Ssimpute.als: no visible global function definition for 'rnorm'
Ssvd.als: no visible global function definition for 'rnorm'
cs.default: no visible binding for global variable 'weighted.mean'
simpute.als: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm weighted.mean
Consider adding
  importFrom("stats", "rnorm", "weighted.mean")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'aqp' 'lattice' 'methods' 'munsell' 'splancs'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' calls in package code:
  'chemometrics' 'spatstat'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.soma: no visible global function definition for 'plot'
soma: no visible global function definition for 'runif'
Undefined global functions or variables:
  plot runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
to your NAMESPACE file.
bm: no visible global function definition for 'rnorm'
bm: no visible global function definition for 'ts'
fbm: no visible global function definition for 'fft'
fbm: no visible global function definition for 'rnorm'
fbm: no visible global function definition for 'ts'
gbm: no visible global function definition for 'rnorm'
gbm: no visible global function definition for 'ts'
Undefined global functions or variables:
  fft rnorm ts
Consider adding
  importFrom("stats", "fft", "rnorm", "ts")
to your NAMESPACE file.
getAlpha: no visible global function definition for 'pbinom'
kfweOrd: no visible global function definition for 'qnbinom'
Undefined global functions or variables:
  pbinom qnbinom
Consider adding
  importFrom("stats", "pbinom", "qnbinom")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from 'someMTP' for: 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
'library' or 'require' call to 'hexbin' which was already attached by Depends.
  Please remove these calls from your code.
hexbinpie: no visible global function definition for 'quantile'
hexbinpie: no visible global function definition for 'polygon'
hexbinpie: no visible global function definition for 'text'
makehexbinplot: no visible global function definition for 'rainbow'
makehexbinplot: no visible global function definition for 'col2rgb'
makehexbinplot: no visible global function definition for 'edit'
makehexbinplot: no visible global function definition for 'dev.new'
makehexbinplot: no visible global function definition for 'plot.new'
makehexbinplot: no visible global function definition for 'plot.window'
makehexbinplot: no visible global function definition for 'box'
makehexbinplot: no visible global function definition for 'axis'
makehexbinplot: no visible global function definition for 'legend'
som.plot: no visible global function definition for 'read.table'
Undefined global functions or variables:
  axis box col2rgb dev.new edit legend plot.new plot.window polygon
  quantile rainbow read.table text
Consider adding
  importFrom("grDevices", "col2rgb", "dev.new", "rainbow")
  importFrom("graphics", "axis", "box", "legend", "plot.new",
             "plot.window", "polygon", "text")
  importFrom("stats", "quantile")
  importFrom("utils", "edit", "read.table")
to your NAMESPACE file.
dfrag: no visible global function definition for 'qgeom'
dfrag: no visible global function definition for 'plogis'
dfrag: no visible global function definition for 'dgeom'
estAbund: no visible global function definition for 'xtabs'
mmN : <anonymous>: no visible global function definition for 'uniroot'
pfrag: no visible global function definition for 'qgeom'
phi.deriv.default: no visible global function definition for
  'model.matrix'
phi.deriv.default: no visible binding for global variable 'sd'
phi.update.default: no visible global function definition for 'glm'
phi.update.default: no visible binding for global variable
  'quasipoisson'
phi.update.default: no visible global function definition for 'predict'
phi.update.lframe: no visible global function definition for 'glm'
phi.update.lframe: no visible binding for global variable
  'quasipoisson'
phi.update.lframe: no visible global function definition for 'predict'
pr.y.given.x : <anonymous>: no visible global function definition for
  'dpois'
pr.y.given.x : <anonymous> : <anonymous>: no visible global function
  definition for 'dpois'
pr.y.given.x : <anonymous>: no visible global function definition for
  'convolve'
qfrag: no visible global function definition for 'qgeom'
rfrag: no visible global function definition for 'qgeom'
simSonic: no visible global function definition for 'rpois'
Undefined global functions or variables:
  convolve dgeom dpois glm model.matrix plogis predict qgeom
  quasipoisson rpois sd uniroot xtabs
Consider adding
  importFrom("stats", "convolve", "dgeom", "dpois", "glm",
             "model.matrix", "plogis", "predict", "qgeom",
             "quasipoisson", "rpois", "sd", "uniroot", "xtabs")
to your NAMESPACE file.
plot.soo_function: no visible global function definition for
  'terrain.colors'
plot.soo_function: no visible binding for global variable 'image'
plot.soo_function: no visible binding for global variable 'contour'
plot3d: no visible global function definition for 'persp3d'
plot3d: no visible global function definition for 'terrain.colors'
random_parameters.soo_function: no visible global function definition
  for 'runif'
random_rotation_matrix: no visible global function definition for
  'runif'
Undefined global functions or variables:
  contour image persp3d runif terrain.colors
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "contour", "image")
  importFrom("stats", "runif")
to your NAMESPACE file.
simdata_contaminated : <anonymous>: no visible global function
  definition for 'rbinom'
simdata_uniform : multivariate_uniform : <anonymous>: no visible global
  function definition for 'runif'
which_min: no visible global function definition for 'head'
which_min: no visible global function definition for 'tail'
Undefined global functions or variables:
  head rbinom runif tail
Consider adding
  importFrom("stats", "rbinom", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
convert_municipality_names: no visible global function definition for
  'read.csv'
regression_plot: no visible binding for global variable 'loess'
regression_plot: no visible global function definition for
  'colorRampPalette'
regression_plot: no visible global function definition for
  'loess.control'
regression_plot: no visible global function definition for 'predict'
regression_plot : <anonymous>: no visible global function definition
  for 'quantile'
regression_plot : <anonymous>: no visible global function definition
  for 'pnorm'
regression_plot: no visible global function definition for
  'flush.console'
regression_plot: no visible global function definition for 'density'
Undefined global functions or variables:
  colorRampPalette density flush.console loess loess.control pnorm
  predict quantile read.csv
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "density", "loess", "loess.control", "pnorm",
             "predict", "quantile")
  importFrom("utils", "flush.console", "read.csv")
to your NAMESPACE file.
'library' or 'require' call to 'rgdal' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: 'r2cytoscape'
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' [193s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("SpaDES.core")
  Loading required package: SpaDES.core
  Loading required package: quickPlot
  Loading required package: reproducible
  
  Attaching package: 'reproducible'
  
  The following object is masked from 'package:testthat':
  
      %>%
  
    Using cached copy of .inputObjects event in test module
    Using cached copy of .inputObjects event in test module
  -- 1. Failure: simList object initializes correctly (@test-simList.R#17)  --------------------------
  length(out) not equal to 75.
  1/1 mismatches
  [1] 73 - 75 == -2
  
    Using cached copy of burn event in fireSpread module
  == testthat results  ===========================================================
  OK: 349 SKIPPED: 33 FAILED: 1
  1. Failure: simList object initializes correctly (@test-simList.R#17) 
  
  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.
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.
Found the following significant warnings:
  sparseSVM.c:367:30: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.6/sparseSVM.Rcheck/00install.out' for details.
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 16.8Mb
  sub-directories of 1Mb or more:
    R      5.0Mb
    doc    4.7Mb
    help   5.0Mb
    libs   1.2Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
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.
randomCorrelations: no visible global function definition for 'cor'
specGlm : <anonymous>: no visible global function definition for 'coef'
specLm : <anonymous>: no visible global function definition for 'coef'
Undefined global functions or variables:
  coef cor
Consider adding
  importFrom("stats", "coef", "cor")
to your NAMESPACE file.
'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.
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 examples in 'splitstackshape-Ex.R' failed
The error most likely occurred in:

> ### Name: cSplit_f
> ### Title: Split Concatenated Cells in a data.frame or a data.table
> ### Aliases: cSplit_f
> 
> ### ** Examples
> 
> 
> ## Sample data. Change `n` to larger values to test on larger data
> set.seed(1)
> n <- 10
> mydf <- data.frame(id = sequence(n))
> mydf <- within(mydf, {
+   v3 <- do.call(paste, c(data.frame(matrix(sample(
+   letters, n*4, TRUE), ncol = 4)), sep = "_"))
+   v2 <- do.call(paste, c(data.frame(matrix(sample(
+   LETTERS, n*3, TRUE), ncol = 3)), sep = "."))
+   v1 <- do.call(paste, c(data.frame(matrix(sample(
+   10, n*2, TRUE), ncol = 2)), sep = "-"))
+ })
> mydf
   id   v1    v2      v3
1   1  4-5 V.M.X g_f_y_m
2   2  9-8 Q.W.H j_e_f_p
3   3  4-4 U.L.L o_r_q_m
4   4  4-4 O.G.I x_j_d_e
5   5  5-8 N.B.Q f_u_g_v
6   6  9-3 U.C.G x_m_k_r
7   7  9-8 A.I.M y_s_a_u
8   8  4-2 M.N.T r_z_j_c
9   9  8-3 T.R.C q_j_w_s
10 10 10-2 S.K.W b_u_i_k
> 
> cSplit_f(mydf, splitCols = c("v1", "v2", "v3"), sep = c("-", ".", "_"))
Error in fread(x, sep[i], header = FALSE) : 
  You can provide 'input=' or 'file=', not both.
Calls: cSplit_f -> fread
Execution halted
Found the following significant warnings:
  timeFuns.c:1084:34: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.6/splusTimeDate.Rcheck/00install.out' for details.
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   2.6Mb
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  6.0Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs   1.9Mb
plotThin: no visible global function definition for 'par'
plotThin: no visible global function definition for 'dev.interactive'
plotThin: no visible global function definition for 'plot'
plotThin: no visible global function definition for 'hist'
thin: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  dev.interactive hist par plot write.csv
Consider adding
  importFrom("grDevices", "dev.interactive")
  importFrom("graphics", "hist", "par", "plot")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
.GameSPT: no visible global function definition for 'runif'
.GameSPT: no visible global function definition for 'points'
.GameST: no visible global function definition for 'runif'
.GameST: no visible global function definition for 'points'
.arc: no visible global function definition for 'lines'
.ptpedal: no visible global function definition for 'polygon'
.sptpedal2: no visible global function definition for 'segments'
.sptpedal3: no visible global function definition for 'polygon'
.sptpedal4: no visible global function definition for 'polygon'
chaos.spt: no visible global function definition for 'plot'
chaos.spt: no visible global function definition for 'polygon'
chaos.spt: no visible global function definition for 'runif'
chaos.spt: no visible global function definition for 'points'
chaos.st: no visible global function definition for 'plot'
chaos.st: no visible global function definition for 'polygon'
chaos.st: no visible global function definition for 'runif'
chaos.st: no visible global function definition for 'points'
plot.spt: no visible global function definition for 'plot'
plot.spt: no visible global function definition for 'polygon'
plot.st: no visible global function definition for 'plot'
plot.st: no visible global function definition for 'polygon'
Undefined global functions or variables:
  lines plot points polygon runif segments
Consider adding
  importFrom("graphics", "lines", "plot", "points", "polygon",
             "segments")
  importFrom("stats", "runif")
to your NAMESPACE file.
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/ssmsn.Rcheck/00install.out' for details.
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.
.ls.objects: no visible binding for global variable 'object.size'
Undefined global functions or variables:
  object.size
Consider adding
  importFrom("utils", "object.size")
to your NAMESPACE file.
.expandLevels: no visible global function definition for 'na.omit'
.ffStack: no visible global function definition for 'na.omit'
.ffffStack: no visible global function definition for 'na.omit'
Stack : <anonymous>: no visible global function definition for
  'na.omit'
ffStack,ffdf-data.frame: no visible global function definition for
  'na.omit'
ffStack,ffdf-ffdf: no visible global function definition for 'na.omit'
ffStack,ffdf-list: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
genericPlot: no visible global function definition for 'dev.new'
genericPlot: no visible global function definition for 'par'
genericPlot: no visible global function definition for 'rainbow'
genericPlot: no visible global function definition for 'plot'
genericPlot: no visible global function definition for 'lines'
genericPlot: no visible global function definition for 'legend'
genericPlot: no visible global function definition for 'dev.copy2pdf'
genericPlot: no visible global function definition for 'dev.copy2eps'
genericPlot: no visible global function definition for 'dev.print'
genericPlot: no visible binding for global variable 'png'
genericPlot: no visible binding for global variable 'tiff'
plotStrains: no visible global function definition for 'rainbow'
plotStrains: no visible global function definition for 'dev.new'
plotStrains: no visible global function definition for 'par'
plotStrains: no visible global function definition for 'plot'
plotStrains: no visible global function definition for 'lines'
plotStrains: no visible global function definition for 'legend'
plotStrains: no visible global function definition for 'dev.copy2pdf'
plotStrains: no visible global function definition for 'dev.copy2eps'
plotStrains: no visible global function definition for 'dev.print'
plotStrains: no visible binding for global variable 'png'
plotStrains: no visible binding for global variable 'tiff'
Undefined global functions or variables:
  dev.copy2eps dev.copy2pdf dev.new dev.print legend lines par plot png
  rainbow tiff
Consider adding
  importFrom("grDevices", "dev.copy2eps", "dev.copy2pdf", "dev.new",
             "dev.print", "png", "rainbow", "tiff")
  importFrom("graphics", "legend", "lines", "par", "plot")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'np' 'sp'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'np' 'sp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
stkde: no visible global function definition for 'npudensbw'
stkde: no visible global function definition for 'npudens'
stkde: no visible global function definition for 'quantile'
stkde: no visible global function definition for 'heat.colors'
stkde: no visible global function definition for 'par'
stkde: no visible global function definition for 'image'
stkde: no visible global function definition for 'contour'
stkde.base: no visible global function definition for 'npudensbw'
stkde.base: no visible global function definition for 'npudens'
stkde.sig: no visible global function definition for 'SpatialPoints'
stkde.sig: no visible global function definition for 'spsample'
stkde.sig: no visible global function definition for 'bbox'
stkde.sig: no visible global function definition for 'quantile'
stkde.sig: no visible global function definition for 'heat.colors'
stkde.sig: no visible global function definition for 'par'
stkde.sig: no visible global function definition for 'image'
stkde.sig: no visible global function definition for 'contour'
Undefined global functions or variables:
  SpatialPoints bbox contour heat.colors image npudens npudensbw par
  quantile spsample
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "contour", "image", "par")
  importFrom("stats", "quantile")
to your NAMESPACE file.
find.names: no visible global function definition for 'na.omit'
generate.names: no visible global function definition for 'na.omit'
standardize.countrynames: no visible global function definition for
  'data'
standardize.names: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    include   8.3Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   5.0Mb
'library' or 'require' call to 'codetools' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'codetools' 'gss'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following hidden files and directories:
  inst/.Renviron.d
  inst/.Rprofile.d
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
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.
Found the following significant warnings:
  ChangePointAnalyzeNorm.cpp:49:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  ChangePointAnalyzePoiss.cpp:42:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.6/StepSignalMargiLike.Rcheck/00install.out' for details.
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.
na.stinterp.default: no visible global function definition for 'time'
na.stinterp.default: no visible global function definition for
  'na.omit'
Undefined global functions or variables:
  na.omit time
Consider adding
  importFrom("stats", "na.omit", "time")
to your NAMESPACE file.
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]
See 'd:/Rcompile/CRANpkg/local/3.6/StMoSim.Rcheck/00install.out' for details.
myQQNorm: no visible global function definition for 'mad'
myQQNorm: no visible global function definition for 'qnorm'
myQQNorm: no visible global function definition for 'plot'
myQQNorm: no visible global function definition for 'matlines'
myQQNorm: no visible global function definition for 'points'
myQQNorm: no visible global function definition for 'qqline'
myQQNorm: no visible global function definition for 'box'
qqnormSim,lm: no visible global function definition for 'resid'
Undefined global functions or variables:
  box mad matlines plot points qnorm qqline resid
Consider adding
  importFrom("graphics", "box", "matlines", "plot", "points")
  importFrom("stats", "mad", "qnorm", "qqline", "resid")
to your NAMESPACE file.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R          2.0Mb
    datasets   2.6Mb
Error in re-building vignettes:
  ...
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "VignetteforSTPGA.ltx" --max-iterations=20 -I "D:/RCompile/recent/R/share/texmf/tex/latex" -I "D:/RCompile/recent/R/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'VignetteforSTPGA.ltx' failed with diagnostics:
running 'texi2dvi' on 'VignetteforSTPGA.ltx' failed

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

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

Execution halted
Packages in Depends field not imported from:
  'cubature' 'deldir' 'splancs'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
HRatio: no visible global function definition for 'qnorm'
icweib: no visible global function definition for 'model.frame'
icweib: no visible binding for global variable 'na.pass'
icweib: no visible global function definition for 'complete.cases'
icweib: no visible global function definition for 'model.matrix'
icweib: no visible global function definition for 'optim'
icweib: no visible global function definition for 'pchisq'
icweib: no visible global function definition for 'pnorm'
plot.icweib : getstat: no visible global function definition for
  'qnorm'
plot.icweib: no visible global function definition for 'plot'
plot.icweib: no visible global function definition for 'lines'
plot.icweib: no visible global function definition for 'legend'
print.icweib: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  complete.cases legend lines model.frame model.matrix na.pass optim
  pchisq plot pnorm qnorm
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "complete.cases", "model.frame", "model.matrix",
             "na.pass", "optim", "pchisq", "pnorm", "qnorm")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.6/streamR.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
'library' or 'require' call to 'ROAuth' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is 35.8Mb
  sub-directories of 1Mb or more:
    libs  35.1Mb
breakpoints.formula: no visible global function definition for
  '%dopar%'
breakpoints.formula: no visible binding for global variable 'i'
efpFunctional: multiple local function definitions for 'plotProcess'
  with different formal arguments
mefp.efp: multiple local function definitions for 'computeEmpProc' with
  different formal arguments
sctest.default: no visible global function definition for 'tail'
Undefined global functions or variables:
  %dopar% i tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
PlotHypTree: no visible global function definition for 'browseURL'
treePValues: no visible global function definition for 'lm'
treePValues: no visible global function definition for 'pf'
plot,GBH-ANY: no visible binding for global variable 'sorted.hyp'
plot,GBH-ANY: no visible binding for global variable 'pval'
plot,GBH-ANY: no visible binding for global variable 'group'
plot,GBH-ANY: no visible binding for global variable 'type'
Undefined global functions or variables:
  browseURL group lm pf pval sorted.hyp type
Consider adding
  importFrom("stats", "lm", "pf")
  importFrom("utils", "browseURL")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from 'stsm.class' for: 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
stsm.model: no visible global function definition for 'is.ts'
stsm.model: no visible global function definition for 'var'
stsm.model: no visible global function definition for 'frequency'
stsm.model: no visible global function definition for 'na.omit'
stsm.model: no visible global function definition for 'fft'
stsm.model: no visible global function definition for 'new'
stsm.sgf: no visible global function definition for 'frequency'
char2numeric,stsm: no visible global function definition for
  'frequency'
set.cpar,stsm: no visible global function definition for 'validObject'
set.nopars,stsm: no visible global function definition for
  'validObject'
set.pars,stsm: no visible global function definition for 'validObject'
transPars,stsm: no visible global function definition for 'var'
Undefined global functions or variables:
  fft frequency is.ts na.omit new validObject var
Consider adding
  importFrom("methods", "new", "validObject")
  importFrom("stats", "fft", "frequency", "is.ts", "na.omit", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
SubLasso: no visible global function definition for 'predict'
SubLasso: no visible global function definition for 'coef'
SubLasso: no visible global function definition for 'dev.new'
SubLasso: no visible global function definition for 'cor'
SubLasso: no visible global function definition for 'boxplot'
predict.sublasso: no visible global function definition for 'predict'
Undefined global functions or variables:
  boxplot coef cor dev.new predict
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "boxplot")
  importFrom("stats", "coef", "cor", "predict")
to your NAMESPACE file.
identifyGraph: no visible global function definition for 'phyper'
mytriangle: no visible global function definition for 'symbols'
plotGraph: no visible global function definition for 'par'
plotGraph: no visible global function definition for 'plot'
updateOrgEnvir: no visible global function definition for 'read.table'
Undefined global functions or variables:
  par phyper plot read.table symbols
Consider adding
  importFrom("graphics", "par", "plot", "symbols")
  importFrom("stats", "phyper")
  importFrom("utils", "read.table")
to your NAMESPACE file.
predict.subsemble: no visible global function definition for 'predict'
predict.subsemble: no visible binding for global variable 'family'
subsemble: no visible global function definition for 'gaussian'
subsemble: no visible global function definition for 'detectCores'
subsemble : .make_Z_l: no visible global function definition for
  'parSapply'
subsemble : .make_Z_l: no visible global function definition for
  'makeCluster'
subsemble : .make_Z_l: no visible global function definition for
  'stopCluster'
subsemble: no visible global function definition for 'parSapply'
subsemble: no visible global function definition for 'makeCluster'
subsemble: no visible global function definition for 'stopCluster'
subsemble: no visible global function definition for 'predict'
Undefined global functions or variables:
  detectCores family gaussian makeCluster parSapply predict stopCluster
Consider adding
  importFrom("stats", "family", "gaussian", "predict")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'ROCR' 'penalized'
  Please remove these calls from your code.
ELF: no visible global function definition for 'pt'
ELF: no visible global function definition for 'qnorm'
ELF: no visible global function definition for 'lm'
ELF: no visible global function definition for 'lowess'
ELF: no visible global function definition for 'dnorm'
ELF: no visible global function definition for 'approx'
subtype: no visible global function definition for 'runif'
subtype: no visible global function definition for 'hclust'
subtype: no visible global function definition for 'dist'
subtype: no visible global function definition for 'cutree'
subtype: no visible global function definition for 'pt'
subtype: no visible global function definition for 'heatmap'
test_subtype_only: no visible global function definition for 'pt'
test_subtype_only: no visible global function definition for 'survdiff'
test_subtype_only: no visible global function definition for 'survfit'
test_subtype_only: no visible global function definition for 'title'
ufun: no visible global function definition for 'dnorm'
ufun: no visible global function definition for 'lowess'
Undefined global functions or variables:
  approx cutree dist dnorm hclust heatmap lm lowess pt qnorm runif
  survdiff survfit title
Consider adding
  importFrom("graphics", "title")
  importFrom("stats", "approx", "cutree", "dist", "dnorm", "hclust",
             "heatmap", "lm", "lowess", "pt", "qnorm", "runif")
to your NAMESPACE file.
playSudoku : replot: no visible global function definition for 'par'
playSudoku : replot: no visible global function definition for 'plot'
playSudoku : replot: no visible global function definition for
  'segments'
playSudoku : replot: no visible global function definition for 'text'
playSudoku: no visible global function definition for 'tktoplevel'
playSudoku: no visible global function definition for 'tkwm.title'
playSudoku: no visible global function definition for 'tkrplot'
playSudoku: no visible global function definition for 'tktext'
playSudoku: no visible global function definition for 'tkscrollbar'
playSudoku : <anonymous>: no visible global function definition for
  'tkyview'
playSudoku: no visible global function definition for 'tkconfigure'
playSudoku : <anonymous>: no visible global function definition for
  'tkset'
playSudoku: no visible global function definition for 'tkpack'
playSudoku: no visible global function definition for 'tcl'
playSudoku: no visible global function definition for 'tkcget'
playSudoku : showz: no visible global function definition for
  'tkrreplot'
playSudoku : type: no visible global function definition for 'tkinsert'
playSudoku : type: no visible global function definition for 'tksee'
playSudoku : kb: no visible global function definition for 'tkdestroy'
playSudoku: no visible global function definition for
  'getGraphicsEvent'
playSudoku: no visible global function definition for 'tkbind'
playSudoku: no visible global function definition for 'tkwait.window'
Undefined global functions or variables:
  getGraphicsEvent par plot segments tcl text tkbind tkcget tkconfigure
  tkdestroy tkinsert tkpack tkrplot tkrreplot tkscrollbar tksee tkset
  tktext tktoplevel tkwait.window tkwm.title tkyview
Consider adding
  importFrom("grDevices", "getGraphicsEvent")
  importFrom("graphics", "par", "plot", "segments", "text")
to your NAMESPACE file.
SUE.fitted.values: no visible global function definition for
  'model.frame'
SUE.lm: no visible global function definition for 'model.frame'
SUE.lm: no visible global function definition for 'lm'
SUE.lm: no visible global function definition for 'anova'
SUE.plot: no visible global function definition for 'plot'
SUE.residuals: no visible global function definition for 'model.frame'
parameters : para2: no visible global function definition for 'uniroot'
parameters: no visible global function definition for 'optimize'
parameters: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  anova lm model.frame optimize plot uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "anova", "lm", "model.frame", "optimize",
             "uniroot")
to your NAMESPACE file.
MCMCCV: no visible global function definition for 'rnorm'
MLCVGauss: no visible global function definition for 'runif'
MLCVGauss: no visible global function definition for 'optim'
SimSunderData: no visible global function definition for 'runif'
SimSunderData: no visible global function definition for 'dist'
SimSunderData: no visible global function definition for 'rnorm'
SimSunderData: no visible global function definition for 'qgamma'
SimSunderData: no visible global function definition for 'pnorm'
SimSunderData: no visible global function definition for 'rmultinom'
Undefined global functions or variables:
  dist optim pnorm qgamma rmultinom rnorm runif
Consider adding
  importFrom("stats", "dist", "optim", "pnorm", "qgamma", "rmultinom",
             "rnorm", "runif")
to your NAMESPACE file.
sunter: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
supcluster : itgamma: no visible global function definition for
  'rgamma'
supcluster : itgamma: no visible global function definition for
  'dgamma'
supcluster : itgamma: no visible global function definition for 'runif'
supcluster : itbeta: no visible global function definition for 'rnorm'
supcluster : itbeta: no visible global function definition for 'runif'
supcluster : itj: no visible global function definition for 'dmultinom'
supcluster: no visible global function definition for 'kmeans'
tab1: no visible global function definition for 'image'
tab1: no visible global function definition for 'gray'
tab1: no visible global function definition for 'var'
Undefined global functions or variables:
  dgamma dmultinom gray image kmeans rgamma rnorm runif var
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "image")
  importFrom("stats", "dgamma", "dmultinom", "kmeans", "rgamma", "rnorm",
             "runif", "var")
to your NAMESPACE file.
Package which this enhances but not available for checking: 'gputools'
HCLtree: no visible global function definition for 'hclust'
HCLtree: no visible global function definition for 'as.dist'
plotProfilesAcrossAllSamples: no visible global function definition for
  'matplot'
plotProfilesAcrossAllSamples: no visible global function definition for
  'matlines'
plotProfilesAcrossAllSamples: no visible global function definition for
  'axis'
plotProfilesAcrossAllSamples: no visible global function definition for
  'box'
plotProfilesWithinBicluster: no visible global function definition for
  'matplot'
plotProfilesWithinBicluster: no visible global function definition for
  'title'
plotProfilesWithinBicluster: no visible global function definition for
  'axis'
plotProfilesWithinBicluster: no visible global function definition for
  'par'
plotProfilesWithinBicluster: no visible global function definition for
  'box'
plotProfilesWithinBicluster: no visible global function definition for
  'matlines'
plotProfilesWithinBicluster: no visible global function definition for
  'legend'
Undefined global functions or variables:
  as.dist axis box hclust legend matlines matplot par title
Consider adding
  importFrom("graphics", "axis", "box", "legend", "matlines", "matplot",
             "par", "title")
  importFrom("stats", "as.dist", "hclust")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'boa' 'coda'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
superdiag: no visible global function definition for 'as.mcmc.list'
superdiag: no visible global function definition for 'as.mcmc'
superdiag: no visible global function definition for 'runif'
superdiag: no visible global function definition for 'geweke.diag'
superdiag: no visible global function definition for 'heidel.diag'
superdiag: no visible global function definition for 'raftery.diag'
superdiag: no visible global function definition for 'gelman.diag'
Undefined global functions or variables:
  as.mcmc as.mcmc.list gelman.diag geweke.diag heidel.diag raftery.diag
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
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.
Files named as vignettes but with no recognized vignette engine:
   'vignettes/copulas-concordance.tex'
   'vignettes/surrosurv.tex'
(Is a VignetteBuilder field missing?)
Est.Var.CCH.trueweights: no visible binding for global variable 'var'
getEstimatesSP: no visible global function definition for 'quantile'
getEstimatesSP: no visible global function definition for 'resid'
prepareDataNP: no visible global function definition for
  'complete.cases'
prepareDataSP: no visible global function definition for
  'complete.cases'
processRawOutput: no visible global function definition for 'qnorm'
survAM.estimate: no visible global function definition for 'median'
survAM.estimate: no visible binding for global variable 'sd'
Undefined global functions or variables:
  complete.cases median qnorm quantile resid sd var
Consider adding
  importFrom("stats", "complete.cases", "median", "qnorm", "quantile",
             "resid", "sd", "var")
to your NAMESPACE file.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

plot.survAUC: no visible global function definition for 'plot'
plot.survAUC: no visible global function definition for 'lines'
plot.survErr: no visible global function definition for 'plot'
plot.survErr: no visible global function definition for 'lines'
schemper: no visible global function definition for 'predict'
schemper: no visible global function definition for 'survfit'
schemper: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx lines plot predict survfit
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "approx", "predict")
to your NAMESPACE file.
Est.PH: no visible global function definition for 'coxph'
Inf.Cval: no visible global function definition for 'rexp'
Inf.Cval: no visible global function definition for 'var'
Inf.Cval.Delta: no visible global function definition for 'rexp'
Inf.Cval.Delta: no visible global function definition for 'var'
cvC: no visible global function definition for 'coxph'
cvC: no visible global function definition for 'weighted.mean'
Undefined global functions or variables:
  coxph rexp var weighted.mean
Consider adding
  importFrom("stats", "rexp", "var", "weighted.mean")
to your NAMESPACE file.
Files named as vignettes but with no recognized vignette engine:
   'vignettes/survClip.Rnw'
(Is a VignetteBuilder field missing?)
pearson: no visible global function definition for 'cor'
plot.survcorr: no visible global function definition for 'pnorm'
plot.survcorr: no visible global function definition for 'par'
plot.survcorr: no visible global function definition for 'plot'
plot.survcorr: no visible global function definition for 'points'
survcorr: no visible global function definition for 'model.frame'
survcorr: no visible global function definition for 'qnorm'
survcorr: no visible global function definition for 'runif'
survcorr: no visible global function definition for 'pnorm'
survcorr: no visible global function definition for 'var'
survcorr: no visible global function definition for 'qt'
Undefined global functions or variables:
  cor model.frame par plot pnorm points qnorm qt runif var
Consider adding
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "cor", "model.frame", "pnorm", "qnorm", "qt",
             "runif", "var")
to your NAMESPACE file.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.3Mb
    help   1.0Mb
    libs   1.7Mb
Running examples in 'surveillance-Ex.R' failed
The error most likely occurred in:

> ### Name: epidataCS
> ### Title: Continuous Space-Time Marked Point Patterns with Grid-Based
> ###   Covariates
> ### Aliases: epidataCS as.epidataCS print.epidataCS nobs.epidataCS
> ###   head.epidataCS tail.epidataCS [.epidataCS subset.epidataCS
> ###   marks.epidataCS summary.epidataCS print.summary.epidataCS
> ###   as.stepfun.epidataCS getSourceDists
> ### Keywords: spatial classes manip
> 
> ### ** Examples
> 
> ## load "imdepi" example data (which is an object of class "epidataCS")
> data("imdepi")
Warning in readChar(con, 5L, useBytes = TRUE) :
  lzma decoder needed more memory
Error in load(zfile, envir = envir) : empty (zero-byte) input file
Calls: data -> load
Execution halted
'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.
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/survHE.Rcheck/00install.out' for details.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
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  5.2Mb
  sub-directories of 1Mb or more:
    doc   2.8Mb
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').
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
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.
completeCol: no visible global function definition for 'colors'
completeCol: no visible global function definition for 'col2rgb'
completeCol: no visible global function definition for 'palette'
Undefined global functions or variables:
  col2rgb colors palette
Consider adding
  importFrom("grDevices", "col2rgb", "colors", "palette")
to your NAMESPACE file.
.formatResult : capture.str: no visible global function definition for
  'str'
createLog: no visible global function definition for 'sessionInfo'
protocol_junit.svSuiteData: no visible global function definition for
  'xmlNode'
protocol_junit.svSuiteData: no visible global function definition for
  'addChildren'
protocol_junit.svSuiteData: no visible global function definition for
  'saveXML'
protocol_junit.svTestData: no visible global function definition for
  'xmlNode'
protocol_junit.svTestData: no visible global function definition for
  'addChildren'
Undefined global functions or variables:
  addChildren saveXML sessionInfo str xmlNode
Consider adding
  importFrom("utils", "sessionInfo", "str")
to your NAMESPACE file.
svycox.calibrate: no visible global function definition for 'quantile'
svycox.calibrate: no visible binding for global variable 'median'
svycox.calibrate: no visible global function definition for
  'as.formula'
svycox.calibrate: no visible global function definition for 'plot'
svycox.calibrate: no visible global function definition for 'arrows'
svycox.calibrate: no visible global function definition for 'abline'
svycox.nomogram: no visible global function definition for 'predict'
svycox.nomogram: no visible global function definition for 'as.formula'
svycox.validate : internal.validate.func: no visible global function
  definition for 'as.formula'
svycox.validate : internal.validate.func: no visible global function
  definition for 'formula'
Undefined global functions or variables:
  abline arrows as.formula formula median plot predict quantile
Consider adding
  importFrom("graphics", "abline", "arrows", "plot")
  importFrom("stats", "as.formula", "formula", "median", "predict",
             "quantile")
to your NAMESPACE file.
additional_comp: no visible global function definition for 'aggregate'
additional_compPV : <anonymous>: no visible global function definition
  for 'aggregate'
cor.aux.func : <anonymous>: no visible global function definition for
  'cov.wt'
eta.func : <anonymous>: no visible global function definition for 'lm'
eta.func : <anonymous>: no visible global function definition for
  'anova'
glm.dummy.no.std: no visible global function definition for
  'as.formula'
pv_by: no visible binding for global variable 'var'
pv_perc: no visible binding for global variable 'var'
pv_quantile: no visible binding for global variable 'var'
svyPVcor: no visible global function definition for 'update'
svyPVcor: no visible global function definition for 'var'
svyPVeta: no visible global function definition for 'update'
svyPVeta: no visible global function definition for 'var'
svyPVglm: no visible global function definition for 'gaussian'
svyPVglm: no visible binding for global variable 'as.formula'
svyPVglm: no visible binding for global variable 'var'
svyPVglm: no visible global function definition for 'pt'
svyPVttest: no visible binding for global variable 'as.formula'
svyPVttest: no visible global function definition for 'var'
svyPVttest: no visible global function definition for 'pt'
svyPVttest: no visible binding for global variable 'var'
t.test.aux: no visible global function definition for 'as.formula'
t.test.aux: no visible global function definition for 'complete.cases'
Undefined global functions or variables:
  aggregate anova as.formula complete.cases cov.wt gaussian lm pt
  update var
Consider adding
  importFrom("stats", "aggregate", "anova", "as.formula",
             "complete.cases", "cov.wt", "gaussian", "lm", "pt",
             "update", "var")
to your NAMESPACE file.
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.
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  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Packages suggested but not available for checking: 'sylly.de' 'sylly.es'
symbol: no visible global function definition for 'plot.new'
symbol: no visible global function definition for 'plot.window'
symbol: no visible global function definition for 'axis'
symbol: no visible global function definition for 'box'
symbol: no visible global function definition for 'title'
symbol: no visible global function definition for 'rainbow'
symbol: no visible global function definition for 'hsv'
symbol: no visible global function definition for 'rect'
symbol: no visible global function definition for 'polygon'
symbol: no visible global function definition for 'lines'
symbol: no visible global function definition for 'text'
Undefined global functions or variables:
  axis box hsv lines plot.new plot.window polygon rainbow rect text
  title
Consider adding
  importFrom("grDevices", "hsv", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "polygon", "rect", "text", "title")
to your NAMESPACE file.
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.
Namespaces with empty importFrom:
  'Rcpp' 'methods'
mainNetFunction: no visible global function definition for 'png'
mainNetFunction: no visible global function definition for 'plot'
mainNetFunction: no visible global function definition for 'lines'
mainNetFunction: no visible global function definition for 'legend'
mainNetFunction: no visible global function definition for 'dev.off'
plotPR: no visible global function definition for 'plot'
plotROC: no visible global function definition for 'plot'
plotROC: no visible global function definition for 'lines'
simulatedData: no visible global function definition for 'rpois'
simulatedData : <anonymous>: no visible global function definition for
  'rpois'
simulatedData : rlognormpois: no visible global function definition for
  'rnorm'
simulatedData : rlognormpois: no visible global function definition for
  'rpois'
Undefined global functions or variables:
  dev.off legend lines plot png rnorm rpois
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "rnorm", "rpois")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'LowRankQP' 'rgenoud'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
fn.V: no visible global function definition for 'LowRankQP'
gaps.plot: no visible global function definition for 'abline'
path.plot: no visible global function definition for 'lines'
path.plot: no visible global function definition for 'abline'
path.plot: no visible global function definition for 'legend'
synth: no visible binding for global variable 'sd'
synth: no visible binding for global variable 'var'
synth: no visible global function definition for 'LowRankQP'
Undefined global functions or variables:
  LowRankQP abline legend lines sd var
Consider adding
  importFrom("graphics", "abline", "legend", "lines")
  importFrom("stats", "sd", "var")
to your NAMESPACE file.
Package unavailable to check Rd xrefs: 'unix'
.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.
S3 methods shown with full name in documentation object 'rbind.tableList':
  'rbind.tableList'

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'library' or 'require' call to 'grid' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to 'perturb' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'grid'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cellgram: no visible global function definition for 'grid.rect'
cellgram: no visible global function definition for 'gpar'
cellgram: no visible global function definition for 'grid.segments'
cellgram: no visible global function definition for 'grid.circle'
cellgram: no visible global function definition for 'grid.polygon'
cellgram: no visible global function definition for 'grid.text'
cellgram: no visible global function definition for 'unit'
compare: no visible global function definition for 'sd'
tableplot.colldiag: no visible global function definition for
  'colldiag'
tableplot.colldiag: no visible global function definition for 'xtabs'
tableplot.default: no visible global function definition for
  'grid.newpage'
tableplot.default: no visible global function definition for
  'grid.layout'
tableplot.default: no visible global function definition for 'unit'
tableplot.default: no visible global function definition for
  'pushViewport'
tableplot.default: no visible global function definition for 'viewport'
tableplot.default: no visible global function definition for
  'grid.text'
tableplot.default: no visible global function definition for
  'upViewport'
tableplot.default: no visible global function definition for 'gpar'
tableplot.default: no visible global function definition for
  'grid.rect'
tableplot.default: no visible global function definition for
  'popViewport'
Undefined global functions or variables:
  colldiag gpar grid.circle grid.layout grid.newpage grid.polygon
  grid.rect grid.segments grid.text popViewport pushViewport sd unit
  upViewport viewport xtabs
Consider adding
  importFrom("stats", "sd", "xtabs")
to your NAMESPACE file.
TCRsink: no visible global function definition for 'head'
Undefined global functions or variables:
  head
Consider adding
  importFrom("utils", "head")
to your NAMESPACE file.
itabplot : <anonymous>: no visible global function definition for
  'capture.output'
itabplot: no visible global function definition for 'browseURL'
Undefined global functions or variables:
  browseURL capture.output
Consider adding
  importFrom("utils", "browseURL", "capture.output")
to your NAMESPACE file.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    java  11.5Mb
NANOVA.test: no visible global function definition for 'ecdf'
NANOVA.test2: no visible global function definition for 'ecdf'
NANOVA.test3: no visible global function definition for 'ecdf'
fdr.table: no visible global function definition for 'median'
fdr.table: no visible global function definition for 'quantile'
gene.classifier1: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  ecdf median quantile write.table
Consider adding
  importFrom("stats", "ecdf", "median", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'gdata' 'ggplot2' 'grid' 'lattice' 'xtable'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
AnalyzeLVZ: no visible global function definition for 'approx'
ConvP2Vdepthinv: no visible global function definition for 'approx'
DistSummary: no visible global function definition for 'heat.colors'
Earthplot: no visible global function definition for 'heat.colors'
Earthplot: no visible global function definition for 'par'
Earthplot: no visible global function definition for 'plot'
Earthplot: no visible global function definition for 'approx'
Earthplot: no visible global function definition for 'image'
Earthplot: no visible binding for global variable 'lines'
FindRoots: no visible global function definition for 'uniroot'
InterpModel: no visible global function definition for 'approx'
LinInterp: no visible global function definition for 'approx'
PolarPlot: no visible binding for global variable 'plot'
Rayfan: no visible binding for global variable 'lines'
polaraxis: no visible global function definition for 'text'
Undefined global functions or variables:
  approx heat.colors image lines par plot text uniroot
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "image", "lines", "par", "plot", "text")
  importFrom("stats", "approx", "uniroot")
to your NAMESPACE file.
BootTree: no visible global function definition for 'hclust'
BootTree: no visible global function definition for 'dist'
BootTree: no visible global function definition for 'as.dist'
BootTree: no visible global function definition for 'cor'
BootTree: no visible binding for global variable 'var'
Pgpd: no visible global function definition for 'optim'
Pgpd : <anonymous>: no visible global function definition for 'optim'
Pgpd: no visible global function definition for 'var'
Pgpd: no visible global function definition for 'rnorm'
Pgpd: no visible global function definition for 'quantile'
Pvalue: no visible global function definition for 'rnorm'
SigTree: no visible global function definition for 'data'
TreeStat: no visible global function definition for 'hclust'
TreeStat: no visible global function definition for 'as.dist'
TreeStat: no visible global function definition for 'dist'
TreeStat: no visible global function definition for 'cor'
plot.best: no visible global function definition for 'hclust'
plot.best: no visible global function definition for 'as.dist'
plot.best: no visible global function definition for 'dist'
plot.best: no visible global function definition for 'cor'
plot.best: no visible global function definition for 'plot'
treetext: no visible global function definition for 'par'
treetext: no visible global function definition for 'text'
Undefined global functions or variables:
  as.dist cor data dist hclust optim par plot quantile rnorm text var
Consider adding
  importFrom("graphics", "par", "plot", "text")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "optim",
             "quantile", "rnorm", "var")
  importFrom("utils", "data")
to your NAMESPACE file.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.9Mb
    libs   1.5Mb
S3 methods shown with full name in documentation object 'top.fun':
  'slice.fun'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
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.
tdt.quad: no visible global function definition for 'runif'
tdt.rr: no visible global function definition for 'pf'
tdt.rr: no visible global function definition for 'qbeta'
Undefined global functions or variables:
  pf qbeta runif
Consider adding
  importFrom("stats", "pf", "qbeta", "runif")
to your NAMESPACE file.
E.2SI: no visible binding for global variable 'var'
E.2SI: no visible global function definition for 'var'
E.BE: no visible global function definition for 'var'
E.Beta: no visible global function definition for 'var'
E.PO: no visible global function definition for 'var'
E.PPS: no visible global function definition for 'var'
E.SI: no visible global function definition for 'var'
E.STPPS: no visible global function definition for 'var'
E.STSI: no visible global function definition for 'var'
E.STpiPS: no visible global function definition for 'var'
E.SY: no visible global function definition for 'var'
E.WR: no visible global function definition for 'var'
E.piPS: no visible global function definition for 'var'
GREG.SI: no visible global function definition for 'var'
S.BE: no visible global function definition for 'runif'
S.PO: no visible global function definition for 'runif'
S.PPS: no visible global function definition for 'runif'
S.SI: no visible global function definition for 'runif'
S.STPPS: no visible global function definition for 'runif'
S.WR: no visible global function definition for 'rbinom'
S.piPS: no visible global function definition for 'runif'
p.WR: no visible global function definition for 'dmultinom'
Undefined global functions or variables:
  dmultinom rbinom runif var
Consider adding
  importFrom("stats", "dmultinom", "rbinom", "runif", "var")
to your NAMESPACE file.
TeachNet: no visible global function definition for 'predict'
createWeights1: no visible global function definition for 'rnorm'
createWeights2: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  predict rnorm
Consider adding
  importFrom("stats", "predict", "rnorm")
to your NAMESPACE file.
aniplotevents: no visible global function definition for 'plot'
aniplotevents: no visible global function definition for 'lines'
cbfs: no visible global function definition for 'rnorm'
cbfs: no visible global function definition for 'runif'
cbfs_red: no visible global function definition for 'arima.sim'
cbfs_red: no visible global function definition for 'runif'
eventCluster: no visible global function definition for 'princomp'
eventCluster: no visible global function definition for 'kmeans'
measures: no visible global function definition for 'sd'
measures: no visible global function definition for 'var'
measures: no visible global function definition for 'PP.test'
noiseTests: no visible global function definition for 'Box.test'
noiseTests: no visible global function definition for 'PP.test'
noiseTests: no visible global function definition for 'ar'
plotevents: no visible global function definition for 'plot'
plotevents: no visible global function definition for 'lines'
ur.za.fast : roll: no visible global function definition for 'coef'
ur.za.fast : roll: no visible global function definition for 'lm'
Undefined global functions or variables:
  Box.test PP.test ar arima.sim coef kmeans lines lm plot princomp
  rnorm runif sd var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "Box.test", "PP.test", "ar", "arima.sim", "coef",
             "kmeans", "lm", "princomp", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
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
Depends: includes the non-default packages:
  'grid' 'quadprog' 'maps' 'maptools' 'mapdata' 'dichromat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  'dichromat' 'grid' 'mapdata' 'maps' 'maptools' 'quadprog'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 45.1Mb
  sub-directories of 1Mb or more:
    libs      13.2Mb
    tessdata  31.0Mb
File which contains pragma(s) suppressing diagnostics:
  'inst/include/testthat/vendor/catch.h'
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    3.6Mb
    libs   2.1Mb
phyper_right: no visible global function definition for 'dhyper'
progression: no visible global function definition for 'density'
progression: no visible global function definition for 'plot'
progression: no visible global function definition for 'points'
progression: no visible global function definition for 'legend'
progression: no visible global function definition for 'text'
specificities.distribution.plot: no visible global function definition
  for 'dhyper'
specificities.distribution.plot: no visible global function definition
  for 'plot'
specificities.distribution.plot: no visible global function definition
  for 'Axis'
specificities.distribution.plot: no visible global function definition
  for 'arrows'
specificities.distribution.plot: no visible global function definition
  for 'text'
specificities.distribution.plot: no visible global function definition
  for 'title'
specificities.probabilities.vector: no visible global function
  definition for 'phyper'
Undefined global functions or variables:
  Axis arrows density dhyper legend phyper plot points text title
Consider adding
  importFrom("graphics", "Axis", "arrows", "legend", "plot", "points",
             "text", "title")
  importFrom("stats", "density", "dhyper", "phyper")
to your NAMESPACE file.
.dea_create_model: no visible global function definition for
  'getSrcFilename'
.wMean: no visible global function definition for 'weighted.mean'
Undefined global functions or variables:
  getSrcFilename weighted.mean
Consider adding
  importFrom("stats", "weighted.mean")
  importFrom("utils", "getSrcFilename")
to your NAMESPACE file.
transfer: no visible global function definition for 'rgamma'
transfer: no visible global function definition for 'rnorm'
transfer: no visible global function definition for 'rnbinom'
transfer: no visible global function definition for 'rpois'
transfer: no visible global function definition for 'rbinom'
transfer: no visible global function definition for 'runif'
plot,transfer: no visible global function definition for 'barplot'
plot,transfer: no visible global function definition for 'axis'
plot,transfer: no visible global function definition for 'par'
plot,transfer: no visible global function definition for 'hist'
Undefined global functions or variables:
  axis barplot hist par rbinom rgamma rnbinom rnorm rpois runif
Consider adding
  importFrom("graphics", "axis", "barplot", "hist", "par")
  importFrom("stats", "rbinom", "rgamma", "rnbinom", "rnorm", "rpois",
             "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Matrix.h:27:18: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.6/TFMPvalue.Rcheck/00install.out' for details.
ParseTrueFX: no visible global function definition for 'read.csv'
TrueFXRef: no visible global function definition for 'download.file'
TrueFXRef: no visible global function definition for 'browseURL'
Undefined global functions or variables:
  browseURL download.file read.csv
Consider adding
  importFrom("utils", "browseURL", "download.file", "read.csv")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    rda    3.8Mb
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').
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidyinftheo)
  > 
  > test_check("tidyinftheo")
  -- 1. Error: right number of columns given (@test-errors.R#10)  ----------------
  argument "expr" is missing, with no default
  1: expect_length(tab %>% select(vs) %>% shannon_entropy(), 1) at testthat/test-errors.R:10
  2: quasi_label(enquo(object))
  3: eval_bare(get_expr(quo), get_env(quo))
  4: tab %>% select(vs) %>% shannon_entropy()
  5: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  6: eval(quote(`_fseq`(`_lhs`)), env, env)
  7: eval(quote(`_fseq`(`_lhs`)), env, env)
  8: `_fseq`(`_lhs`)
  9: freduce(value, `_function_list`)
  10: withVisible(function_list[[k]](value))
  11: function_list[[k]](value)
  12: shannon_entropy(.)
  13: reduce_data(.data, !!enquo(X), numvars = 1, na.rm = na.rm)
  14: tidyselect::vars_select(names(reduced_tab), !!!quos(...))
  15: vars_select_eval(.vars, quos)
  16: map_lgl(quos, quo_is_helper)
  17: .f(.x[[i]], ...)
  18: extract_expr(quo)
  19: is_call(expr, paren_sym)
  
  == testthat results  ===========================================================
  OK: 37 SKIPPED: 0 FAILED: 1
  1. Error: right number of columns given (@test-errors.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
plot.tight.clust: no visible global function definition for 'hclust'
plot.tight.clust: no visible global function definition for 'dist'
plot.tight.clust: no visible global function definition for 'image'
plot.tight.clust: no visible global function definition for
  'colorRampPalette'
plot.tight.clust: no visible global function definition for 'axis'
plot.tight.clust: no visible global function definition for 'lines'
tight.clust : find.candidates : kmeans.classify: no visible global
  function definition for 'kmeans'
write.tight.clust: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  axis colorRampPalette dist hclust image kmeans lines write.table
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "image", "lines")
  importFrom("stats", "dist", "hclust", "kmeans")
  importFrom("utils", "write.table")
to your NAMESPACE file.
'library' or 'require' call to 'shiny' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'ggplot2'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
timeline: no visible global function definition for 'ggplot'
timeline: no visible global function definition for 'geom_segment'
timeline: no visible global function definition for 'aes_string'
timeline: no visible global function definition for 'geom_rect'
timeline: no visible global function definition for 'geom_text'
timeline: no visible global function definition for 'theme'
timeline: no visible global function definition for 'element_blank'
timeline: no visible global function definition for 'xlab'
timeline: no visible global function definition for 'ylab'
timeline: no visible global function definition for 'xlim'
timeline: no visible global function definition for
  'scale_y_continuous'
timeline: no visible global function definition for 'geom_point'
timeline: no visible global function definition for 'scale_color_grey'
timeline: no visible global function definition for 'geom_hline'
Undefined global functions or variables:
  aes_string element_blank geom_hline geom_point geom_rect geom_segment
  geom_text ggplot scale_color_grey scale_y_continuous theme xlab xlim
  ylab
density.tm: no visible global function definition for 'density'
mu.mle: no visible global function definition for 'optimize'
pophistory.tm: no visible binding for global variable 'quantile'
quantile.tm: no visible global function definition for 'quantile'
sample.pop: no visible global function definition for 'runif'
summary.tm: no visible global function definition for 'quantile'
Undefined global functions or variables:
  density optimize quantile runif
Consider adding
  importFrom("stats", "density", "optimize", "quantile", "runif")
to your NAMESPACE file.
generatelatencies: no visible binding for global variable 'allNames'
generatetimedeltas: no visible global function definition for 'head'
generatetimedeltas: no visible global function definition for 'tail'
generatevertexedgelist : <anonymous>: no visible global function
  definition for 'head'
generatevertexedgelist : <anonymous>: no visible global function
  definition for 'tail'
plotnetworkslices: no visible global function definition for 'par'
plotnetworkslices: no visible global function definition for 'text'
plottanet: no visible global function definition for 'plot'
plottonet: no visible global function definition for 'plot'
shortesttimepath : <anonymous>: no visible global function definition
  for 'tail'
Undefined global functions or variables:
  allNames head par plot tail text
Consider adding
  importFrom("graphics", "par", "plot", "text")
  importFrom("methods", "allNames")
  importFrom("utils", "head", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' calls in package code:
  'ggplot2' 'plyr'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'Matrix' 'lubridate' 'timeDate'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
is.Bizday: no visible global function definition for 'isWeekday'
plotCalendarHeatmap: no visible global function definition for 'ddply'
plotCalendarHeatmap: no visible global function definition for '.'
plotCalendarHeatmap: no visible binding for global variable 'year'
plotCalendarHeatmap: no visible binding for global variable 'month'
plotCalendarHeatmap: no visible binding for global variable 'week'
plotCalendarHeatmap: no visible global function definition for 'ggplot'
plotCalendarHeatmap: no visible global function definition for 'aes'
plotCalendarHeatmap: no visible binding for global variable 'monthweek'
plotCalendarHeatmap: no visible binding for global variable 'weekday'
plotCalendarHeatmap: no visible global function definition for
  'geom_tile'
plotCalendarHeatmap: no visible global function definition for
  'facet_grid'
plotCalendarHeatmap: no visible global function definition for
  'scale_fill_gradientn'
projectDate: no visible global function definition for 'holidayNYSE'
projectDate: no visible global function definition for
  'sparse.model.matrix'
Undefined global functions or variables:
  . aes ddply facet_grid geom_tile ggplot holidayNYSE isWeekday month
  monthweek scale_fill_gradientn sparse.model.matrix week weekday year
boot_autocov: no visible global function definition for 'is.ts'
boot_autocov: no visible global function definition for 'tsboot'
boot_autocov: no visible global function definition for 'quantile'
boot_autocov: no visible global function definition for 'par'
boot_autocov: no visible global function definition for 'frequency'
boot_autocov: no visible global function definition for 'polygon'
boot_autocov: no visible global function definition for 'lines'
boot_autocov: no visible global function definition for 'abline'
boot_autocov: no visible global function definition for 'acf'
boot_spec: no visible global function definition for 'is.ts'
boot_spec: no visible global function definition for 'tsboot'
boot_spec: no visible global function definition for 'spec.pgram'
boot_spec: no visible global function definition for 'quantile'
boot_spec: no visible global function definition for 'polygon'
boot_spec: no visible global function definition for 'lines'
redraw: no visible global function definition for 'spec.pgram'
statistic: no visible global function definition for 'acf'
Undefined global functions or variables:
  abline acf frequency is.ts lines par polygon quantile spec.pgram
  tsboot
Consider adding
  importFrom("graphics", "abline", "lines", "par", "polygon")
  importFrom("stats", "acf", "frequency", "is.ts", "quantile",
             "spec.pgram")
to your NAMESPACE file.
createHstore.ts: no visible global function definition for 'time'
exploreDb : <anonymous>: no visible global function definition for
  'plot'
exportTsList : <anonymous>: no visible global function definition for
  'time'
exportTsList: no visible global function definition for 'write.csv2'
importTsList: no visible global function definition for 'read.csv2'
importTsList : <anonymous>: no visible global function definition for
  'as.ts'
plot.tslist: no visible global function definition for 'plot'
plot.tslist : <anonymous>: no visible global function definition for
  'time'
plot.tslist: no visible global function definition for 'par'
plot.tslist: no visible global function definition for 'legend'
readTimeSeries : <anonymous>: no visible global function definition for
  'ts'
resolveOverlap: no visible global function definition for 'is.ts'
resolveOverlap: no visible global function definition for 'frequency'
resolveOverlap: no visible global function definition for 'time'
resolveOverlap: no visible global function definition for 'ts'
storeTimeSeries: no visible binding for global variable 'frequency'
zooLikeDateConvert: no visible global function definition for 'time'
zooLikeDateConvert: no visible global function definition for
  'frequency'
zooLikeDateConvert: no visible global function definition for 'cycle'
Undefined global functions or variables:
  as.ts cycle frequency is.ts legend par plot read.csv2 time ts
  write.csv2
Consider adding
  importFrom("graphics", "legend", "par", "plot")
  importFrom("stats", "as.ts", "cycle", "frequency", "is.ts", "time",
             "ts")
  importFrom("utils", "read.csv2", "write.csv2")
to your NAMESPACE file.
author.search: no visible binding for global variable 'na.omit'
reference.list: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
drawGraph: no visible global function definition for 'pdf'
drawGraph: no visible global function definition for 'par'
drawGraph: no visible global function definition for 'plot'
drawGraph: no visible global function definition for 'segments'
drawGraph: no visible global function definition for 'lines'
drawGraph: no visible global function definition for 'text'
drawGraph: no visible global function definition for 'dev.off'
drugRank: no visible global function definition for 'aggregate'
floating2: no visible global function definition for 'cor'
timma: no visible global function definition for 'median'
timma: no visible global function definition for 'write.table'
Undefined global functions or variables:
  aggregate cor dev.off lines median par pdf plot segments text
  write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "plot", "segments", "text")
  importFrom("stats", "aggregate", "cor", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'ExPosition' 'InPosition' 'TExPosition' 'prettyGraphs'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
Packages in Depends field not imported from:
  'rgl' 'tcltk'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.my.tkdev: no visible global function definition for 'win.metafile'
tkpersp : draw: no visible global function definition for 'par'
tkpersp : draw: no visible global function definition for 'persp'
Undefined global functions or variables:
  par persp win.metafile
Consider adding
  importFrom("grDevices", "win.metafile")
  importFrom("graphics", "par", "persp")
to your NAMESPACE file.
FLXmclust.Density: no visible global function definition for 'dmvnorm'
FLXmclust.Estimate: no visible global function definition for 'flexmix'
FLXmclust.Estimate: no visible global function definition for
  'FLXmclust'
coefmclust: no visible global function definition for 'parameters'
flexmix.Density: no visible global function definition for
  'model.matrix'
flexmix.Density: no visible global function definition for
  'model.response'
flexmix.Density: no visible global function definition for
  'model.frame'
flexmix.Density: no visible global function definition for 'dnorm'
flexmix.Density: no visible global function definition for 'dpois'
flexmix.Density: no visible global function definition for 'dbinom'
flexmix.Estimate: no visible global function definition for 'flexmix'
flexmix.Estimate: no visible global function definition for 'FLXglm'
tleplot,TLE-data.frame: no visible global function definition for
  'legend'
Undefined global functions or variables:
  FLXglm FLXmclust dbinom dmvnorm dnorm dpois flexmix legend
  model.frame model.matrix model.response parameters
Consider adding
  importFrom("graphics", "legend")
  importFrom("stats", "dbinom", "dnorm", "dpois", "model.frame",
             "model.matrix", "model.response")
to your NAMESPACE file.
'library' or 'require' call to 'mvtnorm' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'mvtnorm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
EMN: no visible global function definition for 'dmvnorm'
EMN: no visible global function definition for 'pmvnorm'
EMT: no visible global function definition for 'GenzBretz'
EMT: no visible global function definition for 'dmvt'
EMT: no visible global function definition for 'pmvt'
MomemNT: no visible global function definition for 'pnorm'
MomemNT: no visible global function definition for 'dnorm'
MomemNT: no visible global function definition for 'pmvnorm'
MomemNT: no visible global function definition for 'dmvnorm'
TT.moment: no visible global function definition for 'GenzBretz'
TT.moment: no visible global function definition for 'pmvt'
TT.moment: no visible global function definition for 'dt'
TT.moment: no visible global function definition for 'pt'
TT.moment: no visible global function definition for 'dmvt'
cdfNI: no visible global function definition for 'pnorm'
cdfNI: no visible global function definition for 'pt'
inits: no visible global function definition for 'lm'
Undefined global functions or variables:
  GenzBretz dmvnorm dmvt dnorm dt lm pmvnorm pmvt pnorm pt
Consider adding
  importFrom("stats", "dnorm", "dt", "lm", "pnorm", "pt")
to your NAMESPACE file.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.3Mb
Running examples in 'tmap-Ex.R' failed
The error most likely occurred in:

> ### Name: tm_symbols
> ### Title: Draw symbols
> ### Aliases: tm_symbols tm_squares tm_bubbles tm_dots tm_markers
> ### Keywords: map symbol
> 
> ### ** Examples
> 
> data(World, Europe, metro)
> metro$growth <- (metro$pop2020 - metro$pop2010) / (metro$pop2010 * 10) * 100
> 
> tm_shape(World) +
+     tm_fill("grey70") +
+ tm_shape(metro) +
+     tm_bubbles("pop2010", col = "growth", 
+         border.col = "black", border.alpha = .5, 
+         style="fixed", breaks=c(-Inf, seq(0, 6, by=2), Inf),
+         palette="-RdYlBu", contrast=1, 
+         title.size="Metro population", 
+         title.col="Growth rate (%)") + 
+ tm_format_World()
> 
> tm_shape(metro) +
+ 	tm_symbols(size = "pop2010", col="pop2010", shape="pop2010",
+ 		legend.format = list(text.align="right", text.to.columns = TRUE)) +
+ tm_layout(legend.outside = TRUE, legend.outside.position = "bottom", legend.stack = "horizontal")
> 
> ## Not run: 
> ##D require(tmaptools)
> ##D x <- sample_dots(World, vars="gdp_md_est", convert2density = TRUE, w = 100000)
> ##D tm_shape(x) + 
> ##D 	tm_dots() + 
> ##D tm_layout("World GDP (one dot is 100 billon dollars)", title.position = c("right", "bottom"))
> ## End(Not run)
> 
> qtm(Europe, bbox="Italy") +
+ tm_shape(metro) +
+ 	tm_markers(text="name")
Error in download.file(addr[k], destfile = tmpfile, mode = "wb", quiet = TRUE) : 
  cannot open URL 'http://nominatim.openstreetmap.org/search?q=Italy&format=xml&polygon=0&addressdetails=0'
Calls: <Anonymous> ... do.call -> bb -> get_bb -> geocode_OSM -> lapply -> FUN
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 368-373 (tmap-nutshell.Rmd) 
Error: processing vignette 'tmap-nutshell.Rmd' failed with diagnostics:
cannot open URL 'http://nominatim.openstreetmap.org/search?q=India&format=xml&polygon=0&addressdetails=0'
Execution halted
Running examples in 'tmaptools-Ex.R' failed
The error most likely occurred in:

