: no visible global function definition for 'lines'
plot_moran: no visible global function definition for 'residuals'
print.summary.ssfa: no visible global function definition for
  'printCoefmat'
ssfa: no visible global function definition for 'model.frame'
ssfa: no visible global function definition for 'model.response'
ssfa.fit: no visible global function definition for 'lm'
ssfa.fit: no visible global function definition for 'var'
ssfa.fit: no visible global function definition for 'logLik'
summary.ssfa: no visible global function definition for 'pnorm'
summary.ssfa: no visible global function definition for 'logLik'
summary.ssfa: no visible global function definition for 'pchisq'
summary.ssfa: no visible binding for global variable 'df'
u.ssfa: no visible global function definition for 'dnorm'
u.ssfa: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  df dnorm lines lm logLik model.frame model.response pchisq pnorm
  printCoefmat residuals var
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "df", "dnorm", "lm", "logLik", "model.frame",
             "model.response", "pchisq", "pnorm", "printCoefmat",
             "residuals", "var")
to your NAMESPACE file.
Package in Depends field not imported from: 'survey'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fit.model: no visible global function definition for 'hadamard'
Undefined global functions or variables:
  hadamard
sslCoTrain: no visible global function definition for 'predict'
sslSelfTrain: no visible global function definition for 'predict'
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
map.world: no visible global function definition for 'par'
map.world: no visible global function definition for 'plot.new'
map.world: no visible global function definition for 'plot.window'
map.world: no visible global function definition for 'lines'
map.world: no visible global function definition for 'title'
map.world: no visible global function definition for 'axis'
map.world: no visible global function definition for 'box'
plot.smooth.sspline: no visible global function definition for
  'predict'
plot.smooth.sspline: no visible global function definition for
  'filled.contour'
plot.smooth.sspline: no visible binding for global variable
  'terrain.colors'
plot.smooth.sspline: no visible global function definition for 'title'
plot.smooth.sspline: no visible global function definition for 'axis'
station: no visible binding for global variable 'WTdiff'
station: no visible global function definition for 'points'
Undefined global functions or variables:
  WTdiff axis box filled.contour lines par plot.new plot.window points
  predict terrain.colors title
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "axis", "box", "filled.contour", "lines", "par",
             "plot.new", "plot.window", "points", "title")
  importFrom("stats", "predict")
to your NAMESPACE file.
SS.ID: no visible global function definition for 'var'
SS.sim.chol: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm var
Consider adding
  importFrom("stats", "rnorm", "var")
to your NAMESPACE file.
error.est : <anonymous>: no visible global function definition for
  'median'
holm.robust: no visible global function definition for 'pnorm'
holm.robust: no visible global function definition for 'median'
holm.robust: no visible global function definition for 'mad'
huberize: no visible global function definition for 'quantile'
ssvd.initial: no visible global function definition for 'mad'
ssvd.iter.thresh: no visible global function definition for 'mad'
Undefined global functions or variables:
  mad median pnorm quantile
Consider adding
  importFrom("stats", "mad", "median", "pnorm", "quantile")
to your NAMESPACE file.
.expandLevels: no visible global function definition for 'na.omit'
.ffStack: no visible global function definition for 'na.omit'
.ffffStack: no visible global function definition for 'na.omit'
Stack : <anonymous>: no visible global function definition for
  'na.omit'
ffStack,ffdf-data.frame: no visible global function definition for
  'na.omit'
ffStack,ffdf-ffdf: no visible global function definition for 'na.omit'
ffStack,ffdf-list: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
genericPlot: no visible global function definition for 'dev.new'
genericPlot: no visible global function definition for 'par'
genericPlot: no visible global function definition for 'rainbow'
genericPlot: no visible global function definition for 'plot'
genericPlot: no visible global function definition for 'lines'
genericPlot: no visible global function definition for 'legend'
genericPlot: no visible global function definition for 'dev.copy2pdf'
genericPlot: no visible global function definition for 'dev.copy2eps'
genericPlot: no visible global function definition for 'dev.print'
genericPlot: no visible binding for global variable 'png'
genericPlot: no visible binding for global variable 'tiff'
plotStrains: no visible global function definition for 'rainbow'
plotStrains: no visible global function definition for 'dev.new'
plotStrains: no visible global function definition for 'par'
plotStrains: no visible global function definition for 'plot'
plotStrains: no visible global function definition for 'lines'
plotStrains: no visible global function definition for 'legend'
plotStrains: no visible global function definition for 'dev.copy2pdf'
plotStrains: no visible global function definition for 'dev.copy2eps'
plotStrains: no visible global function definition for 'dev.print'
plotStrains: no visible binding for global variable 'png'
plotStrains: no visible binding for global variable 'tiff'
Undefined global functions or variables:
  dev.copy2eps dev.copy2pdf dev.new dev.print legend lines par plot png
  rainbow tiff
Consider adding
  importFrom("grDevices", "dev.copy2eps", "dev.copy2pdf", "dev.new",
             "dev.print", "png", "rainbow", "tiff")
  importFrom("graphics", "legend", "lines", "par", "plot")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'np' 'sp'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'np' 'sp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
stkde: no visible global function definition for 'npudensbw'
stkde: no visible global function definition for 'npudens'
stkde: no visible global function definition for 'quantile'
stkde: no visible global function definition for 'heat.colors'
stkde: no visible global function definition for 'par'
stkde: no visible global function definition for 'image'
stkde: no visible global function definition for 'contour'
stkde.base: no visible global function definition for 'npudensbw'
stkde.base: no visible global function definition for 'npudens'
stkde.sig: no visible global function definition for 'SpatialPoints'
stkde.sig: no visible global function definition for 'spsample'
stkde.sig: no visible global function definition for 'bbox'
stkde.sig: no visible global function definition for 'quantile'
stkde.sig: no visible global function definition for 'heat.colors'
stkde.sig: no visible global function definition for 'par'
stkde.sig: no visible global function definition for 'image'
stkde.sig: no visible global function definition for 'contour'
Undefined global functions or variables:
  SpatialPoints bbox contour heat.colors image npudens npudensbw par
  quantile spsample
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "contour", "image", "par")
  importFrom("stats", "quantile")
to your NAMESPACE file.
find.names: no visible global function definition for 'na.omit'
generate.names: no visible global function definition for 'na.omit'
standardize.countrynames: no visible global function definition for
  'data'
standardize.names: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    include   9.0Mb
'library' or 'require' call to 'codetools' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'codetools' 'gss'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: 'starsdata'
Found the following hidden files and directories:
  inst/.Renviron.d
  inst/.Rprofile.d
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
actvspred: no visible global function definition for 'quantile'
actvspred: no visible global function definition for 'aggregate'
actvspred: no visible global function definition for 'par'
actvspred: no visible global function definition for 'plot'
actvspred: no visible global function definition for 'lines'
auc: no visible global function definition for 'par'
auc: no visible global function definition for 'plot'
decile: no visible global function definition for 'quantile'
dqcontinuous : numoutliers: no visible global function definition for
  'quantile'
dqcontinuous : <anonymous>: no visible global function definition for
  'sd'
dqcontinuous : <anonymous>: no visible global function definition for
  'quantile'
gini: no visible global function definition for 'par'
gini: no visible global function definition for 'plot'
gini: no visible global function definition for 'abline'
iv: no visible global function definition for 'quantile'
iv: no visible global function definition for 'aggregate'
ks: no visible global function definition for 'aggregate'
ks: no visible global function definition for 'par'
ks: no visible global function definition for 'plot'
ks: no visible global function definition for 'lines'
outliers: no visible global function definition for 'quantile'
outliers: no visible global function definition for 'na.omit'
pentile: no visible global function definition for 'quantile'
Undefined global functions or variables:
  abline aggregate lines na.omit par plot quantile sd
Consider adding
  importFrom("graphics", "abline", "lines", "par", "plot")
  importFrom("stats", "aggregate", "na.omit", "quantile", "sd")
to your NAMESPACE file.
inspect: no visible global function definition for 'par'
inspect: no visible global function definition for 'abline'
inspect: no visible global function definition for 'lines'
inspect: no visible global function definition for 'points'
plotfit: no visible global function definition for 'dev.off'
plotfit: no visible global function definition for 'par'
plotfit: no visible global function definition for 'lines'
plotfit: no visible global function definition for 'points'
plotfit: no visible global function definition for 'legend'
plothill: no visible global function definition for 'par'
plothill: no visible global function definition for 'abline'
plothill: no visible global function definition for 'points'
plotmultifit: no visible global function definition for 'par'
plotmultifit: no visible global function definition for 'lines'
plotmultifit: no visible global function definition for 'points'
plotmultifit: no visible global function definition for 'pexp'
plotmultifit: no visible global function definition for 'plnorm'
plotmultifit: no visible global function definition for 'ppois'
plotmultifit: no visible global function definition for 'legend'
plotols: no visible global function definition for 'dev.off'
plotols: no visible global function definition for 'lm'
plotols: no visible global function definition for 'par'
plotols: no visible global function definition for 'abline'
plotols: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline dev.off legend lines lm par pexp plnorm points ppois
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("graphics", "abline", "legend", "lines", "par", "points")
  importFrom("stats", "lm", "pexp", "plnorm", "ppois")
to your NAMESPACE file.
getStp: no visible global function definition for 'lm'
plot.steeptest: no visible global function definition for 'plot'
plot.steeptest: no visible global function definition for 'axis'
plot.steeptest: no visible global function definition for 'box'
plot.steeptest: no visible global function definition for 'lm'
plot.steeptest: no visible global function definition for 'abline'
plot.steeptest: no visible global function definition for 'legend'
plot.steeptest: no visible global function definition for
  'as.graphicsAnnot'
steeptest: no visible global function definition for 'lm'
summary.steeptest: no visible global function definition for 'var'
summary.steeptest: no visible global function definition for 'quantile'
Undefined global functions or variables:
  abline as.graphicsAnnot axis box legend lm plot quantile var
Consider adding
  importFrom("grDevices", "as.graphicsAnnot")
  importFrom("graphics", "abline", "axis", "box", "legend", "plot")
  importFrom("stats", "lm", "quantile", "var")
to your NAMESPACE file.
Stem.Bootstrap: no visible global function definition for 'runif'
filtering: no visible global function definition for 'is.ts'
filtering: no visible global function definition for 'ts'
filtering: no visible global function definition for 'start'
filtering: no visible global function definition for 'end'
filtering: no visible global function definition for 'frequency'
kalman: no visible global function definition for 'ts'
smoothing: no visible global function definition for 'is.ts'
smoothing: no visible global function definition for 'ts'
smoothing: no visible global function definition for 'start'
smoothing: no visible global function definition for 'end'
smoothing: no visible global function definition for 'frequency'
Undefined global functions or variables:
  end frequency is.ts runif start ts
Consider adding
  importFrom("stats", "end", "frequency", "is.ts", "runif", "start",
             "ts")
to your NAMESPACE file.
d1spectrum: no visible global function definition for 'fft'
d2spectrum: no visible global function definition for 'fft'
plot.d1nat: no visible global function definition for 'plot'
plot.d1nat: no visible global function definition for 'lines'
plot.d1nat: no visible global function definition for 'legend'
plot.d1nat: no visible global function definition for 'title'
plot.d1spec: no visible global function definition for 'plot'
plot.d1spec: no visible global function definition for 'lines'
plot.d1spec: no visible global function definition for 'legend'
plot.d1spec: no visible global function definition for 'title'
plot.d2spec: no visible global function definition for 'plot'
plot.d2spec: no visible global function definition for 'lines'
plot.d2spec: no visible global function definition for 'legend'
plot.d2spec: no visible global function definition for 'title'
plot.pvalign: no visible global function definition for 'plot'
plot.pvalign: no visible global function definition for 'lines'
plot.pvalign: no visible global function definition for 'legend'
plot.pvalign: no visible global function definition for 'title'
print.d1nat: no visible global function definition for 'plot'
print.d1spec: no visible global function definition for 'plot'
print.d2spec: no visible global function definition for 'plot'
print.pvalign: no visible global function definition for 'plot'
utild1bin: no visible global function definition for 'median'
utild1bin: no visible global function definition for 'sd'
utild1clean: no visible global function definition for 'sd'
utild1filt: no visible global function definition for 'convolve'
Undefined global functions or variables:
  convolve fft legend lines median plot sd title
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "title")
  importFrom("stats", "convolve", "fft", "median", "sd")
to your NAMESPACE file.
Error(s) in re-building vignettes:
--- re-building 'stmVignette.Rnw' using Sweave
stm v1.3.3 (2018-1-26) successfully loaded. See ?stm for help. 
 Papers, resources, and other materials at structuraltopicmodel.com
Warning in load(url("http://goo.gl/VPdxlS")) :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine sichere in eine nicht sichere Verbindung.'

Error: processing vignette 'stmVignette.Rnw' failed with diagnostics:
 chunk 7 
Error in load(url("http://goo.gl/VPdxlS")) : cannot open the connection

--- failed re-building 'stmVignette.Rnw'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R          2.0Mb
    datasets   2.6Mb
StratPhyloCongruence: no visible global function definition for 'runif'
StratPhyloCongruence: no visible global function definition for
  'txtProgressBar'
StratPhyloCongruence: no visible global function definition for
  'setTxtProgressBar'
StratPhyloCongruence: no visible global function definition for 'pnorm'
StratPhyloCongruence: no visible global function definition for 'sd'
geoscalePhylo: no visible global function definition for 'data'
geoscalePhylo: no visible global function definition for 'par'
geoscalePhylo: no visible global function definition for 'text'
geoscalePhylo: no visible global function definition for 'segments'
geoscalePhylo: no visible global function definition for 'rect'
geoscalePhylo: no visible global function definition for 'rgb'
Undefined global functions or variables:
  data par pnorm rect rgb runif sd segments setTxtProgressBar text
  txtProgressBar
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "par", "rect", "segments", "text")
  importFrom("stats", "pnorm", "runif", "sd")
  importFrom("utils", "data", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
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:
> zd <- zeq_example
> 
> par(mfrow = c(1,2))
> 
> zijderveld(dec = zd$Dec, inc = zd$Inc, int = zd$Int,
+            xh = "WE", unit = 10^-5)
> 
> zijderveld(dec = zd$Dec, inc = zd$Inc, int = zd$Int,
+            style = "box1", scientific = FALSE, decimals = 5,
+            labels = zd$Treat, nlabels = 2)
> 
> 
> 
> 
> graphics::par(get("par.postscript", pos = 'CheckExEnv'))
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  7.14 0.37 1489.4 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 36.0Mb
  sub-directories of 1Mb or more:
    libs  35.3Mb
Package suggested but not available for checking: 'STRaitRazoR'
breakpoints.formula: no visible global function definition for
  '%dopar%'
breakpoints.formula: no visible binding for global variable 'i'
efpFunctional: multiple local function definitions for 'plotProcess'
  with different formal arguments
mefp.efp: multiple local function definitions for 'computeEmpProc' with
  different formal arguments
sctest.default: no visible global function definition for 'tail'
Undefined global functions or variables:
  %dopar% i tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
PlotHypTree: no visible global function definition for 'browseURL'
treePValues: no visible global function definition for 'lm'
treePValues: no visible global function definition for 'pf'
plot,GBH-ANY: no visible binding for global variable 'sorted.hyp'
plot,GBH-ANY: no visible binding for global variable 'pval'
plot,GBH-ANY: no visible binding for global variable 'group'
plot,GBH-ANY: no visible binding for global variable 'type'
Undefined global functions or variables:
  browseURL group lm pf pval sorted.hyp type
Consider adding
  importFrom("stats", "lm", "pf")
  importFrom("utils", "browseURL")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from 'stsm.class' for: 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
stsm.model: no visible global function definition for 'is.ts'
stsm.model: no visible global function definition for 'var'
stsm.model: no visible global function definition for 'frequency'
stsm.model: no visible global function definition for 'na.omit'
stsm.model: no visible global function definition for 'fft'
stsm.model: no visible global function definition for 'new'
stsm.sgf: no visible global function definition for 'frequency'
char2numeric,stsm: no visible global function definition for
  'frequency'
set.cpar,stsm: no visible global function definition for 'validObject'
set.nopars,stsm: no visible global function definition for
  'validObject'
set.pars,stsm: no visible global function definition for 'validObject'
transPars,stsm: no visible global function definition for 'var'
Undefined global functions or variables:
  fft frequency is.ts na.omit new validObject var
Consider adding
  importFrom("methods", "new", "validObject")
  importFrom("stats", "fft", "frequency", "is.ts", "na.omit", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running 'test-all.R' [22s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("STV")
  Loading required package: STV
  -- 1. Failure: Toy example (@testExt.R#36)  ------------------------------------
  `x` not equal to `expected`.
  1/4 mismatches
  x[2]: "ATL_54"
  y[2]: "ATL_27"
  
  == testthat results  ===========================================================
  OK: 4 SKIPPED: 0 FAILED: 1
  1. Failure: Toy example (@testExt.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
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.
'library' or 'require' calls to packages already attached by Depends:
  'ROCR' 'penalized'
  Please remove these calls from your code.
ELF: no visible global function definition for 'pt'
ELF: no visible global function definition for 'qnorm'
ELF: no visible global function definition for 'lm'
ELF: no visible global function definition for 'lowess'
ELF: no visible global function definition for 'dnorm'
ELF: no visible global function definition for 'approx'
subtype: no visible global function definition for 'runif'
subtype: no visible global function definition for 'hclust'
subtype: no visible global function definition for 'dist'
subtype: no visible global function definition for 'cutree'
subtype: no visible global function definition for 'pt'
subtype: no visible global function definition for 'heatmap'
test_subtype_only: no visible global function definition for 'pt'
test_subtype_only: no visible global function definition for 'survdiff'
test_subtype_only: no visible global function definition for 'survfit'
test_subtype_only: no visible global function definition for 'title'
ufun: no visible global function definition for 'dnorm'
ufun: no visible global function definition for 'lowess'
Undefined global functions or variables:
  approx cutree dist dnorm hclust heatmap lm lowess pt qnorm runif
  survdiff survfit title
Consider adding
  importFrom("graphics", "title")
  importFrom("stats", "approx", "cutree", "dist", "dnorm", "hclust",
             "heatmap", "lm", "lowess", "pt", "qnorm", "runif")
to your NAMESPACE file.
'library' or 'require' call to 'tkrplot' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
playSudoku : replot: no visible global function definition for 'par'
playSudoku : replot: no visible global function definition for 'plot'
playSudoku : replot: no visible global function definition for
  'segments'
playSudoku : replot: no visible global function definition for 'text'
playSudoku: no visible global function definition for 'tktoplevel'
playSudoku: no visible global function definition for 'tkwm.title'
playSudoku: no visible global function definition for 'tkrplot'
playSudoku: no visible global function definition for 'tktext'
playSudoku: no visible global function definition for 'tkscrollbar'
playSudoku : <anonymous>: no visible global function definition for
  'tkyview'
playSudoku: no visible global function definition for 'tkconfigure'
playSudoku : <anonymous>: no visible global function definition for
  'tkset'
playSudoku: no visible global function definition for 'tkpack'
playSudoku: no visible global function definition for 'tcl'
playSudoku: no visible global function definition for 'tkcget'
playSudoku : showz: no visible global function definition for
  'tkrreplot'
playSudoku : type: no visible global function definition for 'tkinsert'
playSudoku : type: no visible global function definition for 'tksee'
playSudoku : kb: no visible global function definition for 'tkdestroy'
playSudoku: no visible global function definition for
  'getGraphicsEvent'
playSudoku: no visible global function definition for 'tkbind'
playSudoku: no visible global function definition for 'tkwait.window'
Undefined global functions or variables:
  getGraphicsEvent par plot segments tcl text tkbind tkcget tkconfigure
  tkdestroy tkinsert tkpack tkrplot tkrreplot tkscrollbar tksee tkset
  tktext tktoplevel tkwait.window tkwm.title tkyview
Consider adding
  importFrom("grDevices", "getGraphicsEvent")
  importFrom("graphics", "par", "plot", "segments", "text")
to your NAMESPACE file.
SUE.fitted.values: no visible global function definition for
  'model.frame'
SUE.lm: no visible global function definition for 'model.frame'
SUE.lm: no visible global function definition for 'lm'
SUE.lm: no visible global function definition for 'anova'
SUE.plot: no visible global function definition for 'plot'
SUE.residuals: no visible global function definition for 'model.frame'
parameters : para2: no visible global function definition for 'uniroot'
parameters: no visible global function definition for 'optimize'
parameters: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  anova lm model.frame optimize plot uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "anova", "lm", "model.frame", "optimize",
             "uniroot")
to your NAMESPACE file.
MCMCCV: no visible global function definition for 'rnorm'
MLCVGauss: no visible global function definition for 'runif'
MLCVGauss: no visible global function definition for 'optim'
SimSunderData: no visible global function definition for 'runif'
SimSunderData: no visible global function definition for 'dist'
SimSunderData: no visible global function definition for 'rnorm'
SimSunderData: no visible global function definition for 'qgamma'
SimSunderData: no visible global function definition for 'pnorm'
SimSunderData: no visible global function definition for 'rmultinom'
Undefined global functions or variables:
  dist optim pnorm qgamma rmultinom rnorm runif
Consider adding
  importFrom("stats", "dist", "optim", "pnorm", "qgamma", "rmultinom",
             "rnorm", "runif")
to your NAMESPACE file.
sunter: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
supcluster : itgamma: no visible global function definition for
  'rgamma'
supcluster : itgamma: no visible global function definition for
  'dgamma'
supcluster : itgamma: no visible global function definition for 'runif'
supcluster : itbeta: no visible global function definition for 'rnorm'
supcluster : itbeta: no visible global function definition for 'runif'
supcluster : itj: no visible global function definition for 'dmultinom'
supcluster: no visible global function definition for 'kmeans'
tab1: no visible global function definition for 'image'
tab1: no visible global function definition for 'gray'
tab1: no visible global function definition for 'var'
Undefined global functions or variables:
  dgamma dmultinom gray image kmeans rgamma rnorm runif var
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "image")
  importFrom("stats", "dgamma", "dmultinom", "kmeans", "rgamma", "rnorm",
             "runif", "var")
to your NAMESPACE file.
HCLtree: no visible global function definition for 'hclust'
HCLtree: no visible global function definition for 'as.dist'
plotProfilesAcrossAllSamples: no visible global function definition for
  'matplot'
plotProfilesAcrossAllSamples: no visible global function definition for
  'matlines'
plotProfilesAcrossAllSamples: no visible global function definition for
  'axis'
plotProfilesAcrossAllSamples: no visible global function definition for
  'box'
plotProfilesWithinBicluster: no visible global function definition for
  'matplot'
plotProfilesWithinBicluster: no visible global function definition for
  'title'
plotProfilesWithinBicluster: no visible global function definition for
  'axis'
plotProfilesWithinBicluster: no visible global function definition for
  'par'
plotProfilesWithinBicluster: no visible global function definition for
  'box'
plotProfilesWithinBicluster: no visible global function definition for
  'matlines'
plotProfilesWithinBicluster: no visible global function definition for
  'legend'
Undefined global functions or variables:
  as.dist axis box hclust legend matlines matplot par title
Consider adding
  importFrom("graphics", "axis", "box", "legend", "matlines", "matplot",
             "par", "title")
  importFrom("stats", "as.dist", "hclust")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'boa' 'coda'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
superdiag: no visible global function definition for 'as.mcmc.list'
superdiag: no visible global function definition for 'as.mcmc'
superdiag: no visible global function definition for 'runif'
superdiag: no visible global function definition for 'geweke.diag'
superdiag: no visible global function definition for 'heidel.diag'
superdiag: no visible global function definition for 'raftery.diag'
superdiag: no visible global function definition for 'gelman.diag'
Undefined global functions or variables:
  as.mcmc as.mcmc.list gelman.diag geweke.diag heidel.diag raftery.diag
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
TrainSuperMDS: no visible global function definition for 'rnorm'
TrainSuperMDSOnce: no visible global function definition for 'cmdscale'
TrainSuperMDSOnce: no visible global function definition for 'quantile'
distmat: no visible global function definition for 'dist'
Undefined global functions or variables:
  cmdscale dist quantile rnorm
Consider adding
  importFrom("stats", "cmdscale", "dist", "quantile", "rnorm")
to your NAMESPACE file.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

plot.survAUC: no visible global function definition for 'plot'
plot.survAUC: no visible global function definition for 'lines'
plot.survErr: no visible global function definition for 'plot'
plot.survErr: no visible global function definition for 'lines'
schemper: no visible global function definition for 'predict'
schemper: no visible global function definition for 'survfit'
schemper: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx lines plot predict survfit
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "approx", "predict")
to your NAMESPACE file.
Est.PH: no visible global function definition for 'coxph'
Inf.Cval: no visible global function definition for 'rexp'
Inf.Cval: no visible global function definition for 'var'
Inf.Cval.Delta: no visible global function definition for 'rexp'
Inf.Cval.Delta: no visible global function definition for 'var'
cvC: no visible global function definition for 'coxph'
cvC: no visible global function definition for 'weighted.mean'
Undefined global functions or variables:
  coxph rexp var weighted.mean
Consider adding
  importFrom("stats", "rexp", "var", "weighted.mean")
to your NAMESPACE file.
pearson: no visible global function definition for 'cor'
plot.survcorr: no visible global function definition for 'pnorm'
plot.survcorr: no visible global function definition for 'par'
plot.survcorr: no visible global function definition for 'plot'
plot.survcorr: no visible global function definition for 'points'
survcorr: no visible global function definition for 'model.frame'
survcorr: no visible global function definition for 'qnorm'
survcorr: no visible global function definition for 'runif'
survcorr: no visible global function definition for 'pnorm'
survcorr: no visible global function definition for 'var'
survcorr: no visible global function definition for 'qt'
Undefined global functions or variables:
  cor model.frame par plot pnorm points qnorm qt runif var
Consider adding
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "cor", "model.frame", "pnorm", "qnorm", "qt",
             "runif", "var")
to your NAMESPACE file.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.3Mb
    help   1.0Mb
    libs   1.7Mb
'library' or 'require' call to 'survival' which was already attached by Depends.
  Please remove these calls from your code.
Survgini: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
Packages in Depends field not imported from:
  'survC1' 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Est.HR.FUN: no visible global function definition for 'coxph'
Est.HR.FUN: no visible global function definition for 'basehaz'
Est.HR.FUN: no visible global function definition for 'approx'
Ghat.FUN: no visible global function definition for 'survfit'
IDI.INF: no visible global function definition for 'kmcens'
IDI.INF: no visible global function definition for 'quantile'
IDI.INF.GRAPH: no visible global function definition for 'plot'
IDI.INF.GRAPH: no visible global function definition for 'lines'
IDI.INF.GRAPH: no visible global function definition for 'abline'
IDI.INF.GRAPH: no visible global function definition for 'points'
IDI.INF.GRAPH: no visible global function definition for 'title'
PTB.IDI.FUN: no visible global function definition for 'rexp'
shade: no visible global function definition for 'polygon'
Undefined global functions or variables:
  abline approx basehaz coxph kmcens lines plot points polygon quantile
  rexp survfit title
Consider adding
  importFrom("graphics", "abline", "lines", "plot", "points", "polygon",
             "title")
  importFrom("stats", "approx", "quantile", "rexp")
to your NAMESPACE file.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   3.0Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
betaEst: no visible global function definition for 'is'
fullKernel: no visible global function definition for 'is'
halfKernel: no visible global function definition for 'is'
kernelAuto: no visible global function definition for 'quantile'
kernelAuto: no visible global function definition for 'lm'
kernelAuto: no visible global function definition for 'pnorm'
kernelFixed: no visible global function definition for 'pnorm'
lastValue: no visible global function definition for 'pnorm'
nearValue: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  is lm pnorm quantile
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "lm", "pnorm", "quantile")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
fitModel: no visible global function definition for 'var'
fitModel: no visible global function definition for 'cov'
svpls: no visible global function definition for 'pt'
Undefined global functions or variables:
  cov pt var
Consider adding
  importFrom("stats", "cov", "pt", "var")
to your NAMESPACE file.
dlgMessage.tcltkGUI: no visible global function definition for 'alarm'
dlgMessage.tcltkGUI: no visible global function definition for
  'bringToTop'
Undefined global functions or variables:
  alarm bringToTop
Consider adding
  importFrom("grDevices", "bringToTop")
  importFrom("utils", "alarm")
to your NAMESPACE file.
svd3dplot: no visible global function definition for 'wireframe'
svd3dplot: no visible global function definition for 'levelplot'
Undefined global functions or variables:
  levelplot wireframe
startHttpServer : <anonymous> : Rjsonp: no visible global function
  definition for 'localeToCharset'
Undefined global functions or variables:
  localeToCharset
Consider adding
  importFrom("utils", "localeToCharset")
to your NAMESPACE file.
.onAttach : svBrowser: no visible global function definition for
  'browseURL'
.onAttach: no visible global function definition for 'loadhistory'
Undefined global functions or variables:
  browseURL loadhistory
Consider adding
  importFrom("utils", "browseURL", "loadhistory")
to your NAMESPACE file.
File 'svmpath/libs/i386/svmpath.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'mi10unix.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'mi10unix.o'
File 'svmpath/libs/x64/svmpath.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'mi10unix.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'mi10unix.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
processSocket: no visible global function definition for 'URLdecode'
Undefined global functions or variables:
  URLdecode
Consider adding
  importFrom("utils", "URLdecode")
to your NAMESPACE file.
.formatResult : capture.str: no visible global function definition for
  'str'
createLog: no visible global function definition for 'sessionInfo'
protocol_junit.svSuiteData: no visible global function definition for
  'xmlNode'
protocol_junit.svSuiteData: no visible global function definition for
  'addChildren'
protocol_junit.svSuiteData: no visible global function definition for
  'saveXML'
protocol_junit.svTestData: no visible global function definition for
  'xmlNode'
protocol_junit.svTestData: no visible global function definition for
  'addChildren'
Undefined global functions or variables:
  addChildren saveXML sessionInfo str xmlNode
Consider adding
  importFrom("utils", "sessionInfo", "str")
to your NAMESPACE file.
svycox.calibrate: no visible global function definition for 'quantile'
svycox.calibrate: no visible binding for global variable 'median'
svycox.calibrate: no visible global function definition for
  'as.formula'
svycox.calibrate: no visible global function definition for 'plot'
svycox.calibrate: no visible global function definition for 'arrows'
svycox.calibrate: no visible global function definition for 'abline'
svycox.nomogram: no visible global function definition for 'predict'
svycox.nomogram: no visible global function definition for 'as.formula'
svycox.validate : internal.validate.func: no visible global function
  definition for 'as.formula'
svycox.validate : internal.validate.func: no visible global function
  definition for 'formula'
Undefined global functions or variables:
  abline arrows as.formula formula median plot predict quantile
Consider adding
  importFrom("graphics", "abline", "arrows", "plot")
  importFrom("stats", "as.formula", "formula", "median", "predict",
             "quantile")
to your NAMESPACE file.
additional_comp: no visible global function definition for 'aggregate'
additional_compPV : <anonymous>: no visible global function definition
  for 'aggregate'
cor.aux.func : <anonymous>: no visible global function definition for
  'cov.wt'
eta.func : <anonymous>: no visible global function definition for 'lm'
eta.func : <anonymous>: no visible global function definition for
  'anova'
glm.dummy.no.std: no visible global function definition for
  'as.formula'
pv_by: no visible binding for global variable 'var'
pv_perc: no visible binding for global variable 'var'
pv_quantile: no visible binding for global variable 'var'
svyPVcor: no visible global function definition for 'update'
svyPVcor: no visible global function definition for 'var'
svyPVeta: no visible global function definition for 'update'
svyPVeta: no visible global function definition for 'var'
svyPVglm: no visible global function definition for 'gaussian'
svyPVglm: no visible binding for global variable 'as.formula'
svyPVglm: no visible binding for global variable 'var'
svyPVglm: no visible global function definition for 'pt'
svyPVttest: no visible binding for global variable 'as.formula'
svyPVttest: no visible global function definition for 'var'
svyPVttest: no visible global function definition for 'pt'
svyPVttest: no visible binding for global variable 'var'
t.test.aux: no visible global function definition for 'as.formula'
t.test.aux: no visible global function definition for 'complete.cases'
Undefined global functions or variables:
  aggregate anova as.formula complete.cases cov.wt gaussian lm pt
  update var
Consider adding
  importFrom("stats", "aggregate", "anova", "as.formula",
             "complete.cases", "cov.wt", "gaussian", "lm", "pt",
             "update", "var")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: GNU Extension: Different type kinds at (1)
  Warning: GNU Extension: initialization of common block variable 'iset' in DATA statement at (1)
  Warning: GNU Extension: Variable 'iset' at (1) is in COMMON but only in BLOCK DATA initialization is allowed
  Warning: GNU Extension: Missing comma at (1)
See 'd:/Rcompile/CRANpkg/local/3.6/SWATmodel.Rcheck/00install.out' for details.
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    libs  25.5Mb
readSWAT: no visible global function definition for 'read.fortran'
runSWAT2005: no visible global function definition for 'read.fortran'
runSWAT2009: no visible global function definition for 'read.fortran'
runSWAT2012: no visible global function definition for 'read.fortran'
Undefined global functions or variables:
  read.fortran
Consider adding
  importFrom("utils", "read.fortran")
to your NAMESPACE file.
Package suggested but not available for checking: 'swephRdata'
Packages in Depends field not imported from:
  'MASS' 'fda' 'splines'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fj_pl: no visible global function definition for 'getbasismatrix'
fj_pl: no visible global function definition for 'create.bspline.basis'
fj_pl: no visible global function definition for 'getbasispenalty'
forward_backward.quantities : <anonymous>: no visible global function
  definition for 'dnorm'
function_cases1AND2: no visible global function definition for 'dnorm'
function_cases3AND4: no visible global function definition for 'dnorm'
pij_iid: no visible global function definition for 'dnorm'
pilj: no visible global function definition for 'dnorm'
updateLambda: no visible global function definition for 'optimize'
Undefined global functions or variables:
  create.bspline.basis dnorm getbasismatrix getbasispenalty optimize
Consider adding
  importFrom("stats", "dnorm", "optimize")
to your NAMESPACE file.
calc_MW: no visible global function definition for 'read.table'
cfba_moment: no visible global function definition for 'median'
cfba_moment: no visible global function definition for 'write.csv'
cfba_moment_mr: no visible global function definition for 'median'
cfba_moment_mr: no visible global function definition for 'write.csv'
cfba_moment_pw: no visible global function definition for 'median'
cfba_moment_pw: no visible global function definition for 'write.csv'
readmodel: no visible global function definition for 'as'
Undefined global functions or variables:
  as median read.table write.csv
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "median")
  importFrom("utils", "read.table", "write.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
symbol: no visible global function definition for 'plot.new'
symbol: no visible global function definition for 'plot.window'
symbol: no visible global function definition for 'axis'
symbol: no visible global function definition for 'box'
symbol: no visible global function definition for 'title'
symbol: no visible global function definition for 'rainbow'
symbol: no visible global function definition for 'hsv'
symbol: no visible global function definition for 'rect'
symbol: no visible global function definition for 'polygon'
symbol: no visible global function definition for 'lines'
symbol: no visible global function definition for 'text'
Undefined global functions or variables:
  axis box hsv lines plot.new plot.window polygon rainbow rect text
  title
Consider adding
  importFrom("grDevices", "hsv", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "polygon", "rect", "text", "title")
to your NAMESPACE file.
integrate.polynomial : f: no visible global function definition for
  'dmvnorm'
Undefined global functions or variables:
  dmvnorm
Package in Depends field not imported from: 'fields'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cwt_fw: no visible global function definition for 'fft'
cwt_iw: no visible global function definition for 'fft'
est_riskshrink_thresh: no visible global function definition for
  'median'
Undefined global functions or variables:
  fft median
Consider adding
  importFrom("stats", "fft", "median")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'tcltk' 'tkrplot'
  Please remove these calls from your code.
mainNetFunction: no visible global function definition for 'png'
mainNetFunction: no visible global function definition for 'plot'
mainNetFunction: no visible global function definition for 'lines'
mainNetFunction: no visible global function definition for 'legend'
mainNetFunction: no visible global function definition for 'dev.off'
plotPR: no visible global function definition for 'plot'
plotROC: no visible global function definition for 'plot'
plotROC: no visible global function definition for 'lines'
simulatedData: no visible global function definition for 'rpois'
simulatedData : <anonymous>: no visible global function definition for
  'rpois'
simulatedData : rlognormpois: no visible global function definition for
  'rnorm'
simulatedData : rlognormpois: no visible global function definition for
  'rpois'
Undefined global functions or variables:
  dev.off legend lines plot png rnorm rpois
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "rnorm", "rpois")
to your NAMESPACE file.
Running examples in 'synthpop-Ex.R' failed
The error most likely occurred in:

