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.
Found the following significant warnings:
  Warning: replacing previous import 'gdalUtils::gdal_rasterize' by 'sf::gdal_rasterize' when loading 'uavRmp'
See 'd:/Rcompile/CRANpkg/local/3.6/uavRmp.Rcheck/00install.out' for details.
Crm: no visible global function definition for 'integrate'
Crm : <anonymous>: no visible global function definition for
  'integrate'
Crm: no visible global function definition for 'optimize'
ail1: no visible global function definition for 'uniroot'
ail2 : fu : <anonymous>: no visible global function definition for
  'integrate'
ail2: no visible global function definition for 'uniroot'
aip : fu : <anonymous>: no visible global function definition for
  'integrate'
aip: no visible global function definition for 'uniroot'
ait1: no visible global function definition for 'uniroot'
ait2 : fu : <anonymous>: no visible global function definition for
  'integrate'
ait2: no visible global function definition for 'uniroot'
sim3p3: no visible global function definition for 'rbinom'
simCrm: no visible global function definition for 'rbinom'
simCrm: no visible global function definition for 'palette'
simCrm: no visible global function definition for 'gray'
simCrm: no visible global function definition for 'plot'
simCrm: no visible global function definition for 'abline'
simCrm: no visible global function definition for 'lines'
ssim3p3: no visible global function definition for 'txtProgressBar'
ssim3p3: no visible global function definition for 'setTxtProgressBar'
ssimCrm: no visible global function definition for 'txtProgressBar'
ssimCrm: no visible global function definition for 'setTxtProgressBar'
Undefined global functions or variables:
  abline gray integrate lines optimize palette plot rbinom
  setTxtProgressBar txtProgressBar uniroot
Consider adding
  importFrom("grDevices", "gray", "palette")
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "integrate", "optimize", "rbinom", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
rmd2pdf: no visible global function definition for 'tail'
rnw2pdf: no visible global function definition for 'tail'
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    doc         5.2Mb
    dummydata   1.4Mb
    libs        4.2Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    8.3Mb
ubRacing : predCandidate: no visible global function definition for
  'predict'
ubRacing : aux2.friedman.edit: no visible global function definition
  for 'pchisq'
ubRacing : aux2.friedman.edit: no visible global function definition
  for 'qt'
ubRacing : aux.friedman.edit: no visible global function definition for
  'wilcox.test'
ubRacing : aux.ttest.edit: no visible global function definition for
  't.test'
ubRacing : aux.ttest.edit: no visible global function definition for
  'p.adjust'
ubRacing : idFolds: no visible global function definition for
  'quantile'
ubRacing: no visible binding for global variable 'sd'
ubSmoteExs: no visible global function definition for 'runif'
Undefined global functions or variables:
  p.adjust pchisq predict qt quantile runif sd t.test wilcox.test
Consider adding
  importFrom("stats", "p.adjust", "pchisq", "predict", "qt", "quantile",
             "runif", "sd", "t.test", "wilcox.test")
to your NAMESPACE file.
med: no visible global function definition for 'quantile'
uh: no visible global function definition for 'mad'
uh.bu: no visible global function definition for 'mad'
Undefined global functions or variables:
  mad quantile
Consider adding
  importFrom("stats", "mad", "quantile")
to your NAMESPACE file.
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
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
Package suggested but not available for checking: 'USAboundariesData'
readSEER: no visible global function definition for 'read.fwf'
Undefined global functions or variables:
  read.fwf
Consider adding
  importFrom("utils", "read.fwf")
to your NAMESPACE file.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'UScensus2000cdp/R/zzz.R':
  .First.lib calls:
    cat(paste("'", ehelp[4], "'\n", "Version ", ehelp[2], " created on ",     ehelp[3], ".\n", sep = ""))
    cat(paste(substring(ehelp[3], first = 16), "\n", "Version ",     substring(ehelp[4], first = 16), " created on ", substring(ehelp[5],         first = 16), ".\n", sep = ""))
    cat(paste("copyright (c) 2009, Zack W. Almquist, University of California-Irvine\n",     sep = ""))
    cat("For citation information, type citation(\"UScensus2000cdp\").\n")
    cat("Type help(package=\"UScensus2000cdp\") to get started.\n")

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

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
Found the following hidden files and directories:
  data/.Rhistory
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
'library' or 'require' call to 'rgdal' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'foreign' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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
installed size is 78.6Mb
  sub-directories of 1Mb or more:
    gdal   3.8Mb
    libs  68.7Mb
    proj   5.0Mb
Mammen: no visible global function definition for 'runif'
PR2: no visible global function definition for 'ar.burg'
PR2: no visible global function definition for 'pt'
PR2: no visible global function definition for 'pf'
PR3: no visible global function definition for 'ar.burg'
PR3: no visible global function definition for 'pt'
PR3: no visible global function definition for 'pf'
VAR.FOR: no visible global function definition for 'qnorm'
VAR.ForeB: no visible global function definition for 'runif'
VAR.LRtest: no visible global function definition for 'pchisq'
VAR.LRtest: no visible global function definition for 'pf'
VAR.PI: no visible global function definition for 'quantile'
VAR.Waldtest: no visible global function definition for 'pf'
VAR.irf: no visible global function definition for 'par'
VAR.irf: no visible global function definition for 'plot'
VAR.irf: no visible global function definition for 'abline'
VAR1.sim: no visible global function definition for 'rnorm'
resamp: no visible global function definition for 'runif'
Undefined global functions or variables:
  abline ar.burg par pchisq pf plot pt qnorm quantile rnorm runif
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("stats", "ar.burg", "pchisq", "pf", "pt", "qnorm",
             "quantile", "rnorm", "runif")
to your NAMESPACE file.
black_scholes: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
burdenPlot: no visible global function definition for 'density'
burdenPlot: no visible global function definition for 'axis'
burdenPlot: no visible global function definition for 'points'
burdenPlot: no visible global function definition for 'lines'
burdenPlot: no visible global function definition for 'abline'
burdenPlot: no visible global function definition for 'text'
burdenPlot: no visible global function definition for 'sd'
burdenPlot: no visible global function definition for 'segments'
vbdm: no visible global function definition for 'var'
vbdm: no visible global function definition for 'pchisq'
vbdmR : run_discrete_mixture_vanilla: no visible global function
  definition for 'var'
vbdmR: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  abline axis density lines pchisq points sd segments text var
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "points", "segments",
             "text")
  importFrom("stats", "density", "pchisq", "sd", "var")
to your NAMESPACE file.
compute_KL : rtnorm: no visible global function definition for 'runif'
compute_KL : rtnorm: no visible global function definition for 'dnorm'
compute_KL: no visible global function definition for 'qnorm'
compute_KL: no visible global function definition for 'dnorm'
compute_KL: no visible global function definition for 'pnorm'
compute_KL: no visible global function definition for 'var'
compute_KL: no visible global function definition for 'rbinom'
compute_KL: no visible global function definition for 'rnorm'
compute_KL: no visible global function definition for 'sd'
vbsr: no visible global function definition for 'qchisq'
vbsr: no visible global function definition for 'var'
vbsr: no visible global function definition for 'pchisq'
vbsr: no visible global function definition for 'sd'
vbsr: no visible binding for global variable 'sd'
Undefined global functions or variables:
  dnorm pchisq pnorm qchisq qnorm rbinom rnorm runif sd var
Consider adding
  importFrom("stats", "dnorm", "pchisq", "pnorm", "qchisq", "qnorm",
             "rbinom", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
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/3.6/VDAP.Rcheck/00install.out' for details.
cv.vda.le.default: no visible global function definition for 'predict'
cv.vda.r.default: no visible global function definition for 'predict'
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
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  9.2Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    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 11.0Mb
  sub-directories of 1Mb or more:
    doc           5.6Mb
    htmlwidgets   3.9Mb
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.
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.
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/3.6/VTrack.Rcheck/00install.out' for details.
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  9.4Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   7.4Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    doc  12.1Mb
Foreign function call to a different package:
  .C("comwr", ..., PACKAGE = "wavethresh")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
changepoints.sbs: no visible global function definition for 'mad'
changepoints.wbs: no visible global function definition for 'var'
changepoints.wbs: no visible global function definition for 'quantile'
plot.sbs: no visible global function definition for 'ts.plot'
plot.sbs: no visible global function definition for 'lines'
plot.sbs: no visible global function definition for 'title'
random.intervals: no visible global function definition for 'runif'
sbs.default: no visible global function definition for 'var'
wbs.default: no visible global function definition for 'var'
Undefined global functions or variables:
  lines mad quantile runif title ts.plot var
Consider adding
  importFrom("graphics", "lines", "title")
  importFrom("stats", "mad", "quantile", "runif", "ts.plot", "var")
to your NAMESPACE file.
onesamplemeantest: no visible global function definition for 'pnorm'
twosamplemeantest: no visible global function definition for 'pnorm'
wcq: no visible global function definition for 'var'
wcq: no visible global function definition for 'pnorm'
wcq.fdrc: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  p.adjust pnorm var
Consider adding
  importFrom("stats", "p.adjust", "pnorm", "var")
to your NAMESPACE file.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    client   8.9Mb
    doc      1.0Mb
Weighted.Box.test: no visible global function definition for 'acf'
Weighted.Box.test: no visible binding for global variable 'na.pass'
Weighted.Box.test: no visible global function definition for 'pgamma'
Weighted.Box.test: no visible global function definition for 'pchisq'
Weighted.LM.test: no visible global function definition for 'acf'
Weighted.LM.test: no visible binding for global variable 'na.pass'
Weighted.LM.test: no visible global function definition for 'pgamma'
Undefined global functions or variables:
  acf na.pass pchisq pgamma
Consider adding
  importFrom("stats", "acf", "na.pass", "pchisq", "pgamma")
to your NAMESPACE file.
'library' or 'require' call to 'markdown' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
dlog.norm: no visible global function definition for 'rnorm'
fun.load.hals.a: no visible global function definition for 'sfExport'
fun.load.hals.a: no visible global function definition for 'sfLibrary'
fun.load.hals.fill: no visible global function definition for
  'sfExport'
fun.load.hals.fill: no visible global function definition for
  'sfLibrary'
fun.load.widals.a: no visible global function definition for 'sfExport'
fun.load.widals.a: no visible global function definition for
  'sfLibrary'
fun.load.widals.fill: no visible global function definition for
  'sfExport'
fun.load.widals.fill: no visible global function definition for
  'sfLibrary'
unif.mh: no visible global function definition for 'runif'
Undefined global functions or variables:
  rnorm runif sfExport sfLibrary
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'genefilter' 'parallel'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.onAttach: no visible global function definition for
  'packageDescription'
.relax.cvcompute: no visible binding for global variable
  'weighted.mean'
.relax.widenet.cv.elnet: no visible global function definition for
  'predict'
.relax.widenet.cv.elnet: no visible binding for global variable
  'weighted.mean'
.relax.widenet.cv.lognet: no visible global function definition for
  'predict'
.relax.widenet.cv.lognet: no visible binding for global variable
  'weighted.mean'
.widenet.cv.elnet: no visible global function definition for 'predict'
.widenet.cv.elnet: no visible binding for global variable
  'weighted.mean'
.widenet.cv.lognet: no visible global function definition for 'predict'
.widenet.cv.lognet: no visible binding for global variable
  'weighted.mean'
predict.widenet: no visible global function definition for 'predict'
screen.cor : <anonymous>: no visible global function definition for
  'var'
screen.cor : <anonymous>: no visible global function definition for
  'cor.test'
screen.ttest: no visible global function definition for 'colttests'
widenet: no visible global function definition for 'mc.reset.stream'
widenet: no visible global function definition for 'mclapply'
widenet: no visible global function definition for 'predict'
Undefined global functions or variables:
  colttests cor.test mc.reset.stream mclapply packageDescription
  predict var weighted.mean
Consider adding
  importFrom("stats", "cor.test", "predict", "var", "weighted.mean")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
Bundesliga.Mannschaft: no visible global function definition for 'data'
Bundesliga.Mannschaft: no visible binding for global variable
  'Bundesliga'
Bundesliga.Tabelle: no visible global function definition for 'data'
Bundesliga.Tabelle: no visible binding for global variable 'Bundesliga'
Bundesliga.XML: no visible global function definition for 'data'
Bundesliga.XML: no visible binding for global variable 'Bundesliga'
sens.spec: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
wilcox.selection.split: no visible global function definition for
  'pnorm'
wilcox.test2: no visible global function definition for 'wilcox.test'
Undefined global functions or variables:
  pnorm wilcox.test
Consider adding
  importFrom("stats", "pnorm", "wilcox.test")
to your NAMESPACE file.
Cs: no visible global function definition for 'wilcox.test'
Don: no visible global function definition for 'points'
Don: no visible global function definition for 'chisq.test'
Lixn: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  chisq.test pchisq points wilcox.test
Consider adding
  importFrom("graphics", "points")
  importFrom("stats", "chisq.test", "pchisq", "wilcox.test")
to your NAMESPACE file.
plotTrait: no visible global function definition for 'plot'
plotTrait: no visible global function definition for 'points'
plotTrait: no visible global function definition for 'legend'
test.windex: no visible global function definition for 'hist'
test.windex: no visible global function definition for 'abline'
test.windex: no visible global function definition for 'legend'
windex: no visible global function definition for 'sd'
windex: no visible global function definition for 'var'
windex: no visible global function definition for 'dist'
windex: no visible global function definition for 'quantile'
Undefined global functions or variables:
  abline dist hist legend plot points quantile sd var
Consider adding
  importFrom("graphics", "abline", "hist", "legend", "plot", "points")
  importFrom("stats", "dist", "quantile", "sd", "var")
to your NAMESPACE file.
.__A__.1 : <anonymous>: no visible binding for global variable '.hwnd'
Undefined global functions or variables:
  .hwnd
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
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.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.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/3.6/word.alignment.Rcheck/00install.out' for details.
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
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
R5.value.default: no visible binding for global variable 'data.table'
R5.value.default: no visible global function definition for
  'as.data.table'
R5.value.parse: no visible binding for global variable 'data.table'
R5.value.parse: no visible global function definition for
  'is.data.table'
R5.value.parse: no visible global function definition for
  'as.data.table'
stampme: no visible global function definition for 'flush.console'
stampmsg: no visible global function definition for 'flush.console'
write.data.table: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  as.data.table data.table flush.console is.data.table write.table
Consider adding
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE file.
Running examples in 'Xmisc-Ex.R' failed
The error most likely occurred in:

> ### Name: is.connection
> ### Title: Is a connection
> ### Aliases: is.connection
> 
> ### ** Examples
> 
> is.connection(textConnection(LETTERS))
[1] TRUE
> 
> 
> 
> cleanEx()
Error: connections left open:
	LETTERS (textConnection)
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
File 'xml2/libs/i386/xml2.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_WriteConnection'
File 'xml2/libs/x64/xml2.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_WriteConnection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    exampleData   1.4Mb
    examples      4.5Mb
    libs          4.2Mb
newXMLDoc: no visible binding for global variable 'doc'
source: no visible binding for global variable 'use_file'
xmlFlatListTree : f: no visible binding for global variable 'nodeNames'
xmlFlatListTree : f: no visible binding for global variable 'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'nodeSet'
xmlFlatListTree : addNode: no visible binding for global variable
  'nodeSet'
xmlFlatListTree : addNode: no visible binding for global variable 'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'nodeNames'
xmlFlatListTree : addNode: no visible binding for global variable
  'nodeNames'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'parentCount'
xmlFlatListTree : addNode: no visible binding for global variable
  'parentCount'
xmlFlatListTree : <anonymous>: no visible binding for global variable
  'e'
xmlFlatTree : <anonymous>: no visible binding for global variable 'e'
Undefined global functions or variables:
  doc e idx nodeNames nodeSet parentCount use_file
LPGM: no visible global function definition for 'flush.console'
PGM: no visible global function definition for 'flush.console'
PGM.path.neighborhood: no visible global function definition for
  'runif'
PGMSim: no visible global function definition for 'rpois'
PGMSim: no visible global function definition for 'par'
WPGMSim: no visible global function definition for 'rpois'
XMRF.Sim: no visible global function definition for 'cov2cor'
XMRF.Sim: no visible global function definition for 'rbinom'
XMRF.Sim: no visible global function definition for 'rnorm'
glm.generic: no visible global function definition for 'flush.console'
mymult: no visible global function definition for 'rmultinom'
plot.GMS: no visible global function definition for 'pdf'
plot.GMS: no visible global function definition for 'dev.off'
plotNet: no visible global function definition for 'pdf'
plotNet: no visible global function definition for 'dev.off'
print.GMS: no visible global function definition for 'str'
processSeq: no visible binding for global variable 'quantile'
processSeq: no visible binding for global variable 'var'
processSeq: no visible global function definition for 'ks.test'
rmpois : <anonymous>: no visible global function definition for 'rpois'
Undefined global functions or variables:
  cov2cor dev.off flush.console ks.test par pdf quantile rbinom
  rmultinom rnorm rpois runif str var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par")
  importFrom("stats", "cov2cor", "ks.test", "quantile", "rbinom",
             "rmultinom", "rnorm", "rpois", "runif", "var")
  importFrom("utils", "flush.console", "str")
to your NAMESPACE file.
File which contains pragma(s) suppressing diagnostics:
  'inst/include/xtensor/xstorage.hpp'
Running examples in 'xtractomatic-Ex.R' failed
The error most likely occurred in:

> ### Name: getInfo
> ### Title: Extract dataset information for a given dtype name or number
> ### Aliases: getInfo
> 
> ### ** Examples
> 
> getInfo('atsstamday')
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Failed to connect to coastwatch.pfeg.noaa.gov port 443: Timed out
Calls: getInfo ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
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.
Running 'test-all.R' [43s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > test_check("zoon")
  Loading required package: zoon
  Loading required package: raster
  Loading required package: sp
  -- 1. Failure: Expected errors (@testTransformCRS.R#39)  -----------------------
  `workflow(...)` did not throw an error.
  
  == testthat results  ===========================================================
  OK: 237 SKIPPED: 30 FAILED: 1
  1. Failure: Expected errors (@testTransformCRS.R#39) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Depends: includes the non-default packages:
  ‘Matrix’ ‘coda’ ‘mvtnorm’ ‘MCMCpack’ ‘spatstat’ ‘parallel’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Dependence on R version ‘3.3.1’ not with patchlevel 0
Found the following significant warnings:
  analyzeFMRI.c:948:3: warning: ‘strncat’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  analyzeFMRI.c:975:5: warning: ‘strncat’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/AnalyzeFMRI.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  ‘sfit’ ‘expectile’ ‘HaarSeg’ ‘mpcbs’
Dependence on R version ‘3.3.2’ not with patchlevel 0
Packages suggested but not available for checking: ‘REBayes’ ‘Rmosek’
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  pa.c:247:2: warning: initialization of ‘struct audio_instance * (*)(struct SEXPREC *, float,  int)’ from incompatible pointer type ‘void * (*)(struct SEXPREC *, float,  int)’ [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/audio.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Quitting from lines 83-86 (use-ballr.Rmd) 
Error: processing vignette ‘use-ballr.Rmd’ failed with diagnostics:
Evaluation error: object ‘age’ not found.
Execution halted
Dependence on R version ‘3.3.3’ not with patchlevel 0
gimli.29466hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Found the following significant warnings:
  Blasso.cpp:451:53: warning: ‘*<unknown>.Blasso::icept’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/bayesCL.Rcheck/00install.out’ for details.
Found the following significant warnings:
  mcmc.c:337:4: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/BayHap.Rcheck/00install.out’ for details.
gimli.31945hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.8002hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.17218hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.24391hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.13592hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.30508hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.22729hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.31380hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.8298hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.19343hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.26680hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘biglmm-Ex.R’ failed
The error most likely occurred in:

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bigglm
> ### Title: Bounded memory linear regression
> ### Aliases: bigglm bigglm.function bigglm.data.frame
> ###   bigglm.SQLiteConnection bigglm.RODBC vcov.bigglm deviance.bigglm
> ###   family.bigglm AIC.bigglm bigglm,ANY,DBIConnection-method
> ### Keywords: regression
> 
> ### ** Examples
> 
> data(trees)
> ff<-log(Volume)~log(Girth)+log(Height)
> a <- bigglm(ff,data=trees, chunksize=10, sandwich=TRUE)
Error in UseMethod("bigglm", data) : 
  no applicable method for 'bigglm' applied to an object of class "data.frame"
Calls: bigglm -> bigglm
Execution halted
Running ‘testthat.R’ [30s/51s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bikedata)
  Data for London, U.K. powered by TfL Open Data:
    Contains OS data Ⓒ Crown copyright and database rights 2016
  Data for New York City provided and owned by:
    NYC Bike Share, LLC and Jersey City Bike Share, LLC ("Bikeshare")
    see https://www.citibikenyc.com/data-sharing-policy
  Data for Washington DC (Captialbikeshare), Chiago (Divvybikes) and Boston (Hubway)
    provided and owned by Motivate International Inc.
    see https://www.capitalbikeshare.com/data-license-agreement
    and https://www.divvybikes.com/data-license-agreement
    and https://www.thehubway.com/data-license-agreement
  Nice Ride Minnesota license  https://www.niceridemn.org/data_license
  > 
  > test_check("bikedata")
  ── 1. Failure: dl_bikedata la (@test-download-data.R#88)  ──────────────────────
  `dl_bikedata(city = "la", data_dir = tempdir(), dates = 2016)` produced unexpected messages.
  Expected match: All data files already exist
  Actual values:
  * Downloading metro-bike-share-trips-2016-q4.csv.zip
  
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 136 SKIPPED: 2 FAILED: 1
  1. Failure: dl_bikedata la (@test-download-data.R#88) 
  
  Error: testthat unit tests failed
  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: tidy.biglm
> ### Title: Tidy a(n) biglm object
> ### Aliases: tidy.biglm
> 
> ### ** Examples
> 
> 
> if (require("biglm", quietly = TRUE)) {
+     bfit <- biglm(mpg ~ wt + disp, mtcars)
+     tidy(bfit)
+     tidy(bfit, conf.int = TRUE)
+     tidy(bfit, conf.int = TRUE, conf.level = .9)
+ 
+     glance(bfit)
+ 
+     # bigglm: logistic regression
+     bgfit <- bigglm(am ~ mpg, mtcars, family = binomial())
+     tidy(bgfit)
+     tidy(bgfit, exponentiate = TRUE)
+     tidy(bgfit, conf.int = TRUE)
+     tidy(bgfit, conf.int = TRUE, conf.level = .9)
+     tidy(bgfit, conf.int = TRUE, conf.level = .9, exponentiate = TRUE)
+ 
+     glance(bgfit)
+ }
Error in UseMethod("bigglm", data) : 
  no applicable method for 'bigglm' applied to an object of class "data.frame"
Calls: bigglm -> bigglm
Execution halted
Running ‘test-all.R’ [30s/34s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("broom")
  Loading required package: broom
  ── 1. Error: (unknown) (@test-biglm.R#7)  ──────────────────────────────────────
  no applicable method for 'bigglm' applied to an object of class "data.frame"
  1: bigglm(am ~ mpg, mtcars, family = binomial()) at testthat/test-biglm.R:7
  2: bigglm(am ~ mpg, mtcars, family = binomial())
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 906 SKIPPED: 2 FAILED: 1
  1. Error: (unknown) (@test-biglm.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘BoomSpikeSlab’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
gimli.10973hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Found the following significant warnings:
  hash.c:144:5: warning: ‘strncpy’ specified bound 2048 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/C50.Rcheck/00install.out’ for details.
Found the following significant warnings:
  catnet_rexport.cpp:202:17: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
  catnet_rexport.cpp:206:15: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:213:16: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 0 and 1023 [-Wformat-overflow=]
  catnet_rexport.cpp:216:18: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
  catnet_rexport.cpp:217:17: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:232:17: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:231:18: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/catnet.Rcheck/00install.out’ for details.
Package required but not available: ‘bsts’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
gimli.20204hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Found the following significant warnings:
  guess_type.c:14:9: warning: ‘strncpy’ specified bound 512 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/checkmate.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [2s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(classyfireR)
  Loading required package: magrittr
  
  Attaching package: 'magrittr'
  
  The following objects are masked from 'package:testthat':
  
      equals, is_less_than, not
  
  > 
  > test_check('classyfireR')
  ── 1. Error: submit-classification (@test-submission.R#16)  ────────────────────
  lexical error: invalid char in json text.
                                         <!DOCTYPE html> <html> <head>  
                       (right here) ------^
  1: expect_true(dplyr::is.tbl(retrieve_classification(inchi_sub$query_id))) at testthat/test-submission.R:16
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: dplyr::is.tbl(retrieve_classification(inchi_sub$query_id))
  5: retrieve_classification(inchi_sub$query_id)
  6: jsonlite::fromJSON(text_content)
  7: fromJSON_string(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame, 
         simplifyMatrix = simplifyMatrix, flatten = flatten, ...)
  8: parseJSON(txt, bigint_as_char)
  9: parse_string(txt, bigint_as_char)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 10 SKIPPED: 0 FAILED: 1
  1. Error: submit-classification (@test-submission.R#16) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  lprintf.c:336:17: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/creditr.Rcheck/00install.out’ for details.
gimli.10970hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Found the following significant warnings:
  hash.c:144:5: warning: ‘strncpy’ specified bound 2048 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Cubist.Rcheck/00install.out’ for details.
Running examples in ‘data.tree-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GetPhyloNr
> ### Title: Determine the number a 'Node' has after conversion to a phylo
> ###   object
> ### Aliases: GetPhyloNr
> 
> ### ** Examples
> 
> library(ape)
> library(data.tree)
> data(acme)
> ap <- as.phylo(acme)
Error in UseMethod("as.phylo") : 
  no applicable method for 'as.phylo' applied to an object of class "c('Node', 'R6')"
Calls: as.phylo
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 502-504 (data.tree.Rmd) 
Error: processing vignette ‘data.tree.Rmd’ failed with diagnostics:
no applicable method for ‘as.igraph’ applied to an object of class "c('Node', 'R6')"
Execution halted
Depends: includes the non-default packages:
  ‘xtable’ ‘akima’ ‘R.oo’ ‘R.methodsS3’ ‘matlab’ ‘lattice’ ‘locfit’
  ‘grid’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  ‘Deducer’ ‘psych’ ‘GPArotation’ ‘mvnormtest’ ‘irr’ ‘klaR’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  ‘JavaGD’ ‘Deducer’ ‘sp’ ‘maptools’ ‘OpenStreetMap’ ‘scales’ ‘rgdal’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Running examples in ‘dendextend-Ex.R’ failed
The error most likely occurred in:

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

Attaching package: ‘ape’

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

    ladderize, rotate

> dend %>% as.phylo %>% di2multi(tol = 0.2) %>% plot(main = "phylo")
Error in UseMethod("as.phylo") : 
  no applicable method for 'as.phylo' applied to an object of class "dendrogram"
Calls: %>% ... eval -> _fseq -> freduce -> <Anonymous> -> as.phylo
Execution halted
Packages which this enhances but not available for checking:
  ‘gurobi’ ‘Rmosek’
Found the following significant warnings:
  GetData.c:342:15: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 3 [-Wformat-overflow=]
  GetData.c:355:15: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 3 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/DetSel.Rcheck/00install.out’ for details.
Found the following significant warnings:
  clipper.cpp:721:34: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct ClipperLib::TEdge’; use assignment or value-initialization instead [-Wclass-memaccess]
  dbfopen.c:1346:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopen.c:1328:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopen.c:879:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  dbfopen.c:1693:9: warning: ‘strncpy’ output may be truncated copying 11 bytes from a string of length 11 [-Wstringop-truncation]
  dbfopen.c:2065:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/dggridR.Rcheck/00install.out’ for details.
Running examples in ‘divest-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: readDicom
> ### Title: Read one or more DICOM directories
> ### Aliases: readDicom sortDicom scanDicom
> 
> ### ** Examples
> 
> path <- system.file("extdata", "raw", package="divest")
> scanDicom(path)
[dcm2niix info] Found 4 DICOM file(s)
[dcm2niix ERROR] You do not have write permissions for the directory /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/divest/extdata/raw
[dcm2niix ERROR] You do not have write permissions for the directory /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/divest/extdata/raw
  label
2  <NA>
1  <NA>
                                                                       rootPath
2 /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/divest/extdata/raw
1 /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/divest/extdata/raw
  files seriesNumber seriesDescription patientName studyDate echoTime
2     2            8        DTIb3000s5        <NA>      <NA>   112.00
1     2            9       fl3D_t1_sag        <NA>      <NA>     4.94
  repetitionTime echoNumber phase diffusion
2           4100         NA FALSE      TRUE
1             11         NA FALSE     FALSE
> readDicom(path, interactive=FALSE)
[dcm2niix info] Found 4 DICOM file(s)
[dcm2niix ERROR] You do not have write permissions for the directory /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/divest/extdata/raw
[dcm2niix info]  Warning: all images appear to be a single slice - please check slice/vector orientation
[dcm2niix ERROR] You do not have write permissions for the directory /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/divest/extdata/raw
Error in .readPath(path.expand(p), flipY, crop, forceStack, verbosity,  : 
  DICOM scan failed
Calls: readDicom -> lapply -> FUN -> .readPath
Execution halted
gimli.23695hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.31742hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.6309hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.14336hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.9417hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.23916hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.18556hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.23593hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.31675hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.7545hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.15846hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/dpglasso.Rcheck/00install.out’ for details.
Found the following significant warnings:
  main.c:334:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:575:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:518:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:805:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:755:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1034:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:983:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1377:7: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1279:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1678:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1962:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1912:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:2316:7: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:2212:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/enviPat.Rcheck/00install.out’ for details.
Found the following significant warnings:
  epanet.c:999:5: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:1000:5: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:1492:3: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:2308:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:2309:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  input1.c:454:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  input1.c:455:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  input3.c:604:2: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/epanet2toolkit.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Creating package 'fakepack' in '/tmp/Rtmput7HZe'
No DESCRIPTION found. Creating with values:


Prerequisite DESCRIPTION found.
Prerequisite R/throw.R found.
Prerequisite R/throw.R found.
Prerequisite R/throw.R found.
Prerequisite R/throw.R found.
* installing *source* package ‘fakepack’ ...
** R
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  ‘fakepack’ 
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (fakepack)
Prerequisite R/throw.R found.
Prerequisite R/throw.R found.
Prerequisite DESCRIPTION found.
Prerequisite R/throw.R found.
Error: processing vignette ‘An_Introduction_to_fakemake.Rmd’ failed with diagnostics:
there is no package called 'spelling'
Execution halted
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/home/hornik/tmp/R.check/r-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  8.3  0.101   8.956
Running examples in ‘ffbase-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bigglm.ffdf
> ### Title: Bounded memory linear regression
> ### Aliases: bigglm.ffdf
> 
> ### ** Examples
> 
> library(biglm)
Loading required package: DBI
> library(ff)
> 
> data(trees)
> x <- as.ffdf(trees)
> a <- bigglm(log(Volume)~log(Girth)+log(Height), 
+             data=x, chunksize=10, sandwich=TRUE)
Error in UseMethod("bigglm", data) : 
  no applicable method for 'bigglm' applied to an object of class "ffdf"
Calls: bigglm -> bigglm
Execution halted
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.
Found the following significant warnings:
  FLAN_Clone.h:131:11: warning: ‘*<unknown>.FLAN_SimClone::mDist’ is used uninitialized in this function [-Wuninitialized]
  FLAN_Clone.h:204:11: warning: ‘*<unknown>.FLAN_SimInhomogeneousClone::mMU’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/flan.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  ‘Rsocp’ ‘Rnlminb2’ ‘Rdonlp2’
Found the following significant warnings:
  RngStream.c:275:7: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/freeknotsplines.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘dggrids’ ‘INLA’
Found the following significant warnings:
  hap_c.c:380:28: warning: ‘%03d’ directive writing between 3 and 10 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  hap_c.c:392:28: warning: ‘%03d’ directive writing between 3 and 10 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gap.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Gdmlib.cpp:2352:19: warning: ‘%lf’ directive writing between 3 and 317 bytes into a region of size between 0 and 1023 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gdm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  rboxlib.c:351:5: warning: ‘strncat’ output may be truncated copying between 0 and 199 bytes from a string of length 199 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/geometry.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_41_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gglasso.Rcheck/00install.out’ for details.
Found the following significant warnings:
  dump_json_ast.cpp:21:12: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound 1000 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/graphql.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  ‘taxstats’ ‘taxstats1516’
gimli.15960hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Found the following significant warnings:
  readstat/readstat_writer.c:82:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  readstat/readstat_writer.c:261:5: warning: ‘strncpy’ specified bound 256 equals destination size [-Wstringop-truncation]
  readstat/readstat_writer.c:316:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  readstat/sas/readstat_sas7bcat_write.c:108:5: warning: ‘strncpy’ output may be truncated copying 64 bytes from a string of length 99 [-Wstringop-truncation]
  readstat/sas/readstat_sas.c:284:5: warning: ‘strncpy’ output may be truncated copying 64 bytes from a string of length 99 [-Wstringop-truncation]
  readstat/sas/readstat_sas.c:337:5: warning: ‘strncpy’ output may be truncated copying 8 bytes from a string of length 31 [-Wstringop-truncation]
  readstat/spss/readstat_sav_write.c:150:5: warning: ‘strncpy’ output may be truncated copying 9 bytes from a string of length 9 [-Wstringop-truncation]
  readstat/spss/readstat_sav_write.c:158:5: warning: ‘strncpy’ output may be truncated copying 8 bytes from a string of length 8 [-Wstringop-truncation]
  readstat/spss/readstat_por_write.c:194:5: warning: ‘strncpy’ output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/haven.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [9s/102s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(hei)
  > 
  > test_check("hei")
  Error in year %in% yearchoices : 
    argument "year" is missing, with no default
  Error in try(if (!day %in% daychoices) stop("must use valid day choice")) : 
    must use valid day choice
  Error in year %in% yearchoices : 
    argument "year" is missing, with no default
  Error in try(if (!day %in% daychoices) stop("must use valid day choice")) : 
    must use valid day choice
  ── 1. Error: (unknown) (@test_diet.R#3)  ───────────────────────────────────────
  attempt to set an attribute on NULL
  1: get_diet("2009/2010", day = "first") at testthat/test_diet.R:3
  
  Processing SAS dataset DR1TOT_F 	 ..
  Processing SAS dataset DR2TOT_F 	 ..
  Processing SAS dataset DEMO_F 	 ..
  Processing SAS dataset DR1TOT_F 	 ..
  Processing SAS dataset DR2TOT_F 	 ..
  Processing SAS dataset DEMO_F 	 ..
  Error in try(if (!year %in% yearchoices) stop("must use valid year choice")) : 
    must use valid year choice
  Error in day %in% daychoices : argument "day" is missing, with no default
  Error in try(if (!year %in% yearchoices) stop("must use valid year choice")) : 
    must use valid year choice
  Error in try(if (!year %in% yearchoices) stop("must use valid year choice")) : 
    must use valid year choice
  Error in day %in% daychoices : argument "day" is missing, with no default
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 8 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_diet.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Error in .requirePackage(package) : 
    unable to find required package 'HiTC'
  Calls: <Anonymous> ... getClass -> getClassDef -> .classEnv -> .requirePackage
  Execution halted
Found the following significant warnings:
  gener.c:39:26: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/hier.part.Rcheck/00install.out’ for details.
Depends: includes the non-default packages:
  ‘lattice’ ‘caTools’ ‘gdata’ ‘gtools’ ‘gplots’ ‘parallel’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Running examples in ‘inca-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: intcalibrate
> ### Title: Integer Calibration Function
> ### Aliases: intcalibrate
> 
> ### ** Examples
> 
> library(inca)
> set.seed(0)
> w <- rpois(150, 4)
> data <- matrix(rbinom(150000, 1, .3) * rpois(150000, 4), 1000, 150)
> y <- data %*% w
> w <- runif(150, 0, 7.5)
> print(sum(abs(y - data %*% w)))
[1] 65229.64
> cw <- intcalibrate(w, ~. + 0, y, lower = 1, upper = 7, sparse = TRUE, data = data)
Error in NextMethod("model.matrix", data = data, contrasts.arg = object$contrasts) : 
  no method to invoke
Calls: intcalibrate -> model.matrix.lm -> NextMethod
Execution halted
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
Running ‘testthat.R’ [0m/16m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ipeaData)
  > 
  > test_check("ipeaData")
  [1] "NA. 05/1999 a 03/2009. Acesso em: 19/10/2018"
  ── 1. Error: ipeaData (@test_functions_ipea_data.R#19)  ────────────────────────
  Recv failure: Connection timed out
  1: suppressWarnings(result <- ipeadata("SERIE SEM RETORNO")) at testthat/test_functions_ipea_data.R:19
  2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  3: ipeadata("SERIE SEM RETORNO")
  4: get_metadata(serie)
  5: basic_call(api_call, type)
  6: GET(api)
  7: request_perform(req, hu$handle$handle)
  8: request_fetch(req$output, req$url, handle)
  9: request_fetch.write_memory(req$output, req$url, handle)
  10: curl::curl_fetch_memory(url, handle = handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 6 SKIPPED: 0 FAILED: 1
  1. Error: ipeaData (@test_functions_ipea_data.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
gimli.5939hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Depends: includes the non-default packages:
  ‘partitions’ ‘VGAM’ ‘MASS’ ‘ape’ ‘apTreeshape’ ‘geiger’ ‘gtools’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:
  jqr.c:11:3: warning: ‘strncpy’ specified bound 1000 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/jqr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  push_parser.c:75:5: warning: ‘strncpy’ specified bound 1024 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/jsonlite.Rcheck/00install.out’ for details.
gimli.27789hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.3058hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.13903hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.22585hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.26862hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.6048hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.3585hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.15183hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.23953hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.30760hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.6748hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Depends: includes the non-default packages:
  ‘sn’ ‘moments’ ‘BB’ ‘Bolstad2’ ‘optimx’ ‘Rmpfr’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Running examples in ‘longpower-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lmmpower
> ### Title: Sample size calculations for linear mixed models of rate of
> ###   change based on lmer, lme, or gee "placebo" pilot estimates.
> ### Aliases: lmmpower lmmpower,ANY-method lmmpower,merMod-method
> ###   lmmpower-methods lmmpower.default lmmpower.gee lmmpower.lme
> ###   lmmpower.numeric
> ### Keywords: effects marginal methods mixed model power random sample size
> 
> ### ** Examples
> 
> 
> ## Not run: 
> ##D browseVignettes(package = "longpower")
> ## End(Not run)
> 
> lmmpower(delta=1.5, t = seq(0,1.5,0.25),
+ 	sig2.i = 55, sig2.s = 24, sig2.e = 10, cov.s.i=0.8*sqrt(55)*sqrt(24), power = 0.80)
Error in UseMethod("lmmpower") : 
  no applicable method for 'lmmpower' applied to an object of class "c('double', 'numeric')"
Calls: lmmpower -> lmmpower
Execution halted
Found the following significant warnings:
  liblwgeom/lwutil.c:317:5: warning: ‘strncat’ specified bound 3 equals source length [-Wstringop-overflow=]
  liblwgeom/lwutil.c:323:5: warning: ‘strncat’ specified bound 3 equals source length [-Wstringop-overflow=]
  liblwgeom/lwutil.c:344:5: warning: ‘strncat’ specified bound 3 equals source length [-Wstringop-overflow=]
  liblwgeom/lwutil.c:349:5: warning: ‘strncat’ specified bound 3 equals source length [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lwgeom.Rcheck/00install.out’ for details.
Depends: includes the non-default packages:
  ‘lattice’ ‘locfit’ ‘maptools’ ‘quantreg’ ‘RANN’ ‘SparseM’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  ‘seqinr’ ‘pcaMethods’ ‘Matrix’ ‘ROCR’ ‘Hmisc’ ‘KernSmooth’ ‘seqLogo’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
gimli.13325hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.18523hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.24218hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.31335hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.25170hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.32754hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.8584hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.19034hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.28146hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
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:
  ...
Quitting from lines 301-306 (miceFast-intro.Rmd) 
Error: processing vignette ‘miceFast-intro.Rmd’ failed with diagnostics:
no method to invoke
Execution halted
Found the following significant warnings:
  migrate.c:179:30: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:186:26: warning: ‘.asc’ directive writing 4 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:199:28: warning: ‘.asc’ directive writing 4 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:286:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:312:29: warning: ‘%d’ directive writing between 1 and 8 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:559:31: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:595:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:603:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MigClim.Rcheck/00install.out’ for details.
gimli.13752hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Found the following significant warnings:
  monetdblite/src/gdk/gdk_heap.c:189:3: warning: ‘strncpy’ output truncated before terminating nul copying 9 bytes from a string of the same length [-Wstringop-truncation]
  monetdblite/src/gdk/gdk_heap.c:260:30: warning: ‘%s’ directive writing likely 3 or more bytes into a region of size between 0 and 99 [-Wformat-overflow=]
  monetdblite/src/mal/sqlbackend/rel_bin.c:2949:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/mal/sqlbackend/rel_bin.c:1083:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/mal/sqlbackend/sql_statement.c:3193:3: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/mal/sqlbackend/sql_statement.c:3196:3: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/mal/sqlbackend/sql_statement.c:3186:3: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/sql/server/rel_planner.c:82:4: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/sql/server/rel_semantic.c:54:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/sql/server/rel_updates.c:1729:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MonetDBLite.Rcheck/00install.out’ for details.
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
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.
Depends: includes the non-default packages:
  ‘car’ ‘pdist’ ‘pls’ ‘gplots’ ‘mvtnorm’ ‘robustbase’ ‘gtools’ ‘bitops’
  ‘caTools’ ‘pcaPP’ ‘rrcov’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
gimli.11485hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
This is lavaan 0.6-3
lavaan is BETA software! Please report any bugs.
This is nonnest2 0.5-2.
nonnest2 has not been tested with all combinations of model classes.
Quitting from lines 64-65 (nonnest2.Rmd) 
Error: processing vignette ‘nonnest2.Rmd’ failed with diagnostics:
no applicable method for ‘estfun’ applied to an object of class "lavaan"
Execution halted
Depends: includes the non-default packages:
  ‘lpSolve’ ‘gdata’ ‘Hmisc’ ‘rms’ ‘geometry’ ‘psych’ ‘pwt’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  ‘R.methodsS3’ ‘MASS’ ‘matrixStats’ ‘R.oo’ ‘R.utils’ ‘aroma.core’
  ‘aroma.affymetrix’ ‘DNAcopy’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:
  medusa.long2text.cpp:16:21: warning: ‘%ld’ directive writing between 1 and 20 bytes into a region of size 16 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Numero.Rcheck/00install.out’ for details.
gimli.7152hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'lubridate'

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

    date


Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Warning in bind_rows_(x, .id) :
  Unequal factor levels: coercing to character
Warning in bind_rows_(x, .id) :
  binding character and factor vector, coercing into character vector
Warning in bind_rows_(x, .id) :
  binding character and factor vector, coercing into character vector
Warning: Removed 5 rows containing missing values (geom_path).
Don't know how to automatically pick scale for object of type difftime. Defaulting to continuous.
Don't know how to automatically pick scale for object of type difftime. Defaulting to continuous.
Don't know how to automatically pick scale for object of type difftime. Defaulting to continuous.
Loading required package: maps
Loading required package: maptools
Loading required package: sp
Checking rgeos availability: TRUE
Loading required package: rgeos
rgeos version: 0.4-1, (SVN revision 579)
 GEOS runtime version: 3.7.0-CAPI-1.11.0 
 Linking to sp version: 1.3-1 
 Polygon checking: TRUE 

Quitting from lines 142-143 (osem-intro.Rmd) 
Error: processing vignette ‘osem-intro.Rmd’ failed with diagnostics:
no simple features geometry column present
Execution halted
Running ‘exporting-methods.R’ [3s/3s]
  Running ‘mahal-dist.R’ [3s/4s]
  Running ‘testthat.R’ [22s/23s]
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
Packages suggested but not available for checking:
  ‘genealogicalSorting’ ‘phybase’
gimli.12866hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Running ‘testthat.R’ [5s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("pacman")
  > options(repos="http://cran.rstudio.com/")
  > 
  > 
  > test_check("pacman")
  ── 1. Error: p_install_gh works (@test-p_install_gh.R#5)  ──────────────────────
  HTTP error 404.
    Not Found
  
    Rate limit remaining: 59
    Rate limit reset at: 2018-10-19 21:07:30 UTC
  1: expect_false(p_install_gh("greg/iDontExistAnywhere")) at testthat/test-p_install_gh.R:5
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: p_install_gh("greg/iDontExistAnywhere")
  5: lapply(package, function(x) {
         devtools::install_github(x, dependencies = dependencies, ...)
     })
  6: FUN(X[[i]], ...)
  7: devtools::install_github(x, dependencies = dependencies, ...)
  8: install_remotes(remotes, auth_token = auth_token, host = host, dependencies = dependencies, 
         upgrade = upgrade, force = force, quiet = quiet, build = build, build_opts = build_opts, 
         repos = repos, type = type, ...)
  9: vapply(remotes, install_remote, ..., FUN.VALUE = character(1))
  10: FUN(X[[i]], ...)
  11: remote_package_name(remote)
  12: remote_package_name.github_remote(remote)
  13: github_DESCRIPTION(username = remote$username, repo = remote$repo, subdir = remote$subdir, 
         host = remote$host, ref = remote$ref, pat = remote$auth_token %||% github_pat(), 
         use_curl = use_curl)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 54 SKIPPED: 3 FAILED: 1
  1. Error: p_install_gh works (@test-p_install_gh.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
gimli.18161hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
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.
Running ‘testthat.R’ [10s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pavo)
  > 
  > test_check("pavo")
  ── 1. Error: classify (@test-images.R#79)  ─────────────────────────────────────
  attempt to set an attribute on NULL
  1: classify(imgfakes, kcols = fake_IDs) at testthat/test-images.R:79
  
  ── 2. Error: adjacency (@test-images.R#156)  ───────────────────────────────────
  attempt to set an attribute on NULL
  1: classify(imgfakes, kcols = 2) at testthat/test-images.R:156
  
  Read 18823 items
  Read 10820 items
  Read 10824 items
  Read 18823 items
  Read 10820 items
  Read 10824 items
  ── 3. Error: getspec (@test-import.R#30)  ──────────────────────────────────────
  write error, closing pipe to the master
  1: suppressMessages(getspec(system.file("testdata", package = "pavo"), ext = "procspec")) at testthat/test-import.R:30
  2: withCallingHandlers(expr, message = function(c) invokeRestart("muffleMessage"))
  3: getspec(system.file("testdata", package = "pavo"), ext = "procspec")
  4: pbmclapply(files, function(x) tryCatch(gsp(x), error = function(e) NULL, warning = function(e) NULL), 
         mc.cores = cores)
  5: mclapply(X, FUN, ..., mc.cores = mc.cores)
  6: lapply(seq_len(cores), inner.do)
  7: FUN(X[[i]], ...)
  8: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
  
  ── 3. Failure: getspec (@test-import.R#31)  ────────────────────────────────────
  `proccase` not identical to `proc`.
  Names: 1 string mismatch
  Length mismatch: comparison on first 3 components
  Component 3: Mean relative difference: 0.5655852
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 143 SKIPPED: 0 FAILED: 3
  1. Error: classify (@test-images.R#79) 
  2. Error: adjacency (@test-images.R#156) 
  3. Failure: getspec (@test-import.R#31) 
  
  Error: testthat unit tests failed
  Execution halted
gimli.9564hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.18077hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.24310hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.18029hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.3106hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.27995hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.4460hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.14040hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.18446hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.24771hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
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.
gimli.10050hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.18461hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.25058hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.30818hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.19478hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.4364hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.29617hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.6775hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.15154hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.20364hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.26173hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
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.
gimli.10187hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.18528hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.