> ### Name: bb
> ### Title: Bounding box generator
> ### Aliases: bb
> 
> ### ** Examples
> 
> if (require(tmap)) {
+ 
+     ## load shapes
+     data(NLD_muni)
+     data(World)
+ 
+     ## get bounding box (similar to sp's function bbox)
+     bb(NLD_muni)
+ 
+     ## extent it by factor 1.10
+     bb(NLD_muni, ext=1.10)
+ 
+     ## convert to longlat
+     bb(NLD_muni, projection="longlat")
+ 
+     ## change existing bounding box
+     bb(NLD_muni, ext=1.5)
+     bb(NLD_muni, width=2, relative = TRUE)
+     bb(NLD_muni, xlim=c(.25, .75), ylim=c(.25, .75), relative = TRUE)
+ 
+     bb("Limburg", projection = "rd")
+     bb_italy <- bb("Italy", projection = "eck4")
+ 
+     tm_shape(World, bbox=bb_italy) + tm_polygons()
+     # shorter alternative: tm_shape(World, bbox="Italy") + tm_polygons()
+ }
Loading required package: tmap
Error in download.file(addr[k], destfile = tmpfile, mode = "wb", quiet = TRUE) : 
  cannot open URL 'http://nominatim.openstreetmap.org/search?q=Limburg&format=xml&polygon=0&addressdetails=0'
Calls: bb -> get_bb -> geocode_OSM -> lapply -> FUN
Execution halted
installed size is 22.6Mb
  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.
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'
Tosls.formula: no visible global function definition for 'model.matrix'
Tosls.formula: no visible global function definition for
  'model.response'
summary: no visible global function definition for 'coef'
summary: no visible global function definition for 'pt'
Undefined global functions or variables:
  coef model.matrix model.response pt
Consider adding
  importFrom("stats", "coef", "model.matrix", "model.response", "pt")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'Cairo' 'RGtk2' 'colorspace' 'gWidgets' 'tourr'
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'TeachingDemos' 'ash'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'Cairo' 'RGtk2' 'colorspace' 'gWidgets' 'tourr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: 'rmongodb'
ConfA: no visible global function definition for 'qf'
EstM2Sn: no visible global function definition for 'nlm'
EstM2Sn: no visible global function definition for 'qnorm'
TV.model: no visible global function definition for 'dev.new'
TV.model: no visible global function definition for 'points'
betaBino: no visible global function definition for 'pbinom'
doseD: no visible global function definition for 'lm'
doseD: no visible global function definition for 'dev.new'
doseD: no visible global function definition for 'par'
doseD: no visible global function definition for 'plot'
doseD: no visible global function definition for 'axTicks'
doseD: no visible global function definition for 'axis'
doseD: no visible global function definition for 'lines'
doseD: no visible global function definition for 'abline'
doseD: no visible global function definition for 'legend'
setD: no visible global function definition for 'dev.new'
setD: no visible global function definition for 'par'
setD: no visible global function definition for 'pbinom'
setD: no visible global function definition for 'abline'
setD: no visible global function definition for 'axis'
setD: no visible global function definition for 'rect'
setD: no visible global function definition for 'lines'
setD: no visible global function definition for 'text'
setD: no visible global function definition for 'axTicks'
setD: no visible global function definition for 'legend'
spoD : spoD_A: no visible global function definition for 'chisq.test'
Undefined global functions or variables:
  abline axTicks axis chisq.test dev.new legend lines lm nlm par pbinom
  plot points qf qnorm rect text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axTicks", "axis", "legend", "lines",
             "par", "plot", "points", "rect", "text")
  importFrom("stats", "chisq.test", "lm", "nlm", "pbinom", "qf", "qnorm")
to your NAMESPACE file.
align1d : obj: no visible global function definition for 'dist'
align2d : obj: no visible global function definition for 'dist'
align2d : pen: no visible global function definition for 'dist'
align2d: no visible global function definition for 'dist'
sumt: no visible global function definition for 'optim'
tpe1d: no visible global function definition for 'hclust'
tpe2d: no visible global function definition for 'hclust'
tpe2d: no visible global function definition for 'cmdscale'
Undefined global functions or variables:
  cmdscale dist hclust optim
Consider adding
  importFrom("stats", "cmdscale", "dist", "hclust", "optim")
to your NAMESPACE file.
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.
microsoftTranslate: no visible global function definition for
  'URLencode'
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
rtrapezoid: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Build_JTree: no visible global function definition for 'flush.console'
Run_JTree: no visible global function definition for 'cov2cor'
Undefined global functions or variables:
  cov2cor flush.console
Consider adding
  importFrom("stats", "cov2cor")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
LikAge: no visible global function definition for 'read.table'
bd.ME.optim: no visible global function definition for 'optim'
bd.ME.optim.rho: no visible global function definition for 'optim'
bd.ME.optim.rho.all: no visible global function definition for 'optim'
bd.MEyule.optim: no visible global function definition for 'optimize'
bd.MEyule.optim: no visible global function definition for 'optim'
bd.age.optim.matlab: no visible global function definition for
  'read.table'
bd.groups.conf: no visible global function definition for 'uniroot'
bd.shifts.plot: no visible global function definition for 'plot'
bd.shifts.plot: no visible global function definition for 'lines'
bdsky.stt.optim: no visible global function definition for 'optim'
create.mat: no visible global function definition for 'write.table'
Undefined global functions or variables:
  lines optim optimize plot read.table uniroot write.table
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "optim", "optimize", "uniroot")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
plot.treeperm: no visible global function definition for 'hist'
plot.treeperm: no visible global function definition for 'points'
plot.treeperm: no visible global function definition for 'text'
treeperm.formula: no visible global function definition for
  'model.frame'
treeperm.formula: no visible global function definition for
  'model.response'
Undefined global functions or variables:
  hist model.frame model.response points text
Consider adding
  importFrom("graphics", "hist", "points", "text")
  importFrom("stats", "model.frame", "model.response")
to your NAMESPACE file.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    4.7Mb
    libs   1.4Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
plot.trifield: no visible global function definition for 'topo.colors'
plot.trifield: no visible global function definition for 'plot'
plot.trifield: no visible global function definition for 'image'
plot.trifield: no visible global function definition for 'contour'
plot.trifield: no visible global function definition for 'text'
ternary.legend: no visible global function definition for 'arrows'
ternary.legend: no visible global function definition for 'text'
triaxes: no visible global function definition for 'lines'
tribox: no visible global function definition for 'polygon'
Undefined global functions or variables:
  arrows contour image lines plot polygon text topo.colors
Consider adding
  importFrom("grDevices", "topo.colors")
  importFrom("graphics", "arrows", "contour", "image", "lines", "plot",
             "polygon", "text")
to your NAMESPACE file.
'library' or 'require' call to 'fpc' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.tkm: no visible global function definition for 'plotcluster'
plot.tkm: no visible global function definition for 'plot'
plot.tkm: no visible global function definition for 'points'
plot.tkm: no visible global function definition for 'lines'
plot.tkm: no visible global function definition for 'discrcoord'
Undefined global functions or variables:
  discrcoord lines plot plotcluster points
Consider adding
  importFrom("graphics", "lines", "plot", "points")
to your NAMESPACE file.
cinbag: no visible global function definition for 'var'
trimTrees: no visible global function definition for 'predict'
Undefined global functions or variables:
  predict var
Consider adding
  importFrom("stats", "predict", "var")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'gtools' 'mgcv'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'gtools' 'mgcv' 'msm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
HtoGp: no visible global function definition for 'odd'
HtoGp: no visible global function definition for 'even'
plot.pirls.gam: no visible global function definition for 'par'
plot.pirls.gam: no visible global function definition for 'plot'
plot.pirls.gam: no visible global function definition for 'title'
plot.pirls.gam: no visible global function definition for 'lines'
plot.pirls.gam: no visible global function definition for 'rug'
plot.pirls.gam: no visible global function definition for 'mtext'
test.trioGxE: no visible global function definition for 'write.table'
trioGxE: no visible global function definition for 'quantile'
trioGxE: no visible global function definition for 'qtnorm'
trioplot: no visible global function definition for 'quantile'
trioplot: no visible global function definition for 'formula'
trioplot: no visible global function definition for 'gam'
trioplot: no visible global function definition for 'binomial'
Undefined global functions or variables:
  binomial even formula gam lines mtext odd par plot qtnorm quantile
  rug title write.table
Consider adding
  importFrom("graphics", "lines", "mtext", "par", "plot", "rug", "title")
  importFrom("stats", "binomial", "formula", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
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.
'library' or 'require' calls to packages already attached by Depends:
  'leaps' 'locfit' 'mgcv'
  Please remove these calls from your code.
':::' calls which should be '::':
  'stats:::ARMAacf' 'stats:::acf' 'stats:::arima'
  See the note in ?`:::` about the use of this operator.
dmvnb: no visible global function definition for 'dbinom'
drvts: no visible global function definition for 'dnorm'
drvts: no visible global function definition for 'dbinom'
dsvts: no visible global function definition for 'dnorm'
rescale: no visible global function definition for 'qlogis'
rescale: no visible global function definition for 'plogis'
tslogl: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dbinom dnorm plogis qlogis
Consider adding
  importFrom("stats", "dbinom", "dnorm", "plogis", "qlogis")
to your NAMESPACE file.
tfDetails: no visible global function definition for 'start'
tfDetails: no visible global function definition for 'end'
Undefined global functions or variables:
  end start
Consider adding
  importFrom("stats", "end", "start")
to your NAMESPACE file.
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.
Package in Depends field not imported from: 'deSolve'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
vintageMap: no visible global function definition for 'read.table'
TSget,character-TSfameLocalConnection: no visible global function
  definition for 'as.ts'
TSget,character-TSfameLocalConnection: no visible global function
  definition for 'zoo'
TSget,character-TSfameLocalConnection: no visible global function
  definition for 'frequency'
TSget,character-TSfameServerConnection: no visible global function
  definition for 'as.ts'
TSget,character-TSfameServerConnection: no visible global function
  definition for 'zoo'
TSget,character-TSfameServerConnection: no visible global function
  definition for 'frequency'
Undefined global functions or variables:
  as.ts frequency read.table zoo
Consider adding
  importFrom("stats", "as.ts", "frequency")
  importFrom("utils", "read.table")
to your NAMESPACE file.
DstandardizedLoadings.TSFmodel: no visible global function definition
  for 'cov'
FAfitStats.TSFmodel: no visible global function definition for 'cov'
FAfitStats.default: no visible global function definition for 'cor'
FAfitStats.default: no visible global function definition for
  'factanal'
FAfitStats.default: no visible global function definition for 'pchisq'
FAmodelFitStats: no visible global function definition for 'pchisq'
checkResiduals.TSFmodel: no visible global function definition for
  'cov'
distribution.factorsEstEval: no visible global function definition for
  'par'
distribution.factorsEstEval: no visible binding for global variable
  'par'
distribution.factorsEstEval: no visible global function definition for
  'density'
distribution.factorsEstEval: no visible global function definition for
  'matplot'
distribution.factorsEstEval: no visible global function definition for
  'title'
summary.TSFmodel: no visible global function definition for 'start'
summary.TSFmodel: no visible global function definition for 'end'
Undefined global functions or variables:
  cor cov density end factanal matplot par pchisq start title
Consider adding
  importFrom("graphics", "matplot", "par", "title")
  importFrom("stats", "cor", "cov", "density", "end", "factanal",
             "pchisq", "start")
to your NAMESPACE file.
Func.SAX: no visible global function definition for 'sd'
Func.SAX: no visible global function definition for 'qnorm'
Func.matrix: no visible global function definition for 'qnorm'
Func.motif: no visible global function definition for 'sd'
Func.motif: no visible global function definition for 'na.omit'
Func.motif: no visible global function definition for 'combn'
Func.motif.multivariate: no visible global function definition for
  'txtProgressBar'
Func.motif.multivariate: no visible global function definition for
  'setTxtProgressBar'
Undefined global functions or variables:
  combn na.omit qnorm sd setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit", "qnorm", "sd")
  importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
dLag : dlag.f: no visible global function definition for
  'complete.cases'
distmat: no visible global function definition for 'dist'
fitCity: no visible global function definition for 'glm.control'
fitCity: no visible global function definition for 'terms'
ldmvnorm: no visible global function definition for 'mahalanobis'
lspline: no visible global function definition for 'quantile'
plot.tsdecomp: no visible global function definition for 'par'
plot.tsdecomp: no visible global function definition for 'plot'
setupFormula: no visible global function definition for 'as.formula'
spatialgibbs: no visible global function definition for 'rnorm'
spatialgibbs: no visible global function definition for 'rgamma'
spatialgibbs: no visible global function definition for 'runif'
tsdecomp: no visible global function definition for 'fft'
Undefined global functions or variables:
  as.formula complete.cases dist fft glm.control mahalanobis par plot
  quantile rgamma rnorm runif terms
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "as.formula", "complete.cases", "dist", "fft",
             "glm.control", "mahalanobis", "quantile", "rgamma", "rnorm",
             "runif", "terms")
to your NAMESPACE file.
covTranspose11: warning in glasso(sc, 2 * rhoc/n, wi.init = gc$wi,
  w.init = gc$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
covTranspose11: warning in glasso(sr, 2 * rhor/p, wi.init = gr$wi,
  w.init = gr$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
.help.ESS: no visible global function definition for 'index.search'
TransSphere : ttin: no visible global function definition for 't.test'
TransSphere: no visible global function definition for 'sd'
TransSphere: no visible global function definition for 'quantile'
TransSphere: no visible global function definition for 'pt'
Undefined global functions or variables:
  index.search pt quantile sd t.test
Consider adding
  importFrom("stats", "pt", "quantile", "sd", "t.test")
to your NAMESPACE file.
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.
Running examples in 'TTR-Ex.R' failed
The error most likely occurred in:

> ### Name: TTR
> ### Title: Functions to create Technical Trading Rules (TTR)
> ### Aliases: TTR TTR-package
> ### Keywords: package
> 
> ### ** Examples
> 
> 
> data(ttrc)
> 
> # Bollinger Bands
> bbands <- BBands( ttrc[,c("High","Low","Close")] )
> 
> # Directional Movement Index
> adx <- ADX(ttrc[,c("High","Low","Close")])
> 
> # Moving Averages
> ema <- EMA(ttrc[,"Close"], n=20)
> sma <- SMA(ttrc[,"Close"], n=20)
> 
> # MACD
> macd <- MACD( ttrc[,"Close"] )
> 
> # RSI
> rsi <- RSI(ttrc[,"Close"])
> 
> # Stochastics
> stochOsc <- stoch(ttrc[,c("High","Low","Close")])
> 
> ### Note: you must have a working internet connection
> ### for the examples below to work!
> 
> # Fetch U.S. symbols from the internet
> nyseSymbols <- stockSymbols("NYSE")
Fetching NYSE symbols...
Warning in file(file, "rt") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in file(file, "rt") : cannot open the connection
Calls: stockSymbols -> read.csv -> read.table -> file
Execution halted
ttScreening: no visible global function definition for 'gaussian'
ttScreening: no visible global function definition for 'glm.control'
ttScreening: no visible global function definition for 'model.response'
ttScreening: no visible global function definition for 'is.empty.model'
ttScreening: no visible global function definition for 'model.matrix'
ttScreening: no visible global function definition for 'na.omit'
ttScreening: no visible global function definition for 'terms'
ttScreening: no visible global function definition for 'capture.output'
ttScreening: no visible global function definition for 'glm'
ttScreening: no visible binding for global variable 'gaussian'
ttScreening: no visible global function definition for 'pt'
ttScreening: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  capture.output gaussian glm glm.control is.empty.model model.matrix
  model.response na.omit p.adjust pt terms
Consider adding
  importFrom("stats", "gaussian", "glm", "glm.control", "is.empty.model",
             "model.matrix", "model.response", "na.omit", "p.adjust",
             "pt", "terms")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
.saveDevice: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  dev.off
Consider adding
  importFrom("grDevices", "dev.off")
to your NAMESPACE file.
ttwa: no visible global function definition for 'aggregate'
ttwa: no visible global function definition for 'txtProgressBar'
ttwa: no visible global function definition for 'setTxtProgressBar'
Undefined global functions or variables:
  aggregate setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "aggregate")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
http.connection: no visible global function definition for 'setNames'
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'gsl' 'igraph' 'snowfall'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
condnorm: no visible global function definition for 'pnorm'
condnorm: no visible global function definition for 'dnorm'
find.p.joint: no visible global function definition for 'integrate'
find.p.joint.alt: no visible global function definition for 'integrate'
termsInt: no visible global function definition for 'pnorm'
termsInt.alt: no visible global function definition for 'pnorm'
twoStageNull: no visible global function definition for 'qnorm'
twoStageNull: no visible global function definition for 'optimize'
twoStagePower: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dnorm integrate optimize pnorm qnorm
Consider adding
  importFrom("stats", "dnorm", "integrate", "optimize", "pnorm", "qnorm")
to your NAMESPACE file.
txtacf: no visible binding for global variable 'na.fail'
txtacf: no visible global function definition for 'acf'
txtboxplot : <anonymous>: no visible global function definition for
  'boxplot.stats'
txtboxplot: no visible global function definition for 'boxplot.stats'
txtdensity: no visible global function definition for 'density'
Undefined global functions or variables:
  acf boxplot.stats density na.fail
Consider adding
  importFrom("grDevices", "boxplot.stats")
  importFrom("stats", "acf", "density", "na.fail")
to your NAMESPACE file.
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 11.9Mb
  sub-directories of 1Mb or more:
    doc         5.3Mb
    dummydata   1.4Mb
    libs        4.2Mb
ubRacing : predCandidate: no visible global function definition for
  'predict'
ubRacing : aux2.friedman.edit: no visible global function definition
  for 'pchisq'
ubRacing : aux2.friedman.edit: no visible global function definition
  for 'qt'
ubRacing : aux.friedman.edit: no visible global function definition for
  'wilcox.test'
ubRacing : aux.ttest.edit: no visible global function definition for
  't.test'
ubRacing : aux.ttest.edit: no visible global function definition for
  'p.adjust'
ubRacing : idFolds: no visible global function definition for
  'quantile'
ubRacing: no visible binding for global variable 'sd'
ubSmoteExs: no visible global function definition for 'runif'
Undefined global functions or variables:
  p.adjust pchisq predict qt quantile runif sd t.test wilcox.test
Consider adding
  importFrom("stats", "p.adjust", "pchisq", "predict", "qt", "quantile",
             "runif", "sd", "t.test", "wilcox.test")
to your NAMESPACE file.
med: no visible global function definition for 'quantile'
uh: no visible global function definition for 'mad'
uh.bu: no visible global function definition for 'mad'
Undefined global functions or variables:
  mad quantile
Consider adding
  importFrom("stats", "mad", "quantile")
to your NAMESPACE file.
permute.rows: no visible global function definition for 'runif'
uniCox: no visible global function definition for 'quantile'
uniCoxCV: no visible global function definition for 'quantile'
uniCoxCV: no visible global function definition for 'coxph'
uniCoxCV: no visible binding for global variable 'var'
Undefined global functions or variables:
  coxph quantile runif var
Consider adding
  importFrom("stats", "quantile", "runif", "var")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'predict.uniCox':
  'predict.uniCox'

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
dudewicz.unif.test: no visible global function definition for 'runif'
frosini.unif.test: no visible global function definition for 'runif'
hegazy.unif.test: no visible global function definition for 'runif'
kolmogorov.unif.test: no visible global function definition for 'runif'
kuiper.unif.test: no visible global function definition for 'runif'
neyman.unif.test: no visible global function definition for 'runif'
quesenberry.unif.test: no visible global function definition for
  'runif'
sarkadi.unif.test: no visible global function definition for 'runif'
sherman.unif.test: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
cumcount: no visible global function definition for 'setNames'
uniqtag: no visible global function definition for 'setNames'
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    1.6Mb
    libs   1.7Mb
plot.upclassfit: no visible global function definition for 'frame'
plot.upclassfit: no visible global function definition for 'par'
plot.upclassfit: no visible global function definition for 'axis'
plot.upclassfit: no visible global function definition for 'matplot'
plot.upclassfit: no visible global function definition for 'legend'
plot.upclassfit: no visible global function definition for 'title'
Undefined global functions or variables:
  axis frame legend matplot par title
Consider adding
  importFrom("graphics", "axis", "frame", "legend", "matplot", "par",
             "title")
to your NAMESPACE file.
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'.
'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.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    extdata   6.2Mb
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 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
Packages suggested but not available for checking: 'vaers' 'vaersND'
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.
Packages in Depends field not imported from:
  'MASS' 'strucchange'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
black_scholes: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
burdenPlot: no visible global function definition for 'density'
burdenPlot: no visible global function definition for 'axis'
burdenPlot: no visible global function definition for 'points'
burdenPlot: no visible global function definition for 'lines'
burdenPlot: no visible global function definition for 'abline'
burdenPlot: no visible global function definition for 'text'
burdenPlot: no visible global function definition for 'sd'
burdenPlot: no visible global function definition for 'segments'
vbdm: no visible global function definition for 'var'
vbdm: no visible global function definition for 'pchisq'
vbdmR : run_discrete_mixture_vanilla: no visible global function
  definition for 'var'
vbdmR: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  abline axis density lines pchisq points sd segments text var
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "points", "segments",
             "text")
  importFrom("stats", "density", "pchisq", "sd", "var")
to your NAMESPACE file.
compute_KL : rtnorm: no visible global function definition for 'runif'
compute_KL : rtnorm: no visible global function definition for 'dnorm'
compute_KL: no visible global function definition for 'qnorm'
compute_KL: no visible global function definition for 'dnorm'
compute_KL: no visible global function definition for 'pnorm'
compute_KL: no visible global function definition for 'var'
compute_KL: no visible global function definition for 'rbinom'
compute_KL: no visible global function definition for 'rnorm'
compute_KL: no visible global function definition for 'sd'
vbsr: no visible global function definition for 'qchisq'
vbsr: no visible global function definition for 'var'
vbsr: no visible global function definition for 'pchisq'
vbsr: no visible global function definition for 'sd'
vbsr: no visible binding for global variable 'sd'
Undefined global functions or variables:
  dnorm pchisq pnorm qchisq qnorm rbinom rnorm runif sd var
Consider adding
  importFrom("stats", "dnorm", "pchisq", "pnorm", "qchisq", "qnorm",
             "rbinom", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
cv.vda.le.default: no visible global function definition for 'predict'
cv.vda.r.default: no visible global function definition for 'predict'
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
Compare2FDS: no visible global function definition for 'runif'
Compare2FDS: no visible global function definition for 'lm'
Compare2FDS: no visible global function definition for 'model.matrix'
Compare2FDS: no visible global function definition for 'plot'
Compare2FDS: no visible global function definition for 'abline'
Compare2FDS: no visible global function definition for 'lines'
Compare2FDS: no visible global function definition for 'text'
Compare2Vdg: no visible global function definition for 'par'
Compare2Vdg: no visible global function definition for 'plot'
Compare2Vdg: no visible global function definition for 'lines'
Compare2Vdg: no visible global function definition for 'legend'
FDSPlot: no visible global function definition for 'runif'
FDSPlot: no visible global function definition for 'lm'
FDSPlot: no visible global function definition for 'model.matrix'
FDSPlot: no visible global function definition for 'plot'
FDSPlot: no visible global function definition for 'abline'
Vdgraph: no visible global function definition for 'par'
Vdgraph: no visible global function definition for 'plot'
Vdgraph: no visible global function definition for 'lines'
Vdgraph: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline legend lines lm model.matrix par plot runif text
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "plot",
             "text")
  importFrom("stats", "lm", "model.matrix", "runif")
to your NAMESPACE file.
calculateParameters,AffineTransformation: no visible global function
  definition for 'lm'
calculateParameters,AffineTransformation: no visible global function
  definition for 'coef'
calculateParameters,SimilarityTransformation: no visible global
  function definition for 'lm'
calculateParameters,SimilarityTransformation: no visible global
  function definition for 'coef'
plotGridTransformation,Cartesian2DCoordinateTransformation: no visible
  global function definition for 'points'
plotGridTransformation,Cartesian2DCoordinateTransformation: no visible
  global function definition for 'legend'
Undefined global functions or variables:
  coef legend lm points
Consider adding
  importFrom("graphics", "legend", "points")
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
DrawDensity3D: no visible global function definition for 'colorRamp'
DrawDensity3D: no visible global function definition for 'rgb'
ReadFromFile3D: no visible global function definition for 'read.table'
Undefined global functions or variables:
  colorRamp read.table rgb
Consider adding
  importFrom("grDevices", "colorRamp", "rgb")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Running examples in 'vegalite-Ex.R' failed
The error most likely occurred in:

> ### Name: from_spec
> ### Title: Take a JSON Vega-Lite Spec and render as an htmlwidget
> ### Aliases: from_spec
> 
> ### ** Examples
> 
> from_spec("http://rud.is/dl/embedded.json")
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in file(con, "r") : cannot open the connection
Calls: from_spec -> readLines -> file
Execution halted
'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  9.1Mb
  sub-directories of 1Mb or more:
    R      3.4Mb
    doc    1.2Mb
    help   2.7Mb
    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.
Package in Depends field not imported from: 'sm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
vioplot: no visible global function definition for 'quantile'
vioplot: no visible global function definition for 'median'
vioplot: no visible global function definition for 'plot.new'
vioplot: no visible global function definition for 'plot.window'
vioplot: no visible global function definition for 'axis'
vioplot: no visible global function definition for 'box'
vioplot: no visible global function definition for 'polygon'
vioplot: no visible global function definition for 'lines'
vioplot: no visible global function definition for 'rect'
vioplot: no visible global function definition for 'points'
Undefined global functions or variables:
  axis box lines median plot.new plot.window points polygon quantile
  rect
Consider adding
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "points", "polygon", "rect")
  importFrom("stats", "median", "quantile")
to your NAMESPACE file.
viopoints.default: no visible global function definition for 'par'
viopoints.default: no visible global function definition for 'plot.new'
viopoints.default: no visible global function definition for
  'plot.window'
viopoints.default: no visible global function definition for 'axis'
viopoints.default: no visible global function definition for 'arrows'
viopoints.default: no visible global function definition for
  'getFromNamespace'
viopoints.default: no visible global function definition for 'title'
viopoints.default: no visible global function definition for 'box'
Undefined global functions or variables:
  arrows axis box getFromNamespace par plot.new plot.window title
Consider adding
  importFrom("graphics", "arrows", "axis", "box", "par", "plot.new",
             "plot.window", "title")
  importFrom("utils", "getFromNamespace")
to your NAMESPACE file.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc           4.7Mb
    htmlwidgets   3.6Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    extdata  10.8Mb
Decile.Plot: no visible global function definition for 'barplot'
Decile.Plot: no visible global function definition for 'axis'
Sliding.Window: no visible global function definition for 'plot'
Sliding.Window: no visible global function definition for 'lines'
Sliding.Window: no visible global function definition for 'legend'
Undefined global functions or variables:
  axis barplot legend lines plot
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines", "plot")
to your NAMESPACE file.
RCplot: no visible global function definition for 'residuals'
RCplot: no visible global function definition for 'predict'
RCplot: no visible global function definition for 'par'
RCplot: no visible global function definition for 'plot.new'
RCplot: no visible global function definition for 'plot.window'
RCplot: no visible global function definition for 'strwidth'
RCplot: no visible global function definition for 'plot'
RCplot: no visible global function definition for 'abline'
RCplot: no visible global function definition for 'text'
RCplot: no visible global function definition for 'mtext'
fitted.vlmc: no visible global function definition for 'predict'
print.vlmc: no visible global function definition for 'AIC'
residuals.vlmc: no visible global function definition for 'predict'
simulate.vlmc: no visible global function definition for 'runif'
summary.vlmc: no visible global function definition for 'predict'
vlmc: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  AIC abline mtext par plot plot.new plot.window predict qchisq
  residuals runif strwidth text
Consider adding
  importFrom("graphics", "abline", "mtext", "par", "plot", "plot.new",
             "plot.window", "strwidth", "text")
  importFrom("stats", "AIC", "predict", "qchisq", "residuals", "runif")
to your NAMESPACE file.
voss1d: no visible global function definition for 'approx'
voss1d: no visible global function definition for 'rnorm'
voss1g: no visible global function definition for 'dchisq'
voss1g: no visible global function definition for 'approx'
voss1g: no visible global function definition for 'rnorm'
voss2d: no visible global function definition for 'rnorm'
voss2g: no visible global function definition for 'dchisq'
voss2g: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  approx dchisq rnorm
Consider adding
  importFrom("stats", "approx", "dchisq", "rnorm")
to your NAMESPACE file.
'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  9.8Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   7.3Mb
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.
Running examples in 'WebGestaltR-Ex.R' failed
The error most likely occurred in:

> ### Name: listGeneSet
> ### Title: List gene sets
> ### Aliases: listGeneSet
> ### Keywords: methods
> 
> ### ** Examples
> 
> 	geneSet <- listGeneSet(organism="hsapiens",hostName="http://www.webgestalt.org/")
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Das Zeitlimit für den Vorgang wurde erreicht.'
Error in file(con, "r") : cannot open the connection
Calls: listGeneSet -> fromJSON -> paste -> readLines -> file
Execution halted
Error in re-building vignettes:
  ...
******************************************

*                                        *

*          Welcome to WebGestaltR !      *

*                                        *

******************************************


Error: processing vignette 'WebGestaltR.Rnw' failed with diagnostics:
 chunk 1 (label = Example) 
Error in fromJSON(file = file.path(hostName, "data", "idtypesummary.json")) : 
  unclosed string

Execution halted
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    client   8.9Mb
    doc      1.0Mb
Running examples in 'webuse-Ex.R' failed
The error most likely occurred in:

> ### Name: webuse
> ### Title: webuse
> ### Aliases: webuse webuselist webuse-package
> 
> ### ** Examples
> 
> webuse("auto")
`curl` package not installed, falling back to using `url()`
Warning in open.connection(con, "rb") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in open.connection(con, "rb") : cannot open the connection
Calls: webuse ... structure -> read_connection -> open -> open.connection
Execution halted
File 'webvis/R/zzz.R':
  .onLoad calls:
    print("Welcome to the webvis pacakge.")

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

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

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Weighted.Box.test: no visible global function definition for 'acf'
Weighted.Box.test: no visible binding for global variable 'na.pass'
Weighted.Box.test: no visible global function definition for 'pgamma'
Weighted.Box.test: no visible global function definition for 'pchisq'
Weighted.LM.test: no visible global function definition for 'acf'
Weighted.LM.test: no visible binding for global variable 'na.pass'
Weighted.LM.test: no visible global function definition for 'pgamma'
Undefined global functions or variables:
  acf na.pass pchisq pgamma
Consider adding
  importFrom("stats", "acf", "na.pass", "pchisq", "pgamma")
to your NAMESPACE file.
Package in Depends field not imported from: 'snpStats'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Z.value: no visible global function definition for 'sd'
Z.value: no visible global function definition for 'pnorm'
pairtest: no visible global function definition for 'is'
pairtest: no visible global function definition for 'new'
pairtest: no visible global function definition for 'rbind2'
pairtest: no visible global function definition for 'p.value'
pairtest: no visible global function definition for 'single.snp.tests'
scoretest: no visible global function definition for 'pchisq'
varplot : <anonymous>: no visible global function definition for 'var'
varplot: no visible global function definition for 'plot'
varplot: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline is new p.value pchisq plot pnorm rbind2 sd single.snp.tests
  var
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("methods", "is", "new", "rbind2")
  importFrom("stats", "pchisq", "pnorm", "sd", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' call to 'markdown' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
dlog.norm: no visible global function definition for 'rnorm'
fun.load.hals.a: no visible global function definition for 'sfExport'
fun.load.hals.a: no visible global function definition for 'sfLibrary'
fun.load.hals.fill: no visible global function definition for
  'sfExport'
fun.load.hals.fill: no visible global function definition for
  'sfLibrary'
fun.load.widals.a: no visible global function definition for 'sfExport'
fun.load.widals.a: no visible global function definition for
  'sfLibrary'
fun.load.widals.fill: no visible global function definition for
  'sfExport'
fun.load.widals.fill: no visible global function definition for
  'sfLibrary'
unif.mh: no visible global function definition for 'runif'
Undefined global functions or variables:
  rnorm runif sfExport sfLibrary
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
'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
dbayes: no visible global function definition for 'mahalanobis'
dbayes: no visible global function definition for 'var'
wmd: no visible global function definition for 'cor'
wmd: no visible global function definition for 'var'
Undefined global functions or variables:
  cor mahalanobis var
Consider adding
  importFrom("stats", "cor", "mahalanobis", "var")
to your NAMESPACE file.
fit,Leader: no visible global function definition for 'lm'
plotfit,Leader: no visible global function definition for 'par'
plotfit,Leader: no visible global function definition for 'plot'
Undefined global functions or variables:
  lm par plot
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "lm")
to your NAMESPACE file.
'library' or 'require' call to 'tm' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'plyr' 'reshape2'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
wordmatch: no visible global function definition for 'llply'
wordmatch : <anonymous>: no visible global function definition for
  'llply'
wordmatch: no visible global function definition for 'melt'
wordmatch: no visible global function definition for 'count'
Undefined global functions or variables:
  count llply melt
pickList : <anonymous>: no visible global function definition for
  'na.omit'
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
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
All packages need a namespace as from R 3.0.0.
R CMD build will produce a suitable starting point, but it is better to
handcraft a NAMESPACE file.
Output(s) listed in 'build/vignette.rds' but not in package:
  'inst/doc/WRS2.pdf'
Found directory 'R' with no source files.
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.
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
.xssfcolor: no visible global function definition for 'col2rgb'
Undefined global functions or variables:
  col2rgb
Consider adding
  importFrom("grDevices", "col2rgb")
to your NAMESPACE file.
R5.value.default: no visible binding for global variable 'data.table'
R5.value.default: no visible global function definition for
  'as.data.table'
R5.value.parse: no visible binding for global variable 'data.table'
R5.value.parse: no visible global function definition for
  'is.data.table'
R5.value.parse: no visible global function definition for
  'as.data.table'
stampme: no visible global function definition for 'flush.console'
stampmsg: no visible global function definition for 'flush.console'
write.data.table: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  as.data.table data.table flush.console is.data.table write.table
Consider adding
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE file.
installed size is  6.7Mb
  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.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
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.
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.
confint.zyp: no visible global function definition for 'qnorm'
confint.zyp: no visible global function definition for 'var'
zyp.sen: no visible global function definition for 'terms'
zyp.sen: no visible global function definition for 'median'
zyp.trend.csv: no visible global function definition for 'read.csv'
zyp.trend.csv: no visible global function definition for 'write.csv'
zyp.yuepilon: no visible global function definition for 'acf'
zyp.yuepilon: no visible binding for global variable 'na.pass'
zyp.yuepilon: no visible global function definition for 'confint'
zyp.yuepilon: no visible global function definition for 'lm'
zyp.zhang: no visible global function definition for 'acf'
zyp.zhang: no visible binding for global variable 'na.pass'
zyp.zhang: no visible global function definition for 'confint'
zyp.zhang: no visible global function definition for 'lm'
Undefined global functions or variables:
  acf confint lm median na.pass qnorm read.csv terms var write.csv
Consider adding
  importFrom("stats", "acf", "confint", "lm", "median", "na.pass",
             "qnorm", "terms", "var")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
Dependence on R version ‘3.3.1’ not with patchlevel 0
Found the following significant warnings:
  ADM3.c:37:12: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  ADM3.c:37:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  ADM3.c:54:21: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ADM3.Rcheck/00install.out’ for details.
Found the following significant warnings:
  WARNING: An illegal reflective access operation has occurred
  WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/tmp/RtmpS9yhFV/RLIBS_617e74e5fa9c/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
  WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
  WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
  WARNING: All illegal access operations will be denied in a future release
  WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/tmp/RtmpS9yhFV/RLIBS_617e1658cdd0/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ANLP.Rcheck/00install.out’ for details.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
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.
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 from incompatible pointer type [-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:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Bayesthresh.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/biclust.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
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/Boom.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/BoomSpikeSlab.Rcheck/00install.out’ for details.
Running examples in ‘broom-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: biglm_tidiers
> ### Title: Tidiers for biglm and bigglm object
> ### Aliases: biglm_tidiers tidy.biglm glance.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’ [10m/13m]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("broom")
  Loading required package: broom
  Killed
Package required but not available: ‘BoomSpikeSlab’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/CircStats.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running ‘testthat.R’ [10m/12m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(clusternomics)
  > 
  > test_check("clusternomics")
  Killed
Found the following significant warnings:
  date.cpp:173:53: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ConvCalendar.Rcheck/00install.out’ for details.
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
              user system elapsed
text_win_rqa 8.577  0.023  11.299
Found the following significant warnings:
  instabCorrection.cpp:34:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/cstab.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ctsem.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running ‘testthat.R’ [166s/202s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(cytominer)
  
  Attaching package: 'cytominer'
  
  The following object is masked from 'package:stats':
  
      aggregate
  
  The following object is masked from 'package:base':
  
      transform
  
  > 
  > test_check("cytominer")
  ── 1. Failure: `replicate_correlation` measures correlationbetween replicates in
  `%>%`(...) not equal to correlations %>% as.data.frame().
  Attributes: < Component "row.names": Numeric: lengths (1, 3) differ >
  Component "variable": Lengths (1, 3) differ (string compare on first 1)
  Component "variable": 1 string mismatch
  Component "median": Numeric: lengths (1, 3) differ
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 232 SKIPPED: 0 FAILED: 1
  1. Failure: `replicate_correlation` measures correlationbetween replicates in each feature (@test-replicate_correlation.R#71) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  convert_util.cpp:299:20: warning: null destination pointer [-Wformat-overflow=]
  convert_util.cpp:307:20: warning: null destination pointer [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/DatABEL.Rcheck/00install.out’ for details.
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
  Warning: 'cBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
     user system elapsed
sdp 7.283  0.017   7.328
Error in re-building vignettes:
  ...
Warning: Removed 92 rows containing missing values (geom_path).
Warning: Removed 71 rows containing missing values (geom_path).
Warning: Removed 120 rows containing missing values (geom_path).
Warning: Removed 125 rows containing missing values (geom_path).
Warning: Removed 30 rows containing missing values (geom_path).
May 17, 2018 7:50:32 AM com.github.fommil.netlib.BLAS <clinit>
WARNING: Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS
May 17, 2018 7:50:32 AM com.github.fommil.netlib.BLAS <clinit>
WARNING: Failed to load implementation from: com.github.fommil.netlib.NativeRefBLAS
May 17, 2018 7:50:32 AM com.github.fommil.netlib.LAPACK <clinit>
WARNING: Failed to load implementation from: com.github.fommil.netlib.NativeSystemLAPACK
May 17, 2018 7:50:32 AM com.github.fommil.netlib.LAPACK <clinit>
WARNING: Failed to load implementation from: com.github.fommil.netlib.NativeRefLAPACK
Killed
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/dhglm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/diffusionMap.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  newmat5.cpp:494:69: warning: throw will always call terminate() [-Wterminate]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/EditImputeCont.Rcheck/00install.out’ for details.
Running examples in ‘elrm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.elrm
> ### Title: Plot Diagnostics for an elrm Object
> ### Aliases: plot.elrm
> ### Keywords: methods
> 
> ### ** Examples
> 
> # Drug dataset example with sex and treatment as the variables of interest
> data(drugDat);
> drug.elrm = elrm(formula=recovered/n~sex+treatment, interest=~sex+treatment, r=4, 
+ 	iter=50000, burnIn=1000, dataset=drugDat);
Generating the Markov chain ...
Progress:   0%  Progress:   5%  Progress:  10%  Progress:  15%  Progress:  20%  Progress:  25%  Progress:  30%  Progress:  35%  Progress:  40%  Progress:  45%  Progress:  50%  Progress:  55%  Progress:  60%  Progress:  65%  Progress:  70%  Progress:  75%  Progress:  80%  Progress:  85%  Progress:  90%  Progress:  95%  Progress: 100%  
Generation of the Markov Chain required 6 secs
Conducting inference ...
Inference required 2 secs
> 
> # Plot the sampled values of the sufficient statistic for each parameter of 
> # interest (sex and treatment)
> plot(drug.elrm,p=0.5,ask=TRUE);
Error in plot.default(drug.elrm, p = 0.5, ask = TRUE) : 
  argument 2 matches multiple formal arguments
Calls: plot
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/EnvStats.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running ‘testthat.R’ [1s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(eurostat)
  > 
  > test_check("eurostat")
  trying URL 'http://ec.europa.eu/eurostat/estat-navtree-portlet-prod/BulkDownloadListing?sort=1&file=data%2Ftsdtr210.tsv.gz'
  downloaded 17 KB
  
  ── 1. Error: (unknown) (@test-all.R#112)  ──────────────────────────────────────
  tsdtr210 does not exist or is not readable
  1: get_eurostat("tsdtr210", type = "label", keepFlags = T, cache = FALSE) at testthat/test-all.R:112
  2: get_eurostat_raw(id)
  3: stop(id, " does not exist or is not readable")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 14 FAILED: 1
  1. Error: (unknown) (@test-all.R#112) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  optile.c:3122:26: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3127:26: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3189:16: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3192:16: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3340:28: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3353:28: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3408:16: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3411:16: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/extracat.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.
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
  Warning: 'cBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
     user system elapsed
fcr 8.183  0.087  10.617
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/fpc.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/frailtyHL.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running examples in ‘funcy-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: funcyOutList-class
> ### Title: Class '"funcyOutList"'
> ### Aliases: funcyOutList-class funcyOutList
> ### Keywords: classes
> 
> ### ** Examples
> 
> set.seed(2808)
> ds <- sampleFuncy(obsNr=30, k=4, timeNr=7)
> data <- Data(ds)
> clusters <- Cluster(ds)
> 
> res <- funcit(data=data, clusters=clusters, seed=2808,
+               methods=1:5, k=4, parallel=TRUE)
4 :4 : *Warning in funclustWrapper(data = data, k = k, reg = reg, regTime = regTime,  :
  It is not possible to set a seed for method funclust.
 * *Loading required namespace: funHDDC
 * *Warning in funHDDCWrapper(data = data, k = k, reg = reg, regTime = regTime,  :
  Clustering with 4 classes is not possible. 3 clusters are used!
 *Warning in Funclustering::funclust(fd = fd, K = k, thd = thd, increaseDimension = increaseDimension,  :
  Convergence of the algorithm to a solution with at least one empty cluster.
            Restart or a choose a smaller value for K = 4
Warning in funHDDCWrapper(data, k, reg, regTime, funcyCtrlMbc, model = "AkBkQkDk",  :
  Clustering with 3 classes is not possible. 2 clusters are used!
Warning in funHDDCWrapper(data, k, reg, regTime, funcyCtrlMbc, model = "AkBkQkDk",  :
  Clustering with 2 classes is not possible. 1 clusters are used!

Warning in funHDDCWrapper(data, k, reg, regTime, funcyCtrlMbc, model = "AkBkQkDk",  :
  Clustering with 1 classes is not possible. 0 clusters are used!

Error in funcit(data = data, clusters = clusters, seed = 2808, methods = 1:5,  : 
  Method funHDDC : Clustering for this data not possible.
Execution halted
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
      user system elapsed
fpca 7.909  0.031   9.472
Found the following significant warnings:
  convert_util.cpp:299:20: warning: null destination pointer [-Wformat-overflow=]
  convert_util.cpp:307:20: warning: null destination pointer [-Wformat-overflow=]
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/GenABEL.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running examples in ‘genderBR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: map_gender
> ### Title: Map the use of Brazilian first names by gender and by state
> ### Aliases: map_gender
> 
> ### ** Examples
> 
> # Map the use of the name 'Joao' for
> # males in Brazil by state
> map_gender('Joao', gender = 'm')
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: Connection timed out after 10000 milliseconds
Calls: map_gender ... request_fetch -> request_fetch.write_memory -> <Anonymous>
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.

Attaching package: 'gglogo'

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

    fortify

Killed
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ggvis)
  > 
  > test_check("ggvis")
  ── 1. Error: (unknown) (@test-specs.r#5)  ──────────────────────────────────────
  no applicable method for 'group_by_' applied to an object of class "ggvis"
  1: suppressMessages(sys.source(spec, envir = new.env(), chdir = TRUE)) at testthat/test-specs.r:5
  2: withCallingHandlers(expr, message = function(c) invokeRestart("muffleMessage"))
  3: sys.source(spec, envir = new.env(), chdir = TRUE)
  4: eval(exprs[i], envir)
  5: eval(exprs[i], envir)
  6: mtcars %>% ggvis(x = ~wt, stroke = ~cyl) %>% group_by(cyl) %>% layer_freqpolys(width = 1) %>% 
         save_spec("layer/freqpoly-grouped.json")
  7: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  8: eval(quote(`_fseq`(`_lhs`)), env, env)
  9: eval(quote(`_fseq`(`_lhs`)), env, env)
  10: `_fseq`(`_lhs`)
  11: freduce(value, `_function_list`)
  12: function_list[[i]](value)
  13: group_by(., cyl)
  14: group_by.default(., cyl)
  15: group_by_(.data, .dots = compat_as_lazy_dots(...), add = add)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 447 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-specs.r#5) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  calculategphmm.cpp:217:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gphmm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rothmana.cpp:123:15: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/graphicalVAR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  _t_array_properties.cpp:10:13: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gRbase.Rcheck/00install.out’ for details.
Running examples in ‘h2o-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: aaa
> ### Title: Starting H2O For examples
> ### Aliases: aaa
> 
> ### ** Examples
> 
> if(Sys.info()['sysname'] == "Darwin" && Sys.info()['release'] == '13.4.0'){
+  quit(save="no")
+ }else{
+  h2o.init(nthreads = 2)
+ }

H2O is not running yet, starting it now...

Note:  In case of errors look at the following log files:
    /tmp/RtmpxofDnM/h2o_UnknownUser_started_from_r.out
    /tmp/RtmpxofDnM/h2o_UnknownUser_started_from_r.err

openjdk version "10.0.1" 2018-04-17
OpenJDK Runtime Environment (build 10.0.1+10-Debian-4)
OpenJDK 64-Bit Server VM (build 10.0.1+10-Debian-4, mixed mode)

Starting H2O JVM and connecting: ............................................................ 
[1] "localhost"
[1] 54321
[1] TRUE
[1] -1
[1] "Failed to connect to localhost port 54321: Connection refused"
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0curl: (7) Failed to connect to localhost port 54321: Connection refused
[1] 7
Error in h2o.init(nthreads = 2) : 
  H2O failed to start, stopping execution.
Execution halted
Running examples in ‘huxtable-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: align
> ### Title: Alignment
> ### Aliases: align align<- set_align align.huxtable align<-.huxtable
> 
> ### ** Examples
> 
> 
> ht <- huxtable(a = 1:3, b = 1:3)
> align(ht) <-  'right'
Error in UseMethod("align<-") : 
  no applicable method for 'align<-' applied to an object of class "c('huxtable', 'data.frame')"
Calls: align<-
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 52-104 (design-principles.Rmd) 
Error: processing vignette ‘design-principles.Rmd’ failed with diagnostics:
no applicable method for ‘bold’ applied to an object of class "c('huxtable', 'data.frame')"
Execution halted
Running ‘ibhm.tests.R’ [4s/5s]
Running the tests in ‘tests/ibhm.tests.R’ failed.
Complete output:
  > library(IBHM)
  Loading required package: compiler
  Loading required package: DEoptim
  Loading required package: parallel
  
  DEoptim package
  Differential Evolution algorithm in R
  Authors: D. Ardia, K. Mullen, B. Peterson and J. Ulrich
  
  Loading required package: cmaes
  Loading required package: Rcpp
  > source('utils.R')
  > 
  > 
  > (test.Tanh <- function(){
  +   x <- seq(-6,6,length.out=400)
  +   y <- tanh(x)
  +   
  +   set.seed(123)  
  +   m <- TrainIBHM(x,y, ConfigureIBHM(scal.candidates='dot.pr', activ.candidates='tanh'))  
  +   stopifnot(summary(m)$rmse<0.1) 
  +   cat('tanh - ok\n')
  + })()
  Error in summary(m)$rmse < 0.1 : $ operator is invalid for atomic vectors
  Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
  Execution halted
Found the following significant warnings:
  regTree.c:317:38: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  regTree.c:336:38: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/iJRF.Rcheck/00install.out’ for details.
Found the following significant warnings:
  transformations.cpp:274:15: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/imager.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [1s/1s]
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)  ────────────────────────────
  no applicable method for 'h5write' applied to an object of class "character"
  1: test_read_write_read(f) at testthat/test_read-write-read.R:8
  2: qwrite(x, outfile) at /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/io.Rcheck/tests/testthat/helper.R:48
  3: .qwrite(x, if (is.filename(file)) as.character(file) else file, if (is.null(type)) .infer_file_type(file) else type, 
         ...)
  4: qwrite.hdf5(x, if (is.filename(file)) as.character(file) else file, if (is.null(type)) .infer_file_type(file) else type, 
         ...)
  5: .write_hdf5_array(x, file)
  6: rhdf5::h5write("array", file, "type")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_read-write-read.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  LBLasso.c:98:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  LBlogistic.c:100:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  LBmultilogistic.c:110:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  ggm.c:69:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  ising.c:83:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  potts.c:99:15: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Libra.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [11s/76s]
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/Rtmp3Qe1qX/h2o_UnknownUser_started_from_r.out
      /tmp/Rtmp3Qe1qX/h2o_UnknownUser_started_from_r.err
  
  openjdk version "10.0.1" 2018-04-17
  OpenJDK Runtime Environment (build 10.0.1+10-Debian-4)
  OpenJDK 64-Bit Server VM (build 10.0.1+10-Debian-4, mixed mode)
  
  Starting H2O JVM and connecting: ............................................................ 
  [1] "localhost"
  [1] 54321
  [1] TRUE
  [1] -1
  [1] "Failed to connect to localhost port 54321: Connection refused"
    % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                   Dload  Upload   Total   Spent    Left  Speed
  
    0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0curl: (7) Failed to connect to localhost port 54321: Connection refused
  [1] 7
  ── 1. Error: (unknown) (@test-h2o.R#4)  ────────────────────────────────────────
  H2O failed to start, stopping execution.
  1: h2o.init() at testthat/test-h2o.R:4
  2: stop("H2O failed to start, stopping execution.")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 22 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-h2o.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  mue_nelmC.cpp:147:15: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  mue_nelmC.cpp:185:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  mue_nelmC.cpp:230:22: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  mue_nrmC.cpp:135:15: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  mue_nrmC.cpp:173:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  mue_nrmC.cpp:218:22: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mcIRT.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mdhglm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Error in re-building vignettes:
  ...
Warning in restoreRecordedPlot(x, reloadPkgs) :
  snapshot recorded in different R version (pre 3.3.0)
Warning in replayPlot(dlStub) :
  snapshot recorded with different graphics engine version (pre 11 - this is version 12)
Quitting from lines 184-185 (meme.Rmd) 
Error: processing vignette ‘meme.Rmd’ failed with diagnostics:
Incompatible graphics state
Execution halted
Found the following significant warnings:
  NMix_RJMCMCcombine.cpp:422:14: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mixAK.Rcheck/00install.out’ for details.
Found the following significant warnings:
  mixCpp.cpp:122:19: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  mixCpp.cpp:167:19: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  mixCpp.cpp:399:22: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  mixCpp.cpp:444:22: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mixR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  confusionMatrix_.cpp:10:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:12:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:14:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:16:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:57:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:104:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:106:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:108:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:110:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ModelMetrics.Rcheck/00install.out’ for details.
Found the following significant warnings:
  weiszfeldIterations.cpp:195:48: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Mposterior.Rcheck/00install.out’ for details.
Found the following significant warnings:
  newmat5.cpp:525:69: warning: throw will always call terminate() [-Wterminate]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MSBVAR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  evallf.c:86:23: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/mvnmle.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(nima)
  nima: Nima Hejazi's R Toolbox
  Version: 0.4.5
  > 
  > test_check("nima")
  ── 1. Failure: attrnames finds the names of the attributes of a data frame (@tes
  attrnames(y) not equal to c("names", "row.names", "class").
  2/3 mismatches
  x[2]: "class"
  y[2]: "row.names"
  
  x[3]: "row.names"
  y[3]: "class"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 21 SKIPPED: 0 FAILED: 1
  1. Failure: attrnames finds the names of the attributes of a data frame (@test-attribute_names.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [17s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > test_check("openxlsx")
  Loading required package: openxlsx
  ── 1. Error: loadWorkbook from different sources (@test-read_sources.R#49)  ────
  subscript out of bounds
  1: expect_true(all.equal.Workbook(wb_url, wb_file), "Loading from URL vs local not equal") at testthat/test-read_sources.R:49
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: all.equal.Workbook(wb_url, wb_file)
  5: sapply(1:nSheets, function(i) isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]])))
  6: lapply(X = X, FUN = FUN, ...)
  7: FUN(X[[i]], ...)
  8: isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]]))
  9: all.equal(x$colWidths[[i]], y$colWidths[[i]])
  10: all.equal.list(x$colWidths[[i]], y$colWidths[[i]])
  11: attr.all.equal(target, current, ...)
  12: mode(current)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 505 SKIPPED: 2 FAILED: 1
  1. Error: loadWorkbook from different sources (@test-read_sources.R#49) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘exporting-methods.R’ [3s/3s]
  Running ‘mahal-dist.R’ [3s/4s]
  Running ‘testthat.R’ [22s/27s]
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
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
        user system elapsed
optrdd 4.949  0.177   6.491
Error in re-building vignettes:
  ...
Killed
Found the following significant warnings:

  Warning: 'cBind' is deprecated.
  Warning: 'rBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
              user system elapsed
AIC.phmm     5.820  0.070   8.118
phmm-package 4.890  0.004   6.113
phmm         4.859  0.004   5.340
Found the following significant warnings:
  cat_pair.c:64:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  cat_pair.c:79:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/PLordprob.Rcheck/00install.out’ for details.
Running ‘MDS.R’ [5s/9s]
Running the tests in ‘tests/MDS.R’ failed.
Complete output:
  > library(qrfactor)
  Loading required package: mvoutlier
  Loading required package: sgeostat
  sROC 0.1-2 loaded
  Loading required package: mgraph
  Loading required package: rgdal
  Loading required package: sp
  rgdal: version: 1.2-20, (SVN revision 725)
   Geospatial Data Abstraction Library extensions to R successfully loaded
   Loaded GDAL runtime: GDAL 2.2.4, released 2018/03/19
   Path to GDAL shared files: /usr/share/gdal/2.2
   GDAL binary built with GEOS: TRUE 
   Loaded PROJ.4 runtime: Rel. 5.0.1, April 1st, 2018, [PJ_VERSION: 501]
   Path to PROJ.4 shared files: (autodetected)
   Linking to sp version: 1.2-7 
  Loading required package: pvclust
  Loading required package: cluster
  Loading required package: maptools
  Checking rgeos availability: FALSE
   	Note: when rgeos is not available, polygon geometry 	computations in maptools depend on gpclib,
   	which has a restricted licence. It is disabled by default;
   	to enable gpclib, type gpclibPermit()
  > #data must be numeric, avoid using categorical and characters
  > data(UScereal, package="MASS")
  > variables=c("calories","protein","sodium","carbo","sugars","potassium")
  > data=UScereal[variables]
  > #Multi dimensional scaling can be simulated as: 
  > plot(qrfactor(data,scale='n'),plot="r",type="mds",factors=c(1,2))
  Error in UseMethod("qrfactor") : 
    no applicable method for 'qrfactor' applied to an object of class "data.frame"
  Calls: plot -> qrfactor
  Execution halted
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: Thu May 17 06:13:26 AM 2018 

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
Found the following significant warnings:
  Warning: replacing previous import ‘Rcmdr::Confint’ by ‘car::Confint’ when loading ‘RcmdrPlugin.BCA’
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RcmdrPlugin.BCA.Rcheck/00install.out’ for details.
Found the following significant warnings:
  cwb/cl/special-chars.c:1771:22: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rcqp.Rcheck/00install.out’ for details.
Running examples in ‘ref-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: refdata
> ### Title: subsettable reference to matrix or data.frame
> ### Aliases: refdata derefdata derefdata<- [.refdata [<-.refdata [[.refdata
> ###   [[<-.refdata $.refdata $<-.refdata dim.refdata dimnames.refdata
> ###   row.names.refdata names.refdata print.refdata
> ### Keywords: programming manip
> 
> ### ** Examples
> 
> 
>   ## Simple usage Example
>   x <- cbind(1:5, 5:1)       # take a matrix or data frame
>   rx <- refdata(x)           # wrap it into an refdata object
>   rx                         # see the autoprinting
list()
attr(,"dat")
<environment: 0x5628b51b5b40>
attr(,"ind")
<environment: 0x5628b51b5f30>
attr(,"class")
[1] "refdata" "matrix" 
>   rm(x)                      # delete original to save memory
>   rx[]                       # extract all data
list()
attr(,"dat")
<environment: 0x5628b51b5b40>
attr(,"ind")
<environment: 0x5628b51b5f30>
>   rx[-1, ]                   # extract part of data
Error in rx[-1, ] : incorrect number of dimensions
Execution halted
Found the following significant warnings:

  Warning: 'cBind' is deprecated.
  Warning: 'rBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                  user system elapsed
simulate_PhenData 4.45  0.039   5.662
Found the following significant warnings:
  simul.cpp:82:21: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/revealedPrefs.Rcheck/00install.out’ for details.
Found the following significant warnings:
  atkClasses.c:1050:25: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  atkClasses.c:1058:34: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  atkClasses.c:1397:51: warning: passing argument 2 of ‘object_class->active_descendant_changed’ from incompatible pointer type [-Wincompatible-pointer-types]
  gdkFuncs.c:6000:36: warning: passing argument 2 of ‘gdk_window_get_user_data’ from incompatible pointer type [-Wincompatible-pointer-types]
  gioClasses.c:1948:17: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gioClasses.c:1964:20: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gtkClasses.c:8665:28: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gtkClasses.c:11110:21: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RGtk2.Rcheck/00install.out’ for details.
Running examples in ‘RISmed-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: EUtilsGet
> ### Title: Results of an NCBI EUtils query
> ### Aliases: EUtilsGet
> 
> ### ** Examples
> 
> 
> # PUBMED QUERY FOR MYELOMA ARTICLES FOR LAST YEAR
> res <- EUtilsSummary("myeloma[ti]",retmax=2,reldate=365)
> 
> summary(res)
Query:
myeloma[ti] AND 2017/05/17[EDAT] : 2018/05/17[EDAT] 

Result count:  1515> 
> fetch <- EUtilsGet(res)
> 
> # PUBMED RETURNS A MEDLINE OBJECT
> fetch
PubMed query:  myeloma[ti] AND 2017/05/17[EDAT] : 2018/05/17[EDAT] 

Records:  0 
> 
> PMID(fetch)
character(0)
> 
> Author(fetch)[[1]]
Error in Author(fetch)[[1]] : subscript out of bounds
Execution halted
Found the following significant warnings:
  Warning: The javah tool is planned to be removed in the next major
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rJava.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’
File ‘rJava/libs/rJava.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  libjson/Source/JSONSharedString.h:297:17: warning: ‘json_shared_string::len’ will be initialized after [-Wreorder]
  libjson/Source/JSONSharedString.h:295:40: warning:   ‘json_shared_string::json_shared_string_internal* json_shared_string::_str’ [-Wreorder]
  libjson/Source/JSONSharedString.h:180:9: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONSharedString.h:182:9: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONStream.h:79:7: warning: ‘JSONStream::state’ will be initialized after [-Wreorder]
  libjson/Source/JSONStream.h:76:28: warning:   ‘void (* JSONStream::call)(void*, void*)’ [-Wreorder]
  JSONStream.cpp:8:1: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONStream.h:77:27: warning: ‘JSONStream::err_call’ will be initialized after [-Wreorder]
  libjson/Source/JSONStream.h:75:17: warning:   ‘json_string JSONStream::buffer’ [-Wreorder]
  JSONStream.cpp:12:1: warning:   when initialized here [-Wreorder]
  libjson/Source/internalJSONNode.h:257:18: warning: ‘internalJSONNode::_name_encoded’ will be initialized after [-Wreorder]
  libjson/Source/internalJSONNode.h:256:17: warning:   ‘json_string internalJSONNode::_name’ [-Wreorder]
  internalJSONNode.cpp:78:1: warning:   when initialized here [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RJSONIO.Rcheck/00install.out’ for details.
Killed
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
Found the following significant warnings:
  PresenceAndAbsence.cpp:536:14: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  PresenceAndAbsence.cpp:537:14: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rlda.Rcheck/00install.out’ for details.
Found the following significant warnings:
  newmat5.cpp:525:69: warning: throw will always call terminate() [-Wterminate]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rmixmod.Rcheck/00install.out’ for details.
Found the following significant warnings:
  npmpois.c:246:38: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  rmg.c:335:38: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rmp.Rcheck/00install.out’ for details.
Running ‘test-all.R’ [3s/42s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > ###
  > library(testthat)
  > test_check('rphylotastic')
  Loading required package: rphylotastic
  ── 1. Error: Loading a tree from NCBI taxonomy (@test_tree.R#17)  ──────────────
  HTTP error 500.
  1: taxa_get_taxonomic_tree(taxa) at testthat/test_tree.R:17
  2: jsonlite::fromJSON(paste(get_base_url(), "gt/pt/get_tree?taxa=", taxa.string, sep = ""))
  3: fromJSON_string(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame, 
         simplifyMatrix = simplifyMatrix, flatten = flatten, ...)
  4: parseJSON(txt, bigint_as_char)
  5: parse_con(txt, bigint_as_char)
  6: open(con, "rb")
  7: open.connection(con, "rb")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 36 SKIPPED: 0 FAILED: 1
  1. Error: Loading a tree from NCBI taxonomy (@test_tree.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [4s/13s]
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-src_translate_env.R#52)  ----------------------
  translate_sql(as(x, 0), con = conn[["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-src_translate_env.R#56)  ----------------------
  translate_sql(pmax(x), con = conn[["con"]]) not equal to dplyr::sql("GREATEST(\"x\")").
  1/1 mismatches
  x[1]: "MAX(\"x\")"
  y[1]: "GREATEST(\"x\")"
  
  -- 3. Failure: as() works (@test-src_translate_env.R#60)  ----------------------
  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-src_translate_env.R#69)  ----------------------
  translate_sql_(list(substituted.expression), con = conn[["con"]]) not equal to dplyr::sql("CAST(\"x\" AS \"DATE\")").
  1/1 mismatches
  x[1]: "AS(\"x\", '2018-05-17')"
  y[1]: "CAST(\"x\" AS \"DATE\")"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 223 SKIPPED: 28 FAILED: 4
  1. Failure: as() works (@test-src_translate_env.R#52) 
  2. Failure: as() works (@test-src_translate_env.R#56) 
  3. Failure: as() works (@test-src_translate_env.R#60) 
  4. Failure: as() works (@test-src_translate_env.R#69) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  regTree.c:242:19: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RRF.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RSEIS.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
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’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘tests.R’ [0s/1s]
Running the tests in ‘tests/tests.R’ failed.
Complete output:
  > require(rtf)
  Loading required package: rtf
  > require(lattice)
  Loading required package: lattice
  > 
  > output<-"test_rtf-package.doc"
  > png.res<-300
  > 
  > rtf<-RTF(output,width=8.5,height=11,font.size=10,omi=c(1,1,1,1))
  > addHeader(rtf,title="Test",subtitle="2011-08-15\n")
  Error in UseMethod("addHeader") : 
    no applicable method for 'addHeader' applied to an object of class "c('RTF', 'Object')"
  Calls: addHeader
  Execution halted
Found the following significant warnings:
  bitmap.c:1594:29: warning: suggest parentheses around comparison in operand of ‘^’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rttf2pt1.Rcheck/00install.out’ for details.
Running examples in ‘sbgcop-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sbgcop.mcmc
> ### Title: Semiparametric Bayesian Gaussian copula estimation and
> ###   imputation
> ### Aliases: sbgcop.mcmc plot.psgc summary.psgc print.sum.psgc
> ### Keywords: multivariate models
> 
> ### ** Examples
> 
> fit<-sbgcop.mcmc(swiss)
10 percent done  Thu May 17 10:11:25 2018 
20 percent done  Thu May 17 10:11:26 2018 
30 percent done  Thu May 17 10:11:26 2018 
40 percent done  Thu May 17 10:11:26 2018 
50 percent done  Thu May 17 10:11:26 2018 
60 percent done  Thu May 17 10:11:27 2018 
70 percent done  Thu May 17 10:11:27 2018 
80 percent done  Thu May 17 10:11:27 2018 
90 percent done  Thu May 17 10:11:28 2018 
100 percent done  Thu May 17 10:11:28 2018 
> summary(fit)
         Length Class  Mode   
C.psamp  3600   -none- numeric
Y.pmean   282   -none- numeric
Y.impute    0   -none- NULL   
LPC       100   -none- numeric
> plot(fit)
Error in xy.coords(x, y, xlabel, ylabel, log) : 
  'x' is a list, but does not have components 'x' and 'y'
Calls: plot -> plot.default -> xy.coords
Execution halted
Running examples in ‘semPlot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: semSyntax
> ### Title: Produce model syntax for various SEM software
> ### Aliases: semSyntax
> 
> ### ** Examples
> 
> # MIMIC model, example 5.8 from mplus user guide:
> Data <- read.table("http://www.statmodel.com/usersguide/chap5/ex5.8.dat")
Warning in file(file, "rt") :
  URL 'http://www.statmodel.com/usersguide/chap5/ex5.8.dat': status was 'Couldn't connect to server'
Error in file(file, "rt") : 
  cannot open the connection to 'http://www.statmodel.com/usersguide/chap5/ex5.8.dat'
Calls: read.table -> file
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 86-91 (snplist.Rnw) 
Error: processing vignette ‘snplist.Rnw’ failed with diagnostics:
Unexpected format to the list of available marts.
Please check the following URL manually, and try ?listMarts for advice.
http://grch37.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
Execution halted
Error in re-building vignettes:
  ...
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

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

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

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

    IQR, mad, sd, var, xtabs

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

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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

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

    expand.grid

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

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

    strsplit

Loading required package: Rsamtools

Error: processing vignette ‘SNPtools.Rnw’ failed with diagnostics:
 chunk 3 
Error in open.TabixFile(con) : 
  [khttp_connect_file] fail to open file (HTTP code: 404).

Execution halted
Running ‘test-all.R’ [181s/237s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("SpaDES.core")
  Loading required package: SpaDES.core
  Loading required package: quickPlot
  Loading required package: reproducible
  
  Attaching package: 'reproducible'
  
  The following object is masked from 'package:testthat':
  
      %>%
  
    Using cached copy of .inputObjects event in test module
    Using cached copy of .inputObjects event in test module
  ── 1. Failure: simList object initializes correctly (@test-simList.R#17)  ──────────────────────────
  length(out) not equal to 75.
  1/1 mismatches
  [1] 73 - 75 == -2
  
    Using cached copy of burn event in fireSpread module
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 349 SKIPPED: 33 FAILED: 1
  1. Failure: simList object initializes correctly (@test-simList.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  sparseSVM.c:367:30: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/sparseSVM.Rcheck/00install.out’ for details.
Found the following significant warnings:
  timeFuns.c:1084:34: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/splusTimeDate.Rcheck/00install.out’ for details.
Found the following significant warnings:
  wdl.cpp:184:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/spp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ChangePointAnalyzeNorm.cpp:49:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  ChangePointAnalyzePoiss.cpp:42:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/StepSignalMargiLike.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/streamR.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running ‘testGBHProcedures.R’ [3s/5s]
  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
Found the following significant warnings:
  gzipdec_ms.cpp:59:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  gzipdec_ms.cpp:61:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  gzipdec_ms.cpp:63:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TAQMNGR.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: data.table
No methods found in package ‘RSQLite’ for request: ‘dbGetQuery’ when loading ‘tcpl’
tcpl (v1.2.2) loaded with the following settings:
  TCPL_DB:    /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/tcpl/sql/tcpldb.sqlite
  TCPL_USER:  NA
  TCPL_HOST:  NA
  TCPL_DRVR:  SQLite
Default settings stored in TCPL.conf. See ?tcplConf for more information.