> ### Name: syn.satcat
> ### Title: Synthesis from a saturated model based on all combinations of
> ###   the predictor variables.
> ### Aliases: syn.satcat
> ### Keywords: datagen
> 
> ### ** Examples
> 
> ods <- SD2011[, c("region", "sex", "agegr", "placesize")]
> 
> s1 <- syn(ods, method = c("sample", "cart", "satcat", "cart"))
Synthesis
-----------
 region sex agegr placesize
> 
> ### mostly fails because too many small categories
> s2 <- syn(ods, method = c("sample", "cart", "cart", "satcat"))  
Synthesis
-----------
 region sex agegr placesize

syn.categories
   Malopolskie-FEMALE-NAtemp   Podkarpackie-FEMALE-NAtemp 
                           1                            1 
Swietokrzyskie-FEMALE-NAtemp 
                           1 
Error: The combined groups above for "satcat" have no records in original data.

         Consider using grouped synthesis with "syn.catall" to overcome this
Execution halted
'library' or 'require' calls in package code:
  'LowRankQP' 'rgenoud'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
fn.V: no visible global function definition for 'LowRankQP'
gaps.plot: no visible global function definition for 'abline'
path.plot: no visible global function definition for 'lines'
path.plot: no visible global function definition for 'abline'
path.plot: no visible global function definition for 'legend'
synth: no visible binding for global variable 'sd'
synth: no visible binding for global variable 'var'
synth: no visible global function definition for 'LowRankQP'
Undefined global functions or variables:
  LowRankQP abline legend lines sd var
Consider adding
  importFrom("graphics", "abline", "legend", "lines")
  importFrom("stats", "sd", "var")
to your NAMESPACE file.
.checkDimAndTest: no visible global function definition for
  'chisq.test'
.checkDimAndTest: no visible global function definition for
  'fisher.test'
plotTable1Heatmap: no visible global function definition for 'par'
plotTable1Heatmap: no visible global function definition for 'image'
plotTable1Heatmap: no visible global function definition for 'abline'
plotTable1Heatmap: no visible global function definition for 'axis'
plotTable1Heatmap: no visible global function definition for 'text'
plotTable1Heatmap: no visible global function definition for 'legend'
plotTable1Heatmap: no visible global function definition for 'box'
Undefined global functions or variables:
  abline axis box chisq.test fisher.test image legend par text
Consider adding
  importFrom("graphics", "abline", "axis", "box", "image", "legend",
             "par", "text")
  importFrom("stats", "chisq.test", "fisher.test")
to your NAMESPACE file.
'library' or 'require' call to 'grid' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to 'perturb' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'grid'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cellgram: no visible global function definition for 'grid.rect'
cellgram: no visible global function definition for 'gpar'
cellgram: no visible global function definition for 'grid.segments'
cellgram: no visible global function definition for 'grid.circle'
cellgram: no visible global function definition for 'grid.polygon'
cellgram: no visible global function definition for 'grid.text'
cellgram: no visible global function definition for 'unit'
compare: no visible global function definition for 'sd'
tableplot.colldiag: no visible global function definition for
  'colldiag'
tableplot.colldiag: no visible global function definition for 'xtabs'
tableplot.default: no visible global function definition for
  'grid.newpage'
tableplot.default: no visible global function definition for
  'grid.layout'
tableplot.default: no visible global function definition for 'unit'
tableplot.default: no visible global function definition for
  'pushViewport'
tableplot.default: no visible global function definition for 'viewport'
tableplot.default: no visible global function definition for
  'grid.text'
tableplot.default: no visible global function definition for
  'upViewport'
tableplot.default: no visible global function definition for 'gpar'
tableplot.default: no visible global function definition for
  'grid.rect'
tableplot.default: no visible global function definition for
  'popViewport'
Undefined global functions or variables:
  colldiag gpar grid.circle grid.layout grid.newpage grid.polygon
  grid.rect grid.segments grid.text popViewport pushViewport sd unit
  upViewport viewport xtabs
Consider adding
  importFrom("stats", "sd", "xtabs")
to your NAMESPACE file.
itabplot : <anonymous>: no visible global function definition for
  'capture.output'
itabplot: no visible global function definition for 'browseURL'
Undefined global functions or variables:
  browseURL capture.output
Consider adding
  importFrom("utils", "browseURL", "capture.output")
to your NAMESPACE file.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    java  11.5Mb
'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.
Running 'testthat.R' [220s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(TauStar)
  > 
  > test_check("TauStar")
  -- 1. Failure: tauStarTest with mixed data. (@test_tauStarTest.R#89)  ----------
  abs(a$pVal - (1 - pMixHoeffInd(n * tval, p))) <= 10^-2 isn't true.
  
  -- 2. Failure: tauStarTest with mixed data. (@test_tauStarTest.R#89)  ----------
  abs(a$pVal - (1 - pMixHoeffInd(n * tval, p))) <= 10^-2 isn't true.
  
  == testthat results  ===========================================================
  OK: 529 SKIPPED: 0 FAILED: 2
  1. Failure: tauStarTest with mixed data. (@test_tauStarTest.R#89) 
  2. Failure: tauStarTest with mixed data. (@test_tauStarTest.R#89) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [110s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(TauStar)
  > 
  > test_check("TauStar")
  -- 1. Failure: tauStarTest with mixed data. (@test_tauStarTest.R#89)  ----------
  abs(a$pVal - (1 - pMixHoeffInd(n * tval, p))) <= 10^-2 isn't true.
  
  -- 2. Failure: tauStarTest with mixed data. (@test_tauStarTest.R#89)  ----------
  abs(a$pVal - (1 - pMixHoeffInd(n * tval, p))) <= 10^-2 isn't true.
  
  == testthat results  ===========================================================
  OK: 529 SKIPPED: 0 FAILED: 2
  1. Failure: tauStarTest with mixed data. (@test_tauStarTest.R#89) 
  2. Failure: tauStarTest with mixed data. (@test_tauStarTest.R#89) 
  
  Error: testthat unit tests failed
  Execution halted
BootTree: no visible global function definition for 'hclust'
BootTree: no visible global function definition for 'dist'
BootTree: no visible global function definition for 'as.dist'
BootTree: no visible global function definition for 'cor'
BootTree: no visible binding for global variable 'var'
Pgpd: no visible global function definition for 'optim'
Pgpd : <anonymous>: no visible global function definition for 'optim'
Pgpd: no visible global function definition for 'var'
Pgpd: no visible global function definition for 'rnorm'
Pgpd: no visible global function definition for 'quantile'
Pvalue: no visible global function definition for 'rnorm'
SigTree: no visible global function definition for 'data'
TreeStat: no visible global function definition for 'hclust'
TreeStat: no visible global function definition for 'as.dist'
TreeStat: no visible global function definition for 'dist'
TreeStat: no visible global function definition for 'cor'
plot.best: no visible global function definition for 'hclust'
plot.best: no visible global function definition for 'as.dist'
plot.best: no visible global function definition for 'dist'
plot.best: no visible global function definition for 'cor'
plot.best: no visible global function definition for 'plot'
treetext: no visible global function definition for 'par'
treetext: no visible global function definition for 'text'
Undefined global functions or variables:
  as.dist cor data dist hclust optim par plot quantile rnorm text var
Consider adding
  importFrom("graphics", "par", "plot", "text")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "optim",
             "quantile", "rnorm", "var")
  importFrom("utils", "data")
to your NAMESPACE file.
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tbltools)
  > 
  > test_check("tbltools")
  -- 1. Failure: filter_data, arrange_data (@test-tbl.R#60)  ---------------------
  nrow(filter_data(d, d$abc == "a")) not equal to 34.
  1/1 mismatches
  [1] 30 - 34 == -4
  
  == testthat results  ===========================================================
  OK: 99 SKIPPED: 0 FAILED: 1
  1. Failure: filter_data, arrange_data (@test-tbl.R#60) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.9Mb
    libs   1.5Mb
cluster_cutoff_at_first_empty_bin: no visible global function
  definition for 'hist'
mapper1D: no visible global function definition for 'dist'
mapper1D: no visible global function definition for 'as.dist'
mapper1D: no visible global function definition for 'hclust'
mapper1D: no visible global function definition for 'cutree'
mapper2D: no visible global function definition for 'dist'
mapper2D: no visible global function definition for 'as.dist'
mapper2D: no visible global function definition for 'hclust'
mapper2D: no visible global function definition for 'cutree'
Undefined global functions or variables:
  as.dist cutree dist hclust hist
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "as.dist", "cutree", "dist", "hclust")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'RSEIS' 'pracma' 'signal'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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  5.4Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   2.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
S3 methods shown with full name in documentation object 'mean.tensor':
  'mean.tensor'

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
TER.deesc.1.B : A1.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.1.B : A1.f: no visible binding for global variable 'ID'
TER.deesc.1.B : A2.n.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.1.B : A2.n.f: no visible binding for global variable 'ID'
TER.deesc.1.B: no visible binding for '<<-' assignment to 'ID'
TER.deesc.1.B: no visible binding for global variable 'ID'
TER.deesc.A.B : A1.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : A1.f: no visible binding for global variable 'ID'
TER.deesc.A.B : A3.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : A3.f: no visible binding for global variable 'ID'
TER.deesc.A.B : A2.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : A2.f: no visible binding for global variable 'ID'
TER.deesc.A.B : B1.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : B1.f: no visible binding for global variable 'ID'
TER.deesc.A.B: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B: no visible binding for global variable 'ID'
Undefined global functions or variables:
  ID
installed size is 28.4Mb
  sub-directories of 1Mb or more:
    doc        1.0Mb
    libs      13.3Mb
    tessdata  14.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   1.5Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    3.6Mb
    libs   2.1Mb
Running examples in 'text2vec-Ex.R' failed
The error most likely occurred in:

> ### Name: itoken
> ### Title: Iterators (and parallel iterators) over input objects
> ### Aliases: itoken itoken.list itoken.character itoken.iterator
> ###   itoken_parallel itoken_parallel.character
> ###   itoken_parallel.ifiles_parallel itoken_parallel.list
> 
> ### ** Examples
> 
> data("movie_review")
> txt = movie_review$review[1:100]
> ids = movie_review$id[1:100]
> it = itoken(txt, tolower, word_tokenizer, n_chunks = 10)
> it = itoken(txt, tolower, word_tokenizer, n_chunks = 10, ids = ids)
> # Example of stemming tokenizer
> # stem_tokenizer =function(x) {
> #   lapply(word_tokenizer(x), SnowballC::wordStem, language="en")
> # }
> #------------------------------------------------
> # PARALLEL iterators
> #------------------------------------------------
> library(text2vec)
> 
> N_WORKERS = 1 # change 1 to number of cores in parallel backend
> if(require(doParallel)) registerDoParallel(N_WORKERS)
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> data("movie_review")
> it = itoken_parallel(movie_review$review[1:100], n_chunks = N_WORKERS)
> system.time(dtm <- create_dtm(it, hash_vectorizer(2**16), type = 'dgTMatrix'))
   user  system elapsed 
   0.00    0.02    2.09 
> 
> 
> 
> cleanEx()

detaching 'package:doParallel', 'package:parallel',
  'package:iterators', 'package:foreach'

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11557 (sockconn)
Execution halted
Running examples in 'text2vec-Ex.R' failed
The error most likely occurred in:

> ### Name: itoken
> ### Title: Iterators (and parallel iterators) over input objects
> ### Aliases: itoken itoken.list itoken.character itoken.iterator
> ###   itoken_parallel itoken_parallel.character
> ###   itoken_parallel.ifiles_parallel itoken_parallel.list
> 
> ### ** Examples
> 
> data("movie_review")
> txt = movie_review$review[1:100]
> ids = movie_review$id[1:100]
> it = itoken(txt, tolower, word_tokenizer, n_chunks = 10)
> it = itoken(txt, tolower, word_tokenizer, n_chunks = 10, ids = ids)
> # Example of stemming tokenizer
> # stem_tokenizer =function(x) {
> #   lapply(word_tokenizer(x), SnowballC::wordStem, language="en")
> # }
> #------------------------------------------------
> # PARALLEL iterators
> #------------------------------------------------
> library(text2vec)
> 
> N_WORKERS = 1 # change 1 to number of cores in parallel backend
> if(require(doParallel)) registerDoParallel(N_WORKERS)
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> data("movie_review")
> it = itoken_parallel(movie_review$review[1:100], n_chunks = N_WORKERS)
> system.time(dtm <- create_dtm(it, hash_vectorizer(2**16), type = 'dgTMatrix'))
   user  system elapsed 
   0.00    0.00    1.95 
> 
> 
> 
> cleanEx()

detaching 'package:doParallel', 'package:parallel',
  'package:iterators', 'package:foreach'

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11600 (sockconn)
Execution halted
Running examples in 'TextForecast-Ex.R' failed
The error most likely occurred in:

> ### Name: tv_sentiment_index
> ### Title: tv sentiment index function
> ### Aliases: tv_sentiment_index
> 
> ### ** Examples
> 
> set.seed(1)
> data("stock_data")
> data("news_data")
> y=as.matrix(stock_data[,2])
> w=as.matrix(stock_data[,3])
> data("news_data")
> X=news_data[,2:ncol(news_data)]
> x=as.matrix(X)
> grid_alphas=0.25
> cont_folds=TRUE
> t=length(y)
> optimal_alphas=optimal_alphas(x[1:(t-1),],w[1:(t-1),],
+ y[2:t],grid_alphas,TRUE,"gaussian")
[1] 1
> tv_index <- tv_sentiment_index(x[1:(t-1),],w[1:(t-1),],y[2:t],
+ optimal_alphas[[1]],optimal_alphas[[2]],x,"gaussian",2)
Error in tv_sentiment_index(x[1:(t - 1), ], w[1:(t - 1), ], y[2:t], optimal_alphas[[1]],  : 
  There is no positive or negative coefficients. Try another alphas and lambdas.
Execution halted
phyper_right: no visible global function definition for 'dhyper'
progression: no visible global function definition for 'density'
progression: no visible global function definition for 'plot'
progression: no visible global function definition for 'points'
progression: no visible global function definition for 'legend'
progression: no visible global function definition for 'text'
specificities.distribution.plot: no visible global function definition
  for 'dhyper'
specificities.distribution.plot: no visible global function definition
  for 'plot'
specificities.distribution.plot: no visible global function definition
  for 'Axis'
specificities.distribution.plot: no visible global function definition
  for 'arrows'
specificities.distribution.plot: no visible global function definition
  for 'text'
specificities.distribution.plot: no visible global function definition
  for 'title'
specificities.probabilities.vector: no visible global function
  definition for 'phyper'
Undefined global functions or variables:
  Axis arrows density dhyper legend phyper plot points text title
Consider adding
  importFrom("graphics", "Axis", "arrows", "legend", "plot", "points",
             "text", "title")
  importFrom("stats", "density", "dhyper", "phyper")
to your NAMESPACE file.
transfer: no visible global function definition for 'rgamma'
transfer: no visible global function definition for 'rnorm'
transfer: no visible global function definition for 'rnbinom'
transfer: no visible global function definition for 'rpois'
transfer: no visible global function definition for 'rbinom'
transfer: no visible global function definition for 'runif'
plot,transfer: no visible global function definition for 'barplot'
plot,transfer: no visible global function definition for 'axis'
plot,transfer: no visible global function definition for 'par'
plot,transfer: no visible global function definition for 'hist'
Undefined global functions or variables:
  axis barplot hist par rbinom rgamma rnbinom rnorm rpois runif
Consider adding
  importFrom("graphics", "axis", "barplot", "hist", "par")
  importFrom("stats", "rbinom", "rgamma", "rnbinom", "rnorm", "rpois",
             "runif")
to your NAMESPACE file.
ParseTrueFX: no visible global function definition for 'read.csv'
TrueFXRef: no visible global function definition for 'download.file'
TrueFXRef: no visible global function definition for 'browseURL'
Undefined global functions or variables:
  browseURL download.file read.csv
Consider adding
  importFrom("utils", "browseURL", "download.file", "read.csv")
to your NAMESPACE file.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    rda    7.1Mb
Thinknum: no visible global function definition for 'URLencode'
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
coef_traceplot: no visible global function definition for 'rainbow'
coef_traceplot: no visible global function definition for 'plot'
coef_traceplot: no visible global function definition for 'abline'
coef_traceplot : <anonymous>: no visible global function definition for
  'lines'
coef_traceplot: no visible global function definition for 'text'
ee.GEE.aux : <anonymous>: no visible global function definition for
  'combn'
Undefined global functions or variables:
  abline combn lines plot rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "plot", "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
summary.tsls: no visible global function definition for 'printCoefmat'
threesls: no visible global function definition for 'cor'
threesls: no visible global function definition for 'pt'
tsls.formula: no visible global function definition for 'model.matrix'
tsls.formula: no visible global function definition for
  'model.response'
Undefined global functions or variables:
  cor model.matrix model.response printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.matrix", "model.response",
             "printCoefmat", "pt")
to your NAMESPACE file.
.LoadTickDataHK: no visible global function definition for 'read.csv'
.LoadTickDataSHSZ: no visible global function definition for 'read.csv'
DrawDown: no visible global function definition for 'na.omit'
PerformanceReport: no visible global function definition for
  'aggregate'
PerformanceReport: no visible global function definition for 'sd'
Undefined global functions or variables:
  aggregate na.omit read.csv sd
Consider adding
  importFrom("stats", "aggregate", "na.omit", "sd")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
newTiddler: no visible global function definition for 'new'
twImage: no visible global function definition for 'new'
twLink: no visible global function definition for 'new'
twList: no visible global function definition for 'new'
twTable: no visible global function definition for 'new'
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.4Mb
'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
'library' or 'require' call to 'boot' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'boot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
boot_autocov: no visible global function definition for 'is.ts'
boot_autocov: no visible global function definition for 'tsboot'
boot_autocov: no visible global function definition for 'quantile'
boot_autocov: no visible global function definition for 'par'
boot_autocov: no visible global function definition for 'frequency'
boot_autocov: no visible global function definition for 'polygon'
boot_autocov: no visible global function definition for 'lines'
boot_autocov: no visible global function definition for 'abline'
boot_autocov: no visible global function definition for 'acf'
boot_spec: no visible global function definition for 'is.ts'
boot_spec: no visible global function definition for 'tsboot'
boot_spec: no visible global function definition for 'spec.pgram'
boot_spec: no visible global function definition for 'quantile'
boot_spec: no visible global function definition for 'polygon'
boot_spec: no visible global function definition for 'lines'
redraw: no visible global function definition for 'spec.pgram'
statistic: no visible global function definition for 'acf'
Undefined global functions or variables:
  abline acf frequency is.ts lines par polygon quantile spec.pgram
  tsboot
Consider adding
  importFrom("graphics", "abline", "lines", "par", "polygon")
  importFrom("stats", "acf", "frequency", "is.ts", "quantile",
             "spec.pgram")
to your NAMESPACE file.
author.search: no visible binding for global variable 'na.omit'
reference.list: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
drawGraph: no visible global function definition for 'pdf'
drawGraph: no visible global function definition for 'par'
drawGraph: no visible global function definition for 'plot'
drawGraph: no visible global function definition for 'segments'
drawGraph: no visible global function definition for 'lines'
drawGraph: no visible global function definition for 'text'
drawGraph: no visible global function definition for 'dev.off'
drugRank: no visible global function definition for 'aggregate'
floating2: no visible global function definition for 'cor'
timma: no visible global function definition for 'median'
timma: no visible global function definition for 'write.table'
Undefined global functions or variables:
  aggregate cor dev.off lines median par pdf plot segments text
  write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "plot", "segments", "text")
  importFrom("stats", "aggregate", "cor", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc         3.7Mb
    rmarkdown   1.3Mb
tipom.car: no visible global function definition for 'abline'
tipom.car: no visible global function definition for 'axis'
tipom.heat: no visible global function definition for 'image'
tipom.heat: no visible global function definition for 'gray'
tipom.lw: no visible global function definition for 'plot'
tipom.lw: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline axis gray image plot
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "image", "plot")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'boot' 'lattice' 'splines' 'tcltk'
  Please remove these calls from your code.
ls.tree: no visible global function definition for 'lm'
ls.tree: no visible global function definition for 'coef'
Undefined global functions or variables:
  coef lm
Consider adding
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
FLXmclust.Density: no visible global function definition for 'dmvnorm'
FLXmclust.Estimate: no visible global function definition for 'flexmix'
FLXmclust.Estimate: no visible global function definition for
  'FLXmclust'
coefmclust: no visible global function definition for 'parameters'
flexmix.Density: no visible global function definition for
  'model.matrix'
flexmix.Density: no visible global function definition for
  'model.response'
flexmix.Density: no visible global function definition for
  'model.frame'
flexmix.Density: no visible global function definition for 'dnorm'
flexmix.Density: no visible global function definition for 'dpois'
flexmix.Density: no visible global function definition for 'dbinom'
flexmix.Estimate: no visible global function definition for 'flexmix'
flexmix.Estimate: no visible global function definition for 'FLXglm'
tleplot,TLE-data.frame: no visible global function definition for
  'legend'
Undefined global functions or variables:
  FLXglm FLXmclust dbinom dmvnorm dnorm dpois flexmix legend
  model.frame model.matrix model.response parameters
Consider adding
  importFrom("graphics", "legend")
  importFrom("stats", "dbinom", "dnorm", "dpois", "model.frame",
             "model.matrix", "model.response")
to your NAMESPACE file.
'library' or 'require' call to 'mvtnorm' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'mvtnorm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
EMN: no visible global function definition for 'dmvnorm'
EMN: no visible global function definition for 'pmvnorm'
EMT: no visible global function definition for 'GenzBretz'
EMT: no visible global function definition for 'dmvt'
EMT: no visible global function definition for 'pmvt'
MomemNT: no visible global function definition for 'pnorm'
MomemNT: no visible global function definition for 'dnorm'
MomemNT: no visible global function definition for 'pmvnorm'
MomemNT: no visible global function definition for 'dmvnorm'
TT.moment: no visible global function definition for 'GenzBretz'
TT.moment: no visible global function definition for 'pmvt'
TT.moment: no visible global function definition for 'dt'
TT.moment: no visible global function definition for 'pt'
TT.moment: no visible global function definition for 'dmvt'
cdfNI: no visible global function definition for 'pnorm'
cdfNI: no visible global function definition for 'pt'
inits: no visible global function definition for 'lm'
Undefined global functions or variables:
  GenzBretz dmvnorm dmvt dnorm dt lm pmvnorm pmvt pnorm pt
Consider adding
  importFrom("stats", "dnorm", "dt", "lm", "pnorm", "pt")
to your NAMESPACE file.
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    examples  19.2Mb
    include    2.9Mb
search_collection: no visible global function definition for
  'URLencode'
search_company: no visible global function definition for 'URLencode'
search_keyword: no visible global function definition for 'URLencode'
search_list: no visible global function definition for 'URLencode'
search_movie: no visible global function definition for 'URLencode'
search_multi: no visible global function definition for 'URLencode'
search_person: no visible global function definition for 'URLencode'
search_tv: no visible global function definition for 'URLencode'
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
Running examples in 'tm.plugin.lexisnexis-Ex.R' failed
The error most likely occurred in:

> ### Name: LexisNexisSource
> ### Title: LexisNexis Source
> ### Aliases: LexisNexisSource getElem.LexisNexisSource eoi.LexisNexisSource
> 
> ### ** Examples
> 
>     library(tm)
Loading required package: NLP
>     file <- system.file("texts", "lexisnexis_test_en.html",
+                         package = "tm.plugin.lexisnexis")
>     corpus <- Corpus(LexisNexisSource(file))
> 
>     # See the contents of the documents
>     inspect(corpus)
<<VCorpus>>
Metadata:  corpus specific: 0, document level (indexed): 0
Content:  documents: 2

[[1]]
<<PlainTextDocument>>
Metadata:  17
Content:  chars: 94

[[2]]
<<PlainTextDocument>>
Metadata:  17
Content:  chars: 66

> 
>     # See meta-data associated with first article
>     meta(corpus[[1]])
  author       : By PAPER AUTHOR
  datetimestamp: 1991-12-19
  description  : character(0)
  heading      : Heading One
  id           : SomeNewsp199112191
  language     : en
  origin       : Some Newspaper
  intro        : character(0)
  section      : Section 5; Part 2; Page 16; Column 2; National Desk
  subject      : character(0)
  coverage     : character(0)
  company      : character(0)
  stocksymbol  : character(0)
  industry     : character(0)
  type         : character(0)
  wordcount    : 584
  rights       : Copyright 1991 My Company
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()

detaching 'package:tm', 'package:NLP'

Error: connections left open:
	as.character(tree) (textConnection)
Execution halted
extractContentDOM: no visible global function definition for
  'capture.output'
extractHTMLStrip: no visible global function definition for
  'capture.output'
Undefined global functions or variables:
  capture.output
Consider adding
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'Rcampdf', 'Rpoppler', 'tm.lexicon.GeneralInquirer'
Package unavailable to check Rd xrefs: 'Rpoppler'
Package suggested but not available for checking: 'corpus.JSS.papers'
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
Tosls.formula: no visible global function definition for 'model.matrix'
Tosls.formula: no visible global function definition for
  'model.response'
summary: no visible global function definition for 'coef'
summary: no visible global function definition for 'pt'
Undefined global functions or variables:
  coef model.matrix model.response pt
Consider adding
  importFrom("stats", "coef", "model.matrix", "model.response", "pt")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'Cairo' 'RGtk2' 'colorspace' 'gWidgets' 'tourr'
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'TeachingDemos' 'ash'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'Cairo' 'RGtk2' 'colorspace' 'gWidgets' 'tourr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ConfA: no visible global function definition for 'qf'
EstM2Sn: no visible global function definition for 'nlm'
EstM2Sn: no visible global function definition for 'qnorm'
TV.model: no visible global function definition for 'dev.new'
TV.model: no visible global function definition for 'points'
betaBino: no visible global function definition for 'pbinom'
doseD: no visible global function definition for 'lm'
doseD: no visible global function definition for 'dev.new'
doseD: no visible global function definition for 'par'
doseD: no visible global function definition for 'plot'
doseD: no visible global function definition for 'axTicks'
doseD: no visible global function definition for 'axis'
doseD: no visible global function definition for 'lines'
doseD: no visible global function definition for 'abline'
doseD: no visible global function definition for 'legend'
setD: no visible global function definition for 'dev.new'
setD: no visible global function definition for 'par'
setD: no visible global function definition for 'pbinom'
setD: no visible global function definition for 'abline'
setD: no visible global function definition for 'axis'
setD: no visible global function definition for 'rect'
setD: no visible global function definition for 'lines'
setD: no visible global function definition for 'text'
setD: no visible global function definition for 'axTicks'
setD: no visible global function definition for 'legend'
spoD : spoD_A: no visible global function definition for 'chisq.test'
Undefined global functions or variables:
  abline axTicks axis chisq.test dev.new legend lines lm nlm par pbinom
  plot points qf qnorm rect text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axTicks", "axis", "legend", "lines",
             "par", "plot", "points", "rect", "text")
  importFrom("stats", "chisq.test", "lm", "nlm", "pbinom", "qf", "qnorm")
to your NAMESPACE file.
align1d : obj: no visible global function definition for 'dist'
align2d : obj: no visible global function definition for 'dist'
align2d : pen: no visible global function definition for 'dist'
align2d: no visible global function definition for 'dist'
sumt: no visible global function definition for 'optim'
tpe1d: no visible global function definition for 'hclust'
tpe2d: no visible global function definition for 'hclust'
tpe2d: no visible global function definition for 'cmdscale'
Undefined global functions or variables:
  cmdscale dist hclust optim
Consider adding
  importFrom("stats", "cmdscale", "dist", "hclust", "optim")
to your NAMESPACE file.
Package in Depends field not imported from: 'lgtdl'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ci.plot: no visible global function definition for 'gaussian'
ci.plot: no visible global function definition for 'qnorm'
ci.plot: no visible global function definition for 'plot'
ci.plot: no visible global function definition for 'lines'
cst.fit.ff: no visible global function definition for 'pnorm'
cstfit.1: no visible global function definition for 'var'
gof.test.boots.pf: no visible binding for global variable 'sd'
gof.test.int.1.ff: no visible global function definition for 'quantile'
gof.test.int.1.ff: no visible global function definition for 'var'
gof.test.int.ff: no visible global function definition for 'pnorm'
gofTest: no visible binding for global variable 'sd'
plotGof: no visible global function definition for 'plot'
plotGof : <anonymous>: no visible global function definition for
  'lines'
plotGof: no visible global function definition for 'lines'
sig.test.int.1.ff: no visible global function definition for 'quantile'
sig.test.int.1.ff: no visible global function definition for 'var'
sig.test.int.ff: no visible global function definition for 'pnorm'
test.boots.1: no visible binding for global variable 'sd'
tpr: no visible global function definition for 'poisson'
tpr: no visible global function definition for 'glm.fit'
tpr: no visible global function definition for 'coef'
tpr: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx coef gaussian glm.fit lines plot pnorm poisson qnorm quantile
  sd var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "approx", "coef", "gaussian", "glm.fit", "pnorm",
             "poisson", "qnorm", "quantile", "sd", "var")
to your NAMESPACE file.
File 'tpr/libs/i386/tpr.dll':
  Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
    Object: 'utils.o'
File 'tpr/libs/x64/tpr.dll':
  Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
    Object: 'utils.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
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.
Package suggested but not available for checking: 'taxidata'
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.
Running examples in 'treatSens-Ex.R' failed
The error most likely occurred in:

> ### Name: treatSens.BART
> ### Title: Dual-Parameter Sensitivity Analysis Using BART
> ### Aliases: treatSens.BART
> 
> ### ** Examples
> 
> N <- 250                      # number of observations
> 
> zetay <- 0.5                  # coefficient on U in the outcome model
> zetaz <- 0.5                  # coefficient on U in the treatment model
> betaz <- c(0.75, -0.5,  0.25) # coefficients of X in the treatment model
> betay <- c(0.5,   1.0, -1.5)  # coefficients of X in the outcome model
> tau   <- 0.25                 # treatment effect
> 
> set.seed(725)
> X <- matrix(rnorm(3 * N), N)  # covariates
> 
> U  <- rbinom(N, 1, 0.5)                        # unmeasured confounder
> ps <- pnorm(X %*% betaz + zetaz * (U - 0.5)) # propensity score
> Z  <- rbinom(N, 1, ps)                         # treatment variable
> epsilon <- rnorm(N, 0.0, 2.0)                  # error term
> 
> Y0 <- X %*% betay + zetay * (U - 0.5) + epsilon       # potential outcome(Z=0)
> Y1 <- X %*% betay + zetay * (U - 0.5) + tau + epsilon # potential outcome(Z=1)
> Y  <- Y0 * (1 - Z) + Y1 * Z                             # realization of potential outcome
> 
> # sensitivity analysis
> out.bin <- treatSens.BART(Y ~ Z + X, nsim = 3, nthin = 2, nburn = 0,
+                           spy.range = c(0, 4), spz.range = c(-2 , 2), grid.dim = c(5, 3),
+                           standardize = FALSE, verbose = TRUE)
Warning in model.matrix.default(mt, mf, contrasts) :
  non-list contrasts argument ignored
Warning in model.matrix.default(mt, mf, contrasts) :
  non-list contrasts argument ignored
Binary U with binomial distribution is assumed.
"ATE" option is selected. Sensitivity analysis is performed with the default Weights for the average treatment effect.
Weight trimming is applied.  The maximum size of weights is set to 25 , which is 10 % of the size of the inferential group.
Computing final grid...
Build_JTree: no visible global function definition for 'flush.console'
Run_JTree: no visible global function definition for 'cov2cor'
Undefined global functions or variables:
  cov2cor flush.console
Consider adding
  importFrom("stats", "cov2cor")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
LikAge: no visible global function definition for 'read.table'
bd.ME.optim: no visible global function definition for 'optim'
bd.ME.optim.rho: no visible global function definition for 'optim'
bd.ME.optim.rho.all: no visible global function definition for 'optim'
bd.MEyule.optim: no visible global function definition for 'optimize'
bd.MEyule.optim: no visible global function definition for 'optim'
bd.age.optim.matlab: no visible global function definition for
  'read.table'
bd.groups.conf: no visible global function definition for 'uniroot'
bd.shifts.plot: no visible global function definition for 'plot'
bd.shifts.plot: no visible global function definition for 'lines'
bdsky.stt.optim: no visible global function definition for 'optim'
create.mat: no visible global function definition for 'write.table'
Undefined global functions or variables:
  lines optim optimize plot read.table uniroot write.table
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "optim", "optimize", "uniroot")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
plot.treeperm: no visible global function definition for 'hist'
plot.treeperm: no visible global function definition for 'points'
plot.treeperm: no visible global function definition for 'text'
treeperm.formula: no visible global function definition for
  'model.frame'
treeperm.formula: no visible global function definition for
  'model.response'
Undefined global functions or variables:
  hist model.frame model.response points text
Consider adding
  importFrom("graphics", "hist", "points", "text")
  importFrom("stats", "model.frame", "model.response")
to your NAMESPACE file.
Running examples in 'treeplyr-Ex.R' failed
The error most likely occurred in:

> ### Name: group_by_.treedata
> ### Title: Function for grouping an object of class 'treedata'
> ### Aliases: group_by_.treedata group_by.treedata ungroup.grouped_treedata
> 
> ### ** Examples
> 
> data(anolis)
> td <- make.treedata(anolis$phy, anolis$dat)
> tdGrouped <- group_by(td, ecomorph)
> summarize(tdGrouped, ntips = length(phy$tip.label), 
+    totalBL = sum(phy$edge.length), meanSVL = mean(SVL), sdSVL = sd(SVL))
Error in envs[[i]] : subscript out of bounds
Calls: summarize -> summarise.grouped_treedata
Execution halted
Running examples in 'TreeSim-Ex.R' failed
The error most likely occurred in:

> ### Name: sim.bd.age
> ### Title: sim.bd.age: Simulating birth-death trees of a fixed age.
> ### Aliases: sim.bd.age
> 
> ### ** Examples
> 
> age<-2
> lambda <- 2.0
> mu <- 0.5
> frac <-0.6
> numbsim<-3
> 
> ##
> # Simulating trees with time age since the origin:
> 
> sim.bd.age(age,numbsim,lambda,mu,mrca=FALSE,complete=TRUE)
[[1]]

Phylogenetic tree with 117 tips and 116 internal nodes.

Tip labels:
	t51, t46, t102, t11, t8, t87, ...

Rooted; includes branch lengths.

[[2]]
[1] 0

[[3]]
[1] 0

> sim.bd.age(age,numbsim,lambda,mu,frac,mrca=FALSE,complete=FALSE)
Warning in max(oldnodes) :
  no non-missing arguments to max; returning -Inf
Error in integer(max(oldnodes)) : vector size cannot be infinite
Calls: sim.bd.age ... drop.extinct -> .drop.tip -> collapse.singles -> integer
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    4.7Mb
    libs   1.5Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
cinbag: no visible global function definition for 'var'
trimTrees: no visible global function definition for 'predict'
Undefined global functions or variables:
  predict var
Consider adding
  importFrom("stats", "predict", "var")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'gtools' 'mgcv'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'gtools' 'mgcv' 'msm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
HtoGp: no visible global function definition for 'odd'
HtoGp: no visible global function definition for 'even'
plot.pirls.gam: no visible global function definition for 'par'
plot.pirls.gam: no visible global function definition for 'plot'
plot.pirls.gam: no visible global function definition for 'title'
plot.pirls.gam: no visible global function definition for 'lines'
plot.pirls.gam: no visible global function definition for 'rug'
plot.pirls.gam: no visible global function definition for 'mtext'
test.trioGxE: no visible global function definition for 'write.table'
trioGxE: no visible global function definition for 'quantile'
trioGxE: no visible global function definition for 'qtnorm'
trioplot: no visible global function definition for 'quantile'
trioplot: no visible global function definition for 'formula'
trioplot: no visible global function definition for 'gam'
trioplot: no visible global function definition for 'binomial'
Undefined global functions or variables:
  binomial even formula gam lines mtext odd par plot qtnorm quantile
  rug title write.table
Consider adding
  importFrom("graphics", "lines", "mtext", "par", "plot", "rug", "title")
  importFrom("stats", "binomial", "formula", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
DrawMargin: no visible global function definition for 'qnorm'
DrawProbability: no visible global function definition for 'pnorm'
Factor: no visible global function definition for 'new'
Gaussian: no visible global function definition for 'new'
LikelihoodFactor: no visible global function definition for 'new'
Parameters: no visible global function definition for 'new'
Player: no visible global function definition for 'new'
PriorFactor: no visible global function definition for 'new'
SumFactor: no visible global function definition for 'new'
TruncateFactor: no visible global function definition for 'new'
Variable: no visible global function definition for 'new'
Vdraw: no visible global function definition for 'dnorm'
Vdraw: no visible global function definition for 'pnorm'
Vwin: no visible global function definition for 'dnorm'
Vwin: no visible global function definition for 'pnorm'
Wdraw: no visible global function definition for 'dnorm'
Wdraw: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dnorm new pnorm qnorm
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "dnorm", "pnorm", "qnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
cdens: no visible global function definition for 'head'
dplot: no visible global function definition for 'knots'
dplot: no visible global function definition for 'median'
dplot: no visible global function definition for 'par'
dplot: no visible global function definition for 'plot.stepfun'
dplot: no visible global function definition for 'abline'
edf: no visible global function definition for 'approxfun'
mctest : rdist: no visible global function definition for 'runif'
mctest : S: no visible global function definition for 'optim'
qplot: no visible global function definition for 'plot'
qplot: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline approxfun head knots median optim par plot plot.stepfun runif
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("stats", "approxfun", "knots", "median", "optim",
             "plot.stepfun", "runif")
  importFrom("utils", "head")
to your NAMESPACE file.
dmvnb: no visible global function definition for 'dbinom'
drvts: no visible global function definition for 'dnorm'
drvts: no visible global function definition for 'dbinom'
dsvts: no visible global function definition for 'dnorm'
rescale: no visible global function definition for 'qlogis'
rescale: no visible global function definition for 'plogis'
tslogl: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dbinom dnorm plogis qlogis
Consider adding
  importFrom("stats", "dbinom", "dnorm", "plogis", "qlogis")
to your NAMESPACE file.
tfDetails: no visible global function definition for 'start'
tfDetails: no visible global function definition for 'end'
Undefined global functions or variables:
  end start
Consider adding
  importFrom("stats", "end", "start")
to your NAMESPACE file.
Qhat: no visible global function definition for 'pnorm'
plrt: no visible global function definition for 'uniroot'
plrt: no visible global function definition for 'optimize'
simulatedata: no visible global function definition for 'rnorm'
tsc.test: no visible global function definition for 'shapiro.test'
tsc.test: no visible global function definition for 'p.adjust'
tsc.test: no visible global function definition for 'glm'
tsc.test : f: no visible global function definition for 'pnorm'
tsc.test: no visible global function definition for 'uniroot'
tsc.test: no visible global function definition for 'optimize'
variance: no visible global function definition for 'density'
variance: no visible global function definition for 'ecdf'
Undefined global functions or variables:
  density ecdf glm optimize p.adjust pnorm rnorm shapiro.test uniroot
Consider adding
  importFrom("stats", "density", "ecdf", "glm", "optimize", "p.adjust",
             "pnorm", "rnorm", "shapiro.test", "uniroot")
to your NAMESPACE file.
vintageMap: no visible global function definition for 'read.table'
TSget,character-TSfameLocalConnection: no visible global function
  definition for 'as.ts'
TSget,character-TSfameLocalConnection: no visible global function
  definition for 'zoo'
TSget,character-TSfameLocalConnection: no visible global function
  definition for 'frequency'
TSget,character-TSfameServerConnection: no visible global function
  definition for 'as.ts'
TSget,character-TSfameServerConnection: no visible global function
  definition for 'zoo'
TSget,character-TSfameServerConnection: no visible global function
  definition for 'frequency'
Undefined global functions or variables:
  as.ts frequency read.table zoo
Consider adding
  importFrom("stats", "as.ts", "frequency")
  importFrom("utils", "read.table")
to your NAMESPACE file.
DstandardizedLoadings.TSFmodel: no visible global function definition
  for 'cov'
FAfitStats.TSFmodel: no visible global function definition for 'cov'
FAfitStats.default: no visible global function definition for 'cor'
FAfitStats.default: no visible global function definition for
  'factanal'
FAfitStats.default: no visible global function definition for 'pchisq'
FAmodelFitStats: no visible global function definition for 'pchisq'
checkResiduals.TSFmodel: no visible global function definition for
  'cov'
distribution.factorsEstEval: no visible global function definition for
  'par'
distribution.factorsEstEval: no visible binding for global variable
  'par'
distribution.factorsEstEval: no visible global function definition for
  'density'
distribution.factorsEstEval: no visible global function definition for
  'matplot'
distribution.factorsEstEval: no visible global function definition for
  'title'
summary.TSFmodel: no visible global function definition for 'start'
summary.TSFmodel: no visible global function definition for 'end'
Undefined global functions or variables:
  cor cov density end factanal matplot par pchisq start title
Consider adding
  importFrom("graphics", "matplot", "par", "title")
  importFrom("stats", "cor", "cov", "density", "end", "factanal",
             "pchisq", "start")
to your NAMESPACE file.
Func.SAX: no visible global function definition for 'sd'
Func.SAX: no visible global function definition for 'qnorm'
Func.matrix: no visible global function definition for 'qnorm'
Func.motif: no visible global function definition for 'sd'
Func.motif: no visible global function definition for 'na.omit'
Func.motif: no visible global function definition for 'combn'
Func.motif.multivariate: no visible global function definition for
  'txtProgressBar'
Func.motif.multivariate: no visible global function definition for
  'setTxtProgressBar'
Undefined global functions or variables:
  combn na.omit qnorm sd setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit", "qnorm", "sd")
  importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
dLag : dlag.f: no visible global function definition for
  'complete.cases'
distmat: no visible global function definition for 'dist'
fitCity: no visible global function definition for 'glm.control'
fitCity: no visible global function definition for 'terms'
ldmvnorm: no visible global function definition for 'mahalanobis'
lspline: no visible global function definition for 'quantile'
plot.tsdecomp: no visible global function definition for 'par'
plot.tsdecomp: no visible global function definition for 'plot'
setupFormula: no visible global function definition for 'as.formula'
spatialgibbs: no visible global function definition for 'rnorm'
spatialgibbs: no visible global function definition for 'rgamma'
spatialgibbs: no visible global function definition for 'runif'
tsdecomp: no visible global function definition for 'fft'
Undefined global functions or variables:
  as.formula complete.cases dist fft glm.control mahalanobis par plot
  quantile rgamma rnorm runif terms
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "as.formula", "complete.cases", "dist", "fft",
             "glm.control", "mahalanobis", "quantile", "rgamma", "rnorm",
             "runif", "terms")
to your NAMESPACE file.
covTranspose11: warning in glasso(sc, 2 * rhoc/n, wi.init = gc$wi,
  w.init = gc$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
covTranspose11: warning in glasso(sr, 2 * rhor/p, wi.init = gr$wi,
  w.init = gr$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
.help.ESS: no visible global function definition for 'index.search'
TransSphere : ttin: no visible global function definition for 't.test'
TransSphere: no visible global function definition for 'sd'
TransSphere: no visible global function definition for 'quantile'
TransSphere: no visible global function definition for 'pt'
Undefined global functions or variables:
  index.search pt quantile sd t.test
Consider adding
  importFrom("stats", "pt", "quantile", "sd", "t.test")
to your NAMESPACE file.
TT.GS : TT.GS.sp: no visible global function definition for 'qt'
TT.GS : TT.GS.sp: no visible global function definition for 'runif'
TT.GS : TT.GS.sp: no visible global function definition for 'pt'
TT.moment: no visible global function definition for 'dt'
TT.moment: no visible global function definition for 'pt'
Undefined global functions or variables:
  dt pt qt runif
Consider adding
  importFrom("stats", "dt", "pt", "qt", "runif")
to your NAMESPACE file.
.saveDevice: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  dev.off
Consider adding
  importFrom("grDevices", "dev.off")
to your NAMESPACE file.
ttwa: no visible global function definition for 'aggregate'
ttwa: no visible global function definition for 'txtProgressBar'
ttwa: no visible global function definition for 'setTxtProgressBar'
Undefined global functions or variables:
  aggregate setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "aggregate")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
http.connection: no visible global function definition for 'setNames'
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
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.
TwoCop: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
txtacf: no visible binding for global variable 'na.fail'
txtacf: no visible global function definition for 'acf'
txtboxplot : <anonymous>: no visible global function definition for
  'boxplot.stats'
txtboxplot: no visible global function definition for 'boxplot.stats'
txtdensity: no visible global function definition for 'density'
Undefined global functions or variables:
  acf boxplot.stats density na.fail
Consider adding
  importFrom("grDevices", "boxplot.stats")
  importFrom("stats", "acf", "density", "na.fail")
to your NAMESPACE file.
Crm: no visible global function definition for 'integrate'
Crm : <anonymous>: no visible global function definition for
  'integrate'
Crm: no visible global function definition for 'optimize'
ail1: no visible global function definition for 'uniroot'
ail2 : fu : <anonymous>: no visible global function definition for
  'integrate'
ail2: no visible global function definition for 'uniroot'
aip : fu : <anonymous>: no visible global function definition for
  'integrate'
aip: no visible global function definition for 'uniroot'
ait1: no visible global function definition for 'uniroot'
ait2 : fu : <anonymous>: no visible global function definition for
  'integrate'
ait2: no visible global function definition for 'uniroot'
sim3p3: no visible global function definition for 'rbinom'
simCrm: no visible global function definition for 'rbinom'
simCrm: no visible global function definition for 'palette'
simCrm: no visible global function definition for 'gray'
simCrm: no visible global function definition for 'plot'
simCrm: no visible global function definition for 'abline'
simCrm: no visible global function definition for 'lines'
ssim3p3: no visible global function definition for 'txtProgressBar'
ssim3p3: no visible global function definition for 'setTxtProgressBar'
ssimCrm: no visible global function definition for 'txtProgressBar'
ssimCrm: no visible global function definition for 'setTxtProgressBar'
Undefined global functions or variables:
  abline gray integrate lines optimize palette plot rbinom
  setTxtProgressBar txtProgressBar uniroot
Consider adding
  importFrom("grDevices", "gray", "palette")
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "integrate", "optimize", "rbinom", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
rmd2pdf: no visible global function definition for 'tail'
rnw2pdf: no visible global function definition for 'tail'
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc         5.3Mb
    dummydata   1.4Mb
    libs        4.2Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    8.3Mb
ubRacing : predCandidate: no visible global function definition for
  'predict'
ubRacing : aux2.friedman.edit: no visible global function definition
  for 'pchisq'
ubRacing : aux2.friedman.edit: no visible global function definition
  for 'qt'
ubRacing : aux.friedman.edit: no visible global function definition for
  'wilcox.test'
ubRacing : aux.ttest.edit: no visible global function definition for
  't.test'
ubRacing : aux.ttest.edit: no visible global function definition for
  'p.adjust'
ubRacing : idFolds: no visible global function definition for
  'quantile'
ubRacing: no visible binding for global variable 'sd'
ubSmoteExs: no visible global function definition for 'runif'
Undefined global functions or variables:
  p.adjust pchisq predict qt quantile runif sd t.test wilcox.test
Consider adding
  importFrom("stats", "p.adjust", "pchisq", "predict", "qt", "quantile",
             "runif", "sd", "t.test", "wilcox.test")
to your NAMESPACE file.
med: no visible global function definition for 'quantile'
uh: no visible global function definition for 'mad'
uh.bu: no visible global function definition for 'mad'
Undefined global functions or variables:
  mad quantile
Consider adding
  importFrom("stats", "mad", "quantile")
to your NAMESPACE file.
Running 'test_unifDAG.R' [7s]
Running the tests in 'tests/test_unifDAG.R' failed.
Complete output:
  > library(unifDAG)
  > 
  > my.wgtMatrix <- function(g, transpose = TRUE) {
  +   res <- as(g, "matrix") # from 'graph' package, now reliable (we hope)
  +   if (transpose) ## default!
  +     t(res) else res
  + }
  > 
  > ## exact
  > set.seed(123)
  > n <- 2
  > reps <- 100
  > res <- matrix(0, reps, 3)
  > for (i in 1:reps) {
  +     gAM <- unifDAG(n)
  +     wm <- my.wgtMatrix(gAM)
  +     if (wm[1,2] != 0) {
  +         res[i,1] <- 1
  +     } else {
  +           if (wm[2,1] != 0) {
  +               res[i,2] <- 1
  +           } else {
  +                 res[i,3] <- 1
  +             }
  +       }
  + }
  > if (!all(round(colMeans(res), 2) == c(0.41, 0.31, 0.28))) {
  +     stop("test_unifDAG: Saved result could not be reproduced (unifDAG).")
  + }
  Error: test_unifDAG: Saved result could not be reproduced (unifDAG).
  Execution halted
dudewicz.unif.test: no visible global function definition for 'runif'
frosini.unif.test: no visible global function definition for 'runif'
hegazy.unif.test: no visible global function definition for 'runif'
kolmogorov.unif.test: no visible global function definition for 'runif'
kuiper.unif.test: no visible global function definition for 'runif'
neyman.unif.test: no visible global function definition for 'runif'
quesenberry.unif.test: no visible global function definition for
  'runif'
sarkadi.unif.test: no visible global function definition for 'runif'
sherman.unif.test: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
cumcount: no visible global function definition for 'setNames'
uniqtag: no visible global function definition for 'setNames'
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    1.6Mb
    libs   1.9Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.6/UpSetR.Rcheck/00install.out' for details.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
Package suggested but not available for checking: 'USAboundariesData'
readSEER: no visible global function definition for 'read.fwf'
Undefined global functions or variables:
  read.fwf
Consider adding
  importFrom("utils", "read.fwf")
to your NAMESPACE file.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'UScensus2000cdp/R/zzz.R':
  .First.lib calls:
    cat(paste("'", ehelp[4], "'\n", "Version ", ehelp[2], " created on ",     ehelp[3], ".\n", sep = ""))
    cat(paste(substring(ehelp[3], first = 16), "\n", "Version ",     substring(ehelp[4], first = 16), " created on ", substring(ehelp[5],         first = 16), ".\n", sep = ""))
    cat(paste("copyright (c) 2009, Zack W. Almquist, University of California-Irvine\n",     sep = ""))
    cat("For citation information, type citation(\"UScensus2000cdp\").\n")
    cat("Type help(package=\"UScensus2000cdp\") to get started.\n")

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

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
Found the following hidden files and directories:
  data/.Rhistory
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
'library' or 'require' call to 'rgdal' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'foreign' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running 'testthat.R' [19s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(utiml)
  Loading required package: mldr
  Loading required package: parallel
  > 
  > test_check("utiml")
  -- 1. Failure: Bipartition measures (@test_evaluation.R#153)  ------------------
  mean(utiml_measure_macro_f1(mlconfmat)) not equal to measures$MacroFMeasure.
  1/1 mismatches
  [1] 0.275 - NaN == NaN
  
  -- 2. Failure: iterative kfold (@test_sampling.R#238)  -------------------------
  length(f1$fold[[2]]) not equal to 25.
  1/1 mismatches
  [1] 24 - 25 == -1
  
  == testthat results  ===========================================================
  OK: 1155 SKIPPED: 21 FAILED: 2
  1. Failure: Bipartition measures (@test_evaluation.R#153) 
  2. Failure: iterative kfold (@test_sampling.R#238) 
  
  Error: testthat unit tests failed
  Execution halted
File 'uuid/libs/i386/uuid.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'gen_uuid.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'gen_uuid.o'
File 'uuid/libs/x64/uuid.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'gen_uuid.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'gen_uuid.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
histw: no visible global function definition for 'plot.new'
histw: no visible global function definition for 'plot.window'
histw: no visible global function definition for 'axis'
histw: no visible global function definition for 'rect'
histw: no visible global function definition for 'lines'
uwham.boot: no visible binding for global variable 'var'
Undefined global functions or variables:
  axis lines plot.new plot.window rect var
Consider adding
  importFrom("graphics", "axis", "lines", "plot.new", "plot.window",
             "rect")
  importFrom("stats", "var")
to your NAMESPACE file.
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    libs  23.2Mb
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("vanddraabe")
  Loading required package: vanddraabe
  -- 1. Failure: the correct mobility values are returned (@test-BoundWaterEnviron
  Mobility(Bvalues, occupancy) not equal to `mobility.answer`.
  14/14 mismatches (average diff: 0.0382)
  [1] 0.224 - 0.225 == -0.00168
  [2] 0.373 - 0.375 == -0.00280
  [3] 0.471 - 0.474 == -0.00354
  [4] 0.621 - 0.626 == -0.00467
  [5] 0.706 - 0.676 ==  0.03025
  [6] 0.824 - 0.876 == -0.05229
  [7] 0.993 - 0.948 ==  0.04521
  [8] 1.006 - 1.013 == -0.00756
  [9] 1.242 - 1.126 ==  0.11578
  ...
  
  -- 2. Failure: counting AtomTypes works (@test-utilities.R#102)  ---------------
  getAtomTypeCounts(atom.types) not equal to `ATCounts.answer`.
  56/167 mismatches (average diff: 5.09)
  [4]  0 - 1 == -1
  [9]  0 - 8 == -8
  [11] 0 - 7 == -7
  [14] 7 - 1 ==  6
  [15] 1 - 0 ==  1
  [18] 0 - 1 == -1
  [21] 0 - 1 == -1
  [23] 0 - 4 == -4
  [31] 1 - 0 ==  1
  ...
  
  == testthat results  ===========================================================
  OK: 63 SKIPPED: 0 FAILED: 2
  1. Failure: the correct mobility values are returned (@test-BoundWaterEnvironments.R#71) 
  2. Failure: counting AtomTypes works (@test-utilities.R#102) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 78.6Mb
  sub-directories of 1Mb or more:
    gdal   3.8Mb
    libs  68.7Mb
    proj   5.0Mb
Mammen: no visible global function definition for 'runif'
PR2: no visible global function definition for 'ar.burg'
PR2: no visible global function definition for 'pt'
PR2: no visible global function definition for 'pf'
PR3: no visible global function definition for 'ar.burg'
PR3: no visible global function definition for 'pt'
PR3: no visible global function definition for 'pf'
VAR.FOR: no visible global function definition for 'qnorm'
VAR.ForeB: no visible global function definition for 'runif'
VAR.LRtest: no visible global function definition for 'pchisq'
VAR.LRtest: no visible global function definition for 'pf'
VAR.PI: no visible global function definition for 'quantile'
VAR.Waldtest: no visible global function definition for 'pf'
VAR.irf: no visible global function definition for 'par'
VAR.irf: no visible global function definition for 'plot'
VAR.irf: no visible global function definition for 'abline'
VAR1.sim: no visible global function definition for 'rnorm'
resamp: no visible global function definition for 'runif'
Undefined global functions or variables:
  abline ar.burg par pchisq pf plot pt qnorm quantile rnorm runif
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("stats", "ar.burg", "pchisq", "pf", "pt", "qnorm",
             "quantile", "rnorm", "runif")
to your NAMESPACE file.
black_scholes: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
burdenPlot: no visible global function definition for 'density'
burdenPlot: no visible global function definition for 'axis'
burdenPlot: no visible global function definition for 'points'
burdenPlot: no visible global function definition for 'lines'
burdenPlot: no visible global function definition for 'abline'
burdenPlot: no visible global function definition for 'text'
burdenPlot: no visible global function definition for 'sd'
burdenPlot: no visible global function definition for 'segments'
vbdm: no visible global function definition for 'var'
vbdm: no visible global function definition for 'pchisq'
vbdmR : run_discrete_mixture_vanilla: no visible global function
  definition for 'var'
vbdmR: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  abline axis density lines pchisq points sd segments text var
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "points", "segments",
             "text")
  importFrom("stats", "density", "pchisq", "sd", "var")
to your NAMESPACE file.
compute_KL : rtnorm: no visible global function definition for 'runif'
compute_KL : rtnorm: no visible global function definition for 'dnorm'
compute_KL: no visible global function definition for 'qnorm'
compute_KL: no visible global function definition for 'dnorm'
compute_KL: no visible global function definition for 'pnorm'
compute_KL: no visible global function definition for 'var'
compute_KL: no visible global function definition for 'rbinom'
compute_KL: no visible global function definition for 'rnorm'
compute_KL: no visible global function definition for 'sd'
vbsr: no visible global function definition for 'qchisq'
vbsr: no visible global function definition for 'var'
vbsr: no visible global function definition for 'pchisq'
vbsr: no visible global function definition for 'sd'
vbsr: no visible binding for global variable 'sd'
Undefined global functions or variables:
  dnorm pchisq pnorm qchisq qnorm rbinom rnorm runif sd var
Consider adding
  importFrom("stats", "dnorm", "pchisq", "pnorm", "qchisq", "qnorm",
             "rbinom", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
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.
Running examples in 'VDA-Ex.R' failed
The error most likely occurred in:

> ### Name: cv.vda.le
> ### Title: Choose the optimal pair of lambdas, lambda_1 and lambda_2
> ### Aliases: cv.vda.le cv.vda.le.default
> 
> ### ** Examples
> 
> ### load zoo data
> ### column 1 is name, columns 2:17 are features, column 18 is class
> data(zoo)
> 
> ### feature matrix 
> x <- zoo[,2:17]
> 
> ### class vector
> y <- zoo[,18]
> 
> ### lambda vector
> lam1 <- (1:5)/100
> lam2 <- (1:5)/100
> 
> ### Searching for the best pair, using both lasso and euclidean penalizations
> cv <- cv.vda.le(x, y, kfold = 3, lam.vec.1 = exp(1:5)/10000, lam.vec.2 = (1:5)/100)
At line 567 of file VDA.f90
Fortran runtime error: Index '7' of dimension 2 of array 'vertex' outside of expected range (1:6)
Compare2FDS: no visible global function definition for 'runif'
Compare2FDS: no visible global function definition for 'lm'
Compare2FDS: no visible global function definition for 'model.matrix'
Compare2FDS: no visible global function definition for 'plot'
Compare2FDS: no visible global function definition for 'abline'
Compare2FDS: no visible global function definition for 'lines'
Compare2FDS: no visible global function definition for 'text'
Compare2Vdg: no visible global function definition for 'par'
Compare2Vdg: no visible global function definition for 'plot'
Compare2Vdg: no visible global function definition for 'lines'
Compare2Vdg: no visible global function definition for 'legend'
FDSPlot: no visible global function definition for 'runif'
FDSPlot: no visible global function definition for 'lm'
FDSPlot: no visible global function definition for 'model.matrix'
FDSPlot: no visible global function definition for 'plot'
FDSPlot: no visible global function definition for 'abline'
Vdgraph: no visible global function definition for 'par'
Vdgraph: no visible global function definition for 'plot'
Vdgraph: no visible global function definition for 'lines'
Vdgraph: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline legend lines lm model.matrix par plot runif text
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "plot",
             "text")
  importFrom("stats", "lm", "model.matrix", "runif")
to your NAMESPACE file.
calculateParameters,AffineTransformation: no visible global function
  definition for 'lm'
calculateParameters,AffineTransformation: no visible global function
  definition for 'coef'
calculateParameters,SimilarityTransformation: no visible global
  function definition for 'lm'
calculateParameters,SimilarityTransformation: no visible global
  function definition for 'coef'
plotGridTransformation,Cartesian2DCoordinateTransformation: no visible
  global function definition for 'points'
plotGridTransformation,Cartesian2DCoordinateTransformation: no visible
  global function definition for 'legend'
Undefined global functions or variables:
  coef legend lm points
Consider adding
  importFrom("graphics", "legend", "points")
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
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: 'Die Serververbindung wurde zurückgesetzt.'
Error in file(con, "r") : cannot open the connection
Calls: from_spec -> readLines -> file
Execution halted
'library' or 'require' call to 'stats' which was already attached by Depends.
  Please remove these calls from your code.
plot.VennDiagram : <anonymous>: no visible global function definition
  for 'hcl'
plot.VennDiagram: no visible global function definition for 'plot.new'
plot.VennDiagram: no visible global function definition for
  'plot.window'
plot.VennDiagram: no visible global function definition for 'col2rgb'
plot.VennDiagram: no visible global function definition for 'rgb'
plot.VennDiagram: no visible global function definition for 'polygon'
plot.VennDiagram: no visible global function definition for 'text'
plot.VennDiagram: no visible global function definition for 'title'
Undefined global functions or variables:
  col2rgb hcl plot.new plot.window polygon rgb text title
Consider adding
  importFrom("grDevices", "col2rgb", "hcl", "rgb")
  importFrom("graphics", "plot.new", "plot.window", "polygon", "text",
             "title")
to your NAMESPACE file.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    doc    1.2Mb
    help   2.8Mb
    libs   1.3Mb
vif: no visible global function definition for 'sd'
vif: no visible global function definition for 'lm'
vif: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  lm pnorm sd
Consider adding
  importFrom("stats", "lm", "pnorm", "sd")
to your NAMESPACE file.
hyperpara: no visible binding for global variable 'var'
hyperpara: no visible global function definition for 'hist'
Undefined global functions or variables:
  hist var
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "var")
to your NAMESPACE file.
panel.meansdplot : meansdplot.stats: no visible global function
  definition for 'sd'
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
viopoints.default: no visible global function definition for 'par'
viopoints.default: no visible global function definition for 'plot.new'
viopoints.default: no visible global function definition for
  'plot.window'
viopoints.default: no visible global function definition for 'axis'
viopoints.default: no visible global function definition for 'arrows'
viopoints.default: no visible global function definition for
  'getFromNamespace'
viopoints.default: no visible global function definition for 'title'
viopoints.default: no visible global function definition for 'box'
Undefined global functions or variables:
  arrows axis box getFromNamespace par plot.new plot.window title
Consider adding
  importFrom("graphics", "arrows", "axis", "box", "par", "plot.new",
             "plot.window", "title")
  importFrom("utils", "getFromNamespace")
to your NAMESPACE file.
Running examples in 'virtualspecies-Ex.R' failed
The error most likely occurred in:

> ### Name: generateRandomSp
> ### Title: Generate a random virtual species distribution from
> ###   environmental variables
> ### Aliases: generateRandomSp
> 
> ### ** Examples
> 
> # Create an example stack with six environmental variables
> a <- matrix(rep(dnorm(1:100, 50, sd = 25)), 
+             nrow = 100, ncol = 100, byrow = TRUE)
> env <- stack(raster(a * dnorm(1:100, 50, sd = 25)),
+              raster(a * 1:100),
+              raster(a * logisticFun(1:100, alpha = 10, beta = 70)),
+              raster(t(a)),
+              raster(exp(a)),
+              raster(log(a)))
> names(env) <- paste("Var", 1:6, sep = "")   
> 
> # More than 6 variables: by default a PCA approach will be used
> generateRandomSp(env)
 - Perfoming the pca

 - Defining the response of the species along PCA axes

 - Calculating suitability values

 - Converting into Presence - Absence

   --- Determing species.prevalence automatically according to alpha and beta


Virtual species generated from 6 variables:
 Var1, Var2, Var3, Var4, Var5, Var6

- Approach used: Response to axes of a PCA
- Axes:  1, 2 ;  81.71 % explained by these axes
- Responses to axes:
   .Axis 1  [min=-3.52; max=3.55] : dnorm (mean=1.399218; sd=2.969177)
   .Axis 2  [min=-1.74; max=3.75] : dnorm (mean=0.2190712; sd=1.881691)
- Environmental suitability was rescaled between 0 and 1

- Converted into presence-absence:
   .Method = probability
   .alpha (slope)           = -0.1
   .beta  (inflexion point) = 0.128128128128128
   .species prevalence      = 0.914> 
> # Manually choosing a response approach
> generateRandomSp(env, approach = "response")
 - Determining species' response to predictor variables

Error in seq.default(cur.rast@data@min, cur.rast@data@max, length = 1000) : 
  'from' must be a finite number
Calls: generateRandomSp -> sample -> seq -> seq.default
Execution halted
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc           5.6Mb
    htmlwidgets   3.9Mb
Missing or unexported object: 'jsonlite::rbind.pages'
Decile.Plot: no visible global function definition for 'barplot'
Decile.Plot: no visible global function definition for 'axis'
Sliding.Window: no visible global function definition for 'plot'
Sliding.Window: no visible global function definition for 'lines'
Sliding.Window: no visible global function definition for 'legend'
Undefined global functions or variables:
  axis barplot legend lines plot
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines", "plot")
to your NAMESPACE file.
voss1d: no visible global function definition for 'approx'
voss1d: no visible global function definition for 'rnorm'
voss1g: no visible global function definition for 'dchisq'
voss1g: no visible global function definition for 'approx'
voss1g: no visible global function definition for 'rnorm'
voss2d: no visible global function definition for 'rnorm'
voss2g: no visible global function definition for 'dchisq'
voss2g: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  approx dchisq rnorm
Consider adding
  importFrom("stats", "approx", "dchisq", "rnorm")
to your NAMESPACE file.
'library' or 'require' call to 'raster' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
level: no visible global function definition for 'quantile'
obj.rec: no visible global function definition for 'txtProgressBar'
obj.rec: no visible global function definition for 'setTxtProgressBar'
project: no visible global function definition for 'aggregate'
raster.proj: no visible global function definition for 'quantile'
raster.proj: no visible global function definition for 'rasterFromXYZ'
raster.proj: no visible global function definition for 'plot.new'
raster.proj: no visible global function definition for 'plot'
raster.proj: no visible global function definition for 'legend'
sub.obj: no visible global function definition for 'aggregate'
sub.obj: no visible global function definition for 'txtProgressBar'
sub.obj: no visible global function definition for 'setTxtProgressBar'
surface: no visible global function definition for 'quantile'
Undefined global functions or variables:
  aggregate legend plot plot.new quantile rasterFromXYZ
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "legend", "plot", "plot.new")
  importFrom("stats", "aggregate", "quantile")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
'library' or 'require' call to 'misc3d' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.vscc: no visible global function definition for 'rainbow'
plot.vscc: no visible global function definition for 'pairs'
Undefined global functions or variables:
  pairs rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "pairs")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'lattice' 'latticeExtra' 'stringdist'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ald: no visible global function definition for 'detectCores'
ald: no visible global function definition for 'mclapply'
coltheart.N: no visible global function definition for 'detectCores'
coltheart.N: no visible global function definition for 'mclapply'
hamming.distance: no visible global function definition for
  'stringdist'
ldknn: no visible global function definition for 'detectCores'
ldknn: no visible global function definition for 'mclapply'
ldknn.odds: no visible global function definition for 'glm'
ldknn.odds: no visible binding for global variable 'binomial'
ldknn.odds: no visible global function definition for 'coefficients'
levenshtein.damerau.distance: no visible global function definition for
  'stringdist'
levenshtein.distance: no visible global function definition for
  'stringdist'
plot.ldknn.run: no visible global function definition for 'histogram'
plot.ldknn.run: no visible global function definition for
  'theEconomist.theme'
plot.ldknn.run: no visible global function definition for 'xyplot'
plot.ldknn.run: no visible global function definition for 'as.layer'
Undefined global functions or variables:
  as.layer binomial coefficients detectCores glm histogram mclapply
  stringdist theEconomist.theme xyplot
Consider adding
  importFrom("stats", "binomial", "coefficients", "glm")
to your NAMESPACE file.
Package in Depends field not imported from: 'Rcpp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File 'waffect/libs/i386/waffect.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'waffect.o'
File 'waffect/libs/x64/waffect.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'waffect.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
summary.whc: no visible global function definition for 'printCoefmat'
wahc.fit: no visible global function definition for 'pt'
wahc.fit: no visible global function definition for 'cor'
whc: no visible global function definition for 'model.frame'
whc: no visible global function definition for 'model.matrix'
whc: no visible global function definition for 'model.response'
Undefined global functions or variables:
  cor model.frame model.matrix model.response printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.frame", "model.matrix",
             "model.response", "printCoefmat", "pt")
to your NAMESPACE file.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   7.5Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    doc  12.1Mb
Foreign function call to a different package:
  .C("comwr", ..., PACKAGE = "wavethresh")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
changepoints.sbs: no visible global function definition for 'mad'
changepoints.wbs: no visible global function definition for 'var'
changepoints.wbs: no visible global function definition for 'quantile'
plot.sbs: no visible global function definition for 'ts.plot'
plot.sbs: no visible global function definition for 'lines'
plot.sbs: no visible global function definition for 'title'
random.intervals: no visible global function definition for 'runif'
sbs.default: no visible global function definition for 'var'
wbs.default: no visible global function definition for 'var'
Undefined global functions or variables:
  lines mad quantile runif title ts.plot var
Consider adding
  importFrom("graphics", "lines", "title")
  importFrom("stats", "mad", "quantile", "runif", "ts.plot", "var")
to your NAMESPACE file.
onesamplemeantest: no visible global function definition for 'pnorm'
twosamplemeantest: no visible global function definition for 'pnorm'
wcq: no visible global function definition for 'var'
wcq: no visible global function definition for 'pnorm'
wcq.fdrc: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  p.adjust pnorm var
Consider adding
  importFrom("stats", "p.adjust", "pnorm", "var")
to your NAMESPACE file.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    client   8.9Mb
    doc      1.0Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc   11.9Mb
    libs   1.6Mb
Weighted.Box.test: no visible global function definition for 'acf'
Weighted.Box.test: no visible binding for global variable 'na.pass'
Weighted.Box.test: no visible global function definition for 'pgamma'
Weighted.Box.test: no visible global function definition for 'pchisq'
Weighted.LM.test: no visible global function definition for 'acf'
Weighted.LM.test: no visible binding for global variable 'na.pass'
Weighted.LM.test: no visible global function definition for 'pgamma'
Undefined global functions or variables:
  acf na.pass pchisq pgamma
Consider adding
  importFrom("stats", "acf", "na.pass", "pchisq", "pgamma")
to your NAMESPACE file.
'library' or 'require' call to 'markdown' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
dlog.norm: no visible global function definition for 'rnorm'
fun.load.hals.a: no visible global function definition for 'sfExport'
fun.load.hals.a: no visible global function definition for 'sfLibrary'
fun.load.hals.fill: no visible global function definition for
  'sfExport'
fun.load.hals.fill: no visible global function definition for
  'sfLibrary'
fun.load.widals.a: no visible global function definition for 'sfExport'
fun.load.widals.a: no visible global function definition for
  'sfLibrary'
fun.load.widals.fill: no visible global function definition for
  'sfExport'
fun.load.widals.fill: no visible global function definition for
  'sfLibrary'
unif.mh: no visible global function definition for 'runif'
Undefined global functions or variables:
  rnorm runif sfExport sfLibrary
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'genefilter' 'parallel'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.onAttach: no visible global function definition for
  'packageDescription'
.relax.cvcompute: no visible binding for global variable
  'weighted.mean'
.relax.widenet.cv.elnet: no visible global function definition for
  'predict'
.relax.widenet.cv.elnet: no visible binding for global variable
  'weighted.mean'
.relax.widenet.cv.lognet: no visible global function definition for
  'predict'
.relax.widenet.cv.lognet: no visible binding for global variable
  'weighted.mean'
.widenet.cv.elnet: no visible global function definition for 'predict'
.widenet.cv.elnet: no visible binding for global variable
  'weighted.mean'
.widenet.cv.lognet: no visible global function definition for 'predict'
.widenet.cv.lognet: no visible binding for global variable
  'weighted.mean'
predict.widenet: no visible global function definition for 'predict'
screen.cor : <anonymous>: no visible global function definition for
  'var'
screen.cor : <anonymous>: no visible global function definition for
  'cor.test'
screen.ttest: no visible global function definition for 'colttests'
widenet: no visible global function definition for 'mc.reset.stream'
widenet: no visible global function definition for 'mclapply'
widenet: no visible global function definition for 'predict'
Undefined global functions or variables:
  colttests cor.test mc.reset.stream mclapply packageDescription
  predict var weighted.mean
Consider adding
  importFrom("stats", "cor.test", "predict", "var", "weighted.mean")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
Bundesliga.Mannschaft: no visible global function definition for 'data'
Bundesliga.Mannschaft: no visible binding for global variable
  'Bundesliga'
Bundesliga.Tabelle: no visible global function definition for 'data'
Bundesliga.Tabelle: no visible binding for global variable 'Bundesliga'
Bundesliga.XML: no visible global function definition for 'data'
Bundesliga.XML: no visible binding for global variable 'Bundesliga'
sens.spec: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
wilcox.selection.split: no visible global function definition for
  'pnorm'
wilcox.test2: no visible global function definition for 'wilcox.test'
Undefined global functions or variables:
  pnorm wilcox.test
Consider adding
  importFrom("stats", "pnorm", "wilcox.test")
to your NAMESPACE file.
Cs: no visible global function definition for 'wilcox.test'
Don: no visible global function definition for 'points'
Don: no visible global function definition for 'chisq.test'
Lixn: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  chisq.test pchisq points wilcox.test
Consider adding
  importFrom("graphics", "points")
  importFrom("stats", "chisq.test", "pchisq", "wilcox.test")
to your NAMESPACE file.
plotTrait: no visible global function definition for 'plot'
plotTrait: no visible global function definition for 'points'
plotTrait: no visible global function definition for 'legend'
test.windex: no visible global function definition for 'hist'
test.windex: no visible global function definition for 'abline'
test.windex: no visible global function definition for 'legend'
windex: no visible global function definition for 'sd'
windex: no visible global function definition for 'var'
windex: no visible global function definition for 'dist'
windex: no visible global function definition for 'quantile'
Undefined global functions or variables:
  abline dist hist legend plot points quantile sd var
Consider adding
  importFrom("graphics", "abline", "hist", "legend", "plot", "points")
  importFrom("stats", "dist", "quantile", "sd", "var")
to your NAMESPACE file.
.__A__.1 : <anonymous>: no visible binding for global variable '.hwnd'
Undefined global functions or variables:
  .hwnd
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    bn   7.1Mb
dbayes: no visible global function definition for 'mahalanobis'
dbayes: no visible global function definition for 'var'
wmd: no visible global function definition for 'cor'
wmd: no visible global function definition for 'var'
Undefined global functions or variables:
  cor mahalanobis var
Consider adding
  importFrom("stats", "cor", "mahalanobis", "var")
to your NAMESPACE file.
fit,Leader: no visible global function definition for 'lm'
plotfit,Leader: no visible global function definition for 'par'
plotfit,Leader: no visible global function definition for 'plot'
Undefined global functions or variables:
  lm par plot
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "lm")
to your NAMESPACE file.
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(WMWssp)
  > 
  > test_check("WMWssp")
  Simulation:
  
  Wilcoxon-Mann-Whitney Sample Size Calculation
   
  Summary
  Call: eval
  Type-I error (two-sided): 0.05
  Power: 0.8
  
                                   Results
  alpha (2-sided)                0.0500000
  Power                          0.8000000
  Simulated Power                0.7600000
  N (total sample size needed)   0.3491124
  t=n1/N                       111.3664650
  n1 in Group 1                  0.4964905
  n2 in Group 2                 55.2923889
  N rounded for t = 1/2         56.0740762
  N rounded                    112.0000000
  n1 rounded                   113.0000000
  n2 rounded                    56.0000000
  12                            57.0000000
  -- 1. Failure: function WMWssp_minimize (@test_MinMax.R#22)  -------------------
  `result_power` not equivalent to `result_simpower`.
  1/1 mismatches
  [1] 0.92 - 0.76 == 0.16
  
  Simulation:
  
  -- 2. Failure: function WMWssp (@test_WMWssp.R#21)  ----------------------------
  `result_power` not equivalent to `result_simpower`.
  1/1 mismatches
  [1] 0.9 - 0.7 == 0.2
  
  == testthat results  ===========================================================
  OK: 14 SKIPPED: 0 FAILED: 2
  1. Failure: function WMWssp_minimize (@test_MinMax.R#22) 
  2. Failure: function WMWssp (@test_WMWssp.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
Packages in Depends field not imported from:
  'plyr' 'reshape2'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
wordmatch: no visible global function definition for 'llply'
wordmatch : <anonymous>: no visible global function definition for
  'llply'
wordmatch: no visible global function definition for 'melt'
wordmatch: no visible global function definition for 'count'
Undefined global functions or variables:
  count llply melt
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   6.5Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.6Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data  11.1Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.3Mb
simul.wsvm: no visible binding for global variable 'mixture.example'
wsvm.boost: no visible global function definition for 'plot'
Undefined global functions or variables:
  mixture.example plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Running 'testthat.R' [32s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(xgboost)
  > 
  > test_check("xgboost")
  [1]	train-error:0.040227 
  -- 1. Failure: xgb.cv works (@test_basic.R#185)  -------------------------------
  cv$evaluation_log[, min(test_error_std)] is not strictly less than 0.004. Difference: 0.00328
  
  [1]	train-logloss:0.380601 
  [2]	train-logloss:0.247327 
  [3]	train-logloss:0.175046 
  [4]	train-logloss:0.122303 
  [5]	train-logloss:0.089890 
  [1]	train-logloss:0.497351 
  [2]	train-logloss:0.357289 
  [3]	train-logloss:0.257217 
  [4]	train-logloss:0.184524 
  [5]	train-logloss:0.132112 
  [1]	train-auc:0.900000	test-auc:0.800000 
  -- 2. Failure: prediction in early-stopping xgb.cv works (@test_callbacks.R#301)
  abs(err_pred - err_log_last) is not strictly more than 1e-04. Difference: -9.99e-05
  
  [1]	eval-error:0.042831	train-error:0.046522 
  [2]	eval-error:0.021726	train-error:0.022263 
  [1]	eval-error:0.042831	train-error:0.046522 
  [2]	eval-error:0.021726	train-error:0.022263 
  [1]	train-error:0.046522 
  [2]	train-error:0.022263 
  [1]	train-error:0.333333 
  == testthat results  ===========================================================
  OK: 552 SKIPPED: 4 FAILED: 2
  1. Failure: xgb.cv works (@test_basic.R#185) 
  2. Failure: prediction in early-stopping xgb.cv works (@test_callbacks.R#301) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [33s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(xgboost)
  > 
  > test_check("xgboost")
  [1]	train-error:0.040227 
  -- 1. Failure: xgb.cv works (@test_basic.R#185)  -------------------------------
  cv$evaluation_log[, min(test_error_std)] is not strictly less than 0.004. Difference: 0.00328
  
  [1]	train-logloss:0.380601 
  [2]	train-logloss:0.247327 
  [3]	train-logloss:0.175046 
  [4]	train-logloss:0.122303 
  [5]	train-logloss:0.089890 
  [1]	train-logloss:0.497351 
  [2]	train-logloss:0.357289 
  [3]	train-logloss:0.257217 
  [4]	train-logloss:0.184524 
  [5]	train-logloss:0.132112 
  [1]	train-auc:0.900000	test-auc:0.800000 
  -- 2. Failure: prediction in early-stopping xgb.cv works (@test_callbacks.R#301)
  abs(err_pred - err_log_last) is not strictly more than 1e-04. Difference: -9.99e-05
  
  [1]	eval-error:0.042831	train-error:0.046522 
  [2]	eval-error:0.021726	train-error:0.022263 
  [1]	eval-error:0.042831	train-error:0.046522 
  [2]	eval-error:0.021726	train-error:0.022263 
  [1]	train-error:0.046522 
  [2]	train-error:0.022263 
  [1]	train-error:0.333333 
  == testthat results  ===========================================================
  OK: 562 SKIPPED: 4 FAILED: 2
  1. Failure: xgb.cv works (@test_basic.R#185) 
  2. Failure: prediction in early-stopping xgb.cv works (@test_callbacks.R#301) 
  
  Error: testthat unit tests failed
  Execution halted
quadplot: no visible global function definition for 'median'
xgobi: no visible global function definition for 'write.table'
Undefined global functions or variables:
  median write.table
Consider adding
  importFrom("stats", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
XHWE: no visible global function definition for 'read.table'
result: no visible global function definition for 'pchisq'
result: no visible global function definition for 'rbinom'
result: no visible global function definition for 'rmultinom'
Undefined global functions or variables:
  pchisq rbinom read.table rmultinom
Consider adding
  importFrom("stats", "pchisq", "rbinom", "rmultinom")
  importFrom("utils", "read.table")
to your NAMESPACE file.
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    java  19.0Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    java   9.8Mb
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.
Running examples in 'Xmisc-Ex.R' failed
The error most likely occurred in:

> ### Name: dfsplit
> ### Title: Split data.frame given one leveled column
> ### Aliases: dfsplit
> 
> ### ** Examples
> 
> x <- read.table(textConnection("
+ chr1  0   100
+ chr2  100 200
+ chr10 200 300
+ "),col.names=c('chr','start','end'))
> 
> ## compare the results by base::split and dfsplit
> split(x,f=x[,'chr'])
$chr1
   chr start end
1 chr1     0 100

$chr10
    chr start end
3 chr10   200 300

$chr2
   chr start end
2 chr2   100 200

> ## $chr1
> ##    chr start end
> ## 1 chr1     0 100
> 
> ## $chr10
> ##     chr start end
> ## 3 chr10   200 300
> 
> ## $chr2
> ##    chr start end
> ## 2 chr2   100 200
> 
> dfsplit(x,'chr',c('chr1','chr2','chr10'))
$chr1
   chr start end
1 chr1     0 100

$chr2
   chr start end
2 chr2   100 200

$chr10
    chr start end
3 chr10   200 300

> ## $chr1
> ##    chr start end
> ## 1 chr1     0 100
> 
> ## $chr2
> ##    chr start end
> ## 2 chr2   100 200
> 
> ## $chr10
> ##     chr start end
> ## 3 chr10   200 300
> 
> 
> 
> cleanEx()
Error: connections left open:
	"\nchr1  0   100\nchr2  100 200\nchr10 200 300\n" (textConnection)
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
File 'xml2/libs/i386/xml2.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_WriteConnection'
File 'xml2/libs/x64/xml2.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_WriteConnection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    exampleData   1.3Mb
    examples      4.5Mb
    libs          4.2Mb
newXMLDoc: no visible binding for global variable 'doc'
source: no visible binding for global variable 'use_file'
xmlFlatListTree : f: no visible binding for global variable 'nodeNames'
xmlFlatListTree : f: no visible binding for global variable 'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'nodeSet'
xmlFlatListTree : addNode: no visible binding for global variable
  'nodeSet'
xmlFlatListTree : addNode: no visible binding for global variable 'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'nodeNames'
xmlFlatListTree : addNode: no visible binding for global variable
  'nodeNames'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'parentCount'
xmlFlatListTree : addNode: no visible binding for global variable
  'parentCount'
xmlFlatListTree : <anonymous>: no visible binding for global variable
  'e'
xmlFlatTree : <anonymous>: no visible binding for global variable 'e'
Undefined global functions or variables:
  doc e idx nodeNames nodeSet parentCount use_file
LPGM: no visible global function definition for 'flush.console'
PGM: no visible global function definition for 'flush.console'
PGM.path.neighborhood: no visible global function definition for
  'runif'
PGMSim: no visible global function definition for 'rpois'
PGMSim: no visible global function definition for 'par'
WPGMSim: no visible global function definition for 'rpois'
XMRF.Sim: no visible global function definition for 'cov2cor'
XMRF.Sim: no visible global function definition for 'rbinom'
XMRF.Sim: no visible global function definition for 'rnorm'
glm.generic: no visible global function definition for 'flush.console'
mymult: no visible global function definition for 'rmultinom'
plot.GMS: no visible global function definition for 'pdf'
plot.GMS: no visible global function definition for 'dev.off'
plotNet: no visible global function definition for 'pdf'
plotNet: no visible global function definition for 'dev.off'
print.GMS: no visible global function definition for 'str'
processSeq: no visible binding for global variable 'quantile'
processSeq: no visible binding for global variable 'var'
processSeq: no visible global function definition for 'ks.test'
rmpois : <anonymous>: no visible global function definition for 'rpois'
Undefined global functions or variables:
  cov2cor dev.off flush.console ks.test par pdf quantile rbinom
  rmultinom rnorm rpois runif str var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par")
  importFrom("stats", "cov2cor", "ks.test", "quantile", "rbinom",
             "rmultinom", "rnorm", "rpois", "runif", "var")
  importFrom("utils", "flush.console", "str")
to your NAMESPACE file.
File which contains pragma(s) suppressing diagnostics:
  'inst/include/xtensor/xstorage.hpp'
big.read.table: no visible global function definition for 'read.table'
big.read.table: no visible global function definition for 'object.size'
sparkline: no visible global function definition for 'is.ts'
sparkline: no visible global function definition for 'time'
sparkline: no visible global function definition for 'boxplot'
Undefined global functions or variables:
  boxplot is.ts object.size read.table time
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "is.ts", "time")
  importFrom("utils", "object.size", "read.table")
to your NAMESPACE file.
bootstrapswapcurve: no visible global function definition for 'ts'
fitted: no visible global function definition for 'ts'
forwardrates: no visible global function definition for 'ts'
residuals: no visible global function definition for 'ts'
tZC_NS: no visible global function definition for 'cmpfun'
tZC_NS_extra: no visible global function definition for 'cmpfun'
tZC_SV: no visible global function definition for 'cmpfun'
tZC_SV_extra: no visible global function definition for 'cmpfun'
ycextra: no visible global function definition for 'new'
ycinter: no visible global function definition for 'new'
ycplot: no visible global function definition for 'par'
ycplot: no visible global function definition for 'points'
ycplot: no visible global function definition for 'abline'
ycplot: no visible global function definition for 'hist'
ycplot: no visible global function definition for 'lines'
ycplot: no visible global function definition for 'density'
ycplot: no visible global function definition for 'qqnorm'
ycplot: no visible global function definition for 'qqline'
ycsummary: no visible global function definition for 'shapiro.test'
ycsummary: no visible global function definition for 'pf'
Undefined global functions or variables:
  abline cmpfun density hist lines new par pf points qqline qqnorm
  shapiro.test ts
Consider adding
  importFrom("graphics", "abline", "hist", "lines", "par", "points")
  importFrom("methods", "new")
  importFrom("stats", "density", "pf", "qqline", "qqnorm",
             "shapiro.test", "ts")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
.NS.estimator: no visible global function definition for 'lm'
.NS.estimator: no visible global function definition for 'coef'
.NS.estimator: no visible global function definition for 'na.omit'
.NS.estimator: no visible global function definition for 'resid'
.NSS.estimator: no visible global function definition for 'lm'
.NSS.estimator: no visible global function definition for 'coef'
.NSS.estimator: no visible global function definition for 'na.omit'
.NSS.estimator: no visible global function definition for 'resid'
NSrates: no visible global function definition for 'time'
Nelson.Siegel: no visible global function definition for 'optimize'
Srates: no visible global function definition for 'time'
Svensson: no visible global function definition for 'median'
Svensson: no visible global function definition for 'optimize'
Undefined global functions or variables:
  coef lm median na.omit optimize resid time
Consider adding
  importFrom("stats", "coef", "lm", "median", "na.omit", "optimize",
             "resid", "time")
to your NAMESPACE file.
kmeansN: no visible global function definition for 'kmeans'
kmeansN: no visible global function definition for 'aggregate'
kmeansN2: no visible global function definition for 'aggregate'
kmeansN2: no visible binding for global variable 'sd'
Undefined global functions or variables:
  aggregate kmeans sd
Consider adding
  importFrom("stats", "aggregate", "kmeans", "sd")
to your NAMESPACE file.
Running examples in 'zFactor-Ex.R' failed
The error most likely occurred in:

> ### Name: z.plot.range
> ### Title: Tile plot of best fit area for a correlation
> ### Aliases: z.plot.range
> 
> ### ** Examples
> 
> # plot Dranchuk-AbouKassem
> z.plot.range("DAK")
Error in n() : could not find function "n"
Calls: z.plot.range ... z.stats -> summarise -> summarise.tbl_df -> summarise_impl
Execution halted
Package suggested but not available for checking: 'zdat'
S3 methods shown with full name in documentation object 'merge':
  'cbind.zoocat'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Depends: includes the non-default packages:
  ‘Matrix’ ‘coda’ ‘mvtnorm’ ‘MCMCpack’ ‘spatstat’ ‘parallel’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Dependence on R version ‘3.3.1’ not with patchlevel 0
Error in re-building vignettes:
  ...
Loading required package: lme4
Loading required package: Matrix
************
Welcome to afex. For support visit: http://afex.singmann.science/
- Functions for ANOVAs: aov_car(), aov_ez(), and aov_4()
- Methods for calculating p-values with mixed(): 'KR', 'S', 'LRT', and 'PB'
- 'afex_aov' and 'mixed' objects can be passed to emmeans() for follow-up tests
- NEWS: library('emmeans') now needs to be called explicitly!
- Get and set global package options with: afex_options()
- Set orthogonal sum-to-zero contrasts globally: set_sum_contrasts()
- For example analyses see: browseVignettes("afex")
************

Attaching package: 'afex'

The following object is masked from 'package:lme4':

    lmer

Loading required package: mvtnorm
Loading required package: survival
Loading required package: TH.data
Loading required package: MASS

Attaching package: 'TH.data'

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

    geyser


Attaching package: 'multcomp'

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

    cld


Attaching package: 'dplyr'

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

    select

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'tidyr'

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

    expand

Loading required package: RColorBrewer

Attaching package: 'latticeExtra'

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

    layer


Attaching package: 'cowplot'

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

    ggsave

Quitting from lines 167-173 (afex_plot_supported_models.Rmd) 
Error: processing vignette ‘afex_plot_supported_models.Rmd’ failed with diagnostics:
no applicable method for ‘recover_data’ applied to an object of class "glmmTMB"
Execution halted
Found the following significant warnings:
  analyzeFMRI.c:948:3: warning: ‘strncat’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  analyzeFMRI.c:975:5: warning: ‘strncat’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/AnalyzeFMRI.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  ‘sfit’ ‘expectile’ ‘HaarSeg’ ‘mpcbs’
Dependence on R version ‘3.3.2’ not with patchlevel 0
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  pa.c:247:2: warning: initialization of ‘struct audio_instance * (*)(struct SEXPREC *, float,  int)’ from incompatible pointer type ‘void * (*)(struct SEXPREC *, float,  int)’ [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/audio.Rcheck/00install.out’ for details.
Dependence on R version ‘3.3.3’ not with patchlevel 0
Found the following significant warnings:
  Blasso.cpp:451:53: warning: ‘*<unknown>.Blasso::icept’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/bayesCL.Rcheck/00install.out’ for details.
Found the following significant warnings:
  mcmc.c:337:4: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/BayHap.Rcheck/00install.out’ for details.
Running examples in ‘biglmm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bigglm
> ### Title: Bounded memory linear regression
> ### Aliases: bigglm bigglm.function bigglm.data.frame
> ###   bigglm.SQLiteConnection bigglm.RODBC vcov.bigglm deviance.bigglm
> ###   family.bigglm AIC.bigglm bigglm,ANY,DBIConnection-method
> ### Keywords: regression
> 
> ### ** Examples
> 
> data(trees)
> ff<-log(Volume)~log(Girth)+log(Height)
> a <- bigglm(ff,data=trees, chunksize=10, sandwich=TRUE)
Error in UseMethod("bigglm", data) : 
  no applicable method for 'bigglm' applied to an object of class "data.frame"
Calls: bigglm -> bigglm
Execution halted
Running examples in ‘biglm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bigglm
> ### Title: Bounded memory linear regression
> ### Aliases: bigglm bigglm.function bigglm.data.frame
> ###   bigglm.SQLiteConnection bigglm.RODBC vcov.bigglm deviance.bigglm
> ###   family.bigglm AIC.bigglm bigglm,ANY,DBIConnection-method
> ### Keywords: regression
> 
> ### ** Examples
> 
> data(trees)
> ff<-log(Volume)~log(Girth)+log(Height)
> a <- bigglm(ff,data=trees, chunksize=10, sandwich=TRUE)
Error in UseMethod("bigglm", data) : 
  no applicable method for 'bigglm' applied to an object of class "data.frame"
Calls: bigglm -> bigglm
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/BinOrdNonNor.Rcheck/00install.out’ for details.
Package required but not available: ‘BinOrdNonNor’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tidy.biglm
> ### Title: Tidy a(n) biglm object
> ### Aliases: tidy.biglm
> 
> ### ** Examples
> 
> 
> if (require("biglm", quietly = TRUE)) {
+     bfit <- biglm(mpg ~ wt + disp, mtcars)
+     tidy(bfit)
+     tidy(bfit, conf.int = TRUE)
+     tidy(bfit, conf.int = TRUE, conf.level = .9)
+ 
+     glance(bfit)
+ 
+     # bigglm: logistic regression
+     bgfit <- bigglm(am ~ mpg, mtcars, family = binomial())
+     tidy(bgfit)
+     tidy(bgfit, exponentiate = TRUE)
+     tidy(bgfit, conf.int = TRUE)
+     tidy(bgfit, conf.int = TRUE, conf.level = .9)
+     tidy(bgfit, conf.int = TRUE, conf.level = .9, exponentiate = TRUE)
+ 
+     glance(bgfit)
+ }
Error in UseMethod("bigglm", data) : 
  no applicable method for 'bigglm' applied to an object of class "data.frame"
Calls: bigglm -> bigglm
Execution halted
Running ‘test-all.R’ [29s/33s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("broom")
  Loading required package: broom
  ── 1. Error: (unknown) (@test-biglm.R#7)  ──────────────────────────────────────
  no applicable method for 'bigglm' applied to an object of class "data.frame"
  1: bigglm(am ~ mpg, mtcars, family = binomial()) at testthat/test-biglm.R:7
  2: bigglm(am ~ mpg, mtcars, family = binomial())
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 951 SKIPPED: 2 FAILED: 1
  1. Error: (unknown) (@test-biglm.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  hash.c:144:5: warning: ‘strncpy’ specified bound 2048 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/C50.Rcheck/00install.out’ for details.
---- unloading

 *** caught segfault ***
address 0x7f353abe1b50, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Found the following significant warnings:
  catnet_rexport.cpp:202:17: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
  catnet_rexport.cpp:206:15: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:213:16: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 0 and 1023 [-Wformat-overflow=]
  catnet_rexport.cpp:216:18: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
  catnet_rexport.cpp:217:17: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:232:17: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:231:18: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/catnet.Rcheck/00install.out’ for details.
Found the following significant warnings:
  hash.c:144:5: warning: ‘strncpy’ specified bound 2048 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Cubist.Rcheck/00install.out’ for details.
Running examples in ‘data.tree-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GetPhyloNr
> ### Title: Determine the number a 'Node' has after conversion to a phylo
> ###   object
> ### Aliases: GetPhyloNr
> 
> ### ** Examples
> 
> library(ape)
> library(data.tree)
> data(acme)
> ap <- as.phylo(acme)
Error in UseMethod("as.phylo") : 
  no applicable method for 'as.phylo' applied to an object of class "c('Node', 'R6')"
Calls: as.phylo
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 502-504 (data.tree.Rmd) 
Error: processing vignette ‘data.tree.Rmd’ failed with diagnostics:
no applicable method for ‘as.igraph’ applied to an object of class "c('Node', 'R6')"
Execution halted
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.
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.
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.
Running examples in ‘dendextend-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: collapse_branch
> ### Title: Collapse branches under a tolerance level
> ### Aliases: collapse_branch
> 
> ### ** Examples
> 
> 
> # # ladderize is like sort(..., type = "node")
> dend <- iris[1:5,-5] %>% dist %>% hclust %>% as.dendrogram 
> par(mfrow = c(1,3))
> dend %>% ladderize %>% plot(horiz = TRUE); abline(v = .2, col = 2, lty = 2)
> dend %>% collapse_branch(tol = 0.2) %>% ladderize %>% plot(horiz = TRUE)
> dend %>% collapse_branch(tol = 0.2) %>% ladderize %>% 
+       hang.dendrogram(hang = 0) %>% plot(horiz = TRUE)
> 
> par(mfrow = c(1,2))
> dend %>% collapse_branch(tol = 0.2, lower = FALSE) %>% plot(horiz = TRUE, main = "dendrogram")
> library(ape)

Attaching package: ‘ape’

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

    ladderize, rotate

> dend %>% as.phylo %>% di2multi(tol = 0.2) %>% plot(main = "phylo")
Error in UseMethod("as.phylo") : 
  no applicable method for 'as.phylo' applied to an object of class "dendrogram"
Calls: %>% ... eval -> _fseq -> freduce -> <Anonymous> -> as.phylo
Execution halted
Found the following significant warnings:
  GetData.c:342:15: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 3 [-Wformat-overflow=]
  GetData.c:355:15: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 3 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/DetSel.Rcheck/00install.out’ for details.
Found the following significant warnings:
  clipper.cpp:721:34: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct ClipperLib::TEdge’; use assignment or value-initialization instead [-Wclass-memaccess]
  dbfopen.c:1346:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopen.c:1328:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopen.c:879:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  dbfopen.c:1693:9: warning: ‘strncpy’ output may be truncated copying 11 bytes from a string of length 11 [-Wstringop-truncation]
  dbfopen.c:2065:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/dggridR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/dpglasso.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...