Found the following apparent S3 methods exported but not registered:
  cbind.ddmatrix rbind.ddmatrix
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
gimli.25092hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.30819hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.23681hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.4753hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.2268hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.12215hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.17257hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.23959hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.30609hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
S3 methods shown with full name in documentation object 'binds':
  ‘rbind.ddmatrix’ ‘cbind.ddmatrix’

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.
gimli.9461hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.17965hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.23956hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.29678hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.22209hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.3161hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.32673hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.9798hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.16213hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.22586hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.27254hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
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.
gimli.18537hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.12639hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.20394hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.26120hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.31950hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.19447hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.5795hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.28926hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.5853hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.14529hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.19617hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.25209hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
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.
gimli.5718hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Running ‘testthat.R’ [232s/335s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(peakPantheR)
  
  This is peakPantheR version 1.2.0 
  
  > 
  > test_check("peakPantheR")
  ── 1. Error: default multiplot (@test_annotationDiagnosticMultiplot.R#180)  ────
  unused arguments (limits, n)
  1: evaluate_promise(annotationDiagnosticMultiplot(input_plots)) at testthat/test_annotationDiagnosticMultiplot.R:180
  2: withr::with_output_sink(temp, withCallingHandlers(withVisible(code), warning = handle_warning, 
         message = handle_message))
  3: force(code)
  4: withCallingHandlers(withVisible(code), warning = handle_warning, message = handle_message)
  5: withVisible(code)
  6: annotationDiagnosticMultiplot(input_plots)
  7: ggplot2::layer_scales(tmp_rtPeakwidthVert)
  8: ggplot_build(plot)
  9: ggplot_build.ggplot(plot)
  10: layout$setup_panel_params()
  ...
  16: f(..., self = self)
  17: parent$setup_panel_params(scale_x, scale_y, params)
  18: f(..., self = self)
  19: train_cartesian(scale_x, self$limits$x, "x")
  20: scale$break_info(range)
  21: f(..., self = self)
  22: ggproto_parent(ScaleContinuous, self)$break_info(range)
  23: f(..., self = self)
  24: self$get_breaks_minor(b = major, limits = range)
  25: f(..., self = self)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1147 SKIPPED: 0 FAILED: 1
  1. Error: default multiplot (@test_annotationDiagnosticMultiplot.R#180) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  fdouble_metaphone.c:268:5: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/PGRdup.Rcheck/00install.out’ for details.
Depends: includes the non-default packages:
  ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’ ‘lattice’ ‘rggobi’ ‘ggplot2’
  ‘proto’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
gimli.32635hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.5463hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.13299hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.20943hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.20046hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.31610hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.26666hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.1571hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.10375hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.18348hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.26982hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
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 .requirePackage(package) : 
    unable to find required package 'raster'
  Calls: <Anonymous> ... getClass -> getClassDef -> .classEnv -> .requirePackage
  Execution halted
Found the following significant warnings:
  zhegv.c:216:27: warning: ‘strncpy’ specified bound 2 equals destination size [-Wstringop-truncation]
  zhegv.c:216:27: warning: ‘strncpy’ specified bound 3 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/PRIMME.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/PSPManalysis.Rcheck/00install.out’ for details.
Found the following significant warnings:
  R4dfp-object.c:253:3: warning: ‘strncpy’ output truncated before terminating nul copying 9 bytes from a string of the same length [-Wstringop-truncation]
  R4dfp-object.c:260:3: warning: ‘strncpy’ output truncated before terminating nul copying 9 bytes from a string of the same length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/R4dfp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  kleinkram.cc:1018:18: warning: ‘ '’ directive writing 2 bytes into a region of size between 1 and 1000 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RandomFieldsUtils.Rcheck/00install.out’ for details.
Found the following significant warnings:
  avc_binwr.c:166:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:173:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:180:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:187:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:1453:29: warning: ‘%4.4d’ directive writing between 4 and 10 bytes into a region of size 5 [-Wformat-overflow=]
  avc_binwr.c:1553:28: warning: ‘%s’ directive writing up to 39 bytes into a region of size between 38 and 77 [-Wformat-overflow=]
  avc_e00write.c:386:30: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  avc_e00write.c:387:30: warning: ‘-ID’ directive writing 3 bytes into a region of size between 1 and 40 [-Wformat-overflow=]
  avc_e00write.c:401:61: warning: ‘%s’ directive writing up to 39 bytes into a region of size 17 [-Wformat-overflow=]
  avc_e00write.c:397:61: warning: ‘%s’ directive writing up to 39 bytes into a region of size 17 [-Wformat-overflow=]
  avc_e00write.c:409:39: warning: ‘%s’ directive writing up to 39 bytes into a region of size 33 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RArcInfo.Rcheck/00install.out’ for details.
Found the following significant warnings:
  samtools/bam.c:118:2: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
  samtools/razf.c:178:2: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
  rbamtools.cpp:126:10: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rbamtools.Rcheck/00install.out’ for details.
Running examples in ‘Rchoice-Ex.R’ failed
The error most likely occurred in:

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

Model: binomial
Model estimated on: Fri Oct 19 06:41:42 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
Depends: includes the non-default packages:
  ‘biclust’ ‘fabia’ ‘iBBiG’ ‘superbiclust’ ‘BcDiag’ ‘rqubic’ ‘BicARE’
  ‘s4vd’ ‘BiBitR’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:
  Rreadsdpa.c:608:15: warning: ‘strncpy’ output may be truncated copying 3999 bytes from a string of length 3999 [-Wstringop-truncation]
  Rreadsdpa.c:1041:13: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  Rreadsdpa.c:1042:13: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  dsdpsetoptions.c:164:4: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  dsdpsetoptions.c:165:4: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rdsdp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  compile.cc:292:69: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class re2::Prog::Inst’; use assignment or value-initialization instead [-Wclass-memaccess]
  regexp.cc:343:33: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class re2::Regexp’ with no trivial copy-assignment [-Wclass-memaccess]
  regexp.cc:344:32: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class re2::Regexp’ with no trivial copy-assignment [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/re2r.Rcheck/00install.out’ for details.
Found the following significant warnings:
  localtime.c:1817:5: warning: ‘strncpy’ specified bound 1000 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/readr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  phonet.c:1207:34: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  phonet.c:1208:34: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RecordLinkage.Rcheck/00install.out’ for details.
gimli.3846hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.6684hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.14916hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.28660hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.5293hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.6229hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.16218hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.20123hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.28427hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.8409hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.17592hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.25782hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running ‘test-all.R’ [2s/2s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("rgbif")
  Loading required package: rgbif
  ── 1. Error: name_usage with single taxon key and return='data': returns issues 
  Not Found
  1: name_usage(key = 143861132, return = "data") at testthat/test-name_usage.r:63
  2: getdata(data, key, uuid, shortname, args, curlopts)
  3: gbif_GET(url, args, FALSE, curlopts)
  4: stop(mssg, call. = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 63 SKIPPED: 117 FAILED: 1
  1. Error: name_usage with single taxon key and return='data': returns issues correctly (@test-name_usage.r#63) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  RhpcMPI.c:301:5: warning: ‘strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rhpc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  cornellout.cpp:99:20: warning: ‘%2d’ directive writing between 2 and 11 bytes into a region of size between 0 and 931 [-Wformat-overflow=]
  cornellout.cpp:137:26: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  cornellout.cpp:129:26: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 988 and 995 [-Wformat-overflow=]
  mat.cpp:315:4: warning: ‘*<unknown>.dataMat::p’ is used uninitialized in this function [-Wuninitialized]
  tilia.cpp:179:14: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 61 bytes from a string of length 199 [-Wstringop-truncation]
  tilia.cpp:180:10: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 19 bytes from a string of length 19 [-Wstringop-truncation]
  tilia.cpp:225:14: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 8 bytes from a string of length 199 [-Wstringop-truncation]
  tilia.cpp:228:17: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 8 bytes from a string of length 29 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rioja.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’,
    ‘R_GlobalContext’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  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.
Found the following significant warnings:
  RngStream.c:347:4: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rlecuyer.Rcheck/00install.out’ for details.
Found the following significant warnings:
  origcmaes.cc:2852:13: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  origcmaes.cc:2855:12: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  origcmaes.cc:2858:12: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rmalschains.Rcheck/00install.out’ for details.
gimli.16562hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.25389hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.2003hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.9770hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.11918hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.18102hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.21836hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.27827hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.2047hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.9725hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.18002hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
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:
  bgc_hmm.c:241:31: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
  rph_tfbs.c:371:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:351:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:819:5: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rphast.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [5s/15s]
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\", '2018-10-19')"
  y[1]: "CAST(\"x\" AS DATE)"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 276 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
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Depends: includes the non-default packages:
  ‘biwt’ ‘cairoDevice’ ‘fBasics’ ‘gplots’ ‘gWidgets’ ‘gWidgetsRGtk2’
  ‘minerva’ ‘parmigene’ ‘stringr’ ‘snowfall’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Running examples in ‘rstpm2-Ex.R’ failed
The error most likely occurred in:

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

Attaching package: ‘rstpm2’

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

    colon


Error: processing vignette ‘predictnl.Rnw’ failed with diagnostics:
 chunk 3 
Error in UseMethod("predictnl") : 
  no applicable method for ‘predictnl’ applied to an object of class "test"
Execution halted
Found the following significant warnings:
  RngStreams.c:332:4: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rstream.Rcheck/00install.out’ for details.
Found the following significant warnings:
  bgc_hmm.c:241:31: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
  rph_tfbs.c:371:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:351:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:819:5: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rtfbs.Rcheck/00install.out’ for details.
Functions or methods with usage in documentation object 'cellFromXY' but not in code:
  cellFromXY
Found the following significant warnings:
  geometry/s2loop.cc:85:73: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘S2Point’ {aka ‘class Vector3<double>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  geometry/s2loop.cc:247:73: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘S2Point’ {aka ‘class Vector3<double>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  geometry/s2polyline.cc:52:73: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘S2Point’ {aka ‘class Vector3<double>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  geometry/s2polyline.cc:94:73: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘S2Point’ {aka ‘class Vector3<double>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  geometry/s2regioncoverer.cc:119:28: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct S2RegionCoverer::Candidate’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/s2.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/scio.Rcheck/00install.out’ for details.
Found the following significant warnings:
  catnet_rexport.cpp:221:17: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
  catnet_rexport.cpp:229:15: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:237:16: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 0 and 1023 [-Wformat-overflow=]
  catnet_rexport.cpp:240:18: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
  catnet_rexport.cpp:241:17: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:258:17: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:257:18: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/sdnet.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_1_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/sdwd.Rcheck/00install.out’ for details.
Depends: includes the non-default packages:
  ‘hdrcde’ ‘coda’ ‘MASS’ ‘bayesm’ ‘mnormt’ ‘spatstat’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
gimli.3866hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.20652hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
prepare_Rd: maxsel.rd:27-29: Dropping empty section \details
prepare_Rd: transf.inter.rd:23-25: Dropping empty section \details
Found the following significant warnings:
  Warning: 'devtools::use_package' is deprecated.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/spectrolab.Rcheck/00install.out’ for details.
gimli.14714hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
prepare_Rd: H.Binv.Rd:48-50: Dropping empty section \note
prepare_Rd: V.theta.Rd:28-30: Dropping empty section \details
prepare_Rd: V.theta.Rd:43-45: Dropping empty section \note
prepare_Rd: V.theta.Rd:49-51: Dropping empty section \seealso
prepare_Rd: V.theta.Rd:52-53: Dropping empty section \examples
prepare_Rd: confid.int.theta.Rd:62-64: Dropping empty section \note
prepare_Rd: dd.est.Rd:39-41: Dropping empty section \note
prepare_Rd: dd.est.Rd:45-47: Dropping empty section \seealso
prepare_Rd: ell.theta.Rd:60-62: Dropping empty section \note
prepare_Rd: ell.theta.Rd:69-70: Dropping empty section \examples
prepare_Rd: grad.hessinv.Rd:47-49: Dropping empty section \note
prepare_Rd: ks.sporm.Rd:43-45: Dropping empty section \note
prepare_Rd: ks.stat.Rd:39-41: Dropping empty section \note
prepare_Rd: mrle.sporm.Rd:66-68: Dropping empty section \note
prepare_Rd: mrle.sporm.Rd:72-74: Dropping empty section \seealso
prepare_Rd: newton.theta.Rd:47-49: Dropping empty section \note
prepare_Rd: phi.Rd:32-38: Dropping empty section \value
prepare_Rd: phi.Rd:48-50: Dropping empty section \note
prepare_Rd: plotor.Rd:26-32: Dropping empty section \value
prepare_Rd: plotor.Rd:42-44: Dropping empty section \note
prepare_Rd: plotor.Rd:48-50: Dropping empty section \seealso
prepare_Rd: sporm-package.Rd:53-54: Dropping empty section \seealso
prepare_Rd: sporm-package.Rd:55-56: Dropping empty section \examples
prepare_Rd: test.theta.Rd:54-56: Dropping empty section \note
prepare_Rd: elltheta.rd:53-55: Dropping empty section \note
prepare_Rd: elltheta.rd:62-63: Dropping empty section \examples
Found the following significant warnings:
  dbfopenSSN.c:1119:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopenSSN.c:1100:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopenSSN.c:663:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  dbfopenSSN.c:1511:2: warning: ‘strncpy’ output may be truncated copying 11 bytes from a string of length 11 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/SSN.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Quitting from lines 47-52 (staple_example.Rmd) 
Error: processing vignette ‘staple_example.Rmd’ failed with diagnostics:
incorrect number of dimensions
Execution halted
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘statnet’
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘statnet’
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/statnet.Rcheck/00install.out’ for details.
Running examples in ‘steemr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: follower_df
> ### Title: A id list of an id's followers from steemdb.com
> ### Aliases: follower_df
> 
> ### ** Examples
> 
> follower_df()
Error in XML::readHTMLTable(theurl, stringsAsFactors = FALSE)[[1]] : 
  subscript out of bounds
Calls: follower_df
Execution halted
Running examples in ‘stplanr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SpatialLinesNetwork
> ### Title: Create object of class SpatialLinesNetwork or sfNetwork
> ### Aliases: SpatialLinesNetwork
> 
> ### ** Examples
> 
> SLN <- SpatialLinesNetwork(route_network)
> class(SLN)
[1] "SpatialLinesNetwork"
attr(,"package")
[1] "stplanr"
> weightfield(SLN) # field used to determine shortest path
[1] "length"
> plot(SLN)
> points(sln2points(SLN)[1,], cex = 5)
> points(sln2points(SLN)[50,], cex = 5)
> shortpath <- sum_network_routes(SLN, 1, 50, sumvars = "length")
> plot(shortpath, col = "red", lwd = 4, add = TRUE)
> points(sln2points(SLN)[35,], cex = 5)
> shortpath <- sum_network_routes(SLN, 1, 35, sumvars = "length")
> plot(shortpath, col = "red", lwd = 4, add = TRUE)
> library(sf)
Linking to GEOS 3.7.0, GDAL 2.3.2, PROJ 5.2.0
> SLN_sf <- SpatialLinesNetwork(route_network_sf)
> plot(SLN_sf)
> shortpath <- sum_network_routes(SLN_sf, 1, 50, sumvars = "length")
Error: Column `do_union` not found in `.data`
Execution halted
Running examples in ‘structSSI-Ex.R’ failed
The error most likely occurred in:

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

Attaching package: ‘igraph’

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

    decompose, spectrum

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

    union

> library('ape')

Attaching package: ‘ape’

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

    edges, mst, ring

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

Quitting from lines 59-76 (UKgrid_vignette.Rmd) 
Error: processing vignette ‘UKgrid_vignette.Rmd’ failed with diagnostics:
there is no package called 'TSstudio'
Execution halted
Packages suggested but not available for checking: ‘vaers’ ‘vaersND’
Found the following significant warnings:
  include/rapidjson/document.h:1952:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘rapidjson::GenericValue<rapidjson::UTF8<> >::Member’ {aka ‘struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::MemoryPoolAllocator<> >’} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class rapidjson::GenericValue<rapidjson::UTF8<> >’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  include/rapidjson/document.h:1952:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>::Member’ {aka ‘struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::CrtAllocator>’} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/validatejsonr.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/varband.Rcheck/00install.out’ for details.
Running examples in ‘vcr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Cassette
> ### Title: Cassette handler
> ### Aliases: Cassette
> ### Keywords: internal
> 
> ### ** Examples
> 
> library(vcr)
> vcr_configure(dir = tempdir())
<vcr configuration>
  Cassette Dir: /tmp/Rtmp00p8hp
  Record: once
  URI Parser: crul::url_parse
  Match Requests on: method, uri
  Preserve Bytes?: FALSE
  Logging?: FALSE
> 
> res <- Cassette$new(name = "bob")
> res$file()
[1] "/tmp/Rtmp00p8hp/bob.yml"
> res$originally_recorded_at()
[1] "2018-10-19 23:48:46 CEST"
> res$recording()
[1] TRUE
> res$serializable_hash()
$http_interactions
list()

$recorded_with
[1] ‘0.1.0’

> res$eject()
ejecting cassette: bob
CrulAdapter disabled!
HttrAdapter disabled!
Error: Please install 'httr'
Execution halted
Running examples in ‘vegdata-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: isc
> ### Title: Indicate site conditions with community weighted mean values of
> ###   traits or with mode of gradient classes (sum of species amplitudes).
> ### Aliases: isc showindiplot
> ### Keywords: misc
> 
> ### ** Examples
> 
> db <- 'elbaue'
> veg <- tv.veg(db, cover.transform='sqrt', check.critical = FALSE)

No Turbowin installation path found. 

############################################################
Turboveg root directory is set to "/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/vegdata/tvdata"
If you want to change this use: options(tv_home="<path_to_your_Turbowin_root>")
############################################################
Reading tvabund.dbf
Taxonomic reference list:  GermanSL 1.3 
Original number of names: 53 
Taxonomic reference list file /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/vegdata/tvdata/Species/GermanSL 1.3/tax.dbf does not exist.

Taxonomic list (tax.dbf) of reflistGermanSL 1.3 not available.


trying URL 'https://germansl.infinitenature.org/GermanSL/1.3/GermanSL.zip'
Content type 'application/zip' length 3092316 bytes (2.9 MB)
==================================================
downloaded 2.9 MB

Warning in unzip(tfile, exdir = file.path(tv_home, "Species")) :
  error -1 in extracting from zip file
Error in load.taxlist(refl = refl, detailed = TRUE, ...) : 
  Reference list file /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/vegdata/tvdata/Species/GermanSL 1.3/tax.dbf does not exist.
Calls: tv.veg -> taxval -> load.taxlist
Execution halted
Running examples in ‘WaterML-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AddSites
> ### Title: AddSites
> ### Aliases: AddSites
> ### Keywords: waterml
> 
> ### ** Examples
> 
> user <- "admin"
> pass <- "password"
> server <- "http://worldwater.byu.edu/app/index.php/default/services/cuahsi_1_1.asmx"
> #make random site codes
> random_codes = sprintf("%04d",sample(1:10000, 2))
> random_names = paste("R","Upload", random_codes)
> random_lats = runif(2, 35.0, 49.0) #two random latitudes inside U.S
> random_lons = runif(2, -110.0, -70.0) #random longitudes inside U.S
> my_sites <- data.frame(SiteCode=random_codes, SiteName=random_names,
+                        Latitude=random_lats, Longitude=random_lons)
> 
> added_sites <- AddSites(server, username=user, password=pass, sites=my_sites)
[1] "{\n \"user\": \"admin\",\n\"password\": \"password\",\n\"SourceID\":      1,\n\"SiteCode\": \"2656\",\n\"SiteName\": \"R Upload 2656\",\n\"Latitude\":  43.02,\n\"Longitude\": -101.93,\n\"SiteType\": \"Atmosphere\",\n\"Elevation_m\":      0,\n\"State\": \"a\",\n\"County\": \"a\",\n\"Comments\": \"a\" \n}"
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Recv failure: Connection timed out
Calls: AddSites ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
Found the following significant warnings:
  tabix/razf.c:188:2: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/WhopGenome.Rcheck/00install.out’ for details.
Found the following significant warnings:
  libxlsxwriter/xmlwriter.c:156:17: warning: ‘strncat’ specified bound 5 equals source length [-Wstringop-overflow=]
  libxlsxwriter/xmlwriter.c:160:17: warning: ‘strncat’ specified bound 4 equals source length [-Wstringop-overflow=]
  libxlsxwriter/xmlwriter.c:164:17: warning: ‘strncat’ specified bound 4 equals source length [-Wstringop-overflow=]
  libxlsxwriter/xmlwriter.c:168:17: warning: ‘strncat’ specified bound 6 equals source length [-Wstringop-overflow=]
  libxlsxwriter/xmlwriter.c:198:17: warning: ‘strncat’ specified bound 5 equals source length [-Wstringop-overflow=]
  libxlsxwriter/xmlwriter.c:202:17: warning: ‘strncat’ specified bound 4 equals source length [-Wstringop-overflow=]
  libxlsxwriter/xmlwriter.c:206:17: warning: ‘strncat’ specified bound 4 equals source length [-Wstringop-overflow=]
  tmpfileplus/tmpfileplus.c:172:3: warning: ‘strncpy’ specified bound 4097 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/writexl.Rcheck/00install.out’ for details.
Running ‘test-all.R’ [18s/29s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > test_check("zoon")
  Loading required package: zoon
  Loading required package: raster
  Loading required package: sp
  ── 1. Failure: Expected errors (@testTransformCRS.R#39)  ───────────────────────
  `workflow(...)` did not throw an error.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 237 SKIPPED: 30 FAILED: 1
  1. Failure: Expected errors (@testTransformCRS.R#39) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/abn.Rcheck/00install.out’ for details.
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    R  14.4Mb
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.

Attaching package: 'lubridate'

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

    date


Attaching package: 'dplyr'

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

    intersect, setdiff, union

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 object is masked from 'package:stats':

    filter

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

    layout

Quitting from lines 91-93 (ActisoftR.Rmd) 
Error: processing vignette 'ActisoftR.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
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
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 66-67 (ahn.Rmd) 
Error: processing vignette 'ahn.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    help   5.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 39-73 (antaresH5.Rmd) 
Error: processing vignette 'antaresH5.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Package suggested but not available for checking: ‘kebabs’
Error in re-building vignettes:
  ...

Attaching package: 'apcluster'

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

    heatmap

Quitting from lines 387-408 (apcluster.Rnw) 
Error: processing vignette 'apcluster.Rnw' failed with diagnostics:
object 'apres2c' not found
Execution halted
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’
Package suggested but not available for checking: ‘MonetDBLite’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    help   1.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.1Mb
    extdata   3.8Mb
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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 51-52 (use-ballr.Rmd) 
Error: processing vignette 'use-ballr.Rmd' failed with diagnostics:
Timeout was reached: Resolving timed out after 10000 milliseconds
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/BANOVA.Rcheck/00install.out’ for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    2.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: survival
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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 46-49 (v01-introduction.Rmd) 
Error: processing vignette 'v01-introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Warning in block_exec(params) :
  failed to tidy R code in chunk <unnamed-chunk-8>
reason: Error in loadNamespace(name) : there is no package called 'formatR'
Installation failed.
See ‘/home/ripley/R/packages/tests32/bayesdfa.Rcheck/00install.out’ for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/BayesFM.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/ripley/R/packages/tests32/bayesLopod.Rcheck/00install.out’ for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.3Mb
    libs   1.7Mb
Package suggested but not available for checking: ‘rstanarm’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   4.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 2-14 (./children/SETTINGS-knitr.txt) 
Quitting from lines NA-14 (./children/SETTINGS-knitr.txt) 
Error: processing vignette 'graphical-ppcs.Rmd' failed with diagnostics:
object 'params' not found
Execution halted
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R         1.0Mb
    data      1.1Mb
    extdata   1.9Mb
Running ‘testthat.R’ [20s/39s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bcgam)
  Loading required package: nimble
  nimble version 0.6-12 is loaded.
  For more information on NIMBLE and a User Manual,
  please visit http://R-nimble.org.
  
  Attaching package: 'nimble'
  
  The following object is masked from 'package:stats':
  
      simulate
  
  > 
  > test_check("bcgam")
  thin = 1: tau, betalpha, sigma, eta
  ── 1. Error: (unknown) (@testthat.R#3)  ────────────────────────────────────────
  Failed to create the shared library
  1: bcgam(income ~ sm.incr(prestige, space = "E") + sm.conv(education) + type, data = duncan) at testthat/testthat.R:3
  2: bcgam.fit(y, xmat0, shapes0, zmat, nums0, ks0, sps0, nloop, burnin, family, xmatnms0, 
         znms)
  3: compileNimble(gaus)
  4: project$compileModel(units[[i]], control = control, showCompilerOutput = showCompilerOutput)
  5: cppProj$compileFile(compileList, showCompilerOutput)
  6: compileDynamicRegistrations(showCompilerOutput = showCompilerOutput)
  7: compileStaticCode(dllName, cppName, showCompilerOutput)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@testthat.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Warning in predictExtrapUp(alpha, lambda, beta, predictPositionsRescaled[depthIndRange],  :
  Unable to find suitable chronologies for top of core - truncated to date of extraction
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.7Mb
Package suggested but not available for checking: ‘BRugs’
Installation failed.
See ‘/home/ripley/R/packages/tests32/beanz.Rcheck/00install.out’ for details.
installed size is 136.9Mb
  sub-directories of 1Mb or more:
    include  136.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: 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]="./webshot2dddfad645a.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot2dddfad645a.png': No such file or directory
Quitting from lines 244-247 (analysis.Rmd) 
Error: processing vignette 'analysis.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package unavailable to check Rd xrefs: ‘bigrquery’
Running examples in ‘BigQuic-Ex.R’ failed
The error most likely occurred in:

> ### Name: BigQuic
> ### Title: Big Quadratic Inverse Covariance Estimation
> ### Aliases: BigQuic
> ### Keywords: BigQUIC package covariance regularization graphical model
> ###   lasso Newton coordinate descent
> 
> ### ** Examples
> 
> lambda <- 0.91
> exampleResult <- BigQuic(inputFileName = paste(path.package("BigQuic"), 
+                          "/extdata/testInput", sep = ""), 
+                          outputFileName = tempfile(pattern = 
+                          "BigQuic_output_matrix", fileext = ".Bmat"),
+                          lambda = lambda, numthreads = 1, memory_size = 512, 
+                          seed = 1, use_ram = TRUE)

 *** caught segfault ***
address 648, cause 'memory not mapped'

Traceback:
 1: BigQuicHelper(argvPasser = c("-l", lambda[i], "-n", numthreads,     "-t", maxit, "-e", epsilon, "-k", k, "-m", memory_size, "-q",     verbose, "-r", isnormalized, inputFileName, outputFileName))
 2: BigQuic(inputFileName = paste(path.package("BigQuic"), "/extdata/testInput",     sep = ""), outputFileName = tempfile(pattern = "BigQuic_output_matrix",     fileext = ".Bmat"), lambda = lambda, numthreads = 1, memory_size = 512,     seed = 1, use_ram = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Package suggested but not available for checking: ‘sodium’
Installation failed.
See ‘/home/ripley/R/packages/tests32/bigrquery.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [47s/117s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bikedata)
  Data for London, U.K. powered by TfL Open Data:
    Contains OS data Ⓒ Crown copyright and database rights 2016
  Data for New York City provided and owned by:
    NYC Bike Share, LLC and Jersey City Bike Share, LLC ("Bikeshare")
    see https://www.citibikenyc.com/data-sharing-policy
  Data for Washington DC (Captialbikeshare), Chiago (Divvybikes) and Boston (Hubway)
    provided and owned by Motivate International Inc.
    see https://www.capitalbikeshare.com/data-license-agreement
    and https://www.divvybikes.com/data-license-agreement
    and https://www.thehubway.com/data-license-agreement
  Nice Ride Minnesota license  https://www.niceridemn.org/data_license
  > 
  > test_check("bikedata")
  ── 1. Failure: dl_bikedata la (@test-download-data.R#88)  ──────────────────────
  `dl_bikedata(city = "la", data_dir = tempdir(), dates = 2016)` produced unexpected messages.
  Expected match: All data files already exist
  Actual values:
  * Downloading metro-bike-share-trips-2016-q4.csv.zip
  
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 136 SKIPPED: 2 FAILED: 1
  1. Failure: dl_bikedata la (@test-download-data.R#88) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 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.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 64-67 (BioCircos.Rmd) 
Error: processing vignette 'BioCircos.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    extdata   7.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 48-51 (BioInstaller.Rmd) 
Error: processing vignette 'BioInstaller.Rmd' failed with diagnostics:
there is no package called 'webshot'
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: cons memory exhausted (limit reached?)
Execution halted
Error in re-building vignettes:
  ...
Loading required package: rtkore
Loading required package: Rcpp

Attaching package: ‘rtkore’

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

    LdFlags

blockcluster version 4.3.2 loaded

----------------
Copyright (C)  <MODAL team @INRIA,Lille & U.M.R. C.N.R.S. 6599 Heudiasyc, UTC>
Please post questions and bugs at: <https://gforge.inria.fr/forum/forum.php?forum_id=11190&group_id=3679>
Running 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 ff55b778, 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 ...
Installation failed.
See ‘/home/ripley/R/packages/tests32/bmlm.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/ripley/R/packages/tests32/BMSC.Rcheck/00install.out’ for details.
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
Error in re-building vignettes:
  ...
Warning 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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Package unavailable to check Rd xrefs: ‘breathteststan’
Installation failed.
See ‘/home/ripley/R/packages/tests32/breathteststan.Rcheck/00install.out’ for details.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R     3.8Mb
    doc   2.7Mb
Packages suggested but not available for checking: ‘rstanarm’ ‘glmmADMB’
Package unavailable to check Rd xrefs: ‘rstanarm’
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    bin    3.1Mb
    doc    1.3Mb
    libs   3.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'c3'

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

    %>%

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

    grid, legend

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot19437beb4fbc.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot19437beb4fbc.png': No such file or directory
Quitting from lines 56-65 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package which this enhances but not available for checking: ‘FastRWeb’
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R        1.3Mb
    data     1.8Mb
    models   2.5Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
CAST                   package:CAST                    R Documentation

'_c_a_r_e_t' _A_p_p_l_i_c_a_t_i_o_n_s _f_o_r _S_p_a_t_i_a_l-_T_e_m_p_o_r_a_l _M_o_d_e_l_s

_D_e_s_c_r_i_p_t_i_o_n:

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

_D_e_t_a_i_l_s:

     'caret' Applications for Spatio-Temporal models

_A_u_t_h_o_r(_s):

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


PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot1c3b68765519.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot1c3b68765519.png': No such file or directory
Quitting from lines 65-73 (CAST-intro.Rmd) 
Error: processing vignette 'CAST-intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running examples in ‘cdcfluview-Ex.R’ failed
The error most likely occurred in:

> ### Name: age_group_distribution
> ### Title: Age Group Distribution of Influenza Positive Tests Reported by
> ###   Public Health Laboratories
> ### Aliases: age_group_distribution
> 
> ### ** Examples
> 
> 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
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
Package suggested but not available for checking: ‘iptools’
Running examples in ‘chillR-Ex.R’ failed
The error most likely occurred in:

> ### Name: getClimateWizardData
> ### Title: Extract climate data from the ClimateWizard database
> ### Aliases: getClimateWizardData
> ### Keywords: utility
> 
> ### ** Examples
> 
> 
> getClimateWizardData(coordinates=c(longitude=10.613975,latitude=34.933439),
+   scenario="historical",
+   start_year=1970,
+   end_year=2000,
+   metric=c("CD18","R02"),
+   GCMs=c("bcc-csm1-1","BNU-ESM"))
Error in open.connection(con, "rb") : 
  Timeout was reached: Resolving timed out after 10000 milliseconds
Calls: getClimateWizardData ... fromJSON_string -> parseJSON -> parse_con -> open -> open.connection
Execution halted
Running examples in ‘ChocoLattes-Ex.R’ failed
The error most likely occurred in:

> ### Name: make_productions_page
> ### Title: Generate HTML page with productions list and summary chart
> ### Aliases: make_productions_page
> 
> ### ** Examples
> 
> 
> # Load example data and convert it to a lattes list
> CV.dir <- system.file("extdata", package="ChocoLattes")
> 
> # Define the aliases of authors "Felipe Campelo" and "Lucas S. Batista":
> # (all aliases will be converted to the first name provided for each author)
> my.aliases <- list(c("Felipe Campelo",
+                      "Felipe Campelo Franca Pinto",
+                      "Felipe Campelo F. Pinto",
+                      "F.C.F. Pinto"),
+                    c("Lucas S. Batista",
+                      "Lucas Batista",
+                      "Lucas de Souza Batista",
+                      "Lucas Souza Batista"))
> 
> lattes.list <- lattes_to_list(CV.dir         = CV.dir,
+                               author.aliases = my.aliases)
> 
> 
> # Build productions page:
> make_productions_page(lattes.list,
+                       chart.type     = "ggplot2",
+                       h1.title       = "ORCS Lab",
+                       h2.title       = "UFMG, Brazil",
+                       language       = "EN")
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    help   1.2Mb
Package suggested but not available for checking: ‘rggobi’
Running ‘testthat.R’ [32s/36s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(classiFunc)
  > 
  > test_check("classiFunc")
  ── 1. Failure: computeDistMat works rucrdtw metrics (@test_computeDistMat.R#100)
  all(as.vector(dist1) <= as.vector(dist3)) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 834 SKIPPED: 0 FAILED: 1
  1. Failure: computeDistMat works rucrdtw metrics (@test_computeDistMat.R#100) 
  
  Error: testthat unit tests failed
  Execution halted
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 404-417 (the_clusterR_package.Rmd) 
Error: processing vignette 'the_clusterR_package.Rmd' failed with diagnostics:
std::bad_alloc
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
    pdf   2.8Mb
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.
Quitting from lines 100-105 (Running-CoDiNA.Rmd) 
Error: processing vignette 'Running-CoDiNA.Rmd' failed with diagnostics:
Saving a widget with selfcontained = TRUE requires pandoc. For details see:
https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
Execution halted
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
Package suggested but not available for checking: ‘rscala’
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.
Installation failed.
See ‘/home/ripley/R/packages/tests32/conStruct.Rcheck/00install.out’ for details.
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$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 176-178 (Extending-cooccurNet.Rmd) 
Error: processing vignette 'Extending-cooccurNet.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
Execution halted
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    R     2.3Mb
    doc   7.4Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/coxrt.Rcheck/00install.out’ for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   6.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 77-78 (cranly.Rmd) 
Error: processing vignette 'cranly.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/csp.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/ripley/R/packages/tests32/ctsem.Rcheck/00install.out’ for details.
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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required namespace: rmarkdown
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 142-152 (truncated_tesseract.Rmd) 
Error: processing vignette 'truncated_tesseract.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 177-179 (cycling_data_analysis.Rmd) 
Error: processing vignette 'cycling_data_analysis.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 27-38 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  5.2Mb
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    img   4.7Mb
installed size is  5.2Mb
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    Pied_Flycatchers_1   2.5Mb
    Pied_Flycatchers_2   1.3Mb
    doc                  1.2Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    java  15.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
sh: whoami:  not found
sh: git:  not found
sh: git:  not found
Data report generation is finished. Please wait while your output file is being rendered.
Quitting from lines 729-768 (extending_dataMaid.Rmd) 
Error: processing vignette 'extending_dataMaid.Rmd' failed with diagnostics:
pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 26-34 (get_started.Rmd) 
Error: processing vignette 'get_started.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  5.1Mb
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    doc    1.3Mb
    libs   2.7Mb
Error in re-building vignettes:
  ...
Warning in engine$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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 512-515 (data.tree.Rmd) 
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Package suggested but not available for checking: ‘RPostgres’
installed size is  6.9Mb
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    data   5.4Mb
installed size is  5.7Mb
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    sample_data   3.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'gridExtra'

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

    combine

Quitting from lines 84-97 (MultiObjectiveDecisionAnalysisinR.Rmd) 
Error: processing vignette 'MultiObjectiveDecisionAnalysisinR.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Running ‘testthat.R’ [92s/117s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(DeclareDesign)
  Loading required package: randomizr
  Loading required package: fabricatr
  Loading required package: estimatr
  > 
  > test_check("DeclareDesign")
  ── 1. Failure: error if you try to draw POs at a level using a variable that doe
  `my_potential_outcomes_formula(pop)` did not throw an error.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 436 SKIPPED: 1 FAILED: 1
  1. Failure: error if you try to draw POs at a level using a variable that doesn't exist at that level (@test-potential-outcomes.R#160) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.1Mb
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Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Joining, by = "key"
Joining, by = "key"
Quitting from lines 102-122 (sjukhus.Rmd) 
Error: processing vignette 'sjukhus.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/DeLorean.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

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

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

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

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


Attaching package: 'dendextend'

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

    cutree

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

Attaching package: 'gplots'

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

    bluered, greenred

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

    lowess

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 931-933 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    1.9Mb
    help   1.4Mb
Packages which this enhances but not available for checking:
  ‘gurobi’ ‘Rcplex’ ‘Rmosek’ ‘Rsymphony’
Installation failed.
See ‘/home/ripley/R/packages/tests32/dfpk.Rcheck/00install.out’ for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   6.4Mb
installed size is  5.0Mb
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    data   3.5Mb
    doc    1.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: rgl
Loading required namespace: rmarkdown
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 230-234 (DGVM3D.Rmd) 
Error: processing vignette 'DGVM3D.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘rsvg’
installed size is  5.0Mb
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    htmlwidgets   3.3Mb
installed size is  9.6Mb
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    doc   9.5Mb
installed size is  6.7Mb
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    doc   5.7Mb
installed size is  6.8Mb
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    doc   6.0Mb
installed size is 15.3Mb
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    include  15.1Mb
installed size is  5.1Mb
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    R      1.5Mb
    data   2.1Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/DMMF.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   2.9Mb
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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Using constraints: b = 1
Using constraints: b = 1
Running default monotherapy fitting. Note that if constraints are needed, run mono fitting manually first
Using constraints: b = 1
Using constraints: b = 1
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot30c22fe133f9.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot30c22fe133f9.png': No such file or directory
Quitting from lines 357-358 (userGuide.Rmd) 
Error: processing vignette 'userGuide.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    media       2.7Mb
    shinyapps   3.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    lucc_MT   3.4Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/DynamicGP.Rcheck/00install.out’ for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    doc    1.6Mb
    libs   1.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include   -KPIC  -O -xlibmieee -xlibmil -xtarget=native -nofstore  -c LinearSDE.c -o LinearSDE.o
cc -xc99 -G -L/usr/local/lib -o LinearSDE.so LinearSDE.o -L/usr/local/lib -lgsl -lgslcblas -lm
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'LinearDiscreteTimeModels.tex' failed.
Messages:
/usr/local/bin/texi2dvi: line 411:  4998 Killed                  "$@" 2>&5 1>&2
/usr/local/bin/texi2dvi: biber failed
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘EasyMx-Ex.R’ failed
The error most likely occurred in:

> ### Name: emxCholeskyComponent
> ### Title: Creates component for a Cholesky Model
> ### Aliases: emxCholeskyComponent
> 
> ### ** Examples
> 
>    
> # Create an ACE model in 22 lines
> require(EasyMx)
> require(OpenMx)
> data(twinData)
> twinVar = names(twinData)
> selVars <- c('ht1', 'bmi1','ht2','bmi2')
> mzdzData <- subset(twinData, zyg %in% c(1, 3), c(selVars, 'zyg'))
> mzdzData$RCoef <- c(1, NA, .5)[mzdzData$zyg]
> nVar = length(selVars)/2
> x <- paste0('x', 1:nVar)
> 
> acomp <- emxCholeskyComponent(x, 'A', hvalues=c(1, .5, 1), hlabels=c(NA, 'data.RCoef', NA))
> ccomp <- emxCholeskyComponent(x, 'C', hvalues=c(1, 1, 1))
> ecomp <- emxCholeskyComponent(x, 'E', hvalues=c(1, 0, 1))
> totalVar <- mxAlgebra(AKron + CKron + EKron, 'V', dimnames=list(selVars, selVars))
> totalMean <- emxMeans(selVars, type='twin')
> expect <- mxExpectationNormal(totalVar$name, totalMean$name)
> fitfun <- mxFitFunctionML()
> 
> comlist <- c(acomp, ccomp, ecomp, list(totalVar, totalMean, expect, fitfun))
> 
> model <- mxModel('model', comlist, mxData(mzdzData, 'raw'))
> run2 <- mxRun(model)
Running model with 11 parameters

 *** caught segfault ***
address 10, cause 'memory not mapped'

Traceback:
 1: runHelper(model, frontendStart, intervals, silent, suppressWarnings,     unsafe, checkpoint, useSocket, onlyFrontend, useOptimizer)
 2: mxRun(model)
An irrecoverable exception occurred. R is aborting now ...
installed size is  7.7Mb
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    htmlwidgets   3.3Mb
installed size is  5.6Mb
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    data   1.3Mb
    hac    4.3Mb
installed size is  6.5Mb
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    data   5.0Mb
    doc    1.3Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/eggCounts.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: foreign
This is vegdata 0.9.3

No Turbowin installation path found. 

############################################################
Turboveg root directory is set to "/home/ripley/R/Lib32/vegdata/tvdata"
If you want to change this use: options(tv_home="<path_to_your_Turbowin_root>")
############################################################
Quitting from lines 51-61 (eHOF.Rnw) 
Error: processing vignette 'eHOF.Rnw' failed with diagnostics:
unsupported conversion from 'CP437' to ''
Execution halted
installed size is  5.0Mb
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    examples   4.2Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data  11.5Mb
Package required but not available: ‘rstanarm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    extdata  10.4Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    xsd   5.9Mb
Packages which this enhances but not available for checking:
  ‘glmmADMB’ ‘rstanarm’
Installation failed.
See ‘/home/ripley/R/packages/tests32/EMMIXgene.Rcheck/00install.out’ for details.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.6Mb
installed size is  5.3Mb
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    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
Running ‘testthat.R’ [59s/69s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(envnames)
  > 
  > test_check("envnames")
  
  Environments involved:
  Current environment: <environment: R_GlobalEnv>
  Parent environment of env1: <environment: R_GlobalEnv>
  Parent environment of env2: <environment: R_GlobalEnv>
  Parent environment of env11: <environment: aa3cd18>
  R_GlobalEnv env_of_envs       envir 
       "env2"      "env2"      "env2" 
  correct memory address: <c358a84> 
  observed result: FALSE 
  ── 1. Failure: T21) is_memory_address(): a string obtained as the memory address
  `observed` not equal to `expected`.
  1 element mismatch
  
  Now inside function g 
  Environment name of calling function (using environmentName() function):  ""
  Environment name of calling function as returned by get_fun_calling(): env1$f
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 265 SKIPPED: 14 FAILED: 1
  1. Failure: T21) is_memory_address(): a string obtained as the memory address of an object is identified as a valid memory address (@test-functions.r#109) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    doc    3.4Mb
    help   3.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 150-151 (epicontacts.Rmd) 
Error: processing vignette 'epicontacts.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 117-120 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Packages required but not available: ‘SNPRelate’ ‘gdsfmt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.2Mb
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    doc   6.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.1Mb
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:  not found
Warning in system(command) : error in running command
Error: pandoc document conversion failed with error 127
Execution halted
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    exiftool  14.2Mb
Running ‘testthat.R’ [48s/63s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(exifr)
  Using ExifTool version 11.1
  > 
  > 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     0    0     0    0     0      0      0 --:--:--  0:00:06 --:--:--     0
    0     0    0     0    0     0      0      0 --:--:--  0:00:07 --:--:--     0
  100 2865k  100 2865k    0     0   409k      0  0:00:07  0:00:07 --:--:--  633k
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 43 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
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: Removed 37 rows containing non-finite values (stat_summary).
Warning: Removed 37 rows containing non-finite values (stat_summary).
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: Removed 37 rows containing non-finite values (stat_summary).
Warning: Removed 37 rows containing non-finite values (stat_summary).
Warning: Removed 37 rows containing non-finite values (stat_summary).
Warning: Removed 37 rows containing non-finite values (stat_summary).
Warning: Removed 37 rows containing non-finite values (stat_summary).
Warning: Removed 37 rows containing non-finite values (stat_summary).
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in make_onset_data(response_window_clean, onset_time = 15500, fixation_window_length = 1,  :
  Very few trials have a legitimate first AOI! Possible incorrect onset time?
Warning in max(SwitchAOI) :
  no non-missing arguments to max; returning -Inf
Warning in min(SwitchAOI) :
  no non-missing arguments to min; returning Inf
Warning in max(df_plot$.Time) :
  no non-missing arguments to max; returning -Inf
Quitting from lines 91-93 (onset_contingent_analysis_vignette.Rmd) 
Error: processing vignette 'onset_contingent_analysis_vignette.Rmd' failed with diagnostics:
replacement has 1 row, data has 0
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Creating package 'fakepack' in '/tmp/Rtmpkaaq5v'
No DESCRIPTION found. Creating with values:


Prerequisite DESCRIPTION found.
Prerequisite R/throw.R found.
Prerequisite R/throw.R found.
Prerequisite R/throw.R found.
Prerequisite R/throw.R found.
* installing *source* package ‘fakepack’ ...
** R
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  ‘fakepack’ 
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (fakepack)
Prerequisite R/throw.R found.
Prerequisite R/throw.R found.
Prerequisite DESCRIPTION found.
Prerequisite R/throw.R found.
Error: processing vignette 'An_Introduction_to_fakemake.Rmd' failed with diagnostics:
there is no package called 'spelling'
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
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Package suggested but not available for checking: ‘Rserve’
Installation failed.
See ‘/home/ripley/R/packages/tests32/FastRWeb.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/ripley/R/packages/tests32/fclust.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [11s/108s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(FedData)
  Loading required package: sp
  > 
  > test_check("FedData")
  ── 1. Error: The SSURGO inventory dataset is available at the correct URL (@test
  Timeout was reached: Operation timed out after 10336 milliseconds with 0 out of 0 bytes received
  1: expect_false(suppressWarnings(httr::http_error(url))) at testthat/test.SSURGO.R:8
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: suppressWarnings(httr::http_error(url))
  5: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  6: httr::http_error(url)
  7: http_error.character(url)
  8: http_error(HEAD(x, ...))
  9: HEAD(x, ...)
  10: request_perform(req, hu$handle$handle)
  11: request_fetch(req$output, req$url, handle)
  12: request_fetch.write_memory(req$output, req$url, handle)
  13: curl::curl_fetch_memory(url, handle = handle)
  
  ── 2. Failure: The SSURGO datasets are available at the correct URL (@test.SSURG
  `suppressWarnings(curl::curl(url) %>% readLines(n = 1))` threw an error.
  Message: Timeout was reached: Operation timed out after 10000 milliseconds with 0 out of 0 bytes received
  Class:   simpleError/error/condition
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 23 SKIPPED: 1 FAILED: 2
  1. Error: The SSURGO inventory dataset is available at the correct URL (@test.SSURGO.R#8) 
  2. Failure: The SSURGO datasets are available at the correct URL (@test.SSURGO.R#32) 
  
  Error: testthat unit tests failed
  Execution halted
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Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Warning: Removed 2 rows containing missing values (geom_point).
Quitting from lines 137-146 (quick_charts.Rmd) 
Error: processing vignette 'quick_charts.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
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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
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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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 168-169 (formattable-data-frame.Rmd) 
Error: processing vignette 'formattable-data-frame.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  6.3Mb
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    R      1.0Mb
    libs   4.7Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/freetypeharfbuzz.Rcheck/00install.out’ for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R   5.8Mb
installed size is  8.1Mb
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    data   4.9Mb
    doc    2.1Mb
Package unavailable to check Rd xrefs: ‘RMark’
Packages suggested but not available for checking: ‘RWeka’ ‘FSelector’
Package unavailable to check Rd xrefs: ‘FSelector’
installed size is  5.4Mb
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    examples   4.6Mb
installed size is 16.4Mb
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Error in re-building vignettes:
  ...
Warning in engine$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 604-605 (futureheatwaves.Rmd) 
Error: processing vignette 'futureheatwaves.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  5.4Mb
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    doc   3.4Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/gastempt.Rcheck/00install.out’ for details.
installed size is  5.4Mb
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    libs      1.9Mb
Error in re-building vignettes:
  ...
Warning in packageDescription("gputools") :
  no package 'gputools' was found
Error: processing vignette 'gcbd.Rnw' failed with diagnostics:
at gcbd.Rnw:860, subscript out of bounds
Execution halted
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Package suggested but not available for checking: ‘reactome.db’
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    extdata   1.4Mb
installed size is  5.4Mb
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Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: spam
Loading required package: dotCall64
Loading required package: grid
Spam version 2.2-0 (2018-06-19) 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) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
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 open.connection(x, "rb") : 
  Timeout was reached: Operation timed out after 10000 milliseconds with 0 out of 0 bytes received
Calls: download_codebook -> read_html -> read_html.default
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 22-24 (gesis.Rmd) 
Error: processing vignette 'gesis.Rmd' failed with diagnostics:
Timeout was reached: Operation timed out after 10000 milliseconds with 0 out of 0 bytes received
Execution halted
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    R           1.1Mb
    doc         2.8Mb
    tutorials   1.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra

Attaching package: 'ggiraphExtra'

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

    addLabelDf, getMapping

Loading required package: plyr
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 45-49 (ggPredict.Rmd) 
Error: processing vignette 'ggPredict.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
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Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 125-126 (ggseas.Rmd) 
Error: processing vignette 'ggseas.Rmd' failed with diagnostics:
Process terminated
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 36-39 (ggspatial.Rmd) 
Error: processing vignette 'ggspatial.Rmd' failed with diagnostics:
object 'DEPTH.M' not found
Execution halted
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    help   2.5Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/gifski.Rcheck/00install.out’ for details.
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
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 34-35 (installation-and-authentication.Rmd) 
Error: processing vignette 'installation-and-authentication.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
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    doc    4.3Mb
Running ‘testthat.R’ [66s/120s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > library(gppm)
  Loading required package: Rcpp
  > 
  > test_check("gppm")
  Error in compileCode(f, code, language = language, verbose = verbose) : 
    Compilation ERROR, function(s)/method(s) not created! In file included from /tmp/Rtmp5zaam1/RLIBS_6a601c4a7ebc/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                   from /tmp/Rtmp5zaam1/RLIBS_6a601c4a7ebc/BH/include/boost/shared_ptr.hpp:17,
                   from /home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/fun/LDLT_factor.hpp:7,
                   from /home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/err/check_ldlt_factor.hpp:6,
                   from /home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat.hpp:33,
                   from /home/ripley/R/Lib32/StanHeaders/include/stan/math/rev/mat.hpp:12,
                   from /home/ripley/R/Lib32/StanHeaders/include/stan/math.hpp:4,
                   from /home/ripley/R/Lib32/StanHeaders/include/src/stan/model/model_header.hpp:4,
                   from file26332f6f7f54.cpp:8:
  /tmp/Rtmp5zaam1/RLIBS_6a601c4a7ebc/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<clas
  Calls: test_check ... cxxfunctionplus -> <Anonymous> -> cxxfunction -> compileCode
  In addition: Warning message:
  In system(cmd, intern = !verbose) :
    running command '/home/ripley/R/gcc/bin/R CMD SHLIB file26332f6f7f54.cpp 2> file26332f6f7f54.cpp.err.txt' had status 1 and error message 'Illegal seek'
  Execution halted
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  sub-directories of 1Mb or more:
    R  25.9Mb
Package suggested but not available for checking: ‘Sxslt’
installed size is  6.5Mb
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    data   6.4Mb
installed size is  5.9Mb
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    R     1.3Mb
    doc   4.4Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Error: processing vignette 'getting_started.Rmd' failed with diagnostics:
invalid multibyte string at '<f0><9f><8c><9f> the repo on GitHub! </li>
<li>If you&#39;re looking to contribute, check out the <a href="https://github.com/h2oai/h2o4gpu/blob/master/CONTRIBUTING.md">CONTRIBUTING.md</a> file.</li>
<li>All open issues that are specific to the R package are <a href="https://github.com/h2oai/h2o4gpu/labels/R">here</a>.</li>
<li>All open issues are <a href="https://github.com/h2oai/h2o4gpu/issues?utf8=%E2%9C%93&amp;q=is%3Aopen">here</a>.</li>
</ul>

<h2>Installation</h2>

<p>The Python package is a prerequisite for the R package. So first, follow the instructions <a href="https://github.com/h2oai/h2o4gpu#installation">here</a> to install the <strong>h2o4gpu</strong> Python package (either at the system level or in a Python virtual envivonment). The easiest thing to do is to <code>pip install</code> either the stable or bleeding edge <code>whl</code> file. To ensure compatibility, the Python pa
Execution halted
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    java  130.7Mb
installed size is 10.0Mb
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Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 335-344 (haplor-vignette.Rmd) 
Error: processing vignette 'haplor-vignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 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:197:17: warning: passing argument 2 of ‘libiconv’ from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/ripley/R/packages/tests32/haven.Rcheck/00install.out’ for details.
Running examples in ‘hdf5r-Ex.R’ failed
The error most likely occurred in:

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

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

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

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

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

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

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

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

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

    error #004: H5FDsec2.c in H5FD_sec2_lock(): line 941: unable to lock file, errno = 14, error message = 'Bad address'
        class: HDF5
        major: File accessibilty
        minor: Bad file ID accessed
Execution halted
installed size is  5.1Mb
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    doc   4.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: plotly
Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Loading required package: viridis
Loading required package: viridisLite

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

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

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

Quitting from lines 88-90 (heatmaply.Rmd) 
Error: processing vignette 'heatmaply.Rmd' failed with diagnostics:
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Execution halted
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Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Highcharts (www.highcharts.com) is a Highsoft software product which is
not free for commercial and Governmental use
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.
installed size is  5.8Mb
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    doc   4.3Mb
installed size is  6.4Mb
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    R     2.1Mb
    doc   2.6Mb
installed size is 15.1Mb
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    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
Package required but not available: ‘FSelector’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
Running examples in ‘IAPWS95-Ex.R’ failed
The error most likely occurred in:

> ### Name: TDh
> ### Title: Temperature, Function of Density and Enthalpy
> ### Aliases: TDh
> 
> ### ** Examples
> 
> D <- 838.025
> h <- 977.181624
> T_Dh <- TDh(D,h)
installed size is  6.3Mb
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    data   6.2Mb
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    R    14.7Mb
    doc   5.5Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/idealstan.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/ripley/R/packages/tests32/idem.Rcheck/00install.out’ for details.
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 ‘testthat.R’ [482s/294s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # NOTE: This will not test an uninstalled package.
  > library(testthat)
  > test_check('ifaTools')
  Loading required package: ifaTools
  Loading required package: shiny
  Loading required package: ggplot2
  Loading required package: reshape2
  Loading required package: rpf
  Loading required package: parallel
  Loading required package: OpenMx
  To take full advantage of multiple cores, use:
    mxOption(NULL, 'Number of Threads', parallel::detectCores()) #now
    Sys.setenv(OMP_NUM_THREADS=parallel::detectCores()) #before library(OpenMx)
  Welcome to ifaTools!
   Use itemModelExplorer() to explore item models.
   Use modelBuilder() to build an IFA model.
  [1] "/home/ripley/R/packages/tests32/ifaTools.Rcheck/tests/testthat"
  ── 1. Failure: addExploratoryFactors (@test-addExploratoryFactor.R#80)  ────────
  m1$output$fit - m2$output$fit not equal to 115.39.
  1/1 mismatches
  [1] -904995 - 115 == -905110
  
  ── 2. Error: univariatePrior (@test-prior.R#24)  ───────────────────────────────
  Setting improper index (1) from vector of Rf_length 0.
  1: checkAnalyticDeriv(mxModel(univariatePrior("lnorm", "x", 1.1), mxMatrix(nrow = 1, 
         ncol = 1, labels = "x", free = TRUE, name = "par", values = 0.3))) at testthat/test-prior.R:24
  2: mxRun(mxModel(m1, mxComputeSequence(list(mxComputeNumericDeriv(checkGradient = FALSE), 
         mxComputeReportDeriv()))), silent = TRUE) at testthat/test-prior.R:10
  3: runHelper(model, frontendStart, intervals, silent, suppressWarnings, unsafe, checkpoint, 
         useSocket, onlyFrontend, useOptimizer)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 6 SKIPPED: 0 FAILED: 2
  1. Failure: addExploratoryFactors (@test-addExploratoryFactor.R#80) 
  2. Error: univariatePrior (@test-prior.R#24) 
  
  Error: testthat unit tests failed
  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
Package required but not available: ‘tesseract’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    doc       1.2Mb
    extdata   1.2Mb
    include   2.9Mb
    libs      4.9Mb
Running examples in ‘Inflation-Ex.R’ failed
The error most likely occurred in:

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

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

Error in checkX13(fail = TRUE, fullcheck = FALSE, htmlcheck = FALSE) : 
  Process terminated
Calls: INFL.core_tf -> <Anonymous> -> checkX13
Execution halted
Running ‘spelling.R’
  Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(inplace)
  > 
  > test_check("inplace")
  ── 1. Failure: in-place operators work in common cases (@test-operators.R#57)  ─
  `X` not identical to `X2`.
  Objects equal but not identical
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 807 SKIPPED: 0 FAILED: 1
  1. Failure: in-place operators work in common cases (@test-operators.R#57) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   7.7Mb
Running ‘testthat.R’ [3s/97s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ipeaData)
  > 
  > test_check("ipeaData")
  [1] "NA. 05/1999 a 03/2009. Acesso em: 18/10/2018"
  ── 1. Error: ipeaData (@test_functions_ipea_data.R#19)  ────────────────────────
  Recv failure: Connection reset by peer
  1: suppressWarnings(result <- ipeadata("SERIE SEM RETORNO")) at testthat/test_functions_ipea_data.R:19
  2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  3: ipeadata("SERIE SEM RETORNO")
  4: get_metadata(serie)
  5: basic_call(api_call, type)
  6: GET(api)
  7: request_perform(req, hu$handle$handle)
  8: request_fetch(req$output, req$url, handle)
  9: request_fetch.write_memory(req$output, req$url, handle)
  10: curl::curl_fetch_memory(url, handle = handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 6 SKIPPED: 0 FAILED: 1
  1. Error: ipeaData (@test_functions_ipea_data.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    dict  19.5Mb
Package suggested but not available for checking: ‘RProtoBuf’
Running examples in ‘jomo-Ex.R’ failed
The error most likely occurred in:

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

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

Traceback:
 1: jomo.clmm(formula, data, nburn = 2, nbetween = 2, nimp = 2)
An irrecoverable exception occurred. R is aborting now ...
installed size is  5.1Mb
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Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: shiny
Loading required package: shinythemes
Loading required package: plyr
Quitting from lines 37-53 (kgc-fine.Rmd) 
Error: processing vignette 'kgc-fine.Rmd' failed with diagnostics:
cannot allocate vector of size 640.7 Mb
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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
installed size is  6.6Mb
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    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] 12673 - 6336 == 6336
  
  ══ 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
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    data   7.3Mb
installed size is  5.7Mb
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    doc       2.5Mb
    extdata   3.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    2.6Mb
    help   1.2Mb
Running ‘config.R’
  Running ‘testthat.R’
Running the tests in ‘tests/config.R’ failed.
Complete output:
  > mac_dir <- "~/Documents/Rtest/"
  > win_dir <- "C:/Rtest"
  > linux_dir <- "~/Documents/Rtest"
  > 
  > switch(Sys.info()['sysname'],
  +        "Darwin" = {working_dir <- mac_dir},
  +        "Windows" = {working_dir <- win_dir},
  +        "Linux" = {working_dir <- linux_dir})
  > 
  > rds_file_name <- "./ranListSmall.rds"
  > llo_file_name <- "./ranListSmall.llo"
  > repeat_time <- 20
  > original <- FALSE
  > compress <- TRUE
  > 
  > # rds_file_name <- "./ranListMid.rds"
  > # llo_file_name <- "./ranListMid.llo"
  > # repeat_time <- 20
  > # original <- FALSE
  > # compress <- TRUE
  > 
  > options(list(largeList.report.progress = FALSE))
  > 
  > if (dir.exists(working_dir)) {
  +   setwd(working_dir)
  +   if (file.exists(rds_file_name)) {
  +     library(futile.logger)
  +     ready_to_test <- TRUE
  +   } else {
  +     ready_to_test <- FALSE
  +   }
  + } else {
  +   ready_to_test <- FALSE
  + }
  Error in dir.exists(working_dir) : object 'working_dir' not found
  Execution halted
installed size is  5.1Mb
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    doc   5.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 41-42 (Intro_to_lavaanPlot.Rmd) 
Error: processing vignette 'Intro_to_lavaanPlot.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
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    geojson  11.5Mb
installed size is  5.5Mb
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    htmlwidgets   4.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs     24.0Mb
Package required but not available: ‘RWeka’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 272-273 (Understanding_lime.Rmd) 
Error: processing vignette 'Understanding_lime.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 109-112 (linkspotterVignette.Rmd) 
Error: processing vignette 'linkspotterVignette.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
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
Running ‘testthat.R’ [11s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(loo)
  This is loo version 2.0.0.
  **NOTE: As of version 2.0.0 loo defaults to 1 core but we recommend using as many as possible. Use the 'cores' argument or set options(mc.cores = NUM_CORES) for an entire session. Visit mc-stan.org/loo/news for details on other changes.
  