Error: processing vignette ‘tcpl_Overview.Rnw’ failed with diagnostics:
 chunk 4 
Error in result_create(conn@ptr, statement) : 
  attempt to write a readonly database
Execution halted
Running examples in ‘tightClust-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tight.clust
> ### Title: Tight Clustering
> ### Aliases: tight.clust
> ### Keywords: cluster
> 
> ### ** Examples
> 
> ## load the test dataset
> data(tclust.test.data)
> ## find 10 tight clusters
> ptm<-proc.time()
> ## k.min=25, tighter clusters will be found
> ## target=1 is used to save time, target=10 is recommended
> tclust1<-tight.clust(tclust.test.data$Data, target=1, k.min=25, random.seed=12345)
Number of points: 1100 	Dimension: 75 

Looking for tight cluster 1 ...
k = 25
k = 26
1 tight cluster(s) found!
Cluster size: 43 	Remaining number of points: 1057 

> proc.time()-ptm
   user  system elapsed 
  3.390   0.141   4.400 
> ## plot the heat map of cluster result
> plot(tclust1)
Error in xy.coords(x, y, xlabel, ylabel, log) : 
  'x' is a list, but does not have components 'x' and 'y'
Calls: plot -> plot.default -> xy.coords
Execution halted
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
          user system elapsed
ViSiElse 6.097  0.034   9.304
Package required but not available: ‘phyloseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
Installation failed.
See ‘/home/ripley/R/packages/tests32/ADMMsigma.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 66-67 (ahn.Rmd) 
Error: processing vignette 'ahn.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 15-19 (ALA4R.Rmd) 
Error: processing vignette 'ALA4R.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    help   5.1Mb
Package suggested but not available for checking: ‘rhdf5’
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 39-73 (antaresH5.Rmd) 
Error: processing vignette 'antaresH5.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 48-50 (aop.Rmd) 
Error: processing vignette 'aop.Rmd' failed with diagnostics:
assignment of an object of class "NULL" is not valid for @'nodes' in an object of class "graphNEL"; is(value, "vector") is not TRUE
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 293-307 (apcluster.Rnw) 
Error: processing vignette 'apcluster.Rnw' failed with diagnostics:
object 'apres1b' not found
Execution halted
Running examples in ‘AR1seg-Ex.R’ failed
The error most likely occurred in:

> ### Name: AR1seg-package
> ### Title: Segmentation of an AR(1) Gaussian process
> ### Aliases: AR1seg-package AR1seg
> 
> ### ** Examples
> 
> library(AR1seg)
> data(y)
> res=AR1seg_func(y,Kmax=15,rho=TRUE)
Error in cumsum(datasize)[breaks[k, 1:k]] : 
  only 0's may be mixed with negative subscripts
Calls: AR1seg_func -> Segmentor -> Segmentor.default
Execution halted
Package suggested but not available for checking: ‘qCBA’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    help   1.1Mb
installed size is 73.8Mb
  sub-directories of 1Mb or more:
    java  73.8Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   9.0Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   6.1Mb
Package suggested but not available for checking: ‘mzR’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 51-52 (use-ballr.Rmd) 
Error: processing vignette 'use-ballr.Rmd' failed with diagnostics:
Timeout was reached: Operation timed out after 10058 milliseconds with 0 out of 0 bytes received
Execution halted
Package suggested but not available for checking: ‘keras’
Package unavailable to check Rd xrefs: ‘keras’
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    2.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: survival
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
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'
Installation failed.
See ‘/home/ripley/R/packages/tests32/BayesFactor.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/ripley/R/packages/tests32/BayesFM.Rcheck/00install.out’ for details.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.3Mb
    libs   1.8Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   3.8Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/ripley/R/packages/tests32/Bayesthresh.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
File ‘BayHap/libs/BayHap.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘mcmc.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘mcmc.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [14s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bcgam)
  Loading required package: nimble
  nimble version 0.6-10 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$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.7Mb
Package suggested but not available for checking: ‘BRugs’
Package suggested but not available for checking: ‘lumi’
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is 136.9Mb
  sub-directories of 1Mb or more:
    include  136.9Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/ripley/R/packages/tests32/biclust.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Error in re-building vignettes:
  ...
Warning in engine$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).
Quitting from lines 240-243 (analysis.Rmd) 
Error: processing vignette 'analysis.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Package unavailable to check Rd xrefs: ‘bigrquery’
Package suggested but not available for checking: ‘sodium’
Installation failed.
See ‘/home/ripley/R/packages/tests32/bigrquery.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/ripley/R/packages/tests32/bikedata.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc           2.3Mb
    htmlwidgets   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 37-44 (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: ‘mzR’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/ripley/R/packages/tests32/bioacoustics.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 64-67 (BioCircos.Rmd) 
Error: processing vignette 'BioCircos.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Parsed with column specification:
cols(
  .default = col_character(),
  X1271 = col_double(),
  X1272 = col_double(),
  X1273 = col_double(),
  X1274 = col_double(),
  X1275 = col_double(),
  X1276 = col_double(),
  X1277 = col_double(),
  X1278 = col_double(),
  X1279 = col_double(),
  X1280 = col_double(),
  X1281 = col_double(),
  X1282 = col_double(),
  X1283 = col_double(),
  X1284 = col_double(),
  X1285 = col_double(),
  X1286 = col_double(),
  X1287 = col_double(),
  X1288 = col_double(),
  X1289 = col_double(),
  X1290 = col_double()
  # ... with 337 more columns
)
See spec(...) for full column specifications.
Parsed with column specification:
cols(
  .default = col_double(),
  FREQ = col_character(),
  Frequency = col_character(),
  REF_AREA = col_character(),
  `Reference area` = col_character(),
  UNIT_MEASURE = col_integer(),
  `Unit of measure` = col_character(),
  `Time Period` = col_character()
)
See spec(...) for full column specifications.

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: 'zoo'

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

    as.Date, as.Date.numeric

Quitting from lines 61-79 (BIS.Rmd) 
Error: processing vignette 'BIS.Rmd' failed with diagnostics:
Evaluation error: yearmon variable can only have one format.
Execution halted
Package suggested but not available for checking: ‘IHW’
Invalid maximum heap size: -Xmx4G
The specified size exceeds the maximum representable size.
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘gtools’ ‘knitr’ ‘nnet’ ‘parallel’ ‘rJava’ ‘reshape’
  ‘rmarkdown’ ‘shinyjs’
  All declared Imports should be used.
Missing or unexported object: ‘xgboost::predict’
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 4.2.6 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 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 5e3de0, cause 'memory not mapped'

Traceback:
 1: optParC(M = M, clu = temppar, 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 ...
Package suggested but not available for checking: ‘processx’
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
File ‘brainwaver/libs/brainwaver.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘connexity_small_world.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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  7.2Mb
  sub-directories of 1Mb or more:
    R     3.8Mb
    doc   2.7Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    bin    3.1Mb
    doc    1.3Mb
    libs   3.1Mb
Package which this enhances but not available for checking: ‘FastRWeb’
File ‘Cairo/libs/Cairo.so’:
  Found non-API calls to R: ‘R_InputHandlers’, ‘addInputHandler’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R        1.3Mb
    data     1.8Mb
    models   2.5Mb
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
> 
> 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
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 55-69 (CDECRetrieve.Rmd) 
Error: processing vignette 'CDECRetrieve.Rmd' failed with diagnostics:
Timeout was reached: Connection timed out after 10000 milliseconds
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
Found the following significant warnings:
  "cec_r.c", line 192: warning: improper pointer/integer combination: op "="
  "cec_r.c", line 267: warning: improper pointer/integer combination: op ":"
See ‘/home/ripley/R/packages/tests32/CEC.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   2.8Mb
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  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/ChoR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/ripley/R/packages/tests32/CircStats.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Package suggested but not available for checking: ‘rggobi’
Running ‘testthat.R’ [28s/31s]
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: 54 SKIPPED: 0 FAILED: 1
  1. Failure: computeDistMat works rucrdtw metrics (@test_computeDistMat.R#100) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/ClinicalTrialSummary.Rcheck/00install.out’ for details.
Packages required but not available: ‘xcms’ ‘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 473-485 (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
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$Counts)
Error in solve.default(H) : 
  system is computationally singular: reciprocal condition number = 0
Calls: cmpproc -> single.cmp -> diag -> solve -> solve.default
Execution halted
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data     3.8Mb
    exdata   5.5Mb
Error in re-building vignettes:
  ...
Warning in engine$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 30-36 (coala-data-import.Rmd) 
Error: processing vignette 'coala-data-import.Rmd' failed with diagnostics:
there is no package called 'PopGenome'
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  5.2Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   2.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    java   5.2Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data      6.5Mb
    extdata   2.8Mb
Package required but not available: ‘bigrquery’

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

> ### Name: coocnet
> ### Title: coocnet
> ### Aliases: coocnet
> 
> ### ** Examples
> 
> cooccurNetwork  = coocnet(dataFile=getexample(dataType="protein"), dataType="protein")
reading file......
completed. (10,329)
preprocess file......Error in if (pred >= memsize * alpha || ncol > 150 || (nrow > 30000 &  : 
  missing value where TRUE/FALSE needed
Calls: coocnet ... cooccur.dataprepreprocess.preprocess -> inmemoryflag
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 176-178 (Extending-cooccurNet.Rmd) 
Error: processing vignette 'Extending-cooccurNet.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
Execution halted
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    R     2.3Mb
    doc   7.4Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 76-77 (cranly.Rmd) 
Error: processing vignette 'cranly.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/csp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/ripley/R/packages/tests32/ctsem.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Error in re-building vignettes:
  ...
Observations with missing time information found - removing 1 rows
Discrete time points created:  4
Extracting first non-missing value for time independent predictors
imputedefs==FALSE (default, recommended) so setting observations with no time value to NA
Running ctsemCarefulFit with 16 parameters

 *** caught segfault ***
address 908, cause 'memory not mapped'
Installation failed.
See ‘/home/ripley/R/packages/tests32/CuCubes.Rcheck/00install.out’ for details.
installed size is 32.2Mb
  sub-directories of 1Mb or more:
    extdata  32.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 177-179 (cycling_data_analysis.Rmd) 
Error: processing vignette 'cycling_data_analysis.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
Error in re-building vignettes:
  ...
Warning in engine$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
  sub-directories of 1Mb or more:
    img   4.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 57-68 (dataexplorer-intro.Rmd) 
Error: processing vignette 'dataexplorer-intro.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
sh: whoami:  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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 26-34 (get_started.Rmd) 
Error: processing vignette 'get_started.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 512-515 (data.tree.Rmd) 
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 152-166 (daymetr-vignette.Rmd) 
Error: processing vignette 'daymetr-vignette.Rmd' failed with diagnostics:
Requested coverage exceeds 6GB file size limit!
Execution halted
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
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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Joining, by = "key"
Joining, by = "key"
Quitting from lines 102-122 (sjukhus.Rmd) 
Error: processing vignette 'sjukhus.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

---------------------
Welcome to dendextend version 1.8.0
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 suggested but not available for checking:
  ‘gurobi’ ‘Rcplex’ ‘Rsymphony’
Installation failed.
See ‘/home/ripley/R/packages/tests32/dexter.Rcheck/00install.out’ for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   6.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    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
Quitting from lines 230-234 (DGVM3D.Rmd) 
Error: processing vignette 'DGVM3D.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/ripley/R/packages/tests32/dhglm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Package suggested but not available for checking: ‘rsvg’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.3Mb
Running ‘testthat.R’ [256s/333s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(diceR)
  > 
  > test_check("diceR")
  Selecting k and imputing non-clustered cases
  Computing consensus functions
  Evaluating output with consensus function results
  Diverse Cluster Ensemble Completed
  Selecting k and imputing non-clustered cases
  Computing consensus functions
  Evaluating output with consensus function results
  Diverse Cluster Ensemble Completed
  Selecting k and imputing non-clustered cases
  Computing consensus functions
  Evaluating output with consensus function results
  Diverse Cluster Ensemble Completed
  Selecting k and imputing non-clustered cases
  Computing consensus functions
  Diverse Cluster Ensemble Completed
  Selecting k and imputing non-clustered cases
  Computing consensus functions
  Diverse Cluster Ensemble Completed
  Selecting k and imputing non-clustered cases
  Computing consensus functions
  Diverse Cluster Ensemble Completed
  Selecting k and imputing non-clustered cases
  Computing consensus functions
  Diverse Cluster Ensemble Completed
  Error: C stack usage  236753812 is too close to the limit
  
  error: Mat::col(): index out of bounds
  
  error: Mat::col(): index out of bounds
  terminate called recursively
  terminate called after throwing an instance of 'std::logic_error'
    what():  Mat::col(): index out of bounds
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc   9.5Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/ripley/R/packages/tests32/diffusionMap.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    include  15.1Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/DMMF.Rcheck/00install.out’ for details.
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.
Using constraints: b = 1
Using constraints: b = 1
Using constraints: b = 1
Using constraints: b = 1
Using constraints: b = 1, h2 = 3.494
Running default monotherapy fitting. Note that if constraints are needed, run mono fitting manually first
Using constraints: b = 1
Using constraints: b = 1
Quitting from lines 357-358 (userGuide.Rmd) 
Error: processing vignette 'userGuide.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    shinyapps   5.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    lucc_MT   3.4Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    doc    1.6Mb
    libs   1.5Mb
File ‘EBS/libs/EBS.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘GeneralFunctions.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  5.6Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    hac    4.3Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
    doc    1.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data      1.8Mb
    doc       1.2Mb
    extdata   1.5Mb
Error in re-building vignettes:
  ...
Loading required package: foreign
This is vegdata 0.9.1

No Turbowin installation path found. 

############################################################
Turboveg root directory is set to "/tmp/RtmpcmaqAG"
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
Package required but not available: ‘iCheck’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘elrm/libs/elrm.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Objects: ‘binomMCMC.o’, ‘functions.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘binomMCMC.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 examples in ‘emIRT-Ex.R’ failed
The error most likely occurred in:

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

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

Iteration: 50

error: inv_sympd(): matrix is singular or not positive definite
terminate called after throwing an instance of 'std::runtime_error'
  what():  inv_sympd(): matrix is singular or not positive definite
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    xsd   5.9Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/EMMIXgene.Rcheck/00install.out’ for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.6Mb
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
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/ripley/R/packages/tests32/EnvStats.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    doc    3.4Mb
    help   3.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   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.
Quitting from lines 150-151 (epicontacts.Rmd) 
Error: processing vignette 'epicontacts.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Packages required but not available: ‘SNPRelate’ ‘gdsfmt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tmap’
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.
Loading required package: xml2
trying URL 'http://ec.europa.eu/eurostat/estat-navtree-portlet-prod/BulkDownloadListing?sort=1&file=data%2Ft2020_rk310.tsv.gz'
Content type 'application/octet-stream;charset=UTF-8' length 4328 bytes
==================================================
downloaded 4328 bytes

Table t2020_rk310 cached at /tmp/RtmpCwaiy3/eurostat/t2020_rk310_num_code_TF.rds

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

trying URL 'http://ec.europa.eu/eurostat/estat-navtree-portlet-prod/BulkDownloadListing?sort=1&file=data%2Ften00081.tsv.gz'
Content type 'application/octet-stream;charset=UTF-8' length 13491 bytes (13 KB)
==================================================
downloaded 13 KB

Table ten00081 cached at /tmp/RtmpCwaiy3/eurostat/ten00081_date_code_TF.rds
Quitting from lines 291-309 (eurostat_tutorial.Rmd) 
Error: processing vignette 'eurostat_tutorial.Rmd' failed with diagnostics:
there is no package called 'tmap'
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   6.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.1Mb
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    exiftool  13.7Mb
Running ‘testthat.R’ [46s/58s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(exifr)
  Using ExifTool version 10.61
  > 
  > test_check("exifr")
  ── 1. Failure: quiet argument supresses messages (@test_read_exif.R#24)  ───────
  `read_exif(test_files)` produced warnings.
  
  ── 2. Failure: recursive option works (@test_read_exif.R#32)  ──────────────────
  `read_exif(images_folder, recursive = TRUE)` produced warnings.
  
  ── 3. Failure: recursive option works (@test_read_exif.R#34)  ──────────────────
  `read_exif(system.file("", package = "exifr"), recursive = TRUE)` produced warnings.
  
    % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                   Dload  Upload   Total   Spent    Left  Speed
  
    0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
    0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
    0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0
    0     0    0     0    0     0      0      0 --:--:--  0:00:03 --:--:--     0
    0     0    0     0    0     0      0      0 --:--:--  0:00:04 --:--:--     0
    0     0    0     0    0     0      0      0 --:--:--  0:00:05 --:--:--     0
    0 2838k    0 13363    0     0   2672      0  0:18:07  0:00:05  0:18:02  2859
  100 2838k  100 2838k    0     0   567k      0  0:00:05  0:00:05 --:--:--  724k
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 42 SKIPPED: 0 FAILED: 3
  1. Failure: quiet argument supresses messages (@test_read_exif.R#24) 
  2. Failure: recursive option works (@test_read_exif.R#32) 
  3. Failure: recursive option works (@test_read_exif.R#34) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘expm-Ex.R’ failed
The error most likely occurred in:

> ### Name: logm
> ### Title: Matrix Logarithm
> ### Aliases: logm
> ### Keywords: algebra math
> 
> ### ** Examples
> 
> m <- diag(2)
> logm(m)
     [,1] [,2]
[1,]    0    0
[2,]    0    0
> expm(logm(m))
     [,1] [,2]
[1,]    1    0
[2,]    0    1
> 
> ## Here, logm() is barely defined, and Higham08 has needed an amendment
> ## in order for not to loop forever:
> D0 <- diag(x=c(1, 0.))
> (L. <- logm(D0))
Warning in logm.Higham08(x) :
  Inverse scaling did not work (t = 1).
The matrix logarithm may not exist for this matrix.Setting m = 3 arbitrarily.
     [,1]     [,2]
[1,]    0        0
[2,]    0 -9576994
> stopifnot( all.equal(D0, expm(L.)) )
> 
> ## A matrix for which clearly no logm(.) exists:
> (m <- cbind(1:2, 1))
     [,1] [,2]
[1,]    1    1
[2,]    2    1
> (l.m <- logm(m)) ## all NA
Warning in sqrt(S[ij, ij]) : NaNs produced
Error in solve.default(X[ii, ii] + X[ij, ij], S[ii, ij] - sumU) : 
  system is computationally singular: reciprocal condition number = 0
Calls: logm ... logm.Higham08 -> rootS -> solve -> solve -> solve.default
Execution halted
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
File ‘fastmatch/libs/fastmatch.so’:
  Found non-API call to R: ‘match5’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘Rserve’
Installation failed.
See ‘/home/ripley/R/packages/tests32/FastRWeb.Rcheck/00install.out’ for details.
installed size is  5.0Mb
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installed size is  6.7Mb
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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 70-72 (lifeExpectancy.Rmd) 
Error: processing vignette 'lifeExpectancy.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/FIT.Rcheck/00install.out’ for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
Package suggested but not available for checking: ‘multipanelfigure’
Package required but not available: ‘flowWorkspace’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.5Mb
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installed size is  7.6Mb
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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 168-169 (formattable-data-frame.Rmd) 
Error: processing vignette 'formattable-data-frame.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/ripley/R/packages/tests32/fpc.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/ripley/R/packages/tests32/frailtyHL.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   4.7Mb
installed size is  5.8Mb
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    R   5.8Mb
installed size is  7.9Mb
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    data   4.9Mb
    doc    1.9Mb
Package unavailable to check Rd xrefs: ‘RMark’
Packages suggested but not available for checking: ‘RWeka’ ‘FSelector’
Package unavailable to check Rd xrefs: ‘FSelector’
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(FSelectorRcpp)
  > library(Matrix)
  > library(Rcpp)
  > library(RcppArmadillo)
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > library(entropy)
  
  Attaching package: 'entropy'
  
  The following object is masked from 'package:FSelectorRcpp':
  
      discretize
  
  > library(lintr)
  > 
  > test_check("FSelectorRcpp")
  ── 1. Error: (unknown) (@test-cutoff.R#2)  ─────────────────────────────────────
  there is no package called 'FSelector'
  1: library(FSelector) at testthat/test-cutoff.R:2
  2: stop(txt, domain = NA)
  
  ── 2. Error: (unknown) (@test-discretize.R#2)  ─────────────────────────────────
  there is no package called 'FSelector'
  1: library(FSelector) at testthat/test-discretize.R:2
  2: stop(txt, domain = NA)
  
  ── 3. Error: (unknown) (@test-information_gain.R#2)  ───────────────────────────
  there is no package called 'FSelector'
  1: library(FSelector) at testthat/test-information_gain.R:2
  2: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 22 SKIPPED: 0 FAILED: 3
  1. Error: (unknown) (@test-cutoff.R#2) 
  2. Error: (unknown) (@test-discretize.R#2) 
  3. Error: (unknown) (@test-information_gain.R#2) 
  
  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 42-45 (benchmarks_discretize.Rmd) 
Error: processing vignette 'benchmarks_discretize.Rmd' failed with diagnostics:
there is no package called 'RWeka'
Execution halted
installed size is  5.4Mb
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    examples   4.6Mb
installed size is 16.4Mb
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Running examples in ‘funcy-Ex.R’ failed
The error most likely occurred in:

> ### Name: funcyOutList-class
> ### Title: Class '"funcyOutList"'
> ### Aliases: funcyOutList-class funcyOutList
> ### Keywords: classes
> 
> ### ** Examples
> 
> set.seed(2808)
> ds <- sampleFuncy(obsNr=30, k=4, timeNr=7)
> data <- Data(ds)
> clusters <- Cluster(ds)
> 
> res <- funcit(data=data, clusters=clusters, seed=2808,
+               methods=1:5, k=4, parallel=TRUE)
4 : * * *4 : *Warning in funclustWrapper(data = data, k = k, reg = reg, regTime = regTime,  :
  It is not possible to set a seed for method funclust.Loading required namespace: funHDDC


 * *Warning in funHDDCWrapper(data = data, k = k, reg = reg, regTime = regTime,  :
  Clustering with 4 classes is not possible. 3 clusters are used!
Warning in funHDDCWrapper(data, k, reg, regTime, funcyCtrlMbc, model = "AkBkQkDk",  :
  Clustering with 3 classes is not possible. 2 clusters are used!
Warning in funHDDCWrapper(data, k, reg, regTime, funcyCtrlMbc, model = "AkBkQkDk",  :
  Clustering with 2 classes is not possible. 1 clusters are used!

Warning in funHDDCWrapper(data, k, reg, regTime, funcyCtrlMbc, model = "AkBkQkDk",  :
  Clustering with 1 classes is not possible. 0 clusters are used!
Error in funcit(data = data, clusters = clusters, seed = 2808, methods = 1:5,  : 
  Method funHDDC : Clustering for this data not possible.
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 604-605 (futureheatwaves.Rmd) 
Error: processing vignette 'futureheatwaves.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
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Error in re-building vignettes:
  ...
Warning in packageDescription("gputools") :
  no package 'gputools' was found
Error: processing vignette 'gcbd.Rnw' failed with diagnostics:
at gcbd.Rnw:860, subscript out of bounds
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/ripley/R/packages/tests32/GenABEL.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    exdata   5.3Mb
Package suggested but not available for checking: ‘reactome.db’
installed size is  5.7Mb
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    examples   1.9Mb
    vign       1.4Mb
installed size is 27.3Mb
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    data  27.2Mb
installed size is  5.6Mb
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    R         3.6Mb
    extdata   1.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: spam
Loading required package: dotCall64
Loading required package: grid
Spam version 2.1-4 (2018-04-12) 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. 
New output format of RFsimulate: S4 object of class 'RFsp';
for a bare, but faster array format use 'RFoptions(spConform=FALSE)'.

     PLEASE NOTE:  The components "delsgs" and "summary" of the
 object returned by deldir() are now DATA FRAMES rather than
 matrices (as they were prior to release 0.0-18).
 See help("deldir").
 
     PLEASE NOTE: The process that deldir() uses for determining
 duplicated points has changed from that used in version
 0.0-9 of this package (and previously). See help("deldir").


Warning in engine$weave(file, quiet = quiet, encoding = enc) :
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Quitting from lines 79-89 (zoningSimu.Rmd) 
Error: processing vignette 'zoningSimu.Rmd' failed with diagnostics:
subscript out of bounds
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 curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: Operation timed out after 10000 milliseconds with 0 out of 0 bytes received
Calls: download_codebook ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
Running ‘testthat.R’ [3s/23s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(gesis)
  > 
  > test_check("gesis")
  ── 1. Error: get_datasets() works (@test-availability.R#10)  ───────────────────
  Timeout was reached: Operation timed out after 10000 milliseconds with 0 out of 0 bytes received
  1: get_datasets("0001") at testthat/test-availability.R:10
  2: read_html(url)
  3: read_html.default(url)
  4: suppressWarnings(read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options))
  5: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  6: read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options)
  7: read_xml.character(x, encoding = encoding, ..., as_html = TRUE, options = options)
  8: read_xml.connection(con, encoding = encoding, ..., as_html = as_html, base_url = x, 
         options = options)
  9: open(x, "rb")
  10: open.connection(x, "rb")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2 SKIPPED: 0 FAILED: 1
  1. Error: get_datasets() works (@test-availability.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 30-32 (gesis.Rmd) 
Error: processing vignette 'gesis.Rmd' failed with diagnostics:
Timeout was reached: Operation timed out after 10000 milliseconds with 0 out of 0 bytes received
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for ‘ggdmc’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/ripley/R/Lib32/ggdmc/libs/ggdmc.so':
  ld.so.1: R: fatal: relocation error: file /home/ripley/R/Lib32/ggdmc/libs/ggdmc.so: symbol GOMP_parallel: referenced symbol not found
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 101-103 (ggimage.Rmd) 
Error: processing vignette 'ggimage.Rmd' failed with diagnostics:
Failed to download https://raw.githubusercontent.com/ionic-team/ionicons/master/png/512/pie-graph.png (HTTP 404)
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra
Quitting from lines 28-33 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  5.0Mb
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    data   4.5Mb
Running ‘testthat.R’ [25s/32s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ggplot2)
  > 
  > test_check("ggplot2")
  ── 1. Failure: inherits timezone from data (@test-scale-date.R#18)  ────────────
  sc$timezone not equal to NULL.
  Types not compatible: character is not NULL
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 804 SKIPPED: 1 FAILED: 1
  1. Failure: inherits timezone from data (@test-scale-date.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 125-126 (ggsdc.Rmd) 
Error: processing vignette 'ggsdc.Rmd' failed with diagnostics:
Process terminated
Execution halted
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
File ‘gnmf/libs/gnmf.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘FactorMatrix.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘FactorMatrix.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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$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
installed size is  5.3Mb
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    data   1.5Mb
    doc    3.5Mb
installed size is 19.5Mb
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Package suggested but not available for checking: ‘Sxslt’
installed size is  5.8Mb
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    R     1.1Mb
    doc   4.4Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/GSCAD.Rcheck/00install.out’ for details.
Running ‘run-tests.R’ [6s/11s]
Running the tests in ‘tests/run-tests.R’ failed.
Complete output:
  > library(testthat)
  > library(gWidgets2)
  Loading required package: digest
  > options(guiToolkit="tcltk")
  > 
  > f <- list.files(system.file("tests", package="gWidgets2"), full=T)
  > f <- Filter(function(x) !grepl("README", x), f)
  > f <- Filter(function(x) !grepl("html", x), f)
  > ## issues
  > f <- Filter(function(x) !grepl("df.R", x), f)
  > f <- Filter(function(x) !grepl("text.R", x), f)
  > f <- Filter(function(x) !grepl("tree.R", x), f)
  > 
  > sapply(f, function(i) {
  +   message("testing ", i)
  +   source(i)
  + })
  testing /home/ripley/R/Lib32/gWidgets2/tests/button.R
  Loading required package: gWidgets2tcltk
  Loading required package: memoise
  Loading required package: tcltk
  testing /home/ripley/R/Lib32/gWidgets2/tests/calendar.R
  testing /home/ripley/R/Lib32/gWidgets2/tests/checkbox.R
  testing /home/ripley/R/Lib32/gWidgets2/tests/combobox.R
  testing /home/ripley/R/Lib32/gWidgets2/tests/containers.R
  Error: svalue(cards) not equal to 1.
  Modes: logical, numeric
  target is logical, current is numeric
  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
installed size is 136.7Mb
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installed size is 10.0Mb
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Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 122-128 (Basic_use.Rmd) 
Error: processing vignette 'Basic_use.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Found the following significant warnings:
  readstat/readstat_convert.c:16:42: warning: passing argument 2 of ‘libiconv’ from incompatible pointer type [-Wincompatible-pointer-types]
  src/spss/readstat_sav_parse.rl:89:17: warning: passing argument 2 of ‘libiconv’ from incompatible pointer type [-Wincompatible-pointer-types]
  src/spss/readstat_sav_parse.rl:195:17: warning: passing argument 2 of ‘libiconv’ from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/ripley/R/packages/tests32/haven.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/ripley/R/packages/tests32/hdf5r.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [33m/16m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(healthcareai)
  healthcareai version 2.0.0
  Please visit https://docs.healthcare.ai for full documentation and vignettes. Join the community at https://healthcare-ai.slack.com
  > Sys.setenv("R_TESTS" = "")
  > test_check("healthcareai")
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
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 0.14.1

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
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    doc          13.8Mb
    htmlwidgets   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.
Highcharts (www.highcharts.com) is a Highsoft software product which is
not free for commercial and Governmental use
Quitting from lines 45-46 (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.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(hogsvdR)
  > 
  > test_check("hogsvdR")
  ── 1. Error: decomposition is correct with arma implementatation (@test.hogsvd.R
  invalid 'type' (complex) of argument
  1: expect_true(all(unlist(lapply(1:N, function(n) {
         max(D[[n]] - res$U[[n]] %*% diag(res$Sigma[[n]]) %*% t(res$V))
     })) < 1e-10)) at testthat/test.hogsvd.R:37
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: unlist(lapply(1:N, function(n) {
         max(D[[n]] - res$U[[n]] %*% diag(res$Sigma[[n]]) %*% t(res$V))
     }))
  5: lapply(1:N, function(n) {
         max(D[[n]] - res$U[[n]] %*% diag(res$Sigma[[n]]) %*% t(res$V))
     })
  6: FUN(X[[i]], ...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 3 SKIPPED: 0 FAILED: 1
  1. Error: decomposition is correct with arma implementatation (@test.hogsvd.R#37) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   2.6Mb
File ‘hSDM/libs/hSDM.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘useful.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Objects: ‘hSDM.Nmixture.o’, ‘hSDM.Nmixture.iCAR.o’, ‘hSDM.ZIB.o’,
      ‘hSDM.ZIB.iCAR.alteration.o’, ‘hSDM.ZIB.iCAR.o’, ‘hSDM.ZIP.o’,
      ‘hSDM.ZIP.iCAR.alteration.o’, ‘hSDM.ZIP.iCAR.o’,
      ‘hSDM.binomial.o’, ‘hSDM.binomial.iCAR.o’, ‘hSDM.poisson.o’,
      ‘hSDM.poisson.iCAR.o’, ‘hSDM.siteocc.o’, ‘hSDM.siteocc.iCAR.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    data  12.9Mb
    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.
trying URL 'https://arxiv.org/e-print/1406.4806v1'
Content type 'application/x-eprint-tar' length 29273 bytes (28 KB)
==================================================
downloaded 28 KB

Quitting from lines 162-165 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Running ‘testthat.R’ [2s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(HURDAT)
  > 
  > test_check("HURDAT")
  ── 1. Error: (unknown) (@test-hurdat.R#4)  ─────────────────────────────────────
  HTTP error 404.
  1: get_hurdat(basin = "AL") at testthat/test-hurdat.R:4
  2: purrr::map_df(.x = basin, .f = parse_hurdat)
  3: map(.x, .f, ...)
  4: .f(.x[[i]], ...)
  5: readr::read_lines(file = url)
  6: datasource(file, skip = skip)
  7: datasource_connection(file, skip, comment)
  8: datasource_raw(read_connection(path), skip, comment = comment)
  9: new_datasource("raw", text, skip = skip, comment = comment)
  10: structure(list(x, skip = skip, comment = comment, ...), class = c(paste0("source_", 
         type), "source"))
  11: read_connection(path)
  12: open(con, "rb")
  13: open.connection(con, "rb")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-hurdat.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘FSelector’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
Running examples in ‘IAPWS95-Ex.R’ failed
The error most likely occurred in:

> ### Name: TDh
> ### Title: Temperature, Function of Density and Enthalpy
> ### Aliases: TDh
> 
> ### ** Examples
> 
> D <- 838.025
> h <- 977.181624
> TDh(D,h)
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   1.4Mb
    doc    5.4Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    libs   2.7Mb
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 ...
Running examples in ‘ifaTools-Ex.R’ failed
The error most likely occurred in:

> ### Name: univariatePrior
> ### Title: Univariate priors commonly used in IFA models
> ### Aliases: univariatePrior
> 
> ### ** Examples
> 
> model <- univariatePrior("logit-norm", "x1", -1)
> model$priorParam$values[1,1] <- -.6
> model <- mxRun(model)
Running univariatePrior with 1 parameter
Error in runHelper(model, frontendStart, intervals, silent, suppressWarnings,  : 
  Setting improper index (1) from vector of Rf_length 0.
Calls: mxRun -> runHelper
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 1345-1400 (pritikin-schmidt.Rnw) 
Error: processing vignette 'pritikin-schmidt.Rnw' failed with diagnostics:
Fit not achieved
Execution halted
Package required but not available: ‘PythonInR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   1.2Mb
    libs   6.4Mb
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    doc       4.9Mb
    extdata   1.2Mb
    include   2.9Mb
    libs      5.2Mb
Package unavailable to check Rd xrefs: ‘minfi’
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
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘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 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.glm.MCMCchain
> ### Title: glm Compatible JM Imputation - A tool to check convergence of
> ###   the MCMC
> ### Aliases: jomo.glm.MCMCchain
> 
> ### ** Examples
> 
>    #First of all we load and attach the data:
>   
>   data(sldata)
>   attach(sldata)
>   
>   #Then we make sure sex is a factor:
>   
>   sex<-factor(sex)
>   
>   # we define the data frame with all the variables 
>   
>   data<-data.frame(measure,age, sex)
>   
>   # And the formula of the substantive lm model 
>   # sex as an outcome only because it is the only binary variable in the dataset...
>   
>   formula<-as.formula(sex~age+measure)
>   
>   #And finally we run the imputation function:
>   
>   imp<-jomo.glm.MCMCchain(formula,data, nburn=10)
This function is beta software. Use carefully and please report any bug to the package mantainer
.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: shiny
Loading required package: shinythemes
Loading required package: plyr
Quitting from lines 37-53 (kgc-fine.Rmd) 
Error: processing vignette 'kgc-fine.Rmd' failed with diagnostics:
cannot allocate vector of size 640.7 Mb
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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
Loading this package had a fatal error status code 1
Loading log:
Loading required package: Rcpp
Error: package or namespace load failed for ‘knor’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/ripley/R/Lib32/knor/libs/knor.so':
  ld.so.1: R: fatal: relocation error: file /home/ripley/R/Lib32/knor/libs/knor.so: symbol GOMP_parallel: referenced symbol not found
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    java   6.2Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    R   7.8Mb
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] 12746 - 6373 == 6373
  
  ══ 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  5.3Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    2.2Mb
    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  6.4Mb
  sub-directories of 1Mb or more:
    doc            1.1Mb
    testdata       2.1Mb
    vignettedata   2.3Mb
Running examples in ‘largeVis-Ex.R’ failed
The error most likely occurred in:

> ### Name: as.dendrogram.hdbscan
> ### Title: as.dendrogram.hdbscan
> ### Aliases: as.dendrogram.hdbscan
> 
> ### ** Examples
> 
> data(iris)
> vis <- largeVis(t(iris[,1:4]), K = 20, sgd_batches = 1, threads = 1)
Error: C stack usage  195007380 is too close to the limit

error: Mat::col(): index out of bounds

error: Mat::col(): index out of bounds
terminate called recursively
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
largeVis was compiled with 32-bit types. This will limit the size of the datasets it can process. Consider recompiling with -DARMA_64BIT_WORD
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in unit(c(t, r, b, l), unit) : NAs introduced by coercion
Error: C stack usage  309236628 is too close to the limit
Quitting from lines 190-214 (momentumandusedata.Rmd) 
Error: processing vignette 'momentumandusedata.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
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:
there is no package called 'webshot'
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
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 272-273 (Understanding_lime.Rmd) 
Error: processing vignette 'Understanding_lime.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R          1.8Mb
    doc        2.8Mb
    testdata   1.8Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/logKDE.Rcheck/00install.out’ for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
Error in re-building vignettes:
  ...
Warning in engine$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
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 0.5-23.1097
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)
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: ‘rsvg’ ‘tesseract’
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
Packages unavailable to check Rd xrefs: ‘rsvg’, ‘tesseract’
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/DrawImage/3308
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.
Running ‘testthat.R’ [17s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > test_check("MALDIrppa")
  Loading required package: MALDIrppa
  Loading required package: MALDIquant
  
  This is MALDIquant version 1.17
  Quantitative Analysis of Mass Spectrometry Data
   See '?MALDIquant' for more information about this package.
  
  Loading required package: signal
  
  Attaching package: 'signal'
  
  The following objects are masked from 'package:stats':
  
      filter, poly
  
  Loading required package: robustbase
  Loading required package: wmtsa
  Loading required package: lattice
  ── 1. Failure: detectOutliers returns expected results (@test_all.R#23)  ───────
  sum(detectOutliers(peaks)) not equal to 63.
  1/1 mismatches
  [1] 64 - 63 == 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 19 SKIPPED: 0 FAILED: 1
  1. Failure: detectOutliers returns expected results (@test_all.R#23) 
  
  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 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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 61-68 (manipulateWidgets.Rmd) 
Error: processing vignette 'manipulateWidgets.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is 33.9Mb
  sub-directories of 1Mb or more:
    mapdata  33.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: igraph

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

Quitting from lines 57-64 (mapfuser.Rmd) 
Error: processing vignette 'mapfuser.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 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
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    java   3.4Mb
File ‘maxent/libs/maxent.so’:
  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.
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  5.1Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   2.8Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/ripley/R/packages/tests32/mdhglm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
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.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.7Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
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 fc120350, 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 = y, v = v, data = my.df, model.name = "No predictor",     suppressWarnings = TRUE, silent = TRUE)
 8: doTryCatch(return(expr), name, parentenv, handler)
 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(meta(y = y, v = v, data = my.df, model.name = "No predictor",     suppressWarnings = TRUE, silent = TRUE), error = function(e) e)
12: meta(y = ln_OR, v = v_ln_OR, data = BCG, x = cbind(scale(Latitude,     scale = FALSE), scale(Year, scale = FALSE)))
13: 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 ...
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   1.1Mb
    doc    1.5Mb
    libs   1.5Mb
    misc   1.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 91-94 (mgwrsar-basic_examples.Rmd) 
Error: processing vignette 'mgwrsar-basic_examples.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mhde_article.tex' failed.
Messages:
/usr/local/bin/texi2dvi: line 411: 18308 Killed                  "$@" 2>&5 1>&2
/usr/local/bin/texi2dvi: biber failed
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
File ‘MigClim/libs/MigClim.so’:
  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.
Running examples in ‘mitml-Ex.R’ failed
The error most likely occurred in:

> ### Name: anova.mitml.result
> ### Title: Compare several nested models
> ### Aliases: anova.mitml.result
> ### Keywords: methods
> 
> ### ** Examples
> 
> require(lme4)
Loading required package: lme4
Loading required package: Matrix
> data(studentratings)
> 
> fml <- ReadDis + SES ~ ReadAchiev + (1|ID)
> imp <- panImpute(studentratings, formula=fml, n.burn=1000, n.iter=100, m=5)
Running burn-in phase ...
Creating imputed data set ( 1 / 5 ) ...
Creating imputed data set ( 2 / 5 ) ...
Creating imputed data set ( 3 / 5 ) ...
Creating imputed data set ( 4 / 5 ) ...
Creating imputed data set ( 5 / 5 ) ...
Error in pan::pan(gy, subj = gclus, gpred, xcol, zcol, prior, seed = rns[ii +  : 
  NA/NaN/Inf in foreign function call (arg 20)
Calls: panImpute -> <Anonymous>
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   2.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   4.1Mb
Running ‘testthat.R’ [38s/45s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mizer)
  > 
  > test_check("mizer")
  ── 1. Failure: retune_abundance reproduces scaling model (@test-wrapper_function
  max(abs(initial_n - pr@initial_n)) is not strictly less than 2e-11. Difference: 2.21e-11
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 508 SKIPPED: 1 FAILED: 1
  1. Failure: retune_abundance reproduces scaling model (@test-wrapper_functions.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘minfi’
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 73-76 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'minfi'
Execution halted
Package suggested but not available for checking: ‘FSelector’
Packages suggested but not available for checking: ‘FSelector’ ‘RWeka’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.4Mb
Error in re-building vignettes:
  ...
Package: mnlogit
Version: 1.2.5
Multinomial Logit Choice Models.
Scientific Computing Group, Sentrana Inc.
Loading required package: Formula
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/

Attaching package: 'mlogit'

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

    hmftest, index, scoretest

Loading required package: stats4
Loading required package: splines

Attaching package: 'VGAM'

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

    lrtest

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

    lrtest
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   5.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.8Mb
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  5.6Mb
  sub-directories of 1Mb or more:
    R     2.4Mb
    doc   2.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.8Mb
File ‘MRwarping/libs/MRwarping.so’:
  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.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 30-37 (msaR.Rmd) 
Error: processing vignette 'msaR.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/MultiBD.Rcheck/00install.out’ for details.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R     2.3Mb
    doc   4.1Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    java  14.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    2.5Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    extdata  16.3Mb
Error in re-building vignettes:
  ...
Warning in engine$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 49-50 (using-nauf.Rmd) 
Error: processing vignette 'using-nauf.Rmd' failed with diagnostics:
Unable to extract deviance function from model fit
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 nc_att.NetCDF nc_att 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 2.1-4 (2018-04-12) 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
File ‘NeatMap/libs/NeatMap.so’:
  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.
Package required but not available: ‘dataone’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘RSiena’
File ‘NetSim/libs/NetSim.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘utils/Random.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘utils/Random.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
Package suggested but not available for checking: ‘tensorflow’
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    CppCode   1.2Mb
    R         6.0Mb
    include   5.3Mb
    tests     1.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data      4.4Mb
    doc       1.2Mb
    reports   3.8Mb
Error in re-building vignettes:
  ...
Warning in engine$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: getRNG1
> ### Title: Extracting RNG Data from NMF Objects
> ### Aliases: .getRNG getRNG1 getRNG1-methods getRNG1,NMFfitX1-method
> ###   getRNG1,NMFfitX-method getRNG1,NMFfitXn-method .getRNG-methods
> ###   .getRNG,NMFfitXn-method
> ### Keywords: methods
> 
> ### ** Examples
> 
> ## Don't show: 
> # roxygen generated flag
> options(R_CHECK_RUNNING_EXAMPLES_=TRUE)
> ## End(Don't show)
> 
> # For multiple NMF runs, the RNG settings used for the first run is also stored
> V <- rmatrix(20,10)
> res <- nmf(V, 3, nrun=4)
# 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: 0.021 0.035 0.061
Execution halted
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
installed size is 39.1Mb
  sub-directories of 1Mb or more:
    extdata  39.0Mb
Package required but not available: ‘rsvg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
File ‘obliclus/libs/obliclus.so’:
  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.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    data   1.0Mb
    help   2.2Mb
Package suggested but not available for checking: ‘RMark’
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    R        2.5Mb
    data     1.0Mb
    libs     2.7Mb
    models   4.5Mb
Running examples in ‘OpenMx-Ex.R’ failed
The error most likely occurred in:

> ### Name: mxExpectationStateSpace
> ### Title: Create an MxExpectationStateSpace Object
> ### Aliases: mxExpectationStateSpace MxExpectationStateSpace-class
> ###   show,MxExpectationStateSpace-method
> ###   print,MxExpectationStateSpace-method
> 
> ### ** Examples
> 
>    
> # Create and fit a model using mxMatrix, mxExpectationStateSpace, and mxFitFunctionML
> require(OpenMx)
> data(demoOneFactor)
> nvar <- ncol(demoOneFactor)
> varnames <- colnames(demoOneFactor)
> ssModel <- mxModel(model="State Space Manual Example",
+     mxMatrix("Full", 1, 1, TRUE, .3, name="A"),
+     mxMatrix("Zero", 1, 1, name="B"),
+     mxMatrix("Full", nvar, 1, TRUE, .6, name="C", dimnames=list(varnames, "F1")),
+     mxMatrix("Zero", nvar, 1, name="D"),
+     mxMatrix("Diag", 1, 1, FALSE, 1, name="Q"),
+     mxMatrix("Diag", nvar, nvar, TRUE, .2, name="R"),
+     mxMatrix("Zero", 1, 1, name="x0"),
+     mxMatrix("Diag", 1, 1, FALSE, 1, name="P0"),
+     mxMatrix("Zero", 1, 1, name="u"),
+     mxData(observed=demoOneFactor[1:100,], type="raw"),#fewer rows = fast
+     mxExpectationStateSpace("A", "B", "C", "D", "Q", "R", "x0", "P0", "u"),
+     mxFitFunctionML()
+ )
> ssRun <- mxRun(ssModel)
Running State Space Manual Example with 11 parameters

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

Traceback:
 1: runHelper(model, frontendStart, intervals, silent, suppressWarnings,     unsafe, checkpoint, useSocket, onlyFrontend, useOptimizer)
 2: mxRun(ssModel)
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
Running ‘testthat.R’ [27s/82s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > test_check("openxlsx")
  Loading required package: openxlsx
  ── 1. Error: loadWorkbook from different sources (@test-read_sources.R#49)  ────
  subscript out of bounds
  1: expect_true(all.equal.Workbook(wb_url, wb_file), "Loading from URL vs local not equal") at testthat/test-read_sources.R:49
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: all.equal.Workbook(wb_url, wb_file)
  5: sapply(1:nSheets, function(i) isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]])))
  6: lapply(X = X, FUN = FUN, ...)
  7: FUN(X[[i]], ...)
  8: isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]]))
  9: all.equal(x$colWidths[[i]], y$colWidths[[i]])
  10: all.equal.list(x$colWidths[[i]], y$colWidths[[i]])
  11: attr.all.equal(target, current, ...)
  12: mode(current)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 505 SKIPPED: 2 FAILED: 1
  1. Error: loadWorkbook from different sources (@test-read_sources.R#49) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in 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
Running examples in ‘osrmr-Ex.R’ failed
The error most likely occurred in:

> ### Name: nearest_api_v5
> ### Title: nearest accessible position for OSRM API v5
> ### Aliases: nearest_api_v5
> 
> ### ** Examples
> 
> osrmr:::nearest_api_v5(47,9, osrmr:::server_address(FALSE))
Warning in file(con, "r") :
  cannot open URL 'http://router.project-osrm.org/nearest/v1/driving/9,47?number=1': HTTP status was '429 Unknown Error'
Error in file(con, "r") : 
  cannot open the connection to 'http://router.project-osrm.org/nearest/v1/driving/9,47?number=1'
Calls: <Anonymous> -> <Anonymous> -> paste -> readLines -> file
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 185-198 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(oxcAAR)
  > 
  > test_check("oxcAAR")
  sh: /home/ripley/R/packages/tests32/oxcAAR.Rcheck/tests/testthat/ox_output.js: cannot execute
  ── 1. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_util
  `quickSetupOxcal()` threw an error.
  Message: argument is of length zero
  Class:   simpleError/error/condition
  
  ── 2. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_util
  dir.exists("OxCal/bin/") isn't true.
  
  ── 3. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_util
  `%in%`(...) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 94 SKIPPED: 0 FAILED: 3
  1. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_utility_functions.R#30) 
  2. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_utility_functions.R#31) 
  3. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_utility_functions.R#32) 
  
  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.
Quitting from lines 24-30 (basic-usage.Rmd) 
Error: processing vignette 'basic-usage.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
Running examples in ‘P2C2M-Ex.R’ failed
The error most likely occurred in:

> ### Name: p2c2m.complete
> ### Title: Execute the complete P2C2M pipeline via a single command
> ### Aliases: p2c2m.complete
> 
> ### ** Examples
> 
> ## Example of the minimal data requirements to run P2C2M
> 
> # The absolute path to the input directory is set
> inPath <- system.file("extdata", "sim.E.003.small/", package="P2C2M")
> 
> # The name of the xml-file generated by BEAUTi and located in 
> # "inPath" is set
> inFile <- "sim.E.003.small.xml"
> 
> # Posterior predictive simulations with a setting of 2 simulation 
> # replicates are preformed
> sim.E.003.small <- p2c2m.complete(inPath, inFile, num.reps=2, save.metadata=TRUE)
Error in python.exec(code, get.exception) : cannot import name izip
Calls: p2c2m.complete -> p2c2m.readstarb -> <Anonymous> -> python.exec
Execution halted
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 196-217 (progressive_packing.Rmd) 
Error: processing vignette 'progressive_packing.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data        1.6Mb
    localdata   3.1Mb
Info message:
Couldn't find 'pandoc'!
Pandoc version is set to '1.16', use `set_pandoc_version` to change the settings if necessary.
File ‘ParallelForest/libs/ParallelForest.so’:
  Found ‘__f90_close’, possibly from ‘close’ (Fortran)
    Object: ‘random_utils.o’
  Found ‘__f90_esfw’, possibly from ‘print’ (Fortran), ‘write’
    (Fortran)
    Object: ‘classification.o’
  Found ‘__f90_eslw’, possibly from ‘print’ (Fortran), ‘write’
    (Fortran)
    Object: ‘classification.o’
  Found ‘__f90_open’, possibly from ‘open’ (Fortran)
    Object: ‘random_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.
File ‘parmigene/libs/parmigene.so’:
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
    Object: ‘points.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 12.0Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    extdata   9.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    1.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc        1.3Mb
    examples   1.8Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    data   2.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.1Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/pdftools.Rcheck/00install.out’ for details.
Running examples in ‘penaltyLearning-Ex.R’ failed
The error most likely occurred in:

> ### Name: modelSelectionC
> ### Title: Exact model selection function
> ### Aliases: modelSelectionC
> 
> ### ** Examples
> 
> 
> library(penaltyLearning)
> data(neuroblastoma, package="neuroblastoma", envir=environment())
> pro <- subset(neuroblastoma$profiles, profile.id==1 & chromosome=="X")
> max.segments <- 20
> fit <- Segmentor3IsBack::Segmentor(pro$logratio, 2, max.segments)
Error in cumsum(datasize)[breaks[k, 1:k]] : 
  only 0's may be mixed with negative subscripts
Calls: <Anonymous> -> Segmentor.default
Execution halted
Running examples in ‘pense-Ex.R’ failed
The error most likely occurred in:

> ### Name: coef.pense
> ### Title: Extract Model Coefficients
> ### Aliases: coef.pense
> 
> ### ** Examples
> 
> # Generate data with highly correlated groups of variables and some outliers
> set.seed(12345)
> n <- 50
> n_out <- 3
> p <- 20
> x <- 1 + matrix(rnorm(n * p), ncol = p)
> x[, 2] <- x[, 1] + rnorm(n, sd = 0.01)
> x[, 3] <- x[, 1] + rnorm(n, sd = 0.01)
> x[, 5] <- x[, 4] + rnorm(n, sd = 0.01)
> x[, 6] <- x[, 4] + rnorm(n, sd = 0.01)
> 
> y <- x %*% c(rep(c(2, 5), each = 3), numeric(p - 6)) + rnorm(n)
> 
> y[seq_len(n_out)] <- rnorm(n_out, -100, sd = 3)
> 
> # Compute the PENSE estimator
> set.seed(1234)
> est_en <- pense(x, y, alpha = 0.5, warm_reset = 1, cv_k = 3)

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

Traceback:
 1: enpy_exact(x, y, alpha, lambda, options, en_options)
 2: enpy(std_data$xs, std_data$yc, alpha, lambda, delta = pense_options$bdp,     cc = pense_options$cc, options = initest_options, en_options = en_options)
 3: pense_init_cold(x = x_train, y = y_train, lambda = job$lambda,     ...)
 4: FUN(X[[i]], ...)
 5: cluster$lapply(jobs_cold_est, get_cold_est, alpha = alpha, standardize = standardize,     pense_options = options, initest_options = init_options,     en_options = en_options)
 6: doTryCatch(return(expr), name, parentenv, handler)
 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8: tryCatchList(expr, classes, parentenv, handlers)
 9: tryCatch({    cold_inits <- cluster$lapply(jobs_cold_est, get_cold_est,         alpha = alpha, standardize = standardize, pense_options = options,         initest_options = init_options, en_options = en_options)}, error = function(e) {    cluster$stopCluster()    stop(e)})
10: pense(x, y, alpha = 0.5, warm_reset = 1, cv_k = 3)
An irrecoverable exception occurred. R is aborting now ...
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      4.5Mb
    data   3.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
File ‘PhaseType/libs/PhaseType.so’:
  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.
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 20-27 (Advanced_Usage.Rmd) 
Error: processing vignette 'Advanced_Usage.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Running ‘testthat.R’ [15s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pillar)
  > 
  > test_check("pillar")
  ── 1. Failure: compute_rhs_digits() works (@test-format_decimal.R#24)  ─────────
  compute_rhs_digits(x, 7) not equal to c(0, 0, 0, 0, 0, 0, 0, 3, 24).
  1/9 mismatches
  [9] 20 - 24 == -4
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 281 SKIPPED: 0 FAILED: 1
  1. Failure: compute_rhs_digits() works (@test-format_decimal.R#24) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: cluster
Loading required package: entropy
Loading required package: parallel
Loading required package: pbmcapply
Loading required package: future
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators

Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   2.0Mb
    doc    2.9Mb
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 65-68 (v01-introduction.Rmd) 
Error: processing vignette 'v01-introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
Packages suggested but not available for checking: ‘Rserve’ ‘RSelenium’
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   6.4Mb
Running ‘testthat.R’ [56s/67s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pmultinom)
  > 
  > test_check("pmultinom")
  ── 1. Failure: Correct behavior when target probability is 0 or 1 (@test_invertp
  invert.pmultinom(...) not equal to 0.
  1/1 mismatches
  [1] 3 - 0 == 3
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1561 SKIPPED: 0 FAILED: 1
  1. Failure: Correct behavior when target probability is 0 or 1 (@test_invertpmultinom.R#37) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Package required but not available: ‘RcppCWB’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R      6.5Mb
    data   2.8Mb
installed size is  5.6Mb
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    doc   5.0Mb
Package suggested but not available for checking: ‘ROI.plugin.symphony’
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    java   5.7Mb
File ‘powell/libs/powell.so’:
  Found ‘printf’, possibly from ‘printf’ (C)
    Object: ‘powell.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking:
  ‘gurobi’ ‘lpsymphony’ ‘Rsymphony’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 31-43 (PRISMA.Rmd) 
Error: processing vignette 'PRISMA.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.1Mb
Running examples in ‘profile-Ex.R’ failed
The error most likely occurred in:

> ### Name: read_rprof
> ### Title: File I/O for profiler data
> ### Aliases: read_rprof read_pprof write_rprof write_pprof
> 
> ### ** Examples
> 
> rprof_file <- system.file("samples/rprof/1.out", package = "profile")
> ds <- read_rprof(rprof_file)
> ds
Profile data: 22 samples
> pprof_file <- tempfile("profile", fileext = ".pb.gz")
> write_pprof(ds, pprof_file)
Error: Package RProtoBuf is required to read pprof files.
Execution halted
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   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.
Loading required package: Rcpp
rstanarm (Version 2.17.4, packaged: 2018-04-13 01:51:52 UTC)
- Do not expect the default priors to remain the same in future rstanarm versions.
Thus, R scripts should specify priors explicitly, even if they are just the defaults.
- For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores())
- Plotting theme set to bayesplot::theme_default().

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: 'plotly'

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

    last_plot

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

    get_x, get_y

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

    filter

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

    layout

We recommend that you use the dev version of ggplot2 with `ggplotly()`
Install it with: `devtools::install_github('hadley/ggplot2')`
Quitting from lines 503-531 (bayesian.Rmd) 
Error: processing vignette 'bayesian.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   1.0Mb
    doc    2.7Mb
    help   1.0Mb
installed size is  5.4Mb
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    R          1.1Mb
    doc        4.8Mb
    examples   2.4Mb
installed size is  7.3Mb
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Running examples in ‘pyinit-Ex.R’ failed
The error most likely occurred in:

> ### Name: pyinit
> ### Title: PY (Pena-Yohai) initial estimates for S-estimates of regression
> ### Aliases: pyinit
> 
> ### ** Examples
> 
> # generate a simple synthetic data set for a linear regression model
> # with true regression coefficients all equal to one "(1, 1, 1, 1, 1)"
> set.seed(123)
> x <- matrix(rnorm(100*4), 100, 4)
> y <- rnorm(100) + rowSums(x) + 1
> # add masked outliers
> a <- svd(var(x))$v[,4]
> x <- rbind(x, t(outer(a, rnorm(20, mean=4, sd=1))))
> y <- c(y, rnorm(20, mean=-2, sd=.2))
> 
> # these outliers are difficult to find
> plot(lm(y~x), ask=FALSE)
> 
> # use pyinit to obtain estimated regression coefficients
> tmp <- pyinit(x=x, y=y, resid_keep_method='proportion', psc_keep = .5, resid_keep_prop=.5)

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

Traceback:
 1: pyinit(x = x, y = y, resid_keep_method = "proportion", psc_keep = 0.5,     resid_keep_prop = 0.5)
An irrecoverable exception occurred. R is aborting now ...
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R   1.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
installed size is 12.9Mb
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installed size is 11.5Mb
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    R         1.9Mb
    contrib   3.7Mb
    doc       3.3Mb
    libs      1.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 83-117 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 92-106 (wilcox1973.Rmd) 
Error: processing vignette 'wilcox1973.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
File ‘QUIC/libs/QUIC.so’:
  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/qVarSel.so’:
  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 examples in ‘R2Cuba-Ex.R’ failed
The error most likely occurred in:

> ### Name: R2Cuba-package
> ### Title: Multidimensional Numerical Integration
> ### Aliases: R2Cuba-package R2Cuba
> ### Keywords: package
> 
> ### ** Examples
> 
> integrand <- function(arg, weight) {
+   x <- arg[1]
+   y <- arg[2]
+   z <- arg[3]
+   ff <- sin(x)*cos(y)*exp(z);
+ return(ff)
+ } # end integrand
> NDIM <-3
> NCOMP <- 1
> vegas(NDIM, NCOMP, integrand, rel.tol=1e-3,  abs.tol=1e-12)
Iteration 1:  1000 integrand evaluations so far
[1] 0.664916 +- 0.0138647  	chisq 0 (0 df)

 *** caught segfault ***
address fd0d6190, cause 'memory not mapped'

Traceback:
 1: vegas(NDIM, NCOMP, integrand, rel.tol = 0.001, abs.tol = 1e-12)
An irrecoverable exception occurred. R is aborting now ...
Package unavailable to check Rd xrefs: ‘BRugs’
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    app   6.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    extdata   1.5Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    htmlwidgets   6.6Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.0Mb
    help   1.2Mb
    libs   1.4Mb
Running examples in ‘RandomFields-Ex.R’ failed
The error most likely occurred in:

> ### Name: RMave
> ### Title: Space-time moving average model
> ### Aliases: RMave
> ### Keywords: spatial models
> 
> ### ** Examples
> 
> RFoptions(seed=0) ## *ANY* simulation will have the random seed 0; set
> ##                   RFoptions(seed=NA) to make them all random again
> 
> ## Example of an evaluation of the ave2-covariance function
> ## in three different ways
> ## ---------------------------------------------------------
> ## some parameters A and z
> A <- matrix(c(2,1,1,2),ncol=2)
> z <- c(1,2)
> ## h for evalutation
> h <- c(1,2)
> ## some abbreviations
> E <- matrix(c(1,0,0,1),ncol=2)
> B <- A %*% h %*% t(h) %*% A
> phi <- function(t){return(RFcov(RMwhittle(1), t))}
> ## ---------------------------------------------------------
> ## the following should yield the same value 3 times
> ## (also for other choices of A,z and h)
> z1 <- RFcov( model=RMave(RMwhittle(1),A=A,z=z) , x=t(c(h,0)) )
> z2 <- RFcov( model=RMave(RMwhittle(1),A=A,z=z,spacetime=FALSE) , x=t(h) )
> z3 <- ( (det(E+2*B))^(-1/2) ) *
+  phi( sqrt( sum(h*h)/2 + (t(z) %*% h)^2 *
+  ( 1-2*t(h) %*% A %*% solve(E+2*B) %*% A %*% h) ) )
> ##
> stopifnot(abs(z1-z2)<1e-12, abs(z2-z3)<1e-12)
Error: abs(z2 - z3) < 1e-12 is not TRUE
Execution halted
Running examples in ‘rapidraker-Ex.R’ failed
The error most likely occurred in:

> ### Name: rapidrake
> ### Title: Rapid RAKE
> ### Aliases: rapidrake
> 
> ### ** Examples
> 
> rapidrake(txt = "some text that has great keywords")
Error in .jfindClass(as.character(class)) : class not found
Calls: rapidrake ... <Anonymous> -> <Anonymous> -> jclassName -> .jfindClass
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.5Mb
Packages suggested but not available for checking: ‘odfWeave’ ‘rggobi’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    etc   2.2Mb
    po    1.5Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/rCBA.Rcheck/00install.out’ for details.
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    cont  23.4Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/rcdk.Rcheck/00install.out’ for details.
Running examples in ‘rchallenge-Ex.R’ failed
The error most likely occurred in:

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

```{r}
library(rchallenge)
```
<link rel="stylesheet" 
 href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css">
`r icon("fa-user")`
`r icon("fa-user fa-lg")`
`r icon("fa-user fa-2x")`
`r icon("fa-user fa-3x")`
`r icon("fa-user fa-3x fa-border")`
> rmarkdown::render(file)
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
Found the following significant warnings:
  Warning: replacing previous import ‘Rcmdr::Confint’ by ‘car::Confint’ when loading ‘RcmdrPlugin.BCA’
See ‘/home/ripley/R/packages/tests32/RcmdrPlugin.BCA.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.5Mb
    po    2.2Mb
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 45-50 (introducao-rcongresso.Rmd) 
Error: processing vignette 'introducao-rcongresso.Rmd' failed with diagnostics:
Not Found (HTTP 404).
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    include   5.0Mb
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    include  25.2Mb
Running examples in ‘RcppBlaze-Ex.R’ failed
The error most likely occurred in:

> ### Name: fastLmPure
> ### Title: linear model fitting function based on RcppBlaze
> ### Aliases: fastLmPure
> 
> ### ** Examples
> 
> # according to fastLm example in RcppArmadillo
> data(trees, package="datasets")
> flm <- fastLmPure(cbind(1, log(trees$Girth)), log(trees$Volume), 0)

 *** caught segfault ***
address fd14b79a, cause 'memory not mapped'

Traceback:
 1: fastLmPure(cbind(1, log(trees$Girth)), log(trees$Volume), 0)
An irrecoverable exception occurred. R is aborting now ...
Running examples in ‘RcppCCTZ-Ex.R’ failed
The error most likely occurred in:

> ### Name: toTz
> ### Title: Shift datetime object from one timezone to another
> ### Aliases: toTz
> 
> ### ** Examples
> 
> toTz(Sys.time(), "America/New_York", "Europe/London")
Error in toTz(Sys.time(), "America/New_York", "Europe/London") : 
  Bad 'from' timezone
Execution halted
Running ‘simpleTests.R’
Running the tests in ‘tests/simpleTests.R’ failed.
Complete output:
  > 
  > library(RcppCCTZ)
  > 
  > ord <- "America/Chicago"
  > lax <- "America/Los_Angeles"
  > lga <- "America/New_York"
  > htr <- "Europe/London"
  > utc <- "UTC"
  > 
  > now <- ISOdatetime(2016, 11, 29, 12, 00, 00, tz="UTC")
  > 
  > format(toTz(now, utc, lax), tz=lax)
  Error in toTz(now, utc, lax) : Bad 'to' timezone
  Calls: format -> toTz
  Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/RcppCWB.Rcheck/00install.out’ for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    include   7.2Mb
Running examples in ‘RcppGetconf-Ex.R’ failed
The error most likely occurred in:

> ### Name: getAll
> ### Title: Return all System Configuration Settings
> ### Aliases: getAll
> 
> ### ** Examples
> 
> head(getAll(), 30)
Error in getAll() : Memory allocation error
Calls: head -> getAll
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/RcppHoney.Rcheck/00install.out’ for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    include   1.5Mb
    lib       3.0Mb
    libs      1.2Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/RcppMsgPack.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [50s/63s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(RcppProgress)
  > 
  > test_check("RcppProgress")
  ── 1. Failure: test_sequential (@test-pkg_examples.R#6)  ───────────────────────
  `test_sequential(nb = 500)` threw an error.
  Message: Command failed (1)
  Class:   simpleError/error/condition
  
  ── 2. Failure: test_multithreaded (@test-pkg_examples.R#13)  ───────────────────
  `test_multithreaded(nb = 1000, threads = 4)` threw an error.
  Message: Command failed (1)
  Class:   simpleError/error/condition
  
  ── 3. Failure: amardillo_multithreaded (@test-pkg_examples.R#20)  ──────────────
  `amardillo_multithreaded(nb = 1000, threads = 4)` threw an error.
  Message: Command failed (1)
  Class:   simpleError/error/condition
  
  ── 4. Failure: eta_progress_bar (@test-pkg_examples.R#28)  ─────────────────────
  `eta_progress_bar(nb = 1000)` threw an error.
  Message: Command failed (1)
  Class:   simpleError/error/condition
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 4
  1. Failure: test_sequential (@test-pkg_examples.R#6) 
  2. Failure: test_multithreaded (@test-pkg_examples.R#13) 
  3. Failure: amardillo_multithreaded (@test-pkg_examples.R#20) 
  4. Failure: eta_progress_bar (@test-pkg_examples.R#28) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    include   8.9Mb
    libs     14.9Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    include   6.6Mb
Running examples in ‘Rcrawler-Ex.R’ failed
The error most likely occurred in:

> ### Name: LinkExtractor
> ### Title: LinkExtractor
> ### Aliases: LinkExtractor
> 
> ### ** Examples
> 
> 
> pageinfo<-LinkExtractor(url="http://www.glofile.com", ExternalLInks = TRUE)
Error in LinkExtractor(url = "http://www.glofile.com", ExternalLInks = TRUE) : 
  object 'Extlinks' not found
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.

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 27-57 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'tmap'
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rdist)
  > 
  > test_check("rdist")
  ── 1. Failure: euclidean metric works as expected (@test-euclidean.R#12)  ──────
  `dist_mat` not equivalent to pdist(x).
  14/10000 mismatches (average diff: 1.64e-08)
  [607]  0 - 2.11e-08 == -2.11e-08
  [809]  0 -      NaN ==       NaN
  [1819] 0 -      NaN ==       NaN
  [2425] 0 -      NaN ==       NaN
  [2728] 0 -      NaN ==       NaN
  [3637] 0 -      NaN ==       NaN
  [4041] 0 -      NaN ==       NaN
  [5354] 0 -      NaN ==       NaN
  [5556] 0 -      NaN ==       NaN
  ...
  