Error: processing vignette ‘empirical.Rnw’ failed with diagnostics:
 chunk 8 
Error in x[seq_len(n)] : object of type ‘closure’ is not subsettable
Execution halted
Found the following significant warnings:
  main.c:334:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:575:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:518:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:805:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:755:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1034:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:983:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1377:7: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1279:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1678:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1962:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1912:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:2316:7: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:2212:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/enviPat.Rcheck/00install.out’ for details.
Found the following significant warnings:
  epanet.c:999:5: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:1000:5: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:1492:3: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:2308:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:2309:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  input1.c:454:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  input1.c:455:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  input3.c:604:2: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/epanet2toolkit.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/FastRWeb.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: rainbow
Loading required package: MASS
Loading required package: pcaPP
Loading required package: RCurl
Loading required package: bitops
Killed
Depends: includes the non-default packages:
  ‘gWidgets’ ‘tcltk’ ‘tkrplot’ ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages suggested but not available for checking:
  ‘Rsocp’ ‘Rnlminb2’ ‘Rdonlp2’
Found the following significant warnings:
  RngStream.c:275:7: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/freeknotsplines.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘dggrids’ ‘INLA’
Found the following significant warnings:
  hap_c.c:380:28: warning: ‘%03d’ directive writing between 3 and 10 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  hap_c.c:392:28: warning: ‘%03d’ directive writing between 3 and 10 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gap.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Gdmlib.cpp:2352:19: warning: ‘%lf’ directive writing between 3 and 317 bytes into a region of size between 0 and 1023 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gdm.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [31s/34s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(getCRUCLdata)
  > 
  > test_check("getCRUCLdata")
  ── 1. Failure: Test that create_stack creates tmn if requested (@test-create_CRU
  raster::maxValue(CRU_stack_list[[1]][[1]]) not equal to 4.3.
  1/1 mismatches
  [1] 4.3 - 4.3 == 1.91e-07
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 398 SKIPPED: 23 FAILED: 1
  1. Failure: Test that create_stack creates tmn if requested (@test-create_CRU_stack.R#1233) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: ‘__var_41_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gglasso.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.

Attaching package: 'gglogo'

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

    fortify

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Anova.glmmTMB
> ### Title: Downstream methods for glmmTMB objects
> ### Aliases: Anova.glmmTMB Effect.glmmTMB recover_data.glmmTMB
> ###   emm_basis.glmmTMB downstream_methods
> 
> ### ** Examples
> 
> warp.lm <- glmmTMB(breaks ~ wool * tension, data = warpbreaks)
> if (require(emmeans)) {
+     emmeans (warp.lm, poly ~ tension | wool)
+ }
Loading required package: emmeans
Error in ref_grid(object, ...) : 
  Can't handle an object of class  “glmmTMB” 
 Use help("models", package = "emmeans") for information on supported models.
Calls: emmeans -> ref_grid
Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'TMB'

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

    tmbroot

Loading required package: carData
Use the command
    lattice::trellis.par.set(effectsTheme())
  to customize lattice options for effects plots.
See ?effectsTheme for details.
Loading required package: mvtnorm
Loading required package: survival
Loading required package: TH.data

Attaching package: 'TH.data'

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

    geyser


Attaching package: 'multcomp'

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

    cld

Quitting from lines 94-96 (model_evaluation.rmd) 
Error: processing vignette ‘model_evaluation.rmd’ failed with diagnostics:
subscript out of bounds
Execution halted
Running examples in ‘gmnl-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getSummary.gmnl
> ### Title: Get Model Summaries for Use with "mtable"
> ### Aliases: getSummary.gmnl
> 
> ### ** Examples
> 
> ## Estimate MNL models
> data("TravelMode", package = "AER")
> library(mlogit)
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

Loading required package: lmtest
> TM <- mlogit.data(TravelMode, choice = "choice", shape = "long", 
+                  alt.levels = c("air", "train", "bus", "car"), chid.var = "individual")
>                  
> mnl.1 <- gmnl(choice ~ wait + vcost + travel + gcost | 0, data = TM)
> mnl.2 <- gmnl(choice ~ wait + vcost                  | 0, data = TM) 
> 
> ## Table
> library(memisc)
Loading required package: lattice
Loading required package: MASS

Attaching package: ‘memisc’

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

    contr.sum, contr.treatment, contrasts

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

    as.array

> mtable("MNL 1"= mnl.1, "MNL 2" = mnl.2, 
+        summary.stats = c("N", "Log-likelihood", "BIC", "AIC"))
Error in UseMethod("getSummary") : 
  no applicable method for 'getSummary' applied to an object of class "gmnl"
Calls: mtable -> lapply -> FUN
Execution halted
Packages suggested but not available for checking:
  ‘taxstats’ ‘taxstats1516’
Running examples in ‘GSE-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TSGS
> ### Title: Two-Step Generalized S-Estimator for cell- and case-wise
> ###   outliers
> ### Aliases: TSGS
> 
> ### ** Examples
> 
> set.seed(12345)
> 
> # Generate 5% cell-wise contaminated normal data
> # using a random correlation matrix with condition number 100
> x <- generate.cellcontam(n=100, p=10, cond=100, contam.size=5, contam.prop=0.05)
> 
> ## Using MLE
> slrt( cov(x$x), x$A)
[1] 84.1606
> 
> ## Using Fast-S
> slrt( rrcov:::CovSest(x$x)@cov, x$A)
[1] 36.74531
> 
> ## Using 2SGS
> slrt( TSGS(x$x)@S, x$A)
Error: 'DetectDeviatingCells' is not an exported object from 'namespace:cellWise'
Execution halted
Found the following significant warnings:
  readstat/readstat_writer.c:82:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  readstat/readstat_writer.c:276:5: warning: ‘strncpy’ specified bound 256 equals destination size [-Wstringop-truncation]
  readstat/readstat_writer.c:331:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  readstat/sas/readstat_sas7bcat_write.c:108:5: warning: ‘strncpy’ output may be truncated copying 64 bytes from a string of length 99 [-Wstringop-truncation]
  readstat/sas/readstat_sas.c:284:5: warning: ‘strncpy’ output may be truncated copying 64 bytes from a string of length 99 [-Wstringop-truncation]
  readstat/sas/readstat_sas.c:337:5: warning: ‘strncpy’ output may be truncated copying 8 bytes from a string of length 31 [-Wstringop-truncation]
  readstat/spss/readstat_sav_write.c:156:5: warning: ‘strncpy’ output may be truncated copying 9 bytes from a string of length 9 [-Wstringop-truncation]
  readstat/spss/readstat_sav_write.c:164:5: warning: ‘strncpy’ output may be truncated copying 8 bytes from a string of length 8 [-Wstringop-truncation]
  readstat/spss/readstat_por_write.c:205:5: warning: ‘strncpy’ output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/haven.Rcheck/00install.out’ for details.
Found the following significant warnings:
  gener.c:39:26: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/hier.part.Rcheck/00install.out’ for details.
Depends: includes the non-default packages:
  ‘lattice’ ‘caTools’ ‘gdata’ ‘gtools’ ‘gplots’ ‘parallel’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Running examples in ‘inca-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: intcalibrate
> ### Title: Integer Calibration Function
> ### Aliases: intcalibrate
> 
> ### ** Examples
> 
> library(inca)
> set.seed(0)
> w <- rpois(150, 4)
> data <- matrix(rbinom(150000, 1, .3) * rpois(150000, 4), 1000, 150)
> y <- data %*% w
> w <- runif(150, 0, 7.5)
> print(sum(abs(y - data %*% w)))
[1] 65229.64
> cw <- intcalibrate(w, ~. + 0, y, lower = 1, upper = 7, sparse = TRUE, data = data)
Error in NextMethod("model.matrix", data = data, contrasts.arg = object$contrasts) : 
  no method to invoke
Calls: intcalibrate -> model.matrix.lm -> NextMethod
Execution halted
Error in re-building vignettes:
  ...
Warning: MathJax doesn't work with self_contained when not using the rmarkdown "default" template.
Quitting from lines 398-401 (interactions.Rmd) 
Error: processing vignette ‘interactions.Rmd’ failed with diagnostics:
No tidy method for objects of class sim_slopes
Execution halted
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.
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    group_rows

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 327-331 (awesome_table_in_html.Rmd) 
Error: processing vignette ‘awesome_table_in_html.Rmd’ failed with diagnostics:
unused arguments ("Group 1", 4, 7)
Execution halted
Packages suggested but not available for checking:
  ‘koRpus.lang.de’ ‘koRpus.lang.es’ ‘koRpus.lang.fr’ ‘koRpus.lang.it’
  ‘koRpus.lang.ru’

Package which this enhances but not available for checking: ‘rkward’
Depends: includes the non-default packages:
  ‘sn’ ‘moments’ ‘BB’ ‘Bolstad2’ ‘optimx’ ‘Rmpfr’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:183:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘value_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:897:16: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:197:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lolog.Rcheck/00install.out’ for details.
Running examples in ‘MARSS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: augment.marssMLE
> ### Title: Return the model predicted values, residuals, and optionally
> ###   confidence intervals
> ### Aliases: augment.marssMLE augment_dfa augment_marss augmentmarxss
> 
> ### ** Examples
> 
>   dat <- t(harborSeal)
>   dat <- dat[c(2,11,12),]
>   MLEobj <- MARSS(dat, model=list(Z=factor(c("WA","OR","OR"))))
Success! abstol and log-log tests passed at 37 iterations.
Alert: conv.test.slope.tol is 0.5.
Test with smaller values (<0.1) to ensure convergence.

MARSS fit is
Estimation method: kem 
Convergence test: conv.test.slope.tol = 0.5, abstol = 0.001
Estimation converged in 37 iterations. 
Log-likelihood: 13.72233 
AIC: -11.44465   AICc: -8.918339   
 
                Estimate
A.OR.SouthCoast  0.49280
R.diag           0.02509
U.WA             0.06171
U.OR             0.03686
Q.(WA,WA)        0.01082
Q.(OR,OR)        0.00439
x0.WA            7.41712
x0.OR            6.56460
Initial states (x0) defined at t=0

Standard errors have not been calculated. 
Use MARSSparamCIs to compute CIs and bias estimates.

> 
> library(broom)
> library(ggplot2)
> theme_set(theme_bw())
> 
> # Make a plot of the observations and model fits
> d <- augment(MLEobj, interval="confidence")
Error: No augment method for objects of class marssMLE
Execution halted
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.
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.
Error in re-building vignettes:
  ...
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-16

Killed
Error in re-building vignettes:
  ...
Quitting from lines 301-306 (miceFast-intro.Rmd) 
Error: processing vignette ‘miceFast-intro.Rmd’ failed with diagnostics:
no method to invoke
Execution halted
Found the following significant warnings:
  migrate.c:179:30: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:186:26: warning: ‘.asc’ directive writing 4 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:199:28: warning: ‘.asc’ directive writing 4 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:286:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:312:29: warning: ‘%d’ directive writing between 1 and 8 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:559:31: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:595:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:603:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MigClim.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Use the user-defined lambda vector.
Using the criterion BIC to choose optimized penalty.
The chosen penalty throuth BIC is 3.6867.
The penalty term is selected automatically with 50 candidates.
Using the criterion BIC to choose optimized penalty.
The chosen penalty throuth BIC is 4.9895.
The penalty term is selected automatically with 50 candidates.
Using the criterion deviance to choose optimized penalty.
The chosen penalty throuth deviance is 2.4657.
trying URL ‘http://www.cs.columbia.edu/~andrews/mil/data/MIL-Data-2002-Musk-Corel-Trec9.tgz’
Content type 'application/x-gzip' length 6249673 bytes (6.0 MB)
==================================================
downloaded 6.0 MB

Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Warning: 'switch' is deprecated.
Use 'strip.position' instead.
See help("Deprecated")
The penalty term is selected automatically with 100 candidates.
Using the criterion deviance to choose optimized penalty.
The chosen penalty throuth deviance is 3.5287.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Killed
Error in re-building vignettes:
  ...

Attaching package: 'mistr'

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

    q

Quitting from lines 180-184 (mistr-extensions.Rmd) 
Error: processing vignette ‘mistr-extensions.Rmd’ failed with diagnostics:
Objects of type trans_contdist/trans_standist/trans_univdist/dist not supported by autoplot.
Execution halted
Found the following significant warnings:
  monetdblite/src/gdk/gdk_heap.c:189:3: warning: ‘strncpy’ output truncated before terminating nul copying 9 bytes from a string of the same length [-Wstringop-truncation]
  monetdblite/src/gdk/gdk_heap.c:260:30: warning: ‘%s’ directive writing likely 3 or more bytes into a region of size between 0 and 99 [-Wformat-overflow=]
  monetdblite/src/mal/sqlbackend/rel_bin.c:2949:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/mal/sqlbackend/rel_bin.c:1083:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/mal/sqlbackend/sql_statement.c:3193:3: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/mal/sqlbackend/sql_statement.c:3196:3: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/mal/sqlbackend/sql_statement.c:3186:3: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/sql/server/rel_planner.c:82:4: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/sql/server/rel_semantic.c:54:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/sql/server/rel_updates.c:1729:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MonetDBLite.Rcheck/00install.out’ for details.
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.
Packages required but not available: ‘BinOrdNonNor’ ‘CorrToolBox’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Depends: includes the non-default packages:
  ‘car’ ‘pdist’ ‘pls’ ‘gplots’ ‘mvtnorm’ ‘robustbase’ ‘gtools’ ‘bitops’
  ‘caTools’ ‘pcaPP’ ‘rrcov’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
This is lavaan 0.6-3
lavaan is BETA software! Please report any bugs.
This is nonnest2 0.5-2.
nonnest2 has not been tested with all combinations of model classes.
Quitting from lines 64-65 (nonnest2.Rmd) 
Error: processing vignette ‘nonnest2.Rmd’ failed with diagnostics:
no applicable method for ‘estfun’ applied to an object of class "lavaan"
Execution halted
Depends: includes the non-default packages:
  ‘lpSolve’ ‘gdata’ ‘Hmisc’ ‘rms’ ‘geometry’ ‘psych’ ‘pwt’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:
  Warning: replacing previous import ‘zip::unzip’ by ‘utils::unzip’ when loading ‘officer’
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/officer.Rcheck/00install.out’ for details.
Running ‘exporting-methods.R’ [2s/3s]
  Running ‘mahal-dist.R’ [3s/4s]
  Running ‘testthat.R’ [22s/24s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(optmatch)
  Loading required package: survival
  The optmatch package has an academic license. Enter relaxinfo() for more information.
  > 
  > test_check("optmatch")
  ── 1. Error: Bigglm distances (@test.match_on.R#298)  ──────────────────────────
  no applicable method for 'bigglm' applied to an object of class "data.frame"
  1: bigglm(Z ~ X1 + X2, data = test.data, family = binomial()) at testthat/test.match_on.R:298
  2: bigglm(Z ~ X1 + X2, data = test.data, family = binomial())
  
  ── 2. Error: scores with bigglm (@test.scores.R#222)  ──────────────────────────
  no applicable method for 'bigglm' applied to an object of class "data.frame"
  1: bigglm(Z ~ X1 + X2, data = test.data, family = binomial()) at testthat/test.scores.R:222
  2: bigglm(Z ~ X1 + X2, data = test.data, family = binomial())
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1308 SKIPPED: 0 FAILED: 2
  1. Error: Bigglm distances (@test.match_on.R#298) 
  2. Error: scores with bigglm (@test.scores.R#222) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Killed
Packages suggested but not available for checking:
  ‘genealogicalSorting’ ‘phybase’
Running ‘testthat.R’ [249s/368s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(peakPantheR)
  
  This is peakPantheR version 1.2.0 
  
  > 
  > test_check("peakPantheR")
  ── 1. Error: default multiplot (@test_annotationDiagnosticMultiplot.R#180)  ────
  unused arguments (limits, n)
  1: evaluate_promise(annotationDiagnosticMultiplot(input_plots)) at testthat/test_annotationDiagnosticMultiplot.R:180
  2: withr::with_output_sink(temp, withCallingHandlers(withVisible(code), warning = handle_warning, 
         message = handle_message))
  3: force(code)
  4: withCallingHandlers(withVisible(code), warning = handle_warning, message = handle_message)
  5: withVisible(code)
  6: annotationDiagnosticMultiplot(input_plots)
  7: ggplot2::layer_scales(tmp_rtPeakwidthVert)
  8: ggplot_build(plot)
  9: ggplot_build.ggplot(plot)
  10: layout$setup_panel_params()
  ...
  16: f(..., self = self)
  17: parent$setup_panel_params(scale_x, scale_y, params)
  18: f(..., self = self)
  19: train_cartesian(scale_x, self$limits$x, "x")
  20: scale$break_info(range)
  21: f(..., self = self)
  22: ggproto_parent(ScaleContinuous, self)$break_info(range)
  23: f(..., self = self)
  24: self$get_breaks_minor(b = major, limits = range)
  25: f(..., self = self)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1147 SKIPPED: 0 FAILED: 1
  1. Error: default multiplot (@test_annotationDiagnosticMultiplot.R#180) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following apparent S3 methods exported but not registered:
  mean.LCL mean.UCL mean.geometric mean.stderr
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  fdouble_metaphone.c:268:5: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/PGRdup.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  zhegv.c:216:27: warning: ‘strncpy’ specified bound 2 equals destination size [-Wstringop-truncation]
  zhegv.c:216:27: warning: ‘strncpy’ specified bound 3 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/PRIMME.Rcheck/00install.out’ for details.
Found the following significant warnings:
  R4dfp-object.c:253:3: warning: ‘strncpy’ output truncated before terminating nul copying 9 bytes from a string of the same length [-Wstringop-truncation]
  R4dfp-object.c:260:3: warning: ‘strncpy’ output truncated before terminating nul copying 9 bytes from a string of the same length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/R4dfp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  avc_binwr.c:166:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:173:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:180:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:187:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:1453:29: warning: ‘%4.4d’ directive writing between 4 and 10 bytes into a region of size 5 [-Wformat-overflow=]
  avc_binwr.c:1553:28: warning: ‘%s’ directive writing up to 39 bytes into a region of size between 38 and 77 [-Wformat-overflow=]
  avc_e00write.c:386:30: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  avc_e00write.c:387:30: warning: ‘-ID’ directive writing 3 bytes into a region of size between 1 and 40 [-Wformat-overflow=]
  avc_e00write.c:401:61: warning: ‘%s’ directive writing up to 39 bytes into a region of size 17 [-Wformat-overflow=]
  avc_e00write.c:397:61: warning: ‘%s’ directive writing up to 39 bytes into a region of size 17 [-Wformat-overflow=]
  avc_e00write.c:409:39: warning: ‘%s’ directive writing up to 39 bytes into a region of size 33 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RArcInfo.Rcheck/00install.out’ for details.
Running examples in ‘Rchoice-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: estfun.Rchoice
> ### Title: Gradient for observations
> ### Aliases: estfun.Rchoice
> 
> ### ** Examples
> 
> ## Probit model
> data("Workmroz")
> probit <- Rchoice(lfp ~ k5 + k618 + age + wc + hc + lwg + inc,  
+                   data = Workmroz , family = binomial('probit'))
> summary(probit)

Model: binomial
Model estimated on: Fri Mar 01 06:45:49 PM 2019 

Call:
Rchoice(formula = lfp ~ k5 + k618 + age + wc + hc + lwg + inc, 
    data = Workmroz, family = binomial("probit"), method = "nr")


Frequencies of categories:
y
     0      1 
0.4316 0.5684 
The estimation took: 0h:0m:0s 

Coefficients:
          Estimate Std. Error z-value Pr(>|z|)    
constant  1.918422   0.380654   5.040 4.66e-07 ***
k5       -0.874711   0.113558  -7.703 1.33e-14 ***
k618     -0.038594   0.040489  -0.953 0.340488    
age      -0.037824   0.007609  -4.971 6.67e-07 ***
wc        0.488314   0.135487   3.604 0.000313 ***
hc        0.057170   0.124005   0.461 0.644776    
lwg       0.365629   0.087779   4.165 3.11e-05 ***
inc      -0.020525   0.004777  -4.297 1.73e-05 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Optimization of log-likelihood by Newton-Raphson maximisation
Log Likelihood: -452.7
Number of observations: 753
Number of iterations: 4
Exit of MLE: gradient close to zero> 
> library(sandwich)
> estfun(probit) 
Error in UseMethod("estfun") : 
  no applicable method for 'estfun' applied to an object of class "Rchoice"
Calls: estfun
Execution halted
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.
Found the following significant warnings:
  Rreadsdpa.c:608:15: warning: ‘strncpy’ output may be truncated copying 3999 bytes from a string of length 3999 [-Wstringop-truncation]
  Rreadsdpa.c:1041:13: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  Rreadsdpa.c:1042:13: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  dsdpsetoptions.c:164:4: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  dsdpsetoptions.c:165:4: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rdsdp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  compile.cc:292:69: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class re2::Prog::Inst’; use assignment or value-initialization instead [-Wclass-memaccess]
  regexp.cc:343:33: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class re2::Regexp’ with no trivial copy-assignment [-Wclass-memaccess]
  regexp.cc:344:32: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class re2::Regexp’ with no trivial copy-assignment [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/re2r.Rcheck/00install.out’ for details.
Found the following significant warnings:
  phonet.c:1207:34: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  phonet.c:1208:34: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RecordLinkage.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  ‘playwith’ ‘pmg’ ‘SVGAnnotation’
Found the following significant warnings:
  RhpcMPI.c:301:5: warning: ‘strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rhpc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  cornellout.cpp:99:20: warning: ‘%2d’ directive writing between 2 and 11 bytes into a region of size between 0 and 931 [-Wformat-overflow=]
  cornellout.cpp:137:26: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  cornellout.cpp:129:26: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 988 and 995 [-Wformat-overflow=]
  mat.cpp:315:4: warning: ‘*<unknown>.dataMat::p’ is used uninitialized in this function [-Wuninitialized]
  tilia.cpp:179:14: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 61 bytes from a string of length 199 [-Wstringop-truncation]
  tilia.cpp:180:10: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 19 bytes from a string of length 19 [-Wstringop-truncation]
  tilia.cpp:225:14: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 8 bytes from a string of length 199 [-Wstringop-truncation]
  tilia.cpp:228:17: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 8 bytes from a string of length 29 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rioja.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’,
    ‘R_GlobalContext’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  RngStream.c:347:4: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rlecuyer.Rcheck/00install.out’ for details.
Found the following significant warnings:
  origcmaes.cc:2852:13: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  origcmaes.cc:2855:12: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  origcmaes.cc:2858:12: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rmalschains.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [9s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rnn)
  > 
  > test_check("rnn")
  ── 1. Failure: (unknown) (@test_rnn.R#66)  ─────────────────────────────────────
  sum(bin2int(B)) not equal to 888626.
  1/1 mismatches
  [1] 995608 - 888626 == 106982
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Failure: (unknown) (@test_rnn.R#66) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  bgc_hmm.c:241:31: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
  rph_tfbs.c:371:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:351:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:819:5: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rphast.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [6s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Copyright (c) 2015-present, Facebook, Inc.
  > # All rights reserved.
  > #
  > # This source code is licensed under the BSD-style license found in the
  > # LICENSE file in the root directory of this source tree. An additional grant
  > # of patent rights can be found in the PATENTS file in the same directory.
  > 
  > library("testthat")
  > library("DBI")
  > library("RPresto")
  > 
  > test_check("RPresto")
  -- 1. Failure: as() works (@test-translate_sql.R#22)  --------------------------
  translate_sql(as(x, 0), con = s[["con"]]) not equal to dplyr::sql("CAST(\"x\" AS DOUBLE)").
  1/1 mismatches
  x[1]: "AS(\"x\", 0.0)"
  y[1]: "CAST(\"x\" AS DOUBLE)"
  
  -- 2. Failure: as() works (@test-translate_sql.R#26)  --------------------------
  translate_sql(pmax(x), con = s[["con"]]) not equal to dplyr::sql("GREATEST(\"x\")").
  1/1 mismatches
  x[1]: "MAX(\"x\")"
  y[1]: "GREATEST(\"x\")"
  
  -- 3. Failure: as() works (@test-translate_sql.R#30)  --------------------------
  translate_sql_(...) not equal to dplyr::sql("CAST(\"x\" AS ARRAY<VARCHAR>)").
  1/1 mismatches
  x[1]: "AS(\"x\", ())"
  y[1]: "CAST(\"x\" AS ARRAY<VARCHAR>)"
  
  -- 4. Failure: as() works (@test-translate_sql.R#39)  --------------------------
  translate_sql_(list(substituted.expression), con = s[["con"]]) not equal to dplyr::sql("CAST(\"x\" AS DATE)").
  1/1 mismatches
  x[1]: "AS(\"x\", '2019-03-01')"
  y[1]: "CAST(\"x\" AS DATE)"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 276 SKIPPED: 28 FAILED: 4
  1. Failure: as() works (@test-translate_sql.R#22) 
  2. Failure: as() works (@test-translate_sql.R#26) 
  3. Failure: as() works (@test-translate_sql.R#30) 
  4. Failure: as() works (@test-translate_sql.R#39) 
  
  Error: testthat unit tests failed
  Execution halted
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Running examples in ‘rstpm2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: predictnl
> ### Title: Estimation of standard errors using the numerical delta method.
> ### Aliases: predictnl predictnl.default predictnl.lm predict.formula
> ###   print.predictnl confint.predictnl
> 
> ### ** Examples
> 
> 
> df <- data.frame(x=0:1, y=c(10, 20))
> fit <- glm(y ~ x, df, family=poisson)
> 
> predictnl(fit,
+           function(obj,newdata)
+           diff(predict(obj,newdata,type="response")))
Error in UseMethod("predictnl") : 
  no applicable method for 'predictnl' applied to an object of class "c('glm', 'lm')"
Calls: predictnl -> predictnl
Execution halted
Error in re-building vignettes:
  ...
Loading required package: survival
Loading required package: splines

Attaching package: ‘rstpm2’

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

    colon


Error: processing vignette ‘predictnl.Rnw’ failed with diagnostics:
 chunk 3 
Error in UseMethod("predictnl") : 
  no applicable method for ‘predictnl’ applied to an object of class "test"
Execution halted
Found the following significant warnings:
  RngStreams.c:332:4: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rstream.Rcheck/00install.out’ for details.
Found the following significant warnings:
  bgc_hmm.c:241:31: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
  rph_tfbs.c:371:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:351:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:819:5: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rtfbs.Rcheck/00install.out’ for details.
Found the following significant warnings:
  geometry/s2loop.cc:85:73: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘S2Point’ {aka ‘class Vector3<double>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  geometry/s2loop.cc:247:73: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘S2Point’ {aka ‘class Vector3<double>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  geometry/s2polyline.cc:52:73: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘S2Point’ {aka ‘class Vector3<double>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  geometry/s2polyline.cc:94:73: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘S2Point’ {aka ‘class Vector3<double>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  geometry/s2regioncoverer.cc:119:28: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct S2RegionCoverer::Candidate’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/s2.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/scio.Rcheck/00install.out’ for details.
Found the following significant warnings:
  catnet_rexport.cpp:221:17: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
  catnet_rexport.cpp:229:15: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:237:16: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 0 and 1023 [-Wformat-overflow=]
  catnet_rexport.cpp:240:18: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
  catnet_rexport.cpp:241:17: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:258:17: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:257:18: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/sdnet.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_1_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/sdwd.Rcheck/00install.out’ for details.
Depends: includes the non-default packages:
  ‘hdrcde’ ‘coda’ ‘MASS’ ‘bayesm’ ‘mnormt’ ‘spatstat’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
prepare_Rd: maxsel.rd:27-29: Dropping empty section \details
prepare_Rd: transf.inter.rd:23-25: Dropping empty section \details
prepare_Rd: H.Binv.Rd:48-50: Dropping empty section \note
prepare_Rd: V.theta.Rd:28-30: Dropping empty section \details
prepare_Rd: V.theta.Rd:43-45: Dropping empty section \note
prepare_Rd: V.theta.Rd:49-51: Dropping empty section \seealso
prepare_Rd: V.theta.Rd:52-53: Dropping empty section \examples
prepare_Rd: confid.int.theta.Rd:62-64: Dropping empty section \note
prepare_Rd: dd.est.Rd:39-41: Dropping empty section \note
prepare_Rd: dd.est.Rd:45-47: Dropping empty section \seealso
prepare_Rd: ell.theta.Rd:60-62: Dropping empty section \note
prepare_Rd: ell.theta.Rd:69-70: Dropping empty section \examples
prepare_Rd: grad.hessinv.Rd:47-49: Dropping empty section \note
prepare_Rd: ks.sporm.Rd:43-45: Dropping empty section \note
prepare_Rd: ks.stat.Rd:39-41: Dropping empty section \note
prepare_Rd: mrle.sporm.Rd:66-68: Dropping empty section \note
prepare_Rd: mrle.sporm.Rd:72-74: Dropping empty section \seealso
prepare_Rd: newton.theta.Rd:47-49: Dropping empty section \note
prepare_Rd: phi.Rd:32-38: Dropping empty section \value
prepare_Rd: phi.Rd:48-50: Dropping empty section \note
prepare_Rd: plotor.Rd:26-32: Dropping empty section \value
prepare_Rd: plotor.Rd:42-44: Dropping empty section \note
prepare_Rd: plotor.Rd:48-50: Dropping empty section \seealso
prepare_Rd: sporm-package.Rd:53-54: Dropping empty section \seealso
prepare_Rd: sporm-package.Rd:55-56: Dropping empty section \examples
prepare_Rd: test.theta.Rd:54-56: Dropping empty section \note
prepare_Rd: elltheta.rd:53-55: Dropping empty section \note
prepare_Rd: elltheta.rd:62-63: Dropping empty section \examples
Found the following significant warnings:
  dbfopenSSN.c:1119:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopenSSN.c:1100:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopenSSN.c:663:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  dbfopenSSN.c:1511:2: warning: ‘strncpy’ output may be truncated copying 11 bytes from a string of length 11 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/SSN.Rcheck/00install.out’ for details.
Running examples in ‘structSSI-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: EstimatedHFDRControl
> ### Title: Estimate FDR control variations for HFDR procedure
> ### Aliases: EstimatedHFDRControl
> ### Keywords: ~htest
> 
> ### ** Examples
> 
> library('igraph')

Attaching package: ‘igraph’

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

    decompose, spectrum

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

    union

> library('ape')

Attaching package: ‘ape’

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

    edges, mst, ring

> 
> alternative.indices <- sample(1:49, 30)
> unadj.p.values <- vector("numeric", length = 49)
> unadj.p.values[alternative.indices] <- runif(30, 0, 0.01)
> unadj.p.values[-alternative.indices] <- runif(19, 0, 1)
> unadj.p.values[c(1:5)] <- runif(5, 0, 0.01)
> names(unadj.p.values) <- paste("Hyp ", c(1:49))
> 
> tree <- as.igraph(rtree(25))
Error in UseMethod("as.igraph") : 
  no applicable method for 'as.igraph' applied to an object of class "phylo"
Calls: as.igraph
Execution halted
Running ‘testGBHProcedures.R’ [3s/4s]
  Running ‘testHierarchicalMethods.R’ [3s/4s]
Running the tests in ‘tests/testHierarchicalMethods.R’ failed.
Complete output:
  > ## Test the hypothesesTree creation class.
  > 
  > set.seed(130229)
  > library('structSSI')
  > library('ape')
  > library('igraph')
  
  Attaching package: 'igraph'
  
  The following objects are masked from 'package:ape':
  
      edges, mst, ring
  
  The following objects are masked from 'package:stats':
  
      decompose, spectrum
  
  The following object is masked from 'package:base':
  
      union
  
  > tree.1 <- as.igraph(rtree(10))
  Error in UseMethod("as.igraph") : 
    no applicable method for 'as.igraph' applied to an object of class "phylo"
  Calls: as.igraph
  Execution halted
Packages suggested but not available for checking: ‘sylly.de’ ‘sylly.es’
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/sparsepp/include/sparsepp/spp_utils.h:422:44: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair<const std::pair<unsigned int, unsigned int>, int>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/sparsepp/include/sparsepp/spp_utils.h:422:44: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair<const std::pair<unsigned int, unsigned int>, float>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/text2vec.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  ‘Rcampdf’ ‘tm.lexicon.GeneralInquirer’
Found the following significant warnings:
  RngStream.c:347:4: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TPmsm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  libqhull/rboxlib.c:351:5: warning: ‘strncat’ output may be truncated copying between 0 and 199 bytes from a string of length 199 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TukeyRegion.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘vaers’ ‘vaersND’
Found the following significant warnings:
  include/rapidjson/document.h:1952:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘rapidjson::GenericValue<rapidjson::UTF8<> >::Member’ {aka ‘struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::MemoryPoolAllocator<> >’} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class rapidjson::GenericValue<rapidjson::UTF8<> >’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  include/rapidjson/document.h:1952:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>::Member’ {aka ‘struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::CrtAllocator>’} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/validatejsonr.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: maps
Loading required package: tuneR
Loading required package: seewave
Loading required package: NatureSounds

NOTE: functions are being renamed (run 'print(new_function_names)' to see new names). Both old and new names are available in this version 
 Please see citation('warbleR') for use in publication
Quitting from lines 82-110 (warbleR_workflow_01.Rmd) 
Error: processing vignette ‘warbleR_workflow_01.Rmd’ failed with diagnostics:
there is no package called 'Rraven'
Execution halted
Found the following significant warnings:
  tabix/razf.c:188:2: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/WhopGenome.Rcheck/00install.out’ for details.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    R  13.6Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    data       2.8Mb
    pictures   2.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R       1.4Mb
    data    1.3Mb
    files   1.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.5Mb
    doc   3.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   3.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       2.9Mb
    extdata   1.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 66-67 (ahn.Rmd) 
Error: processing vignette 'ahn.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 49-64 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
EXPR must be a length 1 vector
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    help   5.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 38-72 (antaresH5.Rmd) 
Error: processing vignette 'antaresH5.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Package suggested but not available for checking: ‘kebabs’
Error in re-building vignettes:
  ...