  Attaching package: 'loo'
  
  The following object is masked from 'package:testthat':
  
      compare
  
  > Sys.setenv("R_TESTS" = "")
  > test_check("loo")
  ── 1. Error: (unknown) (@test_psis.R#2)  ───────────────────────────────────────
  there is no package called 'rstanarm'
  1: suppressPackageStartupMessages(library(rstanarm)) at testthat/test_psis.R:2
  2: withCallingHandlers(expr, packageStartupMessage = function(c) invokeRestart("muffleMessage"))
  3: library(rstanarm)
  4: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 341 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_psis.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 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
Running examples in ‘lori-Ex.R’ failed
The error most likely occurred in:

> ### Name: lori
> ### Title: LORI method.
> ### Aliases: lori
> 
> ### ** Examples
> 
> ## Don't show: 
> X <- matrix(rnorm(50), 25)
> Y <- matrix(rpois(25, 1:25), 5)
> res <- lori(Y, X, 10, 10, size=2)
Error in La.svd(x, nu, nv) : error code 3 from Lapack routine 'dgesdd'
Calls: lori -> altmin -> svd -> La.svd
Execution halted
Package suggested but not available for checking: ‘Rsymphony’
Packages suggested but not available for checking: ‘glmmADMB’ ‘rstanarm’
Error in re-building vignettes:
  ...
Warning 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 0.6-3
lavaan is BETA software! Please report any bugs.

Attaching package: ‘lavaan’

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

    vech

> data(HolzingerSwineford1939)
> Data <- HolzingerSwineford1939[,7:15]
> 
> # Measurement model:
> Lambda <- matrix(0, 9, 3)
> Lambda[1:3,1] <- NA
> Lambda[4:6,2] <- NA
> Lambda[7:9,3] <- NA
> 
> # Fit CFA model:
> CFA <- lvnet(Data, lambda = Lambda)
Error: The job for model 'model' exited abnormally with the error message: Incorrect input to omxRowSortHelper: 0 1 0 9
Execution halted
installed size is 12.6Mb
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    TS_files     6.0Mb
    base_files   6.5Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/MADPop.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  ‘av’ ‘rsvg’ ‘tesseract’ ‘gifski’
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
Packages unavailable to check Rd xrefs: ‘rsvg’, ‘tesseract’, ‘gifski’, ‘av’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'rsvg'
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'rsvg'
Quitting from lines 228-237 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
Magick: non-conforming drawing primitive definition `text' @ error/draw.c/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’ [18s/21s]
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 1.18
  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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot509954816360.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot509954816360.png': No such file or directory
Quitting from lines 61-68 (manipulateWidgets.Rmd) 
Error: processing vignette 'manipulateWidgets.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 33.9Mb
  sub-directories of 1Mb or more:
    mapdata  33.8Mb
Error in re-building vignettes:
  ...
Warning in engine$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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 95-100 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
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installed size is  8.1Mb
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Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in (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
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installed size is  8.5Mb
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Installation failed.
See ‘/home/ripley/R/packages/tests32/meanr.Rcheck/00install.out’ for details.
Package required but not available: ‘gdsfmt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.8Mb
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Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: arm
Loading required package: MASS
Loading required package: Matrix
Loading required package: lme4

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

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

Loading required package: dplyr

Attaching package: 'dplyr'

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

    select

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 390-403 (Using_predictInterval.Rmd) 
Error: processing vignette 'Using_predictInterval.Rmd' failed with diagnostics:
there is no package called 'rstanarm'
Execution halted
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Running examples in ‘metaSEM-Ex.R’ failed
The error most likely occurred in:

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

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

Traceback:
 1: runHelper(model, frontendStart, intervals, silent, suppressWarnings,     unsafe, checkpoint, useSocket, onlyFrontend, useOptimizer)
 2: mxRun(mx.model, intervals = FALSE, suppressWarnings = suppressWarnings,     silent = silent, ...)
 3: doTryCatch(return(expr), name, parentenv, handler)
 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5: tryCatchList(expr, classes, parentenv, handlers)
 6: tryCatch(mxRun(mx.model, intervals = FALSE, suppressWarnings = suppressWarnings,     silent = silent, ...), error = function(e) e)
 7: meta(y = ln_OR, v = v_ln_OR, data = BCG, x = cbind(scale(Latitude,     scale = FALSE), scale(Year, scale = FALSE)))
 8: summary(meta(y = ln_OR, v = v_ln_OR, data = BCG, x = cbind(scale(Latitude,     scale = FALSE), scale(Year, scale = FALSE))))
An irrecoverable exception occurred. R is aborting now ...
Installation failed.
See ‘/home/ripley/R/packages/tests32/MetaStan.Rcheck/00install.out’ for details.
installed size is  7.0Mb
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    R      1.3Mb
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    misc   1.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 91-94 (mgwrsar-basic_examples.Rmd) 
Error: processing vignette 'mgwrsar-basic_examples.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mhde_article.tex' failed.
Messages:
/usr/local/bin/texi2dvi: line 411: 27857 Killed                  "$@" 2>&5 1>&2
/usr/local/bin/texi2dvi: biber failed
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running ‘testthat.R’ [140s/129s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mice)
  Loading required package: lattice
  
  Attaching package: 'mice'
  
  The following objects are masked from 'package:base':
  
      cbind, rbind
  
  > 
  > test_check("mice")
  ── 1. Error: (unknown) (@test-D3.R#26)  ────────────────────────────────────────
  NA/NaN/Inf in foreign function call (arg 20)
  1: mitml::panImpute(studentratings, formula = fml, n.burn = 1000, n.iter = 100, m = 5, 
         silent = TRUE) at testthat/test-D3.R:26
  2: pan::pan(gy, subj = gclus, gpred, xcol, zcol, prior, seed = rns[ii + 1, gg], iter = n.iter, 
         start = glast[[gg]])
  
  ── 2. Error: (unknown) (@test-pool.R#125)  ─────────────────────────────────────
  NA/NaN/Inf in foreign function call (arg 20)
  1: mitml::panImpute(studentratings, formula = fml, n.burn = 1000, n.iter = 100, m = 5, 
         silent = TRUE) at testthat/test-pool.R:125
  2: pan::pan(gy, subj = gclus, gpred, xcol, zcol, prior, seed = rns[ii + 1, gg], iter = n.iter, 
         start = glast[[gg]])
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 277 SKIPPED: 0 FAILED: 2
  1. Error: (unknown) (@test-D3.R#26) 
  2. Error: (unknown) (@test-pool.R#125) 
  
  Error: testthat unit tests failed
  Execution halted
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
Error in re-building vignettes:
  ...
*** This is beta software. Please report any bugs!
*** See the NEWS file for recent changes.
Loading required package: Matrix
Quitting from lines 65-67 (Analysis.Rmd) 
Error: processing vignette 'Analysis.Rmd' failed with diagnostics:
NA/NaN/Inf in foreign function call (arg 20)
Execution halted
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Running ‘testthat.R’ [39s/49s]
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
Packages suggested but not available for checking:
  ‘minfi’ ‘wateRmelon’ ‘IlluminaHumanMethylation450kmanifest’
Error in re-building vignettes:
  ...
Warning 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 73-77 (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
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Installation failed.
See ‘/home/ripley/R/packages/tests32/MMPPsampler.Rcheck/00install.out’ for details.
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
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error in open.connection(con, "rb") : 
  Timeout was reached: Resolving timed out after 10000 milliseconds
Quitting from lines 39-41 (modistools-vignette.Rmd) 
Error: processing vignette 'modistools-vignette.Rmd' failed with diagnostics:
Your requested timed out or the server is unreachable
Execution halted
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    doc    1.9Mb
installed size is  7.6Mb
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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 ...
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Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 30-37 (msaR.Rmd) 
Error: processing vignette 'msaR.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  6.2Mb
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    libs   5.6Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/MultiBD.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 344-346 (Examples.Rmd) 
Error: processing vignette 'Examples.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: geometry
Loading required package: magic
Loading required package: abind
Loading required package: rootSolve
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
xyYfromXYZ(). WARN .  1 of 11 XYZ vectors could not be transformed. 
adaptxyY.CAT(). DEBUG.  11 neutrals (of 11) given special treatment. 
xyYfromXYZ(). WARN .  1 of 11 XYZ vectors could not be transformed. 
adaptxyY.CAT(). DEBUG.  11 neutrals (of 11) given special treatment. 
spacesXYZ::XYZfromxyY(). WARN .  7 of 93 xyY vectors could not be transformed. 
spacesXYZ::XYZfromxyY(). WARN .  7 of 93 xyY vectors could not be transformed. 
spacesXYZ::XYZfromxyY(). WARN .  7 of 93 xyY vectors could not be transformed. 
Quitting from lines 252-268 (munsellinterpol-guide.Rmd) 
Error: processing vignette 'munsellinterpol-guide.Rmd' failed with diagnostics:
`render_flextable` needs to be used as a renderer for a knitr/rmarkdown R code chunk (render by rmarkdown)
Execution halted
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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 2.2-0 (2018-06-19) 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
Package required but not available: ‘dataone’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.8Mb
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installed size is  8.3Mb
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    data   7.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 92-98 (Introducing_nhanesA.Rmd) 
Error: processing vignette 'Introducing_nhanesA.Rmd' failed with diagnostics:
Timeout was reached: Operation timed out after 10000 milliseconds with 0 out of 0 bytes received
Execution halted
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    R         6.7Mb
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    tests     1.4Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 127-133 (geocode.Rmd) 
Error: processing vignette 'geocode.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/nlmixr.Rcheck/00install.out’ for details.
installed size is 10.8Mb
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    data      4.4Mb
    doc       1.2Mb
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Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'walkthrough.Rmd' failed with diagnostics:
(converted from warning) Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Execution halted
Running examples in ‘NMF-Ex.R’ failed
The error most likely occurred in:

> ### Name: NMFfitX-class
> ### Title: Virtual Class to Handle Results from Multiple Runs of NMF
> ###   Algorithms
> ### Aliases: NMFfitX-class
> 
> ### ** Examples
> 
> ## Don't show: 
> # roxygen generated flag
> options(R_CHECK_RUNNING_EXAMPLES_=TRUE)
> ## End(Don't show)
> 
> # generate a synthetic dataset with known classes
> n <- 20; counts <- c(5, 2, 3);
> V <- syntheticNMF(n, counts)
> 
> # perform multiple runs of one algorithm (default is to keep only best fit)
> res <- nmf(V, 3, nrun=3)
# NOTE - CRAN check detected: limiting maximum number of cores [2/16]
Error in big.matrix(nrow = nrow(x), ncol = ncol(x), type = type, init = NULL,  : 
  Error: memory could not be allocated for instance of type big.matrix
Calls: nmf ... gVariable -> <Anonymous> -> <Anonymous> -> big.matrix
Timing stopped at: 0.029 0.03 0.066
Execution halted
Package suggested but not available for checking: ‘redux’
Package unavailable to check Rd xrefs: ‘redux’
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
Running ‘testthat.R’ [33m/39m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(nseval)
  > 
  > test_check("nseval")
installed size is 39.1Mb
  sub-directories of 1Mb or more:
    extdata  39.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R            1.7Mb
    test_files   4.4Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    data   1.0Mb
    doc    1.7Mb
    help   2.4Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    R        2.7Mb
    data     1.0Mb
    libs     3.2Mb
    models   4.5Mb
Running examples in ‘OpenMx-Ex.R’ failed
The error most likely occurred in:

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

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

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R       1.1Mb
    nifti   4.1Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/osqp.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 185-198 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
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
Running ‘testthat.R’ [8s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("pacman")
  > options(repos="http://cran.rstudio.com/")
  > 
  > 
  > test_check("pacman")
  ── 1. Error: p_install_gh works (@test-p_install_gh.R#5)  ──────────────────────
  HTTP error 404.
    Not Found
  
    Rate limit remaining: 54
    Rate limit reset at: 2018-10-19 14:27:14 UTC
  1: expect_false(p_install_gh("greg/iDontExistAnywhere")) at testthat/test-p_install_gh.R:5
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: p_install_gh("greg/iDontExistAnywhere")
  5: lapply(package, function(x) {
         devtools::install_github(x, dependencies = dependencies, ...)
     })
  6: FUN(X[[i]], ...)
  7: devtools::install_github(x, dependencies = dependencies, ...)
  8: install_remotes(remotes, auth_token = auth_token, host = host, dependencies = dependencies, 
         upgrade = upgrade, force = force, quiet = quiet, build = build, build_opts = build_opts, 
         repos = repos, type = type, ...)
  9: vapply(remotes, install_remote, ..., FUN.VALUE = character(1))
  10: FUN(X[[i]], ...)
  11: remote_package_name(remote)
  12: remote_package_name.github_remote(remote)
  13: github_DESCRIPTION(username = remote$username, repo = remote$repo, subdir = remote$subdir, 
         host = remote$host, ref = remote$ref, pat = remote$auth_token %||% github_pat(), 
         use_curl = use_curl)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 54 SKIPPED: 3 FAILED: 1
  1. Error: p_install_gh works (@test-p_install_gh.R#5) 
  
  Error: testthat unit tests failed
  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.
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    extdata   9.8Mb
Running examples in ‘patternize-Ex.R’ failed
The error most likely occurred in:

> ### Name: patRegRGB
> ### Title: Aligns images using 'niftyreg' utilities for automated image
> ###   registration and extracts colors using a predefined RGB values and
> ###   cutoff value.
> ### Aliases: patRegRGB
> 
> ### ** Examples
> 
> IDlist <- c('BC0077','BC0071','BC0050','BC0049','BC0004')
> prepath <- system.file("extdata",  package = 'patternize')
> extension <- '.jpg'
> 
> imageList <- makeList(IDlist, 'image', prepath, extension)
[1] "sample 1 BC0077 added to list"
[1] "sample 2 BC0071 added to list"
[1] "sample 3 BC0050 added to list"
[1] "sample 4 BC0049 added to list"
[1] "sample 5 BC0004 added to list"
> 
> target <- imageList[[1]]
> 
> RGB <- c(114,17,0)
> 
> # Note that this example only aligns one image with the target,
> # remove [2] to run a full examples.
> rasterList_regRGB <- patRegRGB(imageList[2], target, RGB,
+ colOffset= 0.15, crop = c(100,400,40,250), removebgR = 100, plot = TRUE)

 *** caught segfault ***
address f601, cause 'memory not mapped'

Traceback:
 1: retrieveNifti(target)
 2: niftyreg.linear(x, target, "affine", init = transform, nLevels = 0L,     interpolation = interpolation, verbose = FALSE, estimateOnly = FALSE,     internal = internal)
 3: RNiftyReg::applyTransform(RNiftyReg::forward(result), map, interpolation = 0)
 4: patRegRGB(imageList[2], target, RGB, colOffset = 0.15, crop = c(100,     400, 40, 250), removebgR = 100, plot = TRUE)
An irrecoverable exception occurred. R is aborting now ...
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  7.3Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   3.1Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    1.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.1Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/PDFEstimator.Rcheck/00install.out’ for details.
Packages required but not available: ‘MSnbase’ ‘mzR’

Package suggested but not available for checking: ‘faahKO’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
Installation failed.
See ‘/home/ripley/R/packages/tests32/pgdraw.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
Running ‘run_tests.r’ [224s/374s]
Running the tests in ‘tests/run_tests.r’ failed.
Complete output:
  > # Run all unit tests
  > 
  > # This is a wrapper around all the tests specified
  > # in the tests/testthat directory. These tests are visible
  > # to users and serve as small examples as well.
  > testthat::test_check("phenocamr")
  Loading required package: phenocamr
  Downloading: harvard_DB_1000_3day.csv
  Smoothing time series! 
  Downloading: harvard_DB_1000_3day.csv
  Flagging outliers! 
  Smoothing time series! 
  Estimating transition dates! 
  Downloading: harvard_DB_1000_roistats.csv
  Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
    Timeout was reached: Operation timed out after 15002 milliseconds with 7093991 out of 27630063 bytes received
  Error in UseMethod("http_error") : 
    no applicable method for 'http_error' applied to an object of class "try-error"
  Downloading: harvard_DB_1000_3day.csv
  Smoothing time series! 
  Merging Daymet Data! 
  Downloading: harvard_DB_1000_3day.csv
  Contracting Data! 
  Downloading: harvard_DB_1000_3day.csv
  ── 1. Failure: check download options (@test_download_function.r#69)  ──────────
  `check` isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2 SKIPPED: 0 FAILED: 1
  1. Failure: check download options (@test_download_function.r#69) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 20-27 (Advanced_Usage.Rmd) 
Error: processing vignette 'Advanced_Usage.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.0Mb
    doc    3.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 65-68 (v01-introduction.Rmd) 
Error: processing vignette 'v01-introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Running ‘testthat.R’ [11s/53s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pkgdown)
  > 
  > test_check("pkgdown")
  ── 1. Failure: remote_package_url discovers pkgdown site (@test-metadata.R#6)  ─
  remote_package_reference_url("pkgdown") not equal to "http://pkgdown.r-lib.org/reference".
  target is NULL, current is character
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 208 SKIPPED: 21 FAILED: 1
  1. Failure: remote_package_url discovers pkgdown site (@test-metadata.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R             1.0Mb
    htmlwidgets   3.0Mb
Running examples in ‘plotly-Ex.R’ failed
The error most likely occurred in:

> ### Name: partial_bundle
> ### Title: Use a partial bundle of plotly.js
> ### Aliases: partial_bundle
> 
> ### ** Examples
> 
> 
> # ----------------------------------------------------------------------
> # This function is always safe to use when rendering a single 
> # plotly graph. In this case, we get a 3x file reduction.
> # ----------------------------------------------------------------------
> 
> library(plotly)
> p <- plot_ly(x = 1:10, y = 1:10) %>% add_markers()
> save_widget <- function(p, f) {
+   owd <- setwd(dirname(f))
+   on.exit(setwd(owd))
+   htmlwidgets::saveWidget(p, f)
+   mb <- round(file.info(f)$size / 1e6, 3)
+   message("File is: ", mb," MB")
+ }
> f1 <- tempfile(fileext = ".html")
> f2 <- tempfile(fileext = ".html")
> save_widget(p, f1)
Error in htmlwidgets::saveWidget(p, f) : 
  Saving a widget with selfcontained = TRUE requires pandoc. For details see:
https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
Calls: save_widget -> <Anonymous>
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   6.4Mb
Running ‘testthat.R’ [58s/70s]
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
  sub-directories of 1Mb or more:
    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
Running ‘testthat.R’ [20s/447s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(postal)
  > 
  > test_check("postal")
  ── 1. Failure: Extract date works (@test_utils.R#244)  ─────────────────────────
  extract_dates(future_date) %>% as.numeric() is not strictly more than lubridate::today() %>% as.numeric(). Difference: 0
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 108 SKIPPED: 0 FAILED: 1
  1. Failure: Extract date works (@test_utils.R#244) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Package suggested but not available for checking: ‘fclust’
Package unavailable to check Rd xrefs: ‘fclust’
Running examples in ‘ppclust-Ex.R’ failed
The error most likely occurred in:

> ### Name: as.ppclust
> ### Title: Convert object to 'ppclust' class
> ### Aliases: as.ppclust
> 
> ### ** Examples
> 
> data(iris)
> # Create an fclust object
> ofc <- fclust::FKM(X=iris[,1:4], k=3)
Error in loadNamespace(name) : there is no package called ‘fclust’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Welcome! Related Books: `Practical Guide To Cluster Analysis in R` at https://goo.gl/13EFCZ
Quitting from lines 45-48 (fcm.Rmd) 
Error: processing vignette 'fcm.Rmd' failed with diagnostics:
there is no package called 'fclust'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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]="./webshotb5b32e54a10.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotb5b32e54a10.png': No such file or directory
Quitting from lines 125-126 (PPQplan-vignette.Rmd) 
Error: processing vignette 'PPQplan-vignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages suggested but not available for checking:
  ‘gurobi’ ‘lpsymphony’ ‘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 31-44 (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
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
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(projpred)
  This is projpred version 1.0.0
  
  Note: The type of the returned objects of varsel/cv_varsel have changed
  since the latest release, although this does not affect how the functions
  are used.
  > library(rstanarm) # we need rstanarm for running the tests
  Error in library(rstanarm) : there is no package called 'rstanarm'
  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 23-29 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
there is no package called 'rstanarm'
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/prophet.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data      1.8Mb
    extdata   2.8Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/PSPManalysis.Rcheck/00install.out’ for details.
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
  sub-directories of 1Mb or more:
    dict   5.3Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R          1.1Mb
    doc        4.8Mb
    examples   2.4Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.3Mb
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
  sub-directories of 1Mb or more:
    data  12.9Mb
Package required but not available: ‘ssh’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    R         1.9Mb
    contrib   3.7Mb
    doc       3.3Mb
    libs      1.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 83-117 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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:
there is no package called 'webshot'
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
Package unavailable to check Rd xrefs: ‘BRugs’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    3.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    extdata   1.5Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    api           3.0Mb
    htmlwidgets   9.4Mb
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)) : 
  java.lang.UnsupportedClassVersionError: opennlp/tools/stemmer/snowball/SnowballStemmer : Unsupported major.minor version 52.0
Calls: rapidrake ... <Anonymous> -> <Anonymous> -> jclassName -> .jfindClass
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rapidraker)
  > 
  > test_check("rapidraker")
  ── 1. Error: (unknown) (@test-rapidrake.R#3)  ──────────────────────────────────
  no field, method or inner class called 'handled' 
  1: test_that("rapidrake works for non-atomic, non-empty char vectors", {
         out <- rapidrake(slowraker::dog_pubs$abstract[1:10])
         expect_equal(length(out), 10)
     }) at testthat/test-rapidrake.R:3
  2: test_code(desc, code, env = parent.frame())
  3: tryCatch(withCallingHandlers({
         eval(code, test_env)
         if (!handled && !is.null(test)) {
             skip_empty()
         }
     }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, 
         message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) {
     })
  4: tryCatchList(expr, classes, parentenv, handlers)
  5: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], 
         parentenv, handlers[[nh]])
  6: doTryCatch(return(expr), name, parentenv, handler)
  7: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9: value[[3L]](cond)
  10: isTRUE(e$handled)
  11: e$handled
  12: `$.Throwable`(e, "handled")
  13: ._jobjRef_dollar(x[["jobj"]], name)
  14: stop(sprintf("no field, method or inner class called '%s' ", name))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-rapidrake.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.0Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   3.1Mb
    etc    2.2Mb
    po     1.5Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/RBesT.Rcheck/00install.out’ for details.
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    cont  23.4Mb
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
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
Running examples in ‘rcongresso-Ex.R’ failed
The error most likely occurred in:

> ### Name: fetch_deputado
> ### Title: Retrieves details about a deputy
> ### Aliases: fetch_deputado
> 
> ### ** Examples
> 
> abel_mesquita_info <- fetch_deputado(id = 178957)
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: Connection timed out after 10000 milliseconds
Calls: fetch_deputado ... 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.

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 30-31 (introducao-rcongresso.Rmd) 
Error: processing vignette 'introducao-rcongresso.Rmd' failed with diagnostics:
Timeout was reached: Operation timed out after 10000 milliseconds with 0 out of 0 bytes received
Execution halted
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    corpora   8.2Mb
installed size is  6.4Mb
  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 fd14bc4a, cause 'memory not mapped'

Traceback:
 1: fastLmPure(cbind(1, log(trees$Girth)), log(trees$Volume), 0)
An irrecoverable exception occurred. R is aborting now ...
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 95-104 (RcppCNPy-intro.Rmd) 
Error: processing vignette 'RcppCNPy-intro.Rmd' failed with diagnostics:
Python shared library '' not found, Python bindings not loaded.
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.
Installation failed.
See ‘/home/ripley/R/packages/tests32/RcppMeCab.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.
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    include   8.9Mb
    libs     14.9Mb
installed size is 11.9Mb
  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: RobotParser
> ### Title: RobotParser fetch and parse robots.txt
> ### Aliases: RobotParser
> 
> ### ** Examples
> 
> 
> RobotParser("http://www.glofile.com","AgentX")
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: Resolving timed out after 5000 milliseconds
Calls: RobotParser ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
Running ‘testthat.R’ [15s/311s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("rdefra")
  > 
  > test_check("rdefra")
  ── 1. Error: DEFRA server should be running (@test-metadata.R#13)  ─────────────
  HTTP/2 stream 5 was not closed cleanly: CANCEL (err 8)
  1: httr::GET(url = "http://uk-air.defra.gov.uk", path = "networks/find-sites", query = list(site_name = site_name, 
         pollutant = pollutant, group_id = group_id, closed = closed, country_id = country_id, 
         region_id = region_id, location_type = location_type, search = "Search+Network", 
         view = "advanced", action = "results")) at testthat/test-metadata.R:13
  2: request_perform(req, hu$handle$handle)
  3: request_fetch(req$output, req$url, handle)
  4: request_fetch.write_memory(req$output, req$url, handle)
  5: curl::curl_fetch_memory(url, handle = handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 20 SKIPPED: 1 FAILED: 1
  1. Error: DEFRA server should be running (@test-metadata.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    doc   2.6Mb
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.
Loading required package: rJava
Loading required package: Rdroolsjars

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: 'purrr'

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

    set_names

SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
Warning in if (class(intermediateOutput) == "list") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(intermediateOutput) == "list") { :
  the condition has length > 1 and only the first element will be used
Quitting from lines 374-381 (Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd) 
Error: processing vignette 'Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
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
Installation failed.
See ‘/home/ripley/R/packages/tests32/redist.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘Rsymphony’

Package which this enhances but not available for checking: ‘Rcplex’
Error in re-building vignettes:
  ...
Warning 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 296-299 (rentrez_tutorial.Rmd) 
Error: processing vignette 'rentrez_tutorial.Rmd' failed with diagnostics:
Error in the HTTP2 framing layer
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)$CH_4)
Warning in strsplit(raw, split = "\r\n", fixed = T) :
  input string 1 is invalid UTF-8
Error in grep("Date &Time [", f[1:20], fixed = TRUE):length(f) : 
  argument of length 0
Calls: na.omit -> import_witrox
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

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
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
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
Note: information on .o files is not available
File ‘/home/ripley/R/Lib32/rJava/libs/rJava.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API call to R: ‘R_GlobalContext’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor 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  5.4Mb
  sub-directories of 1Mb or more:
    data      1.0Mb
    extdata   3.1Mb
Running examples in ‘Rlibeemd-Ex.R’ failed
The error most likely occurred in:

> ### Name: ceemdan
> ### Title: CEEMDAN decomposition
> ### Aliases: ceemdan
> 
> ### ** Examples
> 
> imfs <- ceemdan(UKgas, threads = 1)
Error reported by gsl_linalg_solve_tridiag: tried to divide by zero
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 0.8.6 [Built: 2018-10-17 20:43:28 UTC]
Push Pin: 'Made of used sample carriers'

Attaching package: 'RLumModel'

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

    model_LuminescenceSignals

Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 125-154 (RLumModel_-_Simulating_luminescence_in_Al2O3.Rmd) 
Error: processing vignette 'RLumModel_-_Simulating_luminescence_in_Al2O3.Rmd' failed with diagnostics:
subscript out of bounds
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    examples   4.9Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    rmd   7.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    java   4.5Mb
Error in re-building vignettes:
  ...
Warning in engine$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
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 11.4Mb
  sub-directories of 1Mb or more:
    R  11.3Mb
Packages suggested but not available for checking:
  ‘affydata’ ‘hgu95av2cdf’ ‘illuminaHumanv3.db’
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’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         2.8Mb
    extdata   2.8Mb
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
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
Installation failed.
See ‘/home/ripley/R/packages/tests32/rrd.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: moonBook
Loading required package: ztable
Welcome to package ztable ver 0.2.0
Loading required package: rrtable

Attaching package: 'rrtable'

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

    roundDf

Loading required package: ggplot2
Quitting from lines 68-69 (rrtable.Rmd) 
Error: processing vignette 'rrtable.Rmd' failed with diagnostics:
`render_flextable` needs to be used as a renderer for a knitr/rmarkdown R code chunk (render by rmarkdown)
Execution halted
Found the following executable file:
  data/GH.RData
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/Rserve.Rcheck/00install.out’ for details.
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 admin module.
Error from REST: Error: Not Found


Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/rstanarm.Rcheck/00install.out’ for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs        6.5Mb
    unitTests   1.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error in file(con, "r") : cannot open the connection
Warning in engine$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 226-236 (rstan.Rmd) 
Error: processing vignette 'rstan.Rmd' failed with diagnostics:
Compilation ERROR, function(s)/method(s) not created! In file included from /tmp/RtmpDEaaDI/RLIBS_44e87eb56c86/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /tmp/RtmpDEaaDI/RLIBS_44e87eb56c86/BH/include/boost/shared_ptr.hpp:17,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/fun/LDLT_factor.hpp:7,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/err/check_ldlt_factor.hpp:6,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat.hpp:33,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/rev/mat.hpp:12,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math.hpp:4,
                 from /home/ripley/R/Lib32/StanHeaders/include/src/stan/model/model_header.hpp:4,
                 from file54345634abd.cpp:8:
/tmp/RtmpDEaaDI/RLIBS_44e87eb56c86/BH/include/boost/smart_ptr/det
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Rcpp
Warning in system(cmd, intern = !verbose) :
  running command '/home/ripley/R/gcc/bin/R CMD SHLIB file1b6b36cac67.cpp 2> file1b6b36cac67.cpp.err.txt' had status 1 and error message 'Illegal seek'
Quitting from lines 74-84 (simulating_data.Rmd) 
Error: processing vignette 'simulating_data.Rmd' failed with diagnostics:
Compilation ERROR, function(s)/method(s) not created! In file included from /tmp/Rtmpf0aagO/RLIBS_50304f6a3607/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /tmp/Rtmpf0aagO/RLIBS_50304f6a3607/BH/include/boost/shared_ptr.hpp:17,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/fun/LDLT_factor.hpp:7,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat/err/check_ldlt_factor.hpp:6,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/prim/mat.hpp:33,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math/rev/mat.hpp:12,
                 from /home/ripley/R/Lib32/StanHeaders/include/stan/math.hpp:4,
                 from /home/ripley/R/Lib32/StanHeaders/include/src/stan/model/model_header.hpp:4,
                 from file1b6b36cac67.cpp:8:
/tmp/Rtmpf0aagO/RLIBS_50304f6a3607/BH/include/boost/sma
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 17-22 (minimal-rstan-package.Rmd) 
Error: processing vignette 'minimal-rstan-package.Rmd' failed with diagnostics:
object 'params' not found
Execution halted
Running examples in ‘RSuite-Ex.R’ failed
The error most likely occurred in:

> ### Name: prj_pack
> ### Title: Prepares project source pack tagged with version.
> ### Aliases: prj_pack
> 
> ### ** Examples
> 
> # create exemplary project base folder
> prj_base <- tempfile("example_")
> dir.create(prj_base, recursive = TRUE, showWarnings = FALSE)
> 
> # start project
> prj <- prj_start("my_project", skip_rc = TRUE, path = prj_base)
2018-10-18 05:02:43 INFO:rsuite:Project my_project has structure compliant with current version of RSuite(v0.33.246).
2018-10-18 05:02:43 INFO:rsuite:Project my_project started.
> 
> # create package in the project
> prj_start_package("mypackage", prj = prj, skip_rc = TRUE)
2018-10-18 05:02:43 INFO:rsuite:Package mypackage started in project my_project.
> 
> # build project source pack
> pack_fpath <- prj_pack(prj = prj, path = tempdir(), pack_ver = "1.0")
2018-10-18 05:02:43 WARNING:rsuite:Project environment is not locked!
2018-10-18 05:02:43 INFO:rsuite:Exporting project from /tmp/Rtmp8Ca4HZ/example_670fbb71296/my_project ...
2018-10-18 05:02:43 INFO:rsuite:Exporting project from /tmp/Rtmp8Ca4HZ/example_670fbb71296/my_project ... done
2018-10-18 05:02:44 WARNING:rsuite:Zip building aborted for
2018-10-18 05:02:44 ERROR:rsuite:Failed to create pack file (zip returned non 0 return status).
Error: Failed to create pack file (zip returned non 0 return status).
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    rmarkdown   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 block_exec(params) :
  failed to tidy R code in chunk <pkg_data>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  failed to tidy R code in chunk <stBooksWP>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  failed to tidy R code in chunk <st_book_series>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  failed to tidy R code in chunk <st_book_series2>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  failed to tidy R code in chunk <stTiles>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  failed to tidy R code in chunk <stGeo>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  failed to tidy R code in chunk <tile_coords>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Quitting from lines 84-89 (rtrek.Rmd) 
Error: processing vignette 'rtrek.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
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  6.1Mb
  sub-directories of 1Mb or more:
    include   2.5Mb
    libs      3.0Mb
Running examples in ‘rvinecopulib-Ex.R’ failed
The error most likely occurred in:

> ### Name: bicop
> ### Title: Bivariate copula models
> ### Aliases: bicop bicop_dist bicop_dist
> 
> ### ** Examples
> 
> ## bicop_dist objects
> bicop_dist("gaussian", 0, 0.5)
Bivariate copula ('bicop_dist'): family = gaussian, rotation = 0, parameters = 0.5
> str(bicop_dist("gauss", 0, 0.5))
List of 4
 $ family    : chr "gaussian"
 $ rotation  : num 0
 $ parameters: num [1, 1] 0.5
 $ npars     : int 1
 - attr(*, "class")= chr "bicop_dist"
> bicop <- bicop_dist("clayton", 90, 3)
> 
> ## bicop objects
> u <- rbicop(500, "gauss", 0, 0.5)
> fit1 <- bicop(u, "par")

 *** caught segfault ***
address fc485610, cause 'memory not mapped'

Traceback:
 1: bicop_select_cpp(data = data, family_set = family_set, par_method = par_method,     nonpar_method = nonpar_method, mult = mult, selcrit = selcrit,     weights = weights, psi0 = psi0, presel = presel, num_threads = cores)
 2: bicop(u, "par")
An irrecoverable exception occurred. R is aborting now ...
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
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  5.3Mb
  sub-directories of 1Mb or more:
    refs   4.5Mb
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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 34-35 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.8Mb
Error in re-building vignettes:
  ...
Warning in engine$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 238-239 (sdcTable.rmd) 
Error: processing vignette 'sdcTable.rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data            1.5Mb
    vignette_data   2.1Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R   7.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.1Mb
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 ...
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    doc     12.3Mb
    docker   1.4Mb
    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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 216-219 (sf5.Rmd) 
Error: processing vignette 'sf5.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.9Mb
Error in re-building vignettes:
  ...
Warning in engine$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  9.4Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    www   7.1Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(shinystan)
  Loading required package: shiny
  
  This is shinystan version 2.5.0
  
  > 
  > test_check("shinystan")
  ── 1. Error: (unknown) (@test_creating_sso.R#3)  ───────────────────────────────
  there is no package called 'rstanarm'
  1: suppressPackageStartupMessages(library(rstanarm)) at testthat/test_creating_sso.R:3
  2: withCallingHandlers(expr, packageStartupMessage = function(c) invokeRestart("muffleMessage"))
  3: library(rstanarm)
  4: stop(txt, domain = NA)
  
  ── 2. Error: (unknown) (@test_misc.R#2)  ───────────────────────────────────────
  there is no package called 'rstanarm'
  1: library(rstanarm) at testthat/test_misc.R:2
  2: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 78 SKIPPED: 0 FAILED: 2
  1. Error: (unknown) (@test_creating_sso.R#3) 
  2. Error: (unknown) (@test_misc.R#2) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   7.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 26-42 (animate.Rmd) 
Error: processing vignette 'animate.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 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
Error in re-building vignettes:
  ...
Warning 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: magrittr
Loading required package: data.table
skm_mls: skm solver via skm_mls_cpp ...

skm_mls: auto_create g w.r.t first letter of s_name.

skm_mls: optimizing on k <1> ...

skm_mls: optimizing on k <1> ... done.

skm_mls: optimizing on k <2> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <2> ... done.

skm_mls: optimizing on k <3> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <3> ... done.

skm_mls: optimizing on k <4> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <4> ... done.

skm_mls: optimizing on k <5> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <5> ... done.

skm_mls: optimizing on k <6> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <6> ... done.

skm_mls: optimizing on k <7> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: encounter better solution at jk <63> run based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <7> ... done.

skm_mls: optimizing on k <8> ...
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
Packages required but not available:
  ‘adaptiveGPCA’ ‘NoiseFiltersR’ ‘FSelector’

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

> ### Name: ExpReport
> ### Title: Function to create HTML EDA report
> ### Aliases: ExpReport
> 
> ### ** Examples
> 
> # Overview of the data
> ExpReport(mtcars,Template=NULL,Target=NULL,label=NULL,op_file="Myreport.html",
+ op_dir=getwd(),sc=2,sn=2,Rc=NULL)
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 125-126 (SmartEDA.Rmd) 
Error: processing vignette 'SmartEDA.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
Running ‘testthat.R’ [169s/213s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(smooth)
  Loading required package: greybox
  Package "greybox", v0.3.1 loaded.
  This is package "smooth", v2.4.6
  
  Attaching package: 'smooth'
  
  The following object is masked from 'package:greybox':
  
      graphmaker
  
  > 
  > test_check("smooth")
  ── 1. Failure: Select exogenous variables for GUMX on N1457 with selection (@tes
  suppressWarnings(testModel$xreg) is not null.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 77 SKIPPED: 0 FAILED: 1
  1. Failure: Select exogenous variables for GUMX on N1457 with selection (@test_ges.R#40) 
  
  Error: testthat unit tests failed
  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: 1.78 secs
Identifing all possible orderings..
Total run time: 2.08 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
Error in re-building vignettes:
  ...
Warning 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':

    %>%


Attaching package: 'SpaDES.core'

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

    end, start

Loading required package: SpaDES.tools
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 366-372 (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
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    R      5.2Mb
    doc    5.2Mb
    help   5.1Mb
    libs   1.3Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data     2.6Mb
    shapes   3.9Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.6Mb
Found the following significant warnings:
  Warning: 'devtools::use_package' is deprecated.
See ‘/home/ripley/R/packages/tests32/spectrolab.Rcheck/00install.out’ for details.
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
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    lsndata   2.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 281-303 (stacomir.Rmd) 
Error: processing vignette 'stacomir.Rmd' failed with diagnostics:
sum(datasub$value, na.rm = TRUE) and sum(datasub2$value, na.rm = TRUE) are not equal:
  Mean relative difference: 0.000996791
Execution halted
installed size is  7.3Mb
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    include   6.4Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   5.5Mb
installed size is  8.2Mb
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    doc   3.8Mb
    nc    3.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 95-99 (blog1.Rmd) 
Error: processing vignette 'blog1.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
Execution halted
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘statnet’
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘statnet’
See ‘/home/ripley/R/packages/tests32/statnet.Rcheck/00install.out’ for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R          2.3Mb
    datasets   2.7Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/stratEst.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Building shared library for Rcpp code chunk...
make: Warning: Ignoring DistributedMake -j option
make: Warning: Ignoring DistributedMake -j option
make: Fatal error: Don't know how to make target `file603277861f01.o'
Current working directory /tmp/RtmpvuaqgW/sourceCpp-i386-pc-solaris2.10-0.12.19/sourcecpp_603226f84659
`/home/ripley/R/gcc/etc/Makeconf' is up to date.
`/home/ripley/R/gcc/etc/Makeconf' is up to date.
Quitting from lines 60-85 (strider.Rmd) 
Error: processing vignette 'strider.Rmd' failed with diagnostics:
Error occurred building shared library.
Execution halted
installed size is 33.2Mb
  sub-directories of 1Mb or more:
    libs  32.4Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 61-64 (stRvignette.Rmd) 
Error: processing vignette 'stRvignette.Rmd' failed with diagnostics:
Process terminated
Execution halted
Running examples in ‘subspaceMOA-Ex.R’ failed
The error most likely occurred in:

> ### Name: DSC_HDDStream
> ### Title: Density-based Projected Clustering over High-Dimensional Data
> ### Aliases: DSC_HDDStream
> 
> ### ** Examples
> 
> dsc <- DSC_HDDStream()
Error in rJava::.jcall("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
Installation failed.
See ‘/home/ripley/R/packages/tests32/survHE.Rcheck/00install.out’ for details.
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
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    libs   6.8Mb
installed size is  5.1Mb
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    R         1.3Mb
    extdata   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: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: 'Hmisc'

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

    format.pval, units

Quitting from lines 44-45 (HTML.Rmd) 
Error: processing vignette 'HTML.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
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)
> tp2 <- tableplot(chp.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
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installed size is  6.4Mb
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    doc    3.9Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/telefit.Rcheck/00install.out’ for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    3.8Mb
installed size is  8.7Mb
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    data   8.6Mb
Package suggested but not available for checking: ‘tesseract’
Package unavailable to check Rd xrefs: ‘tesseract’
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    rda    7.6Mb
Package required but not available: ‘tidyposterior’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Rblpapi’
installed size is  5.4Mb
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    doc   4.4Mb
Package unavailable to check Rd xrefs: ‘Rblpapi’
installed size is  5.4Mb
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    extdata   4.5Mb
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 107-109 (Tigger-Vignette.Rmd) 
Error: processing vignette 'Tigger-Vignette.Rmd' failed with diagnostics:
error in running command: 'Illegal seek'
Execution halted
installed size is  5.9Mb
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    doc         3.9Mb
    rmarkdown   1.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$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 3.6.3, GDAL 2.2.4, PROJ 5.1.0
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 127-131 (tmap-getstarted.Rmd) 
Error: processing vignette 'tmap-getstarted.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/tmbstan.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$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 13-26 (toOrdinal.Rmd) 
Error: processing vignette 'toOrdinal.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
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 14.7Mb
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    doc       2.8Mb
    extdata   8.8Mb
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: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric


Attaching package: 'trackeR'

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

    append

Warning in download.file(url, destfile = tmp, quiet = !messaging, mode = "wb") :
  cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=50.824,-1.7133&zoom=13&size=640x640&scale=2&maptype=terrain&sensor=false': HTTP status was '403 Forbidden'
Quitting from lines 106-108 (TourDetrackeR.Rmd) 
Error: processing vignette 'TourDetrackeR.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  6.4Mb
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    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:
cannot open the connection
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    fonts   5.3Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/trialr.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 130-139 (choropleth_maps_with_tricolore.Rmd) 
Error: processing vignette 'choropleth_maps_with_tricolore.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(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
Running examples in ‘tsibble-Ex.R’ failed
The error most likely occurred in:

> ### Name: as_tsibble
> ### Title: Coerce to a tsibble object
> ### Aliases: as_tsibble as.tsibble as_tsibble.tbl_df as_tsibble.tbl_ts
> ###   as_tsibble.data.frame as_tsibble.list as_tsibble.ts as_tsibble.mts
> ###   as_tsibble.msts as_tsibble.hts
> 
> ### ** Examples
> 
> # coerce tibble to tsibble w/o a key ----
> tbl1 <- tibble(
+   date = as.Date("2017-01-01") + 0:9,
+   value = rnorm(10)
+ )
> as_tsibble(tbl1)
Column `date` is the index.
# A tsibble: 10 x 2 [1D]
   date        value
   <date>      <dbl>
 1 2017-01-01 -0.626
 2 2017-01-02  0.184
 3 2017-01-03 -0.836
 4 2017-01-04  1.60 
 5 2017-01-05  0.330
 6 2017-01-06 -0.820
 7 2017-01-07  0.487
 8 2017-01-08  0.738
 9 2017-01-09  0.576
10 2017-01-10 -0.305
> # specify the index var
> as_tsibble(tbl1, index = date)
# A tsibble: 10 x 2 [1D]
   date        value
   <date>      <dbl>
 1 2017-01-01 -0.626
 2 2017-01-02  0.184
 3 2017-01-03 -0.836
 4 2017-01-04  1.60 
 5 2017-01-05  0.330
 6 2017-01-06 -0.820
 7 2017-01-07  0.487
 8 2017-01-08  0.738
 9 2017-01-09  0.576
10 2017-01-10 -0.305
> 
> # coerce tibble to tsibble with one key ----
> # "date" is automatically considered as the index var, and "group" is the key
> tbl2 <- tibble(
+   mth = rep(yearmonth("201701") + 0:9, 3),
+   group = rep(c("x", "y", "z"), each = 10),
+   value = rnorm(30)
+ )
> as_tsibble(tbl2, key = id(group))
Column `mth` is the index.
Error: Column `mth` (the index) must not contain `NA`.
Execution halted
Package required but not available: ‘ChemmineR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 10.3Mb
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    dummydata   1.5Mb
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Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Quitting from lines 59-76 (UKgrid_vignette.Rmd) 
Error: processing vignette 'UKgrid_vignette.Rmd' failed with diagnostics:
there is no package called 'TSstudio'
Execution halted
Running examples in ‘umx-Ex.R’ failed
The error most likely occurred in:

> ### Name: umx
> ### Title: Helper Functions for Structural Equation Modelling in OpenMx
> ### Aliases: umx umx-package
> 
> ### ** Examples
> 
> require("umx")
> data(demoOneFactor)
> myData = mxData(cov(demoOneFactor), type = "cov", numObs = nrow(demoOneFactor))
> latents = c("G")
> manifests = names(demoOneFactor)
> m1 <- umxRAM("One Factor", data = myData,
+ 	umxPath(latents, to = manifests),
+ 	umxPath(var = manifests),
+ 	umxPath(var = latents  , fixedAt=1)
+ )
A latent variable 'G' was created. 
Running One Factor with 10 parameters
Warning incurred trying to run model
In model 'One Factor' Optimizer returned a non-zero status code 5. The Hessian at the solution does not appear to be convex. See ?mxCheckIdentification for possible diagnosis (Mx status RED).> 
> # umx added informative labels, created starting values, 
> # Ran you model (if autoRun is on), and displayed a brief summary
> # including a comparison if you modified a model...!
> 
> # Let's get some journal-ready fit information
> 
> umxSummary(m1) 
?umxSummary showEstimates='raw|std', digits, report= 'html', filter= 'NS' & more
Error in umx_has_been_run(model, stop = TRUE) : 
  Provided model has no output (probably you have not yet run it?)
Calls: umxSummary -> umxSummary.MxModel -> umx_has_been_run
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: magic
Loading required package: abind

     PLEASE NOTE:  As of version 0.3-5, no degenerate (zero area) 
     regions are returned with the "Qt" option since the R 
     code removes them from the triangulation. 
     See help("delaunayn").


Quitting from lines 93-98 (convexhull.Rmd) 
Error: processing vignette 'convexhull.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
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  7.3Mb
  sub-directories of 1Mb or more:
    extdata   6.4Mb
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’ [19s/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
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
Running examples in ‘vegdata-Ex.R’ failed
The error most likely occurred in:

> ### Name: isc
> ### Title: Indicate site conditions with community weighted mean values of
> ###   traits or with mode of gradient classes (sum of species amplitudes).
> ### Aliases: isc showindiplot
> ### Keywords: misc
> 
> ### ** Examples
> 
> db <- 'elbaue'
> veg <- tv.veg(db, cover.transform='sqrt', check.critical = FALSE)

No Turbowin installation path found. 

############################################################
Turboveg root directory is set to "/home/ripley/R/Lib32/vegdata/tvdata"
If you want to change this use: options(tv_home="<path_to_your_Turbowin_root>")
############################################################
Reading tvabund.dbf
Taxonomic reference list:  GermanSL 1.3 
Original number of names: 53 
Taxonomic reference list file /home/ripley/R/Lib32/vegdata/tvdata/Species/GermanSL 1.3/tax.dbf does not exist.

Taxonomic list (tax.dbf) of reflistGermanSL 1.3 not available.


trying URL 'https://germansl.infinitenature.org/GermanSL/1.3/GermanSL.zip'
Content type 'application/zip' length 3092316 bytes (2.9 MB)
==================================================
downloaded 2.9 MB

5 Synonyms found in dataset. Changed to valid names. 

Number of taxa after harmonisation: 53 
Reading tvhabita.dbf
Error in iconv(site[, i], iconv, "") : 
  unsupported conversion from 'CP437' to ''
Calls: tv.veg -> tv.site -> iconv
Execution halted
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    doc    1.3Mb
    help   2.8Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc           5.7Mb
    htmlwidgets   4.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 22-27 (Introduction-to-visNetwork.Rmd) 
Error: processing vignette 'Introduction-to-visNetwork.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    extdata  11.3Mb
Found the following significant warnings:
  "predict.c", line 111: warning: improper pointer/integer combination: op "<"
See ‘/home/ripley/R/packages/tests32/VLMC.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/ripley/R/packages/tests32/walker.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/ripley/R/packages/tests32/wand.Rcheck/00install.out’ for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   4.3Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc  12.3Mb
Package suggested but not available for checking: ‘rcdk’
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    client  10.1Mb
    doc      1.1Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 37-39 (wordcloud.Rmd) 
Error: processing vignette 'wordcloud.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    data  13.4Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  11.9Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    data  14.3Mb
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.
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 818-843 (Usingxtractomatic.Rmd) 
Error: processing vignette 'Usingxtractomatic.Rmd' failed with diagnostics:
(converted from warning) Removed 4070 rows containing missing values (geom_raster).
Execution halted
Running ‘test-all.R’ [23s/574s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > test_check("zoon")
  Loading required package: zoon
  Loading required package: raster
  Loading required package: sp
  ── 1. Failure: Expected errors (@testTransformCRS.R#39)  ───────────────────────
  `workflow(...)` did not throw an error.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 237 SKIPPED: 30 FAILED: 1
  1. Failure: Expected errors (@testTransformCRS.R#39) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/zstdr.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: moonBook
Welcome to package ztable ver 0.2.0
Warning in engine$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 103-108 (ztable_update.Rmd) 
Error: processing vignette 'ztable_update.Rmd' failed with diagnostics:
`render_flextable` needs to be used as a renderer for a knitr/rmarkdown R code chunk (render by rmarkdown)
In addition: Warning message:
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
Package required but not available: ‘rgl’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘HH’ ‘Hmisc’
Package suggested but not available for checking: ‘rgl’
Packages suggested but not available for checking: ‘DT’ ‘plotly’
Error in re-building vignettes:
  ...
Quitting from lines 29-30 (ActisoftR.Rmd) 
Error: processing vignette ‘ActisoftR.Rmd’ failed with diagnostics:
there is no package called 'DT'
Execution halted
Package required but not available: ‘plotly’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shinystan’
Packages suggested but not available for checking: ‘gge’ ‘HH’ ‘SpATS’
Error in re-building vignettes:
  ...
Quitting from lines 40-49 (agridat_examples.Rmd) 
Error: processing vignette ‘agridat_examples.Rmd’ failed with diagnostics:
there is no package called 'gge'
Execution halted
Package required but not available: ‘visNetwork’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘data.tree’ ‘formattable’ ‘DiagrammeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘hydroPSO’
Error in re-building vignettes:
  ...
Quitting from lines 14-21 (V02.1_param_optim.Rmd) 
Error: processing vignette ‘V02.1_param_optim.Rmd’ failed with diagnostics:
there is no package called 'hydroPSO'
Execution halted
Packages required but not available: ‘dygraphs’ ‘htmlwidgets’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Hmisc’
Packages required but not available: ‘vegan3d’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  analyzeFMRI.c:948:3: warning: ‘strncat’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  analyzeFMRI.c:975:5: warning: ‘strncat’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/AnalyzeFMRI.Rcheck/00install.out’ for details.
Packages required but not available: ‘Hmisc’ ‘weights’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DT’
Error in re-building vignettes:
  ...
Quitting from lines 39-73 (antaresH5.Rmd) 
Error: processing vignette ‘antaresH5.Rmd’ failed with diagnostics:
there is no package called 'DT'
Execution halted
Packages required but not available:
  ‘dygraphs’ ‘plotly’ ‘htmlwidgets’ ‘manipulateWidget’ ‘leaflet’
  ‘leaflet.minicharts’ ‘rAmCharts’

Packages suggested but not available for checking: ‘rbokeh’ ‘visNetwork’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rhandsontable’
Package required but not available: ‘plotKML’

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

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

Packages suggested but not available for checking: ‘soilDB’ ‘sharpshootR’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘EBImage’ ‘sfit’ ‘expectile’ ‘HaarSeg’ ‘mpcbs’
Packages required but not available: ‘Morpho’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘arulesViz’
Packages required but not available: ‘DT’ ‘plotly’ ‘visNetwork’

Package suggested but not available for checking: ‘htmlwidgets’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘Hmisc’ ‘cacheSweave’
Package required but not available: ‘RVAideMemoire’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: compute.ALD
> ### Title: Compute ALD.
> ### Aliases: compute.ALD
> 
> ### ** Examples
> 
> library(asymLD)
> 
> # An example using haplotype frequencies from Wilson(2010)
> data(hla.freqs)
> hla.a_b <- hla.freqs[hla.freqs$locus1=="A" & hla.freqs$locus2=="B",]
> compute.ALD(hla.a_b)
   ALD.x.y is asymmetric LD for locus x conditioned on locus y

  locus1 locus2       F.1    F.1.2        F.2     F.2.1   ALD.1.2   ALD.2.1
1      A      B 0.1021811 0.340332 0.04876543 0.1903394 0.5150291 0.3857872
> hla.freqs$locus <- paste(hla.freqs$locus1, hla.freqs$locus2, sep="-")
> compute.ALD(hla.freqs[hla.freqs$locus=="C-B",])
   ALD.x.y is asymmetric LD for locus x conditioned on locus y

  locus1 locus2        F.1     F.1.2        F.2     F.2.1   ALD.1.2   ALD.2.1
1      C      B 0.08637241 0.7350216 0.05040254 0.4520268 0.8425979 0.6503396
> # Note: additonal columns on the input dataframe (e.g., "locus" above) are allowed, but
> # ignored by the function.
> 
> # An example using genotype data from the haplo.stats package
> require(haplo.stats)
Loading required package: haplo.stats
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘haplo.stats’
> data(hla.demo)
Warning in data(hla.demo) : data set ‘hla.demo’ not found
> geno <- hla.demo[,5:8]  #DPB-DPA
Error: object 'hla.demo' not found
Execution halted
Package suggested but not available for checking: ‘vdiffr’
Running ‘testthat.R’ [18s/23s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(atlantistools)
  > 
  > test_check("atlantistools")
  ── 1. Error: check visually (@test-plot-species.R#12)  ─────────────────────────
  there is no package called 'vdiffr'
  1: vdiffr::expect_doppelganger at testthat/test-plot-species.R:12
  2: getExportedValue(pkg, name)
  3: asNamespace(ns)
  4: getNamespace(ns)
  5: tryCatch(loadNamespace(name), error = function(e) stop(e))
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 197 SKIPPED: 0 FAILED: 1
  1. Error: check visually (@test-plot-species.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  pa.c:247:2: warning: initialization of ‘struct audio_instance * (*)(struct SEXPREC *, float,  int)’ from incompatible pointer type ‘void * (*)(struct SEXPREC *, float,  int)’ [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/audio.Rcheck/00install.out’ for details.
Package required but not available: ‘Rpdb’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/BANOVA.Rcheck/00install.out’ for details.
Package required but not available: ‘htmlwidgets’

Package suggested but not available for checking: ‘listviewer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
gimli.8897hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Package required but not available: ‘hypervolume’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Blasso.cpp:451:53: warning: ‘*<unknown>.Blasso::icept’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/bayesCL.Rcheck/00install.out’ for details.
Packages required but not available: ‘heatmaply’ ‘networkD3’ ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘rstanarm’ ‘shinystan’ ‘vdiffr’
Found the following significant warnings:
  mcmc.c:337:4: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/BayHap.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘rms’ ‘Hmisc’
Packages required but not available: ‘RcmdrMisc’ ‘Rcmdr’

Package suggested but not available for checking: ‘rgl’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘data.tree’ ‘DiagrammeR’ ‘userfriendlyscience’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_datatable_past
> ### Title: Interactive table of results
> ### Aliases: get_datatable_past
> 
> ### ** Examples
> 
> ## Need the DT package
> ## View all results for prog test
> get_datatable_past("prog")
Warning: This function is deprecated and will be removed in the next version. 
              Instead, use https://jumpingrivers.shinyapps.io/benchmarkme/
Error in get_datatable_past("prog") : Install DT package to use datatable
Execution halted
Packages required but not available: ‘plotly’ ‘dygraphs’ ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘DT’ ‘networkD3’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘Hmisc’ ‘intsvy’ ‘LSAmitR’
Package required but not available: ‘haplo.stats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
gimli.6000hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.13377hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.23172hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.29528hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.17144hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.3347hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.27887hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.2846hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.13544hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.22548hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.30338hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
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.
Package required but not available: ‘rgl’

Package suggested but not available for checking: ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [29s/49s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bikedata)
  Data for London, U.K. powered by TfL Open Data:
    Contains OS data Ⓒ Crown copyright and database rights 2016
  Data for New York City provided and owned by:
    NYC Bike Share, LLC and Jersey City Bike Share, LLC ("Bikeshare")
    see https://www.citibikenyc.com/data-sharing-policy
  Data for Washington DC (Captialbikeshare), Chiago (Divvybikes) and Boston (Hubway)
    provided and owned by Motivate International Inc.
    see https://www.capitalbikeshare.com/data-license-agreement
    and https://www.divvybikes.com/data-license-agreement
    and https://www.thehubway.com/data-license-agreement
  Nice Ride Minnesota license  https://www.niceridemn.org/data_license
  > 
  > test_check("bikedata")
  ── 1. Failure: dl_bikedata la (@test-download-data.R#88)  ──────────────────────
  `dl_bikedata(city = "la", data_dir = tempdir(), dates = 2016)` produced unexpected messages.
  Expected match: All data files already exist
  Actual values:
  * Downloading metro-bike-share-trips-2016-q4.csv.zip
  
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 136 SKIPPED: 2 FAILED: 1
  1. Failure: dl_bikedata la (@test-download-data.R#88) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘htmlwidgets’

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

Package suggested but not available for checking: ‘red’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 48-51 (BioInstaller.Rmd) 
Error: processing vignette ‘BioInstaller.Rmd’ failed with diagnostics:
there is no package called 'DT'
Execution halted
Packages suggested but not available for checking: ‘Hmisc’ ‘ecospat’
Packages required but not available: ‘rgl’ ‘shapes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggExtra’
Error in re-building vignettes:
  ...
Quitting from lines 171-174 (Intro.Rmd) 
Error: processing vignette ‘Intro.Rmd’ failed with diagnostics:
there is no package called 'ggExtra'
Execution halted
Packages required but not available: ‘plot3Drgl’ ‘rgl’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mlm_path_plot
> ### Title: Plot 'bmlm"s mediation model as a path diagram
> ### Aliases: mlm_path_plot
> 
> ### ** Examples
> 
> # Draw a template path diagram of the mediation model
> mlm_path_plot()
Error: qgraph package needed for this function. Please install it.
Execution halted
Package required but not available: ‘pec’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘htmlwidgets’
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.
Packages required but not available:
  ‘IsingFit’ ‘qgraph’ ‘mgm’ ‘NetworkToolbox’ ‘graphicalVAR’

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘rstanarm’ ‘brms’ ‘glmmADMB’
Running examples in ‘broom.mixed-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: brms_tidiers
> ### Title: Tidying methods for a brms model
> ### Aliases: brms_tidiers tidy.brmsfit glance.brmsfit augment.brmsfit
> 
> ### ** Examples
> 
>  ## original model
>  ## Not run: 
> ##D     fit <- brm(mpg ~ wt + (1|cyl) + (1+wt|gear), data = mtcars,
> ##D            iter = 500, chains = 2)
> ##D  
> ## End(Not run)
>  ## load stored object
>  fit <- readRDS(system.file("extdata", "brms_example.rds", package="broom.mixed"))
Warning: namespace ‘brms’ is not available and has been replaced
by .GlobalEnv when processing object ‘lmm2’
>  if (require("brms")) {
+    tidy(fit)
+    tidy(fit, parameters = "^sd_", conf.int = FALSE)
+    tidy(fit, effects = "fixed")
+    tidy(fit, effects = "ran_vals")
+    tidy(fit, effects = "ran_pars", robust = TRUE)
+ 
+ }
Loading required package: brms
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘brms’
> 
> # glance method
> glance(fit)
Error in mutate_impl(.data, dots) : 
  Evaluation error: no 'nobs' method is available.
Calls: glance ... glance_stan -> mutate -> mutate.tbl_df -> mutate_impl
Execution halted
Packages suggested but not available for checking:
  ‘brms’ ‘Hmisc’ ‘rstanarm’
Running ‘test-all.R’ [31s/36s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("broom")
  Loading required package: broom
  ── 1. Error: (unknown) (@test-biglm.R#7)  ──────────────────────────────────────
  no applicable method for 'bigglm' applied to an object of class "data.frame"
  1: bigglm(am ~ mpg, mtcars, family = binomial()) at testthat/test-biglm.R:7
  2: bigglm(am ~ mpg, mtcars, family = binomial())
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 903 SKIPPED: 3 FAILED: 1
  1. Error: (unknown) (@test-biglm.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘DESeq2’
Packages required but not available: ‘DiffBind’ ‘DESeq2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘plotly’
Package required but not available: ‘rms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
gimli.20558hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Package required but not available: ‘qgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  hash.c:144:5: warning: ‘strncpy’ specified bound 2048 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/C50.Rcheck/00install.out’ for details.
Packages required but not available: ‘Hmisc’ ‘RcmdrMisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘smoof’
Error in re-building vignettes:
  ...
Quitting from lines 47-69 (Adapting_Algorithm_for_CAISEr.Rmd) 
Error: processing vignette ‘Adapting_Algorithm_for_CAISEr.Rmd’ failed with diagnostics:
there is no package called 'smoof'
Execution halted
Package suggested but not available for checking: ‘leaflet’
Running examples in ‘candisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: heplot.candisc
> ### Title: Canonical Discriminant HE plots
> ### Aliases: heplot.candisc heplot3d.candisc
> ### Keywords: multivariate hplot
> 
> ### ** Examples
> 
> grass.mod <- lm(cbind(N1,N9,N27,N81,N243) ~ Block + Species, data=Grass)
> 
> grass.can1 <-candisc(grass.mod, term="Species")
> grass.canL <-candiscList(grass.mod)
> 
> heplot(grass.can1, scale=6)
> heplot(grass.can1, scale=6, terms=TRUE)
> heplot(grass.canL, terms=TRUE, ask=FALSE)
Vector scale factor set to  4.807288 
Vector scale factor set to  7.150784 
> 
> 
> ## Pottery data, from car package
> pottery.mod <- lm(cbind(Al, Fe, Mg, Ca, Na) ~ Site, data=Pottery)
> pottery.can <-candisc(pottery.mod)
> 
> heplot(pottery.can, var.lwd=3)
Vector scale factor set to  14.83312 
> heplot3d(pottery.can, var.lwd=3, scale=10, zlim=c(-3,3), wire=FALSE)
Loading required namespace: rgl
Failed with error:  ‘there is no package called ‘rgl’’
Error in heplot3d.mlm(can.mod, terms = terms, factor.means = term, xlab = canlab[1],  : 
  rgl package is required.
Calls: heplot3d -> heplot3d.candisc -> heplot3d -> heplot3d.mlm
Execution halted
Package required but not available: ‘qpcR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘DESeq2’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CreateSpacetimeFolds
> ### Title: Create Space-time Folds
> ### Aliases: CreateSpacetimeFolds
> 
> ### ** Examples
> 
> library(GSIF)
Error in library(GSIF) : there is no package called ‘GSIF’
Execution halted
Error in re-building vignettes:
  ...
CAST                   package:CAST                    R Documentation

'_c_a_r_e_t' _A_p_p_l_i_c_a_t_i_o_n_s _f_o_r _S_p_a_t_i_a_l-_T_e_m_p_o_r_a_l _M_o_d_e_l_s

_D_e_s_c_r_i_p_t_i_o_n:

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

_D_e_t_a_i_l_s:

     'caret' Applications for Spatio-Temporal models

_A_u_t_h_o_r(_s):

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


Quitting from lines 65-73 (CAST-intro.Rmd) 
Error: processing vignette ‘CAST-intro.Rmd’ failed with diagnostics:
there is no package called 'mapview'
Execution halted
Packages suggested but not available for checking: ‘rms’ ‘lqa’
Found the following significant warnings:
  catnet_rexport.cpp:202:17: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
  catnet_rexport.cpp:206:15: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:213:16: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 0 and 1023 [-Wformat-overflow=]
  catnet_rexport.cpp:216:18: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
  catnet_rexport.cpp:217:17: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:232:17: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:231:18: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/catnet.Rcheck/00install.out’ for details.
Packages required but not available: ‘rms’ ‘CPE’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggiraph’
Packages required but not available: ‘Hmisc’ ‘rms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘nonlinearTseries’
gimli.13643hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Packages required but not available: ‘rgl’ ‘sphereplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  guess_type.c:14:9: warning: ‘strncpy’ specified bound 512 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/checkmate.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  ‘GenomicInteractions’ ‘Gviz’
Error in re-building vignettes:
  ...
Quitting from lines 41-105 (Visualising_Interactions.Rmd) 
Error: processing vignette ‘Visualising_Interactions.Rmd’ failed with diagnostics:
there is no package called 'GenomicInteractions'
Execution halted
Package suggested but not available for checking: ‘qpcR’
Error in re-building vignettes:
  ...
Quitting from lines 21-92 (cifti_work.Rmd) 
Error: processing vignette ‘cifti_work.Rmd’ failed with diagnostics:
there is no package called 'rgl'
Execution halted
Package suggested but not available for checking: ‘userfriendlyscience’
Package required but not available: ‘htmlTable’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Seurat’
Package required but not available: ‘smoof’

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

Package suggested but not available for checking: ‘shinytest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [14s/140s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(codemetar)
  > 
  > test_check("codemetar")
  ── 1. Error: we can validate this file (@test-codemeta_validate.R#5)  ──────────
  jsonld.InvalidUrl: Dereferencing a URL did not result in a valid JSON-LD object. Possible causes are an inaccessible URL perhaps due to a same-origin policy (ensure the server uses CORS if you are using client-side JavaScript), too many redirects, a non-JSON response, or more than one HTTP Link Header was provided for a remote context.
  1: testthat::expect_true(codemeta_validate("codemeta_test.json")) at testthat/test-codemeta_validate.R:5
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: codemeta_validate("codemeta_test.json")
  5: writeLines(jsonld::jsonld_compact(jsonld::jsonld_expand(codemeta), context), test)
  6: jsonld::jsonld_compact(jsonld::jsonld_expand(codemeta), context)
  7: validate_arg(doc)
  8: jsonld::jsonld_expand(codemeta)
  9: structure(ctx$call("r_expand", compacted, options), class = "json")
  10: ctx$call("r_expand", compacted, options)
  11: this$eval(src)
  12: get_str_output(context_eval(join(src), private$context))
  13: context_eval(join(src), private$context)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 79 SKIPPED: 10 FAILED: 1
  1. Error: we can validate this file (@test-codemeta_validate.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘visNetwork’

Package suggested but not available for checking: ‘wTO’

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

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

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

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

Package suggested but not available for checking: ‘DT’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: arrows3D
> ### Title: arrows in 3D, based on package rgl
> ### Aliases: arrows3D arrows3D.default
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> x <- cbind(rnorm(10),rnorm(10),rnorm(10))
> plot3D(x)
Loading required namespace: rgl
Failed with error:  ‘there is no package called ‘rgl’’
Loading required namespace: rgl
Failed with error:  ‘there is no package called ‘rgl’’
Error in loadNamespace(name) : there is no package called ‘rgl’
Calls: plot3D ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Packages required but not available: ‘rms’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘choroplethr’
Error in re-building vignettes:
  ...
Quitting from lines 111-123 (countytimezones.Rmd) 
Error: processing vignette ‘countytimezones.Rmd’ failed with diagnostics:
there is no package called 'choroplethr'
Execution halted
Running ‘testthat.R’ [44s/74s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > ops <- options("crayon.enabled" = FALSE, warn = 1)
  > library(testthat)
  > library("covr")
  > 
  > # Skip tests on Solaris as gcc is not in the PATH and I do not have an easy way
  > # to mimic the CRAN build environment
  > if (!tolower(Sys.info()[["sysname"]]) == "sunos") {
  +   Sys.setenv("R_TESTS" = "")
  +   test_check("covr")
  + }
  ── 1. Failure: gitlab (@test-gitlab.R#8)  ──────────────────────────────────────
  `gitlab(coverage = cov)` threw an error.
  Message: there is no package called 'DT'
  Class:   simpleError/error/condition
  
  ── 2. Failure: gitlab (@test-gitlab.R#10)  ─────────────────────────────────────
  file.exists("TestS4/public/coverage.html") isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 259 SKIPPED: 2 FAILED: 2
  1. Failure: gitlab (@test-gitlab.R#8) 
  2. Failure: gitlab (@test-gitlab.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘shapes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  lprintf.c:336:17: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/creditr.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘rcrossref’
Running ‘test-all.R’ [1s/2s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  > test_check("crminer")
  Loading required package: crminer
  ── 1. Error: crm_links works (@test-crm_links.R#4)  ────────────────────────────
  package 'rcrossref' not found
  1: crm_links("10.7717/peerj.1268", "pdf") at testthat/test-crm_links.R:4
  2: crm_works_links(dois = doi, ...)
  3: stats::setNames(lapply(dois, get_links, ...), dois)
  4: lapply(dois, get_links, ...)
  5: FUN(X[[i]], ...)
  6: crm_GET(sprintf("works/%s", x), NULL, FALSE, ...)
  7: crul::HttpClient$new(url = url, headers = list(useragent = crminer_ua(), `X-USER-AGENT` = crminer_ua()), 
         opts = list(...))
  8: .subset2(public_bind_env, "initialize")(...)
  9: crminer_ua()
  10: sprintf("rOpenSci(rcrossref/%s)", utils::packageVersion("rcrossref"))
  11: utils::packageVersion("rcrossref")
  12: stop(gettextf("package %s not found", sQuote(pkg)), domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 54 SKIPPED: 20 FAILED: 1
  1. Error: crm_links works (@test-crm_links.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘nbpMatching’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
gimli.29210hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Found the following significant warnings:
  hash.c:144:5: warning: ‘strncpy’ specified bound 2048 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Cubist.Rcheck/00install.out’ for details.
Packages required but not available: ‘feature’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(customLayout)
  > library(vdiffr)
  Error in library(vdiffr) : there is no package called 'vdiffr'
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 142-152 (truncated_tesseract.Rmd) 
Error: processing vignette ‘truncated_tesseract.Rmd’ failed with diagnostics:
there is no package called 'rgl'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 177-179 (cycling_data_analysis.Rmd) 
Error: processing vignette ‘cycling_data_analysis.Rmd’ failed with diagnostics:
there is no package called 'leaflet'
Execution halted
Package suggested but not available for checking: ‘listviewer’
Packages required but not available: ‘rgl’ ‘pca3d’ ‘SNPassoc’ ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘rglwidget’ ‘rgl’
Error in re-building vignettes:
  ...
Quitting from lines 22-34 (DatabionicSwarm.Rmd) 
Error: processing vignette ‘DatabionicSwarm.Rmd’ failed with diagnostics:
there is no package called 'rgl'
Execution halted
Packages required but not available: ‘htmlwidgets’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘networkD3’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘data.tree’
Error in re-building vignettes:
  ...
Quitting from lines 83-93 (usingDataPackageR.Rmd) 
Error: processing vignette ‘usingDataPackageR.Rmd’ failed with diagnostics:
there is no package called 'data.tree'
Execution halted
Package suggested but not available for checking: ‘htmlTable’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Warning in block_exec(params) :
  failed to tidy R code in chunk <workflow>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Quitting from lines 68-131 (dataRetrieval.Rmd) 
Error: processing vignette ‘dataRetrieval.Rmd’ failed with diagnostics:
there is no package called 'htmlTable'
Execution halted
Package required but not available: ‘DiagrammeR’

Packages suggested but not available for checking:
  ‘networkD3’ ‘htmlwidgets’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘plotly’ ‘rgl’ ‘choroplethr’
Package suggested but not available for checking: ‘SASxport’
Packages required but not available: ‘seqHMM’ ‘TraMineR’

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

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

VignetteBuilder package required for checking but not installed: ‘packagedocs’

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

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

Package suggested but not available for checking: ‘ggExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
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 'DT'
Execution halted
Package required but not available: ‘Hmisc’

Depends: includes the non-default packages:
  ‘JavaGD’ ‘Deducer’ ‘sp’ ‘maptools’ ‘OpenStreetMap’ ‘scales’ ‘rgdal’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DiagrammeR’
Packages suggested but not available for checking: ‘heatmaply’ ‘d3heatmap’

Package which this enhances but not available for checking: ‘Hmisc’
Error in re-building vignettes:
  ...

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

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

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

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


Attaching package: 'dendextend'

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

    cutree


Attaching package: 'gplots'

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

    bluered, greenred

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

    lowess

Quitting from lines 931-933 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
there is no package called 'd3heatmap'
Execution halted
Found the following significant warnings:
  GetData.c:342:15: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 3 [-Wformat-overflow=]
  GetData.c:355:15: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 3 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/DetSel.Rcheck/00install.out’ for details.
Packages required but not available:
  ‘dexter’ ‘DT’ ‘htmlwidgets’ ‘ggExtra’ ‘networkD3’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  clipper.cpp:721:34: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct ClipperLib::TEdge’; use assignment or value-initialization instead [-Wclass-memaccess]
  dbfopen.c:1346:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopen.c:1328:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopen.c:879:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  dbfopen.c:1693:9: warning: ‘strncpy’ output may be truncated copying 11 bytes from a string of length 11 [-Wstringop-truncation]
  dbfopen.c:2065:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/dggridR.Rcheck/00install.out’ for details.
Packages required but not available: ‘htmlwidgets’ ‘visNetwork’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rss3d
> ### Title: 3D graphical tool for defect detection of Space-Filling Designs.
> ### Aliases: rss3d
> ### Keywords: design
> 
> ### ** Examples
> 
> 	# An orthogonal array in 3D   
> data(OA131)
> 
> 	# centering the design points of this 7-levels design
> OA <- (OA131 + 0.5)/7
> 
> 	# 2D projections onto coordinate axis 
> pairs(OA, xlim=c(0,1), ylim=c(0,1))
> 	# Now let us look at the 3D properties with the 3D RSS (requires the rgl package)
> rss <- rss3d(OA, lower=c(0,0,0), upper=c(1,1,1))

3D Radial Scanning Statistic (RSS) with GREENWOOD statistic
Discretization step (in degree) : 3

Maximum of RS statistic values (global statistic) per triplet of dimensions
(1,2,3) 0.2621302

[1] "Error : the package rgl is not installed"
Error in rss3d(OA, lower = c(0, 0, 0), upper = c(1, 1, 1)) : 
  object 'dir.max' not found
Execution halted
Package suggested but not available for checking: ‘GPareto’
Package required but not available: ‘rgl’

Packages suggested but not available for checking:
  ‘DiffusionRgqd’ ‘DiffusionRjgqd’

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

Package suggested but not available for checking: ‘DiffusionRgqd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: contToDisc
> ### Title: Continuous to Discrete Transformation
> ### Aliases: contToDisc
> ### Keywords: datagen
> 
> ### ** Examples
> 
> # Example copenhagen stroke study data
> library(pec)
Error in library(pec) : there is no package called ‘pec’
Execution halted
Running ‘UnitTestsDiscSurvDataTransform.R’ [3s/3s]
  Running ‘UnitTestsDiscSurvEstimation.R’ [2s/2s]
  Running ‘UnitTestsDiscSurvEvalShort.R’ [4s/5s]
  Running ‘UnitTestsDiscSurvEvaluation.R’ [2s/3s]
  Running ‘UnitTestsDiscSurvLifeTable.R’ [2s/2s]
  Running ‘UnitTestsDiscSurvSimulation.R’ [3s/3s]
Running the tests in ‘tests/UnitTestsDiscSurvEvaluation.R’ failed.
Complete output:
  > library(discSurv)
  > library(pec)
  Error in library(pec) : there is no package called 'pec'
  Execution halted
Running examples in ‘divest-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: readDicom
> ### Title: Read one or more DICOM directories
> ### Aliases: readDicom sortDicom scanDicom
> 
> ### ** Examples
> 
> path <- system.file("extdata", "raw", package="divest")
> scanDicom(path)
[dcm2niix info] Found 4 DICOM file(s)
[dcm2niix ERROR] You do not have write permissions for the directory /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/divest/extdata/raw
[dcm2niix ERROR] You do not have write permissions for the directory /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/divest/extdata/raw
  label
2  <NA>
1  <NA>
                                                                       rootPath
2 /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/divest/extdata/raw
1 /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/divest/extdata/raw
  files seriesNumber seriesDescription patientName studyDate echoTime
2     2            8        DTIb3000s5        <NA>      <NA>   112.00
1     2            9       fl3D_t1_sag        <NA>      <NA>     4.94
  repetitionTime echoNumber phase diffusion
2           4100         NA FALSE      TRUE
1             11         NA FALSE     FALSE
> readDicom(path, interactive=FALSE)
[dcm2niix info] Found 4 DICOM file(s)
[dcm2niix ERROR] You do not have write permissions for the directory /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/divest/extdata/raw
[dcm2niix info]  Warning: all images appear to be a single slice - please check slice/vector orientation
[dcm2niix ERROR] You do not have write permissions for the directory /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/divest/extdata/raw
Error in .readPath(path.expand(p), flipY, crop, forceStack, verbosity,  : 
  DICOM scan failed
Calls: readDicom -> lapply -> FUN -> .readPath
Execution halted
Package required but not available: ‘RcmdrMisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
gimli.9639hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.19182hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.25430hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.1222hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.31960hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.10556hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.7004hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.12385hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.19907hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.28384hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.4147hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
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.
Package suggested but not available for checking: ‘rms’
Error in re-building vignettes:
  ...
Quitting from lines 330-331 (dosresmeta.Rnw) 
Error: processing vignette ‘dosresmeta.Rnw’ failed with diagnostics:
there is no package called 'rms'
Execution halted
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/dpglasso.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘networkD3’ ‘visNetwork’
Running ‘testthat.R’ [44s/47s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(drake)
  
  Attaching package: 'drake'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  > 
  > test_check("drake")
  ── 1. Error: cache functions work (@test-cache.R#409)  ─────────────────────────
  there is no package called 'visNetwork'
  1: null_graph() at testthat/test-cache.R:409
  2: visNetwork::visNetwork
  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: 315 SKIPPED: 222 FAILED: 1
  1. Error: cache functions work (@test-cache.R#409) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available: ‘BIGL’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘TSclust’ ‘TSdist’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Warning in engine$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: TSclust
Quitting from lines 1576-1584 (dtwclust.Rnw) 
Error: processing vignette ‘dtwclust.Rnw’ failed with diagnostics:
object ‘diss.ACF’ not found
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: raster
Loading required package: sp
Loading required package: snow
Loading required package: ggplot2
Loaded dtwSat v0.2.4. See ?dtwSat for help, citation("dtwSat") for use in publication.

Quitting from lines 97-111 (applying_twdtw.Rmd) 
Error: processing vignette ‘applying_twdtw.Rmd’ failed with diagnostics:
there is no package called 'Hmisc'
Execution halted
Packages required but not available: ‘rms’ ‘plotly’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘d3heatmap’ ‘edgebundleR’ ‘htmlwidgets’ ‘networkD3’ ‘plotly’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tomogRxC3d
> ### Title: Plotting 2x3 Ecological Inference Estimates in 3 dimensions
> ### Aliases: tomogRxC3d
> 
> ### ** Examples
> 
> data(RxCdata)
> formula <- cbind(turnout, noturnout) ~ cbind(white, black, hisp)
> tomogRxC3d(formula, RxCdata, total=NULL, lci=TRUE, estimates=TRUE, ci=TRUE, transparency=.5, 
+ 	light=FALSE, rotate=FALSE)
Error: Package rgl is needed for the tomogRxC3d function to work. Please install it.
Execution halted
Package required but not available: ‘colourpicker’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘prim’
Packages suggested but not available for checking: ‘brms’ ‘mediation’

Packages which this enhances but not available for checking:
  ‘CARBayes’ ‘glmmADMB’ ‘rstanarm’
Error in re-building vignettes:
  ...
Loading required package: emmeans
NOTE: As of emmeans versions > 1.2.3,
      The 'cld' function will be deprecated in favor of 'CLD'.
      You may use 'cld' only if you have package:multcomp attached.
Quitting from lines 105-109 (messy-data.Rmd) 
Error: processing vignette ‘messy-data.Rmd’ failed with diagnostics:
there is no package called 'mediation'
Execution halted
Package required but not available: ‘Hmisc’

Package suggested but not available for checking: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  main.c:334:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:575:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:518:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:805:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:755:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1034:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:983:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1377:7: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1279:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1678:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1962:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1912:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:2316:7: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:2212:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/enviPat.Rcheck/00install.out’ for details.
Running examples in ‘epade-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: box.plot.wtd
> ### Title: weighted Boxplot
> ### Aliases: box.plot.wtd
> ### Keywords: boxplot
> 
> ### ** Examples
> 
> x<-rnorm(1000)
> g<-round(runif(1000))
> w<-abs(rnorm(1000))
> d<- data.frame(x, g, w)
> box.plot.wtd('x', 'g', w='w', data=d)
Error in library(Hmisc) : there is no package called ‘Hmisc’
Calls: box.plot.wtd -> library
Execution halted
Found the following significant warnings:
  epanet.c:999:5: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:1000:5: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:1492:3: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:2308:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:2309:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  input1.c:454:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  input1.c:455:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  input3.c:604:2: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/epanet2toolkit.Rcheck/00install.out’ for details.
Package required but not available: ‘timeROC’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘epicontacts’ ‘leaflet’ ‘htmlwidgets’ ‘visNetwork’

Package suggested but not available for checking: ‘vdiffr’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tmap’
Error in re-building vignettes:
  ...
Loading required package: xml2
trying URL ‘https://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 4490 bytes
==================================================
downloaded 4490 bytes

Table t2020_rk310 cached at /tmp/RtmpBzzsbv/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 ‘https://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 13630 bytes (13 KB)
==================================================
downloaded 13 KB

Table ten00081 cached at /tmp/RtmpBzzsbv/eurostat/ten00081_date_code_TF.rds
Quitting from lines 291-308 (eurostat_tutorial.Rmd) 
Error: processing vignette ‘eurostat_tutorial.Rmd’ failed with diagnostics:
there is no package called 'tmap'
Execution halted
Packages suggested but not available for checking:
  ‘DT’ ‘ggalt’ ‘flexdashboard’ ‘shinytest’
Running ‘testthat.R’ [68s/71s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(evaluator)
  > 
  > test_check("evaluator")
  ── 1. Error: (unknown) (@test-explore-scenarios.R#4)  ──────────────────────────
  there is no package called 'shinytest'
  1: library(shinytest) at testthat/test-explore-scenarios.R:4
  2: stop(txt, domain = NA)
  
  ── 2. Error: (unknown) (@test-openfair-example.R#3)  ───────────────────────────
  there is no package called 'shinytest'
  1: library(shinytest) at testthat/test-openfair-example.R:3
  2: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 84 SKIPPED: 5 FAILED: 2
  1. Error: (unknown) (@test-explore-scenarios.R#4) 
  2. Error: (unknown) (@test-openfair-example.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘geomorph’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘DT’ ‘scatterD3’

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

Package suggested but not available for checking: ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Creating package 'fakepack' in '/tmp/Rtmp8LuXXp'
No DESCRIPTION found. Creating with values:


Prerequisite DESCRIPTION found.
Prerequisite R/throw.R found.
Prerequisite R/throw.R found.
Prerequisite R/throw.R found.
Prerequisite R/throw.R found.
* installing *source* package ‘fakepack’ ...
** R
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  ‘fakepack’ 
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (fakepack)
Prerequisite R/throw.R found.
Prerequisite R/throw.R found.
Prerequisite DESCRIPTION found.
Prerequisite R/throw.R found.
Error: processing vignette ‘An_Introduction_to_fakemake.Rmd’ failed with diagnostics:
there is no package called 'spelling'
Execution halted
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/FastRWeb.Rcheck/00install.out’ for details.
Package required but not available: ‘rgl’

Package suggested but not available for checking: ‘DESeq2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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 8.239   0.12   8.501
Package required but not available: ‘fdapace’

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

Package suggested but not available for checking: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘plot3Drgl’ ‘rgl’
Packages required but not available: ‘soilDB’ ‘Hmisc’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘diveRsity’
Packages required but not available: ‘Rcmdr’ ‘rgl’

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

Package suggested but not available for checking: ‘vdiffr’

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

Package suggested but not available for checking: ‘ExtDist’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotBarrierTree2D
> ### Title: Plot Barrier Tree in 2D
> ### Aliases: plotBarrierTree2D
> 
> ### ** Examples
> 
> # create a feature object
> X = createInitialSample(n.obs = 900, dim = 2)
> f = smoof::makeAckleyFunction(dimensions = 2)
Error in loadNamespace(name) : there is no package called ‘smoof’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Running ‘test-features.R’ [0s/1s]
  Running ‘test-general.R’ [10s/11s]
Running the tests in ‘tests/test-general.R’ failed.
Complete output:
  > library(testthat)
  > 
  > # test general stuff:
  > test_check("flacco", filter = "^base")
  Loading required package: flacco
  ── 1. Error: Usage of regular and smoof functions (@test-base-printFeatureObject
  there is no package called 'smoof'
  1: smoof::makeBBOBFunction at testthat/test-base-printFeatureObject.R:68
  2: getExportedValue(pkg, name)
  3: asNamespace(ns)
  4: getNamespace(ns)
  5: tryCatch(loadNamespace(name), error = function(e) stop(e))
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 152 SKIPPED: 0 FAILED: 1
  1. Error: Usage of regular and smoof functions (@test-base-printFeatureObject.R#68) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  FLAN_Clone.h:131:11: warning: ‘*<unknown>.FLAN_SimClone::mDist’ is used uninitialized in this function [-Wuninitialized]
  FLAN_Clone.h:204:11: warning: ‘*<unknown>.FLAN_SimInhomogeneousClone::mMU’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/flan.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘LogConcDEAD’
Package required but not available: ‘homals’

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

Package suggested but not available for checking: ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  RngStream.c:275:7: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/freeknotsplines.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: oro.nifti
oro.nifti 0.9.1
Quitting from lines 14-29 (exploring_included_data.Rmd) 
Error: processing vignette ‘exploring_included_data.Rmd’ failed with diagnostics:
there is no package called 'rgl'
Execution halted
Package required but not available: ‘Hmisc’

Packages suggested but not available for checking: ‘dggrids’ ‘INLA’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘WGCNA’
Packages suggested but not available for checking: ‘haplo.stats’ ‘rms’
Found the following significant warnings:
  hap_c.c:380:28: warning: ‘%03d’ directive writing between 3 and 10 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  hap_c.c:392:28: warning: ‘%03d’ directive writing between 3 and 10 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/gap.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘WeightedCluster’
Found the following significant warnings:
  Gdmlib.cpp:2352:19: warning: ‘%lf’ directive writing between 3 and 317 bytes into a region of size between 0 and 1023 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/gdm.Rcheck/00install.out’ for details.
Package required but not available: ‘pca3d’

Package suggested but not available for checking: ‘DESeq2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 22-34 (GeneralizedUmatrix.Rmd) 
Error: processing vignette ‘GeneralizedUmatrix.Rmd’ failed with diagnostics:
there is no package called 'rgl'
Execution halted
Packages required but not available: ‘leaflet’ ‘DT’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘reldist’
Package suggested but not available for checking: ‘packagedocs’

VignetteBuilder package required for checking but not installed: ‘packagedocs’

Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/docs.Rmd’
   ‘inst/doc/rd.Rmd’
(Is a VignetteBuilder field missing?)

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  rboxlib.c:351:5: warning: ‘strncat’ output may be truncated copying between 0 and 199 bytes from a string of length 199 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/geometry.Rcheck/00install.out’ for details.
Packages required but not available: ‘leaflet’ ‘rbokeh’ ‘plotly’

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

Packages suggested but not available for checking: ‘vdiffr’ ‘pkgnet’

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

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

Package suggested but not available for checking: ‘vdiffr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: ‘__var_41_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/gglasso.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ggperiodic)
  
  Attaching package: 'ggperiodic'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("ggperiodic")
  ── 1. Error: (unknown) (@test-fortify.R#7)  ────────────────────────────────────
  there is no package called 'vdiffr'
  1: library(vdiffr) at testthat/test-fortify.R:7
  2: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 56 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-fortify.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Packages suggested but not available for checking: ‘Hmisc’ ‘vdiffr’
Running examples in ‘ggplot2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hmisc
> ### Title: A selection of summary functions from Hmisc
> ### Aliases: hmisc mean_cl_boot mean_cl_normal mean_sdl median_hilow
> 
> ### ** Examples
> 
> x <- rnorm(100)
> mean_cl_boot(x)
Error: Hmisc package required for this function
Execution halted
Package required but not available: ‘editData’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘colourpicker’ ‘DT’ ‘Hmisc’ ‘plotly’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hmisc_h
> ### Title: Horizontal versions of summary functions from Hmisc
> ### Aliases: hmisc_h mean_cl_boot_h mean_cl_normal_h mean_sdl_h
> ###   median_hilow_h
> 
> ### ** Examples
> 
> x <- rnorm(100)
> mean_cl_boot_h(x)
Error: Hmisc package required for this function
Execution halted
Packages required but not available: ‘ggExtra’ ‘paletteer’

Package suggested but not available for checking: ‘vdiffr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ggthemes)
  > 
  > test_check("ggthemes")
  ── 1. Error: theme_few draws correctly (@test-few.R#64)  ───────────────────────
  there is no package called 'vdiffr'
  1: expect_doppelganger("theme_few", plot + theme_few()) at testthat/test-few.R:64
  2: vdiffr::expect_doppelganger at /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/ggthemes.Rcheck/tests/testthat/helper-vdiffr.R:18
  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: 274 SKIPPED: 0 FAILED: 1
  1. Error: theme_few draws correctly (@test-few.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘wordcloud2’
Package required but not available: ‘rhandsontable’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 117-117 (GMCM-JStatSoft.Rnw) 
Error: processing vignette ‘GMCM-JStatSoft.Rnw’ failed with diagnostics:
there is no package called 'Hmisc'
Execution halted
Package suggested but not available for checking: ‘mediation’
Packages required but not available: ‘htmlTable’ ‘Hmisc’

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

Package suggested but not available for checking: ‘WGCNA’

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

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

Package suggested but not available for checking: ‘rglwidget’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: granova.2w
> ### Title: Graphical display of data for two-way analysis of variance
> ### Aliases: granova.2w
> ### Keywords: hplot
> 
> ### ** Examples
> 
>  
> # using the R dataset warpbreaks; see documentation 
> #(first surface flat since fit = 'linear' (default); 
> #second surface shows curvature)
> granova.2w(warpbreaks)
Loading required package: rgl
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘rgl’
Loading required package: tcltk
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-24. For overview type 'help("mgcv-package")'.
[1] breaks ~ wool * tension
Loading required namespace: rgl
Failed with error:  ‘there is no package called ‘rgl’’
Error in scatter3d(facA.mn.cntrst, yy, facB.mn.cntrst, xlab = colnames(data.A.B)[2],  : 
  rgl package missing
Calls: granova.2w -> scatter3d
Execution halted
Package required but not available: ‘sparklyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  dump_json_ast.cpp:21:12: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound 1000 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/graphql.Rcheck/00install.out’ for details.
Packages required but not available: ‘Gmisc’ ‘Hmisc’ ‘rms’ ‘htmlTable’

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

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

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

Package suggested but not available for checking: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘plotKML’
gimli.32445hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Running examples in ‘happybiRthday-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: celebrate
> ### Title: Celebrating software birthdays
> ### Aliases: celebrate
> 
> ### ** Examples
> 
> celebrate("Bohdan-Khomtchouk")
Error in gh::gh("/users/:username/repos", username = github_username,  : 
  GitHub API error (403): 403 Forbidden
  API rate limit exceeded for 137.208.57.141. (But here's the good news: Authenticated requests get a higher rate limit. Check out the documentation for more details.)
Calls: celebrate -> <Anonymous> -> gh_process_response
Execution halted
Found the following significant warnings:
  readstat/readstat_writer.c:82:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  readstat/readstat_writer.c:261:5: warning: ‘strncpy’ specified bound 256 equals destination size [-Wstringop-truncation]
  readstat/readstat_writer.c:316:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  readstat/sas/readstat_sas7bcat_write.c:108:5: warning: ‘strncpy’ output may be truncated copying 64 bytes from a string of length 99 [-Wstringop-truncation]
  readstat/sas/readstat_sas.c:284:5: warning: ‘strncpy’ output may be truncated copying 64 bytes from a string of length 99 [-Wstringop-truncation]
  readstat/sas/readstat_sas.c:337:5: warning: ‘strncpy’ output may be truncated copying 8 bytes from a string of length 31 [-Wstringop-truncation]
  readstat/spss/readstat_sav_write.c:150:5: warning: ‘strncpy’ output may be truncated copying 9 bytes from a string of length 9 [-Wstringop-truncation]
  readstat/spss/readstat_sav_write.c:158:5: warning: ‘strncpy’ output may be truncated copying 8 bytes from a string of length 8 [-Wstringop-truncation]
  readstat/spss/readstat_por_write.c:194:5: warning: ‘strncpy’ output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/haven.Rcheck/00install.out’ for details.
Package required but not available: ‘Hmisc’

Package suggested but not available for checking: ‘leaflet’

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

Package suggested but not available for checking: ‘Hmisc’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: update_model
> ### Title: Run Model on New Data
> ### Aliases: update_model update.run_model plot.updated_model
> 
> ### ** Examples
> 
> mod1 <-
+   define_strategy(
+     transition = define_transition(
+       .5, .5,
+       .1, .9
+     ),
+     define_state(
+       cost = 543 + age * 5,
+       ly = 1
+     ),
+     define_state(
+       cost = 432 + age,
+       ly = 1 * age / 100
+     )
+   )
No named state -> generating names.
No named state -> generating names.
> 
> mod2 <-
+   define_strategy(
+     transition = define_transition(
+       .5, .5,
+       .1, .9
+     ),
+     define_state(
+       cost = 789 * age / 10,
+       ly = 1
+     ),
+     define_state(
+       cost = 456 * age / 10,
+       ly = 1 * age / 200
+     )
+   )
No named state -> generating names.
No named state -> generating names.
> 
> res <- run_model(
+   mod1, mod2,
+   parameters = define_parameters(
+     age_init = 60,
+     age = age_init + markov_cycle
+   ),
+   init = 1:0,
+   cycles = 10,
+   cost = cost,
+   effect = ly
+ )
No named model -> generating names.
> 
> # generating table with new parameter sets
> new_tab <- data.frame(
+   age_init = 40:45
+ )
> 
> # with run_model result
> ndt <- update(res, newdata = new_tab)
No weights specified in update, using equal weights.
Updating strategy 'I'...
Updating strategy 'II'...
> 
> summary(ndt)
Loading required namespace: Hmisc
Failed with error:  ‘there is no package called ‘Hmisc’’
Error in wtd_summary(tmp[[x]], tmp$.weights) : 
  'Hmisc' package required to produce weighted summary.
Calls: summary ... summary.updated_model -> lapply -> FUN -> wtd_summary
Execution halted
Error in re-building vignettes:
  ...
Scale for 'colour' is already present. Adding another scale for
'colour', which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for
'colour', which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for
'colour', which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for
'colour', which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for
'colour', which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for
'colour', which will replace the existing scale.
Failed with error:  'there is no package called 'Hmisc''
Quitting from lines 197-198 (g_heterogeneity.Rmd) 
Error: processing vignette ‘g_heterogeneity.Rmd’ failed with diagnostics:
'Hmisc' package required to produce weighted summary.
Execution halted
Package required but not available: ‘nhanesA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘visNetwork’
Packages suggested but not available for checking: ‘rgl’ ‘FRB’
Package required but not available: ‘DESeq2’

Package suggested but not available for checking: ‘glmmADMB’

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

Packages suggested but not available for checking:
  ‘Rcmdr’ ‘RcmdrPlugin.HH’ ‘microplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  gener.c:39:26: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/hier.part.Rcheck/00install.out’ for details.
Packages required but not available: ‘rgl’ ‘tkrgl’

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

Packages suggested but not available for checking: ‘rms’ ‘tables’ ‘plotly’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: HS.normal.means
> ### Title: The horseshoe prior for the sparse normal means problem
> ### Aliases: HS.normal.means
> 
> ### ** Examples
> 
> #Empirical Bayes example with 20 signals, rest is noise
> #Posterior mean for the signals is plotted
> #And variable selection is performed using the credible intervals
> #And the credible intervals are plotted
> truth <- c(rep(0, 80), rep(8, 20))
> data <-  truth + rnorm(100, 1)
> tau.hat <- HS.MMLE(data, Sigma2 = 1)
> res.HS1 <- HS.normal.means(data, method.tau = "fixed", tau = tau.hat,
+ method.sigma = "fixed", Sigma2 = 1)
[1] 1000
[1] 2000
[1] 3000
[1] 4000
[1] 5000
[1] 6000
> #Plot the posterior mean against the data (signals in blue)
> plot(data, res.HS1$BetaHat, col = c(rep("black", 80), rep("blue", 20)))
> #Find the selected betas (ideally, the last 20 are equal to 1)
> HS.var.select(res.HS1, data, method = "intervals")
  [1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 [38] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0
 [75] 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
> #Plot the credible intervals
> library(Hmisc)
Error in library(Hmisc) : there is no package called ‘Hmisc’
Execution halted
Package required but not available: ‘htmlwidgets’

Package suggested but not available for checking: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/htmlwidgets.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘HTSFilter’
Error in re-building vignettes:
  ...
trying URL ‘https://arxiv.org/e-print/1406.4806v1’
Content type 'application/x-eprint-tar' length 29273 bytes (28 KB)
==================================================
downloaded 28 KB

Quitting from lines 162-165 (intro.Rmd) 
Error: processing vignette ‘intro.Rmd’ failed with diagnostics:
there is no package called 'wordcloud2'
Execution halted
Package required but not available: ‘coefplot’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘NSM3’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘EBImage’
Package unavailable to check Rd xrefs: ‘EBImage’
Error in re-building vignettes:
  ...
Using basic display functionality.
  * For better display functionality, install the EBImage package.
  * To install `EBImage`:
    - Install `BiocManager` with `install.packages("BiocManager")`.
    - Then run `BiocManager::install("EBImage")`.
Quitting from lines 50-63 (reading-and-writing-images.Rmd) 
Error: processing vignette ‘reading-and-writing-images.Rmd’ failed with diagnostics:
figure margins too large
Execution halted
Package required but not available: ‘plotly’

Package suggested but not available for checking: ‘mediation’

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

Package suggested but not available for checking: ‘compareGroups’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘rgl’ ‘sphereplot’ ‘INLA’
Packages required but not available: ‘htmlwidgets’ ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
Running ‘testthat.R’ [0m/16m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ipeaData)
  > 
  > test_check("ipeaData")
  [1] "NA. 05/1999 a 03/2009. Acesso em: 20/10/2018"
  ── 1. Error: ipeaData (@test_functions_ipea_data.R#19)  ────────────────────────
  Recv failure: Connection timed out
  1: suppressWarnings(result <- ipeadata("SERIE SEM RETORNO")) at testthat/test_functions_ipea_data.R:19
  2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  3: ipeadata("SERIE SEM RETORNO")
  4: get_metadata(serie)
  5: basic_call(api_call, type)
  6: GET(api)
  7: request_perform(req, hu$handle$handle)
  8: request_fetch(req$output, req$url, handle)
  9: request_fetch.write_memory(req$output, req$url, handle)
  10: curl::curl_fetch_memory(url, handle = handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 6 SKIPPED: 0 FAILED: 1
  1. Error: ipeaData (@test_functions_ipea_data.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available: ‘HH’ ‘Hmisc’ ‘RcmdrPlugin.IPSUR’

Package suggested but not available for checking: ‘RcmdrMisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
gimli.20036hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Package required but not available: ‘iClick’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘semPlot’
Package suggested but not available for checking: ‘BaBooN’
Packages required but not available: ‘jpmesh’ ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  jqr.c:11:3: warning: ‘strncpy’ specified bound 1000 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/jqr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  push_parser.c:75:5: warning: ‘strncpy’ specified bound 1024 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/jsonlite.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘formattable’
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 286-303 (awesome_table_in_html.Rmd) 
Error: processing vignette ‘awesome_table_in_html.Rmd’ failed with diagnostics:
there is no package called 'formattable'
Execution halted
Packages required but not available: ‘nonlinearTseries’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
gimli.10424hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.17264hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.28582hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.4996hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.6779hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.19560hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.18590hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.28949hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.5055hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.11503hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.21261hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages required but not available: ‘rgl’ ‘longitudinalData’ ‘kml’

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dinisurface
> ### Title: Ulisse Dini Data Set Generator
> ### Aliases: dinisurface
> ### Keywords: dataset
> 
> ### ** Examples
> 
> require("rgl")
Loading required package: rgl
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘rgl’
> x=dinisurface()
> open3d()
Error in open3d() : could not find function "open3d"
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 24-28 (copper_mining_2d.Rmd) 
Error: processing vignette ‘copper_mining_2d.Rmd’ failed with diagnostics:
there is no package called 'plotly'
Execution halted
Packages suggested but not available for checking: ‘OceanView’ ‘rgl’
Running examples in ‘ks-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.kdde
> ### Title: Plot for kernel density derivative estimate
> ### Aliases: plot.kdde
> ### Keywords: hplot
> 
> ### ** Examples
> 
> ## univariate example
> data(tempb)
> fhat1 <- kdde(x=tempb[,"tmin"], deriv.order=1)   ## gradient [df/dx, df/dy]
> plot(fhat1, xlab="Min. temp.")                   ## df/dx
> points(20,predict(fhat1, x=20))
> 
> ## bivariate example
> fhat1 <- kdde(x=tempb[,c("tmin", "tmax")], deriv.order=1)
> plot(fhat1, display="quiver")
Error: Install the OceanView package as it is required.
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 124-133 (labelVector.Rmd) 
Error: processing vignette ‘labelVector.Rmd’ failed with diagnostics:
there is no package called 'Hmisc'
Execution halted
Package suggested but not available for checking: ‘crs’
Package required but not available: ‘semPlot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘rgl’ ‘visNetwork’
Package suggested but not available for checking: ‘riskRegression’
Running examples in ‘lavaSearch2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: iidJack
> ### Title: Jackknife iid Decomposition from Model Object
> ### Aliases: iidJack iidJack.default
> 
> ### ** Examples
> 
> n <- 20
> 
> #### glm ####
> set.seed(10)
> m <- lvm(y~x+z)
> distribution(m, ~y+z) <- binomial.lvm("logit")
> d <- lava::sim(m,n)
> g <- glm(y~x+z,data=d,family="binomial")
> iid1 <- iidJack(g, cpus = 1)
> iid2 <- lava::iid(g)
> quantile(iid1-iid2)
           0%           25%           50%           75%          100% 
-2.712906e-01 -2.039810e-02 -9.927842e-05  3.312853e-03  3.360535e-01 
> vcov(g)
            (Intercept)           x             z
(Intercept)  0.47731221 -0.04806632 -4.949054e-01
x           -0.04806632  1.55595994  6.175763e-01
z           -0.49490537  0.61757631  1.853881e+07
> colSums(iid2^2)
(Intercept)           x           z 
  0.5172089   0.5061652   0.6254291 
> colSums(iid1^2)
(Intercept)           x           z 
  0.7651012   1.0746401   1.2131354 
> 
> #### Cox model ####
> library(survival)
> data(Melanoma, package = "riskRegression")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘riskRegression’
Calls: data -> find.package
Execution halted
Running examples in ‘lawn-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lawn_unkinkpolygon
> ### Title: Unkink polygon
> ### Aliases: lawn_unkinkpolygon
> 
> ### ** Examples
> 
> x <- '{
+   "type": "Feature",
+   "properties": {},
+   "geometry": {
+     "type": "Polygon",
+       "coordinates": [[[0, 0], [2, 0], [0, 2], [2, 2], [0, 0]]]
+    }
+ }'
> lawn_unkinkpolygon(x)
<FeatureCollection>
  Bounding box: 0.0 0.0 2.0 2.0
  No. features: 2
  No. points: 16
  Properties: NULL
> view(x)
Error: Please install leaflet
Execution halted
Package required but not available: ‘htmlwidgets’

Package suggested but not available for checking: ‘networkD3’

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

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

Package suggested but not available for checking: ‘htmlwidgets’

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

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

Package suggested but not available for checking: ‘manipulateWidget’

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

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

Package suggested but not available for checking: ‘EBImage’

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_lle
> ### Title: Plot LLE results
> ### Aliases: plot_lle
> 
> ### ** Examples
> 
> 	data( lle_scurve_data )
> 	X <- lle_scurve_data
> 	Y <- lle( X, m=2, k=12 )$Y
finding neighbours
calculating weights
computing coordinates
> 	plot_lle( Y, X, FALSE, col="red", inter=TRUE )
Loading required package: rgl
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘rgl’
Error in plot3d(Y, col = col) : could not find function "plot3d"
Calls: plot_lle
Execution halted
Packages suggested but not available for checking: ‘rgl’ ‘RDRToolbox’
Running ‘testthat.R’ [6s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(loo)
  This is loo version 2.0.0.
  **NOTE: As of version 2.0.0 loo defaults to 1 core but we recommend using as many as possible. Use the 'cores' argument or set options(mc.cores = NUM_CORES) for an entire session. Visit mc-stan.org/loo/news for details on other changes.
  
  Attaching package: 'loo'
  
  The following object is masked from 'package:testthat':
  
      compare
  
  > Sys.setenv("R_TESTS" = "")
  > test_check("loo")
  ── 1. Error: (unknown) (@test_psis.R#2)  ───────────────────────────────────────
  there is no package called 'rstanarm'
  1: suppressPackageStartupMessages(library(rstanarm)) at testthat/test_psis.R:2
  2: withCallingHandlers(expr, packageStartupMessage = function(c) invokeRestart("muffleMessage"))
  3: library(rstanarm)
  4: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 341 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_psis.R#2) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available: ‘shapes’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘mediation’ ‘CARBayes’ ‘glmmADMB’ ‘rstanarm’
Error in re-building vignettes:
  ...
The 'lsmeans' package is being deprecated.
Users are encouraged to switch to 'emmeans'.
See help('transition') for more information, including how
to convert 'lsmeans' objects and scripts to work with 'emmeans'.
Loading required package: mvtnorm
Loading required package: survival
Loading required package: TH.data
Loading required package: MASS

Attaching package: 'TH.data'

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

    geyser

Note: df set to 23
Loading required package: Matrix
Loading required namespace: lmerTest
NOTE: Results may be misleading due to involvement in interactions
Loading required package: lattice
Loading required package: carData
Note: model has aliased coefficients
      sums of squares computed by model comparison
NOTE: Results may be misleading due to involvement in interactions
NOTE: Results may be misleading due to involvement in interactions
NOTE: Results may be misleading due to involvement in interactions
NOTE: Results may be misleading due to involvement in interactions
NOTE: Results may be misleading due to involvement in interactions

Error: processing vignette ‘using-lsmeans.rnw’ failed with diagnostics:
 chunk 85 
Error in library("mediation") : there is no package called 'mediation'
Execution halted
Running examples in ‘lulcc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: allow
> ### Title: Implement decision rules for land use change
> ### Aliases: allow
> 
> ### ** Examples
> 
> 
> ## Plum Island Ecosystems
> 
> ## load observed land use data
> obs <- ObsLulcRasterStack(x=pie,
+                    pattern="lu",
+                    categories=c(1,2,3),
+                    labels=c("forest","built","other"),
+                    t=c(0,6,14))
> 
> ## get land use values
> x <- getValues(obs[[1]])
> x <- x[!is.na(x)]
> 
> ## create vector of arbitrary land use history values
> hist <- sample(1:10, length(x), replace=TRUE)
> 
> ## calculate demand and get change direction for first timestep
> dmd <- approxExtrapDemand(obs=obs, tout=0:14)
Warning in total(x = obs) :
  missing argument 'categories': getting categories from 'x'
Error in loadNamespace(name) : there is no package called ‘Hmisc’
Calls: approxExtrapDemand ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Packages suggested but not available for checking: ‘RLumShiny’ ‘plotly’
Packages required but not available: ‘qgraph’ ‘semPlot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘depth’
Found the following significant warnings:
  liblwgeom/lwutil.c:317:5: warning: ‘strncat’ specified bound 3 equals source length [-Wstringop-overflow=]
  liblwgeom/lwutil.c:323:5: warning: ‘strncat’ specified bound 3 equals source length [-Wstringop-overflow=]
  liblwgeom/lwutil.c:344:5: warning: ‘strncat’ specified bound 3 equals source length [-Wstringop-overflow=]
  liblwgeom/lwutil.c:349:5: warning: ‘strncat’ specified bound 3 equals source length [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/lwgeom.Rcheck/00install.out’ for details.
Packages required but not available: ‘rhandsontable’ ‘DT’

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

Package suggested but not available for checking: ‘rms’

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

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

VignetteBuilder package required for checking but not installed: ‘leaflet’

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

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

Packages suggested but not available for checking:
  ‘dygraphs’ ‘leaflet’ ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘htmlwidgets’ ‘leaflet’ ‘leaflet.extras’ ‘mapview’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 95-100 (intro.Rmd) 
Error: processing vignette ‘intro.Rmd’ failed with diagnostics:
there is no package called 'leaflet'
Execution halted
Packages required but not available: ‘weights’ ‘Hmisc’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spsurvey’
Error in re-building vignettes:
  ...
Quitting from lines 187-200 (MBHdesign.Rnw) 
Error: processing vignette ‘MBHdesign.Rnw’ failed with diagnostics:
there is no package called 'spsurvey'
Execution halted
Package required but not available: ‘ecr’

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

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

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

Depends: includes the non-default packages:
  ‘seqinr’ ‘pcaMethods’ ‘Matrix’ ‘ROCR’ ‘Hmisc’ ‘KernSmooth’ ‘seqLogo’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

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

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

Package suggested but not available for checking: ‘rstanarm’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
gimli.11860hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.20274hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.27309hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.389hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.6079hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.13254hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.23431hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.32127hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.11052hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages suggested but not available for checking: ‘HTSFilter’ ‘DESeq2’
Error in re-building vignettes:
  ...

Error: processing vignette ‘metaRNASeq.Rnw’ failed with diagnostics:
 chunk 2 (label = loadparameters) 
Error in library(DESeq2) : there is no package called ‘DESeq2’
Execution halted
Package required but not available: ‘depth’

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

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

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

Package suggested but not available for checking: ‘htmlTable’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘plotly’ ‘rhandsontable’
Found the following significant warnings:
  migrate.c:179:30: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:186:26: warning: ‘.asc’ directive writing 4 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:199:28: warning: ‘.asc’ directive writing 4 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:286:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:312:29: warning: ‘%d’ directive writing between 1 and 8 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:559:31: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:595:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:603:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/MigClim.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Use the user-defined lambda vector.
Using the criterion BIC to choose optimized penalty.
The chosen penalty throuth BIC is 3.6867.
The penalty term is selected automatically with 50 candidates.
Using the criterion BIC to choose optimized penalty.
The chosen penalty throuth BIC is 4.9895.
The penalty term is selected automatically with 50 candidates.
Using the criterion deviance to choose optimized penalty.
The chosen penalty throuth deviance is 2.4657.
trying URL ‘http://www.cs.columbia.edu/~andrews/mil/data/MIL-Data-2002-Musk-Corel-Trec9.tgz’
Content type 'application/x-gzip' length 6249673 bytes (6.0 MB)
==================================================
downloaded 6.0 MB

Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Warning: 'switch' is deprecated.
Use 'strip.position' instead.
See help("Deprecated")
The penalty term is selected automatically with 100 candidates.
Using the criterion deviance to choose optimized penalty.
The chosen penalty throuth deviance is 3.5287.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Killed
Running examples in ‘misc3d-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: contour3d
> ### Title: Draw an Isosurface, a Three Dimension Contour Plot
> ### Aliases: contour3d
> ### Keywords: hplot
> 
> ### ** Examples
> 
>   #Example 1: Draw a ball
>   f <- function(x, y, z)x^2+y^2+z^2
>   x <- seq(-2,2,len=20)
>   contour3d(f,4,x,x,x)
Error in loadRGL() : rgl is mot available
Calls: contour3d -> drawScene.rgl -> loadRGL
Execution halted
gimli.20731hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Error in re-building vignettes:
  ...
Warning: call dbDisconnect() when finished working with a connection
Warning in getNamespace(ns) :
  closing unused connection 5 (http://gd2.mlb.com/components/game/mlb/year_2018/month_03/day_20/gid_2018_03_20_tbamlb_balmlb_1/inning/inning_all.xml)
Warning: closing unused connection 5 (http://gd2.mlb.com/components/game/mlb/year_2018/month_03/day_24/gid_2018_03_24_sfnmlb_srcaaa_1/inning/inning_all.xml)
Warning: closing unused connection 6 (http://gd2.mlb.com/components/game/mlb/year_2018/month_03/day_26/gid_2018_03_26_chamlb_chraaa_1/inning/inning_all.xml)
Warning: closing unused connection 5 (http://gd2.mlb.com/components/game/mlb/year_2018/month_03/day_26/gid_2018_03_26_balmlb_noraaa_1/inning/inning_all.xml)
Warning in identical(pipe, quote(`%<>%`)) :
  closing unused connection 5 (http://gd2.mlb.com/components/game/mlb/year_2018/month_03/day_26/gid_2018_03_26_kcamlb_omaaaa_1/inning/inning_all.xml)
Warning: closing unused connection 5 (http://gd2.mlb.com/components/game/mlb/year_2018/month_03/day_26/gid_2018_03_26_sdnmlb_elpaaa_1/inning/inning_all.xml)
Warning: closing unused connection 5 (http://gd2.mlb.com/components/game/mlb/year_2018/month_03/day_27/gid_2018_03_27_cinmlb_texmlb_1/inning/inning_all.xml)
Quitting from lines 87-98 (pitch_plotting.Rmd) 
Error: processing vignette ‘pitch_plotting.Rmd’ failed with diagnostics:
there is no package called 'plotly'
Execution halted
Package required but not available: ‘smoof’

Package suggested but not available for checking: ‘cmaesr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘clusterSim’ ‘crs’ ‘Hmisc’ ‘mlrMBO’ ‘smoof’
Packages required but not available: ‘qgraph’ ‘graphicalVAR’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AutoSelectLRM
> ### Title: Automated backward elemination for logistic regression
> ### Aliases: AutoSelectLRM
> 
> ### ** Examples
> 
> library(rms)
Error in library(rms) : there is no package called ‘rms’
Execution halted
Package required but not available: ‘mapedit’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘leaflet’ ‘mapview’ ‘mapedit’
Error in re-building vignettes:
  ...
Quitting from lines 106-114 (Basic_Usage.Rmd) 
Error: processing vignette ‘Basic_Usage.Rmd’ failed with diagnostics:
there is no package called 'smoof'
Execution halted
Package required but not available: ‘tolerance’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  monetdblite/src/gdk/gdk_heap.c:189:3: warning: ‘strncpy’ output truncated before terminating nul copying 9 bytes from a string of the same length [-Wstringop-truncation]
  monetdblite/src/gdk/gdk_heap.c:260:30: warning: ‘%s’ directive writing likely 3 or more bytes into a region of size between 0 and 99 [-Wformat-overflow=]
  monetdblite/src/mal/sqlbackend/rel_bin.c:2949:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/mal/sqlbackend/rel_bin.c:1083:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/mal/sqlbackend/sql_statement.c:3193:3: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/mal/sqlbackend/sql_statement.c:3196:3: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/mal/sqlbackend/sql_statement.c:3186:3: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/sql/server/rel_planner.c:82:4: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/sql/server/rel_semantic.c:54:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/sql/server/rel_updates.c:1729:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/MonetDBLite.Rcheck/00install.out’ for details.
Package required but not available: ‘rgl’

Package suggested but not available for checking: ‘shapes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘matlib’
Package which this enhances but not available for checking: ‘leaflet’
Packages required but not available: ‘Hmisc’ ‘WGCNA’

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

Package suggested but not available for checking: ‘plotly’

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

Package suggested but not available for checking: ‘htmlwidgets’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 82-86 (multiFit.Rmd) 
Error: processing vignette ‘multiFit.Rmd’ failed with diagnostics:
there is no package called 'qgraph'
Execution halted
Running examples in ‘mvQuad-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot (plot.NIGrid)
> ### Title: plots an NIGrid-object
> ### Aliases: 'plot (plot.NIGrid)' plot.NIGrid
> 
> ### ** Examples
> 
> myGrid <- createNIGrid(dim=4, type=c("GHe", "cNC1", "GLe", "oNC1"),
+                        level=c(3,4,5,6))
> plot(myGrid) ## dimension 1-min(3,dim(myGrid)) are plotted
Error in plot.NIGrid(myGrid) : 
  wrong dimensions stated to be plotted (no 'rgl'-package for 3d-plot)
Calls: plot -> plot.NIGrid
Execution halted
Package required but not available: ‘visdat’

Packages suggested but not available for checking: ‘vdiffr’ ‘Hmisc’

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

Package suggested but not available for checking: ‘rglwidget’

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

Package suggested but not available for checking: ‘alphashape3d’

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

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

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

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

Packages suggested but not available for checking: ‘fastshp’ ‘SpaDES.core’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘qgraph’ ‘IsingFit’ ‘NetworkComparisonTest’ ‘smacof’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘wordcloud2’ ‘htmlTable’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages which this enhances but not available for checking:
  ‘jpndistrict’ ‘jpmesh’
Error in re-building vignettes:
  ...
Quitting from lines 15-22 (geocode.Rmd) 
Error: processing vignette ‘geocode.Rmd’ failed with diagnostics:
there is no package called 'leaflet'
Execution halted
Package required but not available: ‘d3heatmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
gimli.11286hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Package required but not available: ‘choroplethr’

Package suggested but not available for checking: ‘hurricaneexposuredata’

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

Depends: includes the non-default packages:
  ‘lpSolve’ ‘gdata’ ‘Hmisc’ ‘rms’ ‘geometry’ ‘psych’ ‘pwt’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  medusa.long2text.cpp:16:21: warning: ‘%ld’ directive writing between 1 and 20 bytes into a region of size 16 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Numero.Rcheck/00install.out’ for details.
gimli.31343hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Package required but not available: ‘optiSolve’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘exporting-methods.R’ [3s/3s]
  Running ‘mahal-dist.R’ [3s/3s]
  Running ‘testthat.R’ [21s/22s]
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
Package required but not available: ‘reldist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
gimli.32366hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Package required but not available: ‘lazyrmd’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 196-217 (progressive_packing.Rmd) 
Error: processing vignette ‘progressive_packing.Rmd’ failed with diagnostics:
there is no package called 'ggiraph'
Execution halted
Running ‘testthat.R’ [5s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("pacman")
  > options(repos="http://cran.rstudio.com/")
  > 
  > 
  > test_check("pacman")
  ── 1. Error: p_install_gh works (@test-p_install_gh.R#5)  ──────────────────────
  HTTP error 404.
    Not Found
  
    Rate limit remaining: 55/60
    Rate limit reset at: 2018-10-20 07:25:39 UTC
  
    
  1: expect_false(p_install_gh("greg/iDontExistAnywhere")) at testthat/test-p_install_gh.R:5
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: p_install_gh("greg/iDontExistAnywhere")
  5: lapply(package, function(x) {
         devtools::install_github(x, dependencies = dependencies, ...)
     })
  6: FUN(X[[i]], ...)
  7: devtools::install_github(x, dependencies = dependencies, ...)
  8: install_remotes(remotes, auth_token = auth_token, host = host, dependencies = dependencies, 
         upgrade = upgrade, force = force, quiet = quiet, build = build, build_opts = build_opts, 
         repos = repos, type = type, ...)
  9: vapply(remotes, install_remote, ..., FUN.VALUE = character(1))
  10: FUN(X[[i]], ...)
  11: remote_package_name(remote)
  12: remote_package_name.github_remote(remote)
  13: github_DESCRIPTION(username = remote$username, repo = remote$repo, subdir = remote$subdir, 
         host = remote$host, ref = remote$ref, pat = remote$auth_token %||% github_pat(), 
         use_curl = use_curl)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 54 SKIPPED: 3 FAILED: 1
  1. Error: p_install_gh works (@test-p_install_gh.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘paleomorph-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotSpecimens
> ### Title: Plot an array of specimen landmark data in an interactive 3D
> ###   frame
> ### Aliases: plotSpecimens
> 
> ### ** Examples
> 
> A <- array(rep(rnorm(3 * 20, sd = 30), by = 6) + rnorm(6 * 20 * 3), 
+        dim = c(20, 3, 6))
> plotSpecimens(A)
Error: Package rgl needed for this function to work. Please install it with install.packages('rgl').
Execution halted
Package required but not available: ‘pals’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘tables’ ‘rms’
Error in re-building vignettes:
  ...
Quitting from lines 13-18 (pander.Rmd) 
Error: processing vignette ‘pander.Rmd’ failed with diagnostics:
there is no package called 'tables'
Execution halted
gimli.7746hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Packages suggested but not available for checking: ‘leaflet’ ‘htmlwidgets’
Error in re-building vignettes:
  ...
Quitting from lines 67-110 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
there is no package called 'leaflet'
Execution halted
Package required but not available: ‘Morpho’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [9s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pavo)
  > 
  > test_check("pavo")
  ── 1. Error: classify (@test-images.R#79)  ─────────────────────────────────────
  attempt to set an attribute on NULL
  1: classify(imgfakes, kcols = fake_IDs) at testthat/test-images.R:79
  
  ── 2. Error: adjacency (@test-images.R#156)  ───────────────────────────────────
  attempt to set an attribute on NULL
  1: classify(imgfakes, kcols = 2) at testthat/test-images.R:156
  
  Read 18823 items
  Read 10820 items
  Read 10824 items
  Read 10820 items
  Read 18823 items
  Read 10824 items
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 143 SKIPPED: 0 FAILED: 2
  1. Error: classify (@test-images.R#79) 
  2. Error: adjacency (@test-images.R#156) 
  
  Error: testthat unit tests failed
  Execution halted
gimli.23356hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.27783hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.2047hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.9664hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.5968hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.17801hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.16633hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.22008hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.29131hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.3229hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.9626hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
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.
gimli.23499hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.28075hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.2989hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.11434hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.7608hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.18426hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.17407hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.23750hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.30613hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.4456hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.12165hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
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.
gimli.23679hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.28205hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.

Found the following apparent S3 methods exported but not registered:
  cbind.ddmatrix rbind.ddmatrix
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
gimli.3283hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.11702hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.14064hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.18630hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.20626hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.28314hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.2613hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.8085hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.16008hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
S3 methods shown with full name in documentation object 'binds':
  ‘rbind.ddmatrix’ ‘cbind.ddmatrix’

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.
gimli.24693hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.29519hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.4031hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.12751hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.14164hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.19160hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.21053hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.28473hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.2590hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.8025hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.15688hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
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.
gimli.13681hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.25220hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.30806hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.4689hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.13219hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.8010hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.19547hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.17366hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.23449hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.30279hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.4251hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.11634hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
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.
gimli.23058hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Packages required but not available: ‘plotly’ ‘qpcR’ ‘visdat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [226s/333s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(peakPantheR)
  
  This is peakPantheR version 1.2.0 
  
  > 
  > test_check("peakPantheR")
  ── 1. Error: default multiplot (@test_annotationDiagnosticMultiplot.R#180)  ────
  unused arguments (limits, n)
  1: evaluate_promise(annotationDiagnosticMultiplot(input_plots)) at testthat/test_annotationDiagnosticMultiplot.R:180
  2: withr::with_output_sink(temp, withCallingHandlers(withVisible(code), warning = handle_warning, 
         message = handle_message))
  3: force(code)
  4: withCallingHandlers(withVisible(code), warning = handle_warning, message = handle_message)
  5: withVisible(code)
  6: annotationDiagnosticMultiplot(input_plots)
  7: ggplot2::layer_scales(tmp_rtPeakwidthVert)
  8: ggplot_build(plot)
  9: ggplot_build.ggplot(plot)
  10: layout$setup_panel_params()
  ...
  16: f(..., self = self)
  17: parent$setup_panel_params(scale_x, scale_y, params)
  18: f(..., self = self)
  19: train_cartesian(scale_x, self$limits$x, "x")
  20: scale$break_info(range)
  21: f(..., self = self)
  22: ggproto_parent(ScaleContinuous, self)$break_info(range)
  23: f(..., self = self)
  24: self$get_breaks_minor(b = major, limits = range)
  25: f(..., self = self)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1147 SKIPPED: 0 FAILED: 1
  1. Error: default multiplot (@test_annotationDiagnosticMultiplot.R#180) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘rms’

Packages suggested but not available for checking: ‘riskRegression’ ‘Hmisc’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Omega
> ### Title: calculate Omega for a return series
> ### Aliases: Omega
> 
> ### ** Examples
> 
> 
>     data(edhec)
>     Omega(edhec)
               Convertible Arbitrage CTA Global Distressed Securities
Omega (L = 0%)              2.602138   1.936841              3.230443
               Emerging Markets Equity Market Neutral Event Driven
Omega (L = 0%)         1.765435              6.213714     2.999655
               Fixed Income Arbitrage Global Macro Long/Short Equity
Omega (L = 0%)               2.585943     3.516616          2.438064
               Merger Arbitrage Relative Value Short Selling Funds of Funds
Omega (L = 0%)         4.595886       3.815368      1.228785       2.460153
>     Omega(edhec[,13],method="interp",output="point")
Error in FUN(newX[, i], ...) : 
  requireNamespace("Hmisc", quietly = TRUE) is not TRUE
Calls: Omega -> apply -> FUN -> stopifnot
Execution halted
Error in re-building vignettes:
  ...
Loading required package: xts
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric


Attaching package: ‘PerformanceAnalytics’

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

    legend


Attaching package: ‘gplots’

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

    textplot

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

    lowess


Error: processing vignette ‘textplotPresentation-CRUG-2011.Rnw’ failed with diagnostics:
 chunk 5 (label = Hmiscformat) 
Error in library(Hmisc) : there is no package called ‘Hmisc’
Execution halted
Packages required but not available: ‘visNetwork’ ‘DiagrammeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  fdouble_metaphone.c:268:5: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/PGRdup.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘leaflet’ ‘plotly’ ‘DT’
Packages required but not available: ‘geomorph’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggsubplot’ ‘rgl’
Packages suggested but not available for checking: ‘htmlwidgets’ ‘leaflet’
Packages required but not available: ‘DT’ ‘visNetwork’

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

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

Packages suggested but not available for checking:
  ‘adehabitat’ ‘Hmisc’ ‘GSIF’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘plotly’
Package suggested but not available for checking: ‘mixOmics’
Running examples in ‘PLSbiplot1-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Mag.Bmat.plot
> ### Title: Magnitude of the Partial Least Squares Regression (PLSR)
> ###   coefficients matrix
> ### Aliases: Mag.Bmat.plot
> 
> ### ** Examples
> 
> if(require(pls))
+ data(oliveoil, package="pls")
Loading required package: pls

Attaching package: ‘pls’

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

    loadings

> X = as.matrix(oliveoil$chemical, ncol=5)
> dimnames(X) = list(paste(c("G1","G2","G3","G4","G5","I1","I2","I3","I4","I5",
+ "S1","S2","S3","S4","S5","S6")),
+ paste(c("Acidity","Peroxide","K232","K270","DK")))
> Y = as.matrix(oliveoil$sensory, ncol=6)
> dimnames(Y) = list(paste(c("G1","G2","G3","G4","G5","I1","I2","I3","I4","I5",
+ "S1","S2","S3","S4","S5","S6")),
+ paste(c("Yellow","Green","Brown","Glossy","Transp","Syrup")))
> Mag.Bmat.plot(X, Y, algorithm=mod.SIMPLS, A=2)
> 
> #nutrimouse data
> if(require(mixOmics))
+ data(nutrimouse, package="mixOmics")
Loading required package: mixOmics
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘mixOmics’
> X1 = as.matrix(nutrimouse$lipid, ncol=21)
Error in as.matrix(nutrimouse$lipid, ncol = 21) : 
  object 'nutrimouse' not found
Execution halted
Packages required but not available: ‘mixOmics’ ‘rms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘htmlwidgets’ ‘visNetwork’
gimli.30401hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.7071hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.18276hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.29384hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.24470hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.6294hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.32461hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.7122hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.14970hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.22329hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.1857hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages required but not available: ‘Hmisc’ ‘weights’ ‘ENmisc’

Package suggested but not available for checking: ‘rgl’

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

Package suggested but not available for checking: ‘pollimetrydata’

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

Package suggested but not available for checking: ‘Hmisc’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘Hmisc’ ‘rhandsontable’
Running ‘testthat.R’ [24s/156s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(postal)
  > 
  > test_check("postal")
  ── 1. Failure: Extract date works (@test_utils.R#244)  ─────────────────────────
  extract_dates(future_date) %>% as.numeric() is not strictly more than lubridate::today() %>% as.numeric(). Difference: 0
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 108 SKIPPED: 0 FAILED: 1
  1. Failure: Extract date works (@test_utils.R#244) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available: ‘htmlwidgets’ ‘leaflet’ ‘tmap’

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

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

Package suggested but not available for checking: ‘GenABEL’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  zhegv.c:216:27: warning: ‘strncpy’ specified bound 2 equals destination size [-Wstringop-truncation]
  zhegv.c:216:27: warning: ‘strncpy’ specified bound 3 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/PRIMME.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘rhandsontable’ ‘gurobi’
Packages required but not available:
  ‘processmapR’ ‘htmlwidgets’ ‘DiagrammeR’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(vdiffr)
  Error in library(vdiffr) : there is no package called 'vdiffr'
  Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(projpred)
  This is projpred version 1.0.0
  
  Note: The type of the returned objects of varsel/cv_varsel have changed
  since the latest release, although this does not affect how the functions
  are used.
  > library(rstanarm) # we need rstanarm for running the tests
  Error in library(rstanarm) : there is no package called 'rstanarm'
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 23-29 (quickstart.Rmd) 
Error: processing vignette ‘quickstart.Rmd’ failed with diagnostics:
there is no package called 'rstanarm'
Execution halted
Packages suggested but not available for checking: ‘plotly’ ‘rgl’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/PSPManalysis.Rcheck/00install.out’ for details.
Packages required but not available: ‘qgraph’ ‘rstanarm’

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘fulltext’
Package required but not available: ‘desctable’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘pec’ ‘riskRegression’ ‘rms’
Running examples in ‘Publish-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: publish.CauseSpecificCox
> ### Title: Tabulizing cause-specific hazard ratio from all causes with
> ###   confidence limits and Wald test p-values.
> ### Aliases: publish.CauseSpecificCox
> 
> ### ** Examples
> 
> library(riskRegression)
Error in library(riskRegression) : 
  there is no package called ‘riskRegression’
Execution halted
Running ‘test-glmSeries.R’ [3s/3s]
  Running ‘test-publish-gls.R’ [3s/3s]
  Running ‘test-publish-mi.R’ [2s/3s]
  Running ‘test-publish.R’ [2s/3s]
  Running ‘test-regressionTable.R’ [3s/3s]
  Running ‘test-univariateTable.R’ [3s/3s]
Running the tests in ‘tests/test-publish-mi.R’ failed.
Complete output:
  > library(testthat)
  > library(Publish)
  Loading required package: prodlim
  > library(mitools)
  > library(smcfcs)
  > library(riskRegression)
  Error in library(riskRegression) : 
    there is no package called 'riskRegression'
  Execution halted
Packages required but not available: ‘dygraphs’ ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 83-117 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
there is no package called 'rgl'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 92-106 (wilcox1973.Rmd) 
Error: processing vignette ‘wilcox1973.Rmd’ failed with diagnostics:
there is no package called 'DT'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 58-68 (create_pkg.Rmd) 
Error: processing vignette ‘create_pkg.Rmd’ failed with diagnostics:
there is no package called 'data.tree'
Execution halted
Package required but not available: ‘htmlwidgets’

Package suggested but not available for checking: ‘shinytest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  R4dfp-object.c:253:3: warning: ‘strncpy’ output truncated before terminating nul copying 9 bytes from a string of the same length [-Wstringop-truncation]
  R4dfp-object.c:260:3: warning: ‘strncpy’ output truncated before terminating nul copying 9 bytes from a string of the same length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/R4dfp.Rcheck/00install.out’ for details.
Package required but not available: ‘FateID’

Packages suggested but not available for checking: ‘DESeq2’ ‘scran’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘radiant.data’ ‘radiant.basics’ ‘data.tree’ ‘DiagrammeR’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘radiant.data’ ‘radiant.design’ ‘radiant.basics’ ‘radiant.model’
  ‘radiant.multivariate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘htmlwidgets’ ‘r2d3’ ‘DiagrammeR’
Package required but not available: ‘rags2ridges’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  kleinkram.cc:1018:18: warning: ‘ '’ directive writing 2 bytes into a region of size between 1 and 1000 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RandomFieldsUtils.Rcheck/00install.out’ for details.
Package required but not available: ‘ecospat’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rankhazard-package
> ### Title: Rank-hazard plots
> ### Aliases: rankhazard-package rankhazard
> ### Keywords: package hplot survival
> 
> ### ** Examples
> 
> library(survival)
> model <- coxph(Surv(time,status) ~ age + sex + ph.karno, data = cancer, x=TRUE)
> rankhazardplot(model, data=cancer)
Y-axis range:  0.608 1.49 
 
Relative hazards for each covarite: 
          Min. 1st Qu. Median 3rd Qu. Max.
age      0.743   0.917      1    1.08 1.27
sex      0.608   0.608      1    1.00 1.00
ph.karno 0.766   0.875      1    1.07 1.49
> library(rms)
Error in library(rms) : there is no package called ‘rms’
Execution halted
Package required but not available: ‘hypervolume’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  avc_binwr.c:166:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:173:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:180:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:187:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:1453:29: warning: ‘%4.4d’ directive writing between 4 and 10 bytes into a region of size 5 [-Wformat-overflow=]
  avc_binwr.c:1553:28: warning: ‘%s’ directive writing up to 39 bytes into a region of size between 38 and 77 [-Wformat-overflow=]
  avc_e00write.c:386:30: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  avc_e00write.c:387:30: warning: ‘-ID’ directive writing 3 bytes into a region of size between 1 and 40 [-Wformat-overflow=]
  avc_e00write.c:401:61: warning: ‘%s’ directive writing up to 39 bytes into a region of size 17 [-Wformat-overflow=]
  avc_e00write.c:397:61: warning: ‘%s’ directive writing up to 39 bytes into a region of size 17 [-Wformat-overflow=]
  avc_e00write.c:409:39: warning: ‘%s’ directive writing up to 39 bytes into a region of size 33 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RArcInfo.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘arulesViz’ ‘Hmisc’
Found the following significant warnings:
  samtools/bam.c:118:2: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
  samtools/razf.c:178:2: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
  rbamtools.cpp:126:10: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/rbamtools.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [61s/64s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(RBesT)
  Loading required package: Rcpp
  This is RBesT version 1.3.4
  > 
  > test_check("RBesT")
  ── 1. Error: (unknown) (@test-gMAP.R#7)  ───────────────────────────────────────
  there is no package called 'rstanarm'
  1: suppressWarnings(suppressPackageStartupMessages(library(rstanarm))) at testthat/test-gMAP.R:7
  2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  3: suppressPackageStartupMessages(library(rstanarm))
  4: withCallingHandlers(expr, packageStartupMessage = function(c) invokeRestart("muffleMessage"))
  5: library(rstanarm)
  6: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 146 SKIPPED: 46 FAILED: 1
  1. Error: (unknown) (@test-gMAP.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Package which this enhances but not available for checking: ‘forestFloor’
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: Sat Oct 20 06:20:41 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
Package required but not available: ‘aspace’

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

Depends: includes the non-default packages:
  ‘biclust’ ‘fabia’ ‘iBBiG’ ‘superbiclust’ ‘BcDiag’ ‘rqubic’ ‘BicARE’
  ‘s4vd’ ‘BiBitR’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

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

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

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

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

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

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

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

Packages suggested but not available for checking: ‘qgraph’ ‘Hmisc’

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

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

Packages suggested but not available for checking: ‘Hmisc’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘networkD3’
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 28-58 (vignette.Rmd) 
Error: processing vignette ‘vignette.Rmd’ failed with diagnostics:
there is no package called 'tmap'
Execution halted
Error in re-building vignettes:
  ...
── Attaching packages ────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.0.0     ✔ purrr   0.2.5
✔ tibble  1.4.2     ✔ dplyr   0.7.7
✔ tidyr   0.8.1     ✔ stringr 1.3.1
✔ 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"
Quitting from lines 39-40 (rdf_intro.Rmd) 
Error: processing vignette ‘rdf_intro.Rmd’ failed with diagnostics:
there is no package called 'DT'
Execution halted
Found the following significant warnings:
  Rreadsdpa.c:608:15: warning: ‘strncpy’ output may be truncated copying 3999 bytes from a string of length 3999 [-Wstringop-truncation]
  Rreadsdpa.c:1041:13: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  Rreadsdpa.c:1042:13: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  dsdpsetoptions.c:164:4: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  dsdpsetoptions.c:165:4: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Rdsdp.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Quitting from lines 22-26 (mapDWD.Rmd) 
Error: processing vignette ‘mapDWD.Rmd’ failed with diagnostics:
there is no package called 'leaflet'
Execution halted
Found the following significant warnings:
  localtime.c:1817:5: warning: ‘strncpy’ specified bound 1000 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/readr.Rcheck/00install.out’ for details.
Running ‘test-all.R’ [2s/3s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  > test_check('rebird')
  Loading required package: rebird
  ── 1. Failure: ebirdtaxonomy works without an API key (@test-ebirdtaxonomy.R#31)
  ncol(tax) not equal to 14.
  1/1 mismatches
  [1] 0 - 14 == -14
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2 SKIPPED: 17 FAILED: 1
  1. Failure: ebirdtaxonomy works without an API key (@test-ebirdtaxonomy.R#31) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: kriging

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 27-33 (recexcavAAR-vignette-1.Rmd) 
Error: processing vignette ‘recexcavAAR-vignette-1.Rmd’ failed with diagnostics:
there is no package called 'rgl'
Execution halted
Found the following significant warnings:
  phonet.c:1207:34: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  phonet.c:1208:34: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RecordLinkage.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘UsingR’
gimli.12524hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Package required but not available: ‘BAT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
gimli.16970hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.25930hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.4613hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.14579hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.19809hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.25175hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.28205hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.7285hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.17269hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.25904hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.1279hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
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:
  ...
Quitting from lines 13-18 (short_intro.Rmd) 
Error: processing vignette ‘short_intro.Rmd’ failed with diagnostics:
there is no package called 'semPlot'
Execution halted
Package suggested but not available for checking: ‘Rcmdr’
Packages required but not available: ‘plotly’ ‘data.tree’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: makeJoinDiagramSpec
> ### Title: Build a drawable specification of the join diagram
> ### Aliases: makeJoinDiagramSpec
> 
> ### ** Examples
> 
> 
> 
> if (requireNamespace("RSQLite", quietly = TRUE)) {
+   # note: employeeanddate is likely built as a cross-product
+   #       join of an employee table and set of dates of interest
+   #       before getting to the join controller step.  We call
+   #       such a table "row control" or "experimental design."
+   my_db <- DBI::dbConnect(RSQLite::SQLite(), ":memory:")
+   RSQLite::initExtension(my_db)
+   tDesc <- example_employeeAndDate(my_db)
+   # fix order by hand, please see replyr::topoSortTables for
+   # how to automate this.
+   ord <- match(c('employeeanddate', 'orgtable', 'activity', 'revenue'),
+                tDesc$tableName)
+   tDesc <- tDesc[ord, , drop=FALSE]
+   columnJoinPlan <- buildJoinPlan(tDesc, check= FALSE)
+   # unify keys
+   columnJoinPlan$resultColumn[columnJoinPlan$resultColumn=='id'] <- 'eid'
+   # look at plan defects
+   print(paste('problems:',
+               inspectDescrAndJoinPlan(tDesc, columnJoinPlan)))
+   diagramSpec <- makeJoinDiagramSpec(columnJoinPlan)
+   # to render as JavaScript:
+   #   DiagrammeR::grViz(diagramSpec)
+   DBI::dbDisconnect(my_db)
+   my_db <- NULL
+ }
Error: The dbplyr package is required to communicate with database backends.
Execution halted
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(replyr)
  Loading required package: wrapr
  > 
  > test_check("replyr")
  ── 1. Error: test_replyr_copy_from.R (@test_replyr_copy_from.R#9)  ─────────────
  The dbplyr package is required to communicate with database backends.
  1: replyr_copy_to(my_db, data.frame(x = c(1, 2)), "d") at testthat/test_replyr_copy_from.R:9
  2: dplyr::copy_to(dest, df, name, temporary = temporary, overwrite = overwrite)
  3: copy_to.DBIConnection(dest, df, name, temporary = temporary, overwrite = overwrite)
  4: check_dbplyr()
  5: check_pkg("dbplyr", "communicate with database backends", install = FALSE)
  6: glubort(NULL, "The {name} package is required to {reason}.", if (install) "\nPlease install it with `install.packages(\"{name}\")`" else "")
  7: .abort(text)
  
  ── 2. Error: test_replyr_copy_to.R (@test_replyr_copy_to.R#9)  ─────────────────
  The dbplyr package is required to communicate with database backends.
  1: replyr_copy_to(my_db, data.frame(x = c(1, 2)), "d") at testthat/test_replyr_copy_to.R:9
  2: dplyr::copy_to(dest, df, name, temporary = temporary, overwrite = overwrite)
  3: copy_to.DBIConnection(dest, df, name, temporary = temporary, overwrite = overwrite)
  4: check_dbplyr()
  5: check_pkg("dbplyr", "communicate with database backends", install = FALSE)
  6: glubort(NULL, "The {name} package is required to {reason}.", if (install) "\nPlease install it with `install.packages(\"{name}\")`" else "")
  7: .abort(text)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1 SKIPPED: 16 FAILED: 2
  1. Error: test_replyr_copy_from.R (@test_replyr_copy_from.R#9) 
  2. Error: test_replyr_copy_to.R (@test_replyr_copy_to.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 13-19 (DependencySorting.Rmd) 
Error: processing vignette ‘DependencySorting.Rmd’ failed with diagnostics:
The dbplyr package is required to communicate with database backends.
Execution halted
Package which this enhances but not available for checking: ‘htmlwidgets’
Package required but not available: ‘UsingR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘DT’ ‘vdiffr’
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 15-26 (rfm-customer-level-data.Rmd) 
Error: processing vignette ‘rfm-customer-level-data.Rmd’ failed with diagnostics:
there is no package called 'DT'
Execution halted
Packages required but not available: ‘htmlwidgets’ ‘manipulateWidget’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘Hmisc’ ‘pmg’ ‘Rcmdr’ ‘rgl’
Found the following significant warnings:
  RhpcMPI.c:301:5: warning: ‘strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Rhpc.Rcheck/00install.out’ for details.
Package required but not available: ‘nonlinearTseries’

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

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

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  cornellout.cpp:99:20: warning: ‘%2d’ directive writing between 2 and 11 bytes into a region of size between 0 and 931 [-Wformat-overflow=]
  cornellout.cpp:137:26: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  cornellout.cpp:129:26: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 988 and 995 [-Wformat-overflow=]
  mat.cpp:315:4: warning: ‘*<unknown>.dataMat::p’ is used uninitialized in this function [-Wuninitialized]
  tilia.cpp:179:14: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 61 bytes from a string of length 199 [-Wstringop-truncation]
  tilia.cpp:180:10: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 19 bytes from a string of length 19 [-Wstringop-truncation]
  tilia.cpp:225:14: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 8 bytes from a string of length 199 [-Wstringop-truncation]
  tilia.cpp:228:17: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 8 bytes from a string of length 29 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/rioja.Rcheck/00install.out’ for details.
Package required but not available: ‘rms’

Packages suggested but not available for checking: ‘Daim’ ‘pec’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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’

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: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:
  RngStream.c:347:4: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/rlecuyer.Rcheck/00install.out’ for details.
Found the following significant warnings:
  origcmaes.cc:2852:13: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  origcmaes.cc:2855:12: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  origcmaes.cc:2858:12: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Rmalschains.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘dygraphs’
Package suggested but not available for checking: ‘merTools’
Error in re-building vignettes:
  ...
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
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'merTools'
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 470-519 (Combined_paper_figures.Rmd) 
Error: processing vignette ‘Combined_paper_figures.Rmd’ failed with diagnostics:
could not find function "predictInterval"
Execution halted
Running examples in ‘Rmisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: group.CI
> ### Title: Group Confidence Interval
> ### Aliases: group.CI
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> require(latticeExtra)
Loading required package: latticeExtra
Loading required package: RColorBrewer
> with(group.CI(weight~feed,chickwts),
+  segplot(feed~weight.lower+weight.upper,center=weight.mean)
+ )
> 
> require(Hmisc)
Loading required package: Hmisc
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘Hmisc’
> with(group.CI(Temp~Month,airquality),
+  xYplot(Cbind(Temp.mean,Temp.lower,Temp.upper)~numericScale(Month),type="b",ylim=c(60,90))
+ )
Error in xYplot(Cbind(Temp.mean, Temp.lower, Temp.upper) ~ numericScale(Month),  : 
  could not find function "xYplot"
Calls: with -> with.default -> eval -> eval
Execution halted
gimli.17702hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.27556hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.6702hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.14602hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.23455hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.28207hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.4246hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.15596hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.23797hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.32144hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.7147hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages required but not available: ‘Hmisc’ ‘htmlTable’

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘DT’ ‘leaflet’ ‘plotly’
Packages suggested but not available for checking: ‘tables’ ‘Hmisc’
Packages required but not available: ‘rgl’ ‘EBImage’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 40-42 (data_mashups.Rmd) 
Error: processing vignette ‘data_mashups.Rmd’ failed with diagnostics:
Timeout was reached: Connection timed out after 10001 milliseconds
Execution halted
Found the following significant warnings:
  bgc_hmm.c:241:31: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
  rph_tfbs.c:371:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:351:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:819:5: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/rphast.Rcheck/00install.out’ for details.
Packages required but not available: ‘leaflet’ ‘mapview’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [5s/15s]
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\", '2018-10-20')"
  y[1]: "CAST(\"x\" AS DATE)"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 276 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
Packages suggested but not available for checking: ‘rgl’ ‘qgraph’
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor 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 suggested but not available for checking: ‘rstanarm’ ‘shinystan’
Found the following significant warnings:
  RngStreams.c:332:4: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/rstream.Rcheck/00install.out’ for details.
Package required but not available: ‘inlmisc’

Packages suggested but not available for checking: ‘leaflet’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  bgc_hmm.c:241:31: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
  rph_tfbs.c:371:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:351:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:819:5: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/rtfbs.Rcheck/00install.out’ for details.
Package required but not available: ‘rbokeh’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in block_exec(params) :
  failed to tidy R code in chunk <pkg_data>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  failed to tidy R code in chunk <stBooksWP>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  failed to tidy R code in chunk <st_book_series>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  failed to tidy R code in chunk <st_book_series2>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  failed to tidy R code in chunk <stTiles>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  failed to tidy R code in chunk <stGeo>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  failed to tidy R code in chunk <tile_coords>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Quitting from lines 84-89 (rtrek.Rmd) 
Error: processing vignette ‘rtrek.Rmd’ failed with diagnostics:
there is no package called 'leaflet'
Execution halted
Packages required but not available: ‘DT’ ‘plotly’ ‘colourpicker’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: checkFaceOrientation
> ### Title: check the orientation of a mesh
> ### Aliases: checkFaceOrientation
> 
> ### ** Examples
> 
> data(dummyhead)
> ## now we invert faces inwards
> checkFaceOrientation(dummyhead.mesh)
[1] TRUE
> dummyinward <- Morpho::invertFaces(dummyhead.mesh)
Error in loadNamespace(name) : there is no package called ‘Morpho’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Found the following significant warnings:
  geometry/s2loop.cc:85:73: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘S2Point’ {aka ‘class Vector3<double>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  geometry/s2loop.cc:247:73: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘S2Point’ {aka ‘class Vector3<double>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  geometry/s2polyline.cc:52:73: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘S2Point’ {aka ‘class Vector3<double>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  geometry/s2polyline.cc:94:73: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘S2Point’ {aka ‘class Vector3<double>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  geometry/s2regioncoverer.cc:119:28: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct S2RegionCoverer::Candidate’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/s2.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/scio.Rcheck/00install.out’ for details.
Packages required but not available: ‘Hmisc’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  catnet_rexport.cpp:221:17: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
  catnet_rexport.cpp:229:15: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:237:16: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 0 and 1023 [-Wformat-overflow=]
  catnet_rexport.cpp:240:18: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
  catnet_rexport.cpp:241:17: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:258:17: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:257:18: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/sdnet.Rcheck/00install.out’ for details.
Package required but not available: ‘spsurvey’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: ‘__var_1_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/sdwd.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘seasonalview’
Packages suggested but not available for checking: ‘dygraphs’ ‘leaflet’
Package required but not available: ‘shiny.semantic’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggExtra’ ‘rgl’
Packages required but not available: ‘plotly’ ‘Hmisc’

Packages suggested but not available for checking: ‘loomR’ ‘DESeq2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘mapview’ ‘tmap’
Error in re-building vignettes:
  ...
Quitting from lines 198-201 (sf5.Rmd) 
Error: processing vignette ‘sf5.Rmd’ failed with diagnostics:
there is no package called 'mapview'
Execution halted
Package suggested but not available for checking: ‘SGP’
Error in re-building vignettes:
  ...
Quitting from lines 2-11 (SGPdata.Rmd) 
Error: processing vignette ‘SGPdata.Rmd’ failed with diagnostics:
there is no package called 'toOrdinal'
Execution halted
Package suggested but not available for checking: ‘threejs’
Packages required but not available: ‘aqp’ ‘soilDB’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shinyjqui’
Packages required but not available:
  ‘heatmaply’ ‘plotly’ ‘DT’ ‘htmlwidgets’

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

Package suggested but not available for checking: ‘highcharter’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘colourpicker’ ‘DT’ ‘dygraphs’ ‘threejs’

Package suggested but not available for checking: ‘rstanarm’

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

Package suggested but not available for checking: ‘flexdashboard’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot2d
> ### Title: Plotting for Class SDE
> ### Aliases: plot2d lines2d points2d plot3D plot2d.default lines2d.default
> ###   points2d.default plot3D.default
> 
> ### ** Examples
> 
> ## Example 1: 
> set.seed(1234)
> 
> fx <- rep(expression(0),2)
> gx <- rep(expression(1),2)
> 
> res <- snssde2d(drift=fx,diffusion=gx,N=10000)
> plot2d(res,type="l")
> 
> ## Example 2: 
> set.seed(1234)
> 
> fx <- rep(expression(0),3)
> gx <- rep(expression(1),3)
> 
> res <- snssde3d(drift=fx,diffusion=gx,N=10000)
> plot3D(res,display="persp")
> plot3D(res,display="rgl")
Error in loadNamespace(name) : there is no package called ‘rgl’
Calls: plot3D ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Package suggested but not available for checking: ‘simmer.plot’
gimli.28837hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Packages suggested but not available for checking: ‘brms’ ‘rstanarm’
Packages suggested but not available for checking:
  ‘brms’ ‘mediation’ ‘rstanarm’
Package required but not available: ‘strataG’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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
gimli.10828hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Packages required but not available: ‘aqp’ ‘Hmisc’

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

Package suggested but not available for checking: ‘plotKML’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘networkD3’ ‘r2cytoscape’
Running examples in ‘SourceSet-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sourceSankeyDiagram
> ### Title: Create a D3 JavaScript Sankey diagram
> ### Aliases: sourceSankeyDiagram
> 
> ### ** Examples
> 
> ## Load the SourceSetObj obtained from the source set analysis of ALL dataset
> 
> # see vignette for more details
> print(load(file=system.file("extdata","ALLsourceresult.RData",package = "SourceSet")))
[1] "results.all"
> class(results.all)
[1] "sourceSetList"
> 
> sourceSankeyDiagram(sourceObj = results.all ,cut.extra.module = FALSE )
Error in loadNamespace(name) : there is no package called ‘networkD3’
Calls: sourceSankeyDiagram ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

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

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

    IQR, mad, sd, var, xtabs

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

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

Identifing all possible orderings..
Total run time: 1.89 secs
Identifing all possible orderings..
Total run time: 1.36 secs
Quitting from lines 346-347 (SourceSet.Rmd) 
Error: processing vignette ‘SourceSet.Rmd’ failed with diagnostics:
there is no package called 'networkD3'
Execution halted
Package required but not available: ‘SpaDES.core’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘profvis’
Package required but not available: ‘htmlwidgets’

Package suggested but not available for checking: ‘formattable’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘r2d3’

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

Package suggested but not available for checking: ‘INLA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plot3Drgl’

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) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 17-58 (spcosa.Rmd) 
Error: processing vignette ‘spcosa.Rmd’ failed with diagnostics:
there is no package called 'rgl'
Execution halted
Packages required but not available: ‘rgl’ ‘MAIT’

Package suggested but not available for checking: ‘rcytoscapejs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'devtools::use_package' is deprecated.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/spectrolab.Rcheck/00install.out’ for details.
gimli.26135hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Package required but not available: ‘mvmesh’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘antaresViz’
Packages required but not available:
  ‘smoof’ ‘SPOT’ ‘rhandsontable’ ‘plotly’

Package suggested but not available for checking: ‘shinytest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  dbfopenSSN.c:1119:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopenSSN.c:1100:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopenSSN.c:663:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  dbfopenSSN.c:1511:2: warning: ‘strncpy’ output may be truncated copying 11 bytes from a string of length 11 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SSN.Rcheck/00install.out’ for details.
Package required but not available: ‘RDS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘rms’
Error in re-building vignettes:
  ...
Loading required package: proxy

Attaching package: ‘proxy’

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

    as.dist, dist

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

    as.matrix

Loading required package: clue
Loading required package: survey
Loading required package: grid
Loading required package: Matrix
Loading required package: survival

Attaching package: ‘survey’

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

    dotchart

Loading required package: RANN
Loading required package: lpSolve
Loading required package: Hmisc

Error: processing vignette ‘Statistical_Matching_with_StatMatch.Rnw’ failed with diagnostics:
 chunk 4 
Error in spearman2(n.income ~ area5 + urb + hsize + age + sex + marital +  : 
  could not find function "spearman2"
Execution halted
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘statnet’
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘statnet’
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/statnet.Rcheck/00install.out’ for details.
Packages required but not available: ‘DT’ ‘Hmisc’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: str_view
> ### Title: View HTML rendering of regular expression match.
> ### Aliases: str_view str_view_all
> 
> ### ** Examples
> 
> str_view(c("abc", "def", "fgh"), "[aeiou]")
Error in loadNamespace(name) : there is no package called ‘htmlwidgets’
Calls: str_view ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Running ‘testGBHProcedures.R’ [3s/3s]
  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
Running examples in ‘styler-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create_node_from_nested_root
> ### Title: Convert a nested tibble into a node tree
> ### Aliases: create_node_from_nested_root
> ### Keywords: internal
> 
> ### ** Examples
> 
> if (getRversion() >= 3.2) {
+ code <- "a <- function(x) { if(x > 1) { 1+1 } else {x} }"
+ nested_pd <- styler:::compute_parse_data_nested(code)
+ initialized <- styler:::pre_visit(nested_pd, c(default_style_guide_attributes))
+ styler:::create_node_from_nested_root(initialized, structure_only = FALSE)
+ }
Error in loadNamespace(name) : there is no package called ‘data.tree’
Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Package required but not available: ‘prim’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: schemper
> ### Title: Distance-based estimator of survival predictive accuracy
> ###   proposed by Schemper and Henderson
> ### Aliases: schemper
> ### Keywords: classif
> 
> ### ** Examples
> 
> 
> library(rms)
Error in library(rms) : there is no package called ‘rms’
Execution halted
Package required but not available: ‘rms’

Packages suggested but not available for checking: ‘shinystan’ ‘INLA’

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

Package suggested but not available for checking: ‘rms’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘LSAmitR’
Error in re-building vignettes:
  ...
Quitting from lines 13-18 (fda-example.Rmd) 
Error: processing vignette ‘fda-example.Rmd’ failed with diagnostics:
there is no package called 'Hmisc'
Execution halted
Package suggested but not available for checking: ‘ggalt’
Error in re-building vignettes:
  ...
Quitting from lines 123-138 (intro_to_tbrf.Rmd) 
Error: processing vignette ‘intro_to_tbrf.Rmd’ failed with diagnostics:
there is no package called 'ggalt'
Execution halted
Package required but not available: ‘SPOT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘radarchart’ ‘DT’ ‘metricsgraphics’ ‘leaflet’ ‘threejs’ ‘d3heatmap’
  ‘plotly’ ‘dygraphs’ ‘networkD3’ ‘DiagrammeR’ ‘visNetwork’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘rgl’ ‘R2wd’
Package required but not available: ‘arulesViz’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/sparsepp/include/sparsepp/spp_utils.h:422:44: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair<const std::pair<unsigned int, unsigned int>, int>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/sparsepp/include/sparsepp/spp_utils.h:422:44: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair<const std::pair<unsigned int, unsigned int>, float>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/text2vec.Rcheck/00install.out’ for details.
Package required but not available: ‘plotly’

Package suggested but not available for checking: ‘networkD3’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages unavailable to check Rd xrefs: ‘DESeq2’, ‘dada2’
Packages suggested but not available for checking:
  ‘vdiffr’ ‘rstanarm’ ‘brms’
Running examples in ‘tidybayes-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gather_emmeans_draws
> ### Title: Extract a tidy data frame of draws of posterior distributions of
> ###   "estimated marginal means" (emmeans/lsmeans) from a Bayesian model
> ###   fit.
> ### Aliases: gather_emmeans_draws
> ### Keywords: manip
> 
> ### ** Examples
> 
> 
> library(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

> library(magrittr)
> library(rstanarm)
Error in library(rstanarm) : there is no package called ‘rstanarm’
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


Attaching package: 'tidyr'

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

    extract

NOTE: As of tidybayes version 1.0, several functions, arguments, and output column names
      have undergone significant name changes in order to adopt a unified naming scheme.
      See help('tidybayes-deprecated') for more information.


Attaching package: 'ggstance'

The following objects are masked from 'package:ggplot2':

    GeomErrorbarh, geom_errorbarh


Attaching package: 'ggridges'

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

    scale_discrete_manual


Attaching package: 'cowplot'

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

    ggsave

Loading required package: StanHeaders
rstan (Version 2.18.1, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)

Attaching package: 'rstan'

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

    extract

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

    extract

Quitting from lines 37-49 (tidy-brms.Rmd) 
Error: processing vignette ‘tidy-brms.Rmd’ failed with diagnostics:
there is no package called 'brms'
Execution halted
Packages required but not available: ‘htmlwidgets’ ‘leaflet’ ‘mapview’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘pca3d’
Error in re-building vignettes:
  ...
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'pca3d'
Quitting from lines 694-697 (tmod.rmd) 
Error: processing vignette ‘tmod.rmd’ failed with diagnostics:
unused argument (group = c("CTRL", "CTRL", "CTRL", "CTRL", "CTRL", "CTRL", "CTRL", "CTRL", "CTRL", "CTRL", "CTRL", "CTRL", "CTRL", "CTRL", "CTRL", "TB", "TB", "TB", "TB", "TB", "TB", "TB", "TB", "TB", "TB", "TB", "TB", "TB", "TB", "TB"))
Execution halted
Packages required but not available: ‘rgl’ ‘qpcR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  RngStream.c:347:4: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/TPmsm.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘rgl’ ‘taxidata’
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(treemapify)
  > 
  > test_check("treemapify")
  ── 1. Error: plots look the way they should (@test_plots.R#4)  ─────────────────
  there is no package called 'vdiffr'
  1: vdiffr::expect_doppelganger at testthat/test_plots.R:4
  2: getExportedValue(pkg, name)
  3: asNamespace(ns)
  4: getNamespace(ns)
  5: tryCatch(loadNamespace(name), error = function(e) stop(e))
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 24 SKIPPED: 0 FAILED: 1
  1. Error: plots look the way they should (@test_plots.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available:
  ‘htmlwidgets’ ‘rgl’ ‘RLumShiny’ ‘scatterD3’

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

Packages suggested but not available for checking:
  ‘rbokeh’ ‘plotly’ ‘packagedocs’

VignetteBuilder package required for checking but not installed: ‘packagedocs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 130-139 (choropleth_maps_with_tricolore.Rmd) 
Error: processing vignette ‘choropleth_maps_with_tricolore.Rmd’ failed with diagnostics:
there is no package called 'leaflet'
Execution halted
Running ‘testthat.R’ [30s/33s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tsbox)
  > 
  > test_check("tsbox")
  "dygraphs"
  ── 1. Error: (unknown) (@test_tricky.R#6)  ─────────────────────────────────────
  Additional packages needed. To install, use:
  
    install.packages("dygraphs")
  1: ts_dygraphs(AirPassengers) at testthat/test_tricky.R:6
  2: load_suggested("dygraphs")
  3: stop("Additional packages needed. To install, use:\n\n  install.packages(\"", pkgv, 
         "\")", call. = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 328 SKIPPED: 11 FAILED: 1
  1. Error: (unknown) (@test_tricky.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available: ‘TSclust’ ‘longitudinalData’

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

Package suggested but not available for checking: ‘DT’

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

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

Package suggested but not available for checking: ‘mapview’

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

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

Package suggested but not available for checking: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 30-32 (convexhull.Rmd) 
Error: processing vignette ‘convexhull.Rmd’ failed with diagnostics:
there is no package called 'rgl'
Execution halted
Packages suggested but not available for checking:
  ‘USAboundariesData’ ‘leaflet’
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

Linking to GEOS 3.7.0, GDAL 2.3.2, PROJ 5.2.0
Quitting from lines 23-30 (usaboundaries-sample-analysis.Rmd) 
Error: processing vignette ‘usaboundaries-sample-analysis.Rmd’ failed with diagnostics:
there is no package called 'leaflet'
Execution halted
Packages required but not available: ‘data.tree’ ‘DiagrammeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘vaers’ ‘vaersND’ ‘rpivotTable’
Packages suggested but not available for checking:
  ‘vaers’ ‘vaersND’ ‘pivottabler’
Found the following significant warnings:
  include/rapidjson/document.h:1952:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘rapidjson::GenericValue<rapidjson::UTF8<> >::Member’ {aka ‘struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::MemoryPoolAllocator<> >’} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class rapidjson::GenericValue<rapidjson::UTF8<> >’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  include/rapidjson/document.h:1952:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>::Member’ {aka ‘struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::CrtAllocator>’} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/validatejsonr.Rcheck/00install.out’ for details.
Running examples in ‘vcdExtra-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mosaic3d
> ### Title: 3D Mosaic Plots
> ### Aliases: mosaic3d mosaic3d.default mosaic3d.loglm
> ### Keywords: hplot
> 
> ### ** Examples
> 
> # 2 x 2 x 2
> mosaic3d(Bartlett, box=TRUE)
Loading required namespace: rgl
Failed with error:  ‘there is no package called ‘rgl’’
Error in mosaic3d.default(Bartlett, box = TRUE) : rgl is required
Calls: mosaic3d -> mosaic3d.default
Execution halted
Running examples in ‘vegdata-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: isc
> ### Title: Indicate site conditions with community weighted mean values of
> ###   traits or with mode of gradient classes (sum of species amplitudes).
> ### Aliases: isc showindiplot
> ### Keywords: misc
> 
> ### ** Examples
> 
> db <- 'elbaue'
> veg <- tv.veg(db, cover.transform='sqrt', check.critical = FALSE)

No Turbowin installation path found. 

############################################################
Turboveg root directory is set to "/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/vegdata/tvdata"
If you want to change this use: options(tv_home="<path_to_your_Turbowin_root>")
############################################################
Reading tvabund.dbf
Taxonomic reference list:  GermanSL 1.3 
Original number of names: 53 
Taxonomic reference list file /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/vegdata/tvdata/Species/GermanSL 1.3/tax.dbf does not exist.

Taxonomic list (tax.dbf) of reflistGermanSL 1.3 not available.


trying URL 'https://germansl.infinitenature.org/GermanSL/1.3/GermanSL.zip'
Content type 'application/zip' length 3092316 bytes (2.9 MB)
==================================================
downloaded 2.9 MB

Warning in unzip(tfile, exdir = file.path(tv_home, "Species")) :
  error -1 in extracting from zip file
Error in load.taxlist(refl = refl, detailed = TRUE, ...) : 
  Reference list file /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/vegdata/tvdata/Species/GermanSL 1.3/tax.dbf does not exist.
Calls: tv.veg -> taxval -> load.taxlist
Execution halted
Package suggested but not available for checking: ‘sparklyr’
Package required but not available: ‘plotly’

Package suggested but not available for checking: ‘vdiffr’

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

Packages suggested but not available for checking:
  ‘colourpicker’ ‘sparkline’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: VoxR-package
> ### Title: Metrics extraction of trees from T-LiDAR data
> ### Aliases: VoxR-package VoxR
> ### Keywords: package 3d point cloud LiDAR
> 
> ### ** Examples
> 
> data(treecloud)
> 
> #-voxelisation using the vox function
> 
> treecloud_vox <- vox(treecloud,res=0.02)
> 
> #-visualisation
> 
> require(rgl)
Loading required package: rgl
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘rgl’
> library(rgl)
Error in library(rgl) : there is no package called ‘rgl’
Execution halted
Packages required but not available: ‘plotKML’ ‘Hmisc’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [18s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(wdm)
  > 
  > test_check("wdm")
  ── 1. Error: method hoeffding is correct (@test_computations_unweighted.R#24)  ─
  there is no package called 'Hmisc'
  1: expect_equal(wdm(x, method = "hoeffd"), Hmisc::hoeffd(x)$D) at testthat/test_computations_unweighted.R:24
  2: quasi_label(enquo(expected), expected.label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: Hmisc::hoeffd
  5: getExportedValue(pkg, name)
  6: asNamespace(ns)
  7: getNamespace(ns)
  8: tryCatch(loadNamespace(name), error = function(e) stop(e))
  9: tryCatchList(expr, classes, parentenv, handlers)
  10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  11: value[[3L]](cond)
  
  ── 2. Error: method hoeffding is correct (@test_computations_unweighted.R#79)  ─
  there is no package called 'Hmisc'
  1: expect_equal(indep_test(x, y, method = "hoeffd")$p_value, Hmisc::hoeffd(x, y)$P[1, 
         2], tol = 0.03) at testthat/test_computations_unweighted.R:79
  2: quasi_label(enquo(expected), expected.label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: Hmisc::hoeffd
  5: getExportedValue(pkg, name)
  6: asNamespace(ns)
  7: getNamespace(ns)
  8: tryCatch(loadNamespace(name), error = function(e) stop(e))
  9: tryCatchList(expr, classes, parentenv, handlers)
  10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  11: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 73 SKIPPED: 0 FAILED: 2
  1. Error: method hoeffding is correct (@test_computations_unweighted.R#24) 
  2. Error: method hoeffding is correct (@test_computations_unweighted.R#79) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘wellknown-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: multilinestring
> ### Title: Make WKT multilinestring objects
> ### Aliases: multilinestring
> 
> ### ** Examples
> 
> ## empty multilinestring
> multilinestring("empty")
[1] "MULTILINESTRING EMPTY"
> # multilinestring("stuff")
> 
> # character string
> x <- "MULTILINESTRING ((30 20, 45 40, 10 40), (15 5, 40 10, 10 20))"
> multilinestring(x)
[1] "MULTILINESTRING ((30 20, 45 40, 10 40), (15 5, 40 10, 10 20))"
> 
> # data.frame
> df <- data.frame(long = c(30, 45, 10), lat = c(20, 40, 40))
> df2 <- data.frame(long = c(15, 40, 10), lat = c(5, 10, 20))
> multilinestring(df, df2, fmt=0)
[1] "MULTILINESTRING ((30 20, 45 40, 10 40), (15 5, 40 10, 10 20))"
> lint(multilinestring(df, df2, fmt=0))
[1] TRUE
> wktview(multilinestring(df, df2), zoom=3)
Error: Please install leaflet
Execution halted
Found the following significant warnings:
  tabix/razf.c:188:2: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/WhopGenome.Rcheck/00install.out’ for details.
Packages required but not available:
  ‘plotly’ ‘DT’ ‘colourpicker’ ‘DESeq2’ ‘heatmaply’

Package suggested but not available for checking: ‘vdiffr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  libxlsxwriter/xmlwriter.c:156:17: warning: ‘strncat’ specified bound 5 equals source length [-Wstringop-overflow=]
  libxlsxwriter/xmlwriter.c:160:17: warning: ‘strncat’ specified bound 4 equals source length [-Wstringop-overflow=]
  libxlsxwriter/xmlwriter.c:164:17: warning: ‘strncat’ specified bound 4 equals source length [-Wstringop-overflow=]
  libxlsxwriter/xmlwriter.c:168:17: warning: ‘strncat’ specified bound 6 equals source length [-Wstringop-overflow=]
  libxlsxwriter/xmlwriter.c:198:17: warning: ‘strncat’ specified bound 5 equals source length [-Wstringop-overflow=]
  libxlsxwriter/xmlwriter.c:202:17: warning: ‘strncat’ specified bound 4 equals source length [-Wstringop-overflow=]
  libxlsxwriter/xmlwriter.c:206:17: warning: ‘strncat’ specified bound 4 equals source length [-Wstringop-overflow=]
  tmpfileplus/tmpfileplus.c:172:3: warning: ‘strncpy’ specified bound 4097 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/writexl.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Quitting from lines 951-952 (WRS2.Rnw) 
Error: processing vignette ‘WRS2.Rnw’ failed with diagnostics:
there is no package called 'mediation'
Execution halted
Running examples in ‘xgboost-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: xgb.plot.multi.trees
> ### Title: Project all trees on one tree and plot it
> ### Aliases: xgb.plot.multi.trees
> 
> ### ** Examples
> 
> 
> data(agaricus.train, package='xgboost')
> 
> bst <- xgboost(data = agaricus.train$data, label = agaricus.train$label, max_depth = 15,
+                eta = 1, nthread = 2, nrounds = 30, objective = "binary:logistic",
+                min_child_weight = 50, verbose = 0)
> 
> p <- xgb.plot.multi.trees(model = bst, features_keep = 3)
Error in loadNamespace(name) : there is no package called ‘DiagrammeR’
Calls: xgb.plot.multi.trees ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Running ‘testthat.R’ [44s/45s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(xgboost)
  > 
  > test_check("xgboost")
  [1]	train-error:0.016275 
  [1]	train-auc:0.900000	test-auc:0.800000 
  [1]	eval-error:0.042831	train-error:0.046522 
  [2]	eval-error:0.021726	train-error:0.022263 
  [1]	eval-error:0.042831	train-error:0.046522 
  [2]	eval-error:0.021726	train-error:0.022263 
  [1]	train-error:0.046522 
  [2]	train-error:0.022263 
  [1]	train-error:0.333333 
  ── 1. Error: xgb.plot.tree works with and without feature names (@test_helpers.R
  DiagrammeR package is required for xgb.plot.tree
  1: xgb.plot.tree(feature_names = feature.names, model = bst.Tree) at testthat/test_helpers.R:290
  2: stop("DiagrammeR package is required for xgb.plot.tree", call. = FALSE)
  
  ── 2. Error: xgb.plot.multi.trees works with and without feature names (@test_he
  there is no package called 'DiagrammeR'
  1: xgb.plot.multi.trees(model = bst.Tree, feature_names = feature.names, features_keep = 3) at testthat/test_helpers.R:295
  2: DiagrammeR::create_node_df
  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: 542 SKIPPED: 2 FAILED: 2
  1. Error: xgb.plot.tree works with and without feature names (@test_helpers.R#290) 
  2. Error: xgb.plot.multi.trees works with and without feature names (@test_helpers.R#295) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘ggbio’
Packages required but not available: ‘colourpicker’ ‘plotly’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getInfo
> ### Title: Extract dataset information for a given dtype name or number
> ### Aliases: getInfo
> 
> ### ** Examples
> 
> getInfo('atsstamday')
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: Connection timed out after 10001 milliseconds
Calls: getInfo ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
Package required but not available: ‘SACCR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    R  13.6Mb
Depends: includes the non-default packages:
  'Matrix' 'coda' 'mvtnorm' 'MCMCpack' 'spatstat' 'parallel'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/AmesHousing.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/AMR.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    help   1.1Mb
Packages suggested but not available for checking:
  'sfit' 'expectile' 'HaarSeg' 'mpcbs'
Packages suggested but not available for checking: 'REBayes' 'Rmosek'
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.
installed size is 67.3Mb
  sub-directories of 1Mb or more:
    java  67.2Mb
Error in re-building vignettes:
  ...
Quitting from lines 83-86 (use-ballr.Rmd) 
Error: processing vignette 'use-ballr.Rmd' failed with diagnostics:
Evaluation error: object 'age' not found.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/BANOVA.Rcheck/00install.out' for details.
Packages which this enhances but not available for checking:
  'doMC' 'rPython'
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.
Packages suggested but not available for checking: 'bcmaps.rdata' 'doMC'
installed size is 142.0Mb
  sub-directories of 1Mb or more:
    include  141.1Mb
Package which this enhances but not available for checking: 'synchronicity'
Package unavailable to check Rd xrefs: 'synchronicity'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      2.6Mb
Running 'testthat.R' [73s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(bikedata)
  Data for London, U.K. powered by TfL Open Data:
    Contains OS data <U+24B8> Crown copyright and database rights 2016
  Data for New York City provided and owned by:
    NYC Bike Share, LLC and Jersey City Bike Share, LLC ("Bikeshare")
    see https://www.citibikenyc.com/data-sharing-policy
  Data for Washington DC (Captialbikeshare), Chiago (Divvybikes) and Boston (Hubway)
    provided and owned by Motivate International Inc.
    see https://www.capitalbikeshare.com/data-license-agreement
    and https://www.divvybikes.com/data-license-agreement
    and https://www.thehubway.com/data-license-agreement
  Nice Ride Minnesota license  https://www.niceridemn.org/data_license
  > 
  > test_check("bikedata")
  -- 1. Failure: dl_bikedata la (@test-download-data.R#88)  ----------------------
  `dl_bikedata(city = "la", data_dir = tempdir(), dates = 2016)` produced unexpected messages.
  Expected match: All data files already exist
  Actual values:
  * Downloading metro-bike-share-trips-2016-q4.csv.zip
  
  
  == testthat results  ===========================================================
  OK: 136 SKIPPED: 2 FAILED: 1
  1. Failure: dl_bikedata la (@test-download-data.R#88) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [49s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(bikedata)
  Data for London, U.K. powered by TfL Open Data:
    Contains OS data <U+24B8> Crown copyright and database rights 2016
  Data for New York City provided and owned by:
    NYC Bike Share, LLC and Jersey City Bike Share, LLC ("Bikeshare")
    see https://www.citibikenyc.com/data-sharing-policy
  Data for Washington DC (Captialbikeshare), Chiago (Divvybikes) and Boston (Hubway)
    provided and owned by Motivate International Inc.
    see https://www.capitalbikeshare.com/data-license-agreement
    and https://www.divvybikes.com/data-license-agreement
    and https://www.thehubway.com/data-license-agreement
  Nice Ride Minnesota license  https://www.niceridemn.org/data_license
  > 
  > test_check("bikedata")
  -- 1. Failure: dl_bikedata la (@test-download-data.R#88)  ----------------------
  `dl_bikedata(city = "la", data_dir = tempdir(), dates = 2016)` produced unexpected messages.
  Expected match: All data files already exist
  Actual values:
  * Downloading metro-bike-share-trips-2016-q4.csv.zip
  
  
  == testthat results  ===========================================================
  OK: 136 SKIPPED: 2 FAILED: 1
  1. Failure: dl_bikedata la (@test-download-data.R#88) 
  
  Error: testthat unit tests failed
  Execution halted
Depends: includes the non-default packages:
  'colorspace' 'deldir' 'rgl' 'tcltk' 'tcltk2' 'tkrplot'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R        1.0Mb
    data     1.5Mb
    models   2.4Mb
Package required but not available: 'OpenCL'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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/ChainLadder.Rcheck/00install.out' for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.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/cosinor2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/cplexAPI.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/cudaBayesreg.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'xtable' 'akima' 'R.oo' 'R.methodsS3' 'matlab' 'lattice' 'locfit'
  'grid'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Running 'testthat.R' [63s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(DeclareDesign)
  Loading required package: randomizr
  Loading required package: fabricatr
  Loading required package: estimatr
  > 
  > test_check("DeclareDesign")
  -- 1. Failure: error if you try to draw POs at a level using a variable that doe
  `my_potential_outcomes_formula(pop)` did not throw an error.
  
  == testthat results  ===========================================================
  OK: 436 SKIPPED: 1 FAILED: 1
  1. Failure: error if you try to draw POs at a level using a variable that doesn't exist at that level (@test-potential-outcomes.R#160) 
  
  Error: testthat unit tests failed
  Execution halted
Depends: includes the non-default packages:
  'Deducer' 'psych' 'GPArotation' 'mvnormtest' 'irr' 'klaR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'JavaGD' 'Deducer' 'sp' 'maptools' 'OpenStreetMap' 'scales' 'rgdal'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
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/define.Rcheck/00install.out' for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.6Mb
    help   1.4Mb
    libs   1.7Mb
Packages which this enhances but not available for checking:
  'gurobi' 'Rcplex' 'Rmosek'
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/DEVis.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/did.Rcheck/00install.out' for details.
Packages which this enhances but not available for checking:
  'gurobi' 'Rmosek'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   3.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    media       2.2Mb
    shinyapps   2.6Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.3Mb
    libs   4.3Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.7Mb
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\RtmpkxPa97\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\RtmpgDnzdK\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
Depends: includes the non-default packages:
  'gWidgets' 'tcltk' 'tkrplot' 'RGtk2' 'gWidgetsRGtk2' 'cairoDevice'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages suggested but not available for checking: 'doMC' 'RSvgDevice'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Packages suggested but not available for checking:
  'Rsocp' 'Rnlminb2' 'Rdonlp2'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/ftsa.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/future.apply.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/gastempt.Rcheck/00install.out' for details.
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  21.2Mb
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")
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/gpuR.Rcheck/00install.out' for details.
installed size is 25.7Mb
  sub-directories of 1Mb or more:
    R  25.7Mb
Packages suggested but not available for checking:
  'taxstats' 'taxstats1516'
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-3.5.1/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.5.1/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.
1/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
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/hNMF.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Depends: includes the non-default packages:
  'lattice' 'caTools' 'gdata' 'gtools' 'gplots' 'parallel'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
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:
  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/Immigrate.Rcheck/00install.out' for details.
Running 'testthat.R' [66s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ipeaData)
  > 
  > test_check("ipeaData")
  [1] "NA. 05/1999 a 03/2009. Acesso em: 19/10/2018"
  -- 1. Error: ipeaData (@test_functions_ipea_data.R#19)  ------------------------
  Recv failure: Connection was reset
  1: suppressWarnings(result <- ipeadata("SERIE SEM RETORNO")) at testthat/test_functions_ipea_data.R:19
  2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  3: ipeadata("SERIE SEM RETORNO")
  4: get_metadata(serie)
  5: basic_call(api_call, type)
  6: GET(api)
  7: request_perform(req, hu$handle$handle)
  8: request_fetch(req$output, req$url, handle)
  9: request_fetch.write_memory(req$output, req$url, handle)
  10: curl::curl_fetch_memory(url, handle = handle)
  
  -- 2. Error: search_serie (@test_functions_ipea_data.R#24)  --------------------
  Timeout was reached: Connection timed out after 10000 milliseconds
  1: search_serie("pib", fields_search = ("SERNOME")) at testthat/test_functions_ipea_data.R:24
  2: basic_call(api_call, type)
  3: GET(api)
  4: request_perform(req, hu$handle$handle)
  5: request_fetch(req$output, req$url, handle)
  6: request_fetch.write_memory(req$output, req$url, handle)
  7: curl::curl_fetch_memory(url, handle = handle)
  
  == testthat results  ===========================================================
  OK: 5 SKIPPED: 0 FAILED: 2
  1. Error: ipeaData (@test_functions_ipea_data.R#19) 
  2. Error: search_serie (@test_functions_ipea_data.R#24) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.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/iprior.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'partitions' 'VGAM' 'MASS' 'ape' 'apTreeshape' 'geiger' 'gtools'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R   7.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      3.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Depends: includes the non-default packages:
  'sn' 'moments' 'BB' 'Bolstad2' 'optimx' 'Rmpfr'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:
  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/LipidMS.Rcheck/00install.out' for details.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    doc        2.4Mb
    libs       2.1Mb
    testdata   1.6Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.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/marmap.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.2Mb
Depends: includes the non-default packages:
  'lattice' 'locfit' 'maptools' 'quantreg' 'RANN' 'SparseM'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'MASS' 'boot' 'RColorBrewer' 'scatterplot3d' 'tcltk' 'tcltk2'
  'tkrplot' 'rpanel' 'rgl'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'seqinr' 'pcaMethods' 'Matrix' 'ROCR' 'Hmisc' 'KernSmooth' 'seqLogo'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
Packages suggested but not available for checking: 'doMC' 'doSMP'
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    1.0Mb
    libs   3.9Mb
    misc   1.1Mb
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.
Package required and available but unsuitable version: 'stringi'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Depends: includes the non-default packages:
  'car' 'pdist' 'pls' 'gplots' 'mvtnorm' 'robustbase' 'gtools' 'bitops'
  'caTools' 'pcaPP' 'rrcov'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
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/nhanesA.Rcheck/00install.out' for details.
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    CppCode   2.5Mb
    R         6.5Mb
    include   5.6Mb
    libs      1.8Mb
    tests     1.3Mb
Depends: includes the non-default packages:
  'lpSolve' 'gdata' 'Hmisc' 'rms' 'geometry' 'psych' 'pwt'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
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-3.5.1/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.5.1/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.
Depends: includes the non-default packages:
  'R.methodsS3' 'MASS' 'matrixStats' 'R.oo' 'R.utils' 'aroma.core'
  'aroma.affymetrix' 'DNAcopy'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    1.5Mb
    help   2.4Mb
    libs   2.0Mb
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/onewaytests.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/OpenCL.Rcheck/00install.out' for details.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    R        2.4Mb
    libs     6.4Mb
    models   4.7Mb
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/optweight.Rcheck/00install.out' for details.
Package required but not available: 'ROracle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
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: 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
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    lib    5.6Mb
    libs   4.6Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.1Mb
    libs   2.3Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      4.4Mb
    data   3.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/pkgload.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'RGtk2' 'gWidgetsRGtk2' 'cairoDevice' 'lattice' 'rggobi' 'ggplot2'
  'proto'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:
  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/ppgmmga.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/prophet.Rcheck/00install.out' for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc        4.6Mb
    examples   2.2Mb
Package required but not available: 'qtbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   3.0Mb
Packages suggested but not available for checking: 'rcom' 'RDCOMClient'
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs   2.8Mb
Error in re-building vignettes:
  ...
Loading required package: sp
Loading required package: RANN
Loading required package: PBSmapping

-----------------------------------------------------------
PBS Mapping 2.70.5 -- 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 
D:/temp/RtmpuQkdyf/RLIBS_1ecf027b3821/PBSmapping/doc/PBSmapping-UG.pdf

Packaged on 2018-06-05
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
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs   2.3Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
Depends: includes the non-default packages:
  'biclust' 'fabia' 'iBBiG' 'superbiclust' 'BcDiag' 'rqubic' 'BicARE'
  's4vd' 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:
  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/RcmdrPlugin.UCA.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/Rcplex.Rcheck/00install.out' for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    include   5.4Mb
    libs      1.6Mb
Running 'testthat.R' [39s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("rdefra")
  > 
  > test_check("rdefra")
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  -- 1. Failure: Metadata should be in the right format (@test-data.R#44)  -------
  `x` not equal to `expected`.
  1 element mismatch
  
  Error in file(file, "rt") : cannot open the connection
  -- 2. Failure: Data should be in the right format (@test-data.R#55)  -----------
  `x` not equal to `expected`.
  'is.NA' value mismatch: 0 in current 1 in target
  
  == testthat results  ===========================================================
  OK: 39 SKIPPED: 1 FAILED: 2
  1. Failure: Metadata should be in the right format (@test-data.R#44) 
  2. Failure: Data should be in the right format (@test-data.R#55) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Running 'test-all.R' [5s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("rgbif")
  Loading required package: rgbif
  -- 1. Error: name_usage with single taxon key and return='data': returns issues 
  Not Found
  1: name_usage(key = 143861132, return = "data") at testthat/test-name_usage.r:63
  2: getdata(data, key, uuid, shortname, args, curlopts)
  3: gbif_GET(url, args, FALSE, curlopts)
  4: stop(mssg, call. = FALSE)
  
  == testthat results  ===========================================================
  OK: 63 SKIPPED: 117 FAILED: 1
  1. Error: name_usage with single taxon key and return='data': returns issues correctly (@test-name_usage.r#63) 
  
  Error: testthat unit tests failed
  Execution halted
Packages suggested but not available for checking: 'pmg' 'SVGAnnotation'
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    R      3.6Mb
    help  10.6Mb
    libs   5.1Mb
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/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 'd:/Rcompile/CRANpkg/local/3.5/RJSONIO.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/Rmosek.Rcheck/00install.out' for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
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.
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.
Depends: includes the non-default packages:
  'biwt' 'cairoDevice' 'fBasics' 'gplots' 'gWidgets' 'gWidgetsRGtk2'
  'minerva' 'parmigene' 'stringr' 'snowfall'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    2.8Mb
    libs  17.4Mb
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 11.6Mb
  sub-directories of 1Mb or more:
    Lib  11.5Mb
Running 'test-all.R' [42s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("rtext")
  Loading required package: rtext
  Loading required package: stringb
  -- 1. Error: rtext tokenize_data_lines (@test_rtext.R#123)  --------------------
  arguments must have same length
  1: expect_true({
         dings <- rtext$new("meine mudder \nschneidet speck\n - ho-narroh")
         dings$char_data_set("test", 1:20, 1)
         dings$char_data_set("toast", 1:dings$char_length(), "uggah")
         dings$char_data_get()
         dings$tokenize_data_lines()$test[1] == 1 & is.na(dings$tokenize_data_lines()$test[2])
     }) at testthat/test_rtext.R:123
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: dings$tokenize_data_lines() at testthat/test_rtext.R:128
  5: self$tokenize_data_regex(split = split, ignore.case = ignore.case, fixed = fixed, 
         perl = perl, useBytes = useBytes, non_token = non_token, join = join, aggregate_function = aggregate_function, 
         ...)
  6: self$tokenize_data_sequences(token = token, join = join, aggregate_function = aggregate_function, 
         ...)
  7: stats::aggregate(chardata[, -c(1:2)], by = list(token_i = token_i), FUN = "modus", 
         multimodal = NA, warn = FALSE)
  8: aggregate.data.frame(chardata[, -c(1:2)], by = list(token_i = token_i), FUN = "modus", 
         multimodal = NA, warn = FALSE)
  9: stop("arguments must have same length")
  
  == testthat results  ===========================================================
  OK: 282 SKIPPED: 0 FAILED: 1
  1. Error: rtext tokenize_data_lines (@test_rtext.R#123) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   1.8Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.9Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    2.4Mb
    libs   3.5Mb
Running examples in 'secrlinear-Ex.R' failed
The error most likely occurred in:

> ### Name: Arvicola
> ### Title: Water Vole Capture Dataset
> ### Aliases: arvicola
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> head(traps(arvicola))
          x      y
0.A  164.86 609.69
0.B  164.86 609.69
20.A 163.85 629.66
20.B 163.85 629.66
40.A 164.88 649.19
40.B 164.88 649.19
> 
> ## for speed, pre-compute distance matrix
> userd <- networkdistance (traps(arvicola), glymemask, glymemask)
> ## fit model
> glymefit <- secr.fit(arvicola, mask = glymemask, trace = FALSE,
+                      details = list(userdist = userd))
Warning in check3D(object) :
  secr 3.0 requires 3-D capthist; using updateCH() to convert
Warning in autoini(ch, msk, binomN = details$binomN, ignoreusage = details$ignoreusage) :
  'autoini' failed to find g0; setting initial g0 = 0.1
installed size is 96.5Mb
  sub-directories of 1Mb or more:
    doc     11.8Mb
    docker   1.3Mb
    gdal     3.9Mb
    libs    70.0Mb
    proj     5.0Mb
    sqlite   1.5Mb
Depends: includes the non-default packages:
  'hdrcde' 'coda' 'MASS' 'bayesm' 'mnormt' 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package suggested but not available for checking: 'rcytoscapejs'
Running examples in 'spm12r-Ex.R' failed
The error most likely occurred in:

> ### Name: install_spm12
> ### Title: Install SPM12 file into directory
> ### Aliases: install_spm12
> 
> ### ** Examples
> 
> tdir = tempfile()
> dir.create(tdir)
> res = install_spm12(install_dir = tdir)
cloning into 'D:\temp\Rtmp6BqWJT\file1f5141ce2335b/spm12'...
Error in git2r::clone("https://github.com/muschellij2/spm12r", branch = "gh-pages",  : 
  Error in 'git2r_clone': unknown certificate check failure
Calls: install_spm12 -> <Anonymous>
Execution halted
Found the following significant warnings:
  Warning: replacing previous import 'statnet.common::sweep.mcmc.list' by 'ergm::sweep.mcmc.list' when loading 'statnet'
  Warning: replacing previous import 'statnet.common::colMeans.mcmc.list' by 'ergm::colMeans.mcmc.list' when loading 'statnet'
See 'd:/Rcompile/CRANpkg/local/3.5/statnet.Rcheck/00install.out' for details.
Running examples in 'steemr-Ex.R' failed
The error most likely occurred in:

> ### Name: follower_df
> ### Title: A id list of an id's followers from steemdb.com
> ### Aliases: follower_df
> 
> ### ** Examples
> 
> follower_df()
Error in function (type, msg, asError = TRUE)  : 
  Failed to connect to steemdb.com port 443: Connection refused
Calls: follower_df -> <Anonymous> -> curlPerform -> <Anonymous> -> fun
Execution halted
Running examples in 'stplanr-Ex.R' failed
The error most likely occurred in:

> ### Name: SpatialLinesNetwork
> ### Title: Create object of class SpatialLinesNetwork or sfNetwork
> ### Aliases: SpatialLinesNetwork
> 
> ### ** Examples
> 
> SLN <- SpatialLinesNetwork(route_network)
> class(SLN)
[1] "SpatialLinesNetwork"
attr(,"package")
[1] "stplanr"
> weightfield(SLN) # field used to determine shortest path
[1] "length"
> plot(SLN)
> points(sln2points(SLN)[1,], cex = 5)
> points(sln2points(SLN)[50,], cex = 5)
> shortpath <- sum_network_routes(SLN, 1, 50, sumvars = "length")
> plot(shortpath, col = "red", lwd = 4, add = TRUE)
> points(sln2points(SLN)[35,], cex = 5)
> shortpath <- sum_network_routes(SLN, 1, 35, sumvars = "length")
> plot(shortpath, col = "red", lwd = 4, add = TRUE)
> library(sf)
Linking to GEOS 3.6.1, GDAL 2.2.3, PROJ 4.9.3
> SLN_sf <- SpatialLinesNetwork(route_network_sf)
> plot(SLN_sf)
> shortpath <- sum_network_routes(SLN_sf, 1, 50, sumvars = "length")
Error: Column `do_union` not found in `.data`
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/stringi.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/survHE.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Packages suggested but not available for checking: 'sylly.de' 'sylly.es'
Packages suggested but not available for checking:
  'Rcampdf' 'Rpoppler' 'tm.lexicon.GeneralInquirer'
Found the following significant warnings:
  Warning: replacing previous import 'gdalUtils::gdal_rasterize' by 'sf::gdal_rasterize' when loading 'uavRmp'
See 'd:/Rcompile/CRANpkg/local/3.5/uavRmp.Rcheck/00install.out' for details.
Running examples in 'urltools-Ex.R' failed
The error most likely occurred in:

> ### Name: tld_extract
> ### Title: Extract TLDs
> ### Aliases: tld_extract
> 
> ### ** Examples
> 
> # Using the inbuilt dataset
> domains <- domain("https://en.wikipedia.org/wiki/Main_Page")
> tld_extract(domains)
            domain tld
1 en.wikipedia.org org
> 
> # Using a refreshed one
> tld_extract(domains, tld_refresh())
Warning in file(con, "r") :
  cannot open URL 'http://data.iana.org/TLD/tlds-alpha-by-domain.txt': HTTP status was '503 Service Unavailable'
Error in file(con, "r") : cannot open the connection
Calls: tld_extract -> tld_refresh -> readLines -> file
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/utilsIPEA.Rcheck/00install.out' for details.
Packages suggested but not available for checking: 'vaers' 'vaersND'
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    doc    1.2Mb
    help   2.7Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc           5.6Mb
    htmlwidgets   3.9Mb
Running 'test-all.R' [40s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > test_check("zoon")
  Loading required package: zoon
  Loading required package: raster
  Loading required package: sp
  -- 1. Failure: Expected errors (@testTransformCRS.R#39)  -----------------------
  `workflow(...)` did not throw an error.
  
  == testthat results  ===========================================================
  OK: 237 SKIPPED: 30 FAILED: 1
  1. Failure: Expected errors (@testTransformCRS.R#39) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/abcdeFBA.Rcheck/00install.out’ for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    bootstrapping_example   1.2Mb
    libs                    6.5Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Error in re-building vignettes:
  ...


Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

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]="./webshot1788e2bb68d48.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot1788e2bb68d48.png': No such file or directory
Quitting from lines 91-93 (ActisoftR.Rmd) 
Error: processing vignette 'ActisoftR.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Namespaces in Imports field not imported from:
  ‘plotly’ ‘shinydashboard’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Error: processing vignette 'additivityTests-vignette.Rmd' failed with diagnostics:
shared object 'stringi.so' not found
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/adiv.Rcheck/00install.out’ for details.
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.
ADM3: no visible global function definition for ‘read.table’
ADM3: no visible global function definition for ‘write.table’
dLRs: no visible global function definition for ‘IQR’
dLRs: no visible global function definition for ‘na.omit’
dLRs: no visible global function definition for ‘qnorm’
plotADM3: no visible global function definition for ‘plot’
plotADM3: no visible global function definition for ‘abline’
plotADM3: no visible global function definition for ‘segments’
Undefined global functions or variables:
  IQR abline na.omit plot qnorm read.table segments write.table
Consider adding
  importFrom("graphics", "abline", "plot", "segments")
  importFrom("stats", "IQR", "na.omit", "qnorm")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/AFM.Rcheck/00install.out’ for details.
IIR: no visible global function definition for ‘qnorm’
TIR: no visible global function definition for ‘qnorm’
agreement: no visible global function definition for ‘var’
agreement: no visible global function definition for ‘pchisq’
agreement: no visible global function definition for ‘dnorm’
agreement: no visible global function definition for ‘qnorm’
html.report: no visible global function definition for ‘plot’
plot.report: no visible global function definition for ‘plot’
plot.report: no visible global function definition for ‘axis’
plot.report: no visible global function definition for ‘points’
unified.agreement: no visible global function definition for ‘lm’
unified.agreement: no visible global function definition for ‘qnorm’
unified.agreement: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  axis dnorm lm pchisq plot pnorm points qnorm var
Consider adding
  importFrom("graphics", "axis", "plot", "points")
  importFrom("stats", "dnorm", "lm", "pchisq", "pnorm", "qnorm", "var")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning 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
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/AIG.Rcheck/00install.out’ for details.
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.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
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 21.3Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
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/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
Error in re-building vignettes:
  ...
Error in loadNamespace(name) : there is no package called 'devtools'
trying URL 'https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.5/apercu_0.2.3.tgz'
Content type 'application/x-gzip' length 27068 bytes (26 KB)
==================================================
downloaded 26 KB

Error in loadNamespace(name) : there is no package called 'BiocInstaller'
Error in loadNamespace(name) : there is no package called 'devtools'
trying URL 'https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.5/apercu_0.2.3.tgz'
Content type 'application/x-gzip' length 27068 bytes (26 KB)
==================================================
downloaded 26 KB

Error in loadNamespace(name) : there is no package called 'BiocInstaller'
Error in loadNamespace(name) : there is no package called 'devtools'
trying URL 'https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.5/apercu_0.2.3.tgz'
Content type 'application/x-gzip' length 27068 bytes (26 KB)
==================================================
downloaded 26 KB

Error in loadNamespace(name) : there is no package called 'BiocInstaller'
Error in loadNamespace(name) : there is no package called 'devtools'
Error: processing vignette 'help.Rmd' failed with diagnostics:
there is no package called ‘markdown’
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’
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
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’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Arothron.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  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
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    libs  20.8Mb
best: no visible global function definition for ‘optim’
randomboards: no visible global function definition for ‘runif’
randomprobs: no visible global function definition for ‘runif’
Undefined global functions or variables:
  optim runif
Consider adding
  importFrom("stats", "optim", "runif")
to your NAMESPACE file.
File ‘aylmer/libs/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.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
    libs   2.4Mb
Package suggested but not available for checking: ‘philr’
Running ‘testthat.R’ [8s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1: philr::phylo2sbp at testthat/test-sbp.R:5
  2: getExportedValue(pkg, name)
  3: asNamespace(ns)
  4: getNamespace(ns)
  5: tryCatch(loadNamespace(name), error = function(e) stop(e))
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 13 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-sbp.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/BALCONY.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  8.6Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.6Mb
    libs   2.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   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.
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
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/BatchGetSymbols.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘doMPI’
Package unavailable to check Rd xrefs: ‘Rmpi’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/BAT.Rcheck/00install.out’ for details.
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 47.6Mb
  sub-directories of 1Mb or more:
    libs  46.9Mb
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [1] "Error in sampler$call_sampler(args_list[[i]]) : "
  [2] "  c++ exception (unknown reason)"                
  Stan model 'dfa' does not contain samples.
  Stan model 'dfa' does not contain samples.
  ── 1. Error: (unknown) (@test-fit.R#8)  ────────────────────────────────────────
  attempt to set an attribute on NULL
  1: fit_dfa(y = y, num_trends = 1, iter = 800, chains = 1) at testthat/test-fit.R:8
  2: rstan::monitor(e)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-fit.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs  11.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   3.9Mb
installed size is 61.2Mb
  sub-directories of 1Mb or more:
    libs  60.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   3.5Mb
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
Depends: includes the non-default packages:
  ‘lme4’ ‘MASS’ ‘VGAM’ ‘mvtnorm’ ‘matrixcalc’ ‘coda’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:
  Note: break 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’.
Packages in Depends field not imported from:
  ‘MASS’ ‘VGAM’ ‘coda’ ‘lme4’ ‘matrixcalc’ ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
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.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   3.2Mb
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
'library' or 'require' call to ‘multcomp’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is 26.3Mb
  sub-directories of 1Mb or more:
    libs  25.3Mb
binommh.default : log_lik: no visible global function definition for
  ‘dbinom’
binommh.default: no visible global function definition for ‘dbinom’
binommh.default: no visible global function definition for ‘runif’
binommh.formula: no visible global function definition for
  ‘model.frame’
binommh.formula: no visible global function definition for
  ‘model.matrix’
binommh.formula: no visible global function definition for
  ‘model.response’
expmh.default : log_lik: no visible global function definition for
  ‘dexp’
expmh.default: no visible global function definition for ‘dexp’
expmh.default: no visible global function definition for ‘runif’
expmh.formula: no visible global function definition for ‘model.frame’
expmh.formula: no visible global function definition for ‘model.matrix’
expmh.formula: no visible global function definition for
  ‘model.response’
poissmh.default : log_lik: no visible global function definition for
  ‘dpois’
poissmh.default: no visible global function definition for ‘dpois’
poissmh.default: no visible global function definition for ‘runif’
poissmh.formula: no visible global function definition for
  ‘model.frame’
poissmh.formula: no visible global function definition for
  ‘model.matrix’
poissmh.formula: no visible global function definition for
  ‘model.response’
Undefined global functions or variables:
  dbinom dexp dpois model.frame model.matrix model.response runif
Consider adding
  importFrom("stats", "dbinom", "dexp", "dpois", "model.frame",
             "model.matrix", "model.response", "runif")
to your NAMESPACE file.
Package required but not available: ‘TargetScore’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 141.1Mb
  sub-directories of 1Mb or more:
    include  141.0Mb
Running ‘testthat.R’ [3s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library("testthat")
  > library("bib2df")
  > test_check("bib2df")
  ── 1. Failure: bib2df() throws error messages (@tests.R#70)  ───────────────────
  `bib2df("https://www.example.com/data/x.bib")` threw an error with unexpected message.
  Expected match: "Invalid URL: File is not readable."
  Actual message: "Timeout was reached: Connection timed out after 10009 milliseconds"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 19 SKIPPED: 0 FAILED: 1
  1. Failure: bib2df() throws error messages (@tests.R#70) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.3Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   6.8Mb
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.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/BIGL.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: 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]="./webshot101686b25b69.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot101686b25b69.png': No such file or directory
Quitting from lines 244-247 (analysis.Rmd) 
Error: processing vignette 'analysis.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
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’.
bigRR: no visible global function definition for ‘gaussian’
bigRR.default: no visible global function definition for ‘gaussian’
bigRR.formula: no visible global function definition for ‘gaussian’
bigRR.formula: no visible global function definition for ‘as.formula’
bigRR.formula: no visible global function definition for ‘model.frame’
bigRR.formula: no visible global function definition for ‘model.matrix’
bigRR.formula: no visible global function definition for
  ‘model.response’
bigRR_update: no visible global function definition for ‘gaussian’
hugeRR: no visible global function definition for ‘gaussian’
hugeRR_update: no visible global function definition for ‘gaussian’
plot.bigRR: no visible global function definition for ‘par’
plot.bigRR: no visible global function definition for ‘plot’
plot.bigRR: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  as.formula gaussian model.frame model.matrix model.response par plot
  rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "par", "plot")
  importFrom("stats", "as.formula", "gaussian", "model.frame",
             "model.matrix", "model.response")
to your NAMESPACE file.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      6.0Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   7.2Mb
Running ‘testthat.R’ [25s/32s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > 
  > test_check("bikedata")
  ── 1. Failure: dl_bikedata la (@test-download-data.R#88)  ──────────────────────
  `dl_bikedata(city = "la", data_dir = tempdir(), dates = 2016)` produced unexpected messages.
  Expected match: All data files already exist
  Actual values:
  * Downloading metro-bike-share-trips-2016-q4.csv.zip
  
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 136 SKIPPED: 2 FAILED: 1
  1. Failure: dl_bikedata la (@test-download-data.R#88) 
  
  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 37-44 (billboarder-intro.Rmd) 
Error: processing vignette 'billboarder-intro.Rmd' failed with diagnostics:
cannot open the connection
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
Packages suggested but not available for checking:
  ‘BiocStyle’ ‘BiocVersion’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Biocomb.Rcheck/00install.out’ for details.
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
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   8.0Mb
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 48-51 (BioInstaller.Rmd) 
Error: processing vignette 'BioInstaller.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/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.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
plot.BIPOD: no visible global function definition for ‘par’
plot.BIPOD: no visible global function definition for ‘matplot’
plot.BIPOD: no visible global function definition for ‘abline’
plot.BIPOD: no visible global function definition for ‘plot’
plot.BIPOD: no visible global function definition for ‘density’
plot.BIPOD: no visible global function definition for ‘curve’
plot.BIPOD: no visible global function definition for ‘dlnorm’
plot.BIPOD: no visible global function definition for ‘dnorm’
plot.BIPOD: no visible global function definition for ‘acf’
plot.BIPOD: no visible global function definition for ‘pairs’
plot.BIPOD : standfun: no visible global function definition for ‘sd’
plot.BIPOD: no visible global function definition for ‘sd’
plot.BIPOD: no visible global function definition for ‘points’
plot.BIPOD: no visible global function definition for ‘tail’
plot.BIPOD: no visible global function definition for ‘matlines’
plot.BIPOD: no visible binding for global variable ‘quantile’
plot.BIPOD: no visible global function definition for ‘lines’
Undefined global functions or variables:
  abline acf curve density dlnorm dnorm lines matlines matplot pairs
  par plot points quantile sd tail
Consider adding
  importFrom("graphics", "abline", "curve", "lines", "matlines",
             "matplot", "pairs", "par", "plot", "points")
  importFrom("stats", "acf", "density", "dlnorm", "dnorm", "quantile",
             "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
Packages required but not available: ‘gWidgetsRGtk2’ ‘RGtk2’ ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
blighty: no visible global function definition for ‘par’
blighty: no visible global function definition for ‘polygon’
blighty: no visible global function definition for ‘points’
blighty: no visible global function definition for ‘box’
blighty: no visible global function definition for ‘axis’
blighty: no visible global function definition for ‘abline’
map.scale: no visible global function definition for ‘locator’
map.scale: no visible global function definition for ‘segments’
map.scale: no visible global function definition for ‘text’
north.pointer: no visible global function definition for ‘locator’
north.pointer: no visible global function definition for ‘text’
north.pointer: no visible global function definition for ‘arrows’
north.pointer: no visible global function definition for ‘segments’
sqlimits: no visible global function definition for ‘frame’
sqlimits: no visible global function definition for ‘par’
Undefined global functions or variables:
  abline arrows axis box frame locator par points polygon segments text
Consider adding
  importFrom("graphics", "abline", "arrows", "axis", "box", "frame",
             "locator", "par", "points", "polygon", "segments", "text")
to your NAMESPACE file.
installed size is 38.1Mb
  sub-directories of 1Mb or more:
    libs  36.9Mb
Running examples in ‘blockingChallenge-Ex.R’ failed
The error most likely occurred in:

> ### Name: makeblocks
> ### Title: Creates strata of size 'bsize' aiming to minimize within strata
> ###   distance.
> ### Aliases: makeblocks
> ### Keywords: Challenge Stratification algorithm
> 
> ### ** Examples
> 
> ## IN THESE EXAMPLES YOU NEED TO LOAD THE R PACKAGE 
> #  'optmatch'.  OTHERWISE, THEY WILL RUN IN A CODE CHECK MODE.
> # library(optmatch)
> ###### 		Usage 1		##########
> data(nh0506)
> ## Don't show: 
> 	nh0506 <- nh0506[1:13,]
> ## End(Don't show)
> res <- makeblocks(nh0506, bsize=4, maxItr=15, 
+          vars=c("female","age","black","hispanic","education","povertyr"))
Iteration no. 1 :: Error in pairmatch(distmat.temp1, controls = bsize - 1) : 
  could not find function "pairmatch"
Calls: makeblocks -> eval -> eval
Execution halted
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
installed size is 35.5Mb
  sub-directories of 1Mb or more:
    libs  35.2Mb
installed size is 45.9Mb
  sub-directories of 1Mb or more:
    libs  45.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
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/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’
print.boolprob: no visible global function definition for ‘plot’
print.boolprof: no visible global function definition for ‘plot’
start_msg: no visible global function definition for
  ‘packageDescription’
Undefined global functions or variables:
  packageDescription plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
installed size is 328.9Mb
  sub-directories of 1Mb or more:
    include    3.0Mb
    lib      325.6Mb
installed size is 69.7Mb
  sub-directories of 1Mb or more:
    libs  69.3Mb
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/bootnet.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/bpca.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘RGtk2’ ‘cairoDevice’
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 34.0Mb
  sub-directories of 1Mb or more:
    libs  33.9Mb
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 24.9Mb
  sub-directories of 1Mb or more:
    libs  23.9Mb
installed size is 79.7Mb
  sub-directories of 1Mb or more:
    libs  79.0Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  18.9Mb
Error in re-building vignettes:
  ...

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

    intersect, setdiff, setequal, union


Attaching package: 'c3'

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

    %>%

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

    grid, legend

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshotb3c71d491160.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotb3c71d491160.png': No such file or directory
Quitting from lines 56-65 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
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.
Error in re-building vignettes:
  ...
Warning 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
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.6Mb
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.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   3.2Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Error in re-building vignettes:
  ...
     validation strategies for spatial-temporal models. To decrease
     overfitting and improve model performances, the package implements
     a forward feature selection that selects suitable predictor
     variables in view to their contribution to the target-oriented
     performance.

_D_e_t_a_i_l_s:

     'caret' Applications for Spatio-Temporal models

_A_u_t_h_o_r(_s):

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


PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshotb12b414ebbf6.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotb12b414ebbf6.png': No such file or directory
Quitting from lines 65-73 (CAST-intro.Rmd) 
Error: processing vignette 'CAST-intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
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  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   2.6Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   9.2Mb
plot.CellularAutomaton: no visible global function definition for
  ‘image’
Undefined global functions or variables:
  image
Consider adding
  importFrom("graphics", "image")
to your NAMESPACE file.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.5Mb
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 hidden files and directories:
  .project
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
get.switch.time: warning in uniroot(f = switch.func, int =
  c(last_boundary, boundary), lower = last_boundary, upper = boundary,
  maxiter = 1000, tol = tol, e): partial argument match of 'int' to
  'interval'
plot.cggd: warning in axis(4, at = b[nrow(b), ], label = paste(cnums),
  cex = 0.8, adj = 0): partial argument match of 'label' to 'labels'
plot.cggd: no visible global function definition for ‘gen.beta’
plotCVcggd: no visible binding for global variable ‘cv’
plotCVcggd: no visible binding for global variable ‘cv.error’
predict.cggd: no visible binding for global variable ‘max.tk’
predict.cggd: no visible global function definition for ‘gen.beta’
Undefined global functions or variables:
  cv cv.error gen.beta max.tk
S3 methods shown with full name in documentation object 'plot.cggd':
  ‘plot.cggd’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
CGH.fused.lasso.one.fast: no visible global function definition for
  ‘lowess’
L2L1ExpandFit: no visible global function definition for
  ‘L2L1PathExtract’
consensusFDR: no visible global function definition for ‘pbinom’
my.mad: no visible global function definition for ‘median’
output.cghFLasso: no visible global function definition for
  ‘write.table’
plot.CGH.FL.All: no visible global function definition for ‘plot’
plot.CGH.FL.All: no visible global function definition for ‘segments’
plot.CGH.FL.All: no visible global function definition for ‘text’
plot.CGH.FL.Consensus: no visible global function definition for
  ‘rainbow’
plot.CGH.FL.Consensus: no visible global function definition for ‘plot’
plot.CGH.FL.Consensus: no visible global function definition for
  ‘segments’
plot.CGH.FL.Consensus: no visible global function definition for ‘gray’
plot.CGH.FL.Consensus: no visible global function definition for ‘text’
plot.CGH.FL.Single: no visible global function definition for ‘plot’
plot.CGH.FL.Single: no visible global function definition for ‘gray’
plot.CGH.FL.Single: no visible global function definition for
  ‘segments’
plot.CGH.FL.Single: no visible global function definition for ‘text’
plot.cghFLasso: no visible global function definition for ‘plot’
plot.cghFLasso: no visible global function definition for ‘gray’
plot.cghFLasso: no visible global function definition for ‘abline’
plot.cghFLasso: no visible global function definition for ‘points’
segment.score: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  L2L1PathExtract abline gray lowess median pbinom plot pnorm points
  rainbow segments text write.table
Consider adding
  importFrom("grDevices", "gray", "rainbow")
  importFrom("graphics", "abline", "plot", "points", "segments", "text")
  importFrom("stats", "lowess", "median", "pbinom", "pnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'plot.cghFLasso':
  ‘plot.cghFLasso’

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 160-170 (checkmate.Rmd) 
Error: processing vignette 'checkmate.Rmd' failed with diagnostics:
package or namespace load failed for 'ggplot2' in library.dynam(lib, package, package.lib):
 shared object 'plyr.so' not found
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 41-105 (Visualising_Interactions.Rmd) 
Error: processing vignette 'Visualising_Interactions.Rmd' failed with diagnostics:
there is no package called 'GenomicInteractions'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 42-44 (access_childes_db.Rmd) 
Error: processing vignette 'access_childes_db.Rmd' failed with diagnostics:
SSL certificate problem: Invalid certificate chain
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.
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  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  18.2Mb
cv.clogitL1 : <anonymous>: no visible global function definition for
  ‘var’
plot.clogitL1: no visible global function definition for ‘matplot’
plot.clogitL1: no visible global function definition for ‘legend’
plot.clogitL1: no visible global function definition for ‘text’
plot.cv.clogitL1: no visible global function definition for ‘matplot’
plot.cv.clogitL1: no visible global function definition for ‘matlines’
plot.cv.clogitL1: no visible global function definition for ‘points’
plot.cv.clogitL1: no visible global function definition for ‘axis’
plot.cv.clogitL1: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline axis legend matlines matplot points text var
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "matlines",
             "matplot", "points", "text")
  importFrom("stats", "var")
to your NAMESPACE file.
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  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Package suggested but not available for checking: ‘SingleCellExperiment’
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
Packages required but not available:
  ‘InteractionSet’ ‘GenomicFeatures’ ‘GenomicInteractions’
  ‘rtracklayer’ ‘BSgenome.Hsapiens.UCSC.hg19’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/colourvision.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/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.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 47.4Mb
  sub-directories of 1Mb or more:
    libs  46.3Mb
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
CosmoPhotoZestimator: no visible global function definition for
  ‘predict’
computeCombPCA: no visible global function definition for ‘prcomp’
computeDiagPhotoZ: no visible global function definition for ‘sd’
computeDiagPhotoZ: no visible global function definition for ‘median’
computeDiagPhotoZ: no visible global function definition for ‘mad’
glmPredictPhotoZ: no visible global function definition for ‘predict’
glmTrainPhotoZ: no visible global function definition for ‘glm’
glmTrainPhotoZ: no visible global function definition for ‘Gamma’
glmTrainPhotoZ: no visible global function definition for
  ‘inverse.gaussian’
plotDiagPhotoZ: no visible global function definition for ‘median’
plotDiagPhotoZ: no visible global function definition for ‘mad’
Undefined global functions or variables:
  Gamma glm inverse.gaussian mad median prcomp predict sd
Consider adding
  importFrom("stats", "Gamma", "glm", "inverse.gaussian", "mad",
             "median", "prcomp", "predict", "sd")
to your NAMESPACE file.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   4.3Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
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
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
find.antimodeMLE: no visible global function definition for ‘par’
find.decreasingMLE: no visible global function definition for ‘chull’
find.decreasingMLE: no visible global function definition for ‘points’
find.increasingMLE: no visible global function definition for ‘chull’
find.increasingMLE: no visible global function definition for ‘points’
find.modeMLE: no visible global function definition for ‘par’
plot.CPHshape: no visible global function definition for ‘plot’
plot.CPHshape: no visible global function definition for ‘segments’
plot.CPHshape: no visible global function definition for ‘abline’
plot.CPHshape: no visible global function definition for ‘grey’
plot.CPHshape: no visible global function definition for ‘points’
Undefined global functions or variables:
  abline chull grey par plot points segments
Consider adding
  importFrom("grDevices", "chull", "grey")
  importFrom("graphics", "abline", "par", "plot", "points", "segments")
to your NAMESPACE file.
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 77-78 (cranly.Rmd) 
Error: processing vignette 'cranly.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘clusterProfiler’
Error in re-building vignettes:
  ...
    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:R.oo':

    trim


Quitting from lines 32-41 (case_study.Rmd) 
Error: processing vignette 'case_study.Rmd' failed with diagnostics:
there is no package called 'clusterProfiler'
Execution halted
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
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/crplyr.Rcheck/00install.out’ for details.
installed size is 21.9Mb
  sub-directories of 1Mb or more:
    libs  20.2Mb
D.SN: no visible global function definition for ‘dnorm’
D.SN: no visible global function definition for ‘pnorm’
beta2cp: no visible global function definition for ‘pnorm’
cSFM.est: no visible global function definition for ‘optim’
cSFM.est: no visible global function definition for ‘qnorm’
cSFM.est: no visible global function definition for ‘cor’
case2.b.initial: no visible global function definition for ‘var’
case2.gr: no visible global function definition for ‘pnorm’
case2.gr: no visible global function definition for ‘dnorm’
case2.unmll.optim: no visible global function definition for ‘pnorm’
cp2beta: no visible global function definition for ‘qnorm’
data.generator.y.F: no visible global function definition for ‘cov2cor’
data.generator.y.F: no visible global function definition for ‘rnorm’
data.generator.y.F : <anonymous>: no visible global function definition
  for ‘pnorm’
g: no visible global function definition for ‘dnorm’
g: no visible global function definition for ‘pnorm’
predict.cSFM : <anonymous>: no visible global function definition for
  ‘qnorm’
predict.cSFM: no visible global function definition for ‘qnorm’
predict.cSFM: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  cor cov2cor dnorm optim pnorm qnorm rnorm var
Consider adding
  importFrom("stats", "cor", "cov2cor", "dnorm", "optim", "pnorm",
             "qnorm", "rnorm", "var")
to your NAMESPACE file.
installed size is 76.4Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
    doc    4.1Mb
    libs  66.1Mb
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.
Packages in Depends field not imported from:
  ‘MCMCpack’ ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cudiaDet: no visible global function definition for ‘model.frame’
cudiaDet: no visible global function definition for ‘model.response’
cudiaDet: no visible binding for global variable ‘sd’
cudiaDet: no visible global function definition for ‘rdirichlet’
cudiaDet: no visible global function definition for ‘rnorm’
cudiaDet: no visible global function definition for ‘lm.ridge’
plot.cudia: no visible global function definition for ‘par’
plot.cudia: no visible global function definition for ‘plot’
Undefined global functions or variables:
  lm.ridge model.frame model.response par plot rdirichlet rnorm sd
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "model.frame", "model.response", "rnorm", "sd")
to your NAMESPACE file.
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
'library' or 'require' call to ‘locfit’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘R.methodsS3’ ‘R.oo’ ‘locfit’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
curvefit: no visible global function definition for ‘model.frame’
curvefit: no visible global function definition for ‘model.response’
curvefit: no visible global function definition for ‘model.matrix’
curvetest: no visible global function definition for ‘model.frame’
curvetest: no visible global function definition for ‘plot’
curvetest.raw: no visible global function definition for ‘pt’
curvetest.raw: no visible global function definition for ‘pnorm’
getoptimalalpha: no visible global function definition for ‘gcvplot’
getoptimalalpha: no visible global function definition for ‘plot’
lines.curvefit: no visible global function definition for ‘lines’
plot.curvefit: no visible global function definition for ‘plot’
plot.curvefit: no visible global function definition for ‘lines’
plot.curvefit: no visible global function definition for ‘points’
Undefined global functions or variables:
  gcvplot lines model.frame model.matrix model.response plot pnorm
  points pt
Consider adding
  importFrom("graphics", "lines", "plot", "points")
  importFrom("stats", "model.frame", "model.matrix", "model.response",
             "pnorm", "pt")
to your NAMESPACE file.
Package which this enhances but not available for checking: ‘RGtk2’
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   4.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs   1.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 177-179 (cycling_data_analysis.Rmd) 
Error: processing vignette 'cycling_data_analysis.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
Error in re-building vignettes:
  ...
Warning in engine$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 27-38 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package required but not available: ‘Rglpk’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/dartR.Rcheck/00install.out’ for details.
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.
get_temporary_file_name: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    4.5Mb
    libs   3.0Mb
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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Data report generation is finished. Please wait while your output file is being rendered.
Quitting from lines 729-768 (extending_dataMaid.Rmd) 
Error: processing vignette 'extending_dataMaid.Rmd' failed with diagnostics:
pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 57.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  55.4Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
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]="./webshot2dd96169dbd5.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot2dd96169dbd5.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’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
DrawAlphas: no visible global function definition for ‘rmultinom’
DrawClasses: no visible global function definition for ‘runif’
GetGammaNames: no visible global function definition for ‘combn’
GetLambdaNamesForItem: no visible global function definition for
  ‘combn’
SampleParameterEstimates: no visible global function definition for
  ‘rnorm’
plot,attribute.class-missing: no visible binding for global variable
  ‘attr.number’
plot,attribute.class-missing: no visible binding for global variable
  ‘mean.attr’
plot,attribute.profile.class-missing: no visible binding for global
  variable ‘attr.profile.number’
plot,attribute.profile.class-missing: no visible binding for global
  variable ‘mean.attr.profile’
summary,attribute.class: no visible binding for global variable ‘value’
summary,attribute.profile.class: no visible binding for global variable
  ‘max.class’
Undefined global functions or variables:
  attr.number attr.profile.number combn max.class mean.attr
  mean.attr.profile rmultinom rnorm runif value
Consider adding
  importFrom("stats", "rmultinom", "rnorm", "runif")
  importFrom("utils", "combn")
to your NAMESPACE file.
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
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: package 'dplyr' was built under R version 3.5.1

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'gridExtra'

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

    combine

Quitting from lines 84-97 (MultiObjectiveDecisionAnalysisinR.Rmd) 
Error: processing vignette 'MultiObjectiveDecisionAnalysisinR.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$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.
installed size is 60.8Mb
  sub-directories of 1Mb or more:
    libs  58.1Mb
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    1.6Mb
    help   1.4Mb
    libs   1.5Mb
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
Running ‘test-that.R’ [197s/208s]
Running the tests in ‘tests/test-that.R’ failed.
Last 13 lines of output:
  9: withr::with_output_sink(tempfile(), pkgdown::build_site(pkg = pkg$path, ...))
  10: force(code)
  11: pkgdown::build_site(pkg = pkg$path, ...)
  12: build_site_external(pkg = pkg, examples = examples, document = document, run_dont_run = run_dont_run, 
         seed = seed, mathjax = mathjax, lazy = lazy, override = override, preview = preview)
  13: callr::r(function(...) pkgdown::build_site(...), args = args, show = TRUE)
  14: get_result(output = out, options)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 48 SKIPPED: 6 FAILED: 2
  1. Error: Package readme can be built  (@test-build-readme.R#8) 
  2. Error: Package pkgdown site can be built  (@test-build-site.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 48.5Mb
  sub-directories of 1Mb or more:
    libs  48.1Mb
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
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.
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"
kf: no visible global function definition for ‘dbinom’
Undefined global functions or variables:
  dbinom
Consider adding
  importFrom("stats", "dbinom")
to your NAMESPACE file.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Found the following hidden files and directories:
  .directory
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
distSegment: no visible global function definition for ‘dist’
distShape: no visible global function definition for ‘dist’
distTriangle: no visible global function definition for ‘dist’
exactHausdorff: no visible global function definition for ‘aggregate’
Undefined global functions or variables:
  aggregate dist
Consider adding
  importFrom("stats", "aggregate", "dist")
to your NAMESPACE file.
Package which this enhances but not available for checking: ‘RobExtremes’
Curvature: no visible global function definition for ‘tail’
gen.rarefac.div: no visible global function definition for ‘sd’
plot.fitsingleMod: no visible global function definition for ‘points’
plot.fitsingleMod: no visible global function definition for ‘lines’
ref.area: no visible global function definition for ‘integrate’
simm: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate lines points sd tail
Consider adding
  importFrom("graphics", "lines", "points")
  importFrom("stats", "integrate", "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
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
Package suggested but not available for checking: ‘FKF’
'library' or 'require' calls in package code:
  ‘FKF’ ‘dlm’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
dlmodeler.extract: no visible global function definition for ‘qnorm’
dlmodeler.fit.MAD: no visible global function definition for ‘optim’
dlmodeler.fit.MAPE: no visible global function definition for ‘optim’
dlmodeler.fit.MLE: no visible global function definition for ‘optim’
dlmodeler.fit.MSE: no visible global function definition for ‘optim’
dlmodeler.fit.sigma : fit.fun: no visible global function definition
  for ‘var’
dlmodeler.fit.sigma: no visible global function definition for ‘optim’
dlmodeler.forecast: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  optim qnorm var
Consider adding
  importFrom("stats", "optim", "qnorm", "var")
to your NAMESPACE file.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   2.1Mb
    libs   3.5Mb
Package in Depends field not imported from: ‘magic’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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 19.1Mb
  sub-directories of 1Mb or more:
    libs  16.9Mb
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.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
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.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/drugCombo.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 rgl.init(initValue, onlyNULL) :
  RGL: unable to open X11 display
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
Using constraints: b = 1
Using constraints: b = 1
Running default monotherapy fitting. Note that if constraints are needed, run mono fitting manually first
Using constraints: b = 1
Using constraints: b = 1
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot100643a05274.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot100643a05274.png': No such file or directory
Quitting from lines 357-358 (userGuide.Rmd) 
Error: processing vignette 'userGuide.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   4.3Mb
dsCHECK: no visible global function definition for ‘na.omit’
dsFC: no visible global function definition for ‘cor’
dsMC: no visible global function definition for ‘cor’
plot.ds: no visible global function definition for ‘plot’
plot.ds: no visible global function definition for ‘par’
plot.ds: no visible global function definition for ‘points’
plot.ds: no visible global function definition for ‘text’
Undefined global functions or variables:
  cor na.omit par plot points text
Consider adding
  importFrom("graphics", "par", "plot", "points", "text")
  importFrom("stats", "cor", "na.omit")
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/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 22.2Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.3Mb
    libs  16.3Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   2.8Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
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 58.7Mb
  sub-directories of 1Mb or more:
    libs  58.0Mb
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/egor.Rcheck/00install.out’ for details.
elmtrain.default: no visible global function definition for ‘runif’
elmtrain.formula: no visible global function definition for
  ‘model.frame’
elmtrain.formula: no visible global function definition for
  ‘model.matrix’
elmtrain.formula: no visible global function definition for
  ‘model.response’
predict.elmNN: no visible global function definition for ‘fitted’
predict.elmNN: no visible global function definition for ‘model.matrix’
print.elmNN: no visible global function definition for ‘head’
print.elmNN: no visible global function definition for ‘fitted’
randomMatrix: no visible global function definition for ‘runif’
Undefined global functions or variables:
  fitted head model.frame model.matrix model.response runif
Consider adding
  importFrom("stats", "fitted", "model.frame", "model.matrix",
             "model.response", "runif")
  importFrom("utils", "head")
to your NAMESPACE file.
Package required but not available: ‘iCheck’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
elrm: no visible global function definition for ‘write.table’
plot.elrm: no visible global function definition for ‘dev.new’
progress: no visible global function definition for ‘flush.console’
update.elrm: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  dev.new flush.console write.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE file.
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’
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/embed.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/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.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot54225f141465.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot54225f141465.png': No such file or directory
Quitting from lines 150-151 (epicontacts.Rmd) 
Error: processing vignette 'epicontacts.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 117-120 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
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:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/EpiStats.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/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’.
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/Equalden.HD.Rcheck/00install.out’ for details.
Package required but not available: ‘rpanel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 27.2Mb
  sub-directories of 1Mb or more:
    libs  26.9Mb
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

trying URL 'https://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 13630 bytes (13 KB)
==================================================
downloaded 13 KB

Table ten00081 cached at /tmp/RtmpsI9cRw/eurostat/ten00081_date_code_TF.rds
trying URL 'https://ec.europa.eu/eurostat/estat-navtree-portlet-prod/BulkDownloadListing?sort=1&file=data%2Ftgs00026.tsv.gz'
Content type 'application/octet-stream;charset=UTF-8' length 5998 bytes
==================================================
downloaded 5998 bytes

Quitting from lines 338-370 (eurostat_tutorial.Rmd) 
Error: processing vignette 'eurostat_tutorial.Rmd' failed with diagnostics:
Recv failure: Connection reset by peer
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
Packages in Depends field not imported from:
  ‘lars’ ‘ncvreg’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plot.path: no visible global function definition for ‘par’
plot.path: no visible global function definition for ‘plot’
plot.path: no visible global function definition for ‘axis’
plot.path: no visible global function definition for ‘points’
plot.path: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline axis par plot points
Consider adding
  importFrom("graphics", "abline", "axis", "par", "plot", "points")
to your NAMESPACE file.
Running examples in ‘exampletestr-Ex.R’ failed
The error most likely occurred in:

> ### Name: make-test-shells
> ### Title: Create test shells.
> ### Aliases: make-test-shells make_test_shell_fun make_tests_shells_file
> ###   make_tests_shells_pkg
> 
> ### ** Examples
> 
> usethis::create_package(tempdir(), open = FALSE)
Error: '/tmp' is not a directory.
Execution halted
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [5s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  6: withVisible(eval(expr, pf))
  7: eval(expr, pf)
  8: eval(expr, pf)
  9: usethis::create_package(tempdir(), open = FALSE)
  10: create_directory(path_dir(path), name)
  11: stop_glue("{value(base_path)} is not a directory.")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 13 SKIPPED: 0 FAILED: 3
  1. Error: `extract_examples()` works (@test-exemplar.R#7) 
  2. Error: `make_test_shell()` works (@test-exemplar.R#47) 
  3. Error: `make_tests_shell_fun()` works (@test-exemplar.R#96) 
  
  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
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    exiftool  12.8Mb
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  5.1Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.9Mb
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  15.5Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.3Mb
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/fastR2.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/FateID.Rcheck/00install.out’ for details.
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 22.6Mb
  sub-directories of 1Mb or more:
    libs  22.3Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   5.5Mb
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
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
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/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’.
plot.cf: no visible global function definition for ‘barplot’
plot.cf: no visible global function definition for ‘lines’
plot.cf: no visible global function definition for ‘abline’
plot.cf: no visible global function definition for ‘axis’
plot.cf: no visible global function definition for ‘curve’
plot.tvm: no visible global function definition for ‘barplot’
plot.tvm: no visible global function definition for ‘lines’
tvm: no visible global function definition for ‘uniroot’
update.tvm: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  abline axis barplot curve lines uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "barplot", "curve", "lines")
  importFrom("stats", "uniroot")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/fingerPro.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 package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Warning: Removed 2 rows containing missing values (geom_point).
Warning in normalizePath(f2) :
  path[1]="./webshot1672e13f906b7.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot1672e13f906b7.png': No such file or directory
Quitting from lines 137-146 (quick_charts.Rmd) 
Error: processing vignette 'quick_charts.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 70-72 (lifeExpectancy.Rmd) 
Error: processing vignette 'lifeExpectancy.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
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’
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
FlimFormula: no visible global function definition for ‘is’
FlimFormula: no visible global function definition for ‘terms’
FlimFormula: no visible global function definition for ‘reformulate’
ImputateMissingValues : RegFun: no visible global function definition
  for ‘lm’
ImputateMissingValues : RegFun: no visible binding for global variable
  ‘na.omit’
ImputateMissingValues: no visible global function definition for
  ‘predict’
ImputateMissingValues: no visible global function definition for
  ‘model.matrix’
ImputateMissingValues: no visible global function definition for ‘coef’
flimList: no visible global function definition for ‘coef’
flimSD: no visible binding for global variable ‘sd’
plot.flim: no visible global function definition for ‘plot’
plot.flim: no visible global function definition for ‘lines’
plot.flim: no visible global function definition for ‘points’
plot.flimList: no visible global function definition for ‘par’
plot.flimList: no visible global function definition for ‘plot’
plot.flimboot: no visible global function definition for ‘plot’
plot.flimboot: no visible global function definition for ‘points’
plot.flimboot: no visible global function definition for ‘lines’
spaplot: no visible global function definition for ‘plot’
spaplot: no visible global function definition for ‘lines’
Undefined global functions or variables:
  coef is lines lm model.matrix na.omit par plot points predict
  reformulate sd terms
Consider adding
  importFrom("graphics", "lines", "par", "plot", "points")
  importFrom("methods", "is")
  importFrom("stats", "coef", "lm", "model.matrix", "na.omit", "predict",
             "reformulate", "sd", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool: more than one input file specified (/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so.dSYM and /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so)
Usage: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool [-change old new] ... [-rpath old new] ... [-add_rpath new] ... [-delete_rpath old] ... [-id name] input
error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool: more than one input file specified (/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so.dSYM and /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so)
Usage: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool [-change old new] ... [-rpath old new] ... [-add_rpath new] ... [-delete_rpath old] ... [-id name] input
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool: more than one input file specified (/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so.dSYM and /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so)
Usage: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool [-change old new] ... [-rpath old new] ... [-add_rpath new] ... [-delete_rpath old] ... [-id name] input
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool: more than one input file specified (/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so.dSYM and /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so)
Usage: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool [-change old new] ... [-rpath old new] ... [-add_rpath new] ... [-delete_rpath old] ... [-id name] input
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool: more than one input file specified (/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so.dSYM and /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so)
Usage: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool [-change old new] ... [-rpath old new] ... [-add_rpath new] ... [-delete_rpath old] ... [-id name] input
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool: more than one input file specified (/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so.dSYM and /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so)
Usage: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool [-change old new] ... [-rpath old new] ... [-add_rpath new] ... [-delete_rpath old] ... [-id name] input
error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool: more than one input file specified (/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so.dSYM and /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so)
Usage: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool [-change old new] ... [-rpath old new] ... [-add_rpath new] ... [-delete_rpath old] ... [-id name] input
error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool: more than one input file specified (/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so.dSYM and /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so)
Usage: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool [-change old new] ... [-rpath old new] ... [-add_rpath new] ... [-delete_rpath old] ... [-id name] input
error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool: more than one input file specified (/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so.dSYM and /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so)
Usage: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool [-change old new] ... [-rpath old new] ... [-add_rpath new] ... [-delete_rpath old] ... [-id name] input
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 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
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 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
Packages suggested but not available for checking:
  ‘Rsocp’ ‘Rnlminb2’ ‘Rdonlp2’ ‘Rsymphony’
Running examples in ‘FREddyPro-Ex.R’ failed
The error most likely occurred in:

> ### Name: buildTimestamp
> ### Title: Build a timestamp
> ### Aliases: buildTimestamp
> 
> ### ** Examples
> 
> ## Load the data
> data(fluxes)
> 
> ## Clean fluxes
> fluxes=cleanFluxes(fluxes,sdCor=TRUE,sdTimes=3,timesList=3,distCor=TRUE,
+                    thresholdList=list(H=c(-100,1000),LE=c(-100,1000)))	
> 
> ## Remove some line as an example
> fluxes=fluxes[-c(832,833,834,835,840,953),]
> 
> ## Create timestamp from date and time
> fluxes=createTimestamp(fluxes)
> 
> ## Now fill the gap timestmaps with NA's
> fluxes=fillTimestamp(fluxes,flux=TRUE)
[1] Discontinuity in 3 instances
[1] 2014-06-14 03:30:00 UTC 2014-06-14 06:00:00 UTC 2014-06-16 14:30:00 UTC
Error in FUN(X[[i]], ...) : subscript out of bounds
Calls: fillTimestamp ... shift_time -> [[ -> [[.POSIXlt -> .POSIXlt -> lapply
Execution halted
add.p.value.legend: no visible global function definition for ‘legend’
cat.freq.post: no visible global function definition for ‘quantile’
draw.signif.post.boxes: no visible global function definition for
  ‘polygon’
plot.freqMAP: no visible global function definition for ‘layout’
plot.freqMAP: no visible global function definition for ‘plot’
plot.freqMAP: no visible global function definition for ‘points’
plot.freqMAP: no visible global function definition for ‘lines’
plot.freqMAP: no visible global function definition for ‘abline’
plot.freqMAP: no visible global function definition for ‘axTicks’
posterior.comparison.freqMAP: no visible global function definition for
  ‘quantile’
rdirichlet: no visible global function definition for ‘rgamma’
Undefined global functions or variables:
  abline axTicks layout legend lines plot points polygon quantile
  rgamma
Consider adding
  importFrom("graphics", "abline", "axTicks", "layout", "legend",
             "lines", "plot", "points", "polygon")
  importFrom("stats", "quantile", "rgamma")
to your NAMESPACE file.
Package suggested but not available for checking: ‘RTCGA.rnaseq’
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   8.8Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
Package in Depends field not imported from: ‘genlasso’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dualpathFusedX.mod: no visible global function definition for
  ‘graph.adjacency’
dualpathFusedX.mod: no visible global function definition for
  ‘clusters’
dualpathFusedX.mod: no visible global function definition for ‘ginv’
dualpathFusedX.mod: no visible global function definition for
  ‘subcomponent’
dualpathFusedX.mod: no visible global function definition for ‘rBind’
fpca.nonscore.cluster: no visible global function definition for
  ‘kmeans’
fpca.score.cluster: no visible global function definition for ‘kmeans’
gen.dcbm: no visible global function definition for ‘rbinom’
gen.sbm: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  clusters ginv graph.adjacency kmeans rBind rbinom subcomponent
Consider adding
  importFrom("stats", "kmeans", "rbinom")
to your NAMESPACE file.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   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 604-605 (futureheatwaves.Rmd) 
Error: processing vignette 'futureheatwaves.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/GADMTools.Rcheck/00install.out’ for details.
GAPerm : pmxCrossover: no visible global function definition for
  ‘runif’
GAReal : twoPointsCrossover: no visible global function definition for
  ‘runif’
GAReal : blendCrossover: no visible global function definition for
  ‘runif’
GAReal : mutateNoise: no visible global function definition for ‘runif’
GAReal : initPopulation: no visible global function definition for
  ‘runif’
plot.GAPerm: no visible global function definition for ‘plot’
plot.GAPerm: no visible global function definition for ‘grid’
plot.GAPerm: no visible global function definition for ‘lines’
plot.GAPerm: no visible global function definition for ‘legend’
plot.GAReal: no visible global function definition for ‘plot’
plot.GAReal: no visible global function definition for ‘grid’
plot.GAReal: no visible global function definition for ‘lines’
plot.GAReal: no visible global function definition for ‘legend’
Undefined global functions or variables:
  grid legend lines plot runif
Consider adding
  importFrom("graphics", "grid", "legend", "lines", "plot")
  importFrom("stats", "runif")
to your NAMESPACE file.
Package which this enhances but not available for checking: ‘doMPI’
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   6.5Mb
installed size is 66.3Mb
  sub-directories of 1Mb or more:
    libs  65.9Mb
installed size is 52.7Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     49.6Mb
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.
Package suggested but not available for checking: ‘VariABEL’
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
Warning: no function found corresponding to methods exports from ‘GenABEL’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
'library' or 'require' calls in package code:
  ‘DatABEL’ ‘genetics’ ‘haplo.stats’ ‘hglm’ ‘qvalue’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘GenABEL.data’ ‘MASS’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following Makefile(s) without a final LF:
  inst/unitTests/Makefile
Some ‘make’ programs ignore lines not ending in LF.
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.
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
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    4.7Mb
    libs   1.5Mb
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.
checkrows: no visible global function definition for ‘rnorm’
cv.trendfilter: no visible binding for global variable ‘sd’
plot.cv.trendfilter: no visible global function definition for ‘plot’
plot.cv.trendfilter: no visible global function definition for ‘lines’
plot.cv.trendfilter: no visible global function definition for ‘points’
plot.cv.trendfilter: no visible global function definition for ‘legend’
plot.gcv.genlasso: no visible global function definition for ‘plot’
plot.gcv.genlasso: no visible global function definition for ‘points’
plot.genlasso: no visible global function definition for ‘par’
plot.genlasso: no visible global function definition for ‘rainbow’
plot.genlasso: no visible global function definition for ‘plot’
plot.genlasso: no visible global function definition for ‘matplot’
plot.genlasso: no visible global function definition for ‘abline’
plot.genlasso: no visible global function definition for ‘text’
plot.genlasso: no visible global function definition for ‘lines’
plot.trendfilter: no visible global function definition for ‘plot’
plot.trendfilter: no visible global function definition for ‘matplot’
predict.genlasso: no visible global function definition for ‘coef’
softthresh: no visible global function definition for ‘coef’
Undefined global functions or variables:
  abline coef legend lines matplot par plot points rainbow rnorm sd
  text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "legend", "lines", "matplot", "par",
             "plot", "points", "text")
  importFrom("stats", "coef", "rnorm", "sd")
to your NAMESPACE file.
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:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/geoelectrics.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   3.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R         3.9Mb
    extdata   1.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/geomorph.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   3.8Mb
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/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
Found the following significant warnings:
  FORCE_certify.c:116:15: 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/GFORCE.Rcheck/00install.out’ for details.
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra
Loading required package: plyr
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 45-49 (ggPredict.Rmd) 
Error: processing vignette 'ggPredict.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ggraptR.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...

Backtrace for this error:
#0  0x123629579
#1  0x123628945
#2  0x7fff93ac4529
sh: line 1: 96924 Trace/BPT trap: 5       /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/x13ashtml /tmp/RtmpLCaVyQ/x1317a8c540f25fd/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  0x1235f6579
#1  0x1235f5945
#2  0x7fff93ac4529
Quitting from lines 125-126 (ggseas.Rmd) 
Error: processing vignette 'ggseas.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
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Warning: no function found corresponding to methods exports from ‘giRaph’ for: ‘coerce’, ‘initialize’, ‘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 ‘mathgraph’ 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 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  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is 40.2Mb
  sub-directories of 1Mb or more:
    libs  39.9Mb
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 38.0Mb
  sub-directories of 1Mb or more:
    libs  37.4Mb
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

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

Waiting for profiling to be done...
trying deprecated constructor; please alert package maintainer
error occurred during calling the sampler; sampling not done
Quitting from lines 134-135 (spatial-glms.Rmd) 
Error: processing vignette 'spatial-glms.Rmd' failed with diagnostics:
incorrect number of dimensions
Execution halted
installed size is 40.3Mb
  sub-directories of 1Mb or more:
    libs  39.4Mb
installed size is 59.7Mb
  sub-directories of 1Mb or more:
    libs  58.5Mb
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
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/GPoM.Rcheck/00install.out’ for details.
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
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    R  19.3Mb
Package in Depends field not imported from: ‘dismo’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages required but not available: ‘RGtk2’ ‘gWidgetsRGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Packages required but not available:
  ‘tximport’ ‘EnsDb.Hsapiens.v86’ ‘EnsDb.Rnorvegicus.v79’
  ‘EnsDb.Mmusculus.v79’ ‘org.Mm.eg.db’ ‘org.Rn.eg.db’ ‘GenomicFeatures’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
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
Namespaces in Imports field not imported from:
  ‘assertthat’ ‘magrittr’ ‘readr’ ‘stringr’ ‘tibble’
  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.
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.
haplo.ccs: no visible global function definition for ‘terms’
haplo.ccs: no visible global function definition for ‘model.response’
haplo.ccs: no visible global function definition for ‘model.matrix’
haplo.ccs.fit: no visible global function definition for ‘glm’
haplo.ccs.fit: no visible global function definition for
  ‘quasibinomial’
haplo.ccs.fit: no visible binding for global variable ‘logit’
haplo.ccs.fit: no visible global function definition for ‘coef’
print.summary.haplo.ccs: no visible global function definition for ‘pt’
sandcov: no visible global function definition for ‘coef’
sandcov: no visible global function definition for ‘model.matrix’
sandcov: no visible global function definition for ‘residuals’
Undefined global functions or variables:
  coef glm logit model.matrix model.response pt quasibinomial residuals
  terms
Consider adding
  importFrom("stats", "coef", "glm", "model.matrix", "model.response",
             "pt", "quasibinomial", "residuals", "terms")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 335-344 (haplor-vignette.Rmd) 
Error: processing vignette 'haplor-vignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 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 10.3Mb
  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 0.15.2

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

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

Quitting from lines 88-90 (heatmaply.Rmd) 
Error: processing vignette 'heatmaply.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
plot.threshpt: no visible global function definition for ‘glm’
plot.threshpt: no visible global function definition for ‘predict’
plot.threshpt: no visible global function definition for ‘plot’
plot.threshpt: no visible global function definition for ‘lines’
plot.threshpt: no visible global function definition for ‘abline’
plot.threshpt: no visible global function definition for ‘points’
print.summary.threshpt: no visible global function definition for
  ‘printCoefmat’
threshpt: no visible global function definition for ‘as.formula’
threshpt: no visible global function definition for ‘glm’
threshpt: no visible global function definition for ‘vcov’
threshpt: no visible global function definition for ‘pnorm’
threshpt: no visible global function definition for ‘predict’
Undefined global functions or variables:
  abline as.formula glm lines plot pnorm points predict printCoefmat
  vcov
Consider adding
  importFrom("graphics", "abline", "lines", "plot", "points")
  importFrom("stats", "as.formula", "glm", "pnorm", "predict",
             "printCoefmat", "vcov")
to your NAMESPACE file.
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’
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  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
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/hypervolume.Rcheck/00install.out’ for details.
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.
ConfigureIBHM : <anonymous>: no visible global function definition for
  ‘dnorm’
FindActiv: no visible global function definition for ‘sd’
OptimizeActivCMAES: no visible global function definition for ‘runif’
OptimizeActivNM: no visible global function definition for ‘optim’
OptimizeActivNM: no visible global function definition for ‘runif’
OptimizeAllParams : goal: no visible global function definition for
  ‘relist’
OptimizeAllParams: no visible global function definition for ‘optim’
OptimizeAllParams: no visible global function definition for ‘relist’
OptimizeAllWeights: no visible global function definition for ‘optim’
OptimizeScalCMAES: no visible global function definition for ‘runif’
OptimizeScalNM: no visible global function definition for ‘optim’
OptimizeScalNM: no visible global function definition for ‘runif’
OptimizeWeights: no visible global function definition for ‘optim’
TrainIBHM: no visible global function definition for ‘enableJIT’
ValidationSC : <anonymous>: no visible global function definition for
  ‘predict’
group.by.samplesPerDim: no visible global function definition for ‘sd’
summary.IBHM: no visible global function definition for ‘predict’
summary.IBHM: no visible global function definition for ‘sd’
summary.IBHM: no visible global function definition for ‘cor’
Undefined global functions or variables:
  cor dnorm enableJIT optim predict relist runif sd
Consider adding
  importFrom("stats", "cor", "dnorm", "optim", "predict", "runif", "sd")
  importFrom("utils", "relist")
to your NAMESPACE file.
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 29.3Mb
  sub-directories of 1Mb or more:
    R     14.5Mb
    doc    5.1Mb
    libs   8.9Mb
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
Package suggested but not available for checking: ‘mixAK’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      2.1Mb
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
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’.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/IFSPlot.Rcheck/00install.out’ for details.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  12.8Mb
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       1.1Mb
    include   2.8Mb
    libs     17.0Mb
Found the following significant warnings:
  IM4ECpp.cpp:24:54: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:24:65: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:33:54: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:33:65: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  ImmigrateCpp.cpp:25:62: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  ImmigrateCpp.cpp:25:73: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  ImmigrateCpp.cpp:35:62: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  ImmigrateCpp.cpp:35:73: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:59: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:67: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:78: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:59: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:67: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:78: 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/Immigrate.Rcheck/00install.out’ for details.
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  8.1Mb
  sub-directories of 1Mb or more:
    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
Packages in Depends field not imported from:
  ‘MASS’ ‘nlme’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
JointRegBC.default : f: no visible global function definition for
  ‘pnorm’
JointRegBC.default : f: no visible global function definition for
  ‘dnorm’
JointRegBC.default: no visible global function definition for ‘nlminb’
JointRegBC.default: no visible global function definition for ‘fdHess’
JointRegBC.default: no visible global function definition for ‘ginv’
Undefined global functions or variables:
  dnorm fdHess ginv nlminb pnorm
Consider adding
  importFrom("stats", "dnorm", "nlminb", "pnorm")
to your NAMESPACE file.
Found the following significant warnings:
  jomo1clmmC.c:105:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo1clmmhrC.c:107:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo2clmmC.c:128:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo2clmmhrC.c:132:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomooprobitC.c:84:3: 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/jomo.Rcheck/00install.out’ for details.
CoxFit : GetEstimate: no visible global function definition for ‘lm’
CoxFit : GetEstimate: no visible global function definition for ‘vcov’
CoxModel_Year: no visible global function definition for ‘model.frame’
CoxModel_Year: no visible global function definition for ‘model.matrix’
joinpoint: no visible global function definition for ‘as.formula’
joinpoint: no visible global function definition for ‘model.frame’
joinpoint: no visible global function definition for ‘model.matrix’
joinpoint : plot.surv: no visible global function definition for
  ‘predict’
joinpoint : plot.surv: no visible global function definition for ‘plot’
joinpoint : plot.surv: no visible global function definition for
  ‘lines’
joinpoint : plot.surv: no visible global function definition for
  ‘legend’
read.seerstat: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  as.formula legend lines lm model.frame model.matrix plot predict
  read.table vcov
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "as.formula", "lm", "model.frame", "model.matrix",
             "predict", "vcov")
  importFrom("utils", "read.table")
to your NAMESPACE file.
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
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
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/kerasformula.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/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.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    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.
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
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   6.7Mb
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’
get.cp: no visible global function definition for ‘cov’
heatmap: no visible global function definition for ‘image’
heatmap: no visible global function definition for ‘grey’
heatmap: no visible global function definition for ‘abline’
heatmap: no visible global function definition for ‘axis’
heatmap: no visible global function definition for ‘box’
ld_lasso: no visible global function definition for ‘cor’
ld_lasso_method: no visible global function definition for ‘pchisq’
plot_beta: no visible global function definition for ‘plot’
plot_beta: no visible global function definition for ‘lines’
plot_ldlasso: no visible global function definition for ‘par’
plot_ldlasso: no visible global function definition for ‘plot’
plot_ldlasso: no visible global function definition for ‘lines’
plot_ldlasso: no visible global function definition for ‘points’
trace.plot: no visible global function definition for ‘plot’
trace.plot: no visible global function definition for ‘lines’
trace.plot: no visible global function definition for ‘points’
Undefined global functions or variables:
  abline axis box cor cov grey image lines par pchisq plot points
Consider adding
  importFrom("grDevices", "grey")
  importFrom("graphics", "abline", "axis", "box", "image", "lines",
             "par", "plot", "points")
  importFrom("stats", "cor", "cov", "pchisq")
to your NAMESPACE file.
chisqfit: no visible global function definition for ‘hist’
drawsample: no visible global function definition for ‘runif’
fitdistribution: no visible global function definition for ‘optimize’
fitdistribution: no visible global function definition for ‘var’
fthetacum: no visible global function definition for ‘integrate’
fthetaf: no visible global function definition for ‘dbeta’
plot.angledist: no visible global function definition for ‘hist’
plot.angledist: no visible global function definition for ‘curve’
plot.angledist: no visible global function definition for ‘box’
plot.angledistlist: no visible global function definition for ‘pdf’
plot.angledistlist: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  box curve dbeta dev.off hist integrate optimize pdf runif var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "box", "curve", "hist")
  importFrom("stats", "dbeta", "integrate", "optimize", "runif", "var")
to your NAMESPACE file.
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
LICurvature.default : f: no visible global function definition for
  ‘dnorm’
LICurvature.default: no visible global function definition for ‘nlminb’
LICurvature.default: no visible global function definition for ‘ginv’
Undefined global functions or variables:
  dnorm ginv nlminb
Consider adding
  importFrom("stats", "dnorm", "nlminb")
to your NAMESPACE file.
Packages suggested but not available for checking: ‘gWidgetsRGtk2’ ‘RGtk2’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 272-273 (Understanding_lime.Rmd) 
Error: processing vignette 'Understanding_lime.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 109-112 (linkspotterVignette.Rmd) 
Error: processing vignette 'linkspotterVignette.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 27.7Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    doc        2.4Mb
    libs      21.3Mb
    testdata   1.6Mb
mq.g.diagnostics : mq_missinggenotype_plot: no visible global function
  definition for ‘plot.missing’
Undefined global functions or variables:
  plot.missing
Running examples in ‘lmem.gwaser-Ex.R’ failed
The error most likely occurred in:

> ### Name: mq.g.diagnostics
> ### Title: Performs molecular markers quality diagnostics.
> ### Aliases: mq.g.diagnostics
> 
> ### ** Examples
> 
> data (QA_geno)
> data (QA_map)
> data (QA_pheno)
> 
> P.data <- QA_pheno
> G.data <- QA_geno
> map.data <- QA_map
> 
> cross.data  <- gwas.cross (P.data, G.data, map.data,
+ cross='gwas', heterozygotes=FALSE)
 --Read the following data:
	 179  individuals
	 811  markers
	 3  phenotypes
Warning in summary.cross(cross) :
  Some markers at the same position on chr 1,2,3,4,5,6,7; use jittermap().
 --Cross type: bc 
> summary (cross.data)
Warning in summary.cross(cross.data) :
  Some markers at the same position on chr 1,2,3,4,5,6,7; use jittermap().
    Doubled haploids

    No. individuals:    179 

    No. phenotypes:     3 
    Percent phenotyped: 100 100 100 

    No. chromosomes:    7 
        Autosomes:      1 2 3 4 5 6 7 

    Total markers:      811 
    No. markers:        117 147 153 48 113 101 132 
    Percent genotyped:  99.9 
    Genotypes (%):      AA:41.7  BB:58.3 
> 
> #Marker Quality
> 
> mq.g.diagnostics (crossobj=cross.data,I.threshold=0.1,
+              p.val=0.01,na.cutoff=0.1)
Error in plot.missing(crossobj) : could not find function "plot.missing"
Calls: mq.g.diagnostics -> mq_missinggenotype_plot
Execution halted
Package required and available but unsuitable version: ‘stats’

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/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
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb
Running ‘tests.R’ [25s/29s]
Running the tests in ‘tests/tests.R’ failed.
Last 13 lines of output:
  > test_check("lolog")
  ── 1. Error: Inline (@test-inline.R#22)  ───────────────────────────────────────
  Evaluation error: ShallowCopyable::vShallowCopy: bad type.
  1: emptyNetwork(10L) at testthat/test-inline.R:22
  
  
   Model is dyad independent. Replications are redundant. Setting nReplicates <- 1L.
  
   Model is dyad independent. Replications are redundant. Setting nReplicates <- 1L.
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 66 SKIPPED: 0 FAILED: 1
  1. Error: Inline (@test-inline.R#22) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘RDRToolbox’
Running ‘testthat.R’ [10s/72s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > 
  > test_check("loose.rock")
  ── 1. Failure: run.cache base.dir in folder that does not have access (@test-run
  `run.cache(sum, 1, 2, 3, 4, 5, show.message = FALSE, base.dir = "/")` did not produce any warnings.
  
  ── 2. Failure: run.cache base.dir in folder that does not have access (@test-run
  `run.cache(sum, 1, 2, 3, 4, 5, show.message = FALSE, base.dir = "/daca")` did not produce any warnings.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 146 SKIPPED: 0 FAILED: 2
  1. Failure: run.cache base.dir in folder that does not have access (@test-run.cache.R#27) 
  2. Failure: run.cache base.dir in folder that does not have access (@test-run.cache.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
S3 methods shown with full name in documentation object 'lqa':
  ‘lqa.update2’

S3 methods shown with full name in documentation object 'lqa.control':
  ‘lqa.control’

S3 methods shown with full name in documentation object 'plot.lqa':
  ‘plot.lqa’

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 46.3Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  44.2Mb
Found the following significant warnings:
  ./pr_queue_k.h:103:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./pr_queue.h:89:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./pr_queue.h:91:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./pr_queue.h:108:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./pr_queue.h:109:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./pr_queue.h:110:4: 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/ltsk.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.1Mb
LVMMCOR.default : f: no visible global function definition for ‘pnorm’
LVMMCOR.default : f: no visible global function definition for ‘dnorm’
LVMMCOR.default: no visible global function definition for ‘nlminb’
LVMMCOR.default: no visible global function definition for ‘fdHess’
LVMMCOR.default: no visible global function definition for ‘ginv’
Undefined global functions or variables:
  dnorm fdHess ginv nlminb pnorm
Consider adding
  importFrom("stats", "dnorm", "nlminb", "pnorm")
to your NAMESPACE file.
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 26.2Mb
  sub-directories of 1Mb or more:
    doc    6.8Mb
    libs  18.9Mb
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/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 15.5Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs  14.1Mb
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
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshotd023306255d6.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotd023306255d6.png': No such file or directory
Quitting from lines 61-68 (manipulateWidgets.Rmd) 
Error: processing vignette 'manipulateWidgets.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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

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 57-64 (mapfuser.Rmd) 
Error: processing vignette 'mapfuser.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 95-100 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   6.6Mb
plot.mathgraph: no visible global function definition for ‘plot’
plot.mathgraph: no visible global function definition for ‘box’
plot.mathgraph: no visible global function definition for ‘segments’
plot.mathgraph: no visible global function definition for ‘arrows’
plot.mathgraph: no visible global function definition for ‘text’
Undefined global functions or variables:
  arrows box plot segments text
Consider adding
  importFrom("graphics", "arrows", "box", "plot", "segments", "text")
to your NAMESPACE file.
Package suggested but not available for checking: ‘ASGSCA’
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
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?
find.cb : plotit: no visible global function definition for ‘plot’
find.cb : plotit: no visible global function definition for ‘points’
find.cb : plotit: no visible global function definition for ‘title’
plot.MCbound: no visible global function definition for ‘par’
plot.MCbound: no visible global function definition for ‘plot’
plot.MCbound: no visible global function definition for ‘lines’
plot.MCbound: no visible global function definition for ‘points’
plot.MCbound: no visible global function definition for ‘axis’
plot.MCbound: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  axis lines mtext par plot points title
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "par", "plot",
             "points", "title")
to your NAMESPACE file.
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
installed size is 16.6Mb
  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
mdr.3WS: no visible global function definition for ‘combn’
mdr.cv: no visible global function definition for ‘combn’
permute.mdr : mdr.lrt: no visible global function definition for
  ‘combn’
permute.mdr : mdr.lrt: no visible global function definition for ‘glm’
permute.mdr : mdr.lrt: no visible global function definition for
  ‘as.formula’
permute.mdr : mdr.lrt: no visible global function definition for
  ‘binomial’
permute.mdr : mdr.lrt: no visible binding for global variable ‘logit’
plot.mdr: no visible global function definition for ‘formula’
Undefined global functions or variables:
  as.formula binomial combn formula glm logit
Consider adding
  importFrom("stats", "as.formula", "binomial", "formula", "glm")
  importFrom("utils", "combn")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/MDSMap.Rcheck/00install.out’ for details.
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: 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
Loading required package: gdsfmt
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
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’ ‘ctc’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/MetabolomicsBasics.Rcheck/00install.out’ for details.
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.
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
installed size is 40.9Mb
  sub-directories of 1Mb or more:
    libs  40.6Mb
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 18.6Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    1.0Mb
    libs  14.1Mb
    misc   1.1Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-16


Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/mgcViz.Rcheck/00install.out’ for details.
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  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
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  7.3Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   5.3Mb
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
npmlt: no visible global function definition for ‘model.frame’
npmlt: no visible binding for global variable ‘na.pass’
npmlt: no visible global function definition for ‘model.matrix’
npmlt: no visible global function definition for ‘na.omit’
npmlt: no visible global function definition for ‘glm’
npmlt: no visible binding for global variable ‘binomial’
npmlt: no visible global function definition for ‘cov2cor’
Undefined global functions or variables:
  binomial cov2cor glm model.frame model.matrix na.omit na.pass
Consider adding
  importFrom("stats", "binomial", "cov2cor", "glm", "model.frame",
             "model.matrix", "na.omit", "na.pass")
to your NAMESPACE file.
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’ [17s/17s]
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’ ‘wateRmelon’
  ‘IlluminaHumanMethylation450kmanifest’
Error in re-building vignettes:
  ...
Warning 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
Error in re-building vignettes:
  ...
The following object is masked from 'package:variables':

    unit

Loading required package: RColorBrewer
Loading required package: mvtnorm
Loading required package: TH.data

Attaching package: 'TH.data'

The following object is masked from 'package:HSAUR3':

    birds

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

    geyser

trying URL 'https://zenodo.org/record/17179/files/DVC.tgz'
Warning in download.file("https://zenodo.org/record/17179/files/DVC.tgz",  :
  cannot open URL 'https://zenodo.org/record/17179/files/DVC.tgz': HTTP status was '404 Not Found'
Quitting from lines 27-80 (mlt.Rnw) 
Error: processing vignette 'mlt.Rnw' failed with diagnostics:
cannot open URL 'https://zenodo.org/record/17179/files/DVC.tgz'
Execution halted
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/mlVAR.Rcheck/00install.out’ for details.
Running ‘testhat.R’ [18s/4s]
Running the tests in ‘tests/testhat.R’ failed.
Last 13 lines of output:
  Loading required package: mlvocab
  Loading required package: Rcpp
  Loading required package: Matrix
  Loading required package: digest
  Loading required package: sparsepp
  ── 1. Failure: vocab is computed correctly (@test_vocab.R#37)  ─────────────────
  `v` not equal to `vt`.
  Component "term": 7 string mismatches
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1199 SKIPPED: 0 FAILED: 1
  1. Failure: vocab is computed correctly (@test_vocab.R#37) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    libs  33.1Mb
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
Fbetaf.ct: no visible global function definition for ‘as’
Fbetaf.it: no visible global function definition for ‘as’
ci: no visible global function definition for ‘pnorm’
initial.values: no visible global function definition for ‘glm’
initial.values: no visible binding for global variable ‘binomial’
initial.values: no visible global function definition for ‘coef’
mseb: no visible global function definition for ‘rnorm’
mseb: no visible global function definition for ‘rmultinom’
msef.ct: no visible global function definition for ‘as’
msef.it: no visible global function definition for ‘as’
phi.direct: no visible global function definition for ‘as’
phi.direct.ct: no visible global function definition for ‘as’
phi.direct.it: no visible global function definition for ‘as’
Undefined global functions or variables:
  as binomial coef glm pnorm rmultinom rnorm
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "binomial", "coef", "glm", "pnorm", "rmultinom",
             "rnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/mnreadR.Rcheck/00install.out’ for details.
'library' or 'require' calls in package code:
  ‘MASS’ ‘parallel’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
dyld: Library not loaded: /Builds/unix/recipes/build/gdal-2.1.3-obj/libgdal.dylib
  Referenced from: /usr/local/bin/gdalinfo
  Reason: image not found
dyld: Library not loaded: /Builds/unix/recipes/build/gdal-2.1.3-obj/libgdal.dylib
  Referenced from: /usr/local/bin/gdalinfo
  Reason: image not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
dyld: Library not loaded: /Builds/unix/recipes/build/gdal-2.1.3-obj/libgdal.dylib
  Referenced from: /usr/local/bin/gdalinfo
  Reason: image not found
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
dyld: Library not loaded: /Builds/unix/recipes/build/gdal-2.1.3-obj/libgdal.dylib
  Referenced from: /usr/local/bin/gdalinfo
  Reason: image not found
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
dyld: Library not loaded: /Builds/unix/recipes/build/gdal-2.1.3-obj/libgdal.dylib
  Referenced from: /usr/local/bin/gdalinfo
  Reason: image not found
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
dyld: Library not loaded: /Builds/unix/recipes/build/gdal-2.1.3-obj/libgdal.dylib
  Referenced from: /usr/local/bin/gdalinfo
  Reason: image not found
dyld: Library not loaded: /Builds/unix/recipes/build/gdal-2.1.3-obj/libgdal.dylib
  Referenced from: /usr/local/bin/gdalinfo
  Reason: image not found
dyld: Library not loaded: /Builds/unix/recipes/build/gdal-2.1.3-obj/libgdal.dylib
  Referenced from: /usr/local/bin/gdalinfo
  Reason: image not found
dyld: Library not loaded: /Builds/unix/recipes/build/gdal-2.1.3-obj/libgdal.dylib
  Referenced from: /usr/local/bin/gdalinfo
  Reason: image not found
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.7Mb
    libs   2.9Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   5.3Mb
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/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’.
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/mosaic.Rcheck/00install.out’ for details.
plot.Mposterior: no visible global function definition for ‘plot’
plot.Mposterior: no visible global function definition for ‘rainbow’
plot.Mposterior: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines plot rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "lines", "plot")
to your NAMESPACE file.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  12.9Mb
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 29.8Mb
  sub-directories of 1Mb or more:
    libs  28.4Mb
installed size is 43.3Mb
  sub-directories of 1Mb or more:
    libs  42.9Mb
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/msigdbr.Rcheck/00install.out’ for details.
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 59.6Mb
  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’.
Undocumented S4 methods:
  generic '[<-' and siglist 'Multiplyr,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘multistateutils-Ex.R’ failed
The error most likely occurred in:

> ### Name: length_of_stay
> ### Title: Estimates length of stay
> ### Aliases: length_of_stay
> 
> ### ** Examples
> 
> 
> library(multistateutils)
> library(mstate)
Loading required package: survival
> library(flexsurv)
> 
> # Convert data to long
> data(ebmt3)
> tmat <- trans.illdeath()
> long <- msprep(time=c(NA, 'prtime', 'rfstime'), 
+                status=c(NA, 'prstat', 'rfsstat'), 
+                data=ebmt3, 
+                trans=tmat, 
+                keep=c('age', 'dissub'))
>                
> # Fit parametric models
> models <- lapply(1:3, function(i) {
+     flexsurvreg(Surv(time, status) ~ age + dissub, data=long, dist='weibull')
+ })
> 
> # New individual to estimate transition probabilities for
> newdata <- data.frame(age="20-40", dissub="AML")
> 
> # Estimate length of stay in each state after a year, given starting in state 1
> length_of_stay(models, 
+                newdata=newdata,
+                tmat, times=365.25,
+                start=1)

 *** caught illegal operation ***
address 0x108aadb00, cause 'illegal opcode'

Traceback:
 1: desCpp(transitions, trans_mat, newdata_mat, start_times, start_states -     1, tcovs)
 2: data.table::as.data.table(desCpp(transitions, trans_mat, newdata_mat,     start_times, start_states - 1, tcovs))
 3: run_sim(transition_list, attr_mat, trans_mat, tcovs, start_times,     start_states)
 4: state_occupancy(models, trans_mat, newdata_ext, tcovs, initial_times,     start_states, ci, M, agelimit, agecol, agescale)
 5: length_of_stay(models, newdata = newdata, tmat, times = 365.25,     start = 1)
An irrecoverable exception occurred. R is aborting now ...
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  26: tryCatchList(expr, classes, parentenv, handlers)
  27: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
  28: test_code(NULL, exprs, env)
  29: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
  30: force(code)
  31: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,     {        lister$start_file(basename(path))        source_file(path, new.env(parent = env), chdir = TRUE,             wrap = wrap)        end_context()    })
  32: FUN(X[[i]], ...)
  33: lapply(paths, test_file, env = env, reporter = current_reporter,     start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
  34: force(code)
  35: with_reporter(reporter = current_reporter, results <- lapply(paths,     test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,     load_helpers = FALSE, wrap = wrap))
  36: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,     stop_on_warning = stop_on_warning, wrap = wrap)
  37: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,     ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     wrap = wrap)
  38: test_package_dir(package = package, test_path = test_path, filter = filter,     reporter = reporter, ..., stop_on_failure = stop_on_failure,     stop_on_warning = stop_on_warning, wrap = wrap)
  39: test_check("multistateutils")
  An irrecoverable exception occurred. R is aborting now ...
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
installed size is 41.3Mb
  sub-directories of 1Mb or more:
    libs  41.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/nat.templatebrains.Rcheck/00install.out’ for details.
Warning: declared S3 method 'plot3d.templatebrain' not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Error in re-building vignettes:
  ...
Warning in engine$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 49-50 (using-nauf.Rmd) 
Error: processing vignette 'using-nauf.Rmd' failed with diagnostics:
Unable to extract deviance function from model fit
Execution halted
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
Package required but not available: ‘sSeq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
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  8.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   4.5Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   4.6Mb
'library' or 'require' call to ‘igraph’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘Rcpp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘NetSim/libs/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.
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  23: tryCatchList(expr, classes, parentenv, handlers)
  24: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
  25: test_code(NULL, exprs, env)
  26: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
  27: force(code)
  28: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,     {        lister$start_file(basename(path))        source_file(path, new.env(parent = env), chdir = TRUE,             wrap = wrap)        end_context()    })
  29: FUN(X[[i]], ...)
  30: lapply(paths, test_file, env = env, reporter = current_reporter,     start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
  31: force(code)
  32: with_reporter(reporter = current_reporter, results <- lapply(paths,     test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,     load_helpers = FALSE, wrap = wrap))
  33: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,     stop_on_warning = stop_on_warning, wrap = wrap)
  34: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,     ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     wrap = wrap)
  35: test_package_dir(package = package, test_path = test_path, filter = filter,     reporter = reporter, ..., stop_on_failure = stop_on_failure,     stop_on_warning = stop_on_warning, wrap = wrap)
  36: test_check("NetworkInference")
  An irrecoverable exception occurred. R is aborting now ...
Packages suggested but not available for checking:
  ‘BiocStyle’ ‘graphite’ ‘NFPdata’
Error in re-building vignettes:
  ...
Quitting from lines 10-11 (NFP.Rnw) 
Error: processing vignette 'NFP.Rnw' failed with diagnostics:
there is no package called 'BiocStyle'
Execution halted
installed size is 35.2Mb
  sub-directories of 1Mb or more:
    CppCode        1.2Mb
    R              6.5Mb
    classic-bugs   1.5Mb
    include        5.6Mb
    libs          18.6Mb
    tests          1.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 127-133 (geocode.Rmd) 
Error: processing vignette 'geocode.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/NNS.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/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.
'library' or 'require' calls in package code:
  ‘SweaveListingUtils’ ‘graphics’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
allsomv: no visible binding for global variable ‘raw_data’
apsomv: no visible binding for global variable ‘raw_data’
apsomv: no visible binding for '<<-' assignment to ‘NAwarning’
cfuinterpolation: no visible binding for global variable
  ‘measured_values’
cfuinterpolation: no visible global function definition for ‘lm’
cfuinterpolation: no visible global function definition for ‘coef’
disconestep: no visible global function definition for ‘runif’
disconestep: no visible binding for global variable ‘measured_values’
disconestep: no visible binding for global variable ‘psteps’
makepdfoutput: no visible binding for '<<-' assignment to ‘textt’
makepdfoutput: no visible global function definition for ‘Sweave’
npmpm: no visible binding for '<<-' assignment to ‘inputsettings’
npmpm: no visible binding for global variable ‘psteps’
npmpm: no visible binding for '<<-' assignment to ‘cfu’
npmpm: no visible binding for '<<-' assignment to ‘countwarnings’
npmpm: no visible binding for global variable ‘cfu’
onestep: no visible binding for global variable ‘measured_values’
onestep: no visible global function definition for ‘var’
onestep: no visible binding for global variable ‘psteps’
onestep: no visible global function definition for ‘rnorm’
psteppar: no visible global function definition for ‘runif’
simpleinterpolation: no visible binding for global variable
  ‘measured_values’
Undefined global functions or variables:
  Sweave cfu coef lm measured_values psteps raw_data rnorm runif var
Consider adding
  importFrom("stats", "coef", "lm", "rnorm", "runif", "var")
  importFrom("utils", "Sweave")
to your NAMESPACE file.
Packages required but not available: ‘gWidgetsRGtk2’ ‘RGtk2Extras’ ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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 10.0Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    1.5Mb
    help   2.5Mb
    libs   2.3Mb
installed size is 77.0Mb
  sub-directories of 1Mb or more:
    libs  76.5Mb
Package in Depends field not imported from: ‘KMsurv’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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
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  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   4.8Mb
installed size is 137.6Mb
  sub-directories of 1Mb or more:
    R         2.4Mb
    libs    127.6Mb
    models    4.7Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.7Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
Package suggested but not available for checking: ‘org.At.tair.db’
Running ‘bdstest.R’ [1s/1s]
  Running ‘hobbs.R’ [4s/4s]
Running the tests in ‘tests/hobbs.R’ failed.
Last 13 lines of output:
  In kktchk(ans$par, fn, wgr, hess = NULL, upper = NULL, lower = NULL,  :
    Eigenvalue failure for projected Hessian
  This problem is unconstrained.
  Error in lbfgsb3::lbfgsb3(prm = spar, fn = efn, gr = egr, control = mcontrol,  : 
    NA/NaN/Inf in foreign function call (arg 7)
  In addition: Warning messages:
  1: In nlm(f = nlmfn, p = spar, iterlim = iterlim, print.level = print.level,  :
    NA/Inf replaced by maximum positive value
  2: In nlm(f = nlmfn, p = spar, iterlim = iterlim, print.level = print.level,  :
    NA/Inf replaced by maximum positive value
  3: In nlm(f = nlmfn, p = spar, iterlim = iterlim, print.level = print.level,  :
    NA/Inf replaced by maximum positive value
  4: In nlm(f = nlmfn, p = spar, iterlim = iterlim, print.level = print.level,  :
    NA/Inf replaced by maximum positive value
  libc++abi.dylib: terminating with uncaught exception of type std::range_error: non-finite x values not allowed in calfun
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/optiSel.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      2.2Mb
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.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Ord.logreg: no visible binding for global variable ‘data’
plot.Ord.logreg: no visible global function definition for ‘par’
plot.Ord.logreg: no visible global function definition for ‘plot’
plot.Ord.logreg: no visible global function definition for ‘mtext’
plot.Ord.logreg: no visible global function definition for ‘plot.new’
Undefined global functions or variables:
  data mtext par plot plot.new
Consider adding
  importFrom("graphics", "mtext", "par", "plot", "plot.new")
  importFrom("utils", "data")
to your NAMESPACE file.
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.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
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
Error in re-building vignettes:
  ...
Warning 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
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.
pass: no visible global function definition for ‘predict’
plot.pass: no visible global function definition for ‘par’
plot.pass: no visible global function definition for ‘plot’
Undefined global functions or variables:
  par plot predict
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "predict")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$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.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc       2.9Mb
    extdata   2.7Mb
    libs      1.8Mb
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 11.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.1Mb
    libs   6.2Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PCRedux.Rcheck/00install.out’ for details.
Package required but not available: ‘strvalidator’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    libs    5.7Mb
    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’.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
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   4.3Mb
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/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.
cdfDist: no visible global function definition for ‘tail’
cor2icc: no visible global function definition for ‘cor’
plot.cdfDist: no visible global function definition for ‘plot’
plot.cdfDist: no visible global function definition for ‘lines’
plot.cdfDist: no visible global function definition for ‘axis’
plot.cdfDist: no visible global function definition for ‘mtext’
plot.cdfDist: no visible global function definition for ‘legend’
Undefined global functions or variables:
  axis cor legend lines mtext plot tail
Consider adding
  importFrom("graphics", "axis", "legend", "lines", "mtext", "plot")
  importFrom("stats", "cor")
  importFrom("utils", "tail")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘Rgraphviz’ ‘cluster’ ‘graph’
  All declared Imports should be used.
dvol.mse.est: no visible global function definition for ‘optim’
ellipsoidSurface: no visible global function definition for ‘integrate’
latscale: no visible global function definition for ‘uniroot’
covariogram,Segment-function: no visible global function definition for
  ‘integrate’
plot,FigLat-missing: no visible global function definition for ‘par’
plot,PointPattern-matrix: no visible global function definition for
  ‘par’
plot,PointPattern-matrix: no visible global function definition for
  ‘lines’
plot,PointPattern-missing: no visible global function definition for
  ‘points’
plot,Quadrat-missing: no visible global function definition for ‘lines’
plot,Segment-matrix: no visible global function definition for ‘par’
plot,Segment-matrix: no visible global function definition for
  ‘polygon’
plot,Segment-missing: no visible global function definition for ‘lines’
Undefined global functions or variables:
  integrate lines optim par points polygon uniroot
Consider adding
  importFrom("graphics", "lines", "par", "points", "polygon")
  importFrom("stats", "integrate", "optim", "uniroot")
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/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.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'Sample-scripts-external-genotype-simulation.Rmd' failed with diagnostics:
Failed to locate the ‘weave’ output file (by engine ‘knitr::rmarkdown’) for vignette with name ‘Sample-scripts-external-genotype-simulation’. The following files exist in directory ‘.’: ‘Sample-scripts-external-genotype-simulation.Rmd’, ‘Sample-scripts-external-genotype-simulation.md’, ‘Simulation-and-LinearModel.Rmd’, ‘SimulationAndLinearModel.bib’, ‘UsagePhenotypeSimulator.Rmd’, ‘UsagePhenotypeSimulator.html’, ‘genotype-simulation.bib’, ‘plos-genetics.csl’, ‘sample-scripts-external-genotype-simulation.html’
Execution halted
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    libs  19.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in 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
Package required and available but unsuitable version: ‘phyloseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot43b167d86d6c.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot43b167d86d6c.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
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.
installed size is 24.1Mb
  sub-directories of 1Mb or more:
    libs  24.0Mb
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
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.1Mb
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.
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.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
... activating corpus: germaparlmini
... activating corpus: reuters
Quitting from lines 139-140 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
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:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/polyPK.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  ‘Rsamtools’ ‘VariantAnnotation’ ‘GenomicFeatures’
Packages unavailable to check Rd xrefs: ‘Rsamtools’, ‘BSgenome’, ‘GenomicFeatures’, ‘VariantAnnotation’
Error in re-building vignettes:
  ...
Warning 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 301-304 (polyRADtutorial.Rmd) 
Error: processing vignette 'polyRADtutorial.Rmd' failed with diagnostics:
there is no package called 'VariantAnnotation'
Execution halted
Package required but not available: ‘EmpiricalBrownsMethod’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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’
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:
  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.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PPQplan.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: Ignoring unknown aesthetics: z
Warning: Ignoring unknown aesthetics: z
Warning in normalizePath(f2) :
  path[1]="./webshot1635920dad531.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot1635920dad531.png': No such file or directory
Quitting from lines 125-126 (PPQplan-vignette.Rmd) 
Error: processing vignette 'PPQplan-vignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Found the following significant warnings:
  ./shared.h:67:9: warning: result of comparison of constant 2147483648 with expression of type 'int' is always false [-Wtautological-constant-out-of-range-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/praznik.Rcheck/00install.out’ for details.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
Error in re-building vignettes:
  ...
Warning in engine$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 31-44 (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 13.5Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   6.4Mb
    libs      5.5Mb
Running examples in ‘ProFit-Ex.R’ failed
The error most likely occurred in:

> ### Name: profitConvolvePSF
> ### Title: High level image convolution
> ### Aliases: profitConvolvePSF
> ### Keywords: PSF convolve convolution
> 
> ### ** Examples
> 
> model = list(
+ 	sersic = list(
+ 		xcen   = c(180, 60),
+ 		ycen   = c(90, 10),
+ 		mag = c(15, 13),
+ 		re  = c(14, 5),
+ 		nser  = c(3, 10),
+ 		ang  = c(46, 80),
+ 		axrat  = c(0.4, 0.6),
+ 		box = c(0.5,-0.5)
+ 	)
+ )
> 
> model.image=profitMakeModel(model=model, dim=c(200,200))$z
> 
> psf=profitMakeGaussianPSF()
> 
> #Do some benchmarking:
> 
> temp=profitBenchmarkConv(model.image, psf=psf)

 *** 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’
Package suggested but not available for checking: ‘ALDEx2’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.8Mb
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/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’.
Error in re-building vignettes:
  ...
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

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]="./webshot6d9639cf936a.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot6d9639cf936a.png': No such file or directory
Quitting from lines 512-540 (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:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PWFSLSmoke.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/PythonInR.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/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:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/qpcR.Rcheck/00install.out’ for details.
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 92-106 (wilcox1973.Rmd) 
Error: processing vignette 'wilcox1973.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 12.3Mb
  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.
draw_legend: no visible global function definition for ‘legend’
draw_legend: no visible global function definition for ‘par’
draw_nodes: no visible global function definition for ‘lines’
draw_nodes: no visible global function definition for ‘points’
draw_nodes: no visible global function definition for ‘text’
draw_vertical_lines: no visible global function definition for ‘lines’
draw_vertical_lines: no visible global function definition for ‘abline’
layout_large_plot: no visible global function definition for ‘par’
layout_large_plot: no visible global function definition for ‘mtext’
layout_large_plot: no visible global function definition for ‘axis’
layout_large_plot: no visible global function definition for ‘lines’
layout_small_plot: no visible global function definition for ‘par’
rquipu: no visible global function definition for ‘colors’
rquipu: no visible global function definition for ‘jpeg’
rquipu: no visible global function definition for ‘png’
rquipu: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  abline axis colors dev.off jpeg legend lines mtext par png points
  text
Consider adding
  importFrom("grDevices", "colors", "dev.off", "jpeg", "png")
  importFrom("graphics", "abline", "axis", "legend", "lines", "mtext",
             "par", "points", "text")
to your NAMESPACE file.
File ‘qVarSel/libs/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.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RaceID.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/radiant.basics.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/radiant.data.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/radiant.design.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/radiant.model.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/radiant.multivariate.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/radiant.Rcheck/00install.out’ for details.
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 14.1Mb
  sub-directories of 1Mb or more:
    api           3.1Mb
    htmlwidgets   9.2Mb
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/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  9.5Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs   5.5Mb
Running examples in ‘RAtmosphere-Ex.R’ failed
The error most likely occurred in:

> ### Encoding: UTF-8
> 
> ### Name: suncalc
> ### Title: Sunrise and Sunset calculations
> ### Aliases: suncalc
> ### Keywords: sun sunset sunrise
> 
> ### ** Examples
> 
> t<-Sys.time()+seq(-3600*12,3600*12,,by=600)
> t0=as.POSIXlt(Sys.time(),tz='UTC')
> plot(t,90-SZA(t,Lat=0,Lon=0),main='SZA',xlab='Time',ylab='El [°deg]')
> sun=suncalc(t0[['yday']],UTC=TRUE)
Error in FUN(X[[i]], ...) : subscript out of bounds
Calls: suncalc -> [[ -> [[.POSIXlt -> .POSIXlt -> lapply
Execution halted
Package suggested but not available for checking: ‘rattle’
Packages suggested but not available for checking:
  ‘cairoDevice’ ‘gWidgetsRGtk2’ ‘playwith’ ‘rggobi’ ‘RGtk2’
  ‘RGtk2Extras’
installed size is 32.3Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  29.9Mb
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
Error in re-building vignettes:
  ...
Loading required package: RCurl
Loading required package: bitops
Loading required package: RJSONIO
Warning in postForm(url, .params = params, .opts = opts, binary = binary) :
  No inputs passed to form

Error: processing vignette 'rbiouml.Rnw' failed with diagnostics:
 chunk 8 
Error in queryJSON("/web/analysis", params = c(jobID = jobID, de = analysisName,  : 
  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
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
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.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
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.
.onAttach: no visible global function definition for ‘palette’
.onAttach: no visible global function definition for ‘dev.off’
helpAboutBCA: no visible global function definition for ‘help’
Undefined global functions or variables:
  dev.off help palette
Consider adding
  importFrom("grDevices", "dev.off", "palette")
  importFrom("utils", "help")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘Rcmdr’ ‘multcomp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Depends: includes the non-default packages:
  ‘Rcmdr’ ‘TeachingDemos’ ‘tseries’ ‘abind’ ‘MASS’ ‘xts’ ‘forecast’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘tseries’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘MASS’ ‘Rcmdr’ ‘TeachingDemos’ ‘abind’ ‘forecast’ ‘tseries’ ‘xts’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Depends: includes the non-default packages:
  ‘Rcmdr’ ‘tcltk’ ‘car’ ‘RColorBrewer’ ‘colorspace’ ‘vcd’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' call to ‘car’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RColorBrewer’ ‘Rcmdr’ ‘car’ ‘colorspace’ ‘vcd’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Error in re-building vignettes:
  ...
Warning 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 62-65 (introducao-rcongresso.Rmd) 
Error: processing vignette 'introducao-rcongresso.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    corpora   7.5Mb
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.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    include   5.4Mb
    libs      1.7Mb
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
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RcppCWB.Rcheck/00install.out’ for details.
installed size is 31.2Mb
  sub-directories of 1Mb or more:
    include   7.6Mb
    libs     23.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RcppMeCab.Rcheck/00install.out’ for details.
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  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    include   8.9Mb
    libs      2.5Mb
installed size is 15.3Mb
  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.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
── 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 11.2Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
Found the following significant warnings:
  dist.cpp:19:33: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
  dist.cpp:65:33: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
  dist.cpp:111:36: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rdist.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...

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

    set_names

SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.thoughtworks.xstream.core.util.Fields (file:/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/Rdroolsjars/java/xstream-1.4.9.jar) to field java.util.TreeMap.comparator
WARNING: Please consider reporting this to the maintainers of com.thoughtworks.xstream.core.util.Fields
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 in if (class(intermediateOutput) == "list") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(intermediateOutput) == "list") { :
  the condition has length > 1 and only the first element will be used
Warning in normalizePath(f2) :
  path[1]="./webshot37525a7a3479.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot37525a7a3479.png': No such file or directory
Quitting from lines 374-381 (Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd) 
Error: processing vignette 'Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
checkForVServer: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning 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]="./webshotd14efb7b68.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotd14efb7b68.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  5.8Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   3.8Mb
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs  15.0Mb
HanoiTower: no visible global function definition for ‘object.size’
plot.HanoiTower: no visible global function definition for ‘plot’
plot.HanoiTower: no visible global function definition for ‘polygon’
plot.HanoiTower: no visible global function definition for ‘text’
Undefined global functions or variables:
  object.size plot polygon text
Consider adding
  importFrom("graphics", "plot", "polygon", "text")
  importFrom("utils", "object.size")
to your NAMESPACE file.
Package required but not available: ‘GenomeGraphs’

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/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 20.8Mb
  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.
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── 2. Error: Testing the introduction presentation (@test-SlideDeck.R#5)  ──────
  Please install pandoc first: http://pandoc.org
  1: Read()$auto(fname, quiet = TRUE) at testthat/test-SlideDeck.R:5
  2: get(fileExt, mode = "function")(fileName, ...)
  3: md(mdFile)
  4: knitr::pandoc(fileName, format = "plain")
  5: stop("Please install pandoc first: http://pandoc.org")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 10 SKIPPED: 0 FAILED: 2
  1. Error:  (@test-Evaluate.R#6) 
  2. Error: Testing the introduction presentation (@test-SlideDeck.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    java   5.8Mb
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 ‘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’
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/revengc.Rcheck/00install.out’ for details.
installed size is 28.1Mb
  sub-directories of 1Mb or more:
    libs  26.9Mb
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.

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 16.3Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
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.
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.
Namespaces in Imports field not imported from:
  ‘httr’ ‘remotes’ ‘rmarkdown’ ‘shiny’
  All declared Imports should be used.
Package unavailable to check Rd xrefs: ‘installr’
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: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rise.Rcheck/00install.out’ for details.
rite : loadHistory: no visible global function definition for
  ‘savehistory’
rite : saveGist: no visible global function definition for ‘browseURL’
rite : uploadToRPubs : processEntry: no visible global function
  definition for ‘browseURL’
rite : runCode: no visible global function definition for ‘savehistory’
rite : runCode: no visible global function definition for ‘loadhistory’
rite : knittxt: no visible global function definition for ‘Sweave’
rite : knittxt: no visible global function definition for ‘browseURL’
rite : addHighlighting : addHighlight: no visible global function
  definition for ‘packageDescription’
rite : addHighlighting : addHighlight: no visible global function
  definition for ‘na.omit’
rite : about : <anonymous>: no visible global function definition for
  ‘browseURL’
rite : <anonymous>: no visible global function definition for
  ‘capture.output’
rite : <anonymous>: no visible global function definition for
  ‘update.packages’
rite : <anonymous>: no visible global function definition for ‘help’
rite : f1: no visible global function definition for ‘help’
rite : f1: no visible global function definition for ‘help.search’
rite : commandCompletion: no visible global function definition for
  ‘apropos’
rite : findreplace : <anonymous>: no visible global function definition
  for ‘browseURL’
Undefined global functions or variables:
  Sweave apropos browseURL capture.output help help.search loadhistory
  na.omit packageDescription savehistory update.packages
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "Sweave", "apropos", "browseURL", "capture.output",
             "help", "help.search", "loadhistory", "packageDescription",
             "savehistory", "update.packages")
to your NAMESPACE file.
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  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  6.0Mb
  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.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
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
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    rmd   6.8Mb
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.
.onLoad: warning in dir(dll.path, pattern = this.ext, full = FALSE):
  partial argument match of 'full' to 'full.names'
diagnos.envel: warning in apply(jumpDistRes, MARG = 2, FUN = quantile,
  probs = perc[1], na.rm = TRUE): partial argument match of 'MARG' to
  'MARGIN'
diagnos.envel: warning in apply(jumpDistRes, MARG = 2, FUN = quantile,
  probs = perc[2], na.rm = TRUE): partial argument match of 'MARG' to
  'MARGIN'
diagnos.envel: no visible global function definition for ‘quantile’
diagnos.envel: no visible global function definition for ‘qnorm’
diagnos.envel: no visible binding for global variable ‘quantile’
hrplot: no visible global function definition for ‘plot’
hrplot: no visible global function definition for ‘lines’
hrplot: no visible global function definition for ‘abline’
hrplot: no visible global function definition for ‘text’
sim.chain: no visible global function definition for ‘rnorm’
simRandWalk: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline lines plot qnorm quantile rnorm text
Consider adding
  importFrom("graphics", "abline", "lines", "plot", "text")
  importFrom("stats", "qnorm", "quantile", "rnorm")
to your NAMESPACE file.
File ‘RMC/libs/RMC.so’:
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
    Objects: ‘RMC.o’, ‘predict.o’
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘ap.o’

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 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
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  8.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   5.2Mb
dbGetDistinct,RMongo-character-character-character: no visible global
  function definition for ‘read.table’
dbGetQueryForKeys,RMongo-character-character-character-numeric-numeric:
  no visible global function definition for ‘read.csv’
Undefined global functions or variables:
  read.csv read.table
Consider adding
  importFrom("utils", "read.csv", "read.table")
to your NAMESPACE file.
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.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
.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  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doxygen   1.3Mb
    libs      3.3Mb
installed size is 94.7Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     92.6Mb
Packages required and available but unsuitable versions:
  ‘impute’ ‘MassSpecWavelet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs  18.7Mb
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.
Packages suggested but not available for checking:
  ‘affydata’ ‘hgu95av2cdf’ ‘beadarrayExampleData’ ‘illuminaHumanv3.db’
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 suggested but not available for checking: ‘ROI.plugin.glpk’
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.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
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
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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'rprojroot.Rmd' failed with diagnostics:
shared object 'stringi.so' not found
Execution halted
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  15.2Mb
Running ‘runUnitTests.R’ [2s/2s]
Running the tests in ‘tests/runUnitTests.R’ failed.
Last 13 lines of output:
  --------------------------- 
  Test file: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RProtoBuf.Rcheck/RProtoBuf/unitTests/runit.serialize_pb.R 
  test.serialize.sublist: (1 checks) ... OK (0.01 seconds)
  test.serialize_pb: (2 checks) ... OK (0.03 seconds)
  test.serialize_pb.alldatasets: (1 checks) ... OK (0.55 seconds)
  > 
  > ## Return success or failure to R CMD CHECK
  > if (getErrors(tests)$nFail > 0) {
  +    stop("TEST FAILED!")
  + }
  > if (getErrors(tests)$nErr > 0) {
  +    stop("TEST HAD ERRORS!")
  + }
  Error: TEST HAD ERRORS!
  Execution halted
'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/rrd.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘biwavelet’
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.
Found the following significant warnings:
  Warning: loading Rplot failed
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RSA.Rcheck/00install.out’ for details.
installed size is 22.0Mb
  sub-directories of 1Mb or more:
    dependencies  20.9Mb
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
filterSD: no visible binding for global variable ‘sd’
filterSD: no visible global function definition for ‘quantile’
fit_lasso: no visible global function definition for ‘coef’
fit_prlasso: no visible global function definition for ‘coef’
rsig: no visible binding for global variable ‘mclapply’
rsig.all: no visible binding for global variable ‘mclapply’
rsig.all : <anonymous>: no visible global function definition for
  ‘flush.console’
rsig.all : <anonymous>: no visible global function definition for
  ‘predict’
Undefined global functions or variables:
  coef flush.console mclapply predict quantile sd
Consider adding
  importFrom("stats", "coef", "predict", "quantile", "sd")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
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
installed size is 48.7Mb
  sub-directories of 1Mb or more:
    libs  48.2Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
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 230.5Mb
  sub-directories of 1Mb or more:
    libs  228.0Mb
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 ...
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  5.8Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       1.8Mb
    projects   2.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$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]="./webshot14ab5585194ff.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot14ab5585194ff.png': No such file or directory
Quitting from lines 84-89 (rtrek.Rmd) 
Error: processing vignette 'rtrek.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
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
Running examples in ‘rviewgraph-Ex.R’ failed
The error most likely occurred in:

> ### Name: rViewGraph
> ### Title: This is a function to create and start the Java graph animation
> ###   GUI.
> ### Aliases: rViewGraph rViewGraph.default rViewGraph.Matrix
> ###   rViewGraph.igraph
> ### Keywords: graph
> 
> ### ** Examples
> 
> # 
> # Viewing an Erdos Renyui random graph specified by random edges.
> f = sample(100,size=200,replace=TRUE)
> t = sample(100,size=200,replace=TRUE)
> vft = rViewGraph(cbind(f,t))
Error in .jnew("rviewgraph/RViewGraph", v, f, t, x, y, directed, running) : 
  java.awt.HeadlessException
Calls: rViewGraph ... rViewGraph.default -> rViewGraphCore -> init -> .jnew
Execution halted
installed size is 46.7Mb
  sub-directories of 1Mb or more:
    include   2.5Mb
    libs     43.9Mb
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.
S3 methods shown with full name in documentation object 'cbind.rv':
  ‘cbind.rv’ ‘rbind.rv’

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:
  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.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs    6.3Mb
    yacas   1.3Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
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.
plot.safidesign: no visible global function definition for ‘par’
plot.safidesign: no visible global function definition for ‘matplot’
plot.safidesign: no visible global function definition for ‘axis’
plot.safimodel : plot.coef: no visible global function definition for
  ‘colorRampPalette’
plot.safimodel : plot.coef: no visible global function definition for
  ‘barplot’
plot.safimodel : plot.coef: no visible global function definition for
  ‘axis’
plot.safimodel : plot.coef: no visible global function definition for
  ‘abline’
plot.safimodel : plot.coef: no visible global function definition for
  ‘box’
plot.safimodel: no visible global function definition for ‘par’
safiModel: no visible global function definition for ‘lm’
Undefined global functions or variables:
  abline axis barplot box colorRampPalette lm matplot par
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "abline", "axis", "barplot", "box", "matplot",
             "par")
  importFrom("stats", "lm")
to your NAMESPACE file.
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
Package required but not available: ‘ConsensusClusterPlus’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/sdStaf.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  5.9Mb
  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.
Packages in Depends field not imported from:
  ‘datautils’ ‘irlba’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
computeKernel: no visible binding for global variable ‘sd’
computeKernel: no visible global function definition for ‘dist’
computeKernel: no visible global function definition for ‘quantile’
computeProjectionFromKernel : <anonymous>: no visible global function
  definition for ‘irlba’
distortions: no visible binding for global variable ‘sd’
distortions: no visible global function definition for ‘dist’
Undefined global functions or variables:
  dist irlba quantile sd
Consider adding
  importFrom("stats", "dist", "quantile", "sd")
to your NAMESPACE file.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.4Mb
Running examples in ‘seoR-Ex.R’ failed
The error most likely occurred in:

> ### Name: lastCached
> ### Title: Function to get the last Google Cache Date for a URL
> ### Aliases: lastCached
> 
> ### ** Examples
> 
> lastCached("https://www.r-project.org/")
Error in if (is.na(res)) { : argument is of length zero
Calls: lastCached
Execution halted
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
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
Packages suggested but not available for checking:
  ‘loomR’ ‘made4’ ‘SingleCellExperiment’ ‘MAST’
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is 115.2Mb
  sub-directories of 1Mb or more:
    doc     11.8Mb
    docker   1.3Mb
    libs    97.5Mb
    sqlite   1.5Mb
Running examples in ‘sf-Ex.R’ failed
The error most likely occurred in:

> ### Name: geos_binary_ops
> ### Title: Geometric operations on pairs of simple feature geometry sets
> ### Aliases: geos_binary_ops st_intersection st_intersection.sfc
> ###   st_intersection.sf st_difference st_difference.sfc st_sym_difference
> ###   st_snap
> 
> ### ** Examples
> 
> set.seed(131)
> library(sf)
> m = rbind(c(0,0), c(1,0), c(1,1), c(0,1), c(0,0))
> p = st_polygon(list(m))
> n = 100
> l = vector("list", n)
> for (i in 1:n)
+   l[[i]] = p + 10 * runif(2)
> s = st_sfc(l)
> plot(s, col = sf.colors(categorical = TRUE, alpha = .5))
> title("overlapping squares")
> d = st_difference(s) # sequential differences: s1, s2-s1, s3-s2-s1, ...
> plot(d, col = sf.colors(categorical = TRUE, alpha = .5))
> title("non-overlapping differences")
> i = st_intersection(s) # all intersections
libc++abi.dylib: terminating with uncaught exception of type std::__1::bad_function_call: std::exception
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/shapes.Rcheck/00install.out’ for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    www   7.7Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    www   6.4Mb
plot.intersect: no visible global function definition for ‘points’
plot.intersect: no visible global function definition for ‘plot’
plot.receiver: no visible global function definition for ‘points’
plot.receiver: no visible global function definition for ‘plot’
plot.receiver: no visible global function definition for ‘segments’
plot.transmitter: no visible global function definition for ‘points’
plot.transmitter: no visible global function definition for ‘plot’
plot.transmitter: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines plot points segments
Consider adding
  importFrom("graphics", "lines", "plot", "points", "segments")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot17b333efda763.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot17b333efda763.png': No such file or directory
Quitting from lines 26-42 (animate.Rmd) 
Error: processing vignette 'animate.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 89-90 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  10.5Mb
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
plot.CorrAn : SAPplot: no visible global function definition for ‘plot’
plot.CorrAn : SAPtitle: no visible global function definition for
  ‘title’
plot.CorrAn : SAPtitle: no visible global function definition for
  ‘mtext’
plot.CorrAn : SAPplotpuntos: no visible global function definition for
  ‘points’
plot.CorrAn : SAPplotpuntos: no visible global function definition for
  ‘text’
plot.CorrAn: no visible global function definition for ‘dev.new’
plot.SimAn : SAPplot: no visible global function definition for ‘plot’
plot.SimAn : SAPtitle: no visible global function definition for
  ‘title’
plot.SimAn : SAPtitle: no visible global function definition for
  ‘mtext’
plot.SimAn : SAPplotpuntos: no visible global function definition for
  ‘points’
plot.SimAn : SAPplotpuntos: no visible global function definition for
  ‘text’
plot.SimAn: no visible global function definition for ‘dev.new’
plot.SimAn: no visible global function definition for ‘points’
plot.SimAn: no visible global function definition for ‘text’
plot.SimAn: no visible global function definition for ‘par’
plot.SimAn: no visible global function definition for ‘plot’
plot.SimAn: no visible global function definition for ‘title’
plot.SimAn: no visible global function definition for ‘axis’
plot.SimAn: no visible global function definition for ‘arrows’
Undefined global functions or variables:
  arrows axis dev.new mtext par plot points text title
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "arrows", "axis", "mtext", "par", "plot",
             "points", "text", "title")
to your NAMESPACE file.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   4.5Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.2Mb
installed size is 29.1Mb
  sub-directories of 1Mb or more:
    libs  27.7Mb
plot.sla: no visible global function definition for ‘title’
plot.sla: no visible global function definition for ‘abline’
print.sla: no visible global function definition for ‘coef’
sla.default: no visible global function definition for ‘lm’
sla.default: no visible global function definition for ‘anova’
Undefined global functions or variables:
  abline anova coef lm title
Consider adding
  importFrom("graphics", "abline", "title")
  importFrom("stats", "anova", "coef", "lm")
to your NAMESPACE file.
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.
'library' or 'require' calls in package code:
  ‘MASS’ ‘survival’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   7.6Mb
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:
  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’.
hsvScale: no visible global function definition for ‘hsv’
plotConcentric: no visible global function definition for ‘plot’
plotConcentric: no visible global function definition for ‘points’
plotConcentric: no visible global function definition for ‘legend’
plotPoints: no visible global function definition for ‘plot’
plotStress: no visible global function definition for ‘plot’
plotStress: no visible global function definition for ‘polygon’
plotStress: no visible global function definition for ‘points’
Undefined global functions or variables:
  hsv legend plot points polygon
Consider adding
  importFrom("grDevices", "hsv")
  importFrom("graphics", "legend", "plot", "points", "polygon")
to your NAMESPACE file.