  ── 2. Failure: euclidean metric works as expected (@test-euclidean.R#13)  ──────
  `dist_mat` not equivalent to cdist(x, x).
  14/10000 mismatches (average diff: 1.64e-08)
  [607]  0 - 2.11e-08 == -2.11e-08
  [809]  0 -      NaN ==       NaN
  [1819] 0 -      NaN ==       NaN
  [2425] 0 -      NaN ==       NaN
  [2728] 0 -      NaN ==       NaN
  [3637] 0 -      NaN ==       NaN
  [4041] 0 -      NaN ==       NaN
  [5354] 0 -      NaN ==       NaN
  [5556] 0 -      NaN ==       NaN
  ...
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 63 SKIPPED: 0 FAILED: 2
  1. Failure: euclidean metric works as expected (@test-euclidean.R#12) 
  2. Failure: euclidean metric works as expected (@test-euclidean.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   2.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 22-26 (mapDWD.Rmd) 
Error: processing vignette 'mapDWD.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 13-17 (recexcavAAR-vignette-1.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-1.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.13.1; older versions will not work.
Execution halted
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.9Mb
Package suggested but not available for checking: ‘Rsymphony’

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

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

> ### Name: calc_MO2
> ### Title: Calculate metabolic rate
> ### Aliases: calc_MO2
> 
> ### ** Examples
> 
> # get O2 data
> file <- system.file('extdata', 'witrox_file.txt', package = 'respirometry')
> o2_data <- na.omit(import_witrox(file, split_channels = TRUE)$CH_4)
Warning in strsplit(raw, split = "\r\n", fixed = T) :
  input string 1 is invalid UTF-8
Error in grep("Date &Time [", f[1:20], fixed = TRUE):length(f) : 
  argument of length 0
Calls: na.omit -> import_witrox
Execution halted
Running examples in ‘revgeo-Ex.R’ failed
The error most likely occurred in:

> ### Name: revgeo
> ### Title: Reverse Geocoding with the Photon Geocoder for OpenStreetMap,
> ###   Google Maps, and Bing.
> ### Aliases: revgeo
> ### Keywords: geocode reverse
> 
> ### ** Examples
> 
> revgeo(longitude=-77.0229529, latitude=38.89283435)
[1] "Getting geocode data from Photon: http://photon.komoot.de/reverse?lon=-77.0229529&lat=38.89283435"

Execution halted
installed size is  5.7Mb
  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.

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 230-274 (rfm-customer-level-data.Rmd) 
Error: processing vignette 'rfm-customer-level-data.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Package unavailable to check Rd xrefs: ‘Rsymphony’
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc     4.1Mb
    fonts   1.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 17-19 (WebGL.Rmd) 
Error: processing vignette 'WebGL.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.14; older versions may not work.
Execution halted
Packages suggested but not available for checking: ‘pmg’ ‘rggobi’
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    extra  10.2Mb
Package required but not available: ‘RPostgres’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  atkClasses.c:1050:25: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  atkClasses.c:1058:34: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  atkClasses.c:1397:51: warning: passing argument 2 of ‘object_class->active_descendant_changed’ from incompatible pointer type [-Wincompatible-pointer-types]
  gdkFuncs.c:6000:36: warning: passing argument 2 of ‘gdk_window_get_user_data’ from incompatible pointer type [-Wincompatible-pointer-types]
  gioClasses.c:1948:17: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gioClasses.c:1964:20: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gtkClasses.c:8665:28: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gtkClasses.c:11110:21: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/ripley/R/packages/tests32/RGtk2.Rcheck/00install.out’ for details.
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    help  10.6Mb
    libs   3.1Mb
File ‘RGtk2/libs/RGtk2.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘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.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc   9.9Mb
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 34-47 (intro_rhandsontable.Rmd) 
Error: processing vignette 'intro_rhandsontable.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
File ‘RInside/libs/RInside.so’:
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLdo1’, ‘R_ReplDLLinit’,
    ‘R_RunExitFinalizers’, ‘R_SetParams’, ‘R_SignalHandlers’,
    ‘R_TempDir’, ‘Rf_endEmbeddedR’, ‘Rf_initEmbeddedR’

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.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
Running examples in ‘RJafroc-Ex.R’ failed
The error most likely occurred in:

> ### Name: PlotRsmOperatingCharacteristics
> ### Title: RSM predicted operating characteristics, ROC pdfs and different
> ###   FOMs possible with FROC data
> ### Aliases: PlotRsmOperatingCharacteristics
> 
> ### ** Examples
> 
> ## Following example is for mu = 2, lambda = 1, nu = 0.6, in one treatment and   
> ## mu = 3, lambda = 1.5, nu = 0.8, in the other treatment. 20% of the diseased 
> ## cases have a single lesion, 40% have two lesions, 10% have 3 lesions, 
> ## and 30% have 4 lesions.  
> lesDistr <- rbind(c(1, 0.2), c(2, 0.4), c(3, 0.1), c(4, 0.3))
> 
> ## On cases with one lesion the weights are 1, on cases with 2 lesions the weights
> ## are 0.4 and 0.6, on cases with three lesions the weights are 0.2, 0.3 and 0.5, and
> ## on cases with 4 lesions the weights are 0.3, 0.4, 0.2 and 0.1: 
> lesionWeights <- rbind(c(1.0, -Inf, -Inf, -Inf), 
+                        c(0.4,  0.6, -Inf, -Inf), 
+                        c(0.2,  0.3,  0.5, -Inf), 
+                        c(0.3,  0.4, 0.2,  0.1))
> ret <- PlotRsmOperatingCharacteristics(mu = c(2, 3), lambda = c(1, 1.5), nu = c(0.6, 0.8),
+    lesDistr = lesDistr, lesionWeights = lesionWeights, 
+    legendPosition = "bottom", nlfRange = c(0, 1), llfRange = c(0, 1))
Error in PlotRsmOperatingCharacteristics(mu = c(2, 3), lambda = c(1, 1.5),  : 
  Line 4 of lesion weights matrix should be summed up to 1.
Execution halted
Note: information on .o files is not available
File ‘/home/ripley/R/Lib32/rJava/libs/rJava.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API call to R: ‘R_GlobalContext’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor 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.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    java  11.2Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    datasets  10.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.0Mb
    extdata   3.1Mb
Found the following significant warnings:
  "lib/vec.c", line 29: warning: improper pointer/integer combination: op "="
See ‘/home/ripley/R/packages/tests32/rlang.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/ripley/R/packages/tests32/rlas.Rcheck/00install.out’ for details.
Running examples in ‘Rlibeemd-Ex.R’ failed
The error most likely occurred in:

> ### Name: ceemdan
> ### Title: CEEMDAN decomposition
> ### Aliases: ceemdan
> 
> ### ** Examples
> 
> imfs <- ceemdan(UKgas, threads = 1)
Error reported by gsl_linalg_solve_tridiag: tried to divide by zero
Error reported by gsl_linalg_solve_tridiag: tried to divide by zero
> # trend extraction
> ts.plot(UKgas, imfs[, ncol(imfs)], col = 1:2, 
+         main = "Quarterly UK gas consumption", ylab = "Million therms")
> 
> # CEEMDAN for logarithmic demand, note that increasing ensemble size 
> # will produce smoother results
> imfs <- ceemdan(log(UKgas), ensemble_size = 50, threads = 1)
Error reported by gsl_linalg_solve_tridiag: tried to divide by zero
> plot(ts.union("log(obs)" = log(UKgas), Seasonal = imfs[, 1], 
+      Irregular = rowSums(imfs[, 2:5]), Trend = imfs[, 6]), 
+      main = "Quarterly UK gas consumption")
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Error in plot.window(...) : need finite 'ylim' values
Calls: plot ... plotts -> plot.default -> localWindow -> plot.window
Execution halted
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: Luminescence
Loading required package: magrittr
Welcome to the R package Luminescence version 0.8.4 [Built: 2018-05-11 15:23:54 UTC]
The NSA: 'O'zapft is.'

Attaching package: 'RLumModel'

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

    model_LuminescenceSignals

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 125-154 (RLumModel_-_Simulating_luminescence_in_Al2O3.Rmd) 
Error: processing vignette 'RLumModel_-_Simulating_luminescence_in_Al2O3.Rmd' failed with diagnostics:
subscript out of bounds
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("rmake")
  Loading required package: rmake
  ── 1. Failure: simple R script (@test-run-simple.R#23)  ────────────────────────
  file.exists(out) isn't true.
  
  ── 2. Error: simple R script (@test-run-simple.R#24)  ──────────────────────────
  cannot open the connection
  1: expect_true(contentGreater(out, dep1)) at testthat/test-run-simple.R:24
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: contentGreater(out, dep1)
  5: read.table(f1)
  6: file(file, "rt")
  
  ── 3. Failure: tasks (@test-run-tasks.R#32)  ───────────────────────────────────
  file.exists(out1) isn't true.
  
  ── 4. Failure: tasks (@test-run-tasks.R#33)  ───────────────────────────────────
  file.exists(out2) isn't true.
  
  ── 5. Error: tasks (@test-run-tasks.R#34)  ─────────────────────────────────────
  cannot open the connection
  1: expect_true(contentGreater(out1, dep11)) at testthat/test-run-tasks.R:34
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: contentGreater(out1, dep11)
  5: read.table(f1)
  6: file(file, "rt")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 60 SKIPPED: 0 FAILED: 5
  1. Failure: simple R script (@test-run-simple.R#23) 
  2. Error: simple R script (@test-run-simple.R#24) 
  3. Failure: tasks (@test-run-tasks.R#32) 
  4. Failure: tasks (@test-run-tasks.R#33) 
  5. Error: tasks (@test-run-tasks.R#34) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    rmd   6.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    java   4.5Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: pwr
Loading required package: psych
Loading required package: RColorBrewer
Loading required package: plotrix

Attaching package: 'plotrix'

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

    rescale

Loading required package: rmcorr
Loading required package: lme4
Loading required package: Matrix
Loading required package: ggplot2

Attaching package: 'ggplot2'

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

    %+%, alpha

Loading required package: merTools
Loading required package: arm
Loading required package: MASS

arm (Version 1.10-1, built: 2018-4-12)

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


Attaching package: 'arm'

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

    rescale

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

    logit, rescale, sim

Loading required package: dplyr

Attaching package: 'dplyr'

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

    select

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'merTools'

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

    ICC

Warning in rmcorr(sub, newX, newY, exampleMat) :
  'sub' coerced into a factor
Warning in rmcorr(sub, newX, newY, exampleMat) :
  'sub' coerced into a factor
Warning in rmcorr(sub, newX, newY, exampleMat2) :
  'sub' coerced into a factor
Warning in rmcorr(sub, newX, newY, exampleMat3) :
  'sub' coerced into a factor
Quitting from lines 523-595 (Combined_paper_figures.Rmd) 
Error: processing vignette 'Combined_paper_figures.Rmd' failed with diagnostics:
Starting values violate bounds
Execution halted
File ‘RMC/libs/RMC.so’:
  Found ‘__1cDstdEcout_’, possibly from ‘std::cout’ (C++)
    Objects: ‘RMC.o’, ‘predict.o’
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘ap.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [8s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rmweather)
  > 
  > test_check("rmweather")
  ── 1. Failure: Test training function (@test_02_rmw_functions.R#53)  ───────────
  model$r.squared not equal to 0.4184627.
  1/1 mismatches
  [1] 0.411 - 0.418 == -0.00721
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 32 SKIPPED: 0 FAILED: 1
  1. Failure: Test training function (@test_02_rmw_functions.R#53) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    java  12.7Mb
Package suggested but not available for checking: ‘rdflib’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    1.7Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    R   9.8Mb
Running examples in ‘robust-Ex.R’ failed
The error most likely occurred in:

> ### Name: overlaidDenPlot.fdfm
> ### Title: Overlaid Density Plot
> ### Aliases: overlaidDenPlot.fdfm
> ### Keywords: hplot
> 
> ### ** Examples
> 
>   data(los, package="robustbase")
>   los.fm <- fit.models(c(Robust = "fitdstnRob", MLE = "fitdstn"),
+                          x = los, densfun = "gamma")

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

Traceback:
 1: Tabgamma(b1, b2, alpha1, alpha2, k, A, maxta, maxtc, maxit, til,     tol)
 2: gammaRob(x, ...)
 3: fitdstnRob(x = los, densfun = "gamma")
 4: eval(model.call, sys.parent())
 5: eval(model.call, sys.parent())
 6: fit.models(c(Robust = "fitdstnRob", MLE = "fitdstn"), x = los,     densfun = "gamma")
An irrecoverable exception occurred. R is aborting now ...
Package suggested but not available for checking: ‘ROI.plugin.symphony’

Package which this enhances but not available for checking: ‘ROI.plugin.cplex’
Installation failed.
See ‘/home/ripley/R/packages/tests32/rpg.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 51-53 (rpivotTableIntroduction.Rmd) 
Error: processing vignette 'rpivotTableIntroduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    extdata  10.9Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/RPostgres.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   4.9Mb
Packages unavailable to check Rd xrefs: ‘keras’, ‘tensorflow’
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/home/ripley/R/packages/tests32/RSEIS.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Installation failed.
See ‘/home/ripley/R/packages/tests32/Rserve.Rcheck/00install.out’ for details.
File ‘rsgcc/libs/rsgcc.so’:
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
    Object: ‘points.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:
  ...
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

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

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

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

    IQR, mad, sd, var, xtabs

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

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


Attaching package: ‘rsolr’

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

    ftable

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

    grouping


Error: processing vignette 'intro.Rnw' failed with diagnostics:
 chunk 3 (label = SolrFrame) 
Error in value[[3L]](cond) : 
  Failed to retrieve schema. rsolr requires schema via REST or as XML from the admin module.
Execution halted
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    3.1Mb
    libs  10.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 2-15 (./children/SETTINGS-knitr.txt) 
Quitting from lines NA-15 (./children/SETTINGS-knitr.txt) 
Error: processing vignette 'aov.Rmd' failed with diagnostics:
object 'params' not found
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs        4.8Mb
    unitTests   1.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 17-22 (minimal-rstan-package.Rmd) 
Error: processing vignette 'minimal-rstan-package.Rmd' failed with diagnostics:
object 'params' not found
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     3.1Mb
    doc   1.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    include   5.6Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Package required but not available: ‘rcdk’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data          1.0Mb
    sample_data   2.7Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/s2.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       1.4Mb
    example   2.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 34-35 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.8Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(scriptexec)
  > 
  > test_check("scriptexec")
  ── 1. Failure: examples: all examples (@test_api_stability.R#156)  ─────────────
  output$status not equal to 0.
  1/1 mismatches
  [1] 1 - 0 == 1
  
  ── 2. Failure: examples: all examples (@test_api_stability.R#157)  ─────────────
  is_string_exists("test_api_stability.R", output$output) not equal to TRUE.
  1 element mismatch
  
  ── 3. Failure: examples: all examples (@test_api_stability.R#162)  ─────────────
  output$status not equal to 0.
  1/1 mismatches
  [1] 1 - 0 == 1
  
  ── 4. Failure: execute: valid command (@test_execute.R#13)  ────────────────────
  output$status not equal to 0.
  1/1 mismatches
  [1] 1 - 0 == 1
  
  ── 5. Failure: execute: valid commands (@test_execute.R#18)  ───────────────────
  output$status not equal to 0.
  1/1 mismatches
  [1] 1 - 0 == 1
  
  ── 6. Failure: execute: runner provided (@test_execute.R#64)  ──────────────────
  output$status not equal to 0.
  1/1 mismatches
  [1] 1 - 0 == 1
  
  ── 7. Failure: execute: print_commands (@test_execute.R#69)  ───────────────────
  output$status not equal to 0.
  1/1 mismatches
  [1] 1 - 0 == 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 62 SKIPPED: 0 FAILED: 7
  1. Failure: examples: all examples (@test_api_stability.R#156) 
  2. Failure: examples: all examples (@test_api_stability.R#157) 
  3. Failure: examples: all examples (@test_api_stability.R#162) 
  4. Failure: execute: valid command (@test_execute.R#13) 
  5. Failure: execute: valid commands (@test_execute.R#18) 
  6. Failure: execute: runner provided (@test_execute.R#64) 
  7. Failure: execute: print_commands (@test_execute.R#69) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data            1.5Mb
    vignette_data   2.1Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   1.1Mb
    doc    1.3Mb
Running examples in ‘Segmentor3IsBack-Ex.R’ failed
The error most likely occurred in:

> ### Name: BestSegmentation
> ### Title: BestSegmentation
> ### Aliases: BestSegmentation
> ### Keywords: R-package PDPA Segmentation
> 
> ### ** Examples
> 
> require(Segmentor3IsBack);
> N=2000 
> x=rnbinom(3*N,size=1.3,prob=rep(c(0.7,0.2,0.01),each=N));
> res=Segmentor(data=x,model=3,Kmax=10, keep=TRUE);  
Error in cumsum(datasize)[breaks[k, 1:k]] : 
  only 0's may be mixed with negative subscripts
Calls: Segmentor -> Segmentor.default
Execution halted
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    6.3Mb
    libs   1.0Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data        1.7Mb
    sequences   2.1Mb
Running examples in ‘seqminer-Ex.R’ failed
The error most likely occurred in:

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

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

$geneFileFormat
[1] "refFlat"

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

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

$upstreamRange
[1] 50

$downstreamRange
[1] 50

$spliceIntoExon
[1] 3

$spliceIntoIntron
[1] 8

$bed
NULL

$genomeScore
NULL

$tabix
NULL

$indexOutput
[1] FALSE

$inputFormat
[1] "vcf"

$checkReference
[1] TRUE

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

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

Traceback:
 1: annotateGene(param, c("1", "1"), c(3, 5), c("A", "C"), c("G",     "C"))
An irrecoverable exception occurred. R is aborting now ...
Package suggested but not available for checking: ‘RPostgres’
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    doc     11.1Mb
    sqlite   1.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 195-198 (sf5.Rmd) 
Error: processing vignette 'sf5.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.9Mb
Error in re-building vignettes:
  ...
Warning in engine$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 13-28 (SGPdata.Rmd) 
Error: processing vignette 'SGPdata.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    doc   3.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-29 (SGP.Rmd) 
Error: processing vignette 'SGP.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    www   7.6Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    www   7.1Mb
Error in re-building vignettes:
  ...
Warning in engine$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 89-90 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.7Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
Package required but not available: ‘rhdf5’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 123-124 (Report_r1.Rmd) 
Error: processing vignette 'Report_r1.Rmd' failed with diagnostics:
unused argument (options = options)
Execution halted
Running examples in ‘SMCP-Ex.R’ failed
The error most likely occurred in:

> ### Name: SMCP
> ### Title: Smoothed minimax concave penalization (SMCP) method for
> ###   genome-wide association studies.
> ### Aliases: SMCP sp
> ### Keywords: model fitting
> 
> ### ** Examples
> 
> x=matrix(rnorm(100*20),100,20)
> y=rnorm(100)
> fit=SMCP(x,y,0.3,0.3,3)
> #solution path for this data
> s.p=sp(x,y,0.3,10,0.05,3)
Error in SMCP(x, y, alpha, delta * i, gamma) : 
  NA/NaN/Inf in foreign function call (arg 6)
Calls: sp -> SMCP
Execution halted
Errors in running code in vignettes:
when running code in ‘SNPtools.Rnw’
  ...

> library(SNPtools)
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

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

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

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

    IQR, mad, sd, var, xtabs

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

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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

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

    expand.grid

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

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

    strsplit

Loading required package: Rsamtools

> snp.file = "http://cgd.jax.org/tools/SNPtools/Build38/sanger.snps.NCBI38.txt.gz"

> mgi.file = "http://cgd.jax.org/tools/SNPtools/MGI/MGI.20130305.sorted.txt.gz"

> available.strains = get.strains(snp.file)

  When sourcing ‘SNPtools.R’:
Error: [khttp_connect_file] fail to open file (HTTP code: 404).
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
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: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

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

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

    IQR, mad, sd, var, xtabs

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

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

Identifing all possible orderings..
Total run time: 1.76 secs
Identifing all possible orderings..
Total run time: 1.74 secs
Quitting from lines 346-347 (SourceSet.Rmd) 
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
Running ‘test-all.R’ [370s/505s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("SpaDES.core")
  Loading required package: SpaDES.core
  Loading required package: quickPlot
  Loading required package: reproducible
  
  Attaching package: 'reproducible'
  
  The following object is masked from 'package:testthat':
  
      %>%
  
    Using cached copy of .inputObjects event in test module
    Using cached copy of .inputObjects event in test module
  ── 1. Failure: simList object initializes correctly (@test-simList.R#17)  ──────────────────────────
  length(out) not equal to 75.
  1/1 mismatches
  [1] 73 - 75 == -2
  
    Using cached copy of burn event in fireSpread module
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 349 SKIPPED: 33 FAILED: 1
  1. Failure: simList object initializes correctly (@test-simList.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

Loading required package: quickPlot
Loading required package: reproducible

Attaching package: 'reproducible'

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

    %>%

Loading required package: RColorBrewer
Loading required package: raster
Loading required package: sp
Loading required package: grid

Attaching package: 'grid'

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

    gpar

Quitting from lines 357-361 (ii-modules.Rmd) 
Error: processing vignette 'ii-modules.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 20-30 (intro_sparkline.Rmd) 
Error: processing vignette 'intro_sparkline.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Quitting from lines 249-254 (SparseIndexTracking-vignette.Rmd) 
Error: processing vignette 'SparseIndexTracking-vignette.Rmd' failed with diagnostics:
The engine "block2" is for R Markdown only
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/spass.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/spatialwarnings.Rcheck/00install.out’ for details.
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    R      5.2Mb
    doc    5.0Mb
    help   5.0Mb
    libs   1.3Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data     2.6Mb
    shapes   3.9Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.6Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
Running examples in ‘sptemExp-Ex.R’ failed
The error most likely occurred in:

> ### Name: extractVNC4
> ### Title: Extract Values for Point from NC4 Image
> ### Aliases: extractVNC4
> ### Keywords: ~kwd1 ~kwd2
> 
> ### ** Examples
> 
> 
> data("samplepnt")
> nc4File=file.path(system.file(package = "sptemExp"), "extdata", "ancdata.nc4")
> ncin0=ncdf4::nc_open(nc4File)
Error in R_nc4_open: NetCDF: HDF error
Error in ncdf4::nc_open(nc4File) : 
  Error in nc_open trying to open file /home/ripley/R/Lib32/sptemExp/extdata/ancdata.nc4
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    lsndata   2.9Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    include   5.7Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   5.5Mb
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.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'gridExtra'

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

    combine

Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=georgia&zoom=5&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false
Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=georgia&sensor=false
Warning: geocode failed with status OVER_QUERY_LIMIT, location = "georgia"
Quitting from lines 220-233 (Details.Rmd) 
Error: processing vignette 'Details.Rmd' failed with diagnostics:
arguments imply differing number of rows: 0, 1
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R          2.2Mb
    datasets   2.7Mb
Package which this enhances but not available for checking: ‘tmap’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Building shared library for Rcpp code chunk...
make: Warning: Ignoring DistributedMake -j option
make: Warning: Ignoring DistributedMake -j option
make: Fatal error: Don't know how to make target `file12c4867c9d.o'
Current working directory /tmp/RtmpQjaGLa/sourceCpp-i386-pc-solaris2.10-0.12.16/sourcecpp_12c4a01c6e
`/home/ripley/R/gcc/etc/Makeconf' is up to date.
`/home/ripley/R/gcc/etc/Makeconf' is up to date.
Quitting from lines 60-85 (strider.Rmd) 
Error: processing vignette 'strider.Rmd' failed with diagnostics:
Error occurred building shared library.
Execution halted
installed size is 33.1Mb
  sub-directories of 1Mb or more:
    libs  32.3Mb
Error in re-building vignettes:
  ...
Warning in engine$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 61-64 (stRvignette.Rmd) 
Error: processing vignette 'stRvignette.Rmd' failed with diagnostics:
Process terminated
Execution halted
Package suggested but not available for checking: ‘phyloseq’
Error in .requirePackage(package) : 
    unable to find required package 'phyloseq'
  Calls: <Anonymous> ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
  Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/subprocess.Rcheck/00install.out’ for details.
Running examples in ‘subspaceMOA-Ex.R’ failed
The error most likely occurred in:

> ### Name: DSC_HDDStream
> ### Title: Density-based Projected Clustering over High-Dimensional Data
> ### Aliases: DSC_HDDStream
> 
> ### ** Examples
> 
> dsc <- DSC_HDDStream()
Error in rJava::.jcall("moa/r_interface/OneStageClusterer", returnSig = "Lmoa/r_interface/RCompatibleDataStreamClusterer;",  : 
  RcallMethod: cannot determine object class
Calls: DSC_HDDStream -> <Anonymous>
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    doc    2.8Mb
    help   1.0Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   3.4Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
Running examples in ‘svd-Ex.R’ failed
The error most likely occurred in:

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

 *** caught segfault ***
address 1f0, cause 'memory not mapped'

Traceback:
 1: ztrlan.eigen(h, neig = 1)
An irrecoverable exception occurred. R is aborting now ...
File ‘svmpath/libs/svmpath.so’:
  Found ‘__f90_close’, possibly from ‘close’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘__f90_eifr’, possibly from ‘read’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi30spec.o’, ‘mi36mps.o’, ‘mi40bfil.o’
  Found ‘__f90_esfr’, possibly from ‘read’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi30spec.o’, ‘mi35mps.o’,
      ‘mi36mps.o’, ‘mi40bfil.o’
  Found ‘__f90_esfw’, possibly from ‘print’ (Fortran), ‘write’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’
  Found ‘__f90_open’, possibly from ‘open’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘__f90_rewind’, possibly from ‘rewind’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi10unix.o’, ‘mi35mps.o’, ‘mi40bfil.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 examples in ‘swapClass-Ex.R’ failed
The error most likely occurred in:

> ### Name: nullModel
> ### Title: SwapClass null model
> ### Aliases: nullModel
> 
> ### ** Examples
> 
> MAT=matrix(sample(0:3,50*20,replace=TRUE,prob=c(.7,.1,.1,.1)),ncol=20)
> 
> #Generation of null communities
> NULL_MATS=nullModel(MAT)

 *** caught segfault ***
address fd8105f0, cause 'memory not mapped'

Traceback:
 1: .Primitive(".C")(<pointer: fd8105f0>, mat0 = as.double(mat0),     mat = as.double(mat), nsim = as.integer(nsim), recursive = as.integer(recursive),     nr = as.integer(nr), nc = as.integer(nc), Kb = as.integer(Kb),     Kt = as.integer(Kt), strata = as.integer(strata), perms = as.double(perms))
 2: swapClass_swapC(mat0 = as.double(mat0), mat = as.double(mat),     nsim = as.integer(nsim), recursive = as.integer(recursive *         1), nr = as.integer(nr), nc = as.integer(nc), Kb = as.integer(burnin),     Kt = as.integer(thin), strata = as.integer(strata), perms = as.double(perms))
 3: swapClass_swapC(mat0 = as.double(mat0), mat = as.double(mat),     nsim = as.integer(nsim), recursive = as.integer(recursive *         1), nr = as.integer(nr), nc = as.integer(nc), Kb = as.integer(burnin),     Kt = as.integer(thin), strata = as.integer(strata), perms = as.double(perms))
 4: nullModel(MAT)
An irrecoverable exception occurred. R is aborting now ...
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.3Mb
Running examples in ‘tabplot-Ex.R’ failed
The error most likely occurred in:

> ### Name: -.tabplot
> ### Title: Compare two tableplots (experimental)
> ### Aliases: -.tabplot
> 
> ### ** Examples
> 
> # load diamonds dataset from ggplot2
> require(ggplot2)
Loading required package: ggplot2
> data(diamonds)
> 
> # calculate normalized prices to be used as sample probabilities
> price.norm <- with(diamonds, price / max(diamonds$price))
> 
> # draw samples
> exp.diamonds <- diamonds[sample(1:nrow(diamonds), size=10000, prob=price.norm, replace=TRUE),]
> chp.diamonds <- diamonds[sample(1:nrow(diamonds), size=10000, prob=1-price.norm, replace=TRUE),]
> 
> tp1 <- tableplot(exp.diamonds)
Error in ff(initdata = initdata, length = length, levels = levels, ordered = ordered,  : 
  write error
Calls: tableplot ... tablePrepare -> lapply -> FUN -> clone -> clone.ff -> assign -> ff
Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    sql   8.9Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    3.9Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    3.8Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   8.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    rda    4.1Mb
Package suggested but not available for checking: ‘Rblpapi’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
Package unavailable to check Rd xrefs: ‘Rblpapi’
Error in re-building vignettes:
  ...
Warning in engine$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: ggplot2

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

sh: nproc:  not found
Quitting from lines 111-113 (Tigger-Vignette.Rmd) 
Error: processing vignette 'Tigger-Vignette.Rmd' failed with diagnostics:
error in running command: 'Illegal seek'
Execution halted
Running examples in ‘TimeMachine-Ex.R’ failed
The error most likely occurred in:

> ### Name: mu.mle
> ### Title: Maximum-Likelihood Estimation of the Mutation Rate
> ### Aliases: mu.mle
> 
> ### ** Examples
> 
> # Load example dataset
> data(pdm)
> transitions <- full.transitions(pdm$unitary.transitions, pdm$loci)
> pi <- stationary.dist(transitions)
> 
> mu.int <- c(0.1, 10)
> samples <- 10
> 
> # MLE of the mutation rate for a single target population size
> n <- 10
> mle.res <- mu.mle(transitions, pi, pdm$population, n, mu.int, samples)
Error: C stack usage  189040340 is too close to the limit
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc         3.9Mb
    rmarkdown   1.9Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    3.4Mb
Error in re-building vignettes:
  ...
Warning in engine$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 13-26 (toOrdinal.Rmd) 
Error: processing vignette 'toOrdinal.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
File ‘tpr/libs/tpr.so’:
  Found ‘__1cDstdEcerr_’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    2.9Mb
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: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: ggplot2

Attaching package: 'trackeR'

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

    append

Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=57.157231,-2.104296&zoom=13&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false
Quitting from lines 96-97 (TourDetrackeR.Rmd) 
Error: processing vignette 'TourDetrackeR.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Package required but not available: ‘phyloseq’

Package suggested but not available for checking: ‘adaptiveGPCA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.4Mb
  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: ape
Loading required package: ade4
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'

   /// adegenet 2.1.1 is loaded ////////////

   > overview: '?adegenet'
   > tutorials/doc/questions: 'adegenetWeb()' 
   > bug reports/feature requests: adegenetIssues()



Attaching package: 'adegenet'

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

    AICc

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

    .render.server.info

Quitting from lines 136-138 (DengueVignette.Rmd) 
Error: processing vignette 'DengueVignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/trialr.Rcheck/00install.out’ for details.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(trustOptim)
  > 
  > test_check("trustOptim")
  Beginning optimization
  
  Iteration has terminated
  
  iter            f           nrm_gr                     status
    50       0.000000       0.000000                    Success
  
  Beginning optimization
  
  Iteration has terminated
  
  iter            f           nrm_gr                     status
   128       0.000000       0.000000                    Success
  
  Beginning optimization
  
  Iteration has terminated
  
  iter            f           nrm_gr                     status
   287       0.000000       0.000000Radius of trust region is less than stop.trust.radius
  
  ── 1. Failure: Rosenbrock (@test_rosenbrock.R#67)  ─────────────────────────────
  opt0\$status does not match "Success".
  Actual value: "Radius of trust region is less than stop\.trust\.radius"
  
  Beginning optimization
  
  Iteration has terminated
  
  iter            f           nrm_gr                     status
    65       0.000000       0.000000                    Success
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 15 SKIPPED: 0 FAILED: 1
  1. Failure: Rosenbrock (@test_rosenbrock.R#67) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: TTR
Version 0.4-0 included new data defaults. See ?getSymbols.
'getSymbols' currently uses auto.assign=TRUE by default, but will
use auto.assign=FALSE in 0.5-0. You will still be able to use
'loadSymbols' to automatically load data. getOption("getSymbols.env")
and getOption("getSymbols.auto.assign") will still be checked for
alternate defaults.

This message is shown once per session and may be disabled by setting 
options("getSymbols.warning4.0"=FALSE). See ?getSymbols for details.


WARNING: There have been significant changes to Yahoo Finance data.
Please see the Warning section of '?getSymbols.yahoo' for details.

This message is shown once per session and may be disabled by setting
options("getSymbols.yahoo.warning"=FALSE).
Quitting from lines 37-64 (TSstudio_Intro.Rmd) 
Error: processing vignette 'TSstudio_Intro.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    doc         5.5Mb
    dummydata   1.5Mb
    libs        1.9Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/unrtf.Rcheck/00install.out’ for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc   8.2Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    data  14.9Mb
installed size is 29.8Mb
  sub-directories of 1Mb or more:
    data  29.1Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   6.5Mb
Running examples in ‘utiml-Ex.R’ failed
The error most likely occurred in:

> ### Name: ctrl
> ### Title: CTRL model for multi-label Classification
> ### Aliases: ctrl
> 
> ### ** Examples
> 
> model <- ctrl(toyml, "RANDOM")
Error in ctrl(toyml, "RANDOM") : 
  There are no installed package 'FSelector' to use CTRL multi-label classifier
Execution halted
Running ‘testthat.R’ [20s/24s]
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. Error: CTRL (@test_brclassifiers.R#94)  ──────────────────────────────────
  There are no installed package 'FSelector' to use CTRL multi-label classifier
  1: ctrl(train, "RANDOM") at testthat/test_brclassifiers.R:94
  2: stop(paste("There are no installed package 'FSelector' to use CTRL", "multi-label classifier"))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1120 SKIPPED: 21 FAILED: 1
  1. Error: CTRL (@test_brclassifiers.R#94) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘uuid/libs/uuid.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘gen_uuid.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘gen_uuid.o’

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.
Quitting from lines 92-93 (regress_intro.Rmd) 
Error: processing vignette 'regress_intro.Rmd' failed with diagnostics:
object 'ttodth' not found
Execution halted
Error in re-building vignettes:
  ...
Loading required package: randomForest
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.

Attaching package: 'randomForest'

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

    importance

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

    margin

Loading required package: parallel
Quitting from lines 123-126 (varrank.Rmd) 
Error: processing vignette 'varrank.Rmd' failed with diagnostics:
there is no package called 'FSelector'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 24-36 (intro_to_vegalite.Rmd) 
Error: processing vignette 'intro_to_vegalite.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    doc    1.3Mb
    help   2.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 157-163 (using_visdat.Rmd) 
Error: processing vignette 'using_visdat.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc           4.8Mb
    htmlwidgets   4.0Mb
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 22-27 (Introduction-to-visNetwork.Rmd) 
Error: processing vignette 'Introduction-to-visNetwork.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    extdata  11.3Mb
Found the following significant warnings:
  "predict.c", line 112: warning: improper pointer/integer combination: op "<"
See ‘/home/ripley/R/packages/tests32/VLMC.Rcheck/00install.out’ for details.
File ‘waffect/libs/waffect.so’:
  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.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   3.9Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/wand.Rcheck/00install.out’ for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   4.5Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc  12.3Mb
Package suggested but not available for checking: ‘rcdk’
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    client  10.1Mb
    doc      1.1Mb
Package suggested but not available for checking: ‘iptools’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 37-39 (wordcloud.Rmd) 
Error: processing vignette 'wordcloud.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 218-220 (wflow-01-getting-started.Rmd) 
Error: processing vignette 'wflow-01-getting-started.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
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    data  13.4Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  11.9Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    data  14.3Mb
Package required but not available: ‘x12’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/ripley/R/packages/tests32/x12.Rcheck/00install.out’ for details.
Package unavailable to check Rd xrefs: ‘RSiena’
Installation failed.
See ‘/home/ripley/R/packages/tests32/xgboost.Rcheck/00install.out’ for details.
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    java  19.3Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    java  10.9Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R             1.0Mb
    exampleData   1.5Mb
    examples      4.6Mb
Running examples in ‘XRJulia-Ex.R’ failed
The error most likely occurred in:

> ### Name: JuliaFunction-class
> ### Title: Proxy Objects in R for Julia Functions
> ### Aliases: JuliaFunction JuliaFunction-class
> ###   initialize,JuliaFunction-method
> 
> ### ** Examples
> 
> if(findJulia(test = TRUE)) {
+   set.seed(228)
+   x <- matrix(rnorm(1000),20,5)
+   xm <- juliaSend(x)
+   svdJ <- JuliaFunction("svdfact")
+   sxm <- svdJ(xm)
+   sxm
+ }
sh: no:  not found
Error in base::system(cmd, intern = TRUE) : 
  error in running command: 'Illegal seek'
Calls: findJulia -> testJSON -> <Anonymous>
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.
date	lon	lat	lowLon	higLon	lowLat	higLat
4/23/2003	203.899	19.664	203.899	203.899	19.664	19.664
4/24/2003	204.151	19.821	203.912597	204.389403	18.78051934	20.86148066
4/30/2003	203.919	20.351	203.6793669	204.1586331	18.79728188	21.90471812
5/1/2003	204.229	20.305	203.9943343	204.4636657	18.90440013	21.70559987
Quitting from lines 1055-1057 (Usingxtractomatic.Rmd) 
Error: processing vignette 'Usingxtractomatic.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/zstdr.Rcheck/00install.out’ for details.
Running ‘testthat.r’ [8s/9s]
Running the tests in ‘tests/testthat.r’ failed.
Complete output:
  > library(testthat)
  > library(adeba)
  > test_check("adeba")
  ── 1. Failure: Expected behaviour (@test-adeba.r#17)  ──────────────────────────
  `volume` is not strictly more than 0.97. Difference: -0.00282
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 8 SKIPPED: 0 FAILED: 1
  1. Failure: Expected behaviour (@test-adeba.r#17) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  ADM3.c:37:12: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  ADM3.c:37:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  ADM3.c:54:21: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/ADM3.Rcheck/00install.out’ for details.
Found the following significant warnings:
  WARNING: An illegal reflective access operation has occurred
  WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/tmp/RtmpW6UlFG/RLIBS_654495ca959/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
  WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
  WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
  WARNING: All illegal access operations will be denied in a future release
  WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/tmp/RtmpW6UlFG/RLIBS_654471d3787f/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/ANLP.Rcheck/00install.out’ for details.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  pa.c:247:2: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/audio.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Bayesthresh.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Error in re-building vignettes:
  ...
Loading required package: leaps
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 579 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running ‘texi2dvi’ on ‘SimExperimentBICq.tex’ failed.
LaTeX errors:
! Package inputenc Error: Invalid UTF-8 byte 150.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/biclust.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Boom.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/BoomSpikeSlab.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/CircStats.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  date.cpp:173:53: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/ConvCalendar.Rcheck/00install.out’ for details.
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
             user system elapsed
text_win_rqa 7.13  0.044  10.463
Found the following significant warnings:
  instabCorrection.cpp:34:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/cstab.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/ctsem.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  convert_util.cpp:299:20: warning: null destination pointer [-Wformat-overflow=]
  convert_util.cpp:307:20: warning: null destination pointer [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/DatABEL.Rcheck/00install.out’ for details.
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
  Warning: 'cBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
     user system elapsed
sdp 6.393  0.024   7.299
'library' or 'require' call to ‘UScensus2010’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘JavaGD’ ‘OpenStreetMap’ ‘maptools’ ‘rgdal’ ‘scales’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
java.lang.NullPointerException
	at org.rosuda.deducer.Deducer.idleEval(Deducer.java:611)
	at org.rosuda.deducer.data.DataViewerController.refreshData(DataViewerController.java:212)
	at org.rosuda.deducer.data.DataRefresher.run(DataViewerController.java:252)
	at java.base/java.lang.Thread.run(Thread.java:844)
Error in re-building vignettes:
  ...
Warning: Removed 92 rows containing missing values (geom_path).
Warning: Removed 71 rows containing missing values (geom_path).
Warning: Removed 120 rows containing missing values (geom_path).
Warning: Removed 125 rows containing missing values (geom_path).
Warning: Removed 30 rows containing missing values (geom_path).
May 17, 2018 7:52:56 PM com.github.fommil.netlib.BLAS <clinit>
WARNING: Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS
May 17, 2018 7:52:57 PM com.github.fommil.netlib.BLAS <clinit>
WARNING: Failed to load implementation from: com.github.fommil.netlib.NativeRefBLAS
May 17, 2018 7:52:57 PM com.github.fommil.netlib.LAPACK <clinit>
WARNING: Failed to load implementation from: com.github.fommil.netlib.NativeSystemLAPACK
May 17, 2018 7:52:57 PM com.github.fommil.netlib.LAPACK <clinit>
WARNING: Failed to load implementation from: com.github.fommil.netlib.NativeRefLAPACK
Killed
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/dhglm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/diffusionMap.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(earthtones)
  > 
  > test_check("earthtones")
  ── 1. Error: returns normal (@test-earth.R#5)  ─────────────────────────────────
  cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=50.759,-125.673&zoom=11&size=640x640&scale=2&maptype=satellite&language=en-EN&sensor=false'
  1: expect_is(get_earthtones(), "palette") at testthat/test-earth.R:5
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: get_earthtones()
  5: ggmap::get_map(location = c(longitude, latitude), maptype = "satellite", zoom = zoom, 
         ...)
  6: get_googlemap(center = location, zoom = zoom, maptype = maptype, scale = scale, messaging = messaging, 
         urlonly = urlonly, force = force, filename = filename, color = color, language = language)
  7: download.file(url, destfile = tmp, quiet = !messaging, mode = "wb")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 3 SKIPPED: 0 FAILED: 1
  1. Error: returns normal (@test-earth.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=36.094994,-111.837962&zoom=12&size=640x640&scale=2&maptype=satellite&language=en-EN&sensor=false
Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=24.2,-77.88&zoom=11&size=640x640&scale=2&maptype=satellite&language=en-EN&sensor=false
Quitting from lines 43-44 (earthtones.rmd) 
Error: processing vignette ‘earthtones.rmd’ failed with diagnostics:
cannot open URL ‘http://maps.googleapis.com/maps/api/staticmap?center=37.89,-122.28&zoom=11&size=640x640&scale=2&maptype=satellite&language=en-EN&sensor=false’
Execution halted
Error in re-building vignettes:
  ...
Processing PubMed data .................................................. done!
Processing PubMed data .Quitting from lines 122-133 (easyPM_vignette_pdf.Rmd) 
Error: processing vignette ‘easyPM_vignette_pdf.Rmd’ failed with diagnostics:
subscript out of bounds
Execution halted
Found the following significant warnings:
  newmat5.cpp:494:69: warning: throw will always call terminate() [-Wterminate]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/EditImputeCont.Rcheck/00install.out’ for details.
Running examples in ‘elrm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.elrm
> ### Title: Plot Diagnostics for an elrm Object
> ### Aliases: plot.elrm
> ### Keywords: methods
> 
> ### ** Examples
> 
> # Drug dataset example with sex and treatment as the variables of interest
> data(drugDat);
> drug.elrm = elrm(formula=recovered/n~sex+treatment, interest=~sex+treatment, r=4, 
+ 	iter=50000, burnIn=1000, dataset=drugDat);
Generating the Markov chain ...
Progress:   0%  Progress:   5%  Progress:  10%  Progress:  15%  Progress:  20%  Progress:  25%  Progress:  30%  Progress:  35%  Progress:  40%  Progress:  45%  Progress:  50%  Progress:  55%  Progress:  60%  Progress:  65%  Progress:  70%  Progress:  75%  Progress:  80%  Progress:  85%  Progress:  90%  Progress:  95%  Progress: 100%  
Generation of the Markov Chain required 5 secs
Conducting inference ...
Inference required 3 secs
> 
> # Plot the sampled values of the sufficient statistic for each parameter of 
> # interest (sex and treatment)
> plot(drug.elrm,p=0.5,ask=TRUE);
Error in plot.default(drug.elrm, p = 0.5, ask = TRUE) : 
  argument 2 matches multiple formal arguments
Calls: plot
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/EnvStats.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  optile.c:3122:26: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3127:26: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3189:16: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3192:16: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3340:28: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3353:28: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3408:16: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3411:16: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/extracat.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-release-gcc/Work/PKGS/FastRWeb.Rcheck/00install.out’ for details.
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
  Warning: 'cBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
     user system elapsed
fcr 8.126  0.082   9.987
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/fpc.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/frailtyHL.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running examples in ‘funcy-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: funcyOutList-class
> ### Title: Class '"funcyOutList"'
> ### Aliases: funcyOutList-class funcyOutList
> ### Keywords: classes
> 
> ### ** Examples
> 
> set.seed(2808)
> ds <- sampleFuncy(obsNr=30, k=4, timeNr=7)
> data <- Data(ds)
> clusters <- Cluster(ds)
> 
> res <- funcit(data=data, clusters=clusters, seed=2808,
+               methods=1:5, k=4, parallel=TRUE)
4 : * * *4 :Warning in funclustWrapper(data = data, k = k, reg = reg, regTime = regTime,  :
  It is not possible to set a seed for method funclust.
 *Loading required namespace: funHDDC
 * *
Warning in funHDDCWrapper(data = data, k = k, reg = reg, regTime = regTime,  :
  Clustering with 4 classes is not possible. 3 clusters are used!
Warning in funHDDCWrapper(data, k, reg, regTime, funcyCtrlMbc, model = "AkBkQkDk",  :
  Clustering with 3 classes is not possible. 2 clusters are used!
Warning in funHDDCWrapper(data, k, reg, regTime, funcyCtrlMbc, model = "AkBkQkDk",  :
  Clustering with 2 classes is not possible. 1 clusters are used!
Warning in funHDDCWrapper(data, k, reg, regTime, funcyCtrlMbc, model = "AkBkQkDk",  :
  Clustering with 1 classes is not possible. 0 clusters are used!
Warning in Funclustering::funclust(fd = fd, K = k, thd = thd, increaseDimension = increaseDimension,  :
  Convergence of the algorithm to a solution with at least one empty cluster.
            Restart or a choose a smaller value for K = 4

Error in funcit(data = data, clusters = clusters, seed = 2808, methods = 1:5,  : 
  Method funHDDC : Clustering for this data not possible.
Execution halted
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
      user system elapsed
fpca 8.038  0.032   9.948
Found the following significant warnings:
  convert_util.cpp:299:20: warning: null destination pointer [-Wformat-overflow=]
  convert_util.cpp:307:20: warning: null destination pointer [-Wformat-overflow=]
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/GenABEL.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running ‘testthat.R’ [4s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ggvis)
  > 
  > test_check("ggvis")
  ── 1. Error: (unknown) (@test-specs.r#5)  ──────────────────────────────────────
  no applicable method for 'group_by_' applied to an object of class "ggvis"
  1: suppressMessages(sys.source(spec, envir = new.env(), chdir = TRUE)) at testthat/test-specs.r:5
  2: withCallingHandlers(expr, message = function(c) invokeRestart("muffleMessage"))
  3: sys.source(spec, envir = new.env(), chdir = TRUE)
  4: eval(exprs[i], envir)
  5: eval(exprs[i], envir)
  6: mtcars %>% ggvis(x = ~wt, stroke = ~cyl) %>% group_by(cyl) %>% layer_freqpolys(width = 1) %>% 
         save_spec("layer/freqpoly-grouped.json")
  7: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  8: eval(quote(`_fseq`(`_lhs`)), env, env)
  9: eval(quote(`_fseq`(`_lhs`)), env, env)
  10: `_fseq`(`_lhs`)
  11: freduce(value, `_function_list`)
  12: function_list[[i]](value)
  13: group_by(., cyl)
  14: group_by.default(., cyl)
  15: group_by_(.data, .dots = compat_as_lazy_dots(...), add = add)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 447 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-specs.r#5) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  calculategphmm.cpp:217:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/gphmm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rothmana.cpp:123:15: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/graphicalVAR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  _t_array_properties.cpp:10:13: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/gRbase.Rcheck/00install.out’ for details.
Running examples in ‘h2o-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: aaa
> ### Title: Starting H2O For examples
> ### Aliases: aaa
> 
> ### ** Examples
> 
> if(Sys.info()['sysname'] == "Darwin" && Sys.info()['release'] == '13.4.0'){
+  quit(save="no")
+ }else{
+  h2o.init(nthreads = 2)
+ }

H2O is not running yet, starting it now...

Note:  In case of errors look at the following log files:
    /tmp/RtmpjYeuuj/h2o_UnknownUser_started_from_r.out
    /tmp/RtmpjYeuuj/h2o_UnknownUser_started_from_r.err

openjdk version "10.0.1" 2018-04-17
OpenJDK Runtime Environment (build 10.0.1+10-Debian-4)
OpenJDK 64-Bit Server VM (build 10.0.1+10-Debian-4, mixed mode)

Starting H2O JVM and connecting: ............................................................ 
[1] "localhost"
[1] 54321
[1] TRUE
[1] -1
[1] "Failed to connect to localhost port 54321: Connection refused"
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0curl: (7) Failed to connect to localhost port 54321: Connection refused
[1] 7
Error in h2o.init(nthreads = 2) : 
  H2O failed to start, stopping execution.
Execution halted
Found the following significant warnings:
  regTree.c:317:38: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  regTree.c:336:38: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/iJRF.Rcheck/00install.out’ for details.
Found the following significant warnings:
  transformations.cpp:274:15: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/imager.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [1s/1s]
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)  ────────────────────────────
  no applicable method for 'h5write' applied to an object of class "character"
  1: test_read_write_read(f) at testthat/test_read-write-read.R:8
  2: qwrite(x, outfile) at /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/io.Rcheck/tests/testthat/helper.R:48
  3: .qwrite(x, if (is.filename(file)) as.character(file) else file, if (is.null(type)) .infer_file_type(file) else type, 
         ...)
  4: qwrite.hdf5(x, if (is.filename(file)) as.character(file) else file, if (is.null(type)) .infer_file_type(file) else type, 
         ...)
  5: .write_hdf5_array(x, file)
  6: rhdf5::h5write("array", file, "type")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_read-write-read.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/ldat.Rcheck/00install.out’ for details.
Found the following significant warnings:
  LBLasso.c:98:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  LBlogistic.c:100:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  LBmultilogistic.c:110:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  ggm.c:69:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  ising.c:83:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  potts.c:99:15: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Libra.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [13s/80s]
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/Rtmp8Jrpzh/h2o_UnknownUser_started_from_r.out
      /tmp/Rtmp8Jrpzh/h2o_UnknownUser_started_from_r.err
  
  openjdk version "10.0.1" 2018-04-17
  OpenJDK Runtime Environment (build 10.0.1+10-Debian-4)
  OpenJDK 64-Bit Server VM (build 10.0.1+10-Debian-4, mixed mode)
  
  Starting H2O JVM and connecting: ............................................................ 
  [1] "localhost"
  [1] 54321
  [1] TRUE
  [1] -1
  [1] "Failed to connect to localhost port 54321: Connection refused"
    % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                   Dload  Upload   Total   Spent    Left  Speed
  
    0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0curl: (7) Failed to connect to localhost port 54321: Connection refused
  [1] 7
  ── 1. Error: (unknown) (@test-h2o.R#4)  ────────────────────────────────────────
  H2O failed to start, stopping execution.
  1: h2o.init() at testthat/test-h2o.R:4
  2: stop("H2O failed to start, stopping execution.")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 22 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-h2o.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  mue_nelmC.cpp:147:15: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  mue_nelmC.cpp:185:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  mue_nelmC.cpp:230:22: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  mue_nrmC.cpp:135:15: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  mue_nrmC.cpp:173:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  mue_nrmC.cpp:218:22: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/mcIRT.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/mdhglm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  NMix_RJMCMCcombine.cpp:422:14: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/mixAK.Rcheck/00install.out’ for details.
Found the following significant warnings:
  mixCpp.cpp:122:19: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  mixCpp.cpp:167:19: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  mixCpp.cpp:399:22: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  mixCpp.cpp:444:22: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/mixR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  confusionMatrix_.cpp:10:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:12:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:14:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:16:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:57:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:104:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:106:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:108:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:110:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/ModelMetrics.Rcheck/00install.out’ for details.
Found the following significant warnings:
  weiszfeldIterations.cpp:195:48: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Mposterior.Rcheck/00install.out’ for details.
Found the following significant warnings:
  newmat5.cpp:525:69: warning: throw will always call terminate() [-Wterminate]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/MSBVAR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  evallf.c:86:23: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/mvnmle.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [68s/87s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mvtboost)
  > 
  > test_check("mvtboost")
  ── 1. Failure: covex-E (@test_covex.R#54)  ─────────────────────────────────────
  covex[covex > 0.01] not equal to rep(a, 3).
  1/3 mismatches
  [2] 0.901 - 1.02 == -0.123
  0.9
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 174 SKIPPED: 2 FAILED: 1
  1. Failure: covex-E (@test_covex.R#54) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(nima)
  nima: Nima Hejazi's R Toolbox
  Version: 0.4.5
  > 
  > test_check("nima")
  ── 1. Failure: attrnames finds the names of the attributes of a data frame (@tes
  attrnames(y) not equal to c("names", "row.names", "class").
  2/3 mismatches
  x[2]: "class"
  y[2]: "row.names"
  
  x[3]: "row.names"
  y[3]: "class"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 21 SKIPPED: 0 FAILED: 1
  1. Failure: attrnames finds the names of the attributes of a data frame (@test-attribute_names.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘OAIHarvester-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: size
> ### Title: OAI-PMH Repository Size
> ### Aliases: oaih_size
> 
> ### ** Examples
> 
> oaih_size("http://www.jstatsoft.org/oai")
Error in curl_fetch_memory(url) : 
  Timeout was reached: Resolving timed out after 10000 milliseconds
Calls: oaih_size
Execution halted
Running ‘testthat.R’ [17s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > test_check("openxlsx")
  Loading required package: openxlsx
  ── 1. Error: loadWorkbook from different sources (@test-read_sources.R#49)  ────
  subscript out of bounds
  1: expect_true(all.equal.Workbook(wb_url, wb_file), "Loading from URL vs local not equal") at testthat/test-read_sources.R:49
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: all.equal.Workbook(wb_url, wb_file)
  5: sapply(1:nSheets, function(i) isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]])))
  6: lapply(X = X, FUN = FUN, ...)
  7: FUN(X[[i]], ...)
  8: isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]]))
  9: all.equal(x$colWidths[[i]], y$colWidths[[i]])
  10: all.equal.list(x$colWidths[[i]], y$colWidths[[i]])
  11: attr.all.equal(target, current, ...)
  12: mode(current)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 505 SKIPPED: 2 FAILED: 1
  1. Error: loadWorkbook from different sources (@test-read_sources.R#49) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘exporting-methods.R’ [3s/3s]
  Running ‘mahal-dist.R’ [3s/3s]
  Running ‘testthat.R’ [22s/27s]
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
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
        user system elapsed
optrdd 5.009  0.128   7.081
Running examples in ‘penalizedSVM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: predict
> ### Title: Predict Method for Feature Selection SVM
> ### Aliases: predict.penSVM
> 
> ### ** Examples
> 
> 
> seed<- 123
> train<-sim.data(n = 200, ng = 100, nsg = 10, corr=FALSE, seed=seed )
> print(str(train)) 
List of 3
 $ x   : num [1:100, 1:200] 0.547 0.635 -0.894 0.786 2.028 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : chr [1:100] "pos1" "pos2" "pos3" "pos4" ...
  .. ..$ : chr [1:200] "1" "2" "3" "4" ...
 $ y   : Named num [1:200] 1 -1 -1 1 -1 -1 1 -1 -1 -1 ...
  ..- attr(*, "names")= chr [1:200] "1" "2" "3" "4" ...
 $ seed: num 123
NULL
> 
> #train standard svm
> my.svm<-svm(x=t(train$x), y=train$y, kernel="linear")
> 
> # test with other data
> test<- sim.data(n = 200, ng = 100, nsg = 10, seed=(seed+1) )
> 
> # Check accuracy standard SVM
> my.pred <-ifelse( predict(my.svm, t(test$x)) >0,1,-1)
> # Check accuracy:
> table(my.pred, test$y)
       
my.pred -1  1
     -1 81 23
     1  30 66
> 
> # define set values of tuning parameter lambda1 for SCAD 
> lambda1.scad <- c (seq(0.01 ,0.05, .01),  seq(0.1,0.5, 0.2), 1 ) 
> # for presentation don't check  all lambdas : time consuming! 
> # computation intensive; for demostration reasons only for the first 100 features
> # and only for 10 Iterations maxIter=10, default maxIter=700
> 
> system.time(fit.scad<- svm.fs(x=t(train$x)[,1:100],y=train$y, fs.method="scad", cross.outer= 0,
+ 	grid.search = "discrete",  lambda1.set=lambda1.scad[1:3], show="none",
+ 	parms.coding = "none", maxIter=10,
+ 	inner.val.method = "cv", cross.inner= 5, seed=seed, verbose=FALSE))
Error in UseMethod("svm.fs") : 
  no applicable method for 'svm.fs' applied to an object of class "c('matrix', 'double', 'numeric')"
Calls: system.time -> svm.fs
Timing stopped at: 0 0 0
Execution halted
Found the following significant warnings:

  Warning: 'cBind' is deprecated.
  Warning: 'rBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
              user system elapsed
AIC.phmm     6.105  0.057   7.653
phmm-package 5.207  0.016   6.652
phmm         5.098  0.004   5.727
Found the following significant warnings:
  cat_pair.c:64:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  cat_pair.c:79:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/PLordprob.Rcheck/00install.out’ for details.
Running ‘MDS.R’ [5s/8s]
Running the tests in ‘tests/MDS.R’ failed.
Complete output:
  > library(qrfactor)
  Loading required package: mvoutlier
  Loading required package: sgeostat
  sROC 0.1-2 loaded
  Loading required package: mgraph
  Loading required package: rgdal
  Loading required package: sp
  rgdal: version: 1.2-20, (SVN revision 725)
   Geospatial Data Abstraction Library extensions to R successfully loaded
   Loaded GDAL runtime: GDAL 2.2.4, released 2018/03/19
   Path to GDAL shared files: /usr/share/gdal/2.2
   GDAL binary built with GEOS: TRUE 
   Loaded PROJ.4 runtime: Rel. 5.0.1, April 1st, 2018, [PJ_VERSION: 501]
   Path to PROJ.4 shared files: (autodetected)
   Linking to sp version: 1.2-7 
  Loading required package: pvclust
  Loading required package: cluster
  Loading required package: maptools
  Checking rgeos availability: FALSE
   	Note: when rgeos is not available, polygon geometry 	computations in maptools depend on gpclib,
   	which has a restricted licence. It is disabled by default;
   	to enable gpclib, type gpclibPermit()
  > #data must be numeric, avoid using categorical and characters
  > data(UScereal, package="MASS")
  > variables=c("calories","protein","sodium","carbo","sugars","potassium")
  > data=UScereal[variables]
  > #Multi dimensional scaling can be simulated as: 
  > plot(qrfactor(data,scale='n'),plot="r",type="mds",factors=c(1,2))
  Error in UseMethod("qrfactor") : 
    no applicable method for 'qrfactor' applied to an object of class "data.frame"
  Calls: plot -> qrfactor
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: sp
Loading required package: RANN
Loading required package: PBSmapping

-----------------------------------------------------------
PBS Mapping 2.70.4 -- Copyright (C) 2003-2018 Fisheries and Oceans Canada

PBS Mapping comes with ABSOLUTELY NO WARRANTY;
for details see the file COPYING.
This is free software, and you are welcome to redistribute
it under certain conditions, as outlined in the above file.

A complete user guide 'PBSmapping-UG.pdf' is located at 
/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/PBSmapping/doc/PBSmapping-UG.pdf

Packaged on 2017-06-28
Pacific Biological Station, Nanaimo

All available PBS packages can be found at
https://github.com/pbs-software

To see demos, type '.PBSfigs()'.
-----------------------------------------------------------


Warning in download.file(urlStr, destfile, mode = "wb", quiet = TRUE) :
  cannot open URL 'http://maps.google.com/maps/api/staticmap?center=37.77173,-122.4306&zoom=13&size=550x550&maptype=mobile&format=png32&sensor=true': HTTP status was '403 Forbidden'

Error: processing vignette ‘RapidPolygonLookup.Rnw’ failed with diagnostics:
 chunk 1 
Error in download.file(urlStr, destfile, mode = "wb", quiet = TRUE) : 
  cannot open URL ‘http://maps.google.com/maps/api/staticmap?center=37.77173,-122.4306&zoom=13&size=550x550&maptype=mobile&format=png32&sensor=true’
Execution halted
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: Thu May 17 06:15:36 PM 2018 

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
Found the following significant warnings:
  Warning: replacing previous import ‘Rcmdr::Confint’ by ‘car::Confint’ when loading ‘RcmdrPlugin.BCA’
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RcmdrPlugin.BCA.Rcheck/00install.out’ for details.
Found the following significant warnings:
  cwb/cl/special-chars.c:1771:22: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/rcqp.Rcheck/00install.out’ for details.
Running examples in ‘ref-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: refdata
> ### Title: subsettable reference to matrix or data.frame
> ### Aliases: refdata derefdata derefdata<- [.refdata [<-.refdata [[.refdata
> ###   [[<-.refdata $.refdata $<-.refdata dim.refdata dimnames.refdata
> ###   row.names.refdata names.refdata print.refdata
> ### Keywords: programming manip
> 
> ### ** Examples
> 
> 
>   ## Simple usage Example
>   x <- cbind(1:5, 5:1)       # take a matrix or data frame
>   rx <- refdata(x)           # wrap it into an refdata object
>   rx                         # see the autoprinting
list()
attr(,"dat")
<environment: 0x55b8f4d8cc90>
attr(,"ind")
<environment: 0x55b8f4d8d080>
attr(,"class")
[1] "refdata" "matrix" 
>   rm(x)                      # delete original to save memory
>   rx[]                       # extract all data
list()
attr(,"dat")
<environment: 0x55b8f4d8cc90>
attr(,"ind")
<environment: 0x55b8f4d8d080>
>   rx[-1, ]                   # extract part of data
Error in rx[-1, ] : incorrect number of dimensions
Execution halted
Found the following significant warnings:
  simul.cpp:82:21: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/revealedPrefs.Rcheck/00install.out’ for details.
Running examples in ‘RgoogleMaps-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GetMap
> ### Title: download a static map from the Google server
> ### Aliases: GetMap
> 
> ### ** Examples
> 
> 
> 
>   lat = c(40.702147,40.718217,40.711614);
> 
> 
>   lon = c(-74.012318,-74.015794,-73.998284);
> 
> 
>   center = c(mean(lat), mean(lon));
> 
> 
>   zoom <- min(MaxZoom(range(lat), range(lon)));
> 
> 
>   #this overhead is taken care of implicitly by GetMap.bbox(); 
> 
> 
>   markers = paste0("&markers=color:blue|label:S|40.702147,-74.015794&markers=color:",
+ 
+ 
+                    "green|label:G|40.711614,-74.012318&markers=color:red|color:red|",
+ 
+ 
+                    "label:C|40.718217,-73.998284")
> 
> 
>   MyMap <- GetMap(center=center, zoom=zoom,markers=markers);
Warning in download.file(urlStr, destfile, mode = "wb", quiet = TRUE) :
  cannot open URL 'http://maps.google.com/maps/api/staticmap?center=40.7106593333333,-74.0087986666667&zoom=15&size=640x640&maptype=mobile&format=png32&sensor=true&markers=color:blue|label:S|40.702147,-74.015794&markers=color:green|label:G|40.711614,-74.012318&markers=color:red|color:red|label:C|40.718217,-73.998284': HTTP status was '403 Forbidden'
Error in download.file(urlStr, destfile, mode = "wb", quiet = TRUE) : 
  cannot open URL 'http://maps.google.com/maps/api/staticmap?center=40.7106593333333,-74.0087986666667&zoom=15&size=640x640&maptype=mobile&format=png32&sensor=true&markers=color:blue|label:S|40.702147,-74.015794&markers=color:green|label:G|40.711614,-74.012318&markers=color:red|color:red|label:C|40.718217,-73.998284'
Calls: GetMap -> download.file
Execution halted
Found the following significant warnings:
  atkClasses.c:1050:25: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  atkClasses.c:1058:34: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  atkClasses.c:1397:51: warning: passing argument 2 of ‘object_class->active_descendant_changed’ from incompatible pointer type [-Wincompatible-pointer-types]
  gdkFuncs.c:6000:36: warning: passing argument 2 of ‘gdk_window_get_user_data’ from incompatible pointer type [-Wincompatible-pointer-types]
  gioClasses.c:1948:17: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gioClasses.c:1964:20: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gtkClasses.c:8665:28: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gtkClasses.c:11110:21: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RGtk2.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: The javah tool is planned to be removed in the next major
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/rJava.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’,
    ‘R_GlobalContext’
File ‘rJava/libs/rJava.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  libjson/Source/JSONSharedString.h:297:17: warning: ‘json_shared_string::len’ will be initialized after [-Wreorder]
  libjson/Source/JSONSharedString.h:295:40: warning:   ‘json_shared_string::json_shared_string_internal* json_shared_string::_str’ [-Wreorder]
  libjson/Source/JSONSharedString.h:180:9: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONSharedString.h:182:9: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONStream.h:79:7: warning: ‘JSONStream::state’ will be initialized after [-Wreorder]
  libjson/Source/JSONStream.h:76:28: warning:   ‘void (* JSONStream::call)(void*, void*)’ [-Wreorder]
  JSONStream.cpp:8:1: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONStream.h:77:27: warning: ‘JSONStream::err_call’ will be initialized after [-Wreorder]
  libjson/Source/JSONStream.h:75:17: warning:   ‘json_string JSONStream::buffer’ [-Wreorder]
  JSONStream.cpp:12:1: warning:   when initialized here [-Wreorder]
  libjson/Source/internalJSONNode.h:257:18: warning: ‘internalJSONNode::_name_encoded’ will be initialized after [-Wreorder]
  libjson/Source/internalJSONNode.h:256:17: warning:   ‘json_string internalJSONNode::_name’ [-Wreorder]
  internalJSONNode.cpp:78:1: warning:   when initialized here [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RJSONIO.Rcheck/00install.out’ for details.
Found the following significant warnings:
  PresenceAndAbsence.cpp:536:14: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  PresenceAndAbsence.cpp:537:14: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Rlda.Rcheck/00install.out’ for details.
Found the following significant warnings:
  newmat5.cpp:525:69: warning: throw will always call terminate() [-Wterminate]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Rmixmod.Rcheck/00install.out’ for details.
Found the following significant warnings:
  npmpois.c:246:38: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  rmg.c:335:38: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/rmp.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [4s/14s]
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-src_translate_env.R#52)  ----------------------
  translate_sql(as(x, 0), con = conn[["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-src_translate_env.R#56)  ----------------------
  translate_sql(pmax(x), con = conn[["con"]]) not equal to dplyr::sql("GREATEST(\"x\")").
  1/1 mismatches
  x[1]: "MAX(\"x\")"
  y[1]: "GREATEST(\"x\")"
  
  -- 3. Failure: as() works (@test-src_translate_env.R#60)  ----------------------
  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-src_translate_env.R#69)  ----------------------
  translate_sql_(list(substituted.expression), con = conn[["con"]]) not equal to dplyr::sql("CAST(\"x\" AS \"DATE\")").
  1/1 mismatches
  x[1]: "AS(\"x\", '2018-05-17')"
  y[1]: "CAST(\"x\" AS \"DATE\")"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 223 SKIPPED: 28 FAILED: 4
  1. Failure: as() works (@test-src_translate_env.R#52) 
  2. Failure: as() works (@test-src_translate_env.R#56) 
  3. Failure: as() works (@test-src_translate_env.R#60) 
  4. Failure: as() works (@test-src_translate_env.R#69) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: robustbase
Scalable Robust Estimators with High Breakdown Point (version 1.4-3)

Warning in arrows(0, 0, y[, 1L] * 0.8, y[, 2L] * 0.8, col = col[[2L]], length = arrow.len) :
  zero-length arrow is of indeterminate angle and so skipped
Warning in arrows(0, 0, y[, 1L] * 0.8, y[, 2L] * 0.8, col = col[[2L]], length = arrow.len) :
  zero-length arrow is of indeterminate angle and so skipped
Warning in arrows(0, 0, y[, 1L] * 0.8, y[, 2L] * 0.8, col = col[[2L]], length = arrow.len) :
  zero-length arrow is of indeterminate angle and so skipped
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 1575 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running ‘texi2dvi’ on ‘rrcov.tex’ failed.
LaTeX errors:
! Package inputenc Error: Invalid UTF-8 byte 252.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  regTree.c:242:19: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RRF.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RSEIS.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  bitmap.c:1594:29: warning: suggest parentheses around comparison in operand of ‘^’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Rttf2pt1.Rcheck/00install.out’ for details.
Running examples in ‘sbgcop-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sbgcop.mcmc
> ### Title: Semiparametric Bayesian Gaussian copula estimation and
> ###   imputation
> ### Aliases: sbgcop.mcmc plot.psgc summary.psgc print.sum.psgc
> ### Keywords: multivariate models
> 
> ### ** Examples
> 
> fit<-sbgcop.mcmc(swiss)
10 percent done  Thu May 17 22:13:21 2018 
20 percent done  Thu May 17 22:13:21 2018 
30 percent done  Thu May 17 22:13:21 2018 
40 percent done  Thu May 17 22:13:22 2018 
50 percent done  Thu May 17 22:13:22 2018 
60 percent done  Thu May 17 22:13:22 2018 
70 percent done  Thu May 17 22:13:22 2018 
80 percent done  Thu May 17 22:13:22 2018 
90 percent done  Thu May 17 22:13:23 2018 
100 percent done  Thu May 17 22:13:23 2018 
> summary(fit)
         Length Class  Mode   
C.psamp  3600   -none- numeric
Y.pmean   282   -none- numeric
Y.impute    0   -none- NULL   
LPC       100   -none- numeric
> plot(fit)
Error in xy.coords(x, y, xlabel, ylabel, log) : 
  'x' is a list, but does not have components 'x' and 'y'
Calls: plot -> plot.default -> xy.coords
Execution halted
Running ‘test-all.R’ [173s/222s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("SpaDES.core")
  Loading required package: SpaDES.core
  Loading required package: quickPlot
  Loading required package: reproducible
  
  Attaching package: 'reproducible'
  
  The following object is masked from 'package:testthat':
  
      %>%
  
    Using cached copy of .inputObjects event in test module
    Using cached copy of .inputObjects event in test module
  ── 1. Failure: simList object initializes correctly (@test-simList.R#17)  ──────────────────────────
  length(out) not equal to 75.
  1/1 mismatches
  [1] 73 - 75 == -2
  
    Using cached copy of burn event in fireSpread module
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 349 SKIPPED: 33 FAILED: 1
  1. Failure: simList object initializes correctly (@test-simList.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  sparseSVM.c:367:30: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/sparseSVM.Rcheck/00install.out’ for details.
Found the following significant warnings:
  timeFuns.c:1084:34: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/splusTimeDate.Rcheck/00install.out’ for details.
Found the following significant warnings:
  wdl.cpp:184:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/spp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ChangePointAnalyzeNorm.cpp:49:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  ChangePointAnalyzePoiss.cpp:42:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/StepSignalMargiLike.Rcheck/00install.out’ for details.
Running ‘testGBHProcedures.R’ [3s/4s]
  Running ‘testHierarchicalMethods.R’ [3s/5s]
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
Found the following significant warnings:
  gzipdec_ms.cpp:59:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  gzipdec_ms.cpp:61:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  gzipdec_ms.cpp:63:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/TAQMNGR.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: data.table
No methods found in package ‘RSQLite’ for request: ‘dbGetQuery’ when loading ‘tcpl’
tcpl (v1.2.2) loaded with the following settings:
  TCPL_DB:    /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/tcpl/sql/tcpldb.sqlite
  TCPL_USER:  NA
  TCPL_HOST:  NA
  TCPL_DRVR:  SQLite
Default settings stored in TCPL.conf. See ?tcplConf for more information.

Error: processing vignette ‘tcpl_Overview.Rnw’ failed with diagnostics:
 chunk 4 
Error in result_create(conn@ptr, statement) : 
  attempt to write a readonly database
Execution halted
Running examples in ‘tightClust-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tight.clust
> ### Title: Tight Clustering
> ### Aliases: tight.clust
> ### Keywords: cluster
> 
> ### ** Examples
> 
> ## load the test dataset
> data(tclust.test.data)
> ## find 10 tight clusters
> ptm<-proc.time()
> ## k.min=25, tighter clusters will be found
> ## target=1 is used to save time, target=10 is recommended
> tclust1<-tight.clust(tclust.test.data$Data, target=1, k.min=25, random.seed=12345)
Number of points: 1100 	Dimension: 75 

Looking for tight cluster 1 ...
k = 25
k = 26
1 tight cluster(s) found!
Cluster size: 43 	Remaining number of points: 1057 

> proc.time()-ptm
   user  system elapsed 
  3.348   0.083   3.988 
> ## plot the heat map of cluster result
> plot(tclust1)
Error in xy.coords(x, y, xlabel, ylabel, log) : 
  'x' is a list, but does not have components 'x' and 'y'
Calls: plot -> plot.default -> xy.coords
Execution halted
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
          user system elapsed
ViSiElse 5.957   0.02   7.568
Error in re-building vignettes:
  ...
Loading required package: survival
Loading required package: Matrix
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 488 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running ‘texi2dvi’ on ‘wgsea.tex’ failed.
LaTeX errors:
! Package inputenc Error: Invalid UTF-8 byte 252.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  ADM3.c:37:12: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  ADM3.c:37:29: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  ADM3.c:54:21: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/ADM3.Rcheck/00install.out' for details.
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.5/audio.Rcheck/00install.out' for details.
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(baseballDBR)
  > 
  > test_check("baseballDBR")
  -- 1. Failure: (unknown) (@test-check_urls.R#25)  ------------------------------
  urlExists("http://www.fangraphs.com/guts.aspx?type=cn") isn't true.
  
  == testthat results  ===========================================================
  OK: 2 SKIPPED: 0 FAILED: 1
  1. Failure: (unknown) (@test-check_urls.R#25) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/BayClone2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/bayesCL.Rcheck/00install.out' for details.
mlike.alt.g.AR: no visible global function definition for 'integrate'
mlike.alt.gtheta.AR: no visible global function definition for 'dbeta'
mlike.null.AR: no visible global function definition for 'dbeta'
multilevel.Gibbs.AR: no visible global function definition for
  'txtProgressBar'
multilevel.Gibbs.AR : pbFun: no visible global function definition for
  'setTxtProgressBar'
trendtest.Gibbs.AR: no visible global function definition for
  'txtProgressBar'
trendtest.Gibbs.AR : pbFun: no visible global function definition for
  'setTxtProgressBar'
trendtest.Gibbs.AR: no visible global function definition for 'dcauchy'
trendtest.Gibbs.AR: no visible global function definition for 'pcauchy'
trendtest.MC.AR: no visible global function definition for
  'txtProgressBar'
trendtest.MC.AR : pbFun: no visible global function definition for
  'setTxtProgressBar'
trendtest.nullMargLikeAR: no visible global function definition for
  'integrate'
ttest.Gibbs.AR: no visible global function definition for
  'txtProgressBar'
ttest.Gibbs.AR : pbFun: no visible global function definition for
  'setTxtProgressBar'
ttest.Gibbs.AR: no visible global function definition for 'dcauchy'
ttest.Gibbs.AR: no visible global function definition for 'pcauchy'
ttest.MCGQ.AR: no visible global function definition for 'integrate'
Undefined global functions or variables:
  dbeta dcauchy integrate pcauchy setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "dbeta", "dcauchy", "integrate", "pcauchy")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/Bayesthresh.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/biclust.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
Running examples in 'BioInstaller-Ex.R' failed
The error most likely occurred in:

> ### Name: install.bioinfo
> ### Title: Download and install biology software or database
> ### Aliases: install.bioinfo
> 
> ### ** Examples
> 
> db <- sprintf('%s/.BioInstaller', tempdir())
> set.biosoftwares.db(db)
> install.bioinfo('bwa', show.all.versions = TRUE)
INFO [2018-05-15 06:46:52] Fetching bwa versions....
Error in function (type, msg, asError = TRUE)  : 
  error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
Calls: install.bioinfo ... github2versions -> getURL -> curlPerform -> <Anonymous> -> fun
Execution halted
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(blscrapeR)
  > 
  > test_check("blscrapeR")
  -- 1. Error: (unknown) (@test_qcew_api.R#8)  -----------------------------------
  cannot open URL 'https://data.bls.gov/cew/data/api/2013/1/industry/5112.csv'
  1: download.file(url, temp, quiet = TRUE) at testthat/test_qcew_api.R:8
  
  == testthat results  ===========================================================
  OK: 2 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_qcew_api.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/BonEV.Rcheck/00install.out' for details.
Package required but not available: 'OpenCL'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'test-all.R' [25s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(cli)
  > library(testthat)
  > old.env <- Sys.getenv("checkpoint.mock.install")
  > Sys.setenv("checkpoint.mock.install" = TRUE)
  > test_check("checkpoint")
  Loading required package: checkpoint
  
  checkpoint: Part of the Reproducible R Toolkit from Microsoft
  https://mran.microsoft.com/documents/rro/reproducibility/
  -- 1. Failure: is.404 (@test-0-is-404.R#11)  -----------------------------------
  is.404("http://mran.microsoft.com/snapshot") isn't false.
  
  -- 2. Failure: is.404 (@test-0-is-404.R#14)  -----------------------------------
  is.404("http://mran.microsoft.com/snapshot/2015-05-01") isn't false.
  
  == testthat results  ===========================================================
  OK: 60 SKIPPED: 7 FAILED: 2
  1. Failure: is.404 (@test-0-is-404.R#11) 
  2. Failure: is.404 (@test-0-is-404.R#14) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/CircStats.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   6.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/cplexAPI.Rcheck/00install.out' for details.
Found the following significant warnings:
  instabCorrection.cpp:34:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/cstab.Rcheck/00install.out' for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/ctsem.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/cudaBayesreg.Rcheck/00install.out' for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.7Mb
    help   1.4Mb
    libs   1.7Mb
Running 'has-devel.R' [2s]
  Running 'test-that.R' [71s]
Running the tests in 'tests/test-that.R' failed.
Complete output:
  > library(testthat)
  > test_check("devtools")
  Loading required package: devtools
  
  Attaching package: 'devtools'
  
  The following object is masked from 'package:testthat':
  
      setup
  
  -- 1. Failure: remote_sha.github_remote returns expected value if remote does ex
  remote_sha(github_remote("hadley/devtools@v1.8.0")) not equal to "ad9aac7b9a522354e1ff363a86f389e32cec181b".
  1/1 mismatches
  x[1]: NA
  y[1]: "ad9aac7b9a522354e1ff363a86f389e32cec181b"
  
  
  == testthat results  ===========================================================
  OK: 400 SKIPPED: 10 FAILED: 1
  1. Failure: remote_sha.github_remote returns expected value if remote does exist (@test-remotes.r#75) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/dhglm.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/diffusionMap.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   3.3Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.2Mb
    libs   3.9Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/EnvStats.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(eurostat)
  > 
  > test_check("eurostat")
  trying URL 'http://ec.europa.eu/eurostat/estat-navtree-portlet-prod/BulkDownloadListing?sort=1&file=data%2Ftsdtr210.tsv.gz'
  Content type 'text/html;charset=UTF-8' length unknown
  .......... .......
  downloaded 17 KB
  
  -- 1. Error: (unknown) (@test-all.R#112)  --------------------------------------
  tsdtr210 does not exist or is not readable
  1: get_eurostat("tsdtr210", type = "label", keepFlags = T, cache = FALSE) at testthat/test-all.R:112
  2: get_eurostat_raw(id)
  3: stop(id, " does not exist or is not readable")
  
  == testthat results  ===========================================================
  OK: 0 SKIPPED: 14 FAILED: 1
  1. Error: (unknown) (@test-all.R#112) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  optile.c:3122:26: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  optile.c:3127:26: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  optile.c:3189:16: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  optile.c:3192:16: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  optile.c:3340:28: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  optile.c:3353:28: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  optile.c:3408:16: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  optile.c:3411:16: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/extracat.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/FastRWeb.Rcheck/00install.out' for details.
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(feather)
  > 
  > test_check("feather")
  -- 1. Error: can read/write with utf-8 filename (@test-read.R#19)  -------------
  IO error: Failed to open file: D:\temp\Rtmpqq3CkA\Ã¥.feather
  1: read_feather(path) at testthat/test-read.R:19
  2: feather(path)
  3: openFeather(path)
  
  == testthat results  ===========================================================
  OK: 50 SKIPPED: 0 FAILED: 1
  1. Error: can read/write with utf-8 filename (@test-read.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(feather)
  > 
  > test_check("feather")
  -- 1. Error: can read/write with utf-8 filename (@test-read.R#19)  -------------
  IO error: Failed to open file: D:\temp\RtmpKod0k3\Ã¥.feather
  1: read_feather(path) at testthat/test-read.R:19
  2: feather(path)
  3: openFeather(path)
  
  == testthat results  ===========================================================
  OK: 50 SKIPPED: 0 FAILED: 1
  1. Error: can read/write with utf-8 filename (@test-read.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/fpc.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/frailtyHL.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(FSelectorRcpp)
  > library(Matrix)
  > library(Rcpp)
  > library(RcppArmadillo)
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > library(entropy)
  
  Attaching package: 'entropy'
  
  The following object is masked from 'package:FSelectorRcpp':
  
      discretize
  
  > library(lintr)
  > 
  > test_check("FSelectorRcpp")
  -- 1. Failure: Catch unit tests pass (@test-cpp.R#5)  --------------------------
  C++ unit tests:
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   is a Catch v1.9.6 host application.
  Run with -? for options
  
  -------------------------------------------------------------------------------
  Entropy tests | test-cpp.cpp
    Numeric entropy - comparsion with entropy package
  -------------------------------------------------------------------------------
  test-cpp.cpp:26
  ...............................................................................
  
  test-cpp.cpp:33: FAILED:
    CATCH_CHECK( entrR[0] == fselector::entropy::numeric_entropy(x.begin(), x.end()) )
  with expansion:
    1.0114042647 == 1.0114042647
  
  ===============================================================================
  test cases: 2 | 1 passed | 1 failed
  assertions: 5 | 4 passed | 1 failed
  
  
  == testthat results  ===========================================================
  OK: 89 SKIPPED: 0 FAILED: 1
  1. Failure: Catch unit tests pass (@test-cpp.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/funbarRF.Rcheck/00install.out' for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/GenABEL.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/git2r.Rcheck/00install.out' for details.
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.data.frame.tbl_df', '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_data_frame.grouped_df', 'as_data_frame.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', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/googledrive.Rcheck/00install.out' for details.
Warning: no function found corresponding to methods exports from 'gpclib' for: 'coerce', 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
read.polyfile: no visible global function definition for 'as'
write.polyfile: no visible global function definition for 'is'
write.polyfile: no visible global function definition for 'as'
[,gpc.poly: no visible global function definition for 'new'
append.poly,gpc.poly-gpc.poly: no visible global function definition
  for 'new'
coerce,data.frame-gpc.poly: no visible global function definition for
  'as'
coerce,list-gpc.poly: no visible global function definition for 'as'
coerce,matrix-gpc.poly: no visible global function definition for 'new'
coerce,numeric-gpc.poly: no visible global function definition for
  'new'
coerce,numeric-gpc.poly.nohole: no visible global function definition
  for 'new'
intersect,gpc.poly-gpc.poly: no visible global function definition for
  'as'
intersect,gpc.poly-gpc.poly: no visible global function definition for
  'new'
setdiff,gpc.poly-gpc.poly: no visible global function definition for
  'as'
setdiff,gpc.poly-gpc.poly: no visible global function definition for
  'new'
tristrip,gpc.poly: no visible global function definition for 'as'
union,gpc.poly-gpc.poly: no visible global function definition for 'as'
union,gpc.poly-gpc.poly: no visible global function definition for
  'new'
Undefined global functions or variables:
  as is new
Consider adding
  importFrom("methods", "as", "is", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running 'bug1.R' [1s]
  Running 'reg-tests.R' [1s]
  Comparing 'reg-tests.Rout' to 'reg-tests.Rout.save' ...58c58
< Formal class 'gpc.poly' [package "gpclib"] with 1 slot
---
> Formal class 'gpc.poly' [package "gpclib"] with 1 slots
68c68
< Formal class 'gpc.poly' [package "gpclib"] with 1 slot
---
> Formal class 'gpc.poly' [package "gpclib"] with 1 slots
83c83
< Formal class 'gpc.poly' [package "gpclib"] with 1 slot
---
> Formal class 'gpc.poly' [package "gpclib"] with 1 slots
Running the tests in 'tests/bug1.R' failed.
Complete output:
  > suppressMessages(library(gpclib))
  > to_numeric <- selectMethod(coerce, c("gpc.poly", "numeric"))
  > load("bug1_data.RData")
  > plot(p)  ## loads a polygon, looks fine
  > plot(as(vec, "gpc.poly"))  ## looks fine
  > clip <- to_numeric(p); str(clip)
   num [1:17] 1 7 0 570545 7890092 ...
  > 
  > ## Crashes R 2.14 and 2.15 (32-bit) on Windows
  > vec <- .Call("Rgpc_polygon_clip", vec, clip, 3, PACKAGE="gpclib")
Found the following significant warnings:
  calculategphmm.cpp:217:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/gphmm.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/gpuR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/graphframes.Rcheck/00install.out' for details.
Found the following significant warnings:
  Rothmana.cpp:123:15: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/graphicalVAR.Rcheck/00install.out' for details.
Found the following significant warnings:
  _t_array_properties.cpp:10:13: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/gRbase.Rcheck/00install.out' for details.
Running examples in 'gtools-Ex.R' failed
The error most likely occurred in:

> ### Name: unByteCode
> ### Title: Convert a Byte-Code Function to an Interpreted-Code Function
> ### Aliases: unByteCode unByteCodeAssign assignEdgewise
> ### Keywords: programming utilites
> 
> ### ** Examples
> 
> datURL <- "https://bugs.r-project.org/bugzilla/attachment.cgi?id=1659"
> dat <- as.matrix(read.csv(file=datURL, row.names=1))
Warning in file(file, "rt") :
  cannot open URL 'https://bugs.r-project.org/bugzilla/attachment.cgi?id=1659': HTTP status was '500 Internal Server Error'
Error in file(file, "rt") : cannot open the connection
Calls: as.matrix -> read.csv -> read.table -> file
Execution halted
Error in re-building vignettes:
  ...
Loading required package: survival
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "ashg2012.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.5.0/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.5.0/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'ashg2012.tex' failed

LaTeX errors:
! LaTeX Error: File `D:/RCompile/recent/R-35\unhbox\voidb@x \penalty \@M \ {}1.
0/share/texmf/tex/latex/Sweave.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Found the following significant warnings:
  Warning: S3 methods 'as.promise.Future', 'as.promise.default', 'as.promise.promise', 'format.promise', 'print.promise' were declared in NAMESPACE but not found
See 'd:/Rcompile/CRANpkg/local/3.5/htmlwidgets.Rcheck/00install.out' for details.
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(HURDAT)
  > 
  > test_check("HURDAT")
  -- 1. Error: (unknown) (@test-hurdat.R#4)  -------------------------------------
  HTTP error 404.
  1: get_hurdat(basin = "AL") at testthat/test-hurdat.R:4
  2: purrr::map_df(.x = basin, .f = parse_hurdat)
  3: map(.x, .f, ...)
  4: .f(.x[[i]], ...)
  5: readr::read_lines(file = url)
  6: datasource(file, skip = skip)
  7: datasource_connection(file, skip, comment)
  8: datasource_raw(read_connection(path), skip, comment = comment)
  9: new_datasource("raw", text, skip = skip, comment = comment)
  10: structure(list(x, skip = skip, comment = comment, ...), class = c(paste0("source_", 
         type), "source"))
  11: read_connection(path)
  12: open(con, "rb")
  13: open.connection(con, "rb")
  
  == testthat results  ===========================================================
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-hurdat.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
'library' or 'require' call to 'tcltk' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'tcltk'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  13.8Mb
Found the following significant warnings:
  regTree.c:317:38: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  regTree.c:336:38: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/iJRF.Rcheck/00install.out' for details.
Found the following significant warnings:
  transformations.cpp:274:15: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/imager.Rcheck/00install.out' for details.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R  10.8Mb
Error in re-building vignettes:
  ...
Warning in read.table(file = file, header = header, sep = sep, quote = quote,  :
  invalid input found on input connection 'D:\temp\RtmpMvRQYV\ex_data21dd875615cc2.csv2'
Warning in read.table(file = file, header = header, sep = sep, quote = quote,  :
  incomplete final line found by readTableHeader on 'D:\temp\RtmpMvRQYV\ex_data21dd875615cc2.csv2'
Quitting from lines 31-32 (incadoc.Rmd) 
Error: processing vignette 'incadoc.Rmd' failed with diagnostics:
cannot open URL 'http://www.cancercentrum.se/globalassets/cancerdiagnoser/lunga-och-lungsack/dokument/styrdokument.pdf'
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      3.4Mb
Found the following significant warnings:
  LBLasso.c:98:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  LBlogistic.c:100:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  LBmultilogistic.c:110:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  ggm.c:69:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  ising.c:83:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  potts.c:99:15: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/Libra.Rcheck/00install.out' for details.
Running 'testthat.R' [2s]
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
Found the following significant warnings:
  mue_nelmC.cpp:147:15: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  mue_nelmC.cpp:185:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  mue_nelmC.cpp:230:22: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  mue_nrmC.cpp:135:15: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  mue_nrmC.cpp:173:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  mue_nrmC.cpp:218:22: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/mcIRT.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.2Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/mdhglm.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   3.8Mb
    misc   1.1Mb
Found the following significant warnings:
  NMix_RJMCMCcombine.cpp:422:14: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/mixAK.Rcheck/00install.out' for details.
Found the following significant warnings:
  mixCpp.cpp:122:19: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
  mixCpp.cpp:167:19: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
  mixCpp.cpp:399:22: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
  mixCpp.cpp:444:22: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/mixR.Rcheck/00install.out' for details.
Found the following significant warnings:
  confusionMatrix_.cpp:10:29: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  confusionMatrix_.cpp:12:29: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  confusionMatrix_.cpp:14:29: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  confusionMatrix_.cpp:16:29: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  confusionMatrix_.cpp:57:29: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  confusionMatrix_.cpp:104:29: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  confusionMatrix_.cpp:106:29: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  confusionMatrix_.cpp:108:29: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  confusionMatrix_.cpp:110:29: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/ModelMetrics.Rcheck/00install.out' for details.
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(mortAAR)
  > 
  > test_check("mortAAR")
  -- 1. Failure: prep.life.table imports a data set correct (@test_input_functions
  names(example_life_table) not equal to c("Unbestimmt", "Weiblich", "Männlich", "All").
  1/4 mismatches
  x[3]: "MÃ¤nnlich"
  y[3]: "Männlich"
  
  == testthat results  ===========================================================
  OK: 78 SKIPPED: 0 FAILED: 1
  1. Failure: prep.life.table imports a data set correct (@test_input_functions.R#22) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  weiszfeldIterations.cpp:195:48: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/Mposterior.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/MSeasy.Rcheck/00install.out' for details.
Found the following significant warnings:
  evallf.c:86:23: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/mvnmle.Rcheck/00install.out' for details.
Error: memory exhausted (limit reached?)
Execution halted
Error: package or namespace load failed for 'ncdump':
 unable to load R code in package 'Rcpp'
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return) 
           message(paste("Error:", msg), domain = NA)
       else stop(msg, call. = FALSE, domain = NA)
   })
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
Error in readRDS(pfile) : error reading from connection
Calls: <Anonymous>
Execution halted
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    CppCode   2.5Mb
    R         5.8Mb
    include   5.6Mb
    libs      1.8Mb
    tests     1.3Mb
It looks like this package (or one of its dependent packages) has an
unstated dependence on a standard package.  All dependencies must be
declared in DESCRIPTION.
See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Fatal error: couldn't allocate memory for pointer stack
Error in re-building vignettes:
  ...
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "nonrandom.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.5.0/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.5.0/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'nonrandom.tex' failed

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

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

Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/npde.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
Packages in Depends field not imported from:
  'mclust' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/NPMOD.Rcheck/00install.out' for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   2.2Mb
    libs   1.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/OpenCL.Rcheck/00install.out' for details.
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    R        2.4Mb
    libs     5.9Mb
    models   4.6Mb
Running 'testthat.R' [26s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > test_check("openxlsx")
  Loading required package: openxlsx
  -- 1. Error: loadWorkbook from different sources (@test-read_sources.R#49)  ----
  subscript out of bounds
  1: expect_true(all.equal.Workbook(wb_url, wb_file), "Loading from URL vs local not equal") at testthat/test-read_sources.R:49
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: all.equal.Workbook(wb_url, wb_file)
  5: sapply(1:nSheets, function(i) isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]])))
  6: lapply(X = X, FUN = FUN, ...)
  7: FUN(X[[i]], ...)
  8: isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]]))
  9: all.equal(x$colWidths[[i]], y$colWidths[[i]])
  10: all.equal.list(x$colWidths[[i]], y$colWidths[[i]])
  11: attr.all.equal(target, current, ...)
  12: mode(current)
  
  == testthat results  ===========================================================
  OK: 505 SKIPPED: 2 FAILED: 1
  1. Error: loadWorkbook from different sources (@test-read_sources.R#49) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: 'ROracle'

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

> ### Name: viaroute
> ### Title: travel time or full information of a route
> ### Aliases: viaroute
> 
> ### ** Examples
> 
> # direct examples of the online API
> link <- "http://router.project-osrm.org/route/v1/driving/8.1,47.1;8.3,46.9?steps=false"
> a <- rjson::fromJSON(file = link)
Warning in file(con, "r") :
  cannot open URL 'http://router.project-osrm.org/route/v1/driving/8.1,47.1;8.3,46.9?steps=false': HTTP status was '429 ???'
Error in file(con, "r") : cannot open the connection
Calls: <Anonymous> -> paste -> readLines -> file
Execution halted
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/3.5/pathological.Rcheck/tests/testthat/CRAN"
  y[1]: "D:/Rcompile/CRANpkg/local/3.5/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/3.5/pathological.Rcheck/tests/testthat/test_dec
  x[1]: ompose_path.R"
  y[1]: "D:/Rcompile/CRANpkg/local/3.5/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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/pcadapt.Rcheck/00install.out' for details.
Found the following significant warnings:
  cat_pair.c:64:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  cat_pair.c:79:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/PLordprob.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
trying URL 'http://goo.gl/BsqnP'
Warning in download.file("http://goo.gl/BsqnP", destfile = "blackouts.txt") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Quitting from lines 418-421 (a_introduction.Rnw) 
Error: processing vignette 'a_introduction.Rnw' failed with diagnostics:
cannot open URL 'http://goo.gl/BsqnP'
Execution halted
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   6.4Mb
    libs      1.7Mb
Package required but not available: 'qtbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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/3.5/randtoolbox.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: replacing previous import 'Rcmdr::Confint' by 'car::Confint' when loading 'RcmdrPlugin.BCA'
See 'd:/Rcompile/CRANpkg/local/3.5/RcmdrPlugin.BCA.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/Rcplex.Rcheck/00install.out' for details.
Running 'testthat.R' [37s]
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: 38 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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/RDieHarder.Rcheck/00install.out' for details.
Package required but not available: 'Rmosek'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  simul.cpp:82:21: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/revealedPrefs.Rcheck/00install.out' for details.
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/3.5/rJava.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.5/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.5/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.
Found the following significant warnings:
  libjson/Source/JSONGlobals.h:43:50: warning: invoking macro json_global_decl argument 3: empty macro arguments are undefined in ISO C90 and ISO C++98
  libjson/Source/JSONGlobals.h:44:49: warning: invoking macro json_global_decl argument 3: empty macro arguments are undefined in ISO C90 and ISO C++98
  libjson/Source/JSONSharedString.h:297:17: warning: 'json_shared_string::len' will be initialized after [-Wreorder]
  libjson/Source/JSONSharedString.h:295:40: warning:   'json_shared_string::json_shared_string_internal* json_shared_string::_str' [-Wreorder]
  libjson/Source/JSONSharedString.h:180:9: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONSharedString.h:182:9: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONStream.h:79:7: warning: 'JSONStream::state' will be initialized after [-Wreorder]
  libjson/Source/JSONStream.h:76:28: warning:   'void (* JSONStream::call)(void*, void*)' [-Wreorder]
  JSONStream.cpp:8:1: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONStream.h:77:27: warning: 'JSONStream::err_call' will be initialized after [-Wreorder]
  libjson/Source/JSONStream.h:75:17: warning:   'json_string JSONStream::buffer' [-Wreorder]
  JSONStream.cpp:12:1: warning:   when initialized here [-Wreorder]
  JSONValidator.cpp:394:105: warning: invoking macro JSON_ASSERT_SAFE argument 3: empty macro arguments are undefined in ISO C90 and ISO C++98
  JSONValidator.cpp:397:104: warning: invoking macro JSON_ASSERT_SAFE argument 3: empty macro arguments are undefined in ISO C90 and ISO C++98
  libjson/Source/internalJSONNode.h:257:18: warning: 'internalJSONNode::_name_encoded' will be initialized after [-Wreorder]
  libjson/Source/internalJSONNode.h:256:17: warning:   'json_string internalJSONNode::_name' [-Wreorder]
  internalJSONNode.cpp:78:1: warning:   when initialized here [-Wreorder]
See 'd:/Rcompile/CRANpkg/local/3.5/RJSONIO.Rcheck/00install.out' for details.
Found the following significant warnings:
  PresenceAndAbsence.cpp:536:14: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  PresenceAndAbsence.cpp:537:14: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/Rlda.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/Rmosek.Rcheck/00install.out' for details.
Found the following significant warnings:
  npmpois.c:246:38: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  rmg.c:335:38: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/rmp.Rcheck/00install.out' for details.
Package required but not available: 'Rcplex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/ROracle.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.5/rpart/libs/i386/rpart.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.5/rpart/libs/x64/rpart.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Running 'test-all.R' [153s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > ###
  > library(testthat)
  > test_check('rphylotastic')
  Loading required package: rphylotastic
  -- 1. Error: Loading names from an online PDF works correctly (@test_names.R#8) 
  HTTP error 400.
  1: url_get_scientific_names("https://www.fws.gov/westvirginiafieldoffice/PDF/beechridgehcp/Appendix_D_Table_D-1.pdf") at testthat/test_names.R:8
  2: jsonlite::fromJSON(paste(get_base_url(), "fn/names_url?url=", URL, "&engine=", search_engine, 
         sep = ""))
  3: fromJSON_string(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame, 
         simplifyMatrix = simplifyMatrix, flatten = flatten, ...)
  4: parseJSON(txt, bigint_as_char)
  5: parse_con(txt, bigint_as_char)
  6: open(con, "rb")
  7: open.connection(con, "rb")
  
  == testthat results  ===========================================================
  OK: 35 SKIPPED: 0 FAILED: 1
  1. Error: Loading names from an online PDF works correctly (@test_names.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  regTree.c:242:19: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/RRF.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/RSAP.Rcheck/00install.out' for details.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/RSEIS.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
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/3.5/Rserve.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.5/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/3.5/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.
Running examples in 'RSVGTipsDevice-Ex.R' failed
The error most likely occurred in:

> ### Name: RSVGTipsDevice
> ### Title: A SVG Graphics Driver with dynamic tips
> ### Aliases: RSVGTipsDevice
> ### Keywords: device package
> 
> ### ** Examples
> 
> library("RSVGTipsDevice")
> sessionInfo()
R Under development (unstable) (2017-12-30 r73992)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server 2008 x64 (build 6002) Service Pack 2

Matrix products: default

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

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

other attached packages:
[1] RSVGTipsDevice_1.0-7

loaded via a namespace (and not attached):
[1] compiler_3.5.0
> devSVGTips("svgplot1.svg", toolTipMode=1,
+     title="SVG example plot 1: Shapes and Points, Tooltips are Title + 1 Line")
> plot(c(0,10),c(0,10), type="n", xlab="x", ylab="y",
+     main="Example SVG plot with title + 1 line tips (mode=1)")
> setSVGShapeToolTip(title="A rectangle", desc="that is yellow")
> rect(1,1,4,6, col='yellow')
> setSVGShapeToolTip(title="1st circle with title only")
> points(5.5,7.5,cex=20,pch=19,col='red')
> setSVGShapeToolTip(title="A triangle", desc="big and green")
> polygon(c(3,6,8), c(3,6,3), col='green')
> # no tooltips on these points
> points(2:8, 8:2, cex=3, pch=19, col='black')
> # tooltips on each these points
> invisible(sapply(1:7, function(x)
+ {setSVGShapeToolTip(title=paste("point", x))
+  points(x+1, 8-x, cex=3, pch=1, col='black')}))
> setSVGShapeToolTip(title="Text", desc="can have a tool tip too!")
> text(x=4, y=9, lab="Poke me!", col="blue")
> dev.off()
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   1.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/Ryacas.Rcheck/00install.out' for details.
installed size is 93.7Mb
  sub-directories of 1Mb or more:
    doc     10.8Mb
    gdal     3.8Mb
    libs    69.9Mb
    proj     5.0Mb
    sqlite   1.5Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    www   6.2Mb
Running 'test-all.R' [207s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("SpaDES.core")
  Loading required package: SpaDES.core
  Loading required package: quickPlot
  Loading required package: reproducible
  
  Attaching package: 'reproducible'
  
  The following object is masked from 'package:testthat':
  
      %>%
  
    Using cached copy of .inputObjects event in test module
    Using cached copy of .inputObjects event in test module
  -- 1. Failure: simList object initializes correctly (@test-simList.R#17)  --------------------------
  length(out) not equal to 75.
  1/1 mismatches
  [1] 73 - 75 == -2
  
    Using cached copy of burn event in fireSpread module
  == testthat results  ===========================================================
  OK: 349 SKIPPED: 33 FAILED: 1
  1. Failure: simList object initializes correctly (@test-simList.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  sparseSVM.c:367:30: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/sparseSVM.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.5/spatial/libs/i386/spatial.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.5/spatial/libs/x64/spatial.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: 'rcytoscapejs'
Found the following significant warnings:
  timeFuns.c:1084:34: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/splusTimeDate.Rcheck/00install.out' for details.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    include   7.8Mb
Found the following significant warnings:
  ChangePointAnalyzeNorm.cpp:49:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  ChangePointAnalyzePoiss.cpp:42:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/StepSignalMargiLike.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "VignetteforSTPGA.ltx" --max-iterations=20 -I "D:/RCompile/recent/R-3.5.0/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.5.0/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'VignetteforSTPGA.ltx' failed with diagnostics:
running 'texi2dvi' on 'VignetteforSTPGA.ltx' failed

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

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

Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/stringi.Rcheck/00install.out' for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data    1.4Mb
    doc     2.6Mb
    tests   1.0Mb
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/3.5/survival/libs/i386/survival.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.5/survival/libs/x64/survival.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidyinftheo)
  > 
  > test_check("tidyinftheo")
  -- 1. Error: right number of columns given (@test-errors.R#10)  ----------------
  argument "expr" is missing, with no default
  1: expect_length(tab %>% select(vs) %>% shannon_entropy(), 1) at testthat/test-errors.R:10
  2: quasi_label(enquo(object))
  3: eval_bare(get_expr(quo), get_env(quo))
  4: tab %>% select(vs) %>% shannon_entropy()
  5: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  6: eval(quote(`_fseq`(`_lhs`)), env, env)
  7: eval(quote(`_fseq`(`_lhs`)), env, env)
  8: `_fseq`(`_lhs`)
  9: freduce(value, `_function_list`)
  10: withVisible(function_list[[k]](value))
  11: function_list[[k]](value)
  12: shannon_entropy(.)
  13: reduce_data(.data, !!enquo(X), numvars = 1, na.rm = na.rm)
  14: tidyselect::vars_select(names(reduced_tab), !!!quos(...))
  15: vars_select_eval(.vars, quos)
  16: map_lgl(quos, quo_is_helper)
  17: .f(.x[[i]], ...)
  18: extract_expr(quo)
  19: is_call(expr, paren_sym)
  
  == testthat results  ===========================================================
  OK: 37 SKIPPED: 0 FAILED: 1
  1. Error: right number of columns given (@test-errors.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R      3.4Mb
    doc    1.2Mb
    help   2.7Mb
Package required but not available: ‘Rglpk’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    bootstrapping_example   1.2Mb
    libs                    3.4Mb
Error in re-building vignettes:
  ...
Error: processing vignette 'additivityTests-vignette.Rmd' failed with diagnostics:
shared object 'stringi.so' not found
Execution halted
Package suggested but not available for checking: ‘HiTC’
Package unavailable to check Rd xrefs: ‘HiTC’
Found the following significant warnings:
  ADM3.c:34:19: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:34:31: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:34:15: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:39:61: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:39:73: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:39:57: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:52:6: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:54:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:54:56: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:55:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:55:42: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:56:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:56:38: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ADM3.Rcheck/00install.out’ for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
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 66-67 (ahn.Rmd) 
Error: processing vignette 'ahn.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
File ‘allelic/libs/allelic.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
    Object: ‘newallelic.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  matrix.c:629:8: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  matrix.c:631:49: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  matrix.c:632:39: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/amei.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
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.


Execution halted
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs  19.8Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/anapuce.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  WARNING: An illegal reflective access operation has occurred
  WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
  WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
  WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
  WARNING: All illegal access operations will be denied in a future release
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ANLP.Rcheck/00install.out’ for details.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Error in re-building vignettes:
  ...
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 39-73 (antaresH5.Rmd) 
Error: processing vignette 'antaresH5.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running examples in ‘apaStyle-Ex.R’ failed
The error most likely occurred in:

> ### Name: apa.descriptives
> ### Title: Generic method to generate an APA style table with descriptives
> ###   for MS Word.
> ### Aliases: apa.descriptives
> 
> ### ** Examples
> 
> 
> # Use apa.descriptives function
> apa.descriptives(
+   data = data.frame(
+     rnorm(100, mean = 0, sd = 1),
+     rnorm(100, mean = 0, sd = 1),
+     rnorm(100, mean = 0, sd = 1),
+     rnorm(100, mean = 0, sd = 1)
+   ),
+   variables = c("Column 1", "Column 2", "Column 3", "Column 4")
+ )
Error in .jnew(class.docx4r.document) : 
  java.lang.NoClassDefFoundError: javax/xml/bind/JAXBException
Calls: apa.descriptives ... apa.table.default -> apaStyleTable -> <Anonymous> -> .jnew
Execution halted
Package suggested but not available for checking: ‘testthat’
Error in re-building vignettes:
  ...

Returned 'NA'!


No TSN found for species 'Juniperus occidentalis'!


Retrieving data for taxon 'Pinus strobus'





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

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


Returned 'NA'!


No TSN found for species 'Pinus strobus'!


Execution halted
Packages suggested but not available for checking:
  ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’
Found the following significant warnings:
  am.c:275:9: warning: comparison of array 'readByte' not equal to a null pointer is always true [-Wtautological-pointer-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/aqr.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘TDA’
Error in re-building vignettes:
  ...
sh: +RTS: command not found
Warning in system(command) : error in running command
Error: processing vignette 'argparse.Rrst' failed with diagnostics:
pandoc document conversion failed with error 127
Execution halted
Package suggested but not available for checking: ‘AffymetrixDataTestFiles’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R             2.2Mb
    help          1.1Mb
    testScripts   1.1Mb
Package suggested but not available for checking: ‘GLAD’
Packages suggested but not available for checking:
  ‘GLAD’ ‘sfit’ ‘expectile’ ‘HaarSeg’ ‘mpcbs’
Package unavailable to check Rd xrefs: ‘GLAD’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.3Mb
Packages suggested but not available for checking: ‘cacheSweave’ ‘weaver’
Packages required but not available: ‘cairoDevice’ ‘gWidgetsRGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  au.c:375:2: warning: incompatible pointer types initializing 'struct audio_instance *(*)(SEXP, float, int)' (aka 'struct audio_instance *(*)(struct SEXPREC *, float, int)') with an expression of type 'au_instance_t *(SEXP, float, int)' (aka 'struct au_instance *(struct SEXPREC *, float, int)') [-Wincompatible-pointer-types]
  au.c:376:2: warning: incompatible pointer types initializing 'struct audio_instance *(*)(SEXP, float, int, int)' (aka 'struct audio_instance *(*)(struct SEXPREC *, float, int, int)') with an expression of type 'au_instance_t *(SEXP, float, int, int)' (aka 'struct au_instance *(struct SEXPREC *, float, int, int)') [-Wincompatible-pointer-types]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/audio.Rcheck/00install.out’ for details.
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
File ‘aylmer/libs/aylmer.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘aylmer.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘aylmer.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package required but not available: ‘glpkAPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/bamboo.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/BANFF.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/BANOVA.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ArrayExpress’
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    2.3Mb
    libs   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.
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 46-49 (v01-introduction.Rmd) 
Error: processing vignette 'v01-introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...

Execution halted
Package suggested but not available for checking: ‘doMPI’
Package unavailable to check Rd xrefs: ‘Rmpi’
Package required but not available: ‘mritc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/bayesCL.Rcheck/00install.out’ for details.
Packages required but not available: ‘gWidgetsRGtk2’ ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs  11.7Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 61.2Mb
  sub-directories of 1Mb or more:
    libs  60.5Mb
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs  15.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    ex-data   4.6Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Bayesthresh.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
File ‘BayHap/libs/BayHap.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘mcmc.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘mcmc.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking:
  ‘beadarrayExampleData’ ‘lumi’
Running examples in ‘beadarrayFilter-Ex.R’ failed
The error most likely occurred in:

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 59.2Mb
  sub-directories of 1Mb or more:
    libs  57.8Mb
installed size is 26.3Mb
  sub-directories of 1Mb or more:
    libs  25.3Mb
installed size is 141.1Mb
  sub-directories of 1Mb or more:
    include  141.0Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/biclust.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   6.5Mb
installed size is 28.1Mb
  sub-directories of 1Mb or more:
    libs  28.0Mb
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [64s/101s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(BIGL)
  > 
  > test_check("BIGL")
  ── 1. Failure: statistics (@test_wrapper.R#14)  ────────────────────────────────
  rs$maxR not equal to maxR(...).
  Component "Ymean": Component "sign": 1 element mismatch
  Component "Ymean": Component "call": 1 string mismatch
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 129 SKIPPED: 0 FAILED: 1
  1. Failure: statistics (@test_wrapper.R#14) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Removed 199 rows containing non-finite values (stat_contour).
Warning in normalizePath(f2) :
  path[1]="./webshot119ff2c0d7f7b.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot119ff2c0d7f7b.png': No such file or directory
Quitting from lines 240-243 (analysis.Rmd) 
Error: processing vignette 'analysis.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/bigpca.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   7.1Mb
Error in re-building vignettes:
  ...
Warning in engine$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 37-44 (billboarder-intro.Rmd) 
Error: processing vignette 'billboarder-intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running ‘testthat.R’ [7s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
             stop("Function ", name, " not found in environment ", environmentName(env), 
                 ".", call. = FALSE)
         mock(name = name, env = env, new = eval(new_values[[qual_name]], eval_env, eval_env))
     })
  4: FUN(X[[i]], ...)
  5: stop("Can't mock functions in base packages (", pkg_name, ")", call. = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 28 SKIPPED: 0 FAILED: 3
  1. Error: canDownloadFiles (@test-download_files.R#9) 
  2. Error: canReturnEmptyDFWhenEmptyDownloadFiles (@test-download_files.R#27) 
  3. Error: canProcessYaml (@test-process_yaml.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available: ‘Rsamtools’ ‘GenomicAlignments’ ‘csaw’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   2.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/bioacoustics.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 64-67 (BioCircos.Rmd) 
Error: processing vignette 'BioCircos.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘BiocStyle’
Running ‘test-all.R’ [9s/13s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  ── 5. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#17)  
  `gbLocation("123^125")` threw an error with unexpected message.
  Expected match: "Inadmissible range"
  Actual message: "c++ exception (unknown reason)"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 267 SKIPPED: 1 FAILED: 5
  1. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#6) 
  2. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#9) 
  3. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#13) 
  4. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#14) 
  5. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#17) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 10-11 (IntroBiofiles.Rnw) 
Error: processing vignette 'IntroBiofiles.Rnw' failed with diagnostics:
there is no package called 'BiocStyle'
Execution halted
Running ‘testthat.R’ [8s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  trying URL 'ftp://ftp.sjtu.edu.cn/pub/CPAN/clpa//README'
  Content type 'unknown' length 107 bytes
  ==================================================
  trying URL 'ftp://ftp.sjtu.edu.cn/pub/CPAN/clpa//index.html'
  Content type 'unknown' length 3574 bytes
  ==================================================
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 61 SKIPPED: 0 FAILED: 4
  1. Error: install.github (@test_install.R#10) 
  2. Error: install.bioinfo (@test_install.R#57) 
  3. Error: dependence (@test_install_uilts.R#88) 
  4. Error: git.download (@test_install_uilts.R#102) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
trying URL 'https://raw.githubusercontent.com/Miachol/ftp/master/files/GRCh37_MT_ensGene.txt'
Content type 'text/plain; charset=utf-8' length 3131 bytes
==================================================
downloaded 3131 bytes

trying URL 'https://raw.githubusercontent.com/Miachol/ftp/master/files/GRCh37_MT_ensGene.txt'
Content type 'text/plain; charset=utf-8' length 3131 bytes
==================================================
downloaded 3131 bytes

trying URL 'https://raw.githubusercontent.com/Miachol/ftp/master/files/GRCh37_MT_ensGene.txt'
Content type 'text/plain; charset=utf-8' length 3131 bytes
==================================================
downloaded 3131 bytes

trying URL 'https://raw.githubusercontent.com/Miachol/ftp/master/files/GRCh37_MT_ensGene.txt'
Content type 'text/plain; charset=utf-8' length 3131 bytes
==================================================
downloaded 3131 bytes

Quitting from lines 102-109 (BioInstaller.Rmd) 
Error: processing vignette 'BioInstaller.Rmd' failed with diagnostics:
Error in 'git2r_clone': SSL error: error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/BioPhysConnectoR.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
extractPDB : atom.select : sel.txt2nums: no visible global function
  definition for ‘na.omit’
extractPDB : read.pdb: no visible global function definition for
  ‘na.omit’
mat.read: no visible global function definition for ‘read.table’
mat.write: no visible global function definition for ‘write.table’
scpcp: no visible global function definition for ‘pgamma’
sim : sim.func: no visible global function definition for ‘write.table’
simc: no visible global function definition for ‘write.table’
simc : simc.func: no visible global function definition for
  ‘write.table’
sims: no visible global function definition for ‘write.table’
sims : sims.func: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  na.omit pgamma read.table write.table
Consider adding
  importFrom("stats", "na.omit", "pgamma")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Package required but not available: ‘rpanel’

Package suggested but not available for checking: ‘soilphysics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘colorspace’
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  ‘deldir’ ‘rgl’ ‘tcltk’ ‘tcltk2’ ‘tkrplot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘bit-Ex.R’ failed
The error most likely occurred in:

> ### Name: regtest.bit
> ### Title: Regressiontests for bit
> ### Aliases: regtest.bit
> ### Keywords: classes logic
> 
> ### ** Examples
> 
>   if (regtest.bit()){
+     message("regtest.bit is OK")
+   }else{
+     message("regtest.bit failed")
+   }

 *** caught segfault ***
address 0x7ff792304174, cause 'memory not mapped'

Traceback:
 1: `[.bit`(b, i)
 2: b[i]
 3: unattr(b[i])
 4: regtest.bit()
An irrecoverable exception occurred. R is aborting now ...
Packages required but not available: ‘gWidgetsRGtk2’ ‘RGtk2’ ‘cairoDevice’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 34.1Mb
  sub-directories of 1Mb or more:
    libs  32.9Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
installed size is 33.7Mb
  sub-directories of 1Mb or more:
    libs  33.4Mb
Found the following significant warnings:
  conditional.least.squares.c:232:20: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  conditional.least.squares.c:233:20: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  conditional.least.squares.c:234:20: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/bnlearn.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ./sampling.h:84:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/BNSP.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/boclust.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Package suggested but not available for checking: ‘sangerseqR’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Boom.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘Boom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘RGtk2’ ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘brainwaver/libs/brainwaver.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘connexity_small_world.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 31.5Mb
  sub-directories of 1Mb or more:
    libs  31.3Mb
Running ‘testthat.R’ [18s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  2/3 mismatches
  x[2]: "c"
  y[2]: "b"
  
  x[3]: "b"
  y[3]: "c"
  
  [1] "liquid_normal" "solid_normal"  "solid_patient"
  [1] "liquid_normal" "solid_normal"  "solid_patient"
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 27 SKIPPED: 7 FAILED: 1
  1. Failure: Result with default parameters is tbl_df with required columns (@test_coef_by_group.R#26) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘pasilla’
Packages required but not available: ‘DiffBind’ ‘Rsamtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  helpers.c:365:19: warning: absolute value function 'fabsf' given an argument of type 'double' but has parameter of type 'float' which may cause truncation of value [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/BSquare.Rcheck/00install.out’ for details.
installed size is 25.0Mb
  sub-directories of 1Mb or more:
    libs  23.8Mb
Packages required and available but unsuitable versions:
  ‘BoomSpikeSlab’ ‘Boom’ ‘Boom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/cairoDevice.Rcheck/00install.out’ for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    5.7Mb
    libs   1.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: sp
rgdal: version: 1.2-18, (SVN revision 718)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.1.3, released 2017/20/01
 Path to GDAL shared files: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/rgdal/gdal
 GDAL binary built with GEOS: FALSE 
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/rgdal/proj
 Linking to sp version: 1.2-7 
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 50-54 (DataExtraction.Rmd) 
Error: processing vignette 'DataExtraction.Rmd' failed with diagnostics:
cannot find ExifTool
Execution halted
Running examples in ‘caRpools-Ex.R’ failed
The error most likely occurred in:

> ### Name: carpools.hit.overview
> ### Title: Analysis: Analysis of pooled CRISPR screening data using a
> ###   Wilcoxon Test
> ### Aliases: carpools.hit.overview
> ### Keywords: ~Analysis
> 
> ### ** Examples
> 
> data(caRpools)
> 
> data.wilcox = stat.wilcox(untreated.list = list(CONTROL1, CONTROL2),
+   treated.list = list(TREAT1,TREAT2), namecolumn=1, fullmatchcolumn=2,
+   normalize=TRUE, norm.fun=median, sorting=FALSE, controls="random",
+   control.picks=NULL)
> 
> 
> data.deseq = stat.DESeq(untreated.list = list(CONTROL1, CONTROL2),
+   treated.list = list(TREAT1,TREAT2), namecolumn=1,
+   fullmatchcolumn=2, extractpattern=expression("^(.+?)(_.+)"),
+   sorting=FALSE, filename.deseq = "ANALYSIS-DESeq2-sgRNA.tab",
+   fitType="parametric")
Error in `rownames<-`(`*tmp*`, value = colnames(countData)) : 
  duplicate rownames not allowed
Calls: stat.DESeq -> <Anonymous> -> rownames<- -> rownames<-
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 1875-1881 (CaRpools.Rmd) 
Error: processing vignette 'CaRpools.Rmd' failed with diagnostics:
duplicate rownames not allowed
Execution halted
Package required but not available: ‘OpenCL’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  slpcovis.cpp:381:12: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/catlearn.Rcheck/00install.out’ for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
Found the following significant warnings:
  ./MCMC_prob.h:2091:41: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/CCMnet.Rcheck/00install.out’ for details.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   9.2Mb
Running examples in ‘census-Ex.R’ failed
The error most likely occurred in:

> ### Name: getCensus
> ### Title: Scrape US Census Data
> ### Aliases: getCensus
> 
> ### ** Examples
> 
> radius <- 5
> cities <- c("Boston", "Los Angeles")
> df <- getCensus(cities, radius)
Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=Boston&sensor=false
Warning: geocode failed with status OVER_QUERY_LIMIT, location = "Boston"
Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=Los%20Angeles&sensor=false
Warning: geocode failed with status OVER_QUERY_LIMIT, location = "Los Angeles"
Error in `[.data.frame`(geo.reply, , c("locality", "lon", "lat")) : 
  undefined columns selected
Calls: getCensus -> [ -> [.data.frame
Execution halted
Found the following significant warnings:
  costfunctions.c:33:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  costfunctions.c:57:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/changepoint.np.Rcheck/00install.out’ for details.
Running ‘test_changepoints.R’ [1s/1s]
Running the tests in ‘tests/test_changepoints.R’ failed.
Last 13 lines of output:
  [1] 88 10
  [1] 12 10
  [1] 89 10
  [1] 11 10
  [1] 90 10
  [1] 10 10
  [1] 77 10
  [1] 23 10
  > stopifnot(changepoints_mod@changepoints == 77)
  > 
  > # test rank one
  > res_ro = rank_one(scp_data, init, update_w=0.1, regularizer=0.1)
  > stopifnot(res_ro$tau == 56)
  Error: res_ro$tau == 56 is not TRUE
  Execution halted
Package suggested but not available for checking: ‘Rmpi’
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/CHAT.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 160-170 (checkmate.Rmd) 
Error: processing vignette 'checkmate.Rmd' failed with diagnostics:
package or namespace load failed for 'ggplot2' in library.dynam(lib, package, package.lib):
 shared object 'plyr.so' not found
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/CircE.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
CircE.Plot: no visible global function definition for ‘dev.new’
CircE.Plot: no visible global function definition for ‘par’
CircE.Plot: no visible global function definition for ‘plot’
CircE.Plot: no visible global function definition for ‘axis’
CircE.Plot: no visible global function definition for ‘title’
CircE.Plot: no visible global function definition for ‘text’
CircE.Plot: no visible global function definition for ‘points’
CircE.Plot: no visible global function definition for ‘abline’
CircE.Plot: no visible global function definition for ‘segments’
Undefined global functions or variables:
  abline axis dev.new par plot points segments text title
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axis", "par", "plot", "points",
             "segments", "text", "title")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/CircStats.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Package required but not available: ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘FRAPO’
Package unavailable to check Rd xrefs: ‘FRAPO’
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  18.2Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/clpAPI.Rcheck/00install.out’ for details.
Packages required but not available: ‘rggobi’ ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Package suggested but not available for checking: ‘SingleCellExperiment’
Package unavailable to check Rd xrefs: ‘SingleCellExperiment’
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘SingleCellExperiment’
Error in .requirePackage(package) : 
  unable to find required package ‘SingleCellExperiment’
Calls: <Anonymous> ... withCallingHandlers -> is -> getClassDef -> .requirePackage
Execution halted
Error in .requirePackage(package) : 
    unable to find required package 'SingleCellExperiment'
  Calls: <Anonymous> ... getClass -> getClassDef -> .classEnv -> .requirePackage
  Execution halted
Running ‘testthat.R’ [19s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: clustree(sim_sc3, prefix = "sc3_", suffix = "_clusters")
  5: .extendsForS3(structure("SingleCellExperiment", package = "SingleCellExperiment"))
  6: extends(Class, maybe = FALSE)
  7: getClassDef(class1)
  8: .requirePackage(package)
  9: stop(gettextf("unable to find required package %s", sQuote(package)), domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 28 SKIPPED: 0 FAILED: 1
  1. Error: SingleCellExperiment interface works (@test-clustree.R#12) 
  
  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 143-147 (clustree.Rmd) 
Error: processing vignette 'clustree.Rmd' failed with diagnostics:
there is no package called 'SingleCellExperiment'
Execution halted
Package suggested but not available for checking: ‘moe430a.db’
Error in re-building vignettes:
  ...

    expand.grid

Loading required package: XML

Attaching package: ‘XML’

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

    toHTML

Loading required package: GO.db

Loading required package: moe430a.db
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘moe430a.db’
Loading required package: RankAggreg
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'clValid.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file ./clValid-022.pdf): PDF inclusion: required page 
does not exist <0>
 ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Combine.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages suggested but not available for checking:
  ‘inSilicoDb’ ‘mogene10sttranscriptcluster.db’
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/CompetingRisk.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  Utility.c:162:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:187:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:211:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:392:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:417:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:442:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/CompRandFld.Rcheck/00install.out’ for details.
Found the following significant warnings:
  date.cpp:167:27: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  date.cpp:167:34: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  date.cpp:167:41: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  date.cpp:169:27: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  date.cpp:169:34: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  date.cpp:169:41: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  date.cpp:171:27: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  date.cpp:171:34: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  date.cpp:171:41: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  date.cpp:173:27: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  date.cpp:173:34: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  date.cpp:173:41: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ConvCalendar.Rcheck/00install.out’ for details.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   6.5Mb
Package suggested but not available for checking: ‘ProData’
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   4.3Mb
Error in re-building vignettes:
  ...

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

    legend

Loading required package: rugarch
Loading required package: parallel

Attaching package: 'rugarch'

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

    sigma


Attaching package: 'rmgarch'

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

    first, last

Quitting from lines 217-225 (CovarianceEstimation.Rmd) 
Error: processing vignette 'CovarianceEstimation.Rmd' failed with diagnostics:
all(sapply(args, function(x) is.zoo(x) || !is.plain(x) || (is.plain(x) &&  .... is not TRUE
Execution halted
Running examples in ‘cowplot-Ex.R’ failed
The error most likely occurred in:

> ### Name: draw_image
> ### Title: Draw an image
> ### Aliases: draw_image
> 
> ### ** Examples
> 
> # Use image as plot background
> p <- ggplot(iris, aes(x = Sepal.Length, fill = Species)) + geom_density(alpha = 0.7)
> ggdraw() +
+   draw_image("http://jeroen.github.io/images/tiger.svg") +
+   draw_plot(p + theme(legend.box.background = element_rect(color = "white")))
Error in magick_image_readpath(path, density, depth, strip) : 
  Magick: unable to open file '/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//Rtmpephi1C/magick-79137e1BGimjmQbQJ': No such file or directory @ error/constitute.c/ReadImage/549
Calls: draw_image -> <Anonymous> -> magick_image_readpath
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: cowplot
Loading required package: ggplot2

Attaching package: 'cowplot'

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

    ggsave

Loading required package: grid
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: viridisLite
Quitting from lines 218-222 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
Magick: unable to open file '/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmpBHxdct/magick-80307qphDOiydIf8w': No such file or directory @ error/constitute.c/ReadImage/549
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is 37.7Mb
  sub-directories of 1Mb or more:
    libs  37.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/cplexAPI.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 76-77 (cranly.Rmd) 
Error: processing vignette 'cranly.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package required but not available: ‘clusterProfiler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Rglpk’
Error in re-building vignettes:
  ...
  Used default patient IDs!
Loading required package: dplyr

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: tidyr
Warning in Data(x = c(25, 50, 50, 75, 100, 100, 225, 300), y = c(0, 0, 0,  :
  Used default patient IDs!
Warning in Data(x = c(25, 50, 50, 75, 100, 100, 225, 300), y = c(0, 0, 0,  :
  Used best guess cohort indices!
Warning: Removed 658 rows containing non-finite values (stat_density).
Warning: Removed 828 rows containing non-finite values (stat_density).
Warning: Removed 1 rows containing missing values (geom_vline).
Warning: Removed 1 rows containing missing values (geom_text).

Timing stopped at: 149.6 1.468 254.9
Execution halted
installed size is 21.9Mb
  sub-directories of 1Mb or more:
    libs  20.2Mb
Running ‘spelling.R’ [8s/8s]
  Comparing ‘spelling.Rout’ to ‘spelling.Rout.save’ ... OK
  Running ‘testthat.R’ [40s/41s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
      table
  
  
  [31m──[39m [31m1. Failure: checkInstalledPackages (@test-misc.R#208) [39m [31m──────────────────────[39m
  `checkInstalledPackages(c("not", "installed"))` threw an error with unexpected message.
  Expected match: "Missing required packages: \"not\" and \"installed\""
  Actual message: "Missing required packages: \"installed\""
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2590 SKIPPED: 14 FAILED: 1
  1. Failure: checkInstalledPackages (@test-misc.R#208) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ctsem.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Error in re-building vignettes:
  ...

Begin fit attempt 2 of at maximum 16 tries

 Lowest minimum so far:  4203.31303320986

Solution found

NPSOL optimizer not available - switching to CSOLNP - consider installing OpenMx using command:  source('http://openmx.psyc.virginia.edu/getOpenMx.R') 
Running ctsem with 19 parameters
Unique discreteDRIFT calculations per step required = 5
Unique discreteCINT calculations per step required = 5
Unique discreteDIFFUSION calculations per step required = 5
2 / 2 latent variables required for covariance calculations
Compiling model, ignore forthcoming warning re number of chains...
the number of chains is less than 1; sampling not done
Sampling...
error occurred during calling the sampler; sampling not done
error occurred during calling the sampler; sampling not done
Warning in .local(object, ...) :
  some chains had errors; consider specifying chains = 1 to debug
here are whatever error messages were returned
Quitting from lines 294-295 (hierarchical.rnw) 
Error: processing vignette 'hierarchical.rnw' failed with diagnostics:
argument is of length zero
Execution halted
Package which this enhances but not available for checking: ‘pbdMPI’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/cudaBayesreg.Rcheck/00install.out’ for details.
Running examples in ‘curl-Ex.R’ failed
The error most likely occurred in:

> ### Name: curl_echo
> ### Title: Echo Service
> ### Aliases: curl_echo
> 
> ### ** Examples
> 
> h <- handle_setform(new_handle(), foo = "blabla", bar = charToRaw("test"),
+ myfile = form_file(system.file("DESCRIPTION"), "text/description"))
> formdata <- curl_echo(h)
Error in curl_fetch_memory(paste0("http://localhost:", port, "/"), handle = handle) : 
  Callback aborted
Calls: curl_echo -> curl_fetch_memory
Execution halted
Running ‘spelling.R’ [1s/2s]
  Comparing ‘spelling.Rout’ to ‘spelling.Rout.save’ ... OK
  Running ‘testthat.R’ [7s/50s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > 
  > test_check("curl")
  This is libcurl version 7.43.0 with SecureTransport 
  Using test server: http://hb.opencpu.org 
  ── 1. Error: echo large data (@test-echo.R#7)  ─────────────────────────────────
  Callback aborted
  1: curl::curl_echo(handle = handle) at testthat/test-echo.R:7
  2: curl_fetch_memory(paste0("http://localhost:", port, "/"), handle = handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 175 SKIPPED: 1 FAILED: 1
  1. Error: echo large data (@test-echo.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Package which this enhances but not available for checking: ‘RGtk2’
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   4.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 177-179 (cycling_data_analysis.Rmd) 
Error: processing vignette 'cycling_data_analysis.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    libs  18.7Mb
Running ‘testthat.R’ [9s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Sparseness = 76.3 %
  Sorting covariates by covariateId and rowId
  ── 1. Failure: Data errors and casting in COO-constructor (@test-xyConstructor.R
  `loadNewSeqlCyclopsDataMultipleX(dataPtr, c(1, 1), c(1, 1), NULL)` threw an error with unexpected message.
  Expected match: "1 - 1"
  Actual message: "c++ exception (unknown reason)"
  
  Sparseness = 99.09 %
  Sorting covariates by covariateId and rowId
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 201 SKIPPED: 17 FAILED: 1
  1. Failure: Data errors and casting in COO-constructor (@test-xyConstructor.R#212) 
  
  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 27-38 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  iterator.cpp:138:17: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  iterator_functions.cpp:12:8: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  iterator_functions.cpp:30:8: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  iterator_functions.cpp:48:8: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/DatABEL.Rcheck/00install.out’ for details.
Packages required but not available: ‘RGtk2’ ‘gWidgets2RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshota85b6d14dca4.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshota85b6d14dca4.png': No such file or directory
Quitting from lines 57-68 (dataexplorer-intro.Rmd) 
Error: processing vignette 'dataexplorer-intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 26-34 (get_started.Rmd) 
Error: processing vignette 'get_started.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 55.7Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  53.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
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]="./webshot59596837133b.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot59596837133b.png': No such file or directory
Quitting from lines 512-515 (data.tree.Rmd) 
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘gWidgetsRGtk2’
Package required but not available: ‘SDD’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   5.3Mb
Running examples in ‘ddeploy-Ex.R’ failed
The error most likely occurred in:

> ### Name: duke_deploy
> ### Title: Deploy model using REST API
> ### Aliases: duke_deploy
> 
> ### ** Examples
> 
> duke_auth <- list(
+ user_name = "try_it",
+ api_key   = "db1542b66f16aba5768d8a19c27dec4facf9168a",
+ endpoint = "/api/v1.0"
+ )
> example_data <- as.data.frame(cbind(gl(3,50),rnorm(150)));names(example_data) <- c("x","y")
> example_fit  <- lm(y~x,data=example_data)
> duke_deploy(auth_details=duke_auth,model_object=example_fit)
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: Connection timed out after 10002 milliseconds
Calls: duke_deploy ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
  Note: next used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/debug.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘debug.Recall’ ‘debug.eval’ ‘debug.eval.guts’ ‘debug.fun.name’
  ‘evaluator’ ‘find.debug.HQ’ ‘mvb.sys.on.exit’ ‘stepping’
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
Packages required but not available:
  ‘BSgenome’ ‘BSgenome.Hsapiens.UCSC.hg19’

Package suggested but not available for checking: ‘VariantAnnotation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...

    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
Found the following significant warnings:
  DEploid/updateHap.cpp:670:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
  DEploid/updateHap.cpp:678:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
  DEploid/updateHap.cpp:681:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
  DEploid/updateHap.cpp:682:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/DEploid.Rcheck/00install.out’ for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.7Mb
    help   1.4Mb
    libs   1.5Mb
Package required but not available: ‘Rglpk’

Packages suggested but not available for checking:
  ‘gurobi’ ‘Rcplex’ ‘Rsymphony’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs  18.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/devEMF.Rcheck/00install.out’ for details.
Running ‘has-devel.R’ [1s/2s]
  Running ‘test-that.R’ [136s/203s]
Running the tests in ‘tests/test-that.R’ failed.
Last 13 lines of output:
      setup
  
  ── 1. Failure: remote_sha.github_remote returns expected value if remote does ex
  remote_sha(github_remote("hadley/devtools@v1.8.0")) not equal to "ad9aac7b9a522354e1ff363a86f389e32cec181b".
  1/1 mismatches
  x[1]: NA
  y[1]: "ad9aac7b9a522354e1ff363a86f389e32cec181b"
  
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 393 SKIPPED: 10 FAILED: 1
  1. Failure: remote_sha.github_remote returns expected value if remote does exist (@test-remotes.r#75) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 48.4Mb
  sub-directories of 1Mb or more:
    libs  48.0Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   9.6Mb
Running examples in ‘dgmb-Ex.R’ failed
The error most likely occurred in:

> ### Name: dgmb-package
> ### Title: Simulating Data for PLS Mode B Structural Models
> ### Aliases: dgmb-package dgmb
> ### Keywords: package
> 
> ### ** Examples
> 
> dgmbGui()
 --------------------------------------------------
| Simulating Data for PLS Mode B Structural Models |
| Version: 1.2                                     |
| Depends: abind, tcltk, MASS                      |
| Licence: GPL >= 2                                |
| System Requirements: tktable, BWidget            |
 --------------------------------------------------
Warning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "ComboBox".
Calls: dgmbGui -> tkwidget -> tcl -> .Tcl.objv -> structure
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: 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
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/dhglm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages required but not available: ‘missMethyl’ ‘methylumi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/diffusionMap.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
Error in globalVariables(c("C", "R", "key.row", "key.col", "label.row",  : 
  could not find function "globalVariables"
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    include  16.2Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   4.5Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading dodgr
Quitting from lines 117-144 (benchmark.Rmd) 
Error: processing vignette 'benchmark.Rmd' failed with diagnostics:
polygon edge not found
Execution halted
Package unavailable to check Rd xrefs: ‘doMPI’
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
Running ‘testthat.R’ [15s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  3: eval_bare(get_expr(quo), get_env(quo))
  4: summarise(gdf, out = 1:2)
  5: summarise.tbl_df(gdf, out = 1:2)
  6: summarise_impl(.data, dots)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2670 SKIPPED: 6 FAILED: 3
  1. Error: mutate() supports unquoted values (@test-mutate.r#721) 
  2. Failure: summarise() supports unquoted values (@test-summarise.r#980) 
  3. Error: summarise() supports unquoted values (@test-summarise.r#985) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  call dbDisconnect() when finished working with a connection 
  Execution halted
Found the following significant warnings:
  gibbsclustersamplealpha.cc:95:8: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  gibbsclustersamplealpha.cc:140:9: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/dpmixsim.Rcheck/00install.out’ for details.
File ‘DPpackage/libs/DPpackage.so’:
  Found ‘__gfortran_st_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 ‘__gfortran_st_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 ‘__gfortran_st_read’, possibly from ‘read’ (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDDPdensity.o’, ‘LDDPsurvival.o’,
      ‘LDPDdoublyintsba.o’, ‘PSgamgam.o’, ‘PSgamgauss.o’,
      ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’, ‘ToolsLDTFP.o’
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDBDPdensity.o’, ‘LDDPdensity.o’,
      ‘LDDPsurvival.o’, ‘LDPDdoublyintsba.o’, ‘LDTFPdensity.o’,
      ‘LDTFPglmmpois.o’, ‘LDTFPsurvival.o’, ‘PSgamgam.o’,
      ‘PSgamgauss.o’, ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  compnoreggilks.cpp:31:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compnoreggilks.cpp:90:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:32:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:88:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:150:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:207:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:380:8: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/DPWeibull.Rcheck/00install.out’ for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   4.2Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/dvfBm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
'library' or 'require' call to ‘wmtsa’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘wmtsa’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
perturbFBM: warning in circFBM(n, H, plot = FALSE): partial argument
  match of 'plot' to 'plotfBm'
circFBM: no visible global function definition for ‘fft’
circFBM: no visible global function definition for ‘rnorm’
circFBM: no visible global function definition for ‘par’
circFBM: no visible global function definition for ‘plot’
dvFBM: no visible global function definition for ‘filter’
dvFBM: no visible global function definition for ‘quantile’
dvFBM: no visible global function definition for ‘lm’
dvFBM: no visible global function definition for ‘plot’
dvFBM: no visible global function definition for ‘abline’
filt: no visible global function definition for ‘wavDaubechies’
perturbFBM: no visible global function definition for ‘rnorm’
perturbFBM: no visible global function definition for ‘rbinom’
perturbFBM: no visible global function definition for ‘par’
perturbFBM: no visible global function definition for ‘segments’
perturbFBM: no visible global function definition for ‘points’
Undefined global functions or variables:
  abline fft filter lm par plot points quantile rbinom rnorm segments
  wavDaubechies
Consider adding
  importFrom("graphics", "abline", "par", "plot", "points", "segments")
  importFrom("stats", "fft", "filter", "lm", "quantile", "rbinom",
             "rnorm")
to your NAMESPACE file.
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.2Mb
    libs  15.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Package required but not available: ‘sdcTable’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘EBS/libs/EBS.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘GeneralFunctions.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ecospat.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is 56.3Mb
  sub-directories of 1Mb or more:
    libs  55.6Mb
File ‘elrm/libs/elrm.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Objects: ‘binomMCMC.o’, ‘functions.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘binomMCMC.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 suggested but not available for checking: ‘hgu133plus2.db’ ‘lumi’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/emIRT.Rcheck/00install.out’ for details.
Running examples in ‘EmiStatR-Ex.R’ failed
The error most likely occurred in:

> ### Name: CInp2TS
> ### Title: Function to convert Constant Input to Time Series
> ### Aliases: CInp2TS
> ### Keywords: CInp2TS
> 
> ### ** Examples
> 
> library(EmiStatR)
> library(xts)
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

> 
> data("Esch_Sure2010")
> 
> cinp            <- 150 # water consumption [m3/h]
> prec            <- Esch_Sure2010[1:1000,] # selecting just the first 1,000 rows
> cinp.daily.dir  <- system.file("shiny/EmiStatR_inputCSO/inputCSO", package = "EmiStatR")
> cinp.daily.file <- paste(cinp.daily.dir, "/qs_factor.csv", sep="")
> cinp.weekly     <- list(mon=1, tue=.83, wed=.83, thu=.83, fri=1, sat=1.25, sun=1.25)  
> # factors average to 1
> cinp.seasonal   <- list(jan=.79, feb=.79, mar=1.15, apr=1.15, may=1.15, jun=1.15,
+                         jul=1.15, aug=1.15, sep=1.15, oct=1.15, nov=.79, dec=.79) 
> # factors average to 1
> 
> ts1 <- CInp2TS(cinp, prec, cinp.daily.file, cinp.weekly, cinp.seasonal)
Error in `[.xts`(cinp.ts.deltap, 1:nrow(P1), ) : subscript out of bounds
Calls: CInp2TS -> [ -> [.xts
Execution halted
Running ‘testthat.R’ [82s/134s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  18: as(set_TextType(methods_file), "description")
  19: .class1(object)
  20: set_TextType(methods_file)
  21: to_docbook(file)
  22: pandoc_convert(basename(file), to = "docbook", output = normalizePath(docbook_file, 
         winslash = "/", mustWork = FALSE), options = "-s")
  23: stop("pandoc document conversion failed with error ", result, call. = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 78 SKIPPED: 5 FAILED: 2
  1. Error: We return TRUE when validating a valid just created eml object with latin1 encoding (@test-validation.R#75) 
  2. Error: We return TRUE when validating a valid just created eml object (@test-validation.R#89) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.5Mb
Packages required but not available: ‘xcms’ ‘MSnbase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/EnvStats.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  input2.c:767:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/epanet2toolkit.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.
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]="./webshot54225f141465.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot54225f141465.png': No such file or directory
Quitting from lines 150-151 (epicontacts.Rmd) 
Error: processing vignette 'epicontacts.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/EpiWeek.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Package required but not available: ‘rpanel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Running ‘testthat.R’ [2s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  trying URL 'http://ec.europa.eu/eurostat/estat-navtree-portlet-prod/BulkDownloadListing?sort=1&file=data%2Ftsdtr210.tsv.gz'
  downloaded 16 KB
  
  ── 1. Error: (unknown) (@test-all.R#112)  ──────────────────────────────────────
  tsdtr210 does not exist or is not readable
  1: get_eurostat("tsdtr210", type = "label", keepFlags = T, cache = FALSE) at testthat/test-all.R:112
  2: get_eurostat_raw(id)
  3: stop(id, " does not exist or is not readable")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 14 FAILED: 1
  1. Error: (unknown) (@test-all.R#112) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/eVenn.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running examples in ‘evolqg-Ex.R’ failed
The error most likely occurred in:

> ### Name: LModularity
> ### Title: L Modularity
> ### Aliases: LModularity
> 
> ### ** Examples
> 
> # A modular matrix:
> modules = matrix(c(rep(c(1, 0, 0), each = 5),
+ rep(c(0, 1, 0), each = 5),
+ rep(c(0, 0, 1), each = 5)), 15)
> cor.hypot = CreateHypotMatrix(modules)[[4]]
> hypot.mask = matrix(as.logical(cor.hypot), 15, 15)
> mod.cor = matrix(NA, 15, 15)
> mod.cor[ hypot.mask] = runif(length(mod.cor[ hypot.mask]), 0.8, 0.9) # within-modules
> mod.cor[!hypot.mask] = runif(length(mod.cor[!hypot.mask]), 0.3, 0.4) # between-modules
> diag(mod.cor) = 1
> mod.cor = (mod.cor + t(mod.cor))/2 # correlation matrices should be symmetric
> 
> LModularity(mod.cor)
Error in method(g, ...) : 
  At optimal_modularity.c:85 : GLPK is not available, Unimplemented function call
Calls: LModularity -> method
Execution halted
Running ‘testthat.R’ [173s/275s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Loading required package: plyr
  ── 1. Error: LModularity resturn resonable results (@test.LModularity.r#12)  ───
  At optimal_modularity.c:85 : GLPK is not available, Unimplemented function call
  1: expect_equal(modules, LModularity(mod.cor)[[2]]) at testthat/test.LModularity.r:12
  2: quasi_label(enquo(expected), expected.label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: LModularity(mod.cor)
  5: method(g, ...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 20953 SKIPPED: 1 FAILED: 1
  1. Error: LModularity resturn resonable results (@test.LModularity.r#12) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘exams-Ex.R’ failed
The error most likely occurred in:

> ### Name: exams2openolat
> ### Title: Generation of Exams for OpenOLAT
> ### Aliases: exams2openolat
> ### Keywords: utilities
> 
> ### ** Examples
> 
> ## load package and enforce par(ask = FALSE)
> library("exams")
> options(device.ask.default = FALSE)
> 
> ## define an exams (= list of exercises)
> myexam <- list(
+   "boxplots",
+   c("tstat", "ttest", "confint"),
+   c("regression", "anova"),
+   c("scatterplot", "boxhist"),
+   "relfreq"
+ )
> 
> ## output directory
> mydir <- tempdir()
> 
> ## generate .zip with OpenOLAT test in temporary directory
> exams2openolat(myexam, n = 3, dir = mydir)
Loading required namespace: rmarkdown
sh: +RTS: command not found
Warning in system(command) : error in running command
Error: pandoc document conversion failed with error 127
Execution halted
Functions or methods with usage in documentation object 'COMStop' but not in code:
  lapply sapply getItemClassName EnumValue createTypeVarName
Running examples in ‘excerptr-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_excerpts
> ### Title: Clone the Excerpts Code from <URL: github.com>
> ### Aliases: get_excerpts
> 
> ### ** Examples
> 
> path <- file.path(tempdir(), "excerpts")
> get_excerpts(directory = path, force = TRUE)
cloning into '/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmpbDe1OS/excerpts'...
Error in git2r::clone(url = "https://github.com/fvafrCU/excerpts/", branch = branch,  : 
  Error in 'git2r_clone': SSL error: error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
Calls: get_excerpts -> <Anonymous> -> <Anonymous>
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > test_check("excerptr")
  cloning into '/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//Rtmpodjq7f'...
  ── 1. Error: get (@test_basic.R#9)  ────────────────────────────────────────────
  SSL error: error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
  1: get_excerpts(directory = tempdir()) at testthat/test_basic.R:9
  2: git2r::clone(url = "https://github.com/fvafrCU/excerpts/", branch = branch, local_path = directory)
  3: git2r::clone(url = "https://github.com/fvafrCU/excerpts/", branch = branch, local_path = directory)
  
  3
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 4 SKIPPED: 0 FAILED: 1
  1. Error: get (@test_basic.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    exiftool  12.3Mb
Packages required but not available: ‘Rsamtools’ ‘GenomicAlignments’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/FACTscorer.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/fArma.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  15.3Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.3Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  16.8Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      4.9Mb
Found the following significant warnings:
  Rconnection.cc:347:12: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  Rconnection.cc:356:12: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/FastRWeb.Rcheck/00install.out’ for details.
Note: information on .o files is not available
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.1Mb
Found the following significant warnings:
  fcnn/level2.cpp:82:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  fcnn/level2.cpp:119:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  fcnn/level2.cpp:165:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/FCNN4R.Rcheck/00install.out’ for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is 35.6Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  32.5Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   5.5Mb
Package required but not available: ‘Fgmutils’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘test-as-dgCMatrix.R’ [3s/4s]
  Running ‘test-empty_array.R’ [3s/4s]
  Running ‘test-existence_collision.R’ [2s/4s]
  Running ‘test-hash.mapping.R’ [2s/4s]
  Running ‘test-hashing.R’ [3s/4s]
Running the tests in ‘tests/test-hashing.R’ failed.
Last 13 lines of output:
  +     if (class(e)[1] != "std::invalid_argument") stop(e)
  +     if (conditionMessage(e) != "Failed to find the column:PlAnT") stop(e)
  +   })
  +   
  +   m <- hashed.model.matrix(~ Plant:Type:Treatment, CO2, create.mapping = TRUE, signed.hash = TRUE)
  +   map <- hash.mapping(m)
  +   map <- map[grepl("\\w+:\\w+:\\w+", names(map))]
  +   checkTrue(all(hashed.interaction.value(names(map)) %% (2^18) + 1== map),
  +             "The hashed.interaction.value gives inconsistent result of hashed.model.matrix")
  + }
  Loading required package: RUnit
  Error in .hashed.model.matrix.dataframe(tf, data, hash.size, transpose,  : 
    c++ exception (unknown reason)
  Calls: tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
  Execution halted
Running ‘testthat.R’ [10s/57s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Invalid query: Cannot open database "SDM" requested by the login. The login failed.
  Login failed for user 'sdawebsql'.
  1: soilDB::SDA_query(q) at testthat/test.SSURGO.R:28
  2: stop(error.msg)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 23 SKIPPED: 0 FAILED: 2
  1. Error: The SoilDB data queries work (@test.SSURGO.R#17) 
  2. Error: The SSURGO datasets are available at the correct URL (@test.SSURGO.R#28) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  In cntns[[class]] <- subs[[i]] :
    closing unused connection 4 (ftp://ftp.ncdc.noaa.gov/pub/data/paleo/treering/chronologies/)
  Execution halted
Package required and available but unsuitable version: ‘bit’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/fifer.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
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:
cannot open the connection
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/FisherEM.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages in Depends field not imported from:
  ‘MASS’ ‘elasticnet’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages required but not available: ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’

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.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 22-24 (fitbitScraper-examples.Rmd) 
Error: processing vignette 'fitbitScraper-examples.Rmd' failed with diagnostics:
login failed
Execution halted
Package suggested but not available for checking: ‘devEMF’
Error in re-building vignettes:
  ...
Warning in engine$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 38-49 (Using_fontHind.Rmd) 
Error: processing vignette 'Using_fontHind.Rmd' failed with diagnostics:
polygon edge not found
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 56-67 (Using_fontMPlus.Rmd) 
Error: processing vignette 'Using_fontMPlus.Rmd' failed with diagnostics:
polygon edge not found
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 168-169 (formattable-data-frame.Rmd) 
Error: processing vignette 'formattable-data-frame.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/fpc.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Package required but not available: ‘Rglpk’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/frailtyHL.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
Found the following significant warnings:
  psplines.c:975:16: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  psplines.c:1087:15: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/freeknotsplines.Rcheck/00install.out’ for details.
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    libs  21.5Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Package suggested but not available for checking: ‘RTCGA.rnaseq’
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   8.7Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
Running examples in ‘funcy-Ex.R’ failed
The error most likely occurred in:

> ### Name: funcyOutList-class
> ### Title: Class '"funcyOutList"'
> ### Aliases: funcyOutList-class funcyOutList
> ### Keywords: classes
> 
> ### ** Examples
> 
> set.seed(2808)
> ds <- sampleFuncy(obsNr=30, k=4, timeNr=7)
> data <- Data(ds)
> clusters <- Cluster(ds)
> 
> res <- funcit(data=data, clusters=clusters, seed=2808,
+               methods=1:5, k=4, parallel=TRUE)
Warning in funclustWrapper(data = data, k = k, reg = reg, regTime = regTime,  :
  It is not possible to set a seed for method funclust.
4 :Loading required namespace: funHDDC
 * *4 : * * *Warning in funHDDCWrapper(data = data, k = k, reg = reg, regTime = regTime,  :
  Clustering with 4 classes is not possible. 3 clusters are used!
 *Warning in funHDDCWrapper(data, k, reg, regTime, funcyCtrlMbc, model = "AkBkQkDk",  :
  Clustering with 3 classes is not possible. 2 clusters are used!

Warning in funHDDCWrapper(data, k, reg, regTime, funcyCtrlMbc, model = "AkBkQkDk",  :
  Clustering with 2 classes is not possible. 1 clusters are used!
Warning in Funclustering::funclust(fd = fd, K = k, thd = thd, increaseDimension = increaseDimension,  :
  Convergence of the algorithm to a solution with at least one empty cluster.
            Restart or a choose a smaller value for K = 4
Warning in funHDDCWrapper(data, k, reg, regTime, funcyCtrlMbc, model = "AkBkQkDk",  :
  Clustering with 1 classes is not possible. 0 clusters are used!

Error in funcit(data = data, clusters = clusters, seed = 2808, methods = 1:5,  : 
  Method funHDDC : Clustering for this data not possible.
Execution halted
Running ‘testMethods.R’ [52s/57s]
Running the tests in ‘tests/testMethods.R’ failed.
Last 13 lines of output:
  + }
  Loading required package: flexclust
  Loading required package: grid
  Loading required package: lattice
  Loading required package: modeltools
  Loading required package: stats4
  Loading required package: splines
  Loading required namespace: Funclustering
  Loading required namespace: funHDDC
  5 : * *5 : * * * *
  5 : * * *
  
  Error in funcit(methods = methods, data = ds@data, k = k, clusters = ds@clusters,  : 
    Method funHDDC : Clustering for this data not possible.
  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 604-605 (futureheatwaves.Rmd) 
Error: processing vignette 'futureheatwaves.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package required but not available: ‘ROI.plugin.glpk’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘doMPI’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   3.5Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   6.4Mb
installed size is 66.3Mb
  sub-directories of 1Mb or more:
    libs  65.9Mb
installed size is 49.5Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     46.3Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  13.9Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Found the following significant warnings:
  cGetHCS.c:9:33: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  cIdentical.c:9:34: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/gdmp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/GenABEL.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.7Mb
Package required but not available: ‘ShortRead’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
timedelay.lm: no visible global function definition for ‘lm’
timedelay.lm: no visible global function definition for ‘AIC’
timedelay.lm: no visible global function definition for ‘pdf’
timedelay.lm: no visible global function definition for ‘x11’
timedelay.lm: no visible global function definition for ‘rainbow’
timedelay.lm: no visible global function definition for ‘title’
timedelay.lm: no visible global function definition for ‘lines’
timedelay.lm: no visible global function definition for ‘predict’
timedelay.lm: no visible global function definition for ‘points’
timedelay.lm: no visible global function definition for ‘legend’
timedelay.lm: no visible global function definition for ‘dev.off’
timedelay.univariate.lm: no visible global function definition for ‘lm’
timedelay.univariate.lm: no visible global function definition for
  ‘AIC’
ts.bspline: no visible global function definition for ‘lm’
ts.bspline: no visible global function definition for ‘predict’
Undefined global functions or variables:
  AIC dev.off legend lines lm pdf points predict rainbow title x11
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "rainbow", "x11")
  importFrom("graphics", "legend", "lines", "points", "title")
  importFrom("stats", "AIC", "lm", "predict")
to your NAMESPACE file.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    exdata   5.0Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'User_manual.tex' failed.
LaTeX errors:
! Package babel Error: Unknown option `USenglish'. Either you misspelled it
(babel)                or the language definition file USenglish.ldf was not fo
und.

See the babel package documentation for explanation.
! Package babel Error: You haven't specified a language option.

See the babel package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘KEGG.db’ ‘reactome.db’
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.4Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/geo.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Unexported objects imported by ':::' calls:
  ‘maps:::makepoly’ ‘maps:::mapgetg’ ‘maps:::mapgetl’ ‘maps:::mapname’
  See the note in ?`:::` about the use of this operator.
Error in setClass("Extent", representation(xmin = "numeric", xmax = "numeric",  : 
  could not find function "setClass"
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/gettingtothebottom.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
example.alpha: no visible global function definition for ‘rnorm’
example.quadratic.approx: no visible global function definition for
  ‘rnorm’
generate_nnm: no visible global function definition for ‘rnorm’
generate_nnm: no visible global function definition for ‘rgamma’
generate_nnm: no visible global function definition for ‘dnorm’
plot_nnm: no visible global function definition for ‘stack’
testmatrix: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  dnorm rgamma rnorm stack
Consider adding
  importFrom("stats", "dnorm", "rgamma", "rnorm")
  importFrom("utils", "stack")
to your NAMESPACE file.
Package suggested but not available for checking: ‘RGtk2’
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 106-107 (IntroductionToGFD.Rmd) 
Error: processing vignette 'IntroductionToGFD.Rmd' failed with diagnostics:
there is no package called 'RGtk2'
Execution halted
Running examples in ‘GGEBiplotGUI-Ex.R’ failed
The error most likely occurred in:

> ### Name: GGEBiplot
> ### Title: GGEBiplotGUI: Interactive GGE Biplots in R
> ### Aliases: GGEBiplot
> 
> ### ** Examples
> 
> data(Ontario)
> GGEBiplot(Data = Ontario)
Warning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "ComboBox".
Calls: GGEBiplot -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
OMP: Error #15: Initializing libomp.dylib, but found libomp.dylib already initialized.
OMP: Hint This means that multiple copies of the OpenMP runtime have been linked into the program. That is dangerous, since it can degrade performance or cause incorrect results. The best thing to do is to ensure that only a single OpenMP runtime is linked into the process, e.g. by avoiding static linking of the OpenMP runtime in any library. As an unsafe, unsupported, undocumented workaround you can set the environment variable KMP_DUPLICATE_LIB_OK=TRUE to allow the program to continue to execute, but that may cause crashes or silently produce incorrect results. For more information, please see http://openmp.llvm.org/
Error in re-building vignettes:
  ...
Warning in engine$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
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]="./webshotb92b226b1dfb.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotb92b226b1dfb.png': No such file or directory
Quitting from lines 28-33 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'gglogo'

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

    fortify

Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Garamond"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Garamond"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Garamond"
Quitting from lines 46-52 (gglogo-alphabet.Rmd) 
Error: processing vignette 'gglogo-alphabet.Rmd' failed with diagnostics:
replacement has 1 row, data has 0
Execution halted
Error in re-building vignettes:
  ...
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Quitting from lines 142-143 (using_ggmcmc.Rmd) 
Error: processing vignette 'using_ggmcmc.Rmd' failed with diagnostics:
polygon edge not found
Execution halted
Error in re-building vignettes:
  ...

Backtrace for this error:
#0  0x129b9e579
#1  0x129b9d945
#2  0x7fff93ac4529
sh: line 1: 89501 Trace/BPT trap: 5       /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/x13ashtml /var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmppExnyS/x1315bc558df5aa/iofile -n -s 2> /dev/null
dyld: lazy symbol binding failed: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib


Program received signal SIGTRAP: Trace/breakpoint trap.

Backtrace for this error:
#0  0x125f5f579
#1  0x125f5e945
#2  0x7fff93ac4529
Quitting from lines 125-126 (ggsdc.Rmd) 
Error: processing vignette 'ggsdc.Rmd' failed with diagnostics:
X-13 has returned a non-zero exist status, which means that the current spec file cannot be processed for an unknown reason.
Execution halted
Running ‘test-all.R’ [1s/3s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  8: git2r::fetch(gitrepo, name = "github", credentials = credentials)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 9 SKIPPED: 0 FAILED: 8
  1. Error: Install a single package (@test_install.R#8) 
  2. Error: Install a single package, removing old install (@test_install.R#14) 
  3. Error: Install a single package w/o vignettes (@test_install.R#19) 
  4. Error: Install from a branch (@test_install.R#25) 
  5. Error: Install from a commit ref (@test_install.R#36) 
  6. Error: Install from a tag (@test_install.R#42) 
  7. Error: Install from a pull request (@test_install.R#49) 
  8. Error: (unknown) (@test_internal.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  openssl.c:420:31: warning: incompatible pointer types assigning to 'int (*)(EVP_CIPHER_CTX *, unsigned char *, const unsigned char *, unsigned int)' (aka 'int (*)(struct evp_cipher_ctx_st *, unsigned char *, const unsigned char *, unsigned int)') from 'int (EVP_CIPHER_CTX *, unsigned char *, const unsigned char *, size_t)' (aka 'int (struct evp_cipher_ctx_st *, unsigned char *, const unsigned char *, unsigned long)') [-Wincompatible-pointer-types]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/git2r.Rcheck/00install.out’ for details.
Package required but not available: ‘rtracklayer’

Packages suggested but not available for checking:
  ‘BSgenome.Hsapiens.UCSC.hg18.masked’
  ‘BSgenome.Hsapiens.UCSC.hg19.masked’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 40.7Mb
  sub-directories of 1Mb or more:
    libs  40.3Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Errors in running code in vignettes:
when running code in ‘openbugs.Rnw’
  ...
+     kResult = try(R2OpenBUGS::bugs(forBugs$ragged, inits = int2, 
+         model.file = "bym.txt", n.chain = 2, n.iter = .... [TRUNCATED] 

> if (!is.null(kResult)) {
+     kParams = restoreParams(kResult, forBugs$ragged)
+ }

  When sourcing ‘openbugs.R’:
Error: $ operator is invalid for atomic vectors
Execution halted
Error in re-building vignettes:
  ...
Linked to JAGS 4.2.0
Loaded modules: basemod,bugs

Attaching package: ‘R2jags’

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

    traceplot

module glm loaded
To access larger datasets in this package, install the spDataLarge
package with: `install.packages('spDataLarge',
repos='https://nowosad.github.io/drat/', type='source'))`

Error: processing vignette 'openbugs.Rnw' failed with diagnostics:
 chunk 12 (label = postprocessKentucky) 
Error : $ operator is invalid for atomic vectors
Execution halted
installed size is 40.3Mb
  sub-directories of 1Mb or more:
    libs  39.4Mb
installed size is 60.4Mb
  sub-directories of 1Mb or more:
    libs  59.2Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/glpkAPI.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Evaluation.cpp:173:9: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to true [-Wtautological-undefined-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/gnmf.Rcheck/00install.out’ for details.
File ‘gnmf/libs/gnmf.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘FactorMatrix.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘FactorMatrix.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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 34-35 (installation-and-authentication.Rmd) 
Error: processing vignette 'installation-and-authentication.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'intro.Rmd' failed with diagnostics:
shared object 'stringi.so' not found
Execution halted
Errors in running code in vignettes:
when running code in ‘GPPFourier.Rnw’
  ...
+     pch = 19, type = "b", xlab = "time", ylab = "GPP", xlim = as.POSIXct(c("2010-01-01 ..." ... [TRUNCATED] 

> par(mfrow = c(2, 1), cex = 2)

> plot(Kruibeke, pch = 20, xlim = as.POSIXct(c("2010-01-01", 
+     "2010-12-31")))

  When sourcing ‘GPPFourier.R’:
Error: figure margins too large
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/GPseq.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
calc_chisq_statistic: no visible global function definition for ‘dpois’
generalized_poisson_likelihood: no visible global function definition
  for ‘var’
perform_permutation_de: no visible binding for global variable ‘rbinom’
perform_permutation_de: no visible global function definition for ‘var’
perform_permutation_ds: no visible binding for global variable ‘rbinom’
perform_permutation_ds: no visible global function definition for ‘var’
Undefined global functions or variables:
  dpois rbinom var
Consider adding
  importFrom("stats", "dpois", "rbinom", "var")
to your NAMESPACE file.
installed size is 44.3Mb
  sub-directories of 1Mb or more:
    libs  41.7Mb
Packages required but not available: ‘RGtk2’ ‘gWidgetsRGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
Running examples in ‘gtools-Ex.R’ failed
The error most likely occurred in:

> ### Name: unByteCode
> ### Title: Convert a Byte-Code Function to an Interpreted-Code Function
> ### Aliases: unByteCode unByteCodeAssign assignEdgewise
> ### Keywords: programming utilites
> 
> ### ** Examples
> 
> datURL <- "https://bugs.r-project.org/bugzilla/attachment.cgi?id=1659"
> dat <- as.matrix(read.csv(file=datURL, row.names=1))
Warning in file(file, "rt") :
  cannot open URL 'https://bugs.r-project.org/bugzilla/attachment.cgi?id=1659': HTTP status was '500 Internal Server Error'
Error in file(file, "rt") : 
  cannot open the connection to 'https://bugs.r-project.org/bugzilla/attachment.cgi?id=1659'
Calls: as.matrix -> read.csv -> read.table -> file
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.
sh: line 1: 29372 Trace/BPT trap: 5       /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/x13ashtml /var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmpjUDYzi/x13717e8f67458/iofile -n -s 2> /dev/null
dyld: lazy symbol binding failed: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib


Program received signal SIGTRAP: Trace/breakpoint trap.

Backtrace for this error:
#0  0x121f26579
#1  0x121f25945
#2  0x7fff93ac4529
Quitting from lines 33-34 (gunsales.Rmd) 
Error: processing vignette 'gunsales.Rmd' failed with diagnostics:
X-13 has returned a non-zero exist status, which means that the current spec file cannot be processed for an unknown reason.
Execution halted
Package required but not available: ‘RGtk2’

Package suggested but not available for checking: ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘RGtk2’ ‘cairoDevice’

Package which this enhances but not available for checking: ‘RGtk2Extras’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/h5.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 122-128 (Basic_use.Rmd) 
Error: processing vignette 'Basic_use.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
Packages required but not available: ‘rtracklayer’ ‘HiTC’

Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
Error in re-building vignettes:
  ...

    filter

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

    layout

Loading required package: viridis
Loading required package: viridisLite

======================
Welcome to heatmaply version 0.14.1

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
Packages required but not available: ‘rtracklayer’ ‘HiTC’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘XMLRPC’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/HierO.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.
Highcharts (www.highcharts.com) is a Highsoft software product which is
not free for commercial and Governmental use
Quitting from lines 45-46 (charting-data-frames.Rmd) 
Error: processing vignette 'charting-data-frames.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    highlight   1.0Mb
    libs        5.9Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   4.8Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/HMMpa.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Package required but not available: ‘Rsamtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘RGtk2’ ‘MenuCollection’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘RGtk2’ ‘cairoDevice’ ‘RGtk2Extras’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
File ‘hSDM/libs/hSDM.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘useful.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Objects: ‘hSDM.Nmixture.o’, ‘hSDM.Nmixture.iCAR.o’, ‘hSDM.ZIB.o’,
      ‘hSDM.ZIB.iCAR.alteration.o’, ‘hSDM.ZIB.iCAR.o’, ‘hSDM.ZIP.o’,
      ‘hSDM.ZIP.iCAR.alteration.o’, ‘hSDM.ZIP.iCAR.o’,
      ‘hSDM.binomial.o’, ‘hSDM.binomial.iCAR.o’, ‘hSDM.poisson.o’,
      ‘hSDM.poisson.iCAR.o’, ‘hSDM.siteocc.o’, ‘hSDM.siteocc.iCAR.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘HTSFilter’
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    dict   1.3Mb
    libs   4.4Mb
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.
trying URL 'https://arxiv.org/e-print/1406.4806v1'
Content type 'application/x-eprint-tar' length 29273 bytes (28 KB)
==================================================
downloaded 28 KB

Quitting from lines 162-165 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   3.6Mb
Found the following significant warnings:
  IBDsim.c:27:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:39:20: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:54:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:61:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/IBDsim.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Running ‘testthat.R’ [5s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Package Rglpk needed for this function to work. Please install it.
  1: calibration(data = data_ex2, marginMatrix = margins, colWeights = "poids", description = FALSE, 
         bounds = "min", method = "min") at testthat/test_calibration_small_dataset.R:127
  2: minBoundsCalib(Xs = matrixCal, d = weights, total = formattedMargins, q = rep(1, 
         nrow(matrixCal)), maxIter = maxIter, description = description, precisionBounds = precisionBounds, 
         forceSimplex = forceSimplex, forceBisection = forceBisection)
  3: solveMinBoundsCalib(Xs, d, total, q, maxIter, calibTolerance, description)
  4: stop("Package Rglpk needed for this function to work. Please install it.", call. = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 59 SKIPPED: 0 FAILED: 1
  1. Error: Calibration on minimum bounds checks out (@test_calibration_small_dataset.R#127) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   1.4Mb
    doc    5.1Mb
    libs  11.2Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
Package suggested but not available for checking: ‘mixAK’
installed size is 41.7Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs  37.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in .local(object, ...) :
  some chains had errors; consider specifying chains = 1 to debug
Quitting from lines 72-73 (Package_Introduction.Rmd) 
Error: processing vignette 'Package_Introduction.Rmd' failed with diagnostics:
object 'all_resid' not found
Execution halted
installed size is 26.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  25.1Mb
Package suggested but not available for checking: ‘PROcess’
Package unavailable to check Rd xrefs: ‘PROcess’
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/IDTurtle.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  12.8Mb
installed size is 30.6Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       4.9Mb
    include   2.8Mb
    libs     19.9Mb
Running examples in ‘iMRMC-Ex.R’ failed
The error most likely occurred in:

> ### Name: doIMRMC
> ### Title: MRMC analysis of the area under the ROC curve
> ### Aliases: doIMRMC
> 
> ### ** Examples
> 
> # Create a sample configuration file
> config <- sim.gRoeMetz.config()
> # Simulate an MRMC ROC data set
> dFrame.imrmc <- sim.gRoeMetz(config)
> # Analyze the MRMC ROC data
> result <- doIMRMC(dFrame.imrmc)
Warning in file(file, "rt") :
  cannot open file '/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmpXpzF0q/imrmcDir/AUCperReader.csv': No such file or directory
Error in file(file, "rt") : cannot open the connection
Calls: doIMRMC -> <Anonymous> -> read.table -> file
Execution halted
Running ‘testthat.R’ [5s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
                AminusB               CminusD AminusB.minus.CminusD 
             0.04765402           -0.04765402            0.09530804 
  
  $var
                AminusB               CminusD AminusB.minus.CminusD 
             0.03198493            0.03198493            0.12793972 
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 11 SKIPPED: 0 FAILED: 3
  1. Error: (unknown) (@test_createANDundoIMRMCdf.R#26) 
  2. Error: (unknown) (@test_doIMRMC.R#26) 
  3. Error: (unknown) (@test_doIMRMCfromFile.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
Packages suggested but not available for checking: ‘rsprng’ ‘Rmpi’
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)
sh: line 1: 29920 Trace/BPT trap: 5       /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/x13ashtml /var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmprnnChM/x136d8f148a3659/iofile -n -s 2> /dev/null
Warning in system(paste(x13.bin, file, flags), intern = TRUE, ignore.stderr = TRUE) :
  running command '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/x13ashtml /var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmprnnChM/x136d8f148a3659/iofile -n -s 2>/dev/null' had status 133
dyld: lazy symbol binding failed: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib


Program received signal SIGTRAP: Trace/breakpoint trap.

Backtrace for this error:
#0  0x123592579
#1  0x123591945
#2  0x7fff93ac4529
Error: X-13 has returned a non-zero exist status, which means that the current spec file cannot be processed for an unknown reason.
Execution halted
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Packages suggested but not available for checking: ‘MLP’ ‘a4Base’
installed size is 25.1Mb
  sub-directories of 1Mb or more:
    libs  24.9Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/intpoint.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
interior_point2d: no visible global function definition for ‘points’
random_problem: no visible global function definition for ‘runif’
show2d: no visible global function definition for ‘plot’
show2d: no visible global function definition for ‘abline’
show2d: no visible global function definition for ‘points’
Undefined global functions or variables:
  abline plot points runif
Consider adding
  importFrom("graphics", "abline", "plot", "points")
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   6.8Mb
Namespaces in Imports field not imported from:
  ‘coda’ ‘lattice’
  All declared Imports should be used.
Running examples in ‘IRATER-Ex.R’ failed
The error most likely occurred in:

> ### Name: clean.admb
> ### Title: delete IRATE (ADMB) run files
> ### Aliases: clean.admb clean.IRATE
> 
> ### ** Examples
> 
> example.setup <- IRATE.examples()
> new.setup <- new.setup.path <- example.setup[1] # select old IRATE setup to reparameterize
> print(new.setup) # print setup name to be run
[1] "HoenigNonMixing"
> old.setup.path <- system.file(paste0("IRATE.examples/",new.setup,".dat"), package = "IRATER")
> 
> system(paste("mkdir -p ",new.setup.path)) # create run folder for new setup
> system(paste("cp",old.setup.path, new.setup.path)) # copy old setup in new run folder
> setwd(new.setup.path)
> 
> run.IRATE(new.setup) # compile and run setup
sh: admb: command not found
Error in R2admb::compile_admb(setup.file, safe = safe, re = re, verbose = verbose,  : 
  base admb command failed: run setup_admb(), or check ADMB installation
Calls: run.IRATE -> <Anonymous>
Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   4.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.0Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   9.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/kmc.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/kmcudaR.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: Matrix
Loading required package: foreach
Loaded glmnet 2.0-16


Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   3.7Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.9Mb
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: 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:
cannot open the connection
Execution halted
Found the following significant warnings:
  W_gamma_Cpp.cpp:14:39: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/LambertW.Rcheck/00install.out’ for details.
installed size is 79.5Mb
  sub-directories of 1Mb or more:
    libs  78.2Mb
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs          12.0Mb
    testdata       1.8Mb
    vignettedata   2.0Mb
Running ‘MASSch04.R’ [1s/1s]
Running the tests in ‘tests/MASSch04.R’ failed.
Complete output:
  > #-*- R -*-
  > 
  > ## Script from Fourth Edition of `Modern Applied Statistics with S'
  > 
  > # Chapter 4   Graphical Output
  > 
  > library(MASS)
  Error: package or namespace load failed for 'MASS' in gzfile(file, "rb"):
   cannot open the connection
  In addition: Warning message:
  In gzfile(file, "rb") :
    cannot open compressed file '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/MASS/data/Rdata.rdx', probable reason 'No such file or directory'
  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 41-42 (Intro_to_lavaanPlot.Rmd) 
Error: processing vignette 'Intro_to_lavaanPlot.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘rtracklayer’
Errors in running code in vignettes:
when running code in ‘addTracks.Rnw’
  ...
+     flip = TRUE)

> ll <- LDheatmap(GIMAP5.CEU$snp.data, GIMAP5.CEU$snp.support$Position, 
+     flip = TRUE)

> grid.newpage()

  When sourcing ‘addTracks.R’:
Error: could not find function "grid.newpage"
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: '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
File ‘leaps/libs/leaps.so’:
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (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  5.1Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      3.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/libstableR.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘gWidgetsRGtk2’ ‘RGtk2’
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 272-273 (Understanding_lime.Rmd) 
Error: processing vignette 'Understanding_lime.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   8.4Mb
Found the following hidden files and directories:
  .DESCRIPTION.swo
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/liso.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages in Depends field not imported from:
  ‘Iso’ ‘MASS’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
S3 methods shown with full name in documentation object 'seq.log':
  ‘seq.log’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    doc        2.4Mb
    libs      21.2Mb
    testdata   1.6Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/LncPriCNet.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running examples in ‘localsolver-Ex.R’ failed
The error most likely occurred in:

> ### Name: add.output.expr
> ### Title: Add expression to output of ls.problem.
> ### Aliases: add.output.expr
> 
> ### ** Examples
> 
> model.text.lsp <- lsp.model.example('extdata/knapsack.txt')
> lsp <- ls.problem(model.text.lsp)
sh: localsolver: command not found
Error in ls.problem(model.text.lsp) : 
  has.localsolver(ls.path) is not TRUE
Calls: ls.problem -> stopifnot
Execution halted
Error in re-building vignettes:
  ...
sh: localsolver: command not found
Quitting from lines 66-68 (localsolver.Rmd) 
Error: processing vignette 'localsolver.Rmd' failed with diagnostics:
has.localsolver(ls.path) is not TRUE
Execution halted
Running examples in ‘LOGIT-Ex.R’ failed
The error most likely occurred in:

> ### Name: confusion_stat
> ### Title: Display confusion or classification matrix following logistic
> ###   regression using glm with binomial family.
> ### Aliases: confusion_stat
> ### Keywords: models
> 
> ### ** Examples
> 
> library(MASS)
> library(LOGIT)
> data(R84)
> R84$cage <- R84$age - mean(R84$age)
> R84$cdoc <- R84$docvis - mean(R84$docvis)
> mylogit <- glm(outwork ~ cdoc + female + kids + cage + factor(edlevel),
+ family=binomial, data=R84)
> mu <- predict(mylogit, type="response")
> cutpoint<-ROCtest(mylogit, fold=10, type="Sensitivity")$cut
> mu[mu>=cutpoint]<-1
> mu[mu<cutpoint]<-0
> confusion_stat(mu, R84$outwork)
Error: `data` and `reference` should be factors with the same levels.
Execution halted
Found the following significant warnings:
  lsdall.c:2078:21: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2200:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2209:12: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2219:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2225:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/logspline.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘RDRToolbox’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
installed size is 46.0Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  44.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.1Mb
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    libs  25.6Mb
installed size is 25.7Mb
  sub-directories of 1Mb or more:
    doc    6.8Mb
    libs  18.5Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/MagneticMap.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages required but not available: ‘RGtk2’ ‘gWidgetsRGtk2’ ‘lumi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
Error in re-building vignettes:
  ...
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

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]="./webshot1b95497e3633.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot1b95497e3633.png': No such file or directory
Quitting from lines 95-96 (manhattanly.Rmd) 
Error: processing vignette 'manhattanly.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot25b878d689ce.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot25b878d689ce.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
Package required but not available: ‘LPmerge’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 95-100 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   5.7Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   6.6Mb
Package suggested but not available for checking: ‘ASGSCA’
Packages required but not available: ‘Rglpk’ ‘glpkAPI’

Package suggested but not available for checking: ‘cplexAPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   6.1Mb
Errors in running code in vignettes:
when running code in ‘mcemGLM-vignette.Rnw’
  ...
         6      :  6   6      :  6   Max.   :1.000  
         (Other):324   (Other):324                  

> fitBernoulli <- mcemGLMM(fixed = Mate ~ 0 + Cross, 
+     random = list(~0 + Female, ~0 + Male), data = salamander, 
+     family = "bernoulli", vcD .... [TRUNCATED] 

Execution halted

... incomplete output.  Crash?
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   2.7Mb
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  16.1Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/mdhglm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   3.9Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   7.8Mb
Package suggested but not available for checking: ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
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: GenABEL
Loading required package: MASS
Loading required package: GenABEL.data
Loading required package: SKAT
Loading required package: pedgene
Loading required package: Matrix
Loading required package: CompQuadForm
Loading required package: survey
Loading required package: grid
Loading required package: survival

Attaching package: 'survey'

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

    dotchart

Loading required package: kinship2
Loading required package: quadprog
Quitting from lines 694-696 (mega2rtutorial.Rmd) 
Error: processing vignette 'mega2rtutorial.Rmd' failed with diagnostics:
there is no package called 'TxDb.Hsapiens.UCSC.hg19.knownGene'
Execution halted
Running ‘testthat.R’ [20s/47s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(memery)
  Loading required package: showtext
  Loading required package: sysfonts
  Loading required package: showtextdb
  > 
  > test_check("memery")
  OMP: Error #15: Initializing libomp.dylib, but found libomp.dylib already initialized.
  OMP: Hint: This means that multiple copies of the OpenMP runtime have been linked into the program. That is dangerous, since it can degrade performance or cause incorrect results. The best thing to do is to ensure that only a single OpenMP runtime is linked into the process, e.g. by avoiding static linking of the OpenMP runtime in any library. As an unsafe, unsupported, undocumented workaround you can set the environment variable KMP_DUPLICATE_LIB_OK=TRUE to allow the program to continue to execute, but that may cause crashes or silently produce incorrect results. For more information, please see http://www.intel.com/software/products/support/.
Packages required but not available: ‘RGtk2’ ‘RGtk2Extras’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘gWidgetsRGtk2’ ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    libs  18.7Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   3.6Mb
Packages suggested but not available for checking: ‘clpAPI’ ‘glpkAPI’ ‘ctc’
Running examples in ‘metaboGSE-Ex.R’ failed
The error most likely occurred in:

> ### Name: rescue
> ### Title: Rescue a model
> ### Aliases: rescue
> 
> ### ** Examples
> 
> data(Ec_core)
> rescue(Ec_core, target=0.1)
Loading required package: glpkAPI
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘glpkAPI’
Error in checkDefaultMethod(solver, method, pType) : 
  package ‘glpkAPI’ not found
Calls: rescue ... optimizeProb -> optimizeProb -> .local -> sysBiolAlg
Execution halted
Error in re-building vignettes:
  ...

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

    backsolve


groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

Attaching package: 'topGO'

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

    members

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

    algorithm, algorithm<-, allGenes, genes

Loading required package: clpAPI
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'clpAPI'
Quitting from lines 37-41 (metaboGSE.Rmd) 
Error: processing vignette 'metaboGSE.Rmd' failed with diagnostics:
package 'clpAPI' not found
Execution halted
Package required but not available: ‘rattle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘gWidgetsRGtk2’

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.
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Quitting from lines 26-27 (MetaIntegrator.Rmd) 
Error: processing vignette 'MetaIntegrator.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
Execution halted
Packages suggested but not available for checking:
  ‘annaffy’ ‘hgu133plus2.db’ ‘hgu133a.db’ ‘hgu95av2.db’
Packages suggested but not available for checking: ‘hgu133plus2.db’ ‘doSMP’
Errors in running code in vignettes:
when running code in ‘metaRNASeq.Rnw’
  ...
    estimateSizeFactorsForMatrix,
    getVarianceStabilizedData,
    varianceStabilizingTransformation


> library(HTSFilter)

  When sourcing ‘metaRNASeq.R’:
Error: there is no package called ‘HTSFilter’
Execution halted
Error in re-building vignettes:
  ...
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: lattice
    Welcome to 'DESeq'. For improved performance,
    usability and functionality, please consider
    migrating to 'DESeq2'.

Attaching package: ‘DESeq’

The following objects are masked from ‘package:DESeq2’:

    estimateSizeFactorsForMatrix,
    getVarianceStabilizedData,
    varianceStabilizingTransformation


Error: processing vignette 'metaRNASeq.Rnw' failed with diagnostics:
 chunk 9 (label = DESeq1study) 
Error in library(HTSFilter) : there is no package called ‘HTSFilter’
Execution halted
Found the following significant warnings:
  Warning: working directory was changed to ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/MetaSubtract.Rcheck/MetaSubtract/extdata’, resetting
Found the following significant warnings:
  binomial-twostage.cpp:78:4: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  binomial-twostage.cpp:280:4: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/mets.Rcheck/00install.out’ for details.
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  13.9Mb
    misc   1.1Mb
Package suggested but not available for checking: ‘grasp2db’
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  20.1Mb
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:
cannot open the connection
Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Package suggested but not available for checking: ‘biotools’
Package unavailable to check Rd xrefs: ‘biotools’
Running examples in ‘micompr-Ex.R’ failed
The error most likely occurred in:

> ### Name: assumptions.cmpoutput
> ### Title: Get assumptions for parametric tests performed on output
> ###   comparisons
> ### Aliases: assumptions.cmpoutput
> 
> ### ** Examples
> 
> 
> # Create a cmpoutput object from the provided datasets
> cmp <- cmpoutput("All", 0.9, pphpc_ok$data[["All"]], pphpc_ok$obs_lvls)
> 
> # Get the assumptions for the parametric tests performed in cmp
> acmp <- assumptions(cmp)
sROC 0.1-2 loaded
MANOVA assumptions require 'MVN' and 'biotools' packages.
Error in `*tmp*`[[i]] : subscript out of bounds
Calls: assumptions -> assumptions.cmpoutput
Execution halted
Running ‘testthat.R’ [19s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  subscript out of bounds
  1: assumptions(mic1a) at testthat/test_micomp.R:281
  2: assumptions.micomp(mic1a)
  3: lapply(obj, function(x) assumptions(x))
  4: FUN(X[[i]], ...)
  5: assumptions(x)
  6: assumptions.cmpoutput(x)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 363 SKIPPED: 0 FAILED: 2
  1. Error: assumptions.cmpoutput creates the correct object (@test_cmpoutput.R#214) 
  2. Error: micomp assumptions have the correct properties (@test_micomp.R#281) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 341-342 (paper.Rnw) 
Error: processing vignette 'paper.Rnw' failed with diagnostics:
subscript out of bounds
Execution halted
File ‘MigClim/libs/MigClim.so’:
  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.
Package suggested but not available for checking: ‘gWidgets2RGtk2’
Package suggested but not available for checking: ‘glpkAPI’
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: lattice
Quitting from lines 21-25 (MINVALintroduction.Rmd) 
Error: processing vignette 'MINVALintroduction.Rmd' failed with diagnostics:
there is no package called 'glpkAPI'
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   5.2Mb
Packages suggested but not available for checking: ‘mixAK’ ‘BRugs’
Package unavailable to check Rd xrefs: ‘mixAK’
Found the following significant warnings:
  simcensor.cpp:91:16: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:91:41: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:95:17: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/missDeaths.Rcheck/00install.out’ for details.
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Running examples in ‘mixKernel-Ex.R’ failed
The error most likely occurred in:

> ### Name: cim.kernel
> ### Title: Compute and display similarities between multiple kernels
> ### Aliases: cim.kernel
> 
> ### ** Examples
> 
> data(TARAoceans)
> 
> # compute one kernel per dataset
> phychem.kernel <- compute.kernel(TARAoceans$phychem, kernel.func = "linear")
> pro.phylo.kernel <- compute.kernel(TARAoceans$pro.phylo, kernel.func = "abundance")
Error in .C("veg_distance", x = as.double(x), nr = N, nc = ncol(x), d = double(N *  : 
  "veg_distance" not available for .C() for package "vegan"
Calls: compute.kernel ... distance -> do.call -> do.call -> vegdist -> vegdist
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/mixor.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running examples in ‘MixSIAR-Ex.R’ failed
The error most likely occurred in:

> ### Name: mixsiar_gui
> ### Title: Run the GUI version of MixSIAR
> ### Aliases: mixsiar_gui
> 
> ### ** Examples
> 
> mixsiar_gui()
Error in mixsiar_gui() : 
  *** gWidgetsRGtk2 package not able to be loaded. ***
        If 'library('gWidgetsRGtk2')' does not work, MixSIAR GUI will not run.
        On Windows/Linux, try 'install.packages('gWidgetsRGtk2')'.
        On Mac, close R, download and install GTK+ from:
        http://r.research.att.com/#other. Then install latest X11 application
        (xQuartz) from http://xquartz.macosforge.org/landing/.

        If installing GTK+ continues to be problematic, consider using the
        script version of MixSIAR. See manual for help and examples.
Execution halted
Running ‘testthat.R’ [16s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mizer)
  > 
  > test_check("mizer")
  ── 1. Failure: retune_abundance reproduces scaling model (@test-wrapper_function
  max(abs(initial_n - pr@initial_n)) is not strictly less than 2e-11. Difference: 1.09e-11
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 508 SKIPPED: 1 FAILED: 1
  1. Failure: retune_abundance reproduces scaling model (@test-wrapper_functions.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Packages suggested but not available for checking:
  ‘Rglpk’ ‘ROI.plugin.glpk’
Package required but not available: ‘rsgcc’

Packages suggested but not available for checking:
  ‘GeneSelector’ ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘minfi’ ‘BiocStyle’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 27-28 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.7Mb
    libs   2.9Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   5.3Mb
Error in re-building vignettes:
  ...
Warning in engine$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 355-357 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
The model needs too many iterations to provide reliable parameter estimates !
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/MortHump.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
File ‘MRwarping/libs/MRwarping.so’:
  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.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 30-37 (msaR.Rmd) 
Error: processing vignette 'msaR.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages required but not available: ‘mzR’ ‘xcms’

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.

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

Package suggested but not available for checking: ‘xcms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 43.3Mb
  sub-directories of 1Mb or more:
    libs  42.9Mb
Running examples in ‘mssqlR-Ex.R’ failed
Errors in running code in vignettes:
when running code in ‘chfls1.Rnw’
  ...

> library("xtable")

> library("car")
Loading required package: carData

  When sourcing ‘chfls1.R’:
Error: package or namespace load failed for ‘car’ in library.dynam(lib, package, package.lib):
 shared object ‘readxl.so’ not found
Execution halted
Error in re-building vignettes:
  ...
Loading required package: carData

Error: processing vignette 'chfls1.Rnw' failed with diagnostics:
 chunk 1 (label = setup) 
Error : package or namespace load failed for ‘car’ in library.dynam(lib, package, package.lib):
 shared object ‘readxl.so’ not found
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is 59.5Mb
  sub-directories of 1Mb or more:
    libs  59.4Mb
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/MultiPhen.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
Found the following significant warnings:
  ./index_heap.h:318:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/nabor.Rcheck/00install.out’ for details.
Errors in running code in vignettes:
when running code in ‘test-vignette.ipynbmeta’
  ...

  When tangling ‘test-vignette.ipynbmeta’:
Error: Either IPython 3+ or Jupyter has to be installed, but neither could be called.
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'test-vignette.ipynbmeta' failed with diagnostics:
Either IPython 3+ or Jupyter has to be installed, but neither could be called.
Execution halted
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ncappc.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/Sub-CommandLineArguments.Rmd’
   ‘vignettes/Sub-EstimatedNCAmetrics.Rmd’
   ‘vignettes/Sub-EstimationMethod.Rmd’
   ‘vignettes/Sub-Output.Rmd’
(Is a VignetteBuilder field missing?)
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   3.9Mb
File ‘NeatMap/libs/NeatMap.so’:
  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.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   4.5Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   4.5Mb
File ‘NetSim/libs/NetSim.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘utils/Random.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘utils/Random.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking:
  ‘BiocStyle’ ‘graphite’ ‘NFPdata’
Error in re-building vignettes:
  ...
Quitting from lines 10-11 (NFP.Rnw) 
Error: processing vignette 'NFP.Rnw' failed with diagnostics:
there is no package called 'BiocStyle'
Execution halted
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── 1. Failure: attrnames finds the names of the attributes of a data frame (@tes
  attrnames(y) not equal to c("names", "row.names", "class").
  2/3 mismatches
  x[2]: "class"
  y[2]: "row.names"
  
  x[3]: "row.names"
  y[3]: "class"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 21 SKIPPED: 0 FAILED: 1
  1. Failure: attrnames finds the names of the attributes of a data frame (@test-attribute_names.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 34.4Mb
  sub-directories of 1Mb or more:
    CppCode        1.2Mb
    R              5.8Mb
    classic-bugs   1.5Mb
    include        5.6Mb
    libs          18.6Mb
    tests          1.3Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
Running ‘testthat.R’ [9s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  10: model.frame(as.Formula(formula), as.data.frame(data), ..., rhs = rhs)
  11: model.frame.Formula(as.Formula(formula), as.data.frame(data), ..., rhs = rhs)
  12: model.frame(terms(formula, lhs = lhs, rhs = rhs, data = data, dot = dot), data = data, 
         ...)
  13: model.frame.default(terms(formula, lhs = lhs, rhs = rhs, data = data, dot = dot), 
         data = data, ...)
  14: eval(predvars, data, env)
  15: eval(predvars, data, env)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 55 SKIPPED: 0 FAILED: 1
  1. Error: mlogit object (@test_llcont.R#207) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/novelist.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
delta.star: no visible global function definition for ‘cov’
delta.star: no visible global function definition for ‘cov2cor’
hardt: no visible global function definition for ‘cov2cor’
novelist.assign: no visible global function definition for ‘cov2cor’
novelist.assign.inv: no visible global function definition for
  ‘cov2cor’
novelist.cov.cv: no visible global function definition for ‘cov’
novelist.cov.cv: no visible global function definition for ‘cor’
novelist.inv.cv: no visible global function definition for ‘cov’
novelist.inv.cv: no visible global function definition for ‘cor’
softt: no visible global function definition for ‘cov2cor’
Undefined global functions or variables:
  cor cov cov2cor
Consider adding
  importFrom("stats", "cor", "cov", "cov2cor")
to your NAMESPACE file.
Found the following significant warnings:
  utilities.c:175:32: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/npcp.Rcheck/00install.out’ for details.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   7.9Mb
Error in re-building vignettes:
  ...
     
     taxi <- etl("nyctaxi", dir = "~/Desktop/nyctaxi/")
     taxi %>% 
        etl_extract(years = 2016, months = 1:2, types = c("yellow","green")) %>% 
        etl_transform(years = 2016, months = 1:2, types = c("yellow","green")) %>% 
        etl_load(years = 2016, months = 1:2, types = c("yellow","green")) 
     ## End(Not run)
     


Attaching package: 'lubridate'

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

    date

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]="./webshot16f9f6d730a2b.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot16f9f6d730a2b.png': No such file or directory
Quitting from lines 61-71 (nyc_taxi.Rmd) 
Error: processing vignette 'nyc_taxi.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
File ‘obliclus/libs/obliclus.so’:
  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.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   2.2Mb
installed size is 77.0Mb
  sub-directories of 1Mb or more:
    libs  76.5Mb
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Expected match: "The length value"
  Actual message: "c++ exception (unknown reason)"
  
  ── 2. Failure: OLC encoding throws an error with odd-numbered requested lengths 
  `x` threw an error with unexpected message.
  Expected match: "The length value"
  Actual message: "c++ exception (unknown reason)"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 34 SKIPPED: 1 FAILED: 2
  1. Failure: OLC encoding throws an error with odd-numbered requested lengths below 8 (@test_encoding.R#20) 
  2. Failure: OLC encoding throws an error with odd-numbered requested lengths below 8 (@test_encoding.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘ROI.plugin.glpk’
Running examples in ‘ompr.roi-Ex.R’ failed
The error most likely occurred in:

> ### Name: with_ROI
> ### Title: Configures a solver based on 'ROI'
> ### Aliases: with_ROI
> 
> ### ** Examples
> 
> library(magrittr)
> library(ompr)
> library(ROI)
ROI.plugin.scs: R Optimization Infrastructure
Registered solver plugins: nlminb, alabama, deoptim, ecos, ipop, lpsolve, msbinlp, nloptr, optimx, quadprog, scs.
Default solver: auto.
> library(ROI.plugin.glpk)
Error in library(ROI.plugin.glpk) : 
  there is no package called ‘ROI.plugin.glpk’
Execution halted
Running ‘testthat.R’ [17s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  Attaching package: 'magrittr'
  
  The following objects are masked from 'package:testthat':
  
      equals, is_less_than, not
  
  > library(ROI)
  ROI.plugin.scs: R Optimization Infrastructure
  Registered solver plugins: nlminb, alabama, deoptim, ecos, ipop, lpsolve, msbinlp, nloptr, optimx, quadprog, scs.
  Default solver: auto.
  > library(ROI.plugin.glpk)
  Error in library(ROI.plugin.glpk) : 
    there is no package called 'ROI.plugin.glpk'
  Execution halted
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.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/OpenCL.Rcheck/00install.out’ for details.
installed size is 115.3Mb
  sub-directories of 1Mb or more:
    R         2.4Mb
    libs    105.5Mb
    models    4.7Mb
Running examples in ‘OpenMx-Ex.R’ failed
The error most likely occurred in:

> ### Name: OpenMx
> ### Title: OpenMx: An package for Structural Equation Modeling and Matrix
> ###   Algebra Optimization
> ### Aliases: OpenMx OpenMx-package
> 
> ### ** Examples
> 
> library(OpenMx)
> data(demoOneFactor)
> # ===============================
> # = Make and run a 1-factor CFA =
> # ===============================
> 
> latents  = c("G") # the latent factor
> manifests = names(demoOneFactor) # manifest variables to be modeled
> # ====================
> # = Make the MxModel =
> # ====================
> m1 <- mxModel("One Factor", type = "RAM", 
+ 	manifestVars = manifests, latentVars = latents, 
+ 	mxPath(from = latents, to = manifests),
+ 	mxPath(from = manifests, arrows = 2),
+ 	mxPath(from = latents, arrows = 2, free = FALSE, values = 1.0),
+ 	mxData(cov(demoOneFactor), type = "cov", numObs = 500)
+ )
> 
> # ===============================
> # = mxRun it and get a summary! =
> # ===============================
> 
> m1 = mxRun(m1)
Running One Factor with 10 parameters
Error in runHelper(model, frontendStart, intervals, silent, suppressWarnings,  : 
  c++ exception (unknown reason)
Calls: mxRun -> runHelper
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/OpenRepGrid.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.7Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
Running ‘testthat.R’ [19s/34s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  5: sapply(1:nSheets, function(i) isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]])))
  6: lapply(X = X, FUN = FUN, ...)
  7: FUN(X[[i]], ...)
  8: isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]]))
  9: all.equal(x$colWidths[[i]], y$colWidths[[i]])
  10: all.equal.list(x$colWidths[[i]], y$colWidths[[i]])
  11: attr.all.equal(target, current, ...)
  12: mode(current)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 505 SKIPPED: 2 FAILED: 1
  1. Error: loadWorkbook from different sources (@test-read_sources.R#49) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘org.At.tair.db’
Error in re-building vignettes:
  ...
sh: +RTS: command not found
Warning in system(command) : error in running command
Error: processing vignette 'optparse.Rrst' failed with diagnostics:
pandoc document conversion failed with error 127
Execution halted
Package required but not available: ‘ROracle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘IsoGene’
File ‘OriGen/libs/OriGen.so’:
  Found ‘__gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__gfortran_st_read’, possibly from ‘read’ (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.
Found the following significant warnings:
  ccaRevolution.c:31:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:44:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:97:23: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:98:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:110:23: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:111:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/osc.Rcheck/00install.out’ for details.
Running examples in ‘osi-Ex.R’ failed
The error most likely occurred in:

> ### Name: extract_id
> ### Title: Extract components from OSI metadata
> ### Aliases: extract_id extract_keywords extract_name extract_superseded
> ###   extractors
> 
> ### ** Examples
> 
> 
> #Get the names of all licenses
> all_license_metadata <- license_list()
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: Resolving timed out after 10005 milliseconds
Calls: license_list ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
Running ‘testthat.R’ [8s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  8: curl::curl_fetch_memory(url, handle = handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 8
  1. Error: All licenses can be retrieved (@test_connectors.R#6) 
  2. Error: Keyword retrieval works (@test_connectors.R#14) 
  3. Error: ID retrieval works (@test_connectors.R#22) 
  4. Error: Content retrieval works (@test_connectors.R#29) 
  5. Error: licenses IDs can be retrieved (@test_extractors.R#4) 
  6. Error: licenses names can be retrieved (@test_extractors.R#11) 
  7. Error: licenses superseded states can be retrieved (@test_extractors.R#18) 
  8. Error: licenses keywords can be retrieved (@test_extractors.R#25) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   4.0Mb
Package required but not available: ‘Rglpk’

Package suggested but not available for checking: ‘Rcplex’

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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 185-198 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages suggested but not available for checking:
  ‘genealogicalSorting’ ‘phybase’ ‘Rmpi’
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PAactivPAL.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Error in re-building vignettes:
  ...
Warning in engine$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 196-217 (progressive_packing.Rmd) 
Error: processing vignette 'progressive_packing.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
File ‘ParallelForest/libs/ParallelForest.so’:
  Found ‘__gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘random_utils.o’
  Found ‘__gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘random_utils.o’
  Found ‘__gfortran_st_read’, possibly from ‘read’ (Fortran)
    Object: ‘random_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.
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.
Linking to GEOS 3.6.1, GDAL 2.1.3, proj.4 4.9.3

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

Downloading constituency data
Warning: Column `party_id` joining character vector and factor, coercing into character vector
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]="./webshotc2552a92add0.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotc2552a92add0.png': No such file or directory
Quitting from lines 67-110 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package required but not available: ‘Rglpk’

Package suggested but not available for checking: ‘Rsymphony’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘parmigene/libs/parmigene.so’:
  Found ‘_rand_r’, possibly from ‘rand_r’ (C)
    Object: ‘points.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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Quitting from lines 58-63 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
Operation was aborted by an application callback
Execution halted
Packages suggested but not available for checking: ‘hu6800.db’ ‘golubEsets’

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

    union

Loading required package: lpSolve

> library(golubEsets)

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

    lowess

Loading required package: igraph

Attaching package: ‘igraph’

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

    normalize, path, union

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

    decompose, spectrum

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

    union

Loading required package: lpSolve

Error: processing vignette 'pathClass.rnw' failed with diagnostics:
 chunk 2 (label = loadALLpackage) 
Error in library(golubEsets) : there is no package called ‘golubEsets’
Execution halted
Package required but not available: ‘pathview’

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘pbdPROF’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/pbdMPI.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/pbdPROF.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/pcaL1.Rcheck/00install.out’ for details.
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   2.1Mb
    libs   6.2Mb
Package required but not available: ‘strvalidator’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    libs    5.6Mb
    share  11.9Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/pdolsms.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  spectrum.c:707:14: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:715:20: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1606:41: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1654:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1654:63: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Peaks.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/pendensity.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/penRvine.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/permGPU.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/phalen.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  LJMA_arms.c:297:11: warning: comparison of array 'env->p' equal to a null pointer is always false [-Wtautological-pointer-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PhaseType.Rcheck/00install.out’ for details.
File ‘PhaseType/libs/PhaseType.so’:
  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.
Running ‘run_tests.r’ [137s/253s]
Running the tests in ‘tests/run_tests.r’ failed.
Last 13 lines of output:
  Smoothing time series! 
  Merging Daymet Data! 
  Error : $ operator is invalid for atomic vectors
  Downloading: harvard_DB_0001_3day.csv
  Contracting Data! 
  Downloading: harvard_DB_0001_3day.csv
  ── 1. Failure: check download options (@test_download_function.r#64)  ──────────
  `check` isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 5 SKIPPED: 0 FAILED: 1
  1. Failure: check download options (@test_download_function.r#64) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'Sample-scripts-external-genotype-simulation.Rmd' failed with diagnostics:
Failed to locate the ‘weave’ output file (by engine ‘knitr::rmarkdown’) for vignette with name ‘Sample-scripts-external-genotype-simulation’. The following files exist in directory ‘.’: ‘Sample-scripts-external-genotype-simulation.Rmd’, ‘Sample-scripts-external-genotype-simulation.md’, ‘Simulation-and-LinearModel.Rmd’, ‘SimulationAndLinearModel.bib’, ‘UsagePhenotypeSimulator.Rmd’, ‘UsagePhenotypeSimulator.html’, ‘genotype-simulation.bib’, ‘plos-genetics.csl’, ‘sample-scripts-external-genotype-simulation.html’
Execution halted
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    libs  18.5Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot19c9635f8145.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot19c9635f8145.png': No such file or directory
Quitting from lines 20-27 (Advanced_Usage.Rmd) 
Error: processing vignette 'Advanced_Usage.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Running examples in ‘phyloseqGraphTest-Ex.R’ failed
The error most likely occurred in:

> ### Name: graph_perm_test
> ### Title: Performs graph-based permutation tests
> ### Aliases: graph_perm_test
> 
> ### ** Examples
> 
> library(phyloseq)
> data(enterotype)
> gt = graph_perm_test(enterotype, sampletype = "SeqTech", type = "mst")
Error in .C("veg_distance", x = as.double(x), nr = N, nc = ncol(x), d = double(N *  : 
  "veg_distance" not available for .C() for package "vegan"
Calls: graph_perm_test ... distance -> do.call -> do.call -> vegdist -> vegdist
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 128-134 (gt_vignette.Rmd) 
Error: processing vignette 'gt_vignette.Rmd' failed with diagnostics:
"veg_distance" not available for .C() for package "vegan"
Execution halted
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PhySortR.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
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]="./webshota5993e30b266.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshota5993e30b266.png': No such file or directory
Quitting from lines 65-68 (v01-introduction.Rmd) 
Error: processing vignette 'v01-introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running ‘testthat.R’ [14s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 201 SKIPPED: 7 FAILED: 12
  1. Error: github links are added to news items (@test-build-news.R#6) 
  2. Error: github links are added to news items (@test-build-news.R#6) 
  3. Error: build_news() uses content in NEWS.md (@test-build-news.R#18) 
  4. Error: build_news() uses content in NEWS.md (@test-build-news.R#18) 
  5. Error: intermediate files cleaned up automatically (@test-build_home.R#29) 
  6. Error: intermediate files cleaned up automatically (@test-build_home.R#37) 
  7. Failure: build_home fails with empty readme.md (@test-build_home.R#152) 
  8. Error: can override defaults in _pkgdown.yml (@test-figure.R#11) 
  9. Error: extra.css and extra.js copied and linked (@test-init.R#12) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘ReportingTools’
Packages required but not available:
  ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’ ‘rggobi’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘cairoDevice’ ‘gWidgetsRGtk2’ ‘RGtk2’

Package suggested but not available for checking: ‘latticist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
dyld: Library not loaded: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libR.dylib
  Reason: no suitable image found.  Did find:
	/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib: pread of first 4K failed: 0
	/Library/Frameworks/R.framework/Resources/lib/libgfortran.3.dylib: file too short
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/plsRglm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
'library' or 'require' calls in package code:
  ‘MASS’ ‘plsdof’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   1.9Mb
Packages required but not available: ‘pbdMPI’ ‘pbdBASE’ ‘pbdDMAT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda

Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/pmlr.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
pmlr: no visible global function definition for ‘model.response’
pmlr: no visible global function definition for ‘model.matrix’
pmlr: no visible global function definition for ‘model.weights’
pmlr: no visible global function definition for ‘pchisq’
pmlr: no visible global function definition for ‘qnorm’
profileCIs: no visible global function definition for ‘qchisq’
test.LR: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  model.matrix model.response model.weights pchisq qchisq qnorm
Consider adding
  importFrom("stats", "model.matrix", "model.response", "model.weights",
             "pchisq", "qchisq", "qnorm")
to your NAMESPACE file.
Running examples in ‘PoloniexR-Ex.R’ failed
The error most likely occurred in:

> ### Name: ReturnTradeHistory,PoloniexPublicAPI-method
> ### Title: Returns the past 200 trades for a given market, or up to 50,000
> ###   trades inside a specified input date range interval.
> ### Aliases: ReturnTradeHistory,PoloniexPublicAPI-method
> 
> ### ** Examples
> 
> Sys.setenv(tz = "UTC")
> poloniex.public <- PoloniexPublicAPI()
> pair   <- "BTC_NXT"
> from   <- as.POSIXct("2017-07-04 00:00:00 UTC")
> to     <- as.POSIXct("2017-07-05 00:00:00 UTC")
> 
> trades.data <- ReturnTradeHistory(theObject = poloniex.public,
+                                   pair      = pair,
+                                   from      = from,
+                                   to        = to)
Error in .ProcessRequest(request.str) : 
  Unable to connect to https://poloniex.com/public?command=returnTradeHistory&currencyPair=BTC_NXT&start=1499140800&end=1499227200 (404)
Calls: ReturnTradeHistory -> ReturnTradeHistory -> .ProcessRequest
Execution halted
Found the following significant warnings:
  heftall.c:1389:2: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  lsdall.c:2077:21: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  lspecall.c:505:12: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  lspecall.c:999:21: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  lspecall.c:1078:18: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2199:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2208:12: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2218:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2224:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/polspline.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘LPmerge’
Package unavailable to check Rd xrefs: ‘LPmerge’
Found the following significant warnings:
  whopgenome/rdnapp_MAF.h:243:12: warning: explicitly assigning value of variable of type 'unsigned int' to itself [-Wself-assign]
  whopgenome/whoptbi_info.cpp:115:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  whopgenome/whoptbi_info.cpp:120:7: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  whopgenome/whoptbi_region.cpp:78:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PopGenome.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Package suggested but not available for checking: ‘VariantAnnotation’
Errors in running code in vignettes:
when running code in ‘poplite.Rnw’
  ...
 8            8         8    18      0      1.68      0.535           2 F    
 9            9         9    20      1      0.911    -0.555           2 F    
10           10        10    12      1      0.237     1.78            1 M    
# ... with more rows

> library(VariantAnnotation)

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

    select

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

    filter

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

Error: processing vignette 'poplite.Rnw' failed with diagnostics:
 chunk 15 
Error in library(VariantAnnotation) : 
  there is no package called ‘VariantAnnotation’
Execution halted
Packages suggested but not available for checking:
  ‘Rglpk’ ‘ROI.plugin.glpk’ ‘ROI.plugin.symphony’
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PortfolioAnalytics.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Errors in running code in vignettes:
when running code in ‘ROI_vignette.Rnw’
  ...

> suppressMessages(library(ROI))

> suppressMessages(library(ROI.plugin.quadprog))

> suppressMessages(library(ROI.plugin.glpk))

  When sourcing ‘ROI_vignette.R’:
Error: there is no package called ‘ROI.plugin.glpk’
Execution halted
when running code in ‘portfolio_vignette.Rnw’
  ...

> maxret <- add.objective(portfolio = init, type = "return", 
+     name = "mean")

> opt_maxret <- optimize.portfolio(R = R, portfolio = maxret, 
+     optimize_method = "ROI", trace = TRUE)

  When sourcing ‘portfolio_vignette.R’:
Error: paste0("package:", plugin) %in% search() || requireNamespace(plugin,  .... is not TRUE
Execution halted
Error in re-building vignettes:
  ...

Error: processing vignette 'ROI_vignette.Rnw' failed with diagnostics:
 chunk 1 
Error in library(ROI.plugin.glpk) : 
  there is no package called ‘ROI.plugin.glpk’
Execution halted
Found the following significant warnings:
  powell.c:700:14: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  powell.c:724:12: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/powell.Rcheck/00install.out’ for details.
File ‘powell/libs/powell.so’:
  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.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/powerCompRisk.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  ppcctest_pearson3.c:19:66: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ppcc.Rcheck/00install.out’ for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Found the following significant warnings:
  ./shared.h:67:9: warning: result of comparison of constant 2147483648 with expression of type 'int' is always false [-Wtautological-constant-out-of-range-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/praznik.Rcheck/00install.out’ for details.
Running ‘testthat-prediction.R’ [27s/44s]
Running the tests in ‘tests/testthat-prediction.R’ failed.
Last 13 lines of output:
  no applicable method for 'predict' applied to an object of class "c('ksvm', 'vm')"
  1: prediction(m, data = genetrain) at testthat/tests-methods.R:255
  2: prediction.ksvm(m, data = genetrain)
  3: predict(model, newdata = out, type = "response", ...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 164 SKIPPED: 0 FAILED: 5
  1. Error: Test prediction() for 'glimML' (@tests-methods.R#33) 
  2. Error: Test prediction() for 'glimQL' (@tests-methods.R#40) 
  3. Error: Test prediction() for 'gausspr' (@tests-methods.R#236) 
  4. Error: Test prediction() for 'kqr' (@tests-methods.R#244) 
  5. Error: Test prediction() for 'ksvm' (@tests-methods.R#255) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
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 31-43 (PRISMA.Rmd) 
Error: processing vignette 'PRISMA.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs  20.9Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PROFANCY.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
getCandidates: no visible binding for global variable ‘envData’
getGraph: no visible binding for global variable ‘envData’
getProvidedDiseaseName: no visible binding for global variable
  ‘envData’
getSeed: no visible binding for global variable ‘envData’
getTopDiseaseMetabolites: no visible binding for global variable
  ‘envData’
Undefined global functions or variables:
  envData
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   6.4Mb
    libs      5.2Mb
Running examples in ‘ProFit-Ex.R’ failed
The error most likely occurred in:

> ### Name: profitBenchmarkResultStripPointers
> ### Title: Return a copy of a data.frame with pointers converted to strings
> ###   for easy printing
> ### Aliases: profitBenchmarkResultStripPointers
> ### Keywords: data
> 
> ### ** Examples
> 
>   openclenvs = profitGetOpenCLEnvs(make.envs=TRUE)
>   print(profitBenchmarkResultStripPointers(openclenvs))

 *** caught segfault ***
address 0x60, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
Packages suggested but not available for checking:
  ‘qtbase’ ‘RGtk2’ ‘cairoDevice’ ‘gWidgetsRGtk2’
Running ‘testthat.R’ [69s/106s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Initial log joint probability = -15.5191
  Optimization terminated normally: 
    Convergence detected: relative gradient magnitude is below tolerance
  Initial log joint probability = -15.5191
  Optimization terminated normally: 
    Convergence detected: relative gradient magnitude is below tolerance
  Initial log joint probability = -15.5191
  Optimization terminated normally: 
    Convergence detected: relative gradient magnitude is below tolerance
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 230 SKIPPED: 0 FAILED: 1
  1. Error: logistic_floor (@test_prophet.R#89) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘ALDEx2’
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PsiHat.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running ‘testthat.R’ [45s/45s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   Elapsed Time: 0.208048 seconds (Warm-up)
                 0.324306 seconds (Sampling)
                 0.532354 seconds (Total)
  
  .0%
  .33%
  .67%
  .100%
  1
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 97 SKIPPED: 0 FAILED: 1
  1. Failure: If it works. (@test-analyze.stanreg.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
    last_plot

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

    get_x, get_y

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

    filter

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

    layout

We recommend that you use the dev version of ggplot2 with `ggplotly()`
Install it with: `devtools::install_github('hadley/ggplot2')`
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot746772bb7fe4.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot746772bb7fe4.png': No such file or directory
Quitting from lines 503-531 (bayesian.Rmd) 
Error: processing vignette 'bayesian.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  pinpolyhedronA.cc:594:7: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  pinpolyhedronA.cc:1766:5: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ptinpoly.Rcheck/00install.out’ for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc        4.6Mb
    examples   2.2Mb
Running ‘testthat.R’ [54s/84s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    jurkat_06_100731121305
  Starting to work on MS/MS Peak shape ...
  
  Memory [MB] prior|after|max(diff) : 91.9 | 91.6 | 4204302 (4204210)
  
  Duration: 1 s
  
  ... MS/MS Peak shape  done
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 252 SKIPPED: 0 FAILED: 2
  1. Failure: createReport (@test_computeQC.R#39) 
  2. Failure: createReport (@test_computeQC.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 34.2Mb
  sub-directories of 1Mb or more:
    libs  33.7Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/QoLR.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  upwindorderedv4.c:542:54: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  upwindorderedv4.c:542:72: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/QPot.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/qtbase.Rcheck/00install.out’ for details.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.7Mb
    doc       2.9Mb
    libs      1.3Mb
Package required but not available: ‘qtbase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 83-117 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 92-106 (wilcox1973.Rmd) 
Error: processing vignette 'wilcox1973.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   9.1Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   3.2Mb
File ‘QUIC/libs/QUIC.so’:
  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/qVarSel.so’:
  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.
FancyPies: no visible global function definition for ‘rainbow’
FancyPies: no visible global function definition for ‘plot’
FancyPies: no visible global function definition for ‘polygon’
Hist2GE: no visible global function definition for ‘dist’
Pies2GE: no visible global function definition for ‘rainbow’
Plots2GE: no visible global function definition for ‘aggregate’
Plots2GE: no visible global function definition for ‘x11’
Plots2GE: no visible global function definition for ‘title’
Plots2GE: no visible global function definition for ‘png’
Plots2GE: no visible global function definition for ‘dev.off’
PolyLines2GE: no visible global function definition for ‘rainbow’
Shapes2GE: no visible global function definition for ‘rainbow’
Undefined global functions or variables:
  aggregate dev.off dist plot png polygon rainbow title x11
Consider adding
  importFrom("grDevices", "dev.off", "png", "rainbow", "x11")
  importFrom("graphics", "plot", "polygon", "title")
  importFrom("stats", "aggregate", "dist")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘RDCOMClient’ ‘rcom’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   4.2Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    htmlwidgets   6.3Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ramidst.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Package suggested but not available for checking: ‘Heatplus’
Package unavailable to check Rd xrefs: ‘Heatplus’
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs   3.9Mb
Packages required but not available: ‘Rsamtools’ ‘GenomicAlignments’

Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RAppArmor.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘rpanel’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs   1.7Mb
Package suggested but not available for checking: ‘rattle’
Packages required but not available: ‘RGtk2’ ‘cairoDevice’

Packages suggested but not available for checking:
  ‘gWidgetsRGtk2’ ‘odfWeave’ ‘playwith’ ‘rggobi’ ‘RGtk2Extras’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 29.7Mb
  sub-directories of 1Mb or more:
    libs  28.3Mb
Errors in running code in vignettes:
when running code in ‘rbiouml.Rnw’
  ...
filterExpression Expression in JavaScript like 'ColumnName1 > 5 && ColumnName2 < 0'
filteringMode                                                  Which rows to select
outputPath                                               Path to the filtered table

> biouml.analysis("Filter table", list(inputPath = "data/Examples/Optimization/Data/Experiments/exp_data_1", 
+     filterExpression = "time < 40", ou .... [TRUNCATED] 

  When sourcing ‘rbiouml.R’:
Error: Internal server error: java.lang.NullPointerException
Execution halted
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    blp    5.9Mb
    libs   4.1Mb
Found the following executable file:
  src/vendor/clickhouse-cpp/contrib/lz4/LICENSE
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘RcppEigen’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Calls with DUP:
   .Call("hclust_from_distance", data = as.double(x), size = as.integer(attributes(x)$Size), 
       link = as.integer(method), DUP = FALSE, NAOK = FALSE, PACKAGE = "Rclusterpp")
   .Call("hclust_from_data", data = x, link = as.integer(method), 
       dist = as.integer(distance), p = as.numeric(p), DUP = FALSE, 
       NAOK = FALSE, PACKAGE = "Rclusterpp")
DUP is no longer supported and will be ignored.
Rclusterpp.package.skeleton: no visible global function definition for
  ‘packageDescription’
Undefined global functions or variables:
  packageDescription
Consider adding
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: replacing previous import ‘Rcmdr::Confint’ by ‘car::Confint’ when loading ‘RcmdrPlugin.BCA’
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RcmdrPlugin.BCA.Rcheck/00install.out’ for details.
Running examples in ‘rcongresso-Ex.R’ failed
The error most likely occurred in:

> ### Name: fetch_votacoes
> ### Title: Fetches all the votings which a proposition went through
> ### Aliases: fetch_votacoes
> 
> ### ** Examples
> 
> votacoes_pec241 <- fetch_votacoes(2088351)
Error in .congresso_api(.$path) : Not Found (HTTP 404).
Calls: fetch_votacoes ... overscope_eval_next -> .congresso_api -> <Anonymous>
Execution halted
Running ‘testthat.R’ [2s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  11: function_list[[i]](value)
  12: dplyr::do(., .congresso_api(.$path)[[1]])
  13: do.rowwise_df(., .congresso_api(.$path)[[1]])
  14: overscope_eval_next(overscope, args[[j]])
  15: .congresso_api(.$path)
  16: httr::stop_for_status(resp)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 19 SKIPPED: 0 FAILED: 3
  1. Failure: GET deputado inexistente (@test_deputados.R#3) 
  2. Error: (unknown) (@test_proposicoes.R#10) 
  3. Error: (unknown) (@test_votacoes.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: '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 45-50 (introducao-rcongresso.Rmd) 
Error: processing vignette 'introducao-rcongresso.Rmd' failed with diagnostics:
Column `id` must be a 1d atomic vector or a list
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rcplex.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RcppAPT.Rcheck/00install.out’ for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    include   5.3Mb
    libs      1.6Mb
Running ‘doRUnit.R’ [140s/140s]
Running the tests in ‘tests/doRUnit.R’ failed.
Last 13 lines of output:
  test.as.dgr2dgc: (5 checks) ... OK (0.01 seconds)
  test.as.dgt2dgc: (18 checks) ... OK (0.09 seconds)
  test.as.dsc2dgc: (8 checks) ... OK (0.03 seconds)
  test.as.dsr2dgc: (4 checks) ... OK (0.02 seconds)
  test.as.dst2dgc: (2 checks) ... OK (0.01 seconds)
  test.as.dtc2dgc: (5 checks) ... OK (0.02 seconds)
  test.as.dtr2dgc: (4 checks) ... OK (0.02 seconds)
  test.as.dtt2dgc: (4 checks) ... OK (0.03 seconds)
  test.as.ind2dgc: (9 checks) ... OK (0.05 seconds)
  test.as.p2dgc: (5 checks) ... OK (0.02 seconds)
  test.as.stm2dgc: (1 checks) ... OK (0 seconds)
  test.as.stm2stm: (1 checks) ... OK (0 seconds)
  test.stop: (7 checks) ... OK (0.04 seconds)
  Error: TEST HAD ERRORS!
  Execution halted
Errors in running code in vignettes:
when running code in ‘RcppArmadillo-unitTests.Rnw’
  ...

> if (err$nFail > 0) stop(sprintf("unit test problems: %d failures", 
+     err$nFail))

> if (err$nErr > 0) stop(sprintf("unit test problems: %d errors", 
+     err$nErr))

  When sourcing ‘RcppArmadillo-unitTests.R’:
Error: unit test problems: 1 errors
Execution halted
Error in re-building vignettes:
  ...
Error in rmultinom(n, size, prob) : NA in probability vector
Error in rmultinomC(n, size, prob) : c++ exception (unknown reason)
Error in rmultinom(n, size, prob) : no positive probabilities
Error in rmultinomC(n, size, prob) : c++ exception (unknown reason)
Timing stopped at: 0.01 0 0.009
Error : $ operator not defined for this S4 class
Error : Only CSC, COO and CSR matrices from SciPy are supported.
dimnames(.) <- NULL:  translated to 
dimnames(.) <- list(NULL,NULL)  <==>  unname(.)
dimnames(.) <- NULL:  translated to 
dimnames(.) <- list(NULL,NULL)  <==>  unname(.)
Error in asSpMat(lm) : lgCMatrix is not supported.
Error in asSpMat(L) : lgTMatrix is not supported.
dimnames(.) <- NULL:  translated to 
dimnames(.) <- list(NULL,NULL)  <==>  unname(.)
Error in asSpMat(nm) : ngCMatrix is not supported.
Error in asSpMat(ngt) : ngTMatrix is not supported.
Error in asSpMat(nM) : ntTMatrix is not supported.
Error in asSpMat(nsc) : nsCMatrix is not supported.
Error in asSpMat(ldi) : ldiMatrix is not supported.

Error: processing vignette 'RcppArmadillo-unitTests.Rnw' failed with diagnostics:
 chunk 2 (label = unitTesting) 
Error in eval(expr, .GlobalEnv) : unit test problems: 1 errors
Execution halted
Found the following warnings:
  ../inst/include/blaze/math/smp/openmp/Functions.h:98:1: warning: control may reach end of non-void function [-Wreturn-type]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RcppBlaze.Rcheck/00install.out’ for details.
installed size is 27.2Mb
  sub-directories of 1Mb or more:
    include  25.3Mb
    libs      1.8Mb
installed size is 31.2Mb
  sub-directories of 1Mb or more:
    include   7.6Mb
    libs     23.0Mb
installed size is 34.5Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib      24.0Mb
    libs      8.6Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    include   6.7Mb
    libs      2.3Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    include   8.9Mb
    libs      2.5Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    include   6.2Mb
    libs      4.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RcppRedis.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rcqp.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rcrypt.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  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

Linking to GEOS 3.6.1, GDAL 2.1.3, proj.4 4.9.3

Attaching package: 'units'

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

    %*%

Quitting from lines 161-186 (vignette.Rmd) 
Error: processing vignette '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
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rDEA.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.
── Attaching packages ────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 2.2.1     ✔ purrr   0.2.4
✔ tibble  1.4.2     ✔ dplyr   0.7.4
✔ tidyr   0.8.0     ✔ stringr 1.3.0
✔ readr   1.1.1     ✔ forcats 0.3.0
── Conflicts ───────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()

Attaching package: 'jsonlite'

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

    flatten

Joining, by = "carrier"
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 39-40 (rdf_intro.Rmd) 
Error: processing vignette 'rdf_intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RDieHarder.Rcheck/00install.out’ for details.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot689656086cc9.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot689656086cc9.png': No such file or directory
Quitting from lines 22-26 (mapDWD.Rmd) 
Error: processing vignette 'mapDWD.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   6.4Mb
Package required but not available: ‘Rmosek’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   3.8Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  14.0Mb
Package required but not available: ‘GenomeGraphs’

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

Package which this enhances but not available for checking: ‘Rcplex’
Running examples in ‘relations-Ex.R’ failed
The error most likely occurred in:

> ### Name: choice
> ### Title: Relation-Based Choices
> ### Aliases: relation_choice
> ### Keywords: math
> 
> ### ** Examples
> 
> data("SVM_Benchmarking_Classification")
> ## Determine the three best classification learners in the above sense.
> relation_choice(SVM_Benchmarking_Classification, k = 3)
Error in loadNamespace(name) : there is no package called ‘Rglpk’
Calls: relation_choice ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Errors in running code in vignettes:
when running code in ‘relations.Rnw’
  ...

> data("Felines")

> relations <- as.relation_ensemble(Felines)

> E <- relation_consensus(relations, "symdiff/E")

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

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

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

    IQR, mad, sd, var, xtabs

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

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

Loading required package: grid

Error: processing vignette 'relations.Rnw' failed with diagnostics:
 chunk 26 (label = consensus1b) 
Error in loadNamespace(name) : there is no package called ‘Rglpk’
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/relax.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
'library' or 'require' call to ‘tkrplot’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  20.2Mb
Found the following significant warnings:
  gar.c:356:29: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  gar.c:356:80: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/repeated.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.
OMP: Error #15: Initializing libomp.dylib, but found libomp.dylib already initialized.
OMP: Hint: This means that multiple copies of the OpenMP runtime have been linked into the program. That is dangerous, since it can degrade performance or cause incorrect results. The best thing to do is to ensure that only a single OpenMP runtime is linked into the process, e.g. by avoiding static linking of the OpenMP runtime in any library. As an unsafe, unsupported, undocumented workaround you can set the environment variable KMP_DUPLICATE_LIB_OK=TRUE to allow the program to continue to execute, but that may cause crashes or silently produce incorrect results. For more information, please see http://www.intel.com/software/products/support/.
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  13: ._jobjRef_dollar(x[["jobj"]], name)
  14: stop(sprintf("no field, method or inner class called '%s' ", name))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 4 SKIPPED: 0 FAILED: 7
  1. Error: (unknown) (@test-docx-bookmarks.R#4) 
  2. Error: (unknown) (@test-docx-img.R#8) 
  3. Error: (unknown) (@test-docx-plot.R#10) 
  4. Error: (unknown) (@test-file-extensions.R#3) 
  5. Error: (unknown) (@test-flextable.R#30) 
  6. Error: (unknown) (@test-pptx-img.R#9) 
  7. Error: (unknown) (@test-pptx-plot.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [20s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 25 SKIPPED: 0 FAILED: 26
  1. Error: can't see environment of caller (@test-env.R#5) 
  2. Error: reprex doesn't write into environment of caller (@test-env.R#11) 
  3. Error: I understand exactly what I'm putting in reprex env (@test-env.R#22) 
  4. Error: reprex: expression input works (@test-input.R#17) 
  5. Error: reprex: character input works (@test-input.R#23) 
  6. Error: reprex: file input works (@test-input.R#31) 
  7. Error: reprex: file input in a subdirectory works (@test-input.R#40) 
  8. Error: Circular use is detected before render (@test-input.R#47) 
  9. Error: Leading prompts are removed (@test-input.R#55) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Running ‘restfulr_unit_tests.R’ [3m/28m]
Running the tests in ‘tests/restfulr_unit_tests.R’ failed.
Last 13 lines of output:
  > require("restfulr") || stop("unable to load restfulr package")
  Loading required package: restfulr
  [1] TRUE
  > restfulr:::.test()
  Loading required namespace: rsolr
  Starting Solr...
  Use options(verbose=TRUE) to diagnose any problems.
  WARNING: An illegal reflective access operation has occurred
  WARNING: Illegal reflective access by org.xnio.nio.NioXnio$2 (file:/Users/urbanek/.local/share/R/rsolr/solr-undertow-1.5.0-RC1-with-solr-5.3.0/lib/xnio-nio-3.4.0.Beta1.jar) to constructor sun.nio.ch.KQueueSelectorProvider()
  WARNING: Please consider reporting this to the maintainers of org.xnio.nio.NioXnio$2
  WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
  WARNING: All illegal access operations will be denied in a future release
  
  Execution halted
  rm: /var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmprsxEQD: Too many open files
Packages suggested but not available for checking:
  ‘gWidgets2RGtk2’ ‘cairoDevice’ ‘RGtk2’
installed size is 29.5Mb
  sub-directories of 1Mb or more:
    libs  28.2Mb
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 230-274 (rfm-customer-level-data.Rmd) 
Error: processing vignette 'rfm-customer-level-data.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 80.1Mb
  sub-directories of 1Mb or more:
    libs      77.3Mb
    pictures   1.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.4Mb
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(rgeolocate)
  > 
  > test_check("rgeolocate")
  ── 1. Failure: non-existent files are detected (@test_maxmind.R#3)  ────────────
  `x` threw an error with unexpected message.
  Expected match: "could not be opened"
  Actual message: "c++ exception (unknown reason)"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 51 SKIPPED: 0 FAILED: 1
  1. Failure: non-existent files are detected (@test_maxmind.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rglpk.Rcheck/00install.out’ for details.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc     3.9Mb
    fonts   1.5Mb
    libs    3.7Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rgnuplot.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RGoogleAnalytics.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages suggested but not available for checking:
  ‘gWidgetsRGtk2’ ‘hyperdraw’ ‘hypergraph’ ‘playwith’ ‘pmg’ ‘rggobi’
  ‘SVGAnnotation’
Running examples in ‘Rgretl-Ex.R’ failed
The error most likely occurred in:

> ### Name: grmod
> ### Title: Interface for _gretl_ estimation commands
> ### Aliases: grmod
> 
> ### ** Examples
> 
> set.seed(13)
> dfr = data.frame(y = rnorm(20), x = rnorm(20))
> grmod("ols y 0 x --simple-print",dfr)

No valid gretl executable: no output is produced
Error: '/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmpNZE4NO/mbundle4ef27a0e3e9.xml' does not exist.
Execution halted
Package required but not available: ‘RGtk2’

Package suggested but not available for checking: ‘gWidgetsRGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RGtk2.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 34-47 (intro_rhandsontable.Rmd) 
Error: processing vignette 'intro_rhandsontable.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rhpc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  filterhr.c:21:11: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  filterhr.c:21:53: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  filterhr.c:21:95: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RHRV.Rcheck/00install.out’ for details.
Found the following significant warnings:
  computePvals.c:488:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ridge.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘httr’ ‘rmarkdown’ ‘shiny’
  All declared Imports should be used.
File ‘RInside/libs/RInside.so’:
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLdo1’, ‘R_ReplDLLinit’,
    ‘R_RunExitFinalizers’, ‘R_SetParams’, ‘R_SignalHandlers’,
    ‘R_TempDir’, ‘Rf_endEmbeddedR’, ‘Rf_initEmbeddedR’

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.
Found the following significant warnings:
  Warning: The javah tool is planned to be removed in the next major
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rJava.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API call to R: ‘R_GlobalContext’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor 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:
  libjson/Source/JSONSharedString.h:180:47: warning: field 'len' will be initialized after field '_str' [-Wreorder]
  libjson/Source/JSONSharedString.h:182:66: warning: field 'len' will be initialized after field '_str' [-Wreorder]
  JSONStream.cpp:8:130: warning: field 'state' will be initialized after field 'call' [-Wreorder]
  JSONStream.cpp:8:157: warning: field 'err_call' will be initialized after field 'buffer' [-Wreorder]
  JSONStream.cpp:12:64: warning: field 'state' will be initialized after field 'call' [-Wreorder]
  JSONStream.cpp:12:100: warning: field 'err_call' will be initialized after field 'buffer' [-Wreorder]
  internalJSONNode.cpp:78:117: warning: field '_name_encoded' will be initialized after field '_name' [-Wreorder]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RJSONIO.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘golubEsets’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rLindo.Rcheck/00install.out’ for details.
Mallows: no visible global function definition for ‘runif’
Mallows: no visible global function definition for ‘x11’
Mallows: no visible global function definition for ‘plot’
Mallows: no visible global function definition for ‘dev.off’
UpdateLambda: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  dev.off plot runif uniroot x11
Consider adding
  importFrom("grDevices", "dev.off", "x11")
  importFrom("graphics", "plot")
  importFrom("stats", "runif", "uniroot")
to your NAMESPACE file.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Package required and available but unsuitable version: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  6: shiny::checkboxInput
  7: getExportedValue(pkg, name)
  8: asNamespace(ns)
  9: getNamespace(ns)
  10: tryCatch(loadNamespace(name), error = function(e) stop(e))
  11: tryCatchList(expr, classes, parentenv, handlers)
  12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  13: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 16 SKIPPED: 25 FAILED: 1
  1. Error: parameters are configurable (@test-params.R#67) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RMark.Rcheck/00install.out’ for details.
File ‘RMC/libs/RMC.so’:
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
    Objects: ‘RMC.o’, ‘predict.o’
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘ap.o’

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 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RmecabKo.Rcheck/00install.out’ for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   5.0Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Running examples in ‘RMongo-Ex.R’ failed
The error most likely occurred in:

> ### Name: dbAggregate-methods
> ### Title: Performing a MongoDB aggregate query
> ### Aliases: dbAggregate dbAggregate-methods
> ###   dbAggregate,RMongo,character,character-method
> 
> ### ** Examples
> 
>   mongo <- mongoDbConnect("test")
>   # insert two records
>   dbInsertDocument(mongo, "test_data", '{"foo": "bar", "size": 5 }')
Error in .jcall(rmongo.object@javaMongo, "S", "dbInsertDocument", collection,  : 
  com.mongodb.MongoException$Network: Write operation to server /127.0.0.1:27017 failed on database test
Calls: dbInsertDocument -> dbInsertDocument -> .jcall -> .jcheck
Execution halted
Running ‘RMongo-Ex.R’ [4s/3s]
Running the tests in ‘tests/RMongo-Ex.R’ failed.
Last 13 lines of output:
  +   dbRemoveQuery(mongo, "test_data", '{}')
  +   dbDisconnect(mongo)
  +   
  +   # print(length(output))
  +   print(as.character(output[1]))
  + 
  +   checkEquals("{ \"_id\" : \"bar\"}", as.character(output[1]))
  +   # checkEquals("bar", as.character(output[1]))
  + }
  > 
  > test.dbInsertDocument()
  Error in .jcall(rmongo.object@javaMongo, "S", "dbInsertDocument", collection,  : 
    com.mongodb.MongoException$Network: Write operation to server /127.0.0.1:27017 failed on database test
  Calls: test.dbInsertDocument ... dbInsertDocument -> dbInsertDocument -> .jcall -> .jcheck
  Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rmosek.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rMouse.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rmpi.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(rmweather)
  > 
  > test_check("rmweather")
  ── 1. Failure: Test training function (@test_02_rmw_functions.R#53)  ───────────
  model$r.squared not equal to 0.4184627.
  1/1 mismatches
  [1] 0.399 - 0.418 == -0.0196
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 32 SKIPPED: 0 FAILED: 1
  1. Failure: Test training function (@test_02_rmw_functions.R#53) 
  
  Error: testthat unit tests failed
  Execution halted
.isPath: no visible global function definition for ‘tail’
.isPath: no visible global function definition for ‘head’
navGraph : <anonymous>: no visible global function definition for
  ‘tail’
navGraph : <anonymous>: no visible global function definition for ‘sd’
navGraph: no visible global function definition for ‘colors’
ng_image_array_gray : <anonymous>: no visible global function
  definition for ‘grey’
scagGraph: no visible global function definition for ‘quantile’
closeViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.off’
initializeViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.new’
initializeViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.cur’
plot,NG_graph-ANY: no visible global function definition for ‘box’
plot,NG_graph-ANY: no visible global function definition for ‘axis’
plot,NG_graph-ANY: no visible global function definition for ‘points’
plot,NG_graph-ANY: no visible global function definition for ‘text’
plot,NG_graph-ANY: no visible global function definition for ‘segments’
updateViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.set’
Undefined global functions or variables:
  axis box colors dev.cur dev.new dev.off dev.set grey head points
  quantile sd segments tail text
Consider adding
  importFrom("grDevices", "colors", "dev.cur", "dev.new", "dev.off",
             "dev.set", "grey")
  importFrom("graphics", "axis", "box", "points", "segments", "text")
  importFrom("stats", "quantile", "sd")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
installed size is 94.7Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     92.6Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
Found the following significant warnings:
  ./hammock.h:369:15: warning: assigning field to itself [-Wself-assign-field]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/robfilter.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘SSOAP’
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  16.0Mb
installed size is 21.3Mb
  sub-directories of 1Mb or more:
    libs  21.0Mb
installed size is 31.4Mb
  sub-directories of 1Mb or more:
    libs  30.3Mb
Running examples in ‘robustX-Ex.R’ failed
The error most likely occurred in:

> ### Name: rbwheel
> ### Title: Multivariate Barrow Wheel Distribution Random Vectors
> ### Aliases: rbwheel
> ### Keywords: distribution robust
> 
> ### ** Examples
> 
> set.seed(17)
> rX8 <- rbwheel(1000,8, fullResult = TRUE, scaleAfter=FALSE)
> with(rX8, stopifnot(all.equal(X, X0 %*% A,    tol = 1e-15),
+                     all.equal(X0, X %*% t(A), tol = 1e-15)))
> ##--> here, don't need to keep X0 (nor A, since that is Qrot(p))
> 
> ## for n = 100,  you  don't see "it", but may guess .. :
> n <- 100
> pairs(r <- rbwheel(n,6))
> n1 <- attr(r,"n1") ; pairs(r, col=1+((1:n) > n1))
> 
> ## for n = 500, you *do* see it :
> n <- 500
> pairs(r <- rbwheel(n,6))
> ## show explicitly
> n1 <- attr(r,"n1") ; pairs(r, col=1+((1:n) > n1))
> 
> ## but increasing sig2 does help:
> pairs(r <- rbwheel(n,6, sig2 = .2))
> 
> ## show explicitly
> n1 <- attr(r,"n1") ; pairs(r, col=1+((1:n) > n1))
> 
> set.seed(12)
> pairs(X <- rbwheel(n, 7, spherize=TRUE))
> colSums(X) # already centered
[1] -3.129441e-15  6.151329e-15 -8.555656e-15  2.352285e-15  2.428613e-16
[6]  3.505876e-15 -3.537101e-15
> 
> if(require("ICS")) {
+   # ICS: Compare M-estimate [Max.Lik. of t_{df = 2}] with high-breakdown :
+   stopifnot(require("MASS"))
+   X.paM <- ics(X, S1 = cov, S2 = function(.) cov.trob(., nu=2)$cov, stdKurt = FALSE)
+   X.paM.<- ics(X, S1 = cov, S2 = function(.) tM(., df=2)$V, stdKurt = FALSE)
+   X.paR <- ics(X, S1 = cov, S2 = function(.) covMcd(.)$cov, stdKurt = FALSE)
+   plot(X.paM) # not at all clear
+   plot(X.paM.)# ditto
+   plot(X.paR)# very clear
+ }
Loading required package: ICS
Loading required package: mvtnorm
Loading required package: MASS
Error in covMcd(.) : could not find function "covMcd"
Calls: ics -> do.call -> S2
Execution halted
Package required but not available: ‘clpAPI’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘test_deoptim.R’ [20s/31s]
Running the tests in ‘tests/test_deoptim.R’ failed.
Last 13 lines of output:
  + 
  +     rt( test_nlp_01() )
  +     rt( test_nlp_02() )
  +     rt( test_nlp_03() )
  + 
  +     if ( ROI_TEST_ERRORS > 0 ) {
  +         stop("ROI_Test_Error ", ROI_TEST_ERRORS, " occurred during testing.")
  +     }
  + }
  Error in test_nlp_03() : equal(solution(nlp), c(20, 11, 15)) is not TRUE
  In addition: Warning message:
  In (function (lower, upper, fn, constr = NULL, meq = 0, eps = 1e-05,  :
    maximum number of iterations reached without convergence
  Error: ROI_Test_Error 1 occurred during testing.
  Execution halted
Package required but not available: ‘Rsymphony’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ROI.plugin.glpk’ ‘ROI.plugin.symphony’

Package which this enhances but not available for checking: ‘ROI.plugin.cplex’
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  18.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ROracle.Rcheck/00install.out’ for details.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.3Mb
    libs   4.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rpanel.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rpg.Rcheck/00install.out’ for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      3.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$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 51-53 (rpivotTableIntroduction.Rmd) 
Error: processing vignette 'rpivotTableIntroduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.1Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    extdata  12.2Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rpoppler.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  11: stringr::str_trim
  12: getExportedValue(pkg, name)
  13: asNamespace(ns)
  14: getNamespace(ns)
  15: tryCatch(loadNamespace(name), error = function(e) stop(e))
  16: tryCatchList(expr, classes, parentenv, handlers)
  17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  18: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 73 SKIPPED: 8 FAILED: 1
  1. Error: thisfile works with knitr (@test-thisfile.R#28) 
  
  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.
Error: processing vignette 'rprojroot.Rmd' failed with diagnostics:
shared object 'stringi.so' not found
Execution halted
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  15.1Mb
'library' or 'require' calls to packages already attached by Depends:
  ‘RSAGA’ ‘shapefiles’
  Please remove these calls from your code.
Packages required but not available: ‘gWidgetsRGtk2’ ‘RGtk2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RQuantLib.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RSAP.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Quitting from lines 307-310 (article.Rnw) 
Error: processing vignette 'article.Rnw' failed with diagnostics:
Please run "rscala::scalaInstall()" or install Scala manually.
Execution halted
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RSEIS.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Namespaces in Imports field not imported from:
  ‘binman’ ‘httr’
  All declared Imports should be used.
Note: information on .o files is not available
File ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_random’, possibly from ‘random’ (C)
  Found ‘_srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor 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.
Packages required but not available: ‘cairoDevice’ ‘gWidgetsRGtk2’

Package suggested but not available for checking: ‘ctc’

Depends: includes the non-default packages:
  ‘biwt’ ‘cairoDevice’ ‘fBasics’ ‘gplots’ ‘gWidgets’ ‘gWidgetsRGtk2’
  ‘minerva’ ‘parmigene’ ‘stringr’ ‘snowfall’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
Running examples in ‘rsolr-Ex.R’ failed
The error most likely occurred in:

> ### Name: SolrCore-class
> ### Title: SolrCore
> ### Aliases: class:SolrCore SolrCore-class name,SolrCore-method
> ###   ndoc,SolrCore-method schema schema,SolrCore-method
> ###   fieldNames,SolrCore-method version version,SolrCore-method SolrCore
> ###   docs docs,SolrCore-method read,SolrCore-method
> ###   eval,SolrQuery,SolrCore-method
> ###   eval,TranslationRequest,SolrCore-method facets facets,SolrCore-method
> ###   groupings groupings,SolrCore-method ngroup,SolrCore-method
> ###   update,SolrCore-method delete,SolrCore-method commit
> ###   commit,SolrCore-method purgeCache,SolrCore-method
> ###   show,SolrCore-method
> ### Keywords: methods classes
> 
> ### ** Examples
> 
>      solr <- TestSolr()
Starting Solr...
Use options(verbose=TRUE) to diagnose any problems.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.xnio.nio.NioXnio$2 (file:/Users/urbanek/.local/share/R/rsolr/solr-undertow-1.5.0-RC1-with-solr-5.3.0/lib/xnio-nio-3.4.0.Beta1.jar) to constructor sun.nio.ch.KQueueSelectorProvider()
WARNING: Please consider reporting this to the maintainers of org.xnio.nio.NioXnio$2
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release

Execution halted
Error: failed to load sRGB colorspace file
Fatal error: error during cleanup

rm: /var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmpxMts3M: Too many open files
installed size is 47.3Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  45.9Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Found the following significant warnings:
  ssl.cpp:110:7: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ssl.cpp:113:11: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ssl.cpp:139:7: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ssl.cpp:165:11: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ssl.cpp:169:8: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ssl.cpp:280:11: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ssl.cpp:284:8: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ssl.cpp:805:11: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ssl.cpp:809:8: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RSSL.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rstanarm.Rcheck/00install.out’ for details.
installed size is 205.1Mb
  sub-directories of 1Mb or more:
    libs  202.5Mb
Running ‘testthat.R’ [252s/415s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > library(rstansim)
  Loading required package: Rcpp
  > 
  > test_check("rstansim")
  
   *** caught segfault ***
  address 0x107f89aa0, cause 'memory not mapped'
  
  Traceback:
   1: .Call(list(name = "CppObject__finalize", address = <pointer: 0x7fcf56212660>,     dll = list(name = "Rcpp", path = "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/Rcpp/libs/Rcpp.so",         dynamicLookup = TRUE, handle = <pointer: 0x7fcf5620b0f0>,         info = <pointer: 0x7fcf5385df00>), numParameters = 2L),     <pointer: 0x7fcf53470440>, .pointer)
   2: x$.self$finalize()
   3: (function (x) x$.self$finalize())(<environment>)
  An irrecoverable exception occurred. R is aborting now ...
Found the following significant warnings:
  c_optim.cpp:427:6: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rstpm2.Rcheck/00install.out’ for details.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rsymphony.Rcheck/00install.out’ for details.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    Lib  11.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       1.8Mb
    projects   2.5Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   2.4Mb
Packages required but not available: ‘cairoDevice’ ‘gWidgetsRGtk2’ ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    libs  25.1Mb
installed size is 46.8Mb
  sub-directories of 1Mb or more:
    libs  45.9Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RVowpalWabbit.Rcheck/00install.out’ for details.
Found the following significant warnings:
  qwiener.c:60:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  qwiener.c:69:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RWiener.Rcheck/00install.out’ for details.
Found the following significant warnings:
  nchg.c:555:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RxCEcolInf.Rcheck/00install.out’ for details.
Found the following significant warnings:
  call_dvode.c:746:18: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  sum.c:221:11: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  sum.c:221:22: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  sum.c:227:45: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  sum.c:227:53: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RxODE.Rcheck/00install.out’ for details.
Found the following significant warnings:
  yacas/src/obmalloc.cpp:584:23: warning: result of comparison of constant 384307168202282325 with expression of type 'unsigned int' is always false [-Wtautological-constant-out-of-range-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Ryacas.Rcheck/00install.out’ for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs    5.2Mb
    yacas   1.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    sample_data   3.1Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SAENET.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
SAENET.nnet: no visible global function definition for ‘as.formula’
SAENET.nnet: no visible global function definition for ‘rnorm’
SAENET.train: no visible global function definition for ‘predict’
Undefined global functions or variables:
  as.formula predict rnorm
Consider adding
  importFrom("stats", "as.formula", "predict", "rnorm")
to your NAMESPACE file.
Found the following significant warnings:
  dists.cc:4239:21: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SafeBayes.Rcheck/00install.out’ for details.
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
Packages suggested but not available for checking:
  ‘mixer’ ‘networkTomography’ ‘org.Sc.sgd.db’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 34-35 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1/1 mismatches
  [1] 1 - 0 == 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 62 SKIPPED: 0 FAILED: 7
  1. Failure: examples: all examples (@test_api_stability.R#156) 
  2. Failure: examples: all examples (@test_api_stability.R#157) 
  3. Failure: examples: all examples (@test_api_stability.R#162) 
  4. Failure: execute: valid command (@test_execute.R#13) 
  5. Failure: execute: valid commands (@test_execute.R#18) 
  6. Failure: execute: runner provided (@test_execute.R#64) 
  7. Failure: execute: print_commands (@test_execute.R#69) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  pointinpolygon.c:60:7: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  slope.aspect.c:128:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  slope.aspect.c:128:33: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  vincenty.geodesics.c:50:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  vincenty.geodesics.c:126:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SDMTools.Rcheck/00install.out’ for details.
Found the following executable file:
  inst/external/env/bio14.bil
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/sdols.Rcheck/00install.out’ for details.
Running ‘cran-tests.R’ [2s/2s]
Running the tests in ‘tests/cran-tests.R’ failed.
Last 13 lines of output:
  
  
  Program received signal SIGTRAP: Trace/breakpoint trap.
  
  Backtrace for this error:
  #0  0x1230e5579
  #1  0x1230e4945
  #2  0x7fff93ac4529
  Error: X-13 has returned a non-zero exist status, which means that the current spec file cannot be processed for an unknown reason.
  In addition: Warning messages:
  1: In system(paste(x13.bin, file, flags), intern = TRUE, ignore.stderr = TRUE) :
    running command '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/x13ashtml /var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmpRVGyFB/x1313b4961ccbe9a/iofile -n -s 2>/dev/null' had status 133
  2: In system(paste(x13.bin, file, flags), intern = TRUE, ignore.stderr = TRUE) :
    running command '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/x13ashtml /var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmpRVGyFB/x1313b4948f5a29f/iofile -n -s 2>/dev/null' had status 133
  Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    data   1.1Mb
    doc    1.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.7Mb
Found the following significant warnings:
  BinNegative.cpp:108:5: warning: assigning field to itself [-Wself-assign-field]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Segmentor3IsBack.Rcheck/00install.out’ for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Packages required but not available: ‘rggobi’ ‘gWidgetsRGtk2’ ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs   6.9Mb
Found the following significant warnings:
  vcf.c:253:15: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/seqminer.Rcheck/00install.out’ for details.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
File ‘sequoia/libs/sequoia.so’:
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Object: ‘sequoia.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 17.5Mb
  sub-directories of 1Mb or more:
    libs  16.8Mb
Packages suggested but not available for checking:
  ‘loomR’ ‘SingleCellExperiment’ ‘MAST’
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is 111.7Mb
  sub-directories of 1Mb or more:
    doc     10.8Mb
    libs    96.7Mb
    sqlite   1.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/shallot.Rcheck/00install.out’ for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    www   7.7Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    www   6.4Mb
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 89-90 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   9.9Mb
Package required but not available: ‘BSgenome’

Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’

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

Packages suggested but not available for checking: ‘clipper’ ‘topologyGSA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.3Mb
Error in re-building vignettes:
  ...
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Shutting down cluster.
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.

Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   4.2Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.2Mb
installed size is 28.5Mb
  sub-directories of 1Mb or more:
    libs  27.2Mb
Found the following significant warnings:
  MCP_efficient.c:114:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  MCP_efficient.c:134:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  MCP_efficient.c:154:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SMCP.Rcheck/00install.out’ for details.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   6.5Mb
Found the following significant warnings:
  ./Scythe_IDE.cpp:70:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:107:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:108:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:109:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:147:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:148:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:149:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:189:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:211:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:212:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:262:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:265:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:266:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/smoothSurv.Rcheck/00install.out’ for details.
Running examples in ‘sm-Ex.R’ failed
The error most likely occurred in:

> ### Name: sm.surface3d
> ### Title: Adding a regression surface to an rgl plot.
> ### Aliases: sm.surface3d
> ### Keywords: nonparametric regression smooth
> 
> ### ** Examples
> 
> with(trawl, {
+    Zone93    <- (Year == 1 & Zone == 1)
+    Position  <- cbind(Longitude - 143, Latitude)
+    model1 <- sm.regression(Position[Zone93,], Score1[Zone93],
+         h= c(0.1, 0.1), display = "rgl", xlab="Longitude - 143")
+    model2 <- sm.regression(Position[Zone93,], Score1[Zone93],
+         h= c(0.2, 0.2), display = "none")
+    sm.surface3d(model2$eval.points, model2$est, model1$scaling, col = "red")
+ })
Error in sm.surface3d(model2$eval.points, model2$est, model1$scaling,  : 
  a scaling must be specified.
Calls: with -> with.default -> eval -> eval -> sm.surface3d
Execution halted
Found the following significant warnings:
  /System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/unicodeobject.h:534:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/unicodeobject.h:553:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/unicodeobject.h:575:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/unicodeobject.h:593:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/stringobject.h:173:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/stringobject.h:174:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/stringobject.h:175:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SnakeCharmR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SocialMediaLab.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages suggested but not available for checking:
  ‘r2cytoscape’ ‘BiocStyle’ ‘graphite’ ‘hgu95av2.db’
Packages unavailable to check Rd xrefs: ‘simPATHy’, ‘graphite’
Error in re-building vignettes:
  ...
    IQR, mad, sd, var, xtabs

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

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

Identifing all possible orderings..
Total run time: 1.21 secs
Identifing all possible orderings..
Total run time: 0.86 secs
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]="./webshotf9064431846f.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotf9064431846f.png': No such file or directory
Quitting from lines 346-347 (SourceSet.Rmd) 
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/spaceExt.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages in Depends field not imported from:
  ‘glasso’ ‘limSolve’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
glasso.miss: no visible global function definition for ‘cov’
glasso.miss: no visible global function definition for ‘glasso’
glasso.miss: no visible global function definition for ‘Solve’
space.miss: no visible global function definition for ‘Solve’
Undefined global functions or variables:
  Solve cov glasso
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
Running ‘test-all.R’ [275s/483s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
    Using cached copy of .inputObjects event in test module
    Using cached copy of .inputObjects event in test module
  ── 1. Error: 3 levels of parent and child modules load and show correctly (@test
  At optimal_modularity.c:85 : GLPK is not available, Unimplemented function call
  1: moduleGraph(mySim, FALSE) at testthat/test-module-deps-methods.R:201
  2: moduleGraph(mySim, FALSE)
  3: cluster_optimal(grph)
  
    Using cached copy of burn event in fireSpread module
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 344 SKIPPED: 33 FAILED: 1
  1. Error: 3 levels of parent and child modules load and show correctly (@test-module-deps-methods.R#201) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...

Loading required package: quickPlot
Loading required package: reproducible

Attaching package: 'reproducible'

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

    %>%

Loading required package: RColorBrewer
Loading required package: raster
Loading required package: sp
Loading required package: grid

Attaching package: 'grid'

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

    gpar

Quitting from lines 357-361 (ii-modules.Rmd) 
Error: processing vignette 'ii-modules.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 32.8Mb
  sub-directories of 1Mb or more:
    libs  31.0Mb
package ‘Matrix’ exists but was not installed under R >= 2.10.0 so xrefs cannot be checked
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot10951185c772.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot10951185c772.png': No such file or directory
Quitting from lines 20-30 (intro_sparkline.Rmd) 
Error: processing vignette 'intro_sparkline.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running ‘run-all.R’ [8s/35s]
Running the tests in ‘tests/run-all.R’ failed.
Last 13 lines of output:
  4: callJStatic("org.apache.spark.ml.r.GeneralizedLinearRegressionWrapper", "fit", formula, 
         data@sdf, tolower(family$family), family$link, tol, as.integer(maxIter), weightCol, 
         regParam, as.double(var.power), as.double(link.power), stringIndexerOrderType, 
         offsetCol)
  5: invokeJava(isStatic = TRUE, className, methodName, ...)
  6: handleErrors(returnStatus, conn)
  7: stop(readString(conn))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 2
  1. Error: create DataFrame from list or data.frame (@test_basic.R#26) 
  2. Error: spark.glm and predict (@test_basic.R#58) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
	at org.apache.spark.sql.Dataset.org$apache$spark$sql$Dataset$$collectFromPlan(Dataset.scala:3272)
	at org.apache.spark.sql.Dataset$$anonfun$collect$1.apply(Dataset.scala:2722)
	at org.apache.spark.sql.Dataset$$anonfun$collect$1.apply(Dataset.scala:2722)
	at org.apache.spark.sql.Dataset$$anonfun$52.apply(Dataset.scala:3253)
	at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:77)
	at org.apache.spark.sql.Dataset.withAction(Dataset.scala:3252)
	at org.apache.spark.sql.Dataset.collect(Dataset.scala:2722)
	at org.apache.spark.sql.api.r.SQLUtils$.dfToCols(SQLUtils.scala:173)
	at org.apache.spark.sql.api.r.SQLUtils.dfToCols(SQLUtils.scala)
	... 36 more
Quitting from lines 102-104 (sparkr-vignettes.Rmd) 
Error: processing vignette 'sparkr-vignettes.Rmd' failed with diagnostics:
java.lang.IllegalArgumentException
	at org.apache.xbean.asm5.ClassReader.<init>(Unknown Source)
	at org.apache.xbean.asm5.ClassReader.<init>(Unknown Source)
	at org.apache.xbean.asm5.ClassReader.<init>(Unknown Source)
	at org.apache.spark.util.ClosureCleaner$.getClassReader(ClosureCleaner.scala:46)
	at org.apache.spark.util.FieldAccessFinder$$anon$3$$anonfun$visitMethodInsn$2.apply(ClosureCleaner.scala:449)
	at org.apache.spark.util.FieldAccessFinder$$anon$3$$anonfun$visitMethodInsn$2.apply(ClosureCleaner.scala:432)
	at scala.collection.TraversableLike$WithFilter$$anonfun$foreach$1.apply(TraversableLike.scala:733)
	at scala.collection.mutable.HashMap$$anon$1$$anonfun$foreach$2.apply(HashMap.scala:103)
	at scala.collection.mutable.HashMap$$anon$1$$anonfun$foreach$2.apply(HashMap.scala:103)
	at scala.collection.mutable.HashTable$class.foreachEntry(HashTable.scala:230)
	at scala.collection.mutable.HashMap.foreachE
Execution halted
Package suggested but not available for checking: ‘RCy3’
Package unavailable to check Rd xrefs: ‘RCy3’
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    R      5.0Mb
    doc    4.7Mb
    help   5.1Mb
    libs   1.7Mb
Running ‘testsAtoF.R’ [37s/60s]
  Running ‘testsGtoK.R’ [120s/187s]
  Running ‘testsLtoM.R’ [165s/261s]
  Running ‘testsNtoP.R’ [28s/44s]
Running the tests in ‘tests/testsNtoP.R’ failed.
Last 13 lines of output:
  + 
  +   ## (6) suffstat.R
  +   fitP <- update(fit, Poisson())
  +   suffstat.poisson(fitP, cells)
  +   fit0 <- killinteraction(fit)
  +   suffstat.poisson(fit0, cells)
  +   
  +   spatstat.options(op)
  + })
  (computing rbord)
  comparing 4 models...
  1, 2, 3,  4.
  fitting optimal model...
  
  Execution halted
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
Packages required but not available: ‘xcms’ ‘MAIT’

Package suggested but not available for checking: ‘rcytoscapejs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: sp
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "10"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "10"
Quitting from lines 45-64 (spew-quickstart.Rmd) 
Error: processing vignette 'spew-quickstart.Rmd' failed with diagnostics:
polygon edge not found
Execution halted
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    libs  23.7Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   6.5Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs  11.4Mb
Running examples in ‘SRRS-Ex.R’ failed
The error most likely occurred in:

> ### Name: SRRS-package
> ### Title: The Stepwise Response Refinement Screener (SRRS)
> ### Aliases: SRRS-package
> 
> ### ** Examples
> 
> SRRS()
Warning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "ComboBox".
Calls: SRRS -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    include   8.7Mb
Packages required but not available:
  ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’ ‘RSCABS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
Running examples in ‘stepwise-Ex.R’ failed
The error most likely occurred in:

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


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

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

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

> WinHalfWidth<-30

> permReps<-10

> a<-maxchi(inputFile, breaks, WinHalfWidth, permReps)
Namespaces in Imports field not imported from:
  ‘lattice’ ‘xtable’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 111-114 (introducing-stplanr.Rmd) 
Error: processing vignette 'introducing-stplanr.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Packages required but not available: ‘Rglpk’ ‘MultAlloc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 33.1Mb
  sub-directories of 1Mb or more:
    libs  32.4Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
sh: line 1: 66959 Trace/BPT trap: 5       /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/x13ashtml /var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//Rtmpegs7NK/x13105287d01a8b5/iofile -n -s 2> /dev/null
dyld: lazy symbol binding failed: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib


Program received signal SIGTRAP: Trace/breakpoint trap.

Backtrace for this error:
#0  0x12cc84579
#1  0x12cc83945
#2  0x7fff93ac4529
Quitting from lines 61-64 (stRvignette.Rmd) 
Error: processing vignette 'stRvignette.Rmd' failed with diagnostics:
X-13 has returned a non-zero exist status, which means that the current spec file cannot be processed for an unknown reason.
Execution halted
Packages required but not available: ‘gWidgets2RGtk2’ ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Found the following significant warnings:
  dists.cc:4239:21: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SuppDists.Rcheck/00install.out’ for details.
Packages required but not available: ‘clipper’ ‘qpgraph’

Packages suggested but not available for checking:
  ‘graphite’ ‘curatedOvarianData’ ‘BiocStyle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.3Mb
    help   1.0Mb
    libs   1.4Mb
installed size is 73.0Mb
  sub-directories of 1Mb or more:
    libs  72.1Mb
Found the following significant warnings:
  trlan/trlcore.c:983:15: warning: comparison of array 'info->oldcpf' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlcore.c:1642:9: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  trlan/trlcore.c:1642:20: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  trlan/trlaux.c:28:13: warning: comparison of array 'info->log_file' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlaux.c:41:13: warning: comparison of array 'info->log_file' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlaux.c:62:13: warning: comparison of array 'info->cpfile' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlan.c:171:20: warning: comparison of array 'info->oldcpf' equal to a null pointer is always false [-Wtautological-pointer-compare]
  trlan/ztrlcore.c:1418:12: warning: comparison of array 'info->oldcpf' not equal to a null pointer is always true [-Wtautological-pointer-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/svd.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘svHttp’
File ‘svmpath/libs/svmpath.so’:
  Found ‘__gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘__gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘__gfortran_st_read’, possibly from ‘read’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi30spec.o’, ‘mi35mps.o’,
      ‘mi36mps.o’, ‘mi40bfil.o’
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: CHARACTER expression will be truncated in assignment (10/13) at (1) [-Wcharacter-truncation]
  Warning: ‘pst_kg’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘burn_frlb’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘hi_ovr’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘harveff’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘frac_harvk’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘lai_init’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘orig_tnylda’ is used uninitialized in this function [-Wuninitialized]
  Warning: CHARACTER expression will be truncated in assignment (1/3) at (1) [-Wcharacter-truncation]
  Warning: ‘fr_curb’ is used uninitialized in this function [-Wuninitialized]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SWATmodel.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘cplexAPI’ ‘glpkAPI’
Running examples in ‘sybilcycleFreeFlux-Ex.R’ failed
The error most likely occurred in:

> ### Name: cfFBA
> ### Title: cycle free flux
> ### Aliases: cfFBA lrFBA
> ### Keywords: cycle free flux loopless FBA
> 
> ### ** Examples
> 
> ##---- Should be DIRECTLY executable !! ----
> ##-- ==>  Define data, use random,
> ##--	or do  help(data=index)  for the standard data sets.
> data(iAF1260)
> model=iAF1260
> fba=optimizeProb(model)
Loading required package: glpkAPI
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘glpkAPI’
Error in checkDefaultMethod(solver, method, pType) : 
  package ‘glpkAPI’ not found
Calls: optimizeProb -> optimizeProb -> .local -> sysBiolAlg
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/sybilEFBA.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
FECorr: no visible global function definition for ‘is’
FECorr: no visible global function definition for ‘write.csv’
FECorr: no visible global function definition for ‘aggregate’
FECorr: no visible global function definition for ‘lm’
FECorr: no visible global function definition for ‘nlm’
eFBA_gene: no visible global function definition for ‘is’
eFBA_gene: no visible global function definition for ‘as’
eFBA_rxn : adjustTol: no visible global function definition for ‘is’
eFBA_rxn: no visible global function definition for ‘is’
eFBA_rxn: no visible global function definition for ‘as’
findFluxGeneExpr: no visible global function definition for ‘as’
findMDCFlux: no visible global function definition for ‘is’
findMDCFlux: no visible global function definition for ‘as’
gene2Rule: no visible global function definition for ‘is’
Undefined global functions or variables:
  aggregate as is lm nlm write.csv
Consider adding
  importFrom("methods", "as", "is")
  importFrom("stats", "aggregate", "lm", "nlm")
  importFrom("utils", "write.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages suggested but not available for checking:
  ‘glpkAPI’ ‘cplexAPI’ ‘clpAPI’
Package unavailable to check Rd xrefs: ‘glpkAPI’
Running examples in ‘sybil-Ex.R’ failed
The error most likely occurred in:

> ### Name: SYBIL_SETTINGS
> ### Title: Set and Get sybil Parameters
> ### Aliases: SYBIL_SETTINGS SOLVER METHOD TOLERANCE MAXIMUM ALGORITHM
> ###   OPT_DIRECTION USE_NAMES PATH_TO_MODEL SOLVER_CTRL_PARM
> ### Keywords: optimize
> 
> ### ** Examples
> 
>   ## show all current parameters
>   SYBIL_SETTINGS()
$MODELORG_VERSION
[1] "2.0"

$SOLVER
[1] "glpkAPI"

$METHOD
[1] "simplex"

$TOLERANCE
[1] 1e-06

$MAXIMUM
[1] 1000

$ALGORITHM
[1] "fba"

$OPT_DIRECTION
[1] "max"

$USE_NAMES
[1] FALSE

$PATH_TO_MODEL
[1] "."

$SOLVER_CTRL_PARM
  NA
1 NA

>   
>   ## show current setting for "SOLVER"
>   SYBIL_SETTINGS("SOLVER")
[1] "glpkAPI"
> 
>   ## change current solver to glpkAPI
>   SYBIL_SETTINGS("SOLVER", "glpkAPI")
Loading required package: glpkAPI
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘glpkAPI’
Error in checkDefaultMethod(solver = value, method = "", probType = "",  : 
  package ‘glpkAPI’ not found
Calls: SYBIL_SETTINGS -> checkDefaultMethod
Execution halted
Errors in running code in vignettes:
when running code in ‘sybil.Rnw’
  ...
number of exchange reactions: 20

> optL <- optimizeProb(Ec_core, algorithm = "fba", retOptSol = FALSE)
Loading required package: glpkAPI
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘glpkAPI’

  When sourcing ‘sybil.R’:
Error: package ‘glpkAPI’ not found
Execution halted
Error in re-building vignettes:
  ...
sybil::fluxVar          Flux Variability Analysis


Type '?PKG::FOO' to inspect entries 'PKG::FOO', or 'TYPE?PKG::FOO' for
entries like 'PKG::FOO-TYPE'.




reading model description, ... OK
reading metabolite list ... OK
parsing reaction list ... OK
GPR mapping ... OK
sub systems ... OK
prepare modelorg object ... OK
validating object ... OK
Loading required package: glpkAPI
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘glpkAPI’

Error: processing vignette 'sybil.Rnw' failed with diagnostics:
 chunk 13 
Error in checkDefaultMethod(solver, method, pType) : 
  package ‘glpkAPI’ not found
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SynergizeR.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages in Depends field not imported from:
  ‘RCurl’ ‘RJSONIO’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   3.3Mb
Found the following significant warnings:
  clean_trade.cpp:22:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  clean_trade.cpp:23:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  clean_trade_ms.cpp:22:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  clean_trade_ms.cpp:23:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  gzipdec.cpp:16:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  gzipdec.cpp:17:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  gzipdec_ms.cpp:59:20: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  gzipdec_ms.cpp:61:21: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  gzipdec_ms.cpp:63:21: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  trstdev.cpp:6:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/TAQMNGR.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [13s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Component 11: Modes: character, numeric
  Component 11: Lengths: 1, 3
  Component 11: names for current but not for target
  Component 11: target is character, current is numeric
  ...
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 4
  1. Failure: COX (@test_COX.R#6) 
  2. Failure: HTC (@test_HTC.R#6) 
  3. Failure: ITC (@test_ITC.R#6) 
  4. Failure: PTC (@test_PTC.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    tklibs   4.7Mb
installed size is 36.9Mb
  sub-directories of 1Mb or more:
    libs  35.6Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/tensorBF.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is 39.3Mb
  sub-directories of 1Mb or more:
    libs       7.3Mb
    tessdata  31.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.6Mb
    libs   4.2Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/textTinyR.Rcheck/00install.out’ for details.
Running examples in ‘threejs-Ex.R’ failed
The error most likely occurred in:

> ### Name: graphjs
> ### Title: Interactive 3D Graph Visualization
> ### Aliases: graphjs
> 
> ### ** Examples
> 
> set.seed(1)
> g <- sample_islands(3, 10, 5/10, 1)
> i <- cluster_optimal(g)
Error in cluster_optimal(g) : 
  At optimal_modularity.c:85 : GLPK is not available, Unimplemented function call
Execution halted
Running ‘testthat.R’ [6s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  14: mutate_as_tbl(.data, !!!dot)
  15: mutate(d_tmp, ...)
  16: mutate.tbl_df(d_tmp, ...)
  17: mutate_impl(.data, dots)
  18: group_optimal()
  19: membership(cluster_optimal(graph = .G(), weights = weights))
  20: cluster_optimal(graph = .G(), weights = weights)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 268 SKIPPED: 0 FAILED: 2
  1. Error: grouping returns integer vector (@test-group.R#14) 
  2. Error: grouping returns integer of correct length (@test-group.R#31) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [2s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  12: shannon_entropy(.)
  13: reduce_data(.data, !!enquo(X), numvars = 1, na.rm = na.rm)
  14: tidyselect::vars_select(names(reduced_tab), !!!quos(...))
  15: vars_select_eval(.vars, quos)
  16: map_lgl(quos, quo_is_helper)
  17: .f(.x[[i]], ...)
  18: extract_expr(quo)
  19: is_call(expr, paren_sym)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 37 SKIPPED: 0 FAILED: 1
  1. Error: right number of columns given (@test-errors.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
File ‘tidyxl/libs/tidyxl.so’:
  Found ‘_abort’, possibly from ‘abort’ (C)
    Object: ‘xlex.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [1] 2015-01-01 23:56:02 - 2015-01-01 == 23.9 hours
  
  ── 3. Failure: updates on ydas works correctly with leap year (@test-update.R#17
  time_update(...) not equal to ymd("2016-01-10", tz = "America/New_York").
  1/1 mismatches
  [1] 2016-01-10 23:56:02 - 2016-01-10 == 23.9 hours
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 685 SKIPPED: 0 FAILED: 3
  1. Failure: updates on ydas works correctly with leap year (@test-update.R#173) 
  2. Failure: updates on ydas works correctly with leap year (@test-update.R#175) 
  3. Failure: updates on ydas works correctly with leap year (@test-update.R#177) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  tm.c:184:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  tm.c:185:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/TimeMachine.Rcheck/00install.out’ for details.
.my.tkdev: no visible global function definition for ‘X11’
tkpersp : draw: no visible global function definition for ‘par’
tkpersp : draw: no visible global function definition for ‘persp’
Undefined global functions or variables:
  X11 par persp
Consider adding
  importFrom("grDevices", "X11")
  importFrom("graphics", "par", "persp")
to your NAMESPACE file.
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    examples  12.1Mb
    include    2.9Mb
Packages suggested but not available for checking:
  ‘Rcampdf’ ‘Rpoppler’ ‘tm.lexicon.GeneralInquirer’
Package unavailable to check Rd xrefs: ‘Rpoppler’
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  tmux not found
  1: stop("tmux not found") at testthat/test-server.R:3
  
  ── 3. Error: (unknown) (@test-session.R#3)  ────────────────────────────────────
  tmux not found
  1: stop("tmux not found") at testthat/test-session.R:3
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 3
  1. Error: (unknown) (@test-pipe.R#3) 
  2. Error: (unknown) (@test-server.R#3) 
  3. Error: (unknown) (@test-session.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Packages suggested but not available for checking: ‘RGtk2’ ‘gWidgetsRGtk2’
Package required but not available: ‘qpgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RGtk2’

Package suggested but not available for checking: ‘rggobi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘tpr/libs/tpr.so’:
  Found ‘__ZNSt3__14cerrE’, 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.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: ggplot2

Attaching package: 'trackeR'

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

    append

Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=57.157231,-2.104296&zoom=13&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false
Quitting from lines 96-97 (TourDetrackeR.Rmd) 
Error: processing vignette 'TourDetrackeR.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Loading required package: ade4
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'

   /// adegenet 2.1.1 is loaded ////////////

   > overview: '?adegenet'
   > tutorials/doc/questions: 'adegenetWeb()' 
   > bug reports/feature requests: adegenetIssues()



Attaching package: 'adegenet'

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

    AICc

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

    .render.server.info

Quitting from lines 136-138 (DengueVignette.Rmd) 
Error: processing vignette 'DengueVignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 39.6Mb
  sub-directories of 1Mb or more:
    libs  39.2Mb
Running ‘testthat.R’ [47s/24s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  6: date_time_to_tsp(wx[[1]])
  7: stop("time column needs to specified as the first date of the period", call. = FALSE)
  
  "blabla"
  ── 2. Failure: heuristic high frequency data works (@test_ts_high_freq.R#91)  ──
  `x` not equal to ts_df(ts_ts(x)).
  Component "time": Mean absolute difference: 86579
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 340 SKIPPED: 9 FAILED: 2
  1. Error: Latest tricky stuff works. (@test_tricky.R#9) 
  2. Failure: heuristic high frequency data works (@test_ts_high_freq.R#91) 
  
  Error: testthat unit tests failed
  Execution halted
Package which this enhances but not available for checking: ‘TSodbc’
Package suggested but not available for checking: ‘TSodbc’
Package unavailable to check Rd xrefs: ‘TSodbc’
Errors in running code in vignettes:
when running code in ‘Guide.Stex’
  ...
> z <- TSget("ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT", 
+     eurostat)
Apr 23, 2018 11:16:19 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: http://ec.europa.eu/eurostat/SDMX/diss-web/rest/dataflow/ESTAT/ei_nama_q/latest/
Apr 23, 2018 11:16:20 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
SEVERE: (500): Error on the provider side.

  When sourcing ‘Guide.R’:
Error: ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.exceptions.SdmxResponseException: (500): Error on the provider side.
Execution halted
when running code in ‘GuideAppendix.Stex’
  ...

> options(continue = "  ")

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

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

  When sourcing ‘GuideAppendix.R’:
Error: Failed to connect to database: Error: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)
Execution halted
Error in re-building vignettes:
  ...
Loading required package: TSdbi
Apr 23, 2018 11:16:26 AM it.bancaditalia.oss.sdmx.util.Configuration init
INFO: No configuration found. Apply defaults.
Apr 23, 2018 11:16:26 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: https://stats.oecd.org/restsdmx/sdmx.ashx/GetDataStructure/QNA
Apr 23, 2018 11:16:28 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: https://stats.oecd.org/restsdmx/sdmx.ashx/GetDataStructure/QNA
Apr 23, 2018 11:16:28 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: https://stats.oecd.org/restsdmx/sdmx.ashx/GetData/QNA/CAN.B1_GE.CARSA.Q?format=compact_v2
Apr 23, 2018 11:16:29 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: https://stats.oecd.org/restsdmx/sdmx.ashx/GetData/QNA/CAN%2BUSA%2BMEX.B1_GE.CARSA.Q?format=compact_v2
Apr 23, 2018 11:16:30 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: http://ec.europa.eu/eurostat/SDMX/diss-web/rest/dataflow/ESTAT/ei_nama_q/latest/
Apr 23, 2018 11:16:30 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
SEVERE: (500): Error on the provider side.

Error: processing vignette 'Guide.Stex' failed with diagnostics:
 chunk 5 
Error in .local(serIDs, con, ...) : 
  ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.exceptions.SdmxResponseException: (500): Error on the provider side.
Execution halted
Error in re-building vignettes:
  ...
Version 0.4-0 included new data defaults. See ?getSymbols.
'getSymbols' currently uses auto.assign=TRUE by default, but will
use auto.assign=FALSE in 0.5-0. You will still be able to use
'loadSymbols' to automatically load data. getOption("getSymbols.env")
and getOption("getSymbols.auto.assign") will still be checked for
alternate defaults.

This message is shown once per session and may be disabled by setting 
options("getSymbols.warning4.0"=FALSE). See ?getSymbols for details.


WARNING: There have been significant changes to Yahoo Finance data.
Please see the Warning section of '?getSymbols.yahoo' for details.

This message is shown once per session and may be disabled by setting
options("getSymbols.yahoo.warning"=FALSE).
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]="./webshot16c10df4f1d8.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot16c10df4f1d8.png': No such file or directory
Quitting from lines 37-64 (TSstudio_Intro.Rmd) 
Error: processing vignette 'TSstudio_Intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 29.8Mb
  sub-directories of 1Mb or more:
    doc         5.3Mb
    dummydata   1.4Mb
    libs       22.0Mb
Running ‘plot.R’ [1s/1s]
  Running ‘set_units.R’ [0s/1s]
Running the tests in ‘tests/set_units.R’ failed.
Last 13 lines of output:
  > library(units)
  
  Attaching package: 'units'
  
  The following object is masked from 'package:base':
  
      %*%
  
  > library(testthat)
  Error: package or namespace load failed for 'testthat' in library.dynam(lib, package, package.lib):
   shared object 'testthat.so' not found
  In addition: Warning message:
  S3 methods 'as.data.frame.testthat_results', 'as.expectation.default', 'as.expectation.error', 'as.expectation.expectation', 'as.expectation.logical', 'as.expectation.skip', 'as.expectation.warning', 'compare.POSIXt', 'compare.character', 'compare.default', 'compare.numeric', 'format.expectation', 'format.expectation_error', 'format.expectation_success', 'format.mismatch_character', 'format.mismatch_numeric', 'print.comparison', 'print.expectation', 'print.mismatch_character', 'print.mismatch_numeric', 'print.testthat_results' were declared in NAMESPACE but not found 
  Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    1.6Mb
    libs   2.2Mb
File ‘uuid/libs/uuid.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘gen_uuid.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘gen_uuid.o’

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 37.7Mb
  sub-directories of 1Mb or more:
    libs  36.9Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    libs  26.8Mb
Running ‘run.R’ [32s/49s]
Running the tests in ‘tests/run.R’ failed.
Last 13 lines of output:
  12/14 type.R: type_alike(sum, sd, vetr_settings(type.mode = 1))
                                                                                  
  12/14 type.R: type_alike(sum, c, vetr_settings(type.mode = 1))
                                                                                  
  12/14 type.R: type_alike(`&&`, `[`, vetr_settings(type.mode = 1))
                                                                                  
  Error: $ operator is invalid for atomic vectors
  In addition: Warning message:
  In FUN(X[[i]], ...) :
    DESCRIPTION file of package 'unitizer' is missing or broken
  | Unexpectedly exited before storing unitizer; if you were reviewing a unitizer 
  | changes to that unitizer were not saved.  Note that any unitizers you *
  | completed* review of should have been saved.
  
  Execution halted
Running examples in ‘viridisLite-Ex.R’ failed
The error most likely occurred in:

> ### Name: viridis
> ### Title: Matplotlib 'viridis' and 'cividis' color map
> ### Aliases: viridis viridisMap magma inferno plasma cividis
> 
> ### ** Examples
> 
> library(ggplot2)
Warning: S3 methods ‘.DollarNames.C++Object’, ‘.DollarNames.Module’, ‘print.bytes’, ‘format.Rcpp_stack_trace’, ‘str.Rcpp_stack_trace’, ‘print.Rcpp_stack_trace’ were declared in NAMESPACE but not found
Error: package or namespace load failed for ‘ggplot2’ in library.dynam(lib, package, package.lib):
 shared object ‘Rcpp.so’ 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 157-163 (using_visdat.Rmd) 
Error: processing vignette 'using_visdat.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc           4.7Mb
    htmlwidgets   3.6Mb
File ‘waffect/libs/waffect.so’:
  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.
installed size is 54.8Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  52.3Mb
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 124-128 (walker.Rmd) 
Error: processing vignette 'walker.Rmd' failed with diagnostics:
argument of length 0
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/wand.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘pbmcapply’ ‘proxy’ ‘signal’
  All declared Imports should be used.
Running ‘testthat.R’ [28s/46s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 26 SKIPPED: 0 FAILED: 18
  1. Error: canCallChrome (@test-chrome.R#3) 
  2. Error: pickUpErrorFromReturnCode (@test-chrome.R#43) 
  3. Error: pickUpErrorFromPortInUse (@test-chrome.R#62) 
  4. Error: canCallGecko (@test-gecko.R#4) 
  5. Error: pickUpErrorFromReturnCode (@test-gecko.R#44) 
  6. Error: pickUpErrorFromPortInUse (@test-gecko.R#63) 
  7. Error: canCallIEDriver (@test-iedriver.R#4) 
  8. Error: pickUpErrorFromReturnCode (@test-iedriver.R#46) 
  9. Error: pickUpErrorFromPortInUse (@test-iedriver.R#68) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    client   9.4Mb
    doc      1.0Mb
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1: curl::curl_echo(h) at testthat/test-echo.R:14
  2: curl_fetch_memory(paste0("http://localhost:", port, "/"), handle = handle)
  
  ── 2. Error: Echo a big file (@test-echo.R#51)  ────────────────────────────────
  Callback aborted
  1: curl::curl_echo(h) at testthat/test-echo.R:51
  2: curl_fetch_memory(paste0("http://localhost:", port, "/"), handle = handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 14 SKIPPED: 0 FAILED: 2
  1. Error: test echo from httpuv (@test-echo.R#14) 
  2. Error: Echo a big file (@test-echo.R#51) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘HotDeckImputation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘org.Mm.eg.db’
Found the following significant warnings:
  t_region.cpp:78:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:115:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:120:7: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/WhopGenome.Rcheck/00install.out’ for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Packages required but not available: ‘gWidgetsRGtk2’ ‘cairoDevice’ ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Warning in initDict() :
  cannot find WordNet 'dict' directory: please set the environment variable WNHOME to its parent

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

Probably some imports need to be declared in the NAMESPACE file.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data  11.2Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    bin   4.1Mb
    lib   2.1Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  17.3Mb
Package required but not available: ‘rtracklayer’

Packages suggested but not available for checking: ‘GenomicScores’ ‘ggbio’

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.
Error: processing vignette 'modification.Rmd' failed with diagnostics:
shared object 'stringi.so' not found
Execution halted
Running ‘doRUnit.R’ [36s/56s]
Running the tests in ‘tests/doRUnit.R’ failed.
Last 13 lines of output:
    Mean relative difference: 8.173474e-05
  
  FAILURE in test.timeSeries_reclass: Error in checkIdentical(sample.timeSeries, reclass(try.xts(sample.timeSeries))) : 
    FALSE 
   
  FAILURE in test.timeSeries_reclass_subset_reclass_j1: Error in checkIdentical(sample.timeSeries[, 1], reclass(try.xts(sample.timeSeries))[,  : 
    FALSE 
   
  DEACTIVATED test.zoo_reclass: rownames are not kept yet in current xts-dev
  DEACTIVATED test.zoo_reclass_subset_reclass_j1: rownames are not kept yet in current xts-dev
  Error: 
  
  unit testing failed (#test failures: 17, #R errors: 0)
  
  Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/zstdr.Rcheck/00install.out’ for details.
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    R  14.3Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data       2.7Mb
    pictures   2.1Mb
Package suggested but not available for checking: 'AffymetrixDataTestFiles'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.5Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    bin   12.0Mb
    misc   2.1Mb
'library' or 'require' calls in package code:
  'cacheSweave' 'weaver'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'utils:::RtangleSetup'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'cacheSweave:::metaChunkName' 'cacheSweave:::metaSetCreationTime'
  'survival:::survmean' 'utils:::.SweaveValidFilenameRegexp'
  'utils:::RtangleFinish' 'utils:::RtangleRuncode'
  'utils:::SweaveParseOptions'
  See the note in ?`:::` about the use of this operator.
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.4/audio.Rcheck/00install.out' for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
    libs   1.8Mb
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    libs  33.0Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    2.3Mb
    libs   1.9Mb
Running 'testthat.R' [17s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(baseballDBR)
  > 
  > test_check("baseballDBR")
  -- 1. Failure: (unknown) (@test-check_urls.R#25)  ------------------------------
  urlExists("http://www.fangraphs.com/guts.aspx?type=cn") isn't true.
  
  == testthat results  ===========================================================
  OK: 2 SKIPPED: 0 FAILED: 1
  1. Failure: (unknown) (@test-check_urls.R#25) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  In .getClassesFromCache(Class) :
    closing unused connection 3 (http://www.fangraphs.com/guts.aspx?type=cn)
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/BayClone2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/bayesCL.Rcheck/00install.out' for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs   2.1Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   4.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R     1.6Mb
    doc   3.6Mb
File 'BayHap/libs/i386/BayHap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'mcmc.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'mcmc.o'
File 'BayHap/libs/x64/BayHap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'mcmc.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'mcmc.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/beanz.Rcheck/00install.out' for details.
installed size is 143.8Mb
  sub-directories of 1Mb or more:
    include  142.9Mb
Running examples in 'BioInstaller-Ex.R' failed
The error most likely occurred in:

> ### Name: install.bioinfo
> ### Title: Download and install biology software or database
> ### Aliases: install.bioinfo
> 
> ### ** Examples
> 
> db <- sprintf('%s/.BioInstaller', tempdir())
> set.biosoftwares.db(db)
> install.bioinfo('bwa', show.all.versions = TRUE)
INFO [2018-05-11 06:19:16] Fetching bwa versions....
Error in function (type, msg, asError = TRUE)  : 
  error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
Calls: install.bioinfo ... getURL -> curlPerform -> .Call -> <Anonymous> -> fun
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/BonEV.Rcheck/00install.out' for details.
installed size is 79.8Mb
  sub-directories of 1Mb or more:
    include   3.1Mb
    lib      76.5Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
File 'brainwaver/libs/i386/brainwaver.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'connexity_small_world.o'
File 'brainwaver/libs/x64/brainwaver.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'connexity_small_world.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/breathteststan.Rcheck/00install.out' for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R     2.7Mb
    doc   2.4Mb
combine_family_info: no visible binding for global variable 'isFALSE'
no_sigma: no visible global function definition for 'isFALSE'
resp_cens : prepare_cens: no visible global function definition for
  'isFALSE'
Undefined global functions or variables:
  isFALSE
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/BrownDog.Rcheck/00install.out' for details.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    5.7Mb
    libs   1.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data     1.5Mb
    models   2.4Mb
Found the following Makefile(s) without a final LF:
  inst/doc/Makefile
Some 'make' programs ignore lines not ending in LF.
Files in the 'vignettes' directory newer than same file in 'inst/doc':
  'figure/glmnet-diagnostic.pdf', 'figure/roc-plot.pdf'
The following files look like leftovers/mistakes:
  'Causata-vignette.log'
Please remove them from your package.
The following directory looks like a leftover from 'knitr':
  'figure'
Please remove from your package.
Running 'test-all.R' [26s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(cli)
  > library(testthat)
  > old.env <- Sys.getenv("checkpoint.mock.install")
  > Sys.setenv("checkpoint.mock.install" = TRUE)
  > test_check("checkpoint")
  Loading required package: checkpoint
  
  checkpoint: Part of the Reproducible R Toolkit from Microsoft
  https://mran.microsoft.com/documents/rro/reproducibility/
  -- 1. Failure: is.404 (@test-0-is-404.R#11)  -----------------------------------
  is.404("http://mran.microsoft.com/snapshot") isn't false.
  
  -- 2. Failure: is.404 (@test-0-is-404.R#14)  -----------------------------------
  is.404("http://mran.microsoft.com/snapshot/2015-05-01") isn't false.
  
  == testthat results  ===========================================================
  OK: 60 SKIPPED: 7 FAILED: 2
  1. Failure: is.404 (@test-0-is-404.R#11) 
  2. Failure: is.404 (@test-0-is-404.R#14) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
    pdf   2.2Mb
Package suggested but not available for checking: 'mogene10sttranscriptcluster.db'
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data      6.5Mb
    extdata   2.6Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   6.5Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.3Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    help   1.4Mb
    libs   1.7Mb
Running 'has-devel.R' [2s]
  Running 'test-that.R' [67s]
Running the tests in 'tests/test-that.R' failed.
Complete output:
  > library(testthat)
  > test_check("devtools")
  Loading required package: devtools
  
  Attaching package: 'devtools'
  
  The following object is masked from 'package:testthat':
  
      setup
  
  -- 1. Failure: remote_sha.github_remote returns expected value if remote does ex
  remote_sha(github_remote("hadley/devtools@v1.8.0")) not equal to "ad9aac7b9a522354e1ff363a86f389e32cec181b".
  1/1 mismatches
  x[1]: NA
  y[1]: "ad9aac7b9a522354e1ff363a86f389e32cec181b"
  
  
  == testthat results  ===========================================================
  OK: 400 SKIPPED: 10 FAILED: 1
  1. Failure: remote_sha.github_remote returns expected value if remote does exist (@test-remotes.r#75) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.8Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    5.1Mb
    libs   1.4Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    5.6Mb
    libs   1.4Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   2.1Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.2Mb
    libs   3.9Mb
Running examples in 'easycsv-Ex.R' failed
The error most likely occurred in:

> ### Name: fread_folder
> ### Title: read multiple csv files into named data frames
> ### Aliases: fread_folder
> ### Keywords: ~utilities ~misc
> 
> ### ** Examples
> 
>   require(easycsv)
>   require("data.table")
>   directory = getwd()
>   write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/table1.csv"))
>   write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/table2.csv"))
>   write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/table3.txt"))
>   write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/table4.txt"))
>   fread_folder(directory, extension = "BOTH")
Error: isTrueFalse(showProgress) is not TRUE
Execution halted
Error in re-building vignettes:
  ...
Processing PubMed data .Quitting from lines 122-133 (easyPM_vignette_html.Rmd) 
Error: processing vignette 'easyPM_vignette_html.Rmd' failed with diagnostics:
subscript out of bounds
Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    xsd   5.4Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   3.4Mb
Running 'testthat.R' [30s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(eurostat)
  > 
  > test_check("eurostat")
  trying URL 'http://ec.europa.eu/eurostat/estat-navtree-portlet-prod/BulkDownloadListing?sort=1&file=data%2Ftsdtr210.tsv.gz'
  Content type 'text/html;charset=UTF-8' length unknown
  .......... .......
  downloaded 17 KB
  
  -- 1. Error: (unknown) (@test-all.R#112)  --------------------------------------
  tsdtr210 does not exist or is not readable
  1: get_eurostat("tsdtr210", type = "label", keepFlags = T, cache = FALSE) at testthat/test-all.R:112
  2: get_eurostat_raw(id)
  3: stop(id, " does not exist or is not readable")
  
  == testthat results  ===========================================================
  OK: 0 SKIPPED: 14 FAILED: 1
  1. Error: (unknown) (@test-all.R#112) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
'LinkingTo' field is unused: package has no 'src' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/FastRWeb.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Warning in parse(file = files, n = -1L) :
  invalid input found on input connection 'fivethirtyeight-Ex.R'
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    1.8Mb
    libs   1.4Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    data  16.2Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   1.5Mb
    libs      1.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   2.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      4.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.3Mb
Error in re-building vignettes:
  ...
Quitting from lines 191-194 (geojson-sf-conversions.Rmd) 
Error: processing vignette 'geojson-sf-conversions.Rmd' failed with diagnostics:
There was an error downloading the geojson
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.7Mb
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg18.masked'
  'BSgenome.Hsapiens.UCSC.hg19.masked'
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    libs  19.8Mb
Error in re-building vignettes:
  ...
Linked to JAGS 4.2.0
Loaded modules: basemod,bugs

Attaching package: 'R2jags'

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

    traceplot

module glm loaded
To access larger datasets in this package, install the spDataLarge
package with: `install.packages('spDataLarge',
repos='https://nowosad.github.io/drat/', type='source'))`

Error: processing vignette 'openbugs.Rnw' failed with diagnostics:
 chunk 12 (label = postprocessKentucky) 
Error : $ operator is invalid for atomic vectors
Execution halted
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    libs  21.4Mb
File 'gnmf/libs/i386/gnmf.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'FactorMatrix.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'FactorMatrix.o'
File 'gnmf/libs/x64/gnmf.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'FactorMatrix.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'FactorMatrix.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Error in re-building vignettes:
  ...
Loading required package: survival
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "ashg2012.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.4.4/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.4.4/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'ashg2012.tex' failed

LaTeX errors:
! LaTeX Error: File `D:/RCompile/recent/R-34\unhbox\voidb@x \penalty \@M \ {}1.
4/share/texmf/tex/latex/Sweave.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/GWASinlps.Rcheck/00install.out' for details.
installed size is 136.0Mb
  sub-directories of 1Mb or more:
    java  134.7Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    doc          13.7Mb
    htmlwidgets   1.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   1.5Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    data  12.8Mb
    doc    1.3Mb
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(HURDAT)
  > 
  > test_check("HURDAT")
  -- 1. Error: (unknown) (@test-hurdat.R#4)  -------------------------------------
  HTTP error 404.
  1: get_hurdat(basin = "AL") at testthat/test-hurdat.R:4
  2: purrr::map_df(.x = basin, .f = parse_hurdat)
  3: map(.x, .f, ...)
  4: .f(.x[[i]], ...)
  5: readr::read_lines(file = url)
  6: datasource(file, skip = skip)
  7: datasource_connection(file, skip, comment)
  8: datasource_raw(read_connection(path), skip, comment = comment)
  9: new_datasource("raw", text, skip = skip, comment = comment)
  10: structure(list(x, skip = skip, comment = comment, ...), class = c(paste0("source_", 
         type), "source"))
  11: read_connection(path)
  12: open(con, "rb")
  13: open.connection(con, "rb")
  
  == testthat results  ===========================================================
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-hurdat.R#4) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  closing unused connection 3 (http://www.nhc.noaa.gov/data/hurdat/hurdat2-1851-2016-041117.txt) 
  Execution halted
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(hyphenatr)
  > 
  > test_check("hyphenatr")
  -- 1. Failure: we can do something (@test-hyphenatr.R#16)  ---------------------
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "tÃ¤=gelÃ®ch"
  y[1]: "tä=gelîch"
  
  == testthat results  ===========================================================
  OK: 4 SKIPPED: 0 FAILED: 1
  1. Failure: we can do something (@test-hyphenatr.R#16) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      1.8Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   5.4Mb
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs  13.8Mb
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       4.9Mb
    include   2.8Mb
    libs     11.6Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R  10.7Mb
Error in re-building vignettes:
  ...
Warning in read.table(file = file, header = header, sep = sep, quote = quote,  :
  invalid input found on input connection 'D:\temp\RtmpCOuED5\ex_data9edcf404c2c.csv2'
Warning in read.table(file = file, header = header, sep = sep, quote = quote,  :
  incomplete final line found by readTableHeader on 'D:\temp\RtmpCOuED5\ex_data9edcf404c2c.csv2'
Quitting from lines 31-32 (incadoc.Rmd) 
Error: processing vignette 'incadoc.Rmd' failed with diagnostics:
cannot open URL 'http://www.cancercentrum.se/globalassets/cancerdiagnoser/lunga-och-lungsack/dokument/styrdokument.pdf'
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   2.2Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R   7.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/lfl.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      3.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.0Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc        2.4Mb
    libs       2.1Mb
    testdata   1.6Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   2.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.6Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    extdata   3.9Mb
    libs      1.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/MetaIntegrator.Rcheck/00install.out' for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.7Mb
    libs   1.8Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.5Mb
Note: significantly better compression could be obtained
        by using R CMD build --resave-data
           old_size new_size compress
  cgps.rda    1.5Mb    1.4Mb       xz
'library' or 'require' calls to packages already attached by Depends:
  'amap' 'clValid' 'cluster' 'fpc' 'xcms'
  Please remove these calls from your code.
'library' or 'require' call to 'tcltk' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'mzR' 'xcms'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' calls to packages already attached by Depends:
  'MSeasy' 'tcltk'
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'grDevices' 'xcms'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.4Mb
    libs   1.5Mb
Loading required package: standardize
Loading required package: lme4
Loading required package: Matrix
Loading required package: rstanarm
Loading required package: Rcpp
Error: package or namespace load failed for 'rstanarm' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 namespace 'Matrix' 1.2-12 is already loaded, but >= 1.2.13 is required
Error: package 'rstanarm' could not be loaded
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
Running examples in 'nauf-Ex.R' failed
The error occurred in:


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> pkgname <- "nauf"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> options(pager = "console")
> library('nauf')
Loading required package: standardize
Loading required package: lme4
Loading required package: Matrix
Loading required package: rstanarm
Loading required package: Rcpp
Error: package or namespace load failed for 'rstanarm' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 namespace 'Matrix' 1.2-12 is already loaded, but >= 1.2.13 is required
Error: package 'rstanarm' could not be loaded
Execution halted
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(nauf)
  Loading required package: standardize
  Loading required package: lme4
  Loading required package: Matrix
  Loading required package: rstanarm
  Loading required package: Rcpp
  Error: package or namespace load failed for 'rstanarm' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
   namespace 'Matrix' 1.2-12 is already loaded, but >= 1.2.13 is required
  Error: package 'rstanarm' could not be loaded
  Execution halted
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   2.2Mb
Running examples in 'netdiffuseR-Ex.R' failed
The error most likely occurred in:

> ### Name: exposure
> ### Title: Ego exposure
> ### Aliases: exposure exposure
> ### Keywords: univar
> 
> ### ** Examples
> 
> # Calculating lagged exposure -----------------------------------------------
> 
> set.seed(8)
> graph <- rdiffnet(20, 4)
> 
> expo0 <- exposure(graph)
> expo1 <- exposure(graph, lags = 1)
> 
> # These should be equivalent
> stopifnot(all(expo0[, -4] == expo1[, -1])) # No stop!
> 
> 
> # Calculating the exposure based on Structural Equivalence ------------------
> set.seed(113132)
> graph <- rdiffnet(100, 10)
> 
> SE <- lapply(struct_equiv(graph), "[[", "SE")
> SE <- lapply(SE, function(x) {
+    x <- 1/x
+    x[!is.finite(x)] <- 0
+    x
+ })
> 
> # Recall setting valued equal to TRUE!
> expo_se <- exposure(graph, alt.graph=SE , valued=TRUE)
> 
> # These three lines are equivalent to:
> expo_se2 <- exposure(graph, alt.graph="se", valued=TRUE)
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   2.1Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    CppCode   2.5Mb
    R         3.4Mb
    include   5.7Mb
    libs      1.8Mb
    tests     1.3Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.2Mb
Error in re-building vignettes:
  ...
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "nonrandom.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.4.4/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.4.4/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'nonrandom.tex' failed

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

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

Execution halted
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc   8.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   2.4Mb
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 the system RNG.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    help   2.2Mb
    libs   1.3Mb
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    R        2.3Mb
    libs     5.9Mb
    models   4.8Mb
Running 'testthat.R' [27s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > test_check("openxlsx")
  Loading required package: openxlsx
  -- 1. Error: loadWorkbook from different sources (@test-read_sources.R#49)  ----
  subscript out of bounds
  1: expect_true(all.equal.Workbook(wb_url, wb_file), "Loading from URL vs local not equal") at testthat/test-read_sources.R:49
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: all.equal.Workbook(wb_url, wb_file)
  5: sapply(1:nSheets, function(i) isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]])))
  6: lapply(X = X, FUN = FUN, ...)
  7: FUN(X[[i]], ...)
  8: isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]]))
  9: all.equal(x$colWidths[[i]], y$colWidths[[i]])
  10: all.equal.list(x$colWidths[[i]], y$colWidths[[i]])
  11: attr.all.equal(target, current, ...)
  12: mode(current)
  
  == testthat results  ===========================================================
  OK: 505 SKIPPED: 2 FAILED: 1
  1. Error: loadWorkbook from different sources (@test-read_sources.R#49) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    nifti   3.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
Running examples in 'osrmr-Ex.R' failed
The error most likely occurred in:

> ### Name: nearest_api_v5
> ### Title: nearest accessible position for OSRM API v5
> ### Aliases: nearest_api_v5
> 
> ### ** Examples
> 
> osrmr:::nearest_api_v5(47,9, osrmr:::server_address(FALSE))
Warning in file(con, "r") :
  cannot open URL 'http://router.project-osrm.org/nearest/v1/driving/9,47?number=1': HTTP status was '429 ???'
Error in file(con, "r") : cannot open the connection
Calls: <Anonymous> -> <Anonymous> -> paste -> readLines -> file
Execution halted
Running 'testthat.R' [13s]
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: 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/3.4/pathological.Rcheck/tests/testthat/test_dec
  x[1]: ompose_path.R"
  y[1]: "D:/Rcompile/CRANpkg/local/3.4/pathological.Rcheck/tests/testthat/test_dec
  y[1]: ompose_path.R"
  
  == testthat results  ===========================================================
  OK: 187 SKIPPED: 18 FAILED: 1
  1. Failure: standardize_path works with missing files with ./ prefix (@test_standardize_path.R#198) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    lib    5.8Mb
    libs   4.8Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   3.9Mb
Running examples in 'phuse-Ex.R' failed
The error most likely occurred in:

> ### Name: cvt_list2df
> ### Title: Convert list to data frame
> ### Aliases: cvt_list2df
> 
> ### ** Examples
> 
>   a <- "https://github.com/phuse-org/phuse-scripts/raw/master"
>   b <- "development/R/scripts"
>   c <- "Draw_Dist2_R.yml"
>   f1 <- paste(a,b,c, sep = '/')
>   r1 <- read_yml(f1)
>   r2 <- cvt_list2df(r1)
Error in a[[k1]] : subscript out of bounds
Calls: cvt_list2df -> typeof
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/PlasmaMutationDetector.Rcheck/00install.out' for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   1.6Mb
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 the system RNG.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   6.4Mb
    libs      1.7Mb
Warning in parse(file = files, n = -1L) :
  invalid input found on input connection 'psycho-Ex.R'
Running examples in 'psycho-Ex.R' failed
The error occurred in:


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> pkgname <- "psycho"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> options(pager = "console")
> library('psycho')
Error: package or namespace load failed for 'psycho' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 namespace 'Matrix' 1.2-12 is already loaded, but >= 1.2.13 is required
Execution halted
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(psycho)
  Error: package or namespace load failed for 'psycho' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
   namespace 'Matrix' 1.2-12 is already loaded, but >= 1.2.13 is required
  Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc        4.6Mb
    examples   2.2Mb
Error in re-building vignettes:
  ...
trying URL 'http://github.com/dobriban/pweight/raw/master/vignettes/iGWAS.cad.example.RData'
Quitting from lines 34-38 (iGWAS-DataExample.Rmd) 
Error: processing vignette 'iGWAS-DataExample.Rmd' failed with diagnostics:
cannot open URL 'http://github.com/dobriban/pweight/raw/master/vignettes/iGWAS.cad.example.RData'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 112-113 (orthography_processing.Rmd) 
Error: processing vignette 'orthography_processing.Rmd' failed with diagnostics:
undefined columns selected
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   3.0Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   2.1Mb
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 the system RNG.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: 'rcom'
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   6.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   2.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/RAPIDR.Rcheck/00install.out' for details.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs   2.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    libs   1.8Mb
Running 'testthat_p1.R' [12s]
  Running 'testthat_p2.R' [1s]
  Running 'testthat_p3.R' [11s]
Running the tests in 'tests/testthat_p3.R' failed.
Complete output:
  > #testing Randy Zwitch solution
  > 
  > library(testthat)
  > library(RClone)
  > test_check("RClone", filter = "p3")
  [1] "Number of MLG sim = 9"
  -- 1. Failure: the genet_dist functions work (@test_package_RClone_p3.R#19)  ---
  length(prev2[[1]]) not equal to 45.
  1/1 mismatches
  [1] 36 - 45 == -9
  
  == testthat results  ===========================================================
  OK: 46 SKIPPED: 1 FAILED: 1
  1. Failure: the genet_dist functions work (@test_package_RClone_p3.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: replacing previous import 'Rcmdr::Confint' by 'car::Confint' when loading 'RcmdrPlugin.BCA'
See 'd:/Rcompile/CRANpkg/local/3.4/RcmdrPlugin.BCA.Rcheck/00install.out' for details.
Running examples in 'rcongresso-Ex.R' failed
The error most likely occurred in:

> ### Name: fetch_votacoes
> ### Title: Fetches all the votings which a proposition went through
> ### Aliases: fetch_votacoes
> 
> ### ** Examples
> 
> votacoes_pec241 <- fetch_votacoes(2088351)
Error in .congresso_api(.$path) : Not Found (HTTP 404).
Calls: fetch_votacoes ... overscope_eval_next -> .congresso_api -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 45-50 (introducao-rcongresso.Rmd) 
Error: processing vignette 'introducao-rcongresso.Rmd' failed with diagnostics:
Column `id` must be a 1d atomic vector or a list
Execution halted
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib       8.9Mb
    libs      1.0Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    include   6.3Mb
    libs      2.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    java   5.2Mb
installed size is 80.0Mb
  sub-directories of 1Mb or more:
    gdal       3.9Mb
    libs      68.7Mb
    pictures   1.3Mb
    proj       5.0Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc     3.9Mb
    fonts   1.5Mb
    libs    2.0Mb
Running examples in 'RgoogleMaps-Ex.R' failed
The error most likely occurred in:

> ### Name: GetMap.bbox
> ### Title: GetMap bbox
> ### Aliases: GetMap.bbox
> 
> ### ** Examples
> 
>  mymarkers <- cbind.data.frame(lat = c(38.898648,38.889112, 38.880940), 
+           lon = c(-77.037692, -77.050273, -77.03660), size =  c('tiny','tiny','tiny'), 
+           col = c('blue', 'green', 'red'), char = c('','',''));
> 
> ##get the bounding box:
>   bb <- qbbox(lat = mymarkers[,"lat"], lon = mymarkers[,"lon"]);
>   
> ##download the map:
>   MyMap <- GetMap.bbox(bb$lonR, bb$latR, destfile = "DC.png", GRAYSCALE =TRUE,
+                 markers = mymarkers);
Warning in download.file(urlStr, destfile, mode = "wb", quiet = TRUE) :
  cannot open URL 'http://maps.google.com/maps/api/staticmap?center=38.889794,-77.0434365&zoom=15&size=640x640&maptype=mobile&format=png32&sensor=true&markers=size:1|col:1|char:1|38.898648,-77.037692&markers=size:1|col:2|char:1|38.889112,-77.050273&markers=size:1|col:3|char:1|38.88094,-77.0366': HTTP status was '403 Forbidden'
Error in download.file(urlStr, destfile, mode = "wb", quiet = TRUE) : 
  cannot open URL 'http://maps.google.com/maps/api/staticmap?center=38.889794,-77.0434365&zoom=15&size=640x640&maptype=mobile&format=png32&sensor=true&markers=size:1|col:1|char:1|38.898648,-77.037692&markers=size:1|col:2|char:1|38.889112,-77.050273&markers=size:1|col:3|char:1|38.88094,-77.0366'
Calls: GetMap.bbox -> GetMap -> download.file
Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    extra   9.3Mb
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    help  10.6Mb
    libs   5.1Mb
Running 'testthat.R' [38s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(RInno)
  Version: 0.2.0
  Maintainer: Jon Hill <jon.mark.hill@gmail.com>
  License: GPL-3 | file LICENSE
  URL: www.ficonsulting.com
  > library(jsonlite)
  > 
  > test_check("RInno")
  -- 1. Error: tasks, code and run return character vectors. (@test_code_run_tasks
  cannot open the connection
  1: expect_is(code_section("iss"), "character") at testthat/test_code_run_tasks.R:3
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: code_section("iss")
  5: unique(stats::na.omit(stringr::str_extract(readLines("https://cran.rstudio.com/bin/windows/base/", 
         warn = F), "[1-3]\\.[0-9]+\\.[0-9]+")))
  6: stats::na.omit(stringr::str_extract(readLines("https://cran.rstudio.com/bin/windows/base/", 
         warn = F), "[1-3]\\.[0-9]+\\.[0-9]+"))
  7: stringr::str_extract(readLines("https://cran.rstudio.com/bin/windows/base/", warn = F), 
         "[1-3]\\.[0-9]+\\.[0-9]+")
  8: stri_extract_first_regex(string, pattern, opts_regex = opts(pattern))
  9: readLines("https://cran.rstudio.com/bin/windows/base/", warn = F)
  10: file(con, "r")
  
  == testthat results  ===========================================================
  OK: 20 SKIPPED: 0 FAILED: 1
  1. Error: tasks, code and run return character vectors. (@test_code_run_tasks.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
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/3.4/rJava.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.4/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.4/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'rJava/libs/i386/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'
File 'rJava/libs/x64/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/RLumModel.Rcheck/00install.out' for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    rmd   5.9Mb
File 'RMC/libs/i386/RMC.dll':
  Found '_ZSt4cout', possibly from 'std::cout' (C++)
    Objects: 'RMC.o', 'predict.o'
  Found 'rand', possibly from 'rand' (C)
    Object: 'ap.o'
File 'RMC/libs/x64/RMC.dll':
  Found '_ZSt4cout', possibly from 'std::cout' (C++)
    Objects: 'RMC.o', 'predict.o'
  Found 'rand', possibly from 'rand' (C)
    Object: 'ap.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      2.8Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.0Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    extdata  12.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.4Mb
Found the following significant warnings:
  d:/RCompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:824:13: warning: this decimal constant is unsigned only in ISO C90
  d:/RCompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:842:13: warning: this decimal constant is unsigned only in ISO C90
  d:/RCompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomlosslatentmodel.hpp:84:13: warning: this decimal constant is unsigned only in ISO C90
  d:/Rcompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:824:13: warning: this decimal constant is unsigned only in ISO C90
  d:/Rcompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:842:13: warning: this decimal constant is unsigned only in ISO C90
  d:/Rcompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomlosslatentmodel.hpp:84:13: warning: this decimal constant is unsigned only in ISO C90
See 'd:/Rcompile/CRANpkg/local/3.4/RQuantLib.Rcheck/00install.out' for details.
installed size is 23.2Mb
  sub-directories of 1Mb or more:
    libs  22.8Mb
Found the following significant warnings:
   #warning Please include winsock2.h before windows.h
  qap_decode.c:200:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:200:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:55: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:60: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.4/Rserve.Rcheck/00install.out' for details.
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/3.4/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/3.4/Rserve/libs/x64/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'Rserve/libs/i386/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs  17.3Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   1.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/Ryacas.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    sample_data   3.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.5Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs   2.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
installed size is 93.4Mb
  sub-directories of 1Mb or more:
    doc     10.8Mb
    gdal     3.9Mb
    libs    69.9Mb
    proj     5.0Mb
    sqlite   1.5Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    www   6.3Mb
Package suggested but not available for checking: 'BSgenome.Hsapiens.UCSC.hg38'
Running examples in 'SIRItoGTFS-Ex.R' failed
The error most likely occurred in:

> ### Name: readGTFS
> ### Title: read GTFS files from a folder into R's environment
> ### Aliases: readGTFS
> ### Keywords: iteration utilities
> 
> ### ** Examples
> 
>   require(SIRItoGTFS)
>   directory = getwd()
>   write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/agency.csv"))
>   write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/calendar.csv"))
>   write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/routes.txt"))
>   write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/shapes.txt"))
>   write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/stop_times.txt"))
>   write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/stops.txt"))
>   write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/translations.txt"))
>   write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/trips.txt"))
> 
>   # now we read just the minimal tables needed for `STG`,
>   # meaning everything besides shapes and translations
>   readGTFS(directory, minimal = TRUE, extension = "BOTH")
Error: isTrueFalse(showProgress) is not TRUE
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/smooth.Rcheck/00install.out' for details.
Running 'test-all.R' [143s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("SpaDES.core")
  Loading required package: SpaDES.core
  Loading required package: quickPlot
  Loading required package: reproducible
  
  Attaching package: 'reproducible'
  
  The following object is masked from 'package:testthat':
  
      %>%
  
    Using cached copy of .inputObjects event in test module
    Using cached copy of .inputObjects event in test module
  -- 1. Failure: simList object initializes correctly (@test-simList.R#17)  --------------------------
  length(out) not equal to 75.
  1/1 mismatches
  [1] 73 - 75 == -2
  
    Using cached copy of burn event in fireSpread module
  == testthat results  ===========================================================
  OK: 349 SKIPPED: 33 FAILED: 1
  1. Failure: simList object initializes correctly (@test-simList.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   2.6Mb
Warning in parse(file = files, n = -1L) :
  invalid input found on input connection 'stability-Ex.R'
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   5.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R          1.9Mb
    datasets   2.6Mb
Error in re-building vignettes:
  ...
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "VignetteforSTPGA.ltx" --max-iterations=20 -I "D:/RCompile/recent/R-3.4.4/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.4.4/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'VignetteforSTPGA.ltx' failed with diagnostics:
running 'texi2dvi' on 'VignetteforSTPGA.ltx' failed

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

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

Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/stringi.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'curatedOvarianData'
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   1.0Mb
    libs   1.7Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
File 'svmpath/libs/i386/svmpath.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Objects: 'mi02lib.o', 'mi05funs.o', 'mi10unix.o', 'mi11sys.o',
      'mi12solv.o', 'mi20amat.o', 'mi25bfac.o', 'mi26bfac.o',
      'mi27lu.o', 'mi30spec.o', 'mi35mps.o', 'mi36mps.o', 'mi40bfil.o',
      'mi50lp.o', 'mi60srch.o', 'mi65rmod.o', 'mi70nobj.o',
      'mi80ncon.o', 'mi81ncon.o'
File 'svmpath/libs/x64/svmpath.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Objects: 'mi02lib.o', 'mi05funs.o', 'mi10unix.o', 'mi11sys.o',
      'mi12solv.o', 'mi20amat.o', 'mi25bfac.o', 'mi26bfac.o',
      'mi27lu.o', 'mi30spec.o', 'mi35mps.o', 'mi36mps.o', 'mi40bfil.o',
      'mi50lp.o', 'mi60srch.o', 'mi65rmod.o', 'mi70nobj.o',
      'mi80ncon.o', 'mi81ncon.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    sql   8.7Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.9Mb
    libs   1.5Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    3.6Mb
    libs   2.1Mb
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidyinftheo)
  > 
  > test_check("tidyinftheo")
  -- 1. Error: right number of columns given (@test-errors.R#10)  ----------------
  argument "expr" is missing, with no default
  1: expect_length(tab %>% select(vs) %>% shannon_entropy(), 1) at testthat/test-errors.R:10
  2: quasi_label(enquo(object))
  3: eval_bare(get_expr(quo), get_env(quo))
  4: tab %>% select(vs) %>% shannon_entropy()
  5: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  6: eval(quote(`_fseq`(`_lhs`)), env, env)
  7: eval(quote(`_fseq`(`_lhs`)), env, env)
  8: `_fseq`(`_lhs`)
  9: freduce(value, `_function_list`)
  10: withVisible(function_list[[k]](value))
  11: function_list[[k]](value)
  12: shannon_entropy(.)
  13: reduce_data(.data, !(!enquo(X)), numvars = 1, na.rm = na.rm)
  14: tidyselect::vars_select(names(reduced_tab), !(!(!quos(...))))
  15: vars_select_eval(.vars, quos)
  16: map_lgl(quos, quo_is_helper)
  17: .f(.x[[i]], ...)
  18: extract_expr(quo)
  19: is_call(expr, paren_sym)
  
  == testthat results  ===========================================================
  OK: 37 SKIPPED: 0 FAILED: 1
  1. Error: right number of columns given (@test-errors.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.3Mb
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    examples  19.2Mb
    include    2.9Mb
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 the system RNG.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.7Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    4.7Mb
    libs   1.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/uaparserjs.Rcheck/00install.out' for details.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
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 the system RNG.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.2Mb
    help   2.7Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc           4.7Mb
    htmlwidgets   3.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/walker.Rcheck/00install.out' for details.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    java   9.8Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    exampleData   1.4Mb
    examples      4.5Mb
    libs          4.2Mb
Package required but not available: 'rPython'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/Zelig.Rcheck/00install.out' for details.
Package suggested but not available for checking: ‘HH’
Packages suggested but not available for checking: ‘INLA’ ‘Rgraphviz’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    bootstrapping_example   1.2Mb
    libs                    3.3Mb
Error in re-building vignettes:
  ...
Loading required package: Cairo
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'abn_v1.0.2.tex' failed.
LaTeX errors:
! LaTeX Error: File `wrapfig.sty' not found.

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

! Emergency stop.
<read *> 
         
l.33 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘aroma.affymetrix’ ‘aroma.core’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 70-71 (ACSN-vignette.Rmd) 
Error: processing vignette 'ACSN-vignette.Rmd' failed with diagnostics:
the table must have a header (column names)
Execution halted
Packages in Depends field not imported from:
  ‘actuar’ ‘hypergeo’ ‘reliaR’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘ActuDistns-Ex.R’ failed
The error most likely occurred in:

> ### Name: dgumbeld
> ### Title: Gumbel pdf
> ### Aliases: dgumbeld
> ### Keywords: Gumbel distribution
> 
> ### ** Examples
> x=runif(10,min=0,max=1)
> y=dgumbeld(x)
Error in dgumbel(x, mu = mu, sigma = sigma) : 
  unused arguments (mu = mu, sigma = sigma)
Calls: dgumbeld -> ifelse
Execution halted
.amdai.initparam: no visible global function definition for ‘cov’
.amdat.initiparam: no visible global function definition for ‘cov’
amdai: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data       2.8Mb
    pictures   2.1Mb
Packages suggested but not available for checking: ‘HiTC’ ‘snpStats’
Packages unavailable to check Rd xrefs: ‘HiTC’, ‘snpStats’
Missing or unexported object: ‘lmerTest::as_lmerModLmerTest’
Package suggested but not available for checking: ‘copula’
aftgee: no visible global function definition for ‘model.extract’
aftgee: no visible global function definition for ‘model.matrix’
aftgee: no visible global function definition for ‘lm’
aftgee: no visible global function definition for ‘vcov’
aftgee.fit: no visible global function definition for ‘lm’
aftgee.fit: no visible global function definition for ‘rexp’
aftgee.fit: no visible global function definition for ‘var’
aftsrr: no visible global function definition for ‘model.extract’
aftsrr: no visible global function definition for ‘model.matrix’
aftsrr.fit: no visible global function definition for ‘lm’
aftsrr.fit: no visible global function definition for ‘rexp’
aftsrr.fit: no visible global function definition for ‘var’
getSmoothSuv: no visible global function definition for ‘pnorm’
print.summary.aftgee: no visible global function definition for
  ‘printCoefmat’
print.summary.aftsrr: no visible global function definition for
  ‘printCoefmat’
solveGehan: no visible global function definition for ‘nlm’
summary.aftgee: no visible global function definition for ‘pnorm’
summary.aftsrr: no visible global function definition for ‘pnorm’
viEmp: no visible global function definition for ‘rexp’
viEmp: no visible global function definition for ‘rnorm’
viEmp: no visible global function definition for ‘var’
zlFun: no visible global function definition for ‘lm’
Undefined global functions or variables:
  lm model.extract model.matrix nlm pnorm printCoefmat rexp rnorm var
  vcov
Consider adding
  importFrom("stats", "lm", "model.extract", "model.matrix", "nlm",
             "pnorm", "printCoefmat", "rexp", "rnorm", "var", "vcov")
to your NAMESPACE file.
Running examples in ‘aftgee-Ex.R’ failed
The error most likely occurred in:

> ### Name: aftgee
> ### Title: Accelerated Failure Time with Generalize Estimating Equation
> ### Aliases: aftgee summary.aftgee
> ### Keywords: aftgee
> 
> ### ** Examples
> 
> library(survival)
> library(copula)
Error in library(copula) : there is no package called ‘copula’
Execution halted
Error in re-building vignettes:
  ...
Warning in adapt(pT = pT, iD = iD, SF = 1, phi = 0, cp = 0.9, theta = 4,  :
  Power may be lower than planned.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

! Emergency stop.
<read *> 
         
l.16 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘Biostrings’
Packages unavailable to check Rd xrefs: ‘Biostrings’, ‘Starr’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'algebraichaplo.tex' failed.
LaTeX errors:
! LaTeX Error: File `ngerman.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [square,comma, numbers,sort&compress]{natbib}   % numbers wor...
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'alleHap.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.64 \setcounter
                {secnumdepth}{5}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
File ‘allelic/libs/allelic.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
    Object: ‘newallelic.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘Biobase’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Error in re-building vignettes:
  ...
Loading required package: Amelia
Loading required package: Rcpp
## 
## Amelia II: Multiple Imputation
## (Version 1.7.4, built: 2015-12-05)
## Copyright (C) 2005-2017 James Honaker, Gary King and Matthew Blackwell
## Refer to http://gking.harvard.edu/amelia/ for more information
## 

Execution halted
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
Error in re-building vignettes:
  ...
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsmath/amsgen.sty))
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsmath/amsbsy.sty)
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsmath/amsopn.sty))
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsfonts/umsa.fd)
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/natbib/natbib.sty)
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/psnfss/times.sty)

! LaTeX Error: File `xy.sty' not found.

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

Enter file name: 
! Emergency stop.
<read *> 
         
l.28 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Transcript written on anchors.log.
make: *** [anchors.pdf] Error 1
Error in buildVignettes(dir = "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/anchors.Rcheck/vign_test/anchors") : 
  running 'make' failed
Execution halted
Package suggested but not available for checking: ‘org.Hs.eg.db’
Error in re-building vignettes:
  ...
Loading required package: TH.data
Loading required package: MASS

Attaching package: 'TH.data'

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

    geyser

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ANOM.tex' failed.
LaTeX errors:
! LaTeX Error: File `doi.sty' not found.

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

! Emergency stop.
<read *> 
         
l.56 \usepackage
                {parskip}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required and available but unsuitable versions:
  ‘antaresRead’ ‘antaresProcessing’

Package suggested but not available for checking: ‘rhdf5’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘Biostrings’ ‘kebabs’
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'apsimr-basics.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.99 \usepackage
                {titletoc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

Loading required package: gWidgets
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'apt.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                [pdftex]{graphicx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in method(..., k = k[i]) : k=13: zs > maxKappa
Warning in method(..., k = k[i]) : k=13: zs > maxKappa
Warning in method(..., k = k[i]) : k=13: zs > maxKappa
Warning in method(..., k = k[i]) : k=14: zs > maxKappa
Warning in method(..., k = k[i]) : k=14: zs > maxKappa
Warning in method(..., k = k[i]) : k=14: zs > maxKappa
Warning in method(..., k = k[i]) : k=15: zs > maxKappa
Warning in axis(1, at = a, ...) : "axes" is not a graphical parameter
Loading required package: grid
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'archetypes.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
sh: +RTS: command not found
Error: processing vignette 'argparse.Rrst' failed with diagnostics:
pandoc document conversion failed with error 127
Execution halted
Package suggested but not available for checking: ‘affxparser’
Package unavailable to check Rd xrefs: ‘affxparser’
Packages required but not available: ‘aroma.core’ ‘PSCBS’

Packages suggested but not available for checking: ‘aroma.light’ ‘GLAD’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘EBImage’ ‘aroma.light’ ‘GLAD’ ‘sfit’ ‘expectile’ ‘HaarSeg’ ‘mpcbs’
Packages unavailable to check Rd xrefs: ‘aroma.light’, ‘GLAD’
Package suggested but not available for checking: ‘Cairo’
Error in re-building vignettes:
  ...
  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

Loading required package: estimability
Loading required package: car

Attaching package: 'car'

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

    recode

Quitting from lines 95-107 (art-contrasts.Rmd) 
Error: processing vignette 'art-contrasts.Rmd' failed with diagnostics:
there is no package called 'Cairo'
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.2Mb
Packages suggested but not available for checking: ‘graph’ ‘Rgraphviz’
Error in re-building vignettes:
  ...
Warning in summary.cross(cross) :
  Some chromosomes > 1000 cM in length; there may be a problem with the genetic map.
  (Perhaps it is in basepairs?)
Warning in summary.cross(cross) :
  Some markers at the same position on chr L.1,L.2,L.3,L.4,L.5,L.6,L.7,L.8,L.9; use jittermap().
Warning in heatMap(mapBC6, chr = c("L.3", "L.5", "L.8", "L.9"), lmax = 70) :
  Running est.rf.
Warning in summary.cross(cross) :
  Some markers at the same position on chr L.1,L.2,L.3,L.4,L.5,L.6,L.7; use jittermap().
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'asmapvignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.34 \usepackage
                [titles]{tocloft}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: ASPBay
Loading required package: hexbin
Loading required package: Rcpp
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ASPBay.tex' failed.
LaTeX errors:
! LaTeX Error: File `moreverb.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘devtools’
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(devtools)
  Error in library(devtools) : there is no package called 'devtools'
  Execution halted
asymp.test.default: no visible global function definition for ‘var’
asymp.test.default: no visible global function definition for ‘pnorm’
asymp.test.default: no visible global function definition for ‘qnorm’
asymp.test.formula: no visible global function definition for ‘terms’
seDMean.default: no visible global function definition for ‘var’
seDMeanG.default: no visible global function definition for ‘var’
seDVar.default: no visible global function definition for ‘var’
seMean.default: no visible global function definition for ‘var’
seRMean.default: no visible global function definition for ‘var’
seRVar.default: no visible global function definition for ‘var’
seVar.default: no visible global function definition for ‘var’
Undefined global functions or variables:
  pnorm qnorm terms var
Consider adding
  importFrom("stats", "pnorm", "qnorm", "terms", "var")
to your NAMESPACE file.
Package suggested but not available for checking: ‘rgdal’
Package suggested but not available for checking: ‘partitions’
File ‘aylmer/libs/aylmer.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘aylmer.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘aylmer.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...

Attaching package: ‘Brobdingnag’

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

    max, min, prod, range, sum

Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘partitions’
Warning in good(icons) :
  Good's method is for matrices with no NA entries.  Answer supplied is indicative only (but should provide an upper bound)
Error: processing vignette 'fishervig.Rnw' failed with diagnostics:
at fishervig.Rnw:753, could not find function "S"
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/BACA.Rcheck/00install.out’ for details.
Package required but not available: ‘glpkAPI’

Package suggested but not available for checking: ‘sybilSBML’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: BACCO
Loading required package: emulator
Loading required package: mvtnorm
Loading required package: calibrator
Loading required package: approximator
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'both_papers.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘pcalg’
Package unavailable to check Rd xrefs: ‘pcalg’
Error in re-building vignettes:
  ...

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

    filter, lag

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

    intersect, setdiff, setequal, union

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'backtestGraphics.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.99 \usepackage
                {titletoc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/bamboo.Rcheck/00install.out’ for details.
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    2.3Mb
    libs   2.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.6Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr

Execution halted
bridge.nmix.R: no visible global function definition for ‘rnorm’
draw.alpha: no visible global function definition for ‘runif’
draw.alpha: no visible global function definition for ‘dbeta’
draw.alpha.2: no visible global function definition for ‘runif’
draw.beta.2: no visible global function definition for ‘runif’
draw.sig2: no visible global function definition for ‘rgamma’
draw.tau: no visible global function definition for ‘rgamma’
draw.u: no visible global function definition for ‘runif’
draw.w: no visible global function definition for ‘runif’
draw.w: no visible global function definition for ‘rgamma’
draw.w.marg: no visible global function definition for ‘runif’
draw.w.marg: no visible global function definition for ‘rgamma’
trace.beta: no visible global function definition for ‘plot’
trace.beta: no visible global function definition for ‘lines’
trace.beta: no visible global function definition for ‘legend’
trace.beta.mcmc: no visible global function definition for ‘sd’
trace.beta.mcmc: no visible binding for global variable ‘sd’
trace.beta.mcmc: no visible global function definition for ‘plot’
trace.beta.mcmc: no visible global function definition for ‘title’
trace.beta.mcmc: no visible global function definition for ‘hsv’
trace.beta.mcmc: no visible global function definition for ‘lines’
trace.beta.mcmc: no visible global function definition for ‘points’
Undefined global functions or variables:
  dbeta hsv legend lines plot points rgamma rnorm runif sd title
Consider adding
  importFrom("grDevices", "hsv")
  importFrom("graphics", "legend", "lines", "plot", "points", "title")
  importFrom("stats", "dbeta", "rgamma", "rnorm", "runif", "sd")
to your NAMESPACE file.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/bayesCL.Rcheck/00install.out’ for details.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   7.4Mb
Found the following significant warnings:
  Warning: Installed Rcpp (0.12.12) different from Rcpp used to build dplyr (0.12.11).
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/BayesianNetwork.Rcheck/00install.out’ for details.
installed size is 56.7Mb
  sub-directories of 1Mb or more:
    libs  55.9Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
 **********   MAMS Version 1.01********** 

Type MAMSNews() to see new features/changes/bug fixes.

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'BayesFreq.tex' failed.
LaTeX errors:
! LaTeX Error: File `doi.sty' not found.

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

! Emergency stop.
<read *> 
         
l.56 \usepackage
                {parskip}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Depends: includes the non-default packages:
  ‘gplots’ ‘xtable’ ‘mnormt’ ‘MASS’ ‘bayesm’ ‘boa’ ‘e1071’ ‘gtools’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  ‘MASS’ ‘bayesm’ ‘boa’ ‘e1071’ ‘gplots’ ‘gtools’ ‘mnormt’ ‘xtable’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs  13.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    ex-data   4.6Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
File ‘BayHap/libs/BayHap.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘mcmc.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘mcmc.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Loading required package: splines
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'bbefkr.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'bbemkr.tex' failed.
LaTeX errors:
! LaTeX Error: File `bbm.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘R2jags’ ‘INLA’
Running examples in ‘BCEA-Ex.R’ failed
The error most likely occurred in:

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

> ### Name: bces0
> ### Title: Bayesian Cost-Effectiveness models in the presence of structural
> ###   zeros
> ### Aliases: bces0 bces0.default
> ### Keywords: JAGS Markov Chain Monte Carlo Bayesian models for
> ###   cost-effectiveness analysis
> 
> ### ** Examples
> 
> data(acupuncture)
> m <- bces0(data,dist.c="gamma",dist.e="beta",n.iter=1000,n.burnin=500,n.chains=2)
Installing package into ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/BCEs0.Rcheck’
(as ‘lib’ is unspecified)
Error in contrib.url(repos, "source") : 
  trying to use CRAN without setting a mirror
Calls: bces0 -> bces0.default -> install.packages -> contrib.url
Execution halted
Error in re-building vignettes:
  ...
Loading required package: plyr
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  plot type 'black' will be truncated to first character
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  plot type 'black' will be truncated to first character
Warning in replayPlot(x) :
  plot type 'black' will be truncated to first character
Warning in replayPlot(x) :
  plot type 'black' will be truncated to first character
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'bcpa.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.60 \usepackage
                {setspace}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
check.summary: no visible global function definition for ‘sd’
risk.summary: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  sd write.csv
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
Package suggested but not available for checking: ‘beadarrayExampleData’
plot.asr: no visible global function definition for ‘plot’
plot.casr: no visible global function definition for ‘plot’
plot.del: no visible global function definition for ‘plot’
plot.q: no visible global function definition for ‘plot’
plot.sr: no visible global function definition for ‘plot’
plot.trace1: no visible global function definition for ‘plot’
plot.trace2: no visible global function definition for ‘plot’
plot.trace3: no visible global function definition for ‘plot’
plot.trace4: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
installed size is 49.7Mb
  sub-directories of 1Mb or more:
    libs  48.3Mb