Attaching package: 'apcluster'

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

    heatmap

Quitting from lines 387-408 (apcluster.Rnw) 
Error: processing vignette 'apcluster.Rnw' failed with diagnostics:
object 'apres2c' not found
Execution halted
Package suggested but not available for checking: ‘qCBA’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    fontawesome-5.3.1   2.8Mb
    help                1.5Mb
Package suggested but not available for checking: ‘MonetDBLite’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    help   1.1Mb
Running examples in ‘arsenal-Ex.R’ failed
The error most likely occurred in:

> ### Name: write2
> ### Title: write2
> ### Aliases: write2 write2.arsenal_table write2.summary.arsenal_table
> ###   write2.compare.data.frame write2.summary.compare.data.frame
> ###   write2.verbatim write2.yaml write2.code.chunk write2.knitr_kable
> ###   write2.xtable write2.character write2.list write2.default
> 
> ### ** Examples
> 
> ## Not run: 
> ##D data(mockstudy)
> ##D # tableby example
> ##D tab1 <- tableby(arm ~ sex + age, data=mockstudy)
> ##D write2(tab1, tempfile(fileext = ".rtf"),
> ##D   toc = TRUE, # passed to rmarkdown::rtf_document, though in this case it's not practical
> ##D   quiet = TRUE, # passed to rmarkdown::render
> ##D   title = "My cool new title", # passed to summary.tableby
> ##D   output_format = rmarkdown::rtf_document)
> ## End(Not run)
> 
> write2html(list(
+   "# Header 1", # a header
+   code.chunk(a <- 1, b <- 2, a + b), # a code chunk
+   verbatim("hi there") # verbatim output
+ ),
+   tempfile(fileext = ".html"),
+   quite = TRUE)
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data      1.1Mb
    extdata   3.8Mb
Package suggested but not available for checking: ‘REBayes’
Error in re-building vignettes:
  ...
Warning in summary.cross(cross) :
  Some markers at the same position on chr 1B1,1D,2B,2D1,3A,3B,3D,4A,5A,5B,5D,6D,7A,7B,7D; use jittermap().
Warning in summary.cross(cross) :
  Some chromosomes > 1000 cM in length; there may be a problem with the genetic map.
  (Perhaps it is in basepairs?)
Warning in summary.cross(cross) :
  Some markers at the same position on chr L.1,L.2,L.3,L.4,L.5,L.6,L.7,L.8,L.9; use jittermap().
Warning in heatMap(mapBC6, chr = c("L.3", "L.5", "L.8", "L.9"), lmax = 70) :
  Running est.rf.
Warning in summary.cross(cross) :
  Some markers at the same position on chr L.1,L.2,L.3,L.4,L.5,L.6,L.7; use jittermap().
Package required but not available: ‘xgboost’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    java   7.5Mb
installed size is 73.8Mb
  sub-directories of 1Mb or more:
    java  73.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   3.4Mb
Package suggested but not available for checking: ‘mzR’
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    2.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: survival
Loading required package: nnet
Loading required package: nlme
Quitting from lines 127-155 (hwbart.Rmd) 
Error: processing vignette 'hwbart.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 46-49 (v01-introduction.Rmd) 
Error: processing vignette 'v01-introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Running ‘testthat.R’ [30s/36s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(BAS)
  > 
  > test_check("BAS")
  ── 1. Failure: herdity and BAS (@test-bas-glm.R#420)  ──────────────────────────
  pima_BAS$probne0 not equal to pima_BAS_no$probne0.
  6/7 mismatches (average diff: 0.0696)
  [2] 0.11013 - 0.1136 == -3.47e-03
  [3] 1.00000 - 1.0000 == -2.54e-06
  [4] 0.63062 - 0.8284 == -1.98e-01
  [5] 0.02193 - 0.0220 == -1.03e-04
  [6] 0.00771 - 0.0101 == -2.42e-03
  [7] 0.31878 - 0.1051 ==  2.14e-01
  
  
   Marginal Posterior Summaries of Coefficients: 
  
   Using  BMA 
  
   Based on the top  16 models 
             post mean  post SD   post p(B != 0)
  Intercept  95.42308    0.67885   1.00000      
  X1          1.40116    0.35351   0.97454      
  X2          0.42326    0.38407   0.76017      
  X3         -0.03997    0.33398   0.30660      
  X4         -0.22077    0.36931   0.44354      
  
  Call:
  bas.lm(formula = Y ~ ., data = Hald, prior = "BIC", modelprior = uniform())
  
  
   Marginal Posterior Inclusion Probabilities: 
  Intercept         X1         X2         X3         X4  
     1.0000     0.9856     0.7921     0.4705     0.5220  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 150 SKIPPED: 0 FAILED: 1
  1. Failure: herdity and BAS (@test-bas-glm.R#420) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-8'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/BayesFM.Rcheck/00install.out’ for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.3Mb
    libs   1.7Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   4.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 2-14 (./children/SETTINGS-knitr.txt) 
Quitting from lines NA-14 (./children/SETTINGS-knitr.txt) 
Error: processing vignette 'graphical-ppcs.Rmd' failed with diagnostics:
object 'params' not found
Execution halted
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R         1.0Mb
    data      1.1Mb
    extdata   1.9Mb
Running ‘testthat.R’ [17s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bcgam)
  Loading required package: nimble
  nimble version 0.7.0.1 is loaded.
  For more information on NIMBLE and a User Manual,
  please visit http://R-nimble.org.
  
  Attaching package: 'nimble'
  
  The following object is masked from 'package:stats':
  
      simulate
  
  > 
  > test_check("bcgam")
  thin = 1: tau, betalpha, sigma, eta
  ── 1. Error: (unknown) (@testthat.R#3)  ────────────────────────────────────────
  Failed to create the shared library.
  1: bcgam(income ~ sm.incr(prestige, space = "E") + sm.conv(education) + type, data = duncan) at testthat/testthat.R:3
  2: bcgam.fit(y, xmat0, shapes0, zmat, nums0, ks0, sps0, nloop, burnin, family, xmatnms0, 
         znms)
  3: compileNimble(gaus)
  4: project$compileModel(units[[i]], control = control, showCompilerOutput = showCompilerOutput)
  5: cppProj$compileFile(compileList, showCompilerOutput)
  6: compileDynamicRegistrations(showCompilerOutput = showCompilerOutput)
  7: compileStaticCode(dllName, cppName, showCompilerOutput)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@testthat.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Warning in predictExtrapUp(alpha, lambda, beta, predictPositionsRescaled[depthIndRange],  :
  Unable to find suitable chronologies for top of core - truncated to date of extraction
Warning in predictExtrapUp(alpha, lambda, beta, predictPositionsRescaled[depthIndRange],  :
  Unable to find suitable chronologies for top of core - truncated to date of extraction
Warning in predictExtrapUp(alpha, lambda, beta, predictPositionsRescaled[depthIndRange],  :
  Unable to find suitable chronologies for top of core - truncated to date of extraction
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.7Mb
Package suggested but not available for checking: ‘BRugs’
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 53-74 (abcd-laagdrempelige_nederlandse_uitleg.Rmd) 
Error: processing vignette 'abcd-laagdrempelige_nederlandse_uitleg.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is 145.8Mb
  sub-directories of 1Mb or more:
    include  145.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Removed 199 rows containing non-finite values (stat_contour).
Warning in normalizePath(f2) :
  path[1]="./webshot32d31cec3f48.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot32d31cec3f48.png': No such file or directory
Quitting from lines 244-247 (analysis.Rmd) 
Error: processing vignette 'analysis.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       3.1Mb
    extdata   2.5Mb
Package unavailable to check Rd xrefs: ‘bigrquery’
Installation failed.
See ‘/home/ripley/R/packages/tests32/bigrquery.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 41-48 (billboarder-intro.Rmd) 
Error: processing vignette 'billboarder-intro.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Package required but not available: ‘csaw’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 64-67 (BioCircos.Rmd) 
Error: processing vignette 'BioCircos.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    extdata   7.8Mb
Packages required but not available: ‘rcdk’ ‘ChemmineR’ ‘fmcsR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.7Mb
Running examples in ‘bioRad-Ex.R’ failed
The error most likely occurred in:

> ### Name: example_scan
> ### Title: Example object of class 'scan'
> ### Aliases: example_scan
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # get summary of example scan:
> summary(example_scan)
                  Polar scan (class scan)

     parameters:  VRADH DBZH ZDR RHOHV PHIDP 
elevation angle:  0.5 deg
           dims:  480 bins x 360 rays
> 
> # example_scan was created with:
> pvolfile <- system.file("extdata", "volume.h5", package = "bioRad")
> pvol <- read_pvolfile(pvolfile)
Error in H5Fopen(file, "H5F_ACC_RDONLY", native = native) : 
  HDF5. File accessibilty. Unable to open file.
Calls: read_pvolfile ... is.odimfile -> h5ls -> h5checktypeOrOpenLoc -> H5Fopen
Execution halted
Running ‘testthat.R’ [12s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bioRad)
  Welcome to bioRad version 0.4.0
  Warning: no running Docker daemon found Warning: bioRad functionality
  requiring Docker has been disabled
  
  To enable Docker functionality, start Docker and run 'check_docker()'
  in R
  > 
  > test_check("bioRad")
  ── 1. Error: Read a vertical profile (@test-read_vpfiles.R#5)  ─────────────────
  HDF5. File accessibilty. Unable to open file.
  1: expect_s3_class(readvp(vpfile), "vp") at testthat/test-read_vpfiles.R:5
  2: quasi_label(enquo(object))
  3: eval_bare(get_expr(quo), get_env(quo))
  4: readvp(vpfile)
  5: read_vpfiles(...)
  6: read_vp(files)
  7: is.vpfile(file)
  8: get_odim_object_type(file)
  9: is.odimfile(file)
  10: h5ls(file, recursive = FALSE)
  11: h5checktypeOrOpenLoc(file, readonly = TRUE, native = native)
  12: H5Fopen(file, "H5F_ACC_RDONLY", native = native)
  
  ── 2. Error: Read multiple vertical profiles (@test-read_vpfiles.R#13)  ────────
  HDF5. File accessibilty. Unable to open file.
  1: expect_is(readvp.list(c(vpfile, vpfile)), "list") at testthat/test-read_vpfiles.R:13
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: readvp.list(c(vpfile, vpfile))
  5: read_vpfiles(...)
  6: lapply(files, read_vp)
  7: FUN(X[[i]], ...)
  8: is.vpfile(file)
  9: get_odim_object_type(file)
  10: is.odimfile(file)
  11: h5ls(file, recursive = FALSE)
  12: h5checktypeOrOpenLoc(file, readonly = TRUE, native = native)
  13: H5Fopen(file, "H5F_ACC_RDONLY", native = native)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 25 SKIPPED: 0 FAILED: 2
  1. Error: Read a vertical profile (@test-read_vpfiles.R#5) 
  2. Error: Read multiple vertical profiles (@test-read_vpfiles.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-4
Loading required package: sna
Loading required package: statnet.common

Attaching package: 'statnet.common'

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

    order

Loading required package: network
network: Classes for Relational Data
Version 1.13.0.1 created on 2015-08-31.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
                    Mark S. Handcock, University of California -- Los Angeles
                    David R. Hunter, Penn State University
                    Martina Morris, University of Washington
                    Skye Bender-deMoll, University of Washington
 For citation information, type citation("network").
 Type help("network-package") to get started.

sna: Tools for Social Network Analysis
Version 2.4 created on 2016-07-23.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
 For citation information, type citation("sna").
 Type help(package="sna") to get started.

 This is bipartite 2.11
 For latest changes see versionlog in  ?"bipartite-package".
 For citation see: citation("bipartite").
 Have a nice time plotting and analysing two-mode networks.


Attaching package: 'bipartite'

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

    nullmodel


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 42-54 (bipartiteD3_Intro.Rmd) 
Error: processing vignette 'bipartiteD3_Intro.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Package suggested but not available for checking: ‘IHW’
Package required but not available: ‘xgboost’

Package suggested but not available for checking: ‘bigrf’

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

> ### Name: blockcluster
> ### Title: Co-Clustering Package
> ### Aliases: blockcluster
> 
> ### ** Examples
> 
> 
> ## Simple example with simulated binary data
> ## load data
> data(binarydata)
> ## usage of coclusterBinary function in its most simplest form
> out<-coclusterBinary(binarydata,nbcocluster=c(2,3))
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

blockcluster version 4.3.2 loaded

----------------
Copyright (C)  <MODAL team @INRIA,Lille & U.M.R. C.N.R.S. 6599 Heudiasyc, UTC>
Please post questions and bugs at: <https://gforge.inria.fr/forum/forum.php?forum_id=11190&group_id=3679>
Running ‘testthat.R’ [489s/144s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(blockForest)
  > 
  > test_check("blockForest")
  ── 1. Failure: Inbag counts match sample fraction, classification (@test_ranger.
  unique(colSums(inbag[51:100, ])) not equal to 45.
  1/1 mismatches
  [1] 44 - 45 == -1
  
  ── 2. Failure: Inbag counts match sample fraction, classification (@test_ranger.
  unique(colSums(inbag[101:150, ])) not equal to 45.
  1/1 mismatches
  [1] 44 - 45 == -1
  
  ── 3. Failure: Inbag counts match sample fraction, probability (@test_ranger.R#8
  unique(colSums(inbag[51:100, ])) not equal to 45.
  1/1 mismatches
  [1] 44 - 45 == -1
  
  ── 4. Failure: Inbag counts match sample fraction, probability (@test_ranger.R#9
  unique(colSums(inbag[101:150, ])) not equal to 45.
  1/1 mismatches
  [1] 44 - 45 == -1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 405 SKIPPED: 0 FAILED: 4
  1. Failure: Inbag counts match sample fraction, classification (@test_ranger.R#71) 
  2. Failure: Inbag counts match sample fraction, classification (@test_ranger.R#80) 
  3. Failure: Inbag counts match sample fraction, probability (@test_ranger.R#89) 
  4. Failure: Inbag counts match sample fraction, probability (@test_ranger.R#98) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘blockmodeling-Ex.R’ failed
The error most likely occurred in:

> ### Name: REGE
> ### Title: REGE - Algorithms for compiting (dis)similarities in terms of
> ###   regular equivalnece
> ### Aliases: REGE REGE.for REGE.nm.for REGE.ow REGE.ow.for REGE.ownm.for
> ###   REGD.for REGD.ow.for REGE.FC REGE.FC.ow REGD.ne.for REGD.ow.ne.for
> ###   REGE.ne.for REGE.nm.diag.for REGE.nm.ne.for REGE.ow.ne.for
> ###   REGE.ownm.diag.for REGE.ownm.ne.for
> ### Keywords: cluster graphs
> 
> ### ** Examples
> 
> n <- 20
> net <- matrix(NA, ncol = n, nrow = n)
> clu <- rep(1:2, times = c(5, 15))
> tclu <- table(clu)
> net[clu == 1, clu == 1] <- 0
> net[clu == 1, clu == 2] <- rnorm(n = tclu[1] * tclu[2], mean = 4, sd = 1) * sample(c(0, 1),
+    size = tclu[1] * tclu[2], replace = TRUE, prob = c(3/5, 2/5))
> net[clu == 2, clu == 1] <- 0
> net[clu == 2, clu == 2] <- 0
> 
> D <- REGE.for(M = net)$E # Any other REGE function can be used
> plot.mat(net, clu = cutree(hclust(d = as.dist(1 - D), method = "ward"),
+    k = 2))
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
> # REGE returns similarities, which have to be converted to
> # disimilarities
> 
> res <- optRandomParC(M = net, k = 2, rep = 10, approaches = "hom", homFun = "ss", blocks = "reg")


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

 *** caught segfault ***
address ebb8b0, cause 'memory not mapped'

Traceback:
 1: optParC(M = M, clu = temppar, approaches = approaches, blocks = blocks,     useMulti = useMulti, save.initial.param = save.initial.param.opt,     ...)
 2: optRandomParC(M = net, k = 2, rep = 10, approaches = "hom", homFun = "ss",     blocks = "reg")
An irrecoverable exception occurred. R is aborting now ...
Installation failed.
See ‘/home/ripley/R/packages/tests32/BMSC.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [13s/258s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bomrang)
  > 
  > test_check("bomrang")
  ── 1. Error: Error handling (@test-get_current_weather.R#7)  ───────────────────
  
  A station was matched.  However, a corresponding JSON file was not found at bom.gov.au.
  1: expect_warning(get_current_weather("Melbourne"), regexp = "Multiple stations match station_name.") at testthat/test-get_current_weather.R:7
  2: quasi_capture(enquo(object), capture_warnings, label = label)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: withCallingHandlers(code, warning = function(condition) {
         out$push(condition)
         invokeRestart("muffleWarning")
     })
  5: eval_bare(get_expr(quo), get_env(quo))
  6: get_current_weather("Melbourne")
  7: tryCatch({
         observations.json <- jsonlite::fromJSON(txt = json_url)
     }, error = function(e) {
         e$message <- paste("\nA station was matched. ", "However, a corresponding JSON file was not found at", 
             "bom.gov.au.\n")
         e$call <- NULL
         stop(e)
     })
  8: tryCatchList(expr, classes, parentenv, handlers)
  9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  10: value[[3L]](cond)
  
  trying URL 'http://www.bom.gov.au/jsp/ncc/cdio/weatherData/av?p_display_type=dailyZippedDataFile&p_stn_num=023000&p_c=-105801732&p_nccObsCode=136'
  downloaded 215 KB
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 28 SKIPPED: 48 FAILED: 1
  1. Error: Error handling (@test-get_current_weather.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...

Error: processing vignette 'BoolNet_package_vignette.Snw' failed with diagnostics:
 chunk 13 
Error in (function (interaction, index, gene)  : 
  No values for the "don't care" entries were specified for gene "Fkh2"!
Execution halted
Package suggested but not available for checking: ‘xgboost’
Package unavailable to check Rd xrefs: ‘xgboost’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 48-53 (get_daily_box_office_info.Rmd) 
Error: processing vignette 'get_daily_box_office_info.Rmd' failed with diagnostics:
is.response(x) is not TRUE
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: lattice
Loading required package: ggplot2
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     3.2Mb
    doc   1.8Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    bin    3.1Mb
    doc    1.3Mb
    libs   3.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'c3'

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

    %>%

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

    grid, legend

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot3bd316734b0d.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot3bd316734b0d.png': No such file or directory
Quitting from lines 56-65 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package which this enhances but not available for checking: ‘FastRWeb’
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R        1.3Mb
    data     1.8Mb
    models   2.5Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
CAST                   package:CAST                    R Documentation

'_c_a_r_e_t' _A_p_p_l_i_c_a_t_i_o_n_s _f_o_r _S_p_a_t_i_a_l-_T_e_m_p_o_r_a_l _M_o_d_e_l_s

_D_e_s_c_r_i_p_t_i_o_n:

     Supporting functionality to run 'caret' with spatial or
     spatial-temporal data. 'caret' is a frequently used package for
     model training and prediction using machine learning. This package
     includes functions to improve spatial-temporal modelling tasks
     using 'caret'. It prepares data for Leave-Location-Out and
     Leave-Time-Out cross-validation which are target-oriented
     validation strategies for spatial-temporal models. To decrease
     overfitting and improve model performances, the package implements
     a forward feature selection that selects suitable predictor
     variables in view to their contribution to the target-oriented
     performance.

_D_e_t_a_i_l_s:

     'caret' Applications for Spatio-Temporal models

_A_u_t_h_o_r(_s):

     Hanna Meyer, Christoph Reudenbach, Marvin Ludwig, Thomas Nauss
     _Maintainer:_ Hanna Meyer <email: hanna.meyer@geo.uni-marburg.de>


PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot191b47669dc.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot191b47669dc.png': No such file or directory
Quitting from lines 65-73 (CAST-intro.Rmd) 
Error: processing vignette 'CAST-intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running examples in ‘cdcfluview-Ex.R’ failed
The error most likely occurred in:

> ### Name: age_group_distribution
> ### Title: Age Group Distribution of Influenza Positive Tests Reported by
> ###   Public Health Laboratories
> ### Aliases: age_group_distribution
> 
> ### ** Examples
> 
> agd <- age_group_distribution(years=2015)
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: Operation timed out after 10000 milliseconds with 0 out of 0 bytes received
Calls: age_group_distribution ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
Running ‘test-all.R’ [6s/25s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("cdcfluview")
  Loading required package: cdcfluview
  ── 1. Error: New API works (@test-cdcfluview.R#5)  ─────────────────────────────
  Timeout was reached: Operation timed out after 10000 milliseconds with 0 out of 0 bytes received
  1: expect_that(age_group_distribution(years = 2017), is_a("data.frame")) at testthat/test-cdcfluview.R:5
  2: condition(object)
  3: expect_is(x, class)
  4: quasi_label(enquo(object), label)
  5: eval_bare(get_expr(quo), get_env(quo))
  6: age_group_distribution(years = 2017)
  7: httr::GET(url = "https://gis.cdc.gov/grasp/fluView6/GetFlu6AllDataP", httr::user_agent(.cdcfluview_ua), 
         httr::add_headers(Accept = "application/json, text/plain, */*", Referer = "https://gis.cdc.gov/grasp/fluview/flu_by_age_virus.html"), 
         httr::timeout(.httr_timeout))
  8: request_perform(req, hu$handle$handle)
  9: request_fetch(req$output, req$url, handle)
  10: request_fetch.write_memory(req$output, req$url, handle)
  11: curl::curl_fetch_memory(url, handle = handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1 SKIPPED: 1 FAILED: 1
  1. Error: New API works (@test-cdcfluview.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    extdata   6.2Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extdata   9.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.9Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Package suggested but not available for checking: ‘iptools’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   2.5Mb
Running examples in ‘ChocoLattes-Ex.R’ failed
The error most likely occurred in:

> ### Name: make_productions_page
> ### Title: Generate HTML page with productions list and summary chart
> ### Aliases: make_productions_page
> 
> ### ** Examples
> 
> 
> # Load example data and convert it to a lattes list
> CV.dir <- system.file("extdata", package="ChocoLattes")
> 
> # Define the aliases of authors "Felipe Campelo" and "Lucas S. Batista":
> # (all aliases will be converted to the first name provided for each author)
> my.aliases <- list(c("Felipe Campelo",
+                      "Felipe Campelo Franca Pinto",
+                      "Felipe Campelo F. Pinto",
+                      "F.C.F. Pinto"),
+                    c("Lucas S. Batista",
+                      "Lucas Batista",
+                      "Lucas de Souza Batista",
+                      "Lucas Souza Batista"))
> 
> lattes.list <- lattes_to_list(CV.dir         = CV.dir,
+                               author.aliases = my.aliases)
> 
> 
> # Build productions page:
> make_productions_page(lattes.list,
+                       chart.type     = "ggplot2",
+                       h1.title       = "ORCS Lab",
+                       h2.title       = "UFMG, Brazil",
+                       language       = "EN")
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    help   1.2Mb
Package suggested but not available for checking: ‘rggobi’
Running ‘testthat.R’ [35s/42s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(classiFunc)
  > 
  > test_check("classiFunc")
  ── 1. Failure: computeDistMat works rucrdtw metrics (@test_computeDistMat.R#100)
  all(as.vector(dist1) <= as.vector(dist3)) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 834 SKIPPED: 0 FAILED: 1
  1. Failure: computeDistMat works rucrdtw metrics (@test_computeDistMat.R#100) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available: ‘xcms’ ‘MSnbase’

Package suggested but not available for checking: ‘CAMERA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘RWeka’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 404-417 (the_clusterR_package.Rmd) 
Error: processing vignette 'the_clusterR_package.Rmd' failed with diagnostics:
std::bad_alloc
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
    pdf   2.8Mb
Package required but not available: ‘quanteda’

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

> ### Name: cmpproc
> ### Title: COM Poisson Process Parameter Estimation.
> ### Aliases: cmpproc
> 
> ### ** Examples
> 
> ## Standard usage
> data(floodcount)
> cmpproc(floodcount$Counts)
Error in solve.default(H) : 
  system is computationally singular: reciprocal condition number = 0
Calls: cmpproc -> single.cmp -> diag -> solve -> solve.default
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 86-87 (codebook.Rmd) 
Error: processing vignette 'codebook.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 100-105 (Running-CoDiNA.Rmd) 
Error: processing vignette 'Running-CoDiNA.Rmd' failed with diagnostics:
Saving a widget with selfcontained = TRUE requires pandoc. For details see:
https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
Execution halted
Running examples in ‘coefplot-Ex.R’ failed
The error most likely occurred in:

> ### Name: extract.coef.xgb.Booster
> ### Title: extract.coef.xgb.Booster
> ### Aliases: extract.coef.xgb.Booster
> 
> ### ** Examples
> 
> library(xgboost)
Error in library(xgboost) : there is no package called ‘xgboost’
Execution halted
Found the following significant warnings:
  "collapsed_lpcm.c", line 74: warning: improper pointer/integer combination: op ">"
See ‘/home/ripley/R/packages/tests32/collpcm.Rcheck/00install.out’ for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   2.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    java   5.2Mb
Package suggested but not available for checking: ‘rscala’
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(commonsMath)
  > 
  > test_check("commonsMath")
  Starting instance. ********************************
  Error in library(rscala) : there is no package called 'rscala'
  Calls: test_check ... source_dir -> lapply -> FUN -> eval -> eval -> library
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 32-37 (commonsMath.Rmd) 
Error: processing vignette 'commonsMath.Rmd' failed with diagnostics:
there is no package called 'rscala'
Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    app   3.1Mb
    doc   2.4Mb
Package required but not available: ‘rminer’

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

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

> ### Name: cham_bill_info
> ### Title: Downloads details of a specific bill by providing type, number
> ###   and year
> ### Aliases: cham_bill_info
> 
> ### ** Examples
> 
> cham_bill_info(type = "PL", number = "3962", year = "2008")
Error in open.connection(x, "rb") : 
  Timeout was reached: Operation timed out after 10206 milliseconds with 0 out of 0 bytes received
Calls: cham_bill_info ... read_xml.character -> read_xml.connection -> open -> open.connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 64-65 (chamber.Rmd) 
Error: processing vignette 'chamber.Rmd' failed with diagnostics:
Timeout was reached: Operation timed out after 10264 milliseconds with 0 out of 0 bytes received
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
Running examples in ‘cooccurNet-Ex.R’ failed
The error most likely occurred in:

> ### Name: coocnet
> ### Title: coocnet
> ### Aliases: coocnet
> 
> ### ** Examples
> 
> cooccurNetwork  = coocnet(dataFile=getexample(dataType="protein"), dataType="protein")
reading file......
completed. (10,329)
preprocess file......Error in if (pred >= memsize * alpha || ncol > 150 || (nrow > 30000 &  : 
  missing value where TRUE/FALSE needed
Calls: coocnet ... cooccur.dataprepreprocess.preprocess -> inmemoryflag
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 176-178 (Extending-cooccurNet.Rmd) 
Error: processing vignette 'Extending-cooccurNet.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
Execution halted
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    R     2.3Mb
    doc   5.9Mb
Package which this enhances but not available for checking: ‘quanteda’
Package suggested but not available for checking: ‘quanteda’
Running examples in ‘corpustools-Ex.R’ failed
The error most likely occurred in:

> ### Name: tCorpus$top_features
> ### Title: Show top features
> ### Aliases: tCorpus$top_features top_features
> 
> ### ** Examples
> 
> tc = tokens_to_tcorpus(corenlp_tokens, token_id_col = 'id')
> 
> tc$top_features('lemma')
Error in value[[3L]](cond) : 
  The dcast generic in data.table has been passed a data.frame (not a data.table) but the reshape2 package is not installed to process this type. Please either install reshape2 and try again, or pass a data.table to dcast instead.
Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 253-341 (introduction_to_coveffectsplot.Rmd) 
Error: processing vignette 'introduction_to_coveffectsplot.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   6.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 77-78 (cranly.Rmd) 
Error: processing vignette 'cranly.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Running examples in ‘crqanlp-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_text_series
> ### Title: Get a text series
> ### Aliases: get_text_series
> ### Keywords: misc
> 
> ### ** Examples
> 
> 
> ## from a literal string
> rsrc = "here is a raw raw raw string, literally"
> ts = get_text_series(rsrc,typ='string')
Warning in tm_map.SimpleCorpus(rawText, tolower) :
  transformation drops documents
Warning in tm_map.SimpleCorpus(rawText, sentencebreak) :
  transformation drops documents
Warning in tm_map.SimpleCorpus(rawText, removepunct) :
  transformation drops documents
Warning in tm_map.SimpleCorpus(rawText, stripWhitespace) :
  transformation drops documents
> print(ts)
[1] 1 2 3 4 4 4 5 6
> 
> ## from tibble
> library(gutenbergr)
> ## let's get Alice's Adventures in Wonderland by Carroll
> # gutenberg_works(author == "Carroll, Lewis") 
> rsrc = gutenberg_download(11) ## take the text
> ts = get_text_series(rsrc, typ = "tibble", removeStopwords = TRUE)
Warning in tm_map.SimpleCorpus(rawText, tolower) :
  transformation drops documents
Warning in tm_map.SimpleCorpus(rawText, sentencebreak) :
  transformation drops documents
Warning in tm_map.SimpleCorpus(rawText, removepunct) :
  transformation drops documents
Warning in tm_map.SimpleCorpus(rawText, removeWords, stopwords("english")) :
  transformation drops documents
Warning in tm_map.SimpleCorpus(rawText, stripWhitespace) :
  transformation drops documents
> print(ts[1:10])
 [1]  1  2  3  4  5  6  7  8  9 10
> 
> ## from URL
> rsrc = "http://www.omegahat.net"
> ts = get_text_series(rsrc, typ = "url")
Error in function (type, msg, asError = TRUE)  : 
  Failed to connect to www.omegahat.net port 80: No route to host
Calls: get_text_series -> getURL -> curlPerform -> <Anonymous> -> fun
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/csp.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/ripley/R/packages/tests32/ctsem.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required namespace: rmarkdown
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 142-152 (truncated_tesseract.Rmd) 
Error: processing vignette 'truncated_tesseract.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 177-179 (cycling_data_analysis.Rmd) 
Error: processing vignette 'cycling_data_analysis.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  5.1Mb
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    doc   4.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 27-38 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  5.2Mb
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installed size is  6.7Mb
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installed size is  5.2Mb
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    Pied_Flycatchers_1   2.5Mb
    Pied_Flycatchers_2   1.3Mb
    doc                  1.2Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    java  15.5Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
sh: whoami:  not found
sh: git:  not found
sh: git:  not found
Data report generation is finished. Please wait while your output file is being rendered.
Quitting from lines 729-768 (extending_dataMaid.Rmd) 
Error: processing vignette 'extending_dataMaid.Rmd' failed with diagnostics:
pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 26-34 (get_started.Rmd) 
Error: processing vignette 'get_started.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  5.1Mb
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    doc    1.3Mb
    libs   2.7Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/data.table.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 512-515 (data.tree.Rmd) 
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Running examples in ‘dbarts-Ex.R’ failed
The error most likely occurred in:

> ### Name: bart
> ### Title: Bayesian Additive Regression Trees
> ### Aliases: bart bart2 plot.bart predict.bart
> ### Keywords: nonparametric tree regression nonlinear
> 
> ### ** Examples
> 
> ## simulate data (example from Friedman MARS paper)
> ## y = f(x) + epsilon , epsilon ~ N(0, sigma)
> ## x consists of 10 variables, only first 5 matter
> 
> f <- function(x) {
+     10 * sin(pi * x[,1] * x[,2]) + 20 * (x[,3] - 0.5)^2 +
+       10 * x[,4] + 5 * x[,5]
+ }
> 
> set.seed(99)
> sigma <- 1.0
> n     <- 100
> 
> x  <- matrix(runif(n * 10), n, 10)
> Ey <- f(x)
> y  <- rnorm(n, Ey, sigma)
> 
> ## run BART
> set.seed(99)
> bartFit <- bart(x, y)

Running BART with numeric y

number of trees: 200
Prior:
	k: 2.000000
	degrees of freedom in sigma prior: 3.000000
	quantile in sigma prior: 0.900000
	scale in sigma prior: 0.002181
	power and base for tree prior: 2.000000 0.950000
	use quantiles for rule cut points: false
data:
	number of training observations: 100
	number of test observations: 0
	number of explanatory variables: 10
	init sigma: 2.756573, curr sigma: 2.756573

Cutoff rules c in x<=c vs x>c
Number of cutoffs: (var: number of possible c):
(1: 100) (2: 100) (3: 100) (4: 100) (5: 100) 
(6: 100) (7: 100) (8: 100) (9: 100) (10: 100) 


 *** caught segfault ***
address bfa21bcc, cause 'memory not mapped'

Traceback:
 1: .Call(C_dbarts_run, ptr, as.integer(numBurnIn), as.integer(numSamples))
 2: sampler$run(0L, control@n.burn, FALSE)
 3: bart(x, y)
An irrecoverable exception occurred. R is aborting now ...
Package suggested but not available for checking: ‘RPostgres’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    sample_data   3.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'gridExtra'

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

    combine

Quitting from lines 84-97 (MultiObjectiveDecisionAnalysisinR.Rmd) 
Error: processing vignette 'MultiObjectiveDecisionAnalysisinR.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Joining, by = "key"
Joining, by = "key"
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 102-122 (sjukhus.Rmd) 
Error: processing vignette 'sjukhus.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

---------------------
Welcome to dendextend version 1.9.0
Type citation('dendextend') for how to cite the package.

Type browseVignettes(package = 'dendextend') for the package vignette.
The github page is: https://github.com/talgalili/dendextend/

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

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


Attaching package: 'dendextend'

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

    cutree

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

Attaching package: 'gplots'

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

    bluered, greenred

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

    lowess

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 931-933 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    1.9Mb
    help   1.4Mb
Packages which this enhances but not available for checking:
  ‘gurobi’ ‘Rcplex’ ‘Rmosek’ ‘Rsymphony’
Running ‘test-that.R’ [108s/206s]
Running the tests in ‘tests/test-that.R’ failed.
Complete output:
  > library(testthat)
  > test_check("devtools")
  Loading required package: devtools
  Error : pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  ── 1. Error: Package readme can be built  (@test-build-readme.R#8)  ────────────
  pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  1: build_readme("testReadme") at testthat/test-build-readme.R:8
  2: callr::r(build, args = list(pkg_path = pkg$path, readme_path = readme_path, ... = ..., 
         quiet = quiet), show = TRUE, spinner = FALSE)
  3: get_result(output = out, options)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 42 SKIPPED: 11 FAILED: 1
  1. Error: Package readme can be built  (@test-build-readme.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.4Mb
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installed size is  5.0Mb
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    data   3.5Mb
    doc    1.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: rgl
Loading required namespace: rmarkdown
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 230-234 (DGVM3D.Rmd) 
Error: processing vignette 'DGVM3D.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘rsvg’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.3Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
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installed size is  6.7Mb
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    doc   5.7Mb
installed size is  6.8Mb
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    doc   6.0Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    include  15.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/DMMF.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading dodgr
Re-compiling dodgr
Quitting from lines 18-19 (benchmark.Rmd) 
Error: processing vignette 'benchmark.Rmd' failed with diagnostics:
System command error
Execution halted
Packages which this enhances but not available for checking:
  ‘gurobi’ ‘Rmosek’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   2.9Mb
File ‘DPpackage/libs/DPpackage.so’:
  Found ‘__f90_close’, possibly from ‘close’ (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDBDPdensity.o’, ‘LDDPdensity.o’,
      ‘LDDPsurvival.o’, ‘LDPDdoublyintsba.o’, ‘LDTFPdensity.o’,
      ‘LDTFPglmmpois.o’, ‘LDTFPsurvival.o’, ‘PSgamgam.o’,
      ‘PSgamgauss.o’, ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’,
      ‘ToolsLDTFP.o’
  Found ‘__f90_esuw’, possibly from ‘write’ (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDBDPdensity.o’, ‘LDDPdensity.o’,
      ‘LDDPsurvival.o’, ‘LDPDdoublyintsba.o’, ‘LDTFPdensity.o’,
      ‘LDTFPglmmpois.o’, ‘LDTFPsurvival.o’, ‘PSgamgam.o’,
      ‘PSgamgauss.o’, ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’
  Found ‘__f90_open’, possibly from ‘open’ (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDBDPdensity.o’, ‘LDDPdensity.o’,
      ‘LDDPsurvival.o’, ‘LDPDdoublyintsba.o’, ‘LDTFPdensity.o’,
      ‘LDTFPglmmpois.o’, ‘LDTFPsurvival.o’, ‘PSgamgam.o’,
      ‘PSgamgauss.o’, ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’,
      ‘ToolsLDTFP.o’
  Found ‘__f90_rewind’, possibly from ‘rewind’ (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDDPdensity.o’, ‘LDDPsurvival.o’,
      ‘LDPDdoublyintsba.o’, ‘PSgamgam.o’, ‘PSgamgauss.o’,
      ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’, ‘ToolsLDTFP.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
drtmle: TMLE with doubly robust inference
Version: 1.0.4
Loading required package: nnls
Super Learner
Version: 2.0-24
Package created on 2018-08-10

Loading required package: nloptr
Loading required package: nloptr
Loading required package: nloptr
Loading required package: nloptr
Loading required package: quadprog
Loading required package: earth
Loading required package: plotmo
Loading required package: plotrix
Loading required package: TeachingDemos
Loading required package: quadprog
Loading required package: earth
Loading required package: plotmo
Loading required package: plotrix
Loading required package: TeachingDemos
Loading required package: quadprog
Loading required package: earth
Loading required package: plotmo
Loading required package: plotrix
Loading required package: TeachingDemos
Loading required package: quadprog
Loading required package: earth
Loading required package: plotmo
Loading required package: plotrix
Loading required package: TeachingDemos
Loading required package: future
Quitting from lines 1049-1062 (using_drtmle.Rmd) 
Error: processing vignette 'using_drtmle.Rmd' failed with diagnostics:
there is no package called 'snow'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Using constraints: b = 1
Using constraints: b = 1
Running default monotherapy fitting. Note that if constraints are needed, run mono fitting manually first
Using constraints: b = 1
Using constraints: b = 1
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot35b241bf198f.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot35b241bf198f.png': No such file or directory
Quitting from lines 357-358 (userGuide.Rmd) 
Error: processing vignette 'userGuide.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    media       2.7Mb
    shinyapps   3.3Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    appinformation  10.2Mb
    media            1.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 163-164 (Designing-33PC.Rmd) 
Error: processing vignette 'Designing-33PC.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    doc    2.8Mb
    libs   1.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include   -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c LinearSDE.c -o LinearSDE.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -G -L/usr/local/lib -o LinearSDE.so LinearSDE.o -L/usr/local/lib -lgsl -lgslcblas -lm
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'LinearDiscreteTimeModels.tex' failed.
Messages:
/usr/local/bin/texi2dvi: line 411: 19465 Killed                  "$@" 2>&5 1>&2
/usr/local/bin/texi2dvi: biber failed
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘EasyMx-Ex.R’ failed
The error most likely occurred in:

> ### Name: emxTwinModel
> ### Title: Creates behavior genetics Twin Model
> ### Aliases: emxTwinModel emxModelTwin
> 
> ### ** Examples
> 
>    
> # Create an ACE model in 10 lines
> # 8 of those are data handling.
> # 2 are the actual model.
> require(EasyMx)
> require(OpenMx)
> data(twinData)
> twinVar = names(twinData)
> selVars <- c('ht1', 'bmi1','ht2','bmi2')
> mzdzData <- subset(twinData, zyg %in% c(1, 3), c(selVars, 'zyg'))
> mzdzData$RCoef <- c(1, NA, .5)[mzdzData$zyg]
> 
> run3 <- emxTwinModel(model='Cholesky', relatedness='RCoef',
+ 	data=mzdzData, use=selVars, run=TRUE, name='TwCh')
Running TwCh with 11 parameters

 *** caught segfault ***
address 8, cause 'memory not mapped'

Traceback:
 1: runHelper(model, frontendStart, intervals, silent, suppressWarnings,     unsafe, checkpoint, useSocket, onlyFrontend, useOptimizer)
 2: OpenMx::mxRun(model)
 3: emxTwinModel(model = "Cholesky", relatedness = "RCoef", data = mzdzData,     use = selVars, run = TRUE, name = "TwCh")
An irrecoverable exception occurred. R is aborting now ...
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    hac    4.3Mb
Running ‘testthat.r’ [2s/21s]
Running the tests in ‘tests/testthat.r’ failed.
Complete output:
  > # Run all unit tests
  > 
  > # This is a wrapper around all the tests specified
  > # in the tests/testthat directory. These tests are visible
  > # to users and serve as small examples as well.
  > testthat::test_check("ecmwfr")
  Loading required package: ecmwfr
  Error in curl::curl_fetch_memory(url, handle = handle) : 
    Timeout was reached: Operation timed out after 10000 milliseconds with 0 out of 0 bytes received
  ── 1. Error: (unknown) (@test_ecmwf.r#40)  ─────────────────────────────────────
  $ operator is invalid for atomic vectors
  1: ecmwf_running(wf_server(service = "webapi")) at testthat/test_ecmwf.r:40
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 3 FAILED: 1
  1. Error: (unknown) (@test_ecmwf.r#40) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Error in re-building vignettes:
  ...
Loading required package: foreign
This is vegdata 0.9.5

No Turbowin installation path found. 

############################################################
Turboveg root directory is set to "/tmp/Rtmpw9aOgr"
If you want to change this use: options(tv_home="<path_to_your_Turbowin_root>")
############################################################
Quitting from lines 51-61 (eHOF.Rnw) 
Error: processing vignette 'eHOF.Rnw' failed with diagnostics:
unsupported conversion from 'CP437' to ''
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    examples   4.2Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data  11.5Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    extdata  10.4Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    xsd   5.9Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.6Mb
Error in re-building vignettes:
  ...

Error: processing vignette 'empirical.Rnw' failed with diagnostics:
 chunk 8 
Error in x[seq_len(n)] : object of type 'closure' is not subsettable
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       1.4Mb
    extdata   1.5Mb
Running examples in ‘eNetXplorer-Ex.R’ failed
The error most likely occurred in:

> ### Name: eNetXplorer
> ### Title: generates family of elastic net models for different alphas
> ### Aliases: eNetXplorer
> 
> ### ** Examples
> 
> ## Don't show: 
> set.seed(123)
> fit = eNetXplorer(x=matrix(rnorm(75),ncol=3),y=rnorm(25),family="gaussian",
+ n_run=5,n_perm_null=4,alpha=c(0.5,1))
Error in if (any(lambda < 0)) stop("lambdas should be non-negative") : 
  missing value where TRUE/FALSE needed
Calls: eNetXplorer -> eNetXplorerGaussian -> glmnet
Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    doc    3.4Mb
    help   3.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 150-151 (epicontacts.Rmd) 
Error: processing vignette 'epicontacts.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 117-120 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 367-368 (EpiReport_Vignette.Rmd) 
Error: processing vignette 'EpiReport_Vignette.Rmd' failed with diagnostics:
`render_flextable` needs to be used as a renderer for a knitr/rmarkdown R code chunk (render by rmarkdown)
Execution halted
Running examples in ‘EpiSignalDetection-Ex.R’ failed
The error most likely occurred in:

> ### Name: runEpiSDReport
> ### Title: Run the EpiSignalDetection report (HTML markdown)
> ### Aliases: runEpiSDReport
> 
> ### ** Examples
> 
> #---> OR
> 
> #-- First setting the parameters to run the report for
> input <- list(
+ disease = "Salmonellosis",
+ country = "Portugal",
+ indicator = "Reported cases",
+ stratification = "Confirmed cases",
+ unit = "Month",
+ daterange = c("2011-01-01", "2016-12-31"),
+ algo = "FarringtonFlexible",
+ testingperiod = 6
+ )
> 
> #-- Second running the report based on the EpiSignalDetection::SignalData dataset
> #-- and store it in a temporary folder
> runEpiSDReport(input = input)
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
Packages required but not available: ‘SNPRelate’ ‘gdsfmt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.1Mb
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    exiftool  14.4Mb
Package suggested but not available for checking: ‘tesseract’
Package suggested but not available for checking: ‘RWeka’
Package unavailable to check Rd xrefs: ‘RWeka’
Running ‘run-all.R’
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("farff")
  Loading required package: farff
  ── 1. Error: quick test with small arffs (@test_quick.R#6)  ────────────────────
  there is no package called 'RWeka'
  1: compareRWeka(INST_ARFF_DIR, "iris.arff", data.reader = dreader) at testthat/test_quick.R:6
  2: RWeka::read.arff at /home/ripley/R/packages/tests32/farff.Rcheck/tests/testthat/helper.R:17
  3: getExportedValue(pkg, name)
  4: asNamespace(ns)
  5: getNamespace(ns)
  6: tryCatch(loadNamespace(name), error = function(e) stop(e))
  7: tryCatchList(expr, classes, parentenv, handlers)
  8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 8 SKIPPED: 0 FAILED: 1
  1. Error: quick test with small arffs (@test_quick.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
Package suggested but not available for checking: ‘Rserve’
Installation failed.
See ‘/home/ripley/R/packages/tests32/FastRWeb.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [8s/106s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(FedData)
  Loading required package: sp
  > 
  > test_check("FedData")
  ── 1. Error: The SSURGO inventory dataset is available at the correct URL (@test
  Timeout was reached: Operation timed out after 10338 milliseconds with 0 out of 0 bytes received
  1: expect_false(suppressWarnings(httr::http_error(url))) at testthat/test.SSURGO.R:7
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: suppressWarnings(httr::http_error(url))
  5: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  6: httr::http_error(url)
  7: http_error.character(url)
  8: http_error(HEAD(x, ...))
  9: HEAD(x, ...)
  10: request_perform(req, hu$handle$handle)
  11: request_fetch(req$output, req$url, handle)
  12: request_fetch.write_memory(req$output, req$url, handle)
  13: curl::curl_fetch_memory(url, handle = handle)
  
  ── 2. Failure: The SSURGO datasets are available at the correct URL (@test.SSURG
  `suppressWarnings(curl::curl(url) %>% readLines(n = 1))` threw an error.
  Message: Timeout was reached: Operation timed out after 10002 milliseconds with 0 out of 0 bytes received
  Class:   simpleError/error/condition
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 23 SKIPPED: 1 FAILED: 2
  1. Error: The SSURGO inventory dataset is available at the correct URL (@test.SSURGO.R#7) 
  2. Failure: The SSURGO datasets are available at the correct URL (@test.SSURGO.R#31) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [5s/24s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fedregs)
  > 
  > test_check("fedregs")
  terminate called after throwing an instance of 'Rcpp::exception'
    what():  Space required after the Public Identifier [65]
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Warning: Removed 2 rows containing missing values (geom_point).
Quitting from lines 137-146 (quick_charts.Rmd) 
Error: processing vignette 'quick_charts.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 70-72 (lifeExpectancy.Rmd) 
Error: processing vignette 'lifeExpectancy.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 46-49 (layout.Rmd) 
Error: processing vignette 'layout.Rmd' failed with diagnostics:
`render_flextable` needs to be used as a renderer for a knitr/rmarkdown R code chunk (render by rmarkdown)
Execution halted
Package suggested but not available for checking: ‘multipanelfigure’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    fonts   6.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    fonts   7.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 168-169 (formattable-data-frame.Rmd) 
Error: processing vignette 'formattable-data-frame.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Packages suggested but not available for checking:
  ‘Rsocp’ ‘Rnlminb2’ ‘Rdonlp2’ ‘Rsymphony’
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   5.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R   5.8Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
    doc    2.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Package unavailable to check Rd xrefs: ‘RMark’
Packages suggested but not available for checking: ‘RWeka’ ‘FSelector’
Package unavailable to check Rd xrefs: ‘FSelector’
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    data  16.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 604-605 (futureheatwaves.Rmd) 
Error: processing vignette 'futureheatwaves.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   3.4Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      1.9Mb
Error in re-building vignettes:
  ...
Warning in packageDescription("gputools") :
  no package 'gputools' was found
Error: processing vignette 'gcbd.Rnw' failed with diagnostics:
at gcbd.Rnw:860, subscript out of bounds
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    exdata   5.3Mb
Package suggested but not available for checking: ‘reactome.db’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc        1.5Mb
    examples   1.9Mb
    vign       1.4Mb
installed size is 27.3Mb
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    data  27.2Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R         6.3Mb
    extdata   1.4Mb
Error in re-building vignettes:
  ...
Loading required package: sf
Linking to GEOS 3.6.3, GDAL 2.2.4, PROJ 5.1.0
Loading required package: sp
Loading required package: geoR
--------------------------------------------------------------
 Analysis of Geostatistical Data
 For an Introduction to geoR go to http://www.leg.ufpr.br/geoR
 geoR version 1.7-5.2.1 (built on 2016-05-02) is now loaded
--------------------------------------------------------------

Loading required package: maxLik
Loading required package: miscTools

Please cite the 'maxLik' package as:
Henningsen, Arne and Toomet, Ott (2011). maxLik: A package for maximum likelihood estimation in R. Computational Statistics 26(3), 443-458. DOI 10.1007/s00180-010-0217-1.

If you have questions, suggestions, or comments regarding the 'maxLik' package, please use a forum or 'tracker' at maxLik's R-Forge site:
https://r-forge.r-project.org/projects/maxlik/
Loading required package: raster
Loading required package: pdist
Loading required package: Matrix
Quitting from lines 476-516 (geosample-vignette.Rnw) 
Error: processing vignette 'geosample-vignette.Rnw' failed with diagnostics:
cannot allocate vector of size 3.0 Gb
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 53-60 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
EXPR must be a length 1 vector
Execution halted
Running examples in ‘gesis-Ex.R’ failed
The error most likely occurred in:

> ### Name: download_codebook
> ### Title: Download the codebook for a Gesis data set
> ### Aliases: download_codebook
> 
> ### ** Examples
> 
> download_codebook(doi = "0078")
Error in open.connection(x, "rb") : 
  Timeout was reached: Operation timed out after 10000 milliseconds with 0 out of 0 bytes received
Calls: download_codebook -> read_html -> read_html.default
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 60-61 (gesis.Rmd) 
Error: processing vignette 'gesis.Rmd' failed with diagnostics:
Timeout was reached: Operation timed out after 10000 milliseconds with 0 out of 0 bytes received
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 99-112 (gitrd-vignette-introduction.Rmd) 
Error: processing vignette 'gitrd-vignette-introduction.Rmd' failed with diagnostics:
cannot open URL 'http://www.rad.cvm.gov.br/enetconsulta/frmDownloadDocumento.aspx?CodigoInstituicao=2&NumeroSequencialDocumento=8203'
Execution halted
Packages suggested but not available for checking: ‘av’ ‘gifski’
Running ‘testthat.R’ [7s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(gganimate)
  Loading required package: ggplot2
  > 
  > test_check("gganimate")
  ── 1. Error: anim_save overwrites existing files (@test-anim_save.R#8)  ────────
  The `gifski_renderer()` is selected by default but requires the gifski
  package to be installed. Either install gifski or use another renderer.
  See `?renderers` for a list of available ones.
  1: capture.output({
         a1 <- animate(p, nframes = 2)
         a2 <- animate(p, nframes = 3)
     }) at testthat/test-anim_save.R:8
  2: evalVis(expr)
  3: withVisible(eval(expr, pf))
  4: eval(expr, pf)
  5: eval(expr, pf)
  6: animate(p, nframes = 2)
  7: animate.gganim(p, nframes = 2)
  8: prepare_args(nframes = nframes, fps = fps, duration = duration, detail = detail, 
         renderer = renderer, device = device, ref_frame = ref_frame, start_pause = start_pause, 
         end_pause = end_pause, rewind = rewind, ...)
  9: renderer %?% chunk_args$renderer %||% getOption("gganimate.renderer", gifski_renderer())
  10: getOption("gganimate.renderer", gifski_renderer())
  11: gifski_renderer()
  12: stop("The `gifski_renderer()` is selected by default but requires the gifski\n", 
         "package to be installed. Either install gifski or use another renderer.\n", 
         "See `?renderers` for a list of available ones.", call. = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 6 SKIPPED: 0 FAILED: 1
  1. Error: anim_save overwrites existing files (@test-anim_save.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
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Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 51-57 (gganimate.Rmd) 
Error: processing vignette 'gganimate.Rmd' failed with diagnostics:
The `gifski_renderer()` is selected by default but requires the gifski
package to be installed. Either install gifski or use another renderer.
See `?renderers` for a list of available ones.
Execution halted
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    R           1.1Mb
    doc         2.8Mb
    tutorials   1.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 99-101 (ggimage.Rmd) 
Error: processing vignette 'ggimage.Rmd' failed with diagnostics:
there is no package called 'rsvg'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra

Attaching package: 'ggiraphExtra'

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

    addLabelDf, getMapping

Loading required package: plyr
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 45-49 (ggPredict.Rmd) 
Error: processing vignette 'ggPredict.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
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Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 125-126 (ggseas.Rmd) 
Error: processing vignette 'ggseas.Rmd' failed with diagnostics:
Process terminated
Execution halted
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Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 63-64 (msgimme-vignette.Rmd) 
Error: processing vignette 'msgimme-vignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Running examples in ‘glmnet-Ex.R’ failed
The error most likely occurred in:

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 34-35 (installation-and-authentication.Rmd) 
Error: processing vignette 'installation-and-authentication.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
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installed size is 27.9Mb
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installed size is  6.5Mb
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Running examples in ‘GSE-Ex.R’ failed
The error most likely occurred in:

> ### Name: TSGS
> ### Title: Two-Step Generalized S-Estimator for cell- and case-wise
> ###   outliers
> ### Aliases: TSGS
> 
> ### ** Examples
> 
> set.seed(12345)
> 
> # Generate 5% cell-wise contaminated normal data
> # using a random correlation matrix with condition number 100
> x <- generate.cellcontam(n=100, p=10, cond=100, contam.size=5, contam.prop=0.05)
> 
> ## Using MLE
> slrt( cov(x$x), x$A)
[1] 84.1606
> 
> ## Using Fast-S
> slrt( rrcov:::CovSest(x$x)@cov, x$A)
[1] 36.74531
> 
> ## Using 2SGS
> slrt( TSGS(x$x)@S, x$A)
Error: 'DetectDeviatingCells' is not an exported object from 'namespace:cellWise'
Execution halted
Running examples in ‘GSIF-Ex.R’ failed
The error most likely occurred in:

> ### Name: fit.regModel-methods
> ### Title: Fits a regression model to spatial data
> ### Aliases: fit.regModel
> ###   fit.regModel,formula,data.frame,SpatialPixelsDataFrame,character-method
> 
> ### ** Examples
> 
> library(sp)
> library(rpart)
> library(nlme)
> library(gstat)
> library(randomForest)
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
> library(quantregForest)
Loading required package: RColorBrewer
> library(xgboost)
Error in library(xgboost) : there is no package called ‘xgboost’
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Error: processing vignette 'getting_started.Rmd' failed with diagnostics:
invalid multibyte string at '<f0><9f><8c><9f> the repo on GitHub! </li>
<li>If you&#39;re looking to contribute, check out the <a href="https://github.com/h2oai/h2o4gpu/blob/master/CONTRIBUTING.md">CONTRIBUTING.md</a> file.</li>
<li>All open issues that are specific to the R package are <a href="https://github.com/h2oai/h2o4gpu/labels/R">here</a>.</li>
<li>All open issues are <a href="https://github.com/h2oai/h2o4gpu/issues?utf8=%E2%9C%93&amp;q=is%3Aopen">here</a>.</li>
</ul>

<h2>Installation</h2>

<p>The Python package is a prerequisite for the R package. So first, follow the instructions <a href="https://github.com/h2oai/h2o4gpu#installation">here</a> to install the <strong>h2o4gpu</strong> Python package (either at the system level or in a Python virtual envivonment). The easiest thing to do is to <code>pip install</code> either the stable or bleeding edge <code>whl</code> file. To ensure compatibility, the Python pa
Execution halted
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    java  123.5Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 95-107 (retype.Rmd) 
Error: processing vignette 'retype.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
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Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 165-168 (haplor-vignette.Rmd) 
Error: processing vignette 'haplor-vignette.Rmd' failed with diagnostics:
undefined columns selected
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 122-128 (Basic_use.Rmd) 
Error: processing vignette 'Basic_use.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Found the following significant warnings:
  readstat/readstat_convert.c:18:42: warning: passing argument 2 of ‘libiconv’ from incompatible pointer type [-Wincompatible-pointer-types]
  src/spss/readstat_sav_parse.rl:89:17: warning: passing argument 2 of ‘libiconv’ from incompatible pointer type [-Wincompatible-pointer-types]
  src/spss/readstat_sav_parse.rl:197:17: warning: passing argument 2 of ‘libiconv’ from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/ripley/R/packages/tests32/haven.Rcheck/00install.out’ for details.
Running examples in ‘hdf5r-Ex.R’ failed
The error most likely occurred in:

> ### Name: H5A-class
> ### Title: Class for representing HDF5 attributes
> ### Aliases: H5A-class H5A
> 
> ### ** Examples
> 
> fname <- tempfile(fileext = ".h5")
> file <- H5File$new(fname, mode = "a")
Error in H5File.open(filename, mode, file_create_pl, file_access_pl) : 
  HDF5-API Errors:
    error #000: H5F.c in H5Fcreate(): line 444: unable to create file
        class: HDF5
        major: File accessibilty
        minor: Unable to open file

    error #001: H5Fint.c in H5F__create(): line 1364: unable to open file
        class: HDF5
        major: File accessibilty
        minor: Unable to open file

    error #002: H5Fint.c in H5F_open(): line 1615: unable to lock the file
        class: HDF5
        major: File accessibilty
        minor: Unable to open file

    error #003: H5FD.c in H5FD_lock(): line 1640: driver lock request failed
        class: HDF5
        major: Virtual File Layer
        minor: Can't update object

    error #004: H5FDsec2.c in H5FD_sec2_lock(): line 941: unable to lock file, errno = 14, error message = 'Bad address'
        class: HDF5
        major: File accessibilty
        minor: Bad file ID accessed
Calls: <Anonymous> -> <Anonymous> -> H5File.open
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-2'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Quitting from lines 73-77 (hdf5r.Rmd) 
Error: processing vignette 'hdf5r.Rmd' failed with diagnostics:
HDF5-API Errors:
    error #000: H5F.c in H5Fcreate(): line 444: unable to create file
        class: HDF5
        major: File accessibilty
        minor: Unable to open file

    error #001: H5Fint.c in H5F__create(): line 1364: unable to open file
        class: HDF5
        major: File accessibilty
        minor: Unable to open file

    error #002: H5Fint.c in H5F_open(): line 1615: unable to lock the file
        class: HDF5
        major: File accessibilty
        minor: Unable to open file

    error #003: H5FD.c in H5FD_lock(): line 1640: driver lock request failed
        class: HDF5
        major: Virtual File Layer
        minor: Can't update object

    error #004: H5FDsec2.c in H5FD_sec2_lock(): line 941: unable to lock file, errno = 14, error message = 'Bad address'
        class: HDF5
        major: File accessibilty
        minor: Bad file ID accessed
Execution halted
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    doc   4.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: plotly
Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Loading required package: viridis
Loading required package: viridisLite

======================
Welcome to heatmaply version 0.15.2

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

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

Quitting from lines 88-90 (heatmaply.Rmd) 
Error: processing vignette 'heatmaply.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
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Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Highcharts (www.highcharts.com) is a Highsoft software product which is
not free for commercial and Governmental use

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 52-53 (charting-data-frames.Rmd) 
Error: processing vignette 'charting-data-frames.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Package required but not available: ‘xcms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘RProtoBuf’
Package unavailable to check Rd xrefs: ‘RProtoBuf’
Package required but not available: ‘bamsignals’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  9.3Mb
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installed size is 16.8Mb
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Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
trying URL 'https://arxiv.org/e-print/1406.4806v1'
Content type 'application/x-eprint-tar' length 29273 bytes (28 KB)
==================================================
downloaded 28 KB

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Error: processing vignette 'intro.Rmd' failed with diagnostics:
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Execution halted
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Running examples in ‘IAPWS95-Ex.R’ failed
The error most likely occurred in:

> ### Name: TDh
> ### Title: Temperature, Function of Density and Enthalpy
> ### Aliases: TDh
> 
> ### ** Examples
> 
> D <- 838.025
> h <- 977.181624
> T_Dh <- TDh(D,h)
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 25-37 (ibmsunburst.Rmd) 
Error: processing vignette 'ibmsunburst.Rmd' failed with diagnostics:
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Execution halted
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Running examples in ‘ifa-Ex.R’ failed
The error most likely occurred in:

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

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

Traceback:
 1: sub(".*\\.", "", x)
 2: fileExt(file)
 3: data(memory)
An irrecoverable exception occurred. R is aborting now ...
Error in re-building vignettes:
  ...
Quitting from lines 1345-1400 (pritikin-schmidt.Rnw) 
Error: processing vignette 'pritikin-schmidt.Rnw' failed with diagnostics:
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Execution halted
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    help   1.2Mb
    libs   6.6Mb
installed size is 16.8Mb
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    doc       5.4Mb
    extdata   1.2Mb
    include   2.9Mb
    libs      4.9Mb
Running examples in ‘Inflation-Ex.R’ failed
The error most likely occurred in:

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

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

Error in checkX13(fail = TRUE, fullcheck = FALSE, htmlcheck = FALSE) : 
  Process terminated
Calls: INFL.core_tf -> <Anonymous> -> checkX13
Execution halted
Running ‘spelling.R’
  Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(inplace)
  > 
  > test_check("inplace")
  ── 1. Failure: in-place operators work in common cases (@test-operators.R#82)  ─
  `X` not identical to `X2`.
  Objects equal but not identical
  
  ── 2. Failure: in-place operators work in common cases (@test-operators.R#84)  ─
  `X` not identical to `X2`.
  Objects equal but not identical
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 806 SKIPPED: 0 FAILED: 2
  1. Failure: in-place operators work in common cases (@test-operators.R#82) 
  2. Failure: in-place operators work in common cases (@test-operators.R#84) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(stringr)
  > library(io)
  Loading required package: filenamer
  > 
  > test_check("io")
  ── 1. Error: (unknown) (@test_read-write-read.R#8)  ────────────────────────────
  HDF5. File accessibilty. Unable to open file.
  1: test_read_write_read(f) at testthat/test_read-write-read.R:8
  2: qread(infile) at /home/ripley/R/packages/tests32/io.Rcheck/tests/testthat/helper.R:47
  3: .qread(file, if (is.null(type)) .infer_file_type(file) else type, ...)
  4: qread.hdf5(file, if (is.null(type)) .infer_file_type(file) else type, ...)
  5: trimws(rhdf5::h5ls(file)$name)
  6: mysub("[ \t\r\n]+$", mysub("^[ \t\r\n]+", x))
  7: sub(re, "", x, perl = TRUE)
  8: mysub("^[ \t\r\n]+", x)
  9: sub(re, "", x, perl = TRUE)
  10: rhdf5::h5ls(file)
  11: h5checktypeOrOpenLoc(file, readonly = TRUE, native = native)
  12: H5Fopen(file, "H5F_ACC_RDONLY", native = native)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_read-write-read.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
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Package suggested but not available for checking: ‘redux’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
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ndvi                    package:irg                    R Documentation

_R_a_w _N_D_V_I _T_i_m_e _S_e_r_i_e_s

_D_e_s_c_r_i_p_t_i_o_n:

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

_F_o_r_m_a_t:

     A data.table with 2530 rows and 5 variables:

        • id - individual identifier

        • yr - year of sample

        • DayOfYear - julian day/day of year of sample

        • NDVI - sampled value

        • SummaryQA - Summary quality assessment value

     SummaryQA details:

        • 0 - Good data, use with confidence

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

        • 2 - Pixel covered with snow/ice

        • 3 - Pixel is cloudy

_E_x_a_m_p_l_e_s:

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

Quitting from lines 99-153 (getting-started-with-irg.Rmd) 
Error: processing vignette 'getting-started-with-irg.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Packages suggested but not available for checking:
  ‘gurobi’ ‘Rcplex’ ‘cplexAPI’
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    dict  19.5Mb
Package suggested but not available for checking: ‘RProtoBuf’
Running examples in ‘jomo-Ex.R’ failed
The error most likely occurred in:

> ### Name: jomo.clmm
> ### Title: Joint Modelling Imputation Compatible with Cumulative Link Mixed
> ###   Model
> ### Aliases: jomo.clmm
> 
> ### ** Examples
> 
> 
> 
>   # make sure social is a factor:
>   
>   cldata<-within(cldata, social<-factor(social))
>   
>   # we define the data frame with all the variables 
>   
>   data<-cldata[,c("measure","age", "social", "city")]
>   
>   # And the formula of the substantive lm model 
>   # social as an outcome only because it is the only ordinal variable in the dataset...
>   
>   formula<-as.formula(social~age+measure+(1|city))
>   
>   #And finally we run the imputation function:
>   
>   imp<-jomo.clmm(formula,data, nburn=2, nbetween=2, nimp=2)
This function is beta software. Please use carefully and report any bug to the package mantainer

 *** caught segfault ***
address 70a, cause 'memory not mapped'

Traceback:
 1: factor(from)
 2: fac2sparse(from, to = "d")
 3: asMethod(object)
 4: as(ff, "sparseMatrix")
 5: FUN(X[[i]], ...)
 6: lapply(barlist, function(x) {    ff <- eval(substitute(as.factor(fac)[, drop = TRUE], list(fac = x[[3]])),         fullmf)    Zti <- as(ff, "sparseMatrix")    mm <- model.matrix(eval(substitute(~expr, list(expr = x[[2]]))),         fullmf)    Zt = do.call(rbind, lapply(seq_len(ncol(mm)), function(j) {        Zti@x <- mm[, j]        Zti    }))    ST <- matrix(0, ncol(mm), ncol(mm), dimnames = list(colnames(mm),         colnames(mm)))    list(f = ff, Zt = Zt, ST = ST)})
 7: getREterms(frames = frames, formulae$formula)
 8: ordinal::clmm(formula, data = data, na.action = na.omit, Hess = T,     link = "probit")
 9: jomo.clmm(formula, data, nburn = 2, nbetween = 2, nimp = 2)
An irrecoverable exception occurred. R is aborting now ...
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    group_rows

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 327-331 (awesome_table_in_html.Rmd) 
Error: processing vignette 'awesome_table_in_html.Rmd' failed with diagnostics:
unused arguments ("Group 1", 4, 7)
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: shiny
Loading required package: shinythemes
Loading required package: plyr
Quitting from lines 37-53 (kgc-fine.Rmd) 
Error: processing vignette 'kgc-fine.Rmd' failed with diagnostics:
cannot allocate vector of size 640.7 Mb
Execution halted
Package suggested but not available for checking: ‘gifski’
Running examples in ‘knitr-Ex.R’ failed
The error most likely occurred in:

> ### Name: raw_block
> ### Title: Mark character strings as raw blocks in R Markdown
> ### Aliases: raw_block raw_latex raw_html
> 
> ### ** Examples
> 
> knitr::raw_latex("\\emph{some text}")
Error in if (rmarkdown::pandoc_version() < "2.0.0") warning("raw_block() requires Pandoc >= 2.0.0") : 
  argument is of length zero
Calls: <Anonymous> -> raw_block
Execution halted
Running ‘run-all.R’ [20s/26s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library(testit)
  > test_pkg("knitr")
  Error from eval(expr, envir = envir, enclos = NULL) 
  Error in if (rmarkdown::pandoc_version() < "2.0.0") warning("raw_block() requires Pandoc >= 2.0.0") : 
    argument is of length zero
  Calls: test_pkg ... assert -> assert2 -> eval -> eval -> raw_latex -> raw_block
  In addition: Warning messages:
  1: In write_bib(pkgs, tempfile(), tweak = FALSE) :
    package(s) KernSmooth, boot, class, cluster, foreign, nnet, rpart, spatial, survival not found
  2: In write_bib(pkgs, tweak = TRUE) :
    package(s) KernSmooth, boot, class, cluster, foreign, nnet, rpart, spatial, survival not found
  3: In kable_markdown(x, padding = padding, ...) :
    The table should have a header (column names)
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-16
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    java   6.2Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(KRIG)
  > 
  > test_check("KRIG")
  ── 1. Failure: Same result sequencial and parallel code (@test1.R#15)  ─────────
  `kw` not equal to `nw`.
  1/1 mismatches
  [1] 12795 - 6398 == 6398
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Failure: Same result sequencial and parallel code (@test1.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Quitting from lines 120-123 (copper_mining_2d.Rmd) 
Error: processing vignette 'copper_mining_2d.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   7.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   3.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    2.6Mb
    help   1.2Mb
Running ‘config.R’
  Running ‘testthat.R’
Running the tests in ‘tests/config.R’ failed.
Complete output:
  > mac_dir <- "~/Documents/Rtest/"
  > win_dir <- "C:/Rtest"
  > linux_dir <- "~/Documents/Rtest"
  > 
  > switch(Sys.info()['sysname'],
  +        "Darwin" = {working_dir <- mac_dir},
  +        "Windows" = {working_dir <- win_dir},
  +        "Linux" = {working_dir <- linux_dir})
  > 
  > rds_file_name <- "./ranListSmall.rds"
  > llo_file_name <- "./ranListSmall.llo"
  > repeat_time <- 20
  > original <- FALSE
  > compress <- TRUE
  > 
  > # rds_file_name <- "./ranListMid.rds"
  > # llo_file_name <- "./ranListMid.llo"
  > # repeat_time <- 20
  > # original <- FALSE
  > # compress <- TRUE
  > 
  > options(list(largeList.report.progress = FALSE))
  > 
  > if (dir.exists(working_dir)) {
  +   setwd(working_dir)
  +   if (file.exists(rds_file_name)) {
  +     library(futile.logger)
  +     ready_to_test <- TRUE
  +   } else {
  +     ready_to_test <- FALSE
  +   }
  + } else {
  +   ready_to_test <- FALSE
  + }
  Error in dir.exists(working_dir) : object 'working_dir' not found
  Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 41-42 (Intro_to_lavaanPlot.Rmd) 
Error: processing vignette 'Intro_to_lavaanPlot.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    geojson  11.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    htmlwidgets   4.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 67-77 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.9Mb
File ‘leaps/libs/leaps.so’:
  Found ‘__f90_esfw’, possibly from ‘print’ (Fortran), ‘write’
    (Fortran)
    Object: ‘leaps.o’
  Found ‘__f90_eslw’, possibly from ‘print’ (Fortran), ‘write’
    (Fortran)
    Object: ‘leaps.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs     24.0Mb
Running ‘testthat.R’ [171s/207s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(lidR)
  Loading required package: raster
  Loading required package: sp
  > 
  > options(lidR.progress = FALSE)
  > 
  > test_check("lidR")
  ── 1. Failure: grid_terrain return the same both with LAScatalog and LAS (@test-
  mean(error) not equal to 0.048.
  1/1 mismatches
  [1] NA - 0.048 == NA
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 571 SKIPPED: 0 FAILED: 1
  1. Failure: grid_terrain return the same both with LAScatalog and LAS (@test-grid_terrain.R#107) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘lime-Ex.R’ failed
The error most likely occurred in:

> ### Name: interactive_text_explanations
> ### Title: Interactive explanations
> ### Aliases: interactive_text_explanations text_explanations_output
> ###   render_text_explanations
> 
> ### ** Examples
> 
> library(text2vec)
> library(xgboost)
Error in library(xgboost) : there is no package called ‘xgboost’
Execution halted
Running ‘testthat.R’ [17s/58s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(lime)
  > 
  > test_check("lime")
  
  H2O is not running yet, starting it now...
  
  Note:  In case of errors look at the following log files:
      /tmp/RtmpHJaqTt/h2o_ripley_started_from_r.out
      /tmp/RtmpHJaqTt/h2o_ripley_started_from_r.err
  
  java version "1.7.0_65"
  Java(TM) SE Runtime Environment (build 1.7.0_65-b17)
  Java HotSpot(TM) Server VM (build 24.65-b04, mixed mode)
  
  Starting H2O JVM and connecting: ... Connection successful!
  
  R is connected to the H2O cluster: 
      H2O cluster uptime:         6 seconds 300 milliseconds 
      H2O cluster timezone:       Europe/London 
      H2O data parsing timezone:  UTC 
      H2O cluster version:        3.22.1.1 
      H2O cluster version age:    1 month and 30 days  
      H2O cluster name:           H2O_started_from_R_ripley_dqj247 
      H2O cluster total nodes:    1 
      H2O cluster total memory:   0.89 GB 
      H2O cluster total cores:    16 
      H2O cluster allowed cores:  16 
      H2O cluster healthy:        TRUE 
      H2O Connection ip:          localhost 
      H2O Connection port:        54321 
      H2O Connection proxy:       NA 
      H2O Internal Security:      FALSE 
      H2O API Extensions:         AutoML, Algos, Core V3, Core V4 
      R Version:                  R version 3.5.2 Patched (2019-02-20 r76141) 
  
  ── 1. Error: (unknown) (@test-text.R#3)  ───────────────────────────────────────
  there is no package called 'xgboost'
  1: library(xgboost) at testthat/test-text.R:3
  2: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 18 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-text.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 185-224 (Understanding_lime.Rmd) 
Error: processing vignette 'Understanding_lime.Rmd' failed with diagnostics:
there is no package called 'xgboost'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 109-112 (linkspotterVignette.Rmd) 
Error: processing vignette 'linkspotterVignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.3Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R          1.8Mb
    doc        2.8Mb
    testdata   1.8Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/lmSubsets.Rcheck/00install.out’ for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 2-13 (./children/SETTINGS-knitr.txt) 
Quitting from lines NA-13 (./children/SETTINGS-knitr.txt) 
Error: processing vignette 'loo2-example.Rmd' failed with diagnostics:
object 'params' not found
Execution halted
Package suggested but not available for checking: ‘Rsymphony’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 18-23 (lspline.Rmd) 
Error: processing vignette 'lspline.Rmd' failed with diagnostics:
object 'params' not found
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 62-63 (LUCIDus-vignette.Rmd) 
Error: processing vignette 'LUCIDus-vignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Running examples in ‘lvnet-Ex.R’ failed
The error most likely occurred in:

> ### Name: lvnet
> ### Title: Confirmatory Latent Variable Network Models
> ### Aliases: lvnet
> 
> ### ** Examples
> 
> # Load dataset:
> library("lavaan")
This is lavaan 0.6-3
lavaan is BETA software! Please report any bugs.

Attaching package: ‘lavaan’

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

    vech

> data(HolzingerSwineford1939)
> Data <- HolzingerSwineford1939[,7:15]
> 
> # Measurement model:
> Lambda <- matrix(0, 9, 3)
> Lambda[1:3,1] <- NA
> Lambda[4:6,2] <- NA
> Lambda[7:9,3] <- NA
> 
> # Fit CFA model:
> CFA <- lvnet(Data, lambda = Lambda)
Error: The job for model 'model' exited abnormally with the error message: Incorrect input to omxRowSortHelper: 0 1 0 9
Execution halted
Running examples in ‘MachineShop-Ex.R’ failed
The error most likely occurred in:

> ### Name: XGBModel
> ### Title: Extreme Gradient Boosting Models
> ### Aliases: XGBModel XGBDARTModel XGBLinearModel XGBTreeModel
> 
> ### ** Examples
> 
> modelfit <- fit(Species ~ ., data = iris, model = XGBTreeModel())
Loading required namespace: xgboost
Failed with error:  ‘there is no package called ‘xgboost’’
Error in requireModelNamespaces(model@packages) : 
  install required packages: xgboost
Calls: fit ... fit.ModelFrame -> .fit -> .fit.MLModel -> requireModelNamespaces
Execution halted
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    TS_files     6.0Mb
    base_files   6.5Mb
Packages suggested but not available for checking:
  ‘av’ ‘rsvg’ ‘tesseract’ ‘gifski’
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
Packages unavailable to check Rd xrefs: ‘rsvg’, ‘tesseract’, ‘gifski’, ‘av’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'rsvg'
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'rsvg'
Quitting from lines 228-237 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
Magick: non-conforming drawing primitive definition `text' @ error/draw.c/RenderMVGContent/4354
Execution halted
Warning in find_bad_exprs(exprs[[i]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in find_bad_exprs(exprs[[i]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in find_bad_exprs(exprs[[i]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in find_bad_exprs(exprs[[i]]) :
  it is not known that wchar_t is Unicode on this platform
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Quitting from lines 95-96 (manhattanly.Rmd) 
Error: processing vignette 'manhattanly.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot59f61ae05835.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot59f61ae05835.png': No such file or directory
Quitting from lines 61-68 (manipulateWidgets.Rmd) 
Error: processing vignette 'manipulateWidgets.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 33.9Mb
  sub-directories of 1Mb or more:
    mapdata  33.8Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data          1.0Mb
    doc           1.3Mb
    htmlwidgets   1.6Mb
    libs          3.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 95-100 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    mapdata   4.2Mb
Packages required but not available: ‘CausalImpact’ ‘bsts’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    java   3.4Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in (function (filename = "Rplot%03d.png", width = 480, height = 480,  :
  cairo error 'invalid value (typically too big) for the size of the input (surface, pattern, etc.)'
Quitting from lines 39-41 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
unable to start device 'png'
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   3.0Mb
XIO:  fatal IO error 146 (Connection refused) on X server ":5.0"
      after 0 requests (0 known processed) with 0 events remaining.
Installation failed.
See ‘/home/ripley/R/packages/tests32/mDAG.Rcheck/00install.out’ for details.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   6.0Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/meanr.Rcheck/00install.out’ for details.
Package required but not available: ‘gdsfmt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.7Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
Running examples in ‘metaSEM-Ex.R’ failed
The error most likely occurred in:

> ### Name: BCG
> ### Title: Dataset on the Effectiveness of the BCG Vaccine for Preventing
> ###   Tuberculosis
> ### Aliases: BCG
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(BCG)
> 
> ## Univariate meta-analysis on the log of the odds ratio
> summary( meta(y=ln_OR, v=v_ln_OR, data=BCG,
+               x=cbind(scale(Latitude,scale=FALSE),
+               scale(Year,scale=FALSE))) )

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

Traceback:
 1: runHelper(model, frontendStart, intervals, silent, suppressWarnings,     unsafe, checkpoint, useSocket, onlyFrontend, useOptimizer)
 2: mxRun(mx.model, intervals = FALSE, suppressWarnings = suppressWarnings,     silent = silent, ...)
 3: doTryCatch(return(expr), name, parentenv, handler)
 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5: tryCatchList(expr, classes, parentenv, handlers)
 6: tryCatch(mxRun(mx.model, intervals = FALSE, suppressWarnings = suppressWarnings,     silent = silent, ...), error = function(e) e)
 7: meta(y = ln_OR, v = v_ln_OR, data = BCG, x = cbind(scale(Latitude,     scale = FALSE), scale(Year, scale = FALSE)))
 8: summary(meta(y = ln_OR, v = v_ln_OR, data = BCG, x = cbind(scale(Latitude,     scale = FALSE), scale(Year, scale = FALSE))))
An irrecoverable exception occurred. R is aborting now ...
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 31-39 (Working-with-data.Rmd) 
Error: processing vignette 'Working-with-data.Rmd' failed with diagnostics:
Error in nc_open trying to open file /home/ripley/R/Lib32/metR/extdata/temperature.nc
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    data   1.1Mb
    doc    1.2Mb
    libs   1.7Mb
    misc   1.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 91-94 (mgwrsar-basic_examples.Rmd) 
Error: processing vignette 'mgwrsar-basic_examples.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mhde_article.tex' failed.
Messages:
/usr/local/bin/texi2dvi: line 411: 12220 Killed                  "$@" 2>&5 1>&2
/usr/local/bin/texi2dvi: biber failed
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.0Mb
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    doc       1.5Mb
    extdata   3.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
*** This is beta software. Please report any bugs!
*** See the NEWS file for recent changes.
Loading required package: Matrix
Quitting from lines 109-112 (Analysis.Rmd) 
Error: processing vignette 'Analysis.Rmd' failed with diagnostics:
objective in x0 returns NA
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   2.9Mb
Packages suggested but not available for checking: ‘REBayes’ ‘Rmosek’
Packages unavailable to check Rd xrefs: ‘REBayes’, ‘Rmosek’
Packages suggested but not available for checking:
  ‘minfi’ ‘IlluminaHumanMethylation450kmanifest’
Package suggested but not available for checking: ‘FSelector’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 5-183 (./toc/vignettetoc.Rmd) 
Quitting from lines 5-183 (./toc/vignettetoc.Rmd) 
Error: processing vignette 'a_1_getting_started.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
Packages suggested but not available for checking:
  ‘FSelector’ ‘RWeka’ ‘xgboost’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   5.2Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
Package which this enhances but not available for checking: ‘MonetDBLite’
Running examples in ‘monoreg-Ex.R’ failed
The error most likely occurred in:

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

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

Traceback:
 1: monoreg(niter = 5000, burnin = 2500, adapt = 2500, refresh = 10,     thin = 5, birthdeath = 10, seed = 1, rhoa = 0.1, rhob = 0.1,     deltai = 0.1, drange = 2, predict = rep(1, nobs), include = rep(1,         nobs), response = y, offset = NULL, axes = cbind(x1,         x2), covariates = rep(1, nobs), settozero = getcmat(2),     package = rep(1, 3))
An irrecoverable exception occurred. R is aborting now ...
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   3.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 30-37 (msaR.Rmd) 
Error: processing vignette 'msaR.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Running ‘test-all.R’ [65s/78s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > 
  > library(testthat)
  > 
  > test_check("mudata2")
  Loading required package: mudata2
  
  Attaching package: 'mudata2'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  ── 1. Error: read/write functions work inside RMarkdown (@test_mudata.io.R#554) 
  pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  1: rmarkdown::render(tf, quiet = TRUE) at testthat/test_mudata.io.R:554
  2: pandoc_available(required_pandoc, error = TRUE)
  3: stop(paste(msg, collapse = " "), call. = FALSE)
  
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 967 SKIPPED: 0 FAILED: 1
  1. Error: read/write functions work inside RMarkdown (@test_mudata.io.R#554) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/MultiBD.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: geometry
Loading required package: rootSolve
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 252-268 (munsellinterpol-guide.Rmd) 
Error: processing vignette 'munsellinterpol-guide.Rmd' failed with diagnostics:
`render_flextable` needs to be used as a renderer for a knitr/rmarkdown R code chunk (render by rmarkdown)
Execution halted
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    java  14.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    2.5Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    extdata  16.3Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(namer)
  > 
  > test_check("namer")
  ── 1. Error: unname_all_chunks works (@test-unname_all_chunks.R#22)  ───────────
  pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  1: rmarkdown::render(temp_file_path) at testthat/test-unname_all_chunks.R:22
  2: pandoc_available(required_pandoc, error = TRUE)
  3: stop(paste(msg, collapse = " "), call. = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 9 SKIPPED: 0 FAILED: 1
  1. Error: unname_all_chunks works (@test-unname_all_chunks.R#22) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data   9.5Mb
Running examples in ‘ncdump-Ex.R’ failed
The error most likely occurred in:

> ### Name: NetCDF
> ### Title: Information about a NetCDF file, in convenient form.
> ### Aliases: NetCDF
> 
> ### ** Examples
> 
> rnc <- NetCDF(system.file("extdata", "S2008001.L3m_DAY_CHL_chlor_a_9km.nc", package= "ncdump"))
Error in R_nc4_open: NetCDF: HDF error
Error in ncdf4::nc_open(x) : 
  Error in nc_open trying to open file /home/ripley/R/Lib32/ncdump/extdata/S2008001.L3m_DAY_CHL_chlor_a_9km.nc
Calls: NetCDF -> <Anonymous>
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ncdump)
  > 
  > test_check("ncdump")
  Error in R_nc4_open: NetCDF: HDF error
  ── 1. Error: (unknown) (@testbasic.r#6)  ───────────────────────────────────────
  Error in nc_open trying to open file /home/ripley/R/Lib32/ncdump/extdata/S2008001.L3m_DAY_CHL_chlor_a_9km.nc
  1: NetCDF(ifile) at testthat/testbasic.r:6
  2: ncdf4::nc_open(x)
  3: stop(paste("Error in nc_open trying to open file", filename))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@testbasic.r#6) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘ncmeta-Ex.R’ failed
The error most likely occurred in:

> ### Name: nc_att
> ### Title: NetCDF attributes
> ### Aliases: nc_att nc_att.NetCDF nc_att.character
> 
> ### ** Examples
> 
> f <- system.file("extdata", "S2008001.L3m_DAY_CHL_chlor_a_9km.nc", package = "ncmeta")
> nc_att(f, 0, 0)
Error: NetCDF: HDF error
Execution halted
Running examples in ‘NCutYX-Ex.R’ failed
The error most likely occurred in:

> ### Name: ancut
> ### Title: Cluster the Columns of Y into K Groups with the Help of External
> ###   Features X.
> ### Aliases: ancut
> 
> ### ** Examples
> 
> #This sets up the initial parameters for the simulation.
> library(MASS)#for mvrnorm
> library(fields)
Loading required package: spam
Loading required package: dotCall64
Loading required package: grid
Spam version 2.2-1 (2018-12-20) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: ‘spam’

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

    backsolve, forwardsolve

Loading required package: maps
See www.image.ucar.edu/~nychka/Fields for
 a vignette and other supplements. 
> n=30 #Sample size
> B=50 #Number of iterations in the simulated annealing algorithm.
> L=10000 #Temperature coefficient.
> p=50 #Number of columns of Y.
> q=p #Number of columns of X.
> h1=0.15
> h2=0.25
> 
> S=matrix(0.2,q,q)
> S[1:(q/2),(q/2+1):q]=0
> S[(q/2+1):q,1:(q/2)]=0
> S=S-diag(diag(S))+diag(q)
> 
> mu=rep(0,q)
> 
> W0=matrix(1,p,p)
> W0[1:(p/2),1:(p/2)]=0
> W0[(p/2+1):p,(p/2+1):p]=0
> Denum=sum(W0)
> 
> B2=matrix(0,q,p)
> for (i in 1:(p/2)){
+    B2[1:(q/2),i]=runif(q/2,h1,h2)
+    in1=sample.int(q/2,6)
+    B2[-in1,i]=0
+ }
> 
> for (i in (p/2+1):p){
+    B2[(q/2+1):q,i]=runif(q/2,h1,h2)
+    in2=sample(seq(q/2+1,q),6)
+    B2[-in2,i]=0
+ }
> 
> X=mvrnorm(n, mu, S)
> Z=X%*%B2
> Y=Z+matrix(rnorm(n*p,0,1),n,p)
> #Our method
> Res=ancut(Y=Y,X=X,B=B,L=L,alpha=0,ncv=3)
Error in if (J2 > J) { : missing value where TRUE/FALSE needed
Calls: ancut
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
installed size is  7.8Mb
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    data   7.8Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 92-98 (Introducing_nhanesA.Rmd) 
Error: processing vignette 'Introducing_nhanesA.Rmd' failed with diagnostics:
Timeout was reached: Operation timed out after 10007 milliseconds with 0 out of 0 bytes received
Execution halted
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    CppCode   1.2Mb
    R         6.9Mb
    include   5.3Mb
    tests     1.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 127-133 (geocode.Rmd) 
Error: processing vignette 'geocode.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data      4.4Mb
    doc       1.2Mb
    reports   3.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'walkthrough.Rmd' failed with diagnostics:
(converted from warning) Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Execution halted
Running examples in ‘NMF-Ex.R’ failed
The error most likely occurred in:

> ### Name: NMFfitX-class
> ### Title: Virtual Class to Handle Results from Multiple Runs of NMF
> ###   Algorithms
> ### Aliases: NMFfitX-class
> 
> ### ** Examples
> 
> ## Don't show: 
> # roxygen generated flag
> options(R_CHECK_RUNNING_EXAMPLES_=TRUE)
> ## End(Don't show)
> 
> # generate a synthetic dataset with known classes
> n <- 20; counts <- c(5, 2, 3);
> V <- syntheticNMF(n, counts)
> 
> # perform multiple runs of one algorithm (default is to keep only best fit)
> res <- nmf(V, 3, nrun=3)
# NOTE - CRAN check detected: limiting maximum number of cores [2/16]
Error in big.matrix(nrow = nrow(x), ncol = ncol(x), type = type, init = NULL,  : 
  Error: memory could not be allocated for instance of type big.matrix
Calls: nmf ... gVariable -> <Anonymous> -> <Anonymous> -> big.matrix
Timing stopped at: 0.032 0.043 0.194
Execution halted
Package unavailable to check Rd xrefs: ‘redux’
Running examples in ‘norm2-Ex.R’ failed
The error most likely occurred in:

> ### Name: emNorm
> ### Title: EM algorithm for incomplete multivariate normal data
> ### Aliases: emNorm emNorm.default emNorm.formula emNorm.norm
> ### Keywords: multivariate NA
> 
> ### ** Examples
> 
> ## run EM for marijuana data with strict convergence criterion
> data(marijuana)
> result <- emNorm(marijuana, criterion=1e-06)

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

Traceback:
 1: emNorm.default(marijuana, criterion = 1e-06)
 2: emNorm(marijuana, criterion = 1e-06)
An irrecoverable exception occurred. R is aborting now ...
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc   8.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 192-194 (NormalizeMets_vignette.Rmd) 
Error: processing vignette 'NormalizeMets_vignette.Rmd' failed with diagnostics:
Saving a widget with selfcontained = TRUE requires pandoc. For details see:
https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 39-42 (downloading_data_nsrr.Rmd) 
Error: processing vignette 'downloading_data_nsrr.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 2-30 (NumeroGuide.rmd) 
Error: processing vignette 'NumeroGuide.rmd' failed with diagnostics:
could not find function "pkg_ver"
Execution halted
installed size is 39.1Mb
  sub-directories of 1Mb or more:
    extdata  39.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R            1.7Mb
    test_files   4.4Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    data   1.0Mb
    doc    1.7Mb
    help   2.4Mb
Packages suggested but not available for checking: ‘RMark’ ‘R2ucare’
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    R        2.7Mb
    data     1.0Mb
    libs     3.5Mb
    models   4.6Mb
Running examples in ‘OpenMx-Ex.R’ failed
The error most likely occurred in:

> ### Name: mxModelAverage
> ### Title: Information-Theoretic Model-Averaging and Multimodel Inference
> ### Aliases: mxModelAverage omxAkaikeWeights omxAICWeights
> 
> ### ** Examples
> 
> require(OpenMx)
> data(demoOneFactor)
> factorModel1 <- mxModel(
+ 	"OneFactor1",
+ 	mxMatrix(
+ 		"Full", 5, 1, values=0.8, 
+ 		labels=paste("a",1:5,sep=""),
+ 		free=TRUE, name="A"),
+ 	mxMatrix(
+ 		"Full", 5, 1, values=1,
+ 		labels=paste("u",1:5,sep=""),
+ 		free=TRUE, name="Udiag"),
+ 	mxMatrix(
+ 		"Symm", 1, 1, values=1,
+ 		free=FALSE, name="L"),
+ 	mxAlgebra(vec2diag(Udiag),name="U"),
+ 	mxAlgebra(A %*% L %*% t(A) + U, name="R"),
+ 	mxExpectationNormal(
+ 		covariance = "R",
+ 		dimnames = names(demoOneFactor)),
+ 	mxFitFunctionML(),
+ 	mxData(cov(demoOneFactor), type="cov", numObs=500))
> factorFit1 <- mxRun(factorModel1)
Running OneFactor1 with 10 parameters

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

Traceback:
 1: runHelper(model, frontendStart, intervals, silent, suppressWarnings,     unsafe, checkpoint, useSocket, onlyFrontend, useOptimizer)
 2: mxRun(factorModel1)
An irrecoverable exception occurred. R is aborting now ...
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    java     1.3Mb
    models   6.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
invalid multibyte string at '<f0><9f><95><9b></h2>

<p><strong>OptimClassifier</strong> provides a set of tools for creating models, selecting the best parameters combination for a model, and select the best threshold for your binary classification. The package contains tools for:</p>

<ul>
<li>Linear Model (LM) </li>
<li>Generalized Linear Model (GLM) </li>
<li>Linear Mixed Model (LMM) </li>
<li>Classification And Regression Tree (CART)</li>
<li>Discriminant Analysis (DA)</li>
<li>Neural Networks (NN)</li>
<li>Support Vector Machines (SVM)</li>
</ul>

<h2>Take a quick look at functions</h2>

<p>The main function could summarize in this table:</p>

<style type="text/css">
table td {padding: 0px 0px;border-width: 1px; border-style: inset;}
.tg  {border-collapse:collapse;border-spacing:0;}
.tg {border-style:solid;padding: 0px  0px; border-width:1px; overflow:hidden;word-break:normal;border-color:black;}
.tgd{border-style:soli
Execution halted
File ‘OriGen/libs/OriGen.so’:
  Found ‘__f90_close’, possibly from ‘close’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__f90_esfr’, possibly from ‘read’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__f90_open’, possibly from ‘open’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__f90_rewind’, possibly from ‘rewind’ (Fortran)
    Object: ‘OriGen.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R       1.1Mb
    nifti   4.1Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/osqp.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 185-198 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted