flowField: no visible global function definition for 'plot'
flowField: no visible global function definition for 'arrows'
nullclines: no visible global function definition for 'contour'
numericalSolution: no visible global function definition for 'locator'
numericalSolution: no visible global function definition for 'plot'
numericalSolution: no visible global function definition for 'lines'
phasePortrait: no visible global function definition for 'plot'
phasePortrait: no visible global function definition for 'arrows'
stability: no visible global function definition for 'locator'
trajectory: no visible global function definition for 'locator'
trajectory: no visible global function definition for 'plot'
trajectory: no visible global function definition for 'lines'
trajectory: no visible global function definition for 'points'
Undefined global functions or variables:
  arrows contour lines locator plot points
Consider adding
  importFrom("graphics", "arrows", "contour", "lines", "locator", "plot",
             "points")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'ggplot2' 'reshape'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plot.phtMCMC: no visible global function definition for 'ggplot'
plot.phtMCMC: no visible global function definition for 'melt'
plot.phtMCMC: no visible global function definition for 'geom_line'
plot.phtMCMC: no visible global function definition for 'aes_string'
plot.phtMCMC: no visible global function definition for 'geom_smooth'
plot.phtMCMC: no visible global function definition for 'facet_wrap'
plot.phtMCMC: no visible global function definition for 'ggtitle'
plot.phtMCMC: no visible global function definition for 'xlab'
plot.phtMCMC: no visible global function definition for 'ylab'
plot.phtMCMC: no visible global function definition for 'geom_density'
Undefined global functions or variables:
  aes_string facet_wrap geom_density geom_line geom_smooth ggplot
  ggtitle melt xlab ylab
File 'PhaseType/libs/i386/PhaseType.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'LJMA_arms.o'
File 'PhaseType/libs/x64/PhaseType.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'LJMA_arms.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
deforestation: no visible global function definition for 'model.frame'
deforestation: no visible global function definition for 'model.matrix'
deforestation: no visible global function definition for
  'model.response'
deforestation: no visible global function definition for 'vcov'
deforestation: no visible global function definition for 'glm'
demography: no visible global function definition for 'model.frame'
demography: no visible global function definition for 'model.matrix'
demography: no visible global function definition for 'model.response'
form.beta.start: no visible global function definition for 'coef'
form.beta.start: no visible global function definition for 'glm'
form.sigma2.start: no visible global function definition for 'var'
form.sigma2.start: no visible global function definition for
  'residuals'
form.sigma2.start: no visible global function definition for 'glm'
rinvgamma: no visible global function definition for 'rgamma'
rwish: no visible global function definition for 'rchisq'
rwish: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  coef glm model.frame model.matrix model.response rchisq residuals
  rgamma rnorm var vcov
Consider adding
  importFrom("stats", "coef", "glm", "model.frame", "model.matrix",
             "model.response", "rchisq", "residuals", "rgamma", "rnorm",
             "var", "vcov")
to your NAMESPACE file.
Package has both 'src/Makevars.in' and 'src/Makevars'.
Installation with --no-configure' is unlikely to work.  If you intended
'src/Makevars' to be used on Windows, rename it to 'src/Makevars.win'
otherwise remove it.  If 'configure' created 'src/Makevars', you need a
'cleanup' script.
fox: no visible binding for global variable 'sd'
fox: no visible global function definition for 'cor'
fox: no visible global function definition for 'interaction.plot'
fox: no visible global function definition for 'reorder'
fox: no visible global function definition for 'plot'
kang: no visible global function definition for 'var'
kang: no visible binding for global variable 'sd'
kang: no visible global function definition for 'cor'
kang: no visible global function definition for 'interaction.plot'
kang: no visible global function definition for 'reorder'
kang: no visible global function definition for 'plot'
nahu: no visible global function definition for 'interaction.plot'
nahu: no visible global function definition for 'reorder'
nahu: no visible global function definition for 'plot'
thsu: no visible global function definition for 'median'
thsu: no visible binding for global variable 'sd'
thsu: no visible global function definition for 'cor'
thsu: no visible global function definition for 'interaction.plot'
thsu: no visible global function definition for 'reorder'
thsu: no visible global function definition for 'plot'
Undefined global functions or variables:
  cor interaction.plot median plot reorder sd var
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "cor", "interaction.plot", "median", "reorder",
             "sd", "var")
to your NAMESPACE file.
pheno.ddm: no visible global function definition for 'new'
pheno.flm.fit: no visible binding for global variable 'na.exclude'
pheno.flm.fit: no visible global function definition for 'terms'
pheno.flm.fit: no visible global function definition for 'residuals'
pheno.flm.fit: no visible global function definition for 'qt'
pheno.lad.fit: no visible binding for global variable 'na.exclude'
pheno.mlm.fit: no visible binding for global variable 'na.exclude'
pheno.mlm.fit: no visible global function definition for 'residuals'
Undefined global functions or variables:
  na.exclude new qt residuals terms
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "na.exclude", "qt", "residuals", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in 'phuse-Ex.R' failed
The error most likely occurred in:

> ### Name: cvt_list2df
> ### Title: Convert list to data frame
> ### Aliases: cvt_list2df
> 
> ### ** Examples
> 
>   a <- "https://github.com/phuse-org/phuse-scripts/raw/master"
>   b <- "development/R/scripts"
>   c <- "Draw_Dist2_R.yml"
>   f1 <- paste(a,b,c, sep = '/')
>   r1 <- read_yml(f1)
>   r2 <- cvt_list2df(r1)
Error in a[[k1]] : subscript out of bounds
Calls: cvt_list2df
Execution halted
Package in Depends field not imported from: 'raster'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following hidden files and directories:
  data/.Rhistory
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
plotData: no visible global function definition for 'plot'
plotData: no visible global function definition for 'abline'
plotData: no visible global function definition for 'text'
Undefined global functions or variables:
  abline plot text
Consider adding
  importFrom("graphics", "abline", "plot", "text")
to your NAMESPACE file.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/PhySortR.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
incident: no visible global function definition for 'splinefun'
incident: no visible global function definition for 'integrate'
phytoprod: no visible global function definition for 'approx'
phytoprod: no visible global function definition for 'splinefun'
phytoprod: no visible global function definition for 'integrate'
reflectance: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx integrate splinefun
Consider adding
  importFrom("stats", "approx", "integrate", "splinefun")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/picante.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
'library' or 'require' calls in package code:
  'brglm' 'quantreg'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
File which contains pragma(s) suppressing diagnostics:
  'src/pijavski.cpp'
plot.pred.int: no visible global function definition for 'plot.default'
plot.pred.int: no visible global function definition for 'axis'
plot.pred.int: no visible global function definition for 'box'
plot.pred.int : cidist: no visible global function definition for
  'ecdf'
plot.pred.int : negcidist: no visible global function definition for
  'ecdf'
plot.pred.int : pi.col.fun: no visible global function definition for
  'gray'
plot.pred.int: no visible global function definition for 'segments'
plot.pred.int: no visible global function definition for 'points'
plot.pred.int: no visible global function definition for 'abline'
pred.int: no visible binding for global variable 'sd'
prop.test.mult: no visible global function definition for 'qnorm'
sim.basic: no visible global function definition for 'rbinom'
sim.basic: no visible global function definition for 'rnorm'
t.test.mult: no visible global function definition for 'qt'
Undefined global functions or variables:
  abline axis box ecdf gray plot.default points qnorm qt rbinom rnorm
  sd segments
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "box", "plot.default",
             "points", "segments")
  importFrom("stats", "ecdf", "qnorm", "qt", "rbinom", "rnorm", "sd")
to your NAMESPACE file.
Package suggested but not available for checking: 'ggsubplot'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.4Mb
'library' or 'require' calls in package code:
  'argparse' 'devtools' 'knitr'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Depends: includes the non-default packages:
  'RGtk2' 'gWidgetsRGtk2' 'cairoDevice' 'lattice' 'rggobi' 'ggplot2'
  'proto'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'RGtk2' 'gWidgetsRGtk2'
A package should be listed in only one of these fields.
Package in Depends field not imported from: 'cairoDevice'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
PKmod: no visible global function definition for 'deriv'
Undefined global functions or variables:
  deriv
Consider adding
  importFrom("stats", "deriv")
to your NAMESPACE file.
PKadjust: no visible binding for global variable 'jpeg'
PKadjust: no visible binding for global variable 'bmp'
PKadjust: no visible binding for global variable 'png'
PKadjust: no visible binding for global variable 'tiff'
PKadjust: no visible binding for global variable 'dev.new'
PKadjust: no visible global function definition for 'dev.off'
PKfigure: no visible global function definition for 'dev.cur'
PKfigure: no visible global function definition for 'dev.off'
PKoutput: no visible global function definition for 'heatmap'
PKoutput: no visible global function definition for
  'packageDescription'
PKshow: no visible global function definition for 'browseURL'
addList1: no visible global function definition for 'formula'
addList1.old: no visible global function definition for 'formula'
addList2: no visible global function definition for 'formula'
generate.plot: no visible global function definition for 'dev.off'
writeHTML: no visible global function definition for
  'packageDescription'
writeLst: no visible global function definition for
  'packageDescription'
writeLst.tab: no visible global function definition for
  'packageDescription'
writeTable: no visible global function definition for
  'packageDescription'
writeTable: no visible global function definition for 'quantile'
initialize,nonmem: no visible global function definition for
  'read.table'
Undefined global functions or variables:
  bmp browseURL dev.cur dev.new dev.off formula heatmap jpeg
  packageDescription png quantile read.table tiff
Consider adding
  importFrom("grDevices", "bmp", "dev.cur", "dev.new", "dev.off", "jpeg",
             "png", "tiff")
  importFrom("stats", "formula", "heatmap", "quantile")
  importFrom("utils", "browseURL", "packageDescription", "read.table")
to your NAMESPACE file.
plot.burndown: no visible global function definition for 'par'
plot.burndown: no visible global function definition for 'hcl'
plot.burndown: no visible global function definition for 'plot'
plot.burndown: no visible global function definition for 'polygon'
plot.burndown: no visible global function definition for 'lm'
plot.burndown: no visible global function definition for 'abline'
plot.burndown: no visible global function definition for 'lines'
plot.burndown: no visible global function definition for 'points'
plot.burndown: no visible global function definition for 'legend'
plot.burndown: no visible global function definition for 'mtext'
plot.gantt: no visible global function definition for 'gray'
plot.gantt: no visible global function definition for 'par'
plot.gantt: no visible global function definition for 'strheight'
plot.gantt: no visible global function definition for 'strwidth'
plot.gantt: no visible global function definition for 'plot'
plot.gantt: no visible global function definition for 'box'
plot.gantt: no visible global function definition for 'mtext'
plot.gantt: no visible global function definition for 'axis.POSIXct'
plot.gantt: no visible global function definition for 'rug'
plot.gantt: no visible global function definition for 'abline'
plot.gantt: no visible global function definition for 'axis'
plot.gantt: no visible global function definition for 'lines'
plot.gantt: no visible global function definition for 'rect'
Undefined global functions or variables:
  abline axis axis.POSIXct box gray hcl legend lines lm mtext par plot
  points polygon rect rug strheight strwidth
Consider adding
  importFrom("grDevices", "gray", "hcl")
  importFrom("graphics", "abline", "axis", "axis.POSIXct", "box",
             "legend", "lines", "mtext", "par", "plot", "points",
             "polygon", "rect", "rug", "strheight", "strwidth")
  importFrom("stats", "lm")
to your NAMESPACE file.
Package suggested but not available for checking: 'latticist'
'library' or 'require' call to 'lattice' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to 'latticist' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'cairoDevice' 'gWidgetsRGtk2' 'grid' 'lattice'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  'lattice:::lattice.getStatus' 'stats:::biplot.prcomp'
  See the note in ?`:::` about the use of this operator.
S3 methods shown with full name in documentation object 'plotCoords':
  'plotCoords.plot' 'plotCoords.biplot'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
bwfw.hmm: no visible global function definition for 'dnorm'
bwfw1.hmm: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'R.oo' 'limma' 'splines'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fitBspline: no visible global function definition for 'median'
fitBspline: no visible global function definition for 'quantile'
fitGAPLM: no visible global function definition for 'poisson'
fitGAPLM: no visible global function definition for 'quantile'
fitGAPLM: no visible global function definition for 'anova'
fitGAPLM: no visible global function definition for 'as.formula'
fitGAPLM: no visible global function definition for 'glm'
fitGAPLM: no visible global function definition for 'pf'
fitGAPLM: no visible global function definition for 'lm'
fitGAPLM: no visible global function definition for 'p.adjust'
head.DEresults: no visible global function definition for 'head'
head.plmDE: no visible global function definition for 'head'
hist.DEresults: no visible global function definition for 'hist'
hist.DEresults: no visible global function definition for 'colors'
hist.DEresults: no visible global function definition for 'box'
limmaPLM: no visible global function definition for 'quantile'
plot.DEresults: no visible global function definition for 'as.formula'
plot.DEresults: no visible global function definition for 'lm'
plot.DEresults: no visible global function definition for 'glm'
plot.DEresults: no visible global function definition for 'plot'
plot.DEresults: no visible global function definition for 'lines'
plot.DEresults: no visible global function definition for 'points'
plot.DEresults: no visible global function definition for 'predict'
Undefined global functions or variables:
  anova as.formula box colors glm head hist lines lm median p.adjust pf
  plot points poisson predict quantile
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "box", "hist", "lines", "plot", "points")
  importFrom("stats", "anova", "as.formula", "glm", "lm", "median",
             "p.adjust", "pf", "poisson", "predict", "quantile")
  importFrom("utils", "head")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'Formula' 'sm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
nrmlepln: no visible global function definition for 'pchisq'
nrmlerasch: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
Found the following significant warnings:
  cat_pair.c:64:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  cat_pair.c:79:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/PLordprob.Rcheck/00install.out' for details.
Running examples in 'plotKML-Ex.R' failed
The error most likely occurred in:

> ### Name: plotKML-method
> ### Title: Methods for plotting results of spatial analysis in Google Earth
> ### Aliases: plotKML-method plotKML plotKML,SpatialPointsDataFrame-method
> ###   plotKML,SpatialLinesDataFrame-method
> ###   plotKML,SpatialPolygonsDataFrame-method
> ###   plotKML,SoilProfileCollection-method
> ###   plotKML,SpatialGridDataFrame-method
> ###   plotKML,SpatialPixelsDataFrame-method plotKML,RasterLayer-method
> ###   plotKML,SpatialPhotoOverlay-method plotKML,STIDF-method
> ###   plotKML,STFDF-method plotKML,STSDF-method plotKML,STTDF-method
> ###   plotKML,SpatialPredictions-method
> ###   plotKML,RasterBrickSimulations-method
> ###   plotKML,SpatialVectorsSimulations-method
> ###   plotKML,SpatialMaxEntOutput-method
> ###   plotKML,RasterBrickTimeSeries-method
> ###   plotKML,SpatialSamplingPattern-method plotKML,list-method
> ### Keywords: spatial methods
> 
> ### ** Examples
> 
> plotKML.env(silent = FALSE, kmz = FALSE)
Search for SAGA command line program and modules... 
SAGA command line program not found in the following default paths:
C:/Progra~1/SAGA-GIS
C:/SAGA-GIS
C:/OSGeo4W64/apps/saga
C:/OSGeo4W64/apps/saga-ltr
Search on the entire hard drive...
Error in paths(show.paths = TRUE) : object 'saga.version' not found
Calls: plotKML.env -> paths
Execution halted
Error in re-building vignettes:
  ...
Loading required package: gstat
Loading required package: raster
Loading required package: sp
Loading required package: plotKML
plotKML version 0.5-8 (2017-05-12)
URL: http://plotkml.r-forge.r-project.org/
Loading required package: GSIF
GSIF version 0.5-4 (2017-04-25)
URL: http://gsif.r-forge.r-project.org/

Attaching package: 'XML'

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

    toHTML

Reprojecting to +proj=longlat +datum=WGS84 ...
KML file opened for writing...
Writing to KML...
Closing  eberg.ll__CLYMHT_A__.kml
KML file opened for writing...
Writing to KML...
Closing  eberg.ll.kml
KML file opened for writing...
Reprojecting to +proj=longlat +datum=WGS84 ...

Error: processing vignette 'jss1079.Rnw' failed with diagnostics:
 chunk 12 
Error in paths(show.paths = TRUE) : object 'saga.version' not found
Execution halted
plotAuto: no visible global function definition for 'window'
plotAuto: no visible global function definition for 'title'
plotAuto: no visible global function definition for 'axis'
plotAuto: no visible global function definition for 'box'
plotCumu: no visible global function definition for 'title'
plotCumu: no visible global function definition for 'axis'
plotCumu: no visible global function definition for 'box'
plotDens : panel.dens: no visible global function definition for 'var'
plotDens : panel.dens: no visible global function definition for
  'quantile'
plotDens : panel.dens: no visible global function definition for
  'median'
plotDens: no visible global function definition for 'tail'
plotQuant: no visible global function definition for 'par'
plotQuant: no visible binding for global variable 'quantile'
plotQuant: no visible global function definition for 'plot'
plotQuant: no visible global function definition for 'lines'
plotQuant: no visible global function definition for 'bxp'
plotQuant: no visible global function definition for 'matplot'
plotQuant: no visible global function definition for 'axis'
plotQuant: no visible global function definition for 'box'
plotQuant: no visible global function definition for 'title'
plotSplom: no visible global function definition for 'pairs'
plotTrace : panel.trace: no visible global function definition for
  'var'
plotTrace : panel.trace: no visible global function definition for
  'median'
plotTrace: no visible global function definition for 'tail'
Undefined global functions or variables:
  axis box bxp lines matplot median pairs par plot quantile tail title
  var window
Consider adding
  importFrom("graphics", "axis", "box", "bxp", "lines", "matplot",
             "pairs", "par", "plot", "title")
  importFrom("stats", "median", "quantile", "var", "window")
  importFrom("utils", "tail")
to your NAMESPACE file.
generateEnvelope: no visible global function definition for 'tail'
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
llla.bi: no visible global function definition for 'as.formula'
llla.bi: no visible global function definition for 'glm'
llla.bi: no visible global function definition for 'binomial'
llla.bi: no visible binding for global variable 'logit'
llla.bi: no visible global function definition for 'vcov'
llla.bi: no visible global function definition for 'coef'
llla.mc: no visible global function definition for 'model.matrix'
llla.mc: no visible global function definition for 'as.formula'
llla.mc: no visible global function definition for 'coxph'
llla.mc: no visible global function definition for 'vcov'
llla.mc: no visible global function definition for 'coef'
llla.mle: no visible global function definition for 'as.formula'
llla.mle: no visible global function definition for 'glm'
llla.mle: no visible global function definition for 'poisson'
llla.mle: no visible global function definition for 'coef'
llla.mle: no visible global function definition for 'vcov'
mclgen: no visible global function definition for 'reshape'
simRasch.1D: no visible global function definition for 'rnorm'
simRasch.1D: no visible global function definition for 'runif'
vcov.sandwich.glm: no visible global function definition for
  'model.matrix'
vcov.sandwich.glm: no visible global function definition for 'weights'
vcov.sandwich.glm: no visible global function definition for
  'residuals'
vcov.sandwich.glm: no visible global function definition for 'vcov'
Undefined global functions or variables:
  as.formula binomial coef coxph glm logit model.matrix poisson reshape
  residuals rnorm runif vcov weights
Consider adding
  importFrom("stats", "as.formula", "binomial", "coef", "glm",
             "model.matrix", "poisson", "reshape", "residuals", "rnorm",
             "runif", "vcov", "weights")
to your NAMESPACE file.
compute.lower.bound: no visible global function definition for 'cor'
kernel.pls.fit: no visible binding for global variable 'sd'
linear.pls.fit: no visible binding for global variable 'sd'
pcr: no visible binding for global variable 'sd'
pcr: no visible global function definition for 'cor'
pcr.cv: no visible global function definition for 'cor'
pcr.cv: no visible global function definition for 'plot'
pls.model: no visible binding for global variable 'sd'
ridge.cv: no visible global function definition for 'coef'
ridge.cv: no visible global function definition for 'cor'
ridge.cv: no visible global function definition for 'plot'
Undefined global functions or variables:
  coef cor plot sd
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "coef", "cor", "sd")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/plsRglm.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
'library' or 'require' calls in package code:
  'MASS' 'plsdof'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
print.densityEHpi: no visible global function definition for 'str'
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'rbind.fill':
  'rbind.fill'

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

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:
  Groups.cc:322:46: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/PMA.Rcheck/00install.out' for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   1.6Mb
Packages in Depends field not imported from:
  'impute' 'plyr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.MCM: no visible global function definition for 'runif'
.MCM: no visible global function definition for 'rmultinom'
.MCM: no visible global function definition for 'mahalanobis'
.MCM: no visible global function definition for 'optimize'
.MCM : f: no visible global function definition for 'mahalanobis'
.MCM: no visible global function definition for 'alarm'
.igpark: no visible global function definition for 'kmeans'
.loglik: no visible global function definition for 'mahalanobis'
.plot.gpcm: no visible global function definition for 'plot'
.plot.gpcm: no visible global function definition for 'lines'
.plot.gpcm: no visible global function definition for 'legend'
.rwgpar: no visible global function definition for 'rexp'
.weights: no visible global function definition for 'mahalanobis'
Undefined global functions or variables:
  alarm kmeans legend lines mahalanobis optimize plot rexp rmultinom
  runif
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "kmeans", "mahalanobis", "optimize", "rexp",
             "rmultinom", "runif")
  importFrom("utils", "alarm")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/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.
dbm: no visible global function definition for 'optim'
dbm: no visible global function definition for 'new'
destat: no visible global function definition for 'weighted.mean'
local.knn: no visible global function definition for 'sd'
local.knn: no visible global function definition for 'optim'
mdpref: no visible global function definition for 'sd'
mdpref: no visible global function definition for 'text'
mdpref: no visible global function definition for 'lines'
phicom: no visible global function definition for 'optim'
phicom: no visible global function definition for 'new'
pl: no visible global function definition for 'optim'
pl: no visible global function definition for 'new'
rol: no visible global function definition for 'nlm'
rol: no visible global function definition for 'new'
wdbm: no visible global function definition for 'optim'
wdbm: no visible global function definition for 'new'
Undefined global functions or variables:
  lines new nlm optim sd text weighted.mean
Consider adding
  importFrom("graphics", "lines", "text")
  importFrom("methods", "new")
  importFrom("stats", "nlm", "optim", "sd", "weighted.mean")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' call to 'MASS' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'MASS'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
pnmtrem1: no visible global function definition for 'pnorm'
pnmtrem1: no visible global function definition for 'dnorm'
pnmtrem1: no visible global function definition for 'ginv'
pnmtrem1 : fun: no visible global function definition for 'pnorm'
pnmtrem1 : derf: no visible global function definition for 'dnorm'
pnmtrem1 : derf: no visible global function definition for 'pnorm'
pnmtrem1 : fun: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm ginv pnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm")
to your NAMESPACE file.
'library' or 'require' call to 'rgenoud' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.sigma: no visible global function definition for 'plot'
smooth: no visible global function definition for 'genoud'
Undefined global functions or variables:
  genoud plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
ppoibin: no visible global function definition for 'pnorm'
ppoibin: no visible global function definition for 'dnorm'
rpoibin: no visible global function definition for 'runif'
Undefined global functions or variables:
  dnorm pnorm runif
Consider adding
  importFrom("stats", "dnorm", "pnorm", "runif")
to your NAMESPACE file.
ColorDendrogram: no visible global function definition for 'plot'
ColorDendrogram: no visible global function definition for 'segments'
CountDataSet: no visible global function definition for 'rexp'
CountDataSet: no visible global function definition for 'runif'
CountDataSet: no visible global function definition for 'rnorm'
CountDataSet: no visible global function definition for 'rnbinom'
NullModel: no visible binding for global variable 'quantile'
NullModel : <anonymous>: no visible global function definition for
  'median'
NullModelTest: no visible binding for global variable 'quantile'
NullModelTest : <anonymous>: no visible global function definition for
  'median'
PoissonDistance: no visible global function definition for 'as.dist'
permute.rows: no visible global function definition for 'runif'
print.poiclacv: no visible global function definition for 'write.table'
se: no visible global function definition for 'sd'
Undefined global functions or variables:
  as.dist median plot quantile rexp rnbinom rnorm runif sd segments
  write.table
Consider adding
  importFrom("graphics", "plot", "segments")
  importFrom("stats", "as.dist", "median", "quantile", "rexp", "rnbinom",
             "rnorm", "runif", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
bipoilogMLE: no visible global function definition for 'optim'
bipoilogMLE: no visible global function definition for 'write.table'
poilogMLE: no visible global function definition for 'optim'
rbipoilog : sim: no visible global function definition for 'rnorm'
rbipoilog : sim: no visible global function definition for 'rpois'
rpoilog : sim: no visible global function definition for 'rnorm'
rpoilog : sim: no visible global function definition for 'rpois'
Undefined global functions or variables:
  optim rnorm rpois write.table
Consider adding
  importFrom("stats", "optim", "rnorm", "rpois")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Running examples in 'pointblank-Ex.R' failed
The error most likely occurred in:

> ### Name: col_exists
> ### Title: Verify that one or more columns exist
> ### Aliases: col_exists
> 
> ### ** Examples
> 
> # Validate that column `a` exists in
> # the `small_table` CSV file; do this
> # by creating an agent, focussing on
> # that table, creating a `col_exists()`
> # step, and then interrogating the table
> agent <-
+   create_agent() %>%
+   focus_on(
+     file_name = 
+       system.file(
+         "extdata", "small_table.csv",
+         package = "pointblank"),
+     col_types = "TDicidlc") %>%
+   col_exists(column = a) %>%
+   interrogate()
Error: `UQ()` can only be used within a quasiquoted argument
Execution halted
approxMargMLE: no visible global function definition for 'optim'
approxMargMLECI : ciFunction: no visible global function definition for
  'qchisq'
approxMargMLECI: no visible global function definition for 'uniroot'
margMLE: no visible global function definition for 'optim'
margMLECI: no visible global function definition for 'optim'
margMLECI : unNormLikeMinusVal: no visible global function definition
  for 'qchisq'
margMLECI: no visible global function definition for 'uniroot'
profMLECI : ciFunction: no visible global function definition for
  'qchisq'
profMLECI: no visible global function definition for 'uniroot'
rtbinom: no visible global function definition for 'rbinom'
rtpois: no visible global function definition for 'rpois'
waldCI: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  optim qchisq qnorm rbinom rpois uniroot
Consider adding
  importFrom("stats", "optim", "qchisq", "qnorm", "rbinom", "rpois",
             "uniroot")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'combinat' 'splines'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Est.Depth: no visible global function definition for 'quantile'
PS.FDR: no visible global function definition for 'quantile'
Permu.Ind: no visible global function definition for 'permn'
Permu.Ind: no visible global function definition for 'hcube'
Trans.Data: no visible global function definition for 'write.table'
Trans.Data: no visible global function definition for 'predict'
Trans.Data: no visible global function definition for 'lm'
Undefined global functions or variables:
  hcube lm permn predict quantile write.table
Consider adding
  importFrom("stats", "lm", "predict", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
rpoistweedie: no visible global function definition for 'runif'
testOmegaPT: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'MASS' 'scatterplot3d'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plot.poLCA: no visible global function definition for 'layout'
plot.poLCA: no visible global function definition for 'par'
poLCA: no visible global function definition for 'model.frame'
poLCA: no visible global function definition for 'model.response'
poLCA: no visible global function definition for 'model.matrix'
poLCA: no visible global function definition for 'runif'
poLCA: no visible global function definition for 'ginv'
poLCA: no visible global function definition for 'flush.console'
poLCA.makeplot.dich: no visible global function definition for
  'scatterplot3d'
poLCA.makeplot.poly: no visible global function definition for
  'scatterplot3d'
poLCA.se: no visible global function definition for 'ginv'
poLCA.simdata: no visible global function definition for 'runif'
poLCA.simdata: no visible global function definition for 'rnorm'
poLCA.table: no visible global function definition for 'model.frame'
print.poLCA: no visible global function definition for 'pt'
print.poLCA: no visible global function definition for 'flush.console'
rmulti: no visible global function definition for 'runif'
Undefined global functions or variables:
  flush.console ginv layout model.frame model.matrix model.response par
  pt rnorm runif scatterplot3d
Consider adding
  importFrom("graphics", "layout", "par")
  importFrom("stats", "model.frame", "model.matrix", "model.response",
             "pt", "rnorm", "runif")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'polmineR.Rcpp' 'europarl.en' 'rcqp'
qPolyaAeppliSingle: no visible global function definition for 'qgamma'
rPolyaAeppli: no visible global function definition for 'rpois'
rPolyaAeppli: no visible global function definition for 'rgeom'
Undefined global functions or variables:
  qgamma rgeom rpois
Consider adding
  importFrom("stats", "qgamma", "rgeom", "rpois")
to your NAMESPACE file.
Running examples in 'polywog-Ex.R' failed
The error most likely occurred in:

> ### Name: bootPolywog
> ### Title: Bootstrap a fitted polywog model
> ### Aliases: bootPolywog control.bp
> 
> ### ** Examples
> 
> ## Using occupational prestige data
> data(Prestige, package = "car")
Warning in data(Prestige, package = "car") :
  data set 'Prestige' not found
> Prestige <- transform(Prestige, income = income / 1000)
Error in transform(Prestige, income = income/1000) : 
  object 'Prestige' not found
Execution halted
'library' or 'require' call to 'matrixcalc' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'matrixcalc'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
print.mixed.pom: no visible global function definition for 'pnorm'
print.pom: no visible global function definition for 'pnorm'
siteocc : get.mod.matrix: no visible binding for global variable
  'na.pass'
siteocc : get.mod.matrix: no visible global function definition for
  'formula'
siteocc : get.mod.matrix: no visible global function definition for
  'model.matrix'
siteocc: no visible global function definition for 'nlminb'
siteocc: no visible global function definition for
  'is.positive.definite'
Undefined global functions or variables:
  formula is.positive.definite model.matrix na.pass nlminb pnorm
Consider adding
  importFrom("stats", "formula", "model.matrix", "na.pass", "nlminb",
             "pnorm")
to your NAMESPACE file.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/PopGenome.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
asymmetricIntervals: no visible global function definition for 'stack'
bonferroniIntervals: no visible global function definition for 'stack'
bonferroniIntervals: no visible global function definition for 'lm'
bonferroniIntervals: no visible global function definition for
  'predict'
bootstrapIntervals: no visible global function definition for 'stack'
component1a: no visible global function definition for 'pnorm'
component1b: no visible global function definition for 'pnorm'
component2: no visible global function definition for 'dgamma'
eqnForMin: no visible global function definition for 'pnorm'
eqnForMin: no visible global function definition for 'integrate'
integrand : <anonymous>: no visible global function definition for
  'pnorm'
integrand: no visible global function definition for 'dnorm'
integrate2: no visible global function definition for 'integrate'
integrate2a: no visible global function definition for 'integrate'
integrate2b: no visible global function definition for 'integrate'
integrate4a: no visible global function definition for 'integrate'
integrate4b: no visible global function definition for 'integrate'
optimalCScalar2: no visible global function definition for 'uniroot'
optimalLambda: no visible global function definition for 'optimise'
optimalLambdaC: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dgamma dnorm integrate lm optimise pnorm predict stack uniroot
Consider adding
  importFrom("stats", "dgamma", "dnorm", "integrate", "lm", "optimise",
             "pnorm", "predict", "uniroot")
  importFrom("utils", "stack")
to your NAMESPACE file.
popRangeSim: no visible global function definition for 'write.table'
Undefined global functions or variables:
  write.table
Consider adding
  importFrom("utils", "write.table")
to your NAMESPACE file.
Running examples in 'popRange-Ex.R' failed
The error most likely occurred in:

> ### Name: popRangeSim
> ### Title: popRangeSim
> ### Aliases: popRangeSim
> 
> ### ** Examples
>  
> ## Example: In this scenario, we are simulating a 3x3 grid of populations for 50 
> ## generations. Each population starts with 100 diploid individuals. Each individual 
> ## has a 0.01 probability of migrating away from their populations. There are 100 
> ## SNPs that all have a starting frequency of 0.5, and the program outputs the standard 
> ## "results" file, as well as a PLINK file. 
> 
> ## Commands
> 
> mat = matrix(1,nrow=3,ncol=3) 
> popRangeSim(world = mat, popSize = 100, diploid = TRUE, nGens = 50,
+               mig = 0.01, SNP_model = 0, nSNPs = 100, SNPs_starting_freq = 0.5, 
+               outfile= "outFile1", PLINK=TRUE)
Error in loadNamespace(name) : there is no package called 'reticulate'
[1] "Could not find an acceptable version of python with numpy installed. This should be able to locate python \n      anywhere on your computer, but perhaps try adding python to your PATH if you think this message is an error."
Error in popRangeSim(world = mat, popSize = 100, diploid = TRUE, nGens = 50,  : 
  
Execution halted
estMod.rinvGamma.mar29: no visible global function definition for
  'rgamma'
life.expectancy.stationary: no visible global function definition for
  'head'
life.expectancy.stationary: no visible global function definition for
  'tail'
log.lhood.mar29: no visible global function definition for 'dnorm'
log.post.mar29: no visible global function definition for 'dnorm'
popRecon.sampler: no visible global function definition for 'rnorm'
popRecon.sampler: no visible global function definition for 'runif'
Undefined global functions or variables:
  dnorm head rgamma rnorm runif tail
Consider adding
  importFrom("stats", "dnorm", "rgamma", "rnorm", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Missing or unexported object: 'forecast::simulate.Arima'
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/PortfolioAnalytics.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
'library' or 'require' call to 'methods' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'lattice' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File 'portfolioSim/R/AllClasses.R':
  .onLoad calls:
    require(methods)

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

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

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

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/powerCompRisk.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
fnfam: no visible global function definition for 'qnorm'
fx: no visible global function definition for 'qnorm'
normplot : <local> : replot: no visible global function definition for
  'qnorm'
normplot : <local> : replot: no visible global function definition for
  'pnorm'
normplot : <local> : replot: no visible global function definition for
  'plot'
normplot : <local> : replot: no visible global function definition for
  'dnorm'
normplot : <local> : replot: no visible global function definition for
  'points'
normplot : <local> : replot: no visible global function definition for
  'lines'
normplot : <local> : regen: no visible global function definition for
  'rnorm'
normplot : <local> : regen: no visible global function definition for
  'rexp'
nsibs: no visible global function definition for 'qnorm'
ntdt: no visible global function definition for 'uniroot'
plotDom: no visible global function definition for 'plot'
plotNsibs: no visible global function definition for 'plot'
plotNtdt: no visible global function definition for 'plot'
plotNtdt: no visible global function definition for 'lines'
plotNtdt: no visible global function definition for 'legend'
ptdt: no visible global function definition for 'optimize'
ptdt: no visible global function definition for 'uniroot'
ptdt: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dnorm legend lines optimize plot pnorm points qnorm rexp rnorm
  uniroot
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points")
  importFrom("stats", "dnorm", "optimize", "pnorm", "qnorm", "rexp",
             "rnorm", "uniroot")
to your NAMESPACE file.
graphic.ppls.splines: no visible global function definition for 'par'
graphic.ppls.splines: no visible global function definition for 'plot'
graphic.ppls.splines: no visible global function definition for 'lines'
jack.ppls: no visible global function definition for 'cov'
penalized.pls: no visible binding for global variable 'var'
penalized.pls.default: no visible global function definition for 'var'
penalized.pls.kernel: no visible global function definition for 'var'
penalized.pls.select: no visible global function definition for 'var'
sim.data.ppls: no visible global function definition for 'runif'
sim.data.ppls: no visible global function definition for 'var'
sim.data.ppls: no visible global function definition for 'rnorm'
ttest.ppls: no visible global function definition for 'coef'
ttest.ppls: no visible global function definition for 'vcov'
ttest.ppls: no visible global function definition for 'pt'
Undefined global functions or variables:
  coef cov lines par plot pt rnorm runif var vcov
Consider adding
  importFrom("graphics", "lines", "par", "plot")
  importFrom("stats", "coef", "cov", "pt", "rnorm", "runif", "var",
             "vcov")
to your NAMESPACE file.
pps1: no visible global function definition for 'runif'
ppss: no visible global function definition for 'runif'
ppswr: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
LDA.Tree : Find.proj: no visible binding for global variable 'var'
LDA.Tree : Find.proj: no visible binding for global variable 'IQR'
LDA.Tree : Find.proj: no visible binding for global variable 'median'
PDA.Tree : Find.proj: no visible binding for global variable 'var'
PDA.Tree : Find.proj: no visible binding for global variable 'median'
PDA.Tree : Find.proj: no visible binding for global variable 'IQR'
PP.Tree : Find.proj: no visible binding for global variable 'var'
PP.Tree : Find.proj: no visible binding for global variable 'median'
PP.Tree : Find.proj: no visible binding for global variable 'IQR'
PP.optimize.Huber: no visible binding for global variable 'sd'
PP.optimize.anneal: no visible binding for global variable 'sd'
PP.optimize.plot: no visible binding for global variable 'sd'
PP.optimize.plot: no visible global function definition for 'hist'
PP.optimize.plot: no visible global function definition for 'text'
PP.optimize.plot: no visible global function definition for 'par'
PP.optimize.plot: no visible global function definition for 'plot'
PP.optimize.plot: no visible global function definition for 'colors'
PP.optimize.plot: no visible global function definition for 'pairs'
PP.optimize.random: no visible binding for global variable 'sd'
Undefined global functions or variables:
  IQR colors hist median pairs par plot sd text var
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "hist", "pairs", "par", "plot", "text")
  importFrom("stats", "IQR", "median", "sd", "var")
to your NAMESPACE file.
prais.winsten: no visible global function definition for 'model.frame'
prais.winsten: no visible global function definition for 'as.formula'
prais.winsten: no visible global function definition for 'tail'
Undefined global functions or variables:
  as.formula model.frame tail
Consider adding
  importFrom("stats", "as.formula", "model.frame")
  importFrom("utils", "tail")
to your NAMESPACE file.
TT.test : <anonymous>: no visible global function definition for
  't.test'
TT.test: no visible binding for global variable 'sd'
TT.test: no visible global function definition for 'setNames'
kirjelda : combo: no visible binding for global variable 'sd'
kor.tabel: no visible binding for global variable 'cor.test'
Undefined global functions or variables:
  cor.test sd setNames t.test
Consider adding
  importFrom("stats", "cor.test", "sd", "setNames", "t.test")
to your NAMESPACE file.
gausspred: no visible global function definition for 'qt'
mvapred: no visible global function definition for 'qt'
Undefined global functions or variables:
  qt
Consider adding
  importFrom("stats", "qt")
to your NAMESPACE file.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'predmixcor/R/firstlib.r':
  .First.lib calls:
    cat("predmixcor loaded\n", "COPY RIGHT: Longhai Li\n", "http://math.usask.ca/~longhai\n",     "Type ?begin.predmixcor for help\n", sep = "")

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

Predict.mix: no visible global function definition for 'dbinom'
abs_cor: no visible global function definition for 'cor'
gen.alpha.IGamma: no visible global function definition for 'qgamma'
gendata.mix: no visible global function definition for 'runif'
gendata.mix: no visible global function definition for 'rbeta'
mh1.unif: no visible global function definition for 'runif'
train_predict_mix: no visible global function definition for 'dbinom'
training: no visible global function definition for 'runif'
training: no visible global function definition for 'dbinom'
Undefined global functions or variables:
  cor dbinom qgamma rbeta runif
Consider adding
  importFrom("stats", "cor", "dbinom", "qgamma", "rbeta", "runif")
to your NAMESPACE file.
Found the following hidden files and directories:
  data/.Rapp.history
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
'library' or 'require' call to 'deSolve' which was already attached by Depends.
  Please remove these calls from your code.
LVCompGames: no visible global function definition for 'runif'
LVCompGames: no visible global function definition for 'plot'
LVCompGames: no visible global function definition for 'axis'
LVCompGames: no visible global function definition for 'box'
LVCompGames: no visible global function definition for 'lines'
LVCompGames: no visible global function definition for 'points'
MetaSim: no visible global function definition for 'runif'
chesson: no visible global function definition for 'rbeta'
chesson: no visible global function definition for 'dbeta'
chesson : rhof: no visible global function definition for 'dbeta'
chesson: no visible global function definition for 'integrate'
pimmlawton: no visible global function definition for 'runif'
Undefined global functions or variables:
  axis box dbeta integrate lines plot points rbeta runif
Consider adding
  importFrom("graphics", "axis", "box", "lines", "plot", "points")
  importFrom("stats", "dbeta", "integrate", "rbeta", "runif")
to your NAMESPACE file.
bias.correct.curve: no visible global function definition for 'approx'
lines.principal.curve: no visible global function definition for
  'lines'
periodic.lowess: no visible global function definition for 'lowess'
periodic.lowess: no visible global function definition for 'approx'
plot.principal.curve: no visible global function definition for 'plot'
points.principal.curve: no visible global function definition for
  'points'
principal.curve : <anonymous>: no visible global function definition
  for 'lowess'
principal.curve : <anonymous>: no visible global function definition
  for 'smooth.spline'
principal.curve : <anonymous>: no visible global function definition
  for 'predict'
principal.curve: no visible global function definition for 'var'
principal.curve: no visible global function definition for 'plot'
principal.curve: no visible global function definition for 'lines'
Undefined global functions or variables:
  approx lines lowess plot points predict smooth.spline var
Consider adding
  importFrom("graphics", "lines", "plot", "points")
  importFrom("stats", "approx", "lowess", "predict", "smooth.spline",
             "var")
to your NAMESPACE file.
basisplot: no visible global function definition for 'plot'
basisplot: no visible global function definition for 'abline'
basisplot: no visible global function definition for 'text'
basisplot: no visible global function definition for 'par'
plot.prinsimp: no visible global function definition for 'screeplot'
plot.simpart: no visible global function definition for 'par'
position_text: no visible global function definition for 'par'
position_text: no visible global function definition for 'strwidth'
simpart.formula: no visible global function definition for 'terms'
simpart.formula: no visible global function definition for
  'model.matrix'
varperc: no visible global function definition for 'plot'
varperc: no visible global function definition for 'lines'
varperc: no visible global function definition for 'text'
varsimp: no visible global function definition for 'plot'
varsimp: no visible global function definition for 'points'
varsimp: no visible global function definition for 'text'
varsimp: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline lines model.matrix par plot points screeplot strwidth terms
  text
Consider adding
  importFrom("graphics", "abline", "lines", "par", "plot", "points",
             "strwidth", "text")
  importFrom("stats", "model.matrix", "screeplot", "terms")
to your NAMESPACE file.
Package suggested but not available for checking: 'gurobi'
pr.conditional: no visible global function definition for 'qnorm'
pr.marginal: no visible global function definition for 'qnorm'
prLogisticDelta: no visible global function definition for 'glm'
prLogisticDelta: no visible binding for global variable 'binomial'
Undefined global functions or variables:
  binomial glm qnorm
Consider adding
  importFrom("stats", "binomial", "glm", "qnorm")
to your NAMESPACE file.
.pfda.fstep: no visible global function definition for 'dist'
.pfda.main: no visible global function definition for 'plot'
.pfda.mstep: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov dist plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "cov", "dist")
to your NAMESPACE file.
File 'processx/libs/i386/processx.dll':
  Found non-API call to R: 'R_new_custom_connection'
File 'processx/libs/x64/processx.dll':
  Found non-API call to R: 'R_new_custom_connection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
GPois: no visible global function definition for 'dnorm'
GPois: no visible binding for global variable 'poisson'
GPois: no visible global function definition for 'predict'
GPois: no visible global function definition for 'fitted'
GPois: no visible global function definition for 'residuals'
GPois: no visible global function definition for 'smooth.spline'
ProDenICA: no visible global function definition for 'rnorm'
d.gaussmix: no visible global function definition for 'dnorm'
djordan: no visible global function definition for 'dt'
djordan: no visible global function definition for 'dunif'
mixmat: no visible global function definition for 'rnorm'
mixmat: no visible global function definition for 'runif'
plot.ProDenICA: no visible global function definition for 'plot'
r.gaussmix: no visible global function definition for 'rmultinom'
r.gaussmix: no visible global function definition for 'rnorm'
rjordan: no visible global function definition for 'rt'
rjordan: no visible global function definition for 'runif'
rmix.dexp: no visible global function definition for 'runif'
Undefined global functions or variables:
  dnorm dt dunif fitted plot poisson predict residuals rmultinom rnorm
  rt runif smooth.spline
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dnorm", "dt", "dunif", "fitted", "poisson",
             "predict", "residuals", "rmultinom", "rnorm", "rt", "runif",
             "smooth.spline")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/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
profBinary: no visible global function definition for 'model.frame'
profBinary: no visible global function definition for 'model.matrix'
profLinear: no visible global function definition for 'model.frame'
profLinear: no visible global function definition for 'model.matrix'
profLinear: no visible global function definition for 'model.response'
profLinear: no visible global function definition for 'model.extract'
summary.profBinary: no visible global function definition for 'terms'
summary.profBinary: no visible global function definition for 'qbeta'
summary.profLinear: no visible global function definition for 'terms'
Undefined global functions or variables:
  model.extract model.frame model.matrix model.response qbeta terms
Consider adding
  importFrom("stats", "model.extract", "model.frame", "model.matrix",
             "model.response", "qbeta", "terms")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/profileR.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   6.4Mb
    libs      1.7Mb
.simplify : <anonymous>: no visible binding for global variable 'hist'
.simplify : <anonymous>: no visible binding for global variable 'start'
.simplify: no visible binding for global variable 'start'
.simplify: no visible binding for global variable 'end'
ggplot.profr: no visible global function definition for 'ggplot'
ggplot.profr: no visible global function definition for 'geom_rect'
ggplot.profr: no visible global function definition for 'aes'
ggplot.profr: no visible binding for global variable 'start'
ggplot.profr: no visible binding for global variable 'end'
ggplot.profr: no visible global function definition for 'geom_text'
ggplot.profr: no visible binding for global variable 'time'
ggplot.profr: no visible global function definition for
  'scale_y_continuous'
ggplot.profr: no visible global function definition for
  'scale_x_continuous'
plot.profr: no visible global function definition for 'plot'
plot.profr: no visible global function definition for 'rect'
plot.profr: no visible binding for global variable 'time'
plot.profr: no visible global function definition for 'text'
profr: no visible global function definition for 'Rprof'
Undefined global functions or variables:
  Rprof aes end geom_rect geom_text ggplot hist plot rect
  scale_x_continuous scale_y_continuous start text time
Consider adding
  importFrom("graphics", "hist", "plot", "rect", "text")
  importFrom("stats", "end", "start", "time")
  importFrom("utils", "Rprof")
to your NAMESPACE file.
Package suggested but not available for checking: 'qtbase'
Packages in Depends field not imported from:
  'splines' 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
IndividualPROC: no visible global function definition for 'survfit'
IndividualPROC: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile survfit
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
Running 'run-all.R' [29s]
Running the tests in 'tests/run-all.R' failed.
Complete output:
  > library(testthat)
  > 
  > test_check("ProjectTemplate")
  Loading required package: ProjectTemplate
  Read 1 item
  v | OK F W S | Context
  
  - |  1       | 0
  == Results =====================================================================
  Duration: 0.1 s
  
  OK:       1
  Failed:   0
  Warnings: 0
  Skipped:  0
  v | OK F W S | Context
  
  - |  1       | 0
  == Results =====================================================================
  OK:       1
  Failed:   0
  Warnings: 0
  Skipped:  0
  -- 1. Failure: ignored data files are not loaded (@test-load.R#183)  -----------
  `load.project(override.config = list(data_ignore = ""))` threw an error with unexpected message.
  Expected match: "file is encrypted or is not a database"
  Actual message: "file is not a database"
  
  WARNING: Perl module Compress::Raw::Zlib cannot be loaded.
  WARNING: Perl module Spreadsheet::ParseXLSX cannot be loaded.
  WARNING: Microsoft Excel 2007 'XLSX' formatted files will not be processed.
  == testthat results  ===========================================================
  OK: 636 SKIPPED: 4 FAILED: 1
  1. Failure: ignored data files are not loaded (@test-load.R#183) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Found the following significant warnings:
  backend.cpp:207:12: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
  backend.cpp:210:14: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  backend.cpp:239:13: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/propr.Rcheck/00install.out' for details.
addpi: no visible global function definition for 'lines'
genPerms: no visible global function definition for 'combn'
getVar: no visible global function definition for 'glm'
getVar: no visible global function definition for 'binomial'
getVar: no visible global function definition for 'var'
pba: no visible global function definition for 'glm'
pba: no visible global function definition for 'binomial'
pba: no visible global function definition for 'predict'
pba: no visible global function definition for 'rbinom'
pcr: no visible global function definition for 'quantile'
plotpi: no visible global function definition for 'plot'
plotpi: no visible global function definition for 'axis'
plotpi: no visible global function definition for 'abline'
plotpi: no visible global function definition for 'lines'
Undefined global functions or variables:
  abline axis binomial combn glm lines plot predict quantile rbinom var
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "plot")
  importFrom("stats", "binomial", "glm", "predict", "quantile", "rbinom",
             "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
Cul: no visible global function definition for 'qf'
blockScale: no visible binding for global variable 'sd'
cochranTest: no visible global function definition for 'prcomp'
cochranTest: no visible binding for global variable 'var'
cochranTest: no visible global function definition for 'matplot'
cochranTest: no visible global function definition for 'legend'
continuumRemoval : crfun: no visible global function definition for
  'chull'
continuumRemoval : crfun: no visible global function definition for
  'approx'
continuumRemoval : crfun: no visible global function definition for
  'splinefun'
detrend: no visible binding for global variable 'sd'
duplex: no visible global function definition for 'prcomp'
e2m: no visible global function definition for 'cov'
kenStone: no visible global function definition for 'prcomp'
naes: no visible global function definition for 'prcomp'
naes: no visible global function definition for 'kmeans'
puchwein: no visible global function definition for 'prcomp'
readASD: no visible global function definition for 'read.table'
resample : resfun: no visible global function definition for 'approx'
resample : resfun: no visible global function definition for
  'splinefun'
shenkWest: no visible global function definition for 'prcomp'
spliceCorrection : extrapfun: no visible global function definition for
  'lm'
standardNormalVariate: no visible binding for global variable 'sd'
Undefined global functions or variables:
  approx chull cov kmeans legend lm matplot prcomp qf read.table sd
  splinefun var
Consider adding
  importFrom("grDevices", "chull")
  importFrom("graphics", "legend", "matplot")
  importFrom("stats", "approx", "cov", "kmeans", "lm", "prcomp", "qf",
             "sd", "splinefun", "var")
  importFrom("utils", "read.table")
to your NAMESPACE file.
addIonSatistics: no visible binding for global variable 'median'
adjustOne: no visible binding for global variable 'median'
attachModifications: no visible global function definition for
  'na.omit'
avrgLoadingCalculation: no visible binding for global variable 'median'
channelResponses : estimate: no visible binding for global variable
  'var'
responseStatisics : func: no visible global function definition for
  'aggregate'
testing: no visible global function definition for 'aov'
testingOneshot: no visible global function definition for 'anova'
testingTukey: no visible global function definition for 'TukeyHSD'
Undefined global functions or variables:
  TukeyHSD aggregate anova aov median na.omit var
Consider adding
  importFrom("stats", "TukeyHSD", "aggregate", "anova", "aov", "median",
             "na.omit", "var")
to your NAMESPACE file.
estimateLSEparam: no visible global function definition for 'lm'
estimateMLEparam: no visible global function definition for 'optim'
getCCnlL: no visible global function definition for 'dnorm'
iterateScampi: no visible global function definition for 'quantile'
plot.scampi: no visible global function definition for 'hist'
plot.scampiVal: no visible global function definition for 'par'
plot.scampiVal: no visible global function definition for 'hist'
plot.scampiVal: no visible global function definition for 'abline'
plot.scampiVal: no visible global function definition for 'qqnorm'
plot.scampiVal: no visible global function definition for 'qqline'
sampleInitialVector: no visible global function definition for 'runif'
Undefined global functions or variables:
  abline dnorm hist lm optim par qqline qqnorm quantile runif
Consider adding
  importFrom("graphics", "abline", "hist", "par")
  importFrom("stats", "dnorm", "lm", "optim", "qqline", "qqnorm",
             "quantile", "runif")
to your NAMESPACE file.
'library' or 'require' call to 'class' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'class'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
addcircle: no visible global function definition for 'lines'
addclassifierboundary: no visible global function definition for 'par'
addclassifierboundary: no visible global function definition for
  'contour'
plot.protoclass: no visible global function definition for 'plot'
plot.protoclass: no visible global function definition for 'box'
plot.protoclass: no visible global function definition for 'rgb2hsv'
plot.protoclass: no visible global function definition for 'col2rgb'
plot.protoclass: no visible global function definition for 'points'
plot.protoclass: no visible global function definition for 'hsv'
predict.protoclass: no visible global function definition for 'knn1'
Undefined global functions or variables:
  box col2rgb contour hsv knn1 lines par plot points rgb2hsv
Consider adding
  importFrom("grDevices", "col2rgb", "hsv", "rgb2hsv")
  importFrom("graphics", "box", "contour", "lines", "par", "plot",
             "points")
to your NAMESPACE file.
plotwithprototypes: no visible global function definition for 'plot'
plotwithprototypes: no visible global function definition for
  'strwidth'
plotwithprototypes: no visible global function definition for
  'strheight'
plotwithprototypes: no visible global function definition for 'rect'
plotwithprototypes: no visible global function definition for 'text'
protoclust: no visible global function definition for 'as.dist'
protocut: no visible global function definition for 'cutree'
Undefined global functions or variables:
  as.dist cutree plot rect strheight strwidth text
Consider adding
  importFrom("graphics", "plot", "rect", "strheight", "strwidth", "text")
  importFrom("stats", "as.dist", "cutree")
to your NAMESPACE file.
Extract_plant_grapevine_function: no visible global function definition
  for 'na.omit'
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Package in Depends field not imported from: 'rpart'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
mahalanobisComposite: no visible global function definition for
  'princomp'
prepareComposite: no visible global function definition for 'cov'
winsorizor : f: no visible global function definition for 'quantile'
Undefined global functions or variables:
  cov princomp quantile
Consider adding
  importFrom("stats", "cov", "princomp", "quantile")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/psidR.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/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'.
candidate.overlap: no visible global function definition for
  'write.table'
fisher: no visible global function definition for 'fisher.test'
fisher.iteration: no visible global function definition for
  'download.file'
fisher.iteration: no visible global function definition for
  'read.table'
pSI.list: no visible global function definition for 'write.table'
specificity.index: no visible global function definition for 'png'
specificity.index: no visible global function definition for 'par'
specificity.index: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  dev.off download.file fisher.test par png read.table write.table
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "par")
  importFrom("stats", "fisher.test")
  importFrom("utils", "download.file", "read.table", "write.table")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/PSM.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 'numDeriv' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
test.problem : g: no visible global function definition for 'grad'
test.problem: no visible global function definition for 'new'
psoptim,test.problem-missing-missing-missing-missing: no visible global
  function definition for 'new'
show,test.result: no visible global function definition for 'show'
show,test.result: no visible global function definition for 'sd'
Undefined global functions or variables:
  grad new sd show
Consider adding
  importFrom("methods", "new", "show")
  importFrom("stats", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
pspearman: no visible global function definition for 'pt'
spearman.test: no visible global function definition for
  'complete.cases'
spearman.test: no visible global function definition for 'cor'
Undefined global functions or variables:
  complete.cases cor pt
Consider adding
  importFrom("stats", "complete.cases", "cor", "pt")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'EffectsRelBaseline' 'boot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
catEffectBootAdaptor: no visible binding for global variable 'sumSqCat'
compExclusionFraction: no visible global function definition for
  'rpois'
compExclusionFraction: no visible global function definition for
  't.test'
compExclusionFraction: no visible global function definition for 'glm'
compExclusionFraction: no visible global function definition for
  'anova'
compPowerCatSelectivity: no visible binding for global variable
  'fRatioStat'
compPowerGeneralRespDetection: no visible binding for global variable
  'sumSqCat'
compPowerRespDetection: no visible binding for global variable
  'sumSqCat'
compRejectionFraction: no visible global function definition for
  'rpois'
compRejectionFraction: no visible global function definition for
  't.test'
compRejectionFraction: no visible global function definition for 'glm'
compRejectionFraction: no visible global function definition for
  'anova'
simCatResp: no visible global function definition for 'rpois'
simNormCatResp: no visible global function definition for 'rnorm'
testCatEffectBoot: no visible global function definition for 'boot'
Undefined global functions or variables:
  anova boot fRatioStat glm rnorm rpois sumSqCat t.test
Consider adding
  importFrom("stats", "anova", "glm", "rnorm", "rpois", "t.test")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'multilevel' 'nlme'
A package should be listed in only one of these fields.
'library' or 'require' calls to packages already attached by Depends:
  'multilevel' 'nlme'
  Please remove these calls from your code.
Running examples in 'psychotools-Ex.R' failed
The error most likely occurred in:

> ### Name: pcmodel
> ### Title: Partial Credit Model Fitting Function
> ### Aliases: pcmodel PCModel.fit print.pcmodel summary.pcmodel
> ###   print.summary.pcmodel coef.pcmodel bread.pcmodel estfun.pcmodel
> ###   logLik.pcmodel vcov.pcmodel
> ### Keywords: regression
> 
> ### ** Examples
> 
> o <- options(digits = 4)
> 
> ## Verbal aggression data
> data("VerbalAggression", package = "psychotools")
> 
> ## Partial credit model for the other-to-blame situations
> pcm <- pcmodel(VerbalAggression$resp[, 1:12])
Warning in log(elementary_symmetric_functions(par = esf_par, order = 0,  :
  NaNs produced
Warning in log(elementary_symmetric_functions(par = esf_par, order = 0,  :
  NaNs produced
Warning in log(elementary_symmetric_functions(par = esf_par, order = 0,  :
  NaNs produced
Warning in log(elementary_symmetric_functions(par = esf_par, order = 0,  :
  NaNs produced
Error in solve.default(vc) : 
  system is computationally singular: reciprocal condition number = 2.17723e-302
Calls: pcmodel -> solve -> solve.default
Execution halted
Packages in Depends field not imported from:
  'R.utils' 'rmeta'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ChisqTest_expect: no visible global function definition for 'pchisq'
plot_chase_observed_expected: no visible global function definition for
  'meta.MH'
plot_chase_observed_expected: no visible global function definition for
  'txtProgressBar'
plot_chase_observed_expected: no visible global function definition for
  'setTxtProgressBar'
test.one.treated: no visible global function definition for
  'fisher.test'
test_one: no visible global function definition for 'rbinom'
test_one: no visible global function definition for 'fisher.test'
Undefined global functions or variables:
  fisher.test meta.MH pchisq rbinom setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "fisher.test", "pchisq", "rbinom")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
PurBayes: no visible global function definition for 'update'
PurBayes: no visible global function definition for 'sd'
plot.PurBayes: no visible global function definition for 'plot'
plot.PurBayes: no visible global function definition for 'quantile'
plot.PurBayes: no visible global function definition for 'lines'
summary.PurBayes : <anonymous>: no visible global function definition
  for 'quantile'
Undefined global functions or variables:
  lines plot quantile sd update
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "quantile", "sd", "update")
to your NAMESPACE file.
CandidateBio.getBio : <anonymous>: no visible global function
  definition for 'na.omit'
Committee.getCommittee : <anonymous>: no visible global function
  definition for 'na.omit'
getAllBios: no visible global function definition for 'txtProgressBar'
getAllBios: no visible global function definition for
  'setTxtProgressBar'
getAllLocalOfficials: no visible global function definition for
  'txtProgressBar'
getAllLocalOfficials: no visible global function definition for
  'setTxtProgressBar'
getAllVotes: no visible global function definition for 'txtProgressBar'
getAllVotes: no visible global function definition for
  'setTxtProgressBar'
Undefined global functions or variables:
  na.omit setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
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.
trying URL 'http://github.com/dobriban/pweight/raw/master/vignettes/iGWAS.cad.example.RData'
Quitting from lines 34-38 (iGWAS-DataExample.Rmd) 
Error: processing vignette 'iGWAS-DataExample.Rmd' failed with diagnostics:
cannot open URL 'http://github.com/dobriban/pweight/raw/master/vignettes/iGWAS.cad.example.RData'
Execution halted
.grid.matrix: no visible global function definition for 'slot'
.matrix2grid: no visible global function definition for 'as'
.poly2grid: no visible global function definition for 'is'
.poly2grid: no visible global function definition for 'slot'
.poly2grid: no visible global function definition for 'as'
.pycno.core : smooth2D : s1d: no visible global function definition for
  'filter'
.pycno.core: no visible global function definition for 'flush.console'
.pycno2matrix: no visible global function definition for 'slot'
Undefined global functions or variables:
  as filter flush.console is slot
Consider adding
  importFrom("methods", "as", "is", "slot")
  importFrom("stats", "filter")
  importFrom("utils", "flush.console")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
pyramid: no visible global function definition for 'plot'
pyramid: no visible global function definition for 'segments'
pyramid: no visible global function definition for 'lines'
pyramid: no visible global function definition for 'text'
pyramid: no visible global function definition for 'rect'
pyramidf: no visible global function definition for 'segments'
pyramidf: no visible global function definition for 'lines'
pyramidf: no visible global function definition for 'text'
pyramidf: no visible global function definition for 'rect'
Undefined global functions or variables:
  lines plot rect segments text
Consider adding
  importFrom("graphics", "lines", "plot", "rect", "segments", "text")
to your NAMESPACE file.
csQCAbinTest: no visible global function definition for 'p.adjust'
fsQCApermTest: no visible global function definition for 'p.adjust'
mvQCAbinTest: no visible global function definition for 'p.adjust'
p.threshold.adjust: no visible global function definition for
  'p.adjust'
plot.fsQCApt: no visible global function definition for 'dev.cur'
plot.fsQCApt: no visible global function definition for 'dev.new'
plot.fsQCApt: no visible global function definition for 'par'
plot.fsQCApt: no visible global function definition for 'plot'
plot.fsQCApt: no visible global function definition for 'density'
plot.fsQCApt: no visible global function definition for 'axis'
plot.fsQCApt: no visible global function definition for 'polygon'
plot.fsQCApt: no visible global function definition for 'points'
plot.fsQCApt: no visible global function definition for 'hist'
summary.csQCAbt: no visible global function definition for
  'printCoefmat'
summary.fsQCApt: no visible global function definition for
  'printCoefmat'
summary.mvQCAbt: no visible global function definition for
  'printCoefmat'
Undefined global functions or variables:
  axis density dev.cur dev.new hist p.adjust par plot points polygon
  printCoefmat
Consider adding
  importFrom("grDevices", "dev.cur", "dev.new")
  importFrom("graphics", "axis", "hist", "par", "plot", "points",
             "polygon")
  importFrom("stats", "density", "p.adjust", "printCoefmat")
to your NAMESPACE file.
dmm_fn: no visible global function definition for 'dnorm'
dmm_noweights_fn: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
Package suggested but not available for checking: 'biom'
chooseMDoubleBootstrap: no visible global function definition for
  'model.matrix'
chooseMDoubleBootstrap: no visible global function definition for
  'as.formula'
chooseMDoubleBootstrap: no visible global function definition for
  'model.frame'
chooseMDoubleBootstrap: no visible global function definition for 'lm'
chooseMDoubleBootstrap: no visible global function definition for
  'coef'
chooseMDoubleBootstrap: no visible global function definition for
  'quantile'
chooseMDoubleBootstrap: no visible global function definition for
  'qnorm'
getModel: no visible global function definition for 'lm'
getModel: no visible global function definition for 'model.matrix'
getModel: no visible global function definition for 'as.formula'
getModel: no visible global function definition for 'model.frame'
getModel: no visible global function definition for 'model.response'
getModel: no visible global function definition for 'coef'
getModel: no visible global function definition for 'qnorm'
qLearn: no visible global function definition for 'model.matrix'
qLearn: no visible global function definition for 'as.formula'
qLearn: no visible global function definition for 'model.frame'
qLearn: no visible global function definition for 'coef'
qLearn: no visible global function definition for 'lm'
qLearn: no visible global function definition for 'quantile'
Undefined global functions or variables:
  as.formula coef lm model.frame model.matrix model.response qnorm
  quantile
Consider adding
  importFrom("stats", "as.formula", "coef", "lm", "model.frame",
             "model.matrix", "model.response", "qnorm", "quantile")
to your NAMESPACE file.
pcAxisCubeMake: no visible global function definition for 'aggregate'
pcAxisCubeToCSV: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  aggregate write.csv
Consider adding
  importFrom("stats", "aggregate")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/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'.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

Calc.Expr: no visible global function definition for 'read.csv'
Calc.Expr: no visible binding for global variable 'Type'
Calc.Expr: no visible binding for global variable 'Identifier'
Calc.Expr: no visible binding for global variable 'Fluor'
GroupPlot: no visible global function definition for 'read.csv'
GroupPlot: no visible binding for global variable 'Type'
GroupPlot: no visible global function definition for
  'aggregate.data.frame'
plot.CT: no visible global function definition for 'sd'
plot.CT: no visible global function definition for 'barplot'
plot.CT: no visible binding for global variable 'tr_gene_name'
plot.CT : errorbars: no visible global function definition for 'arrows'
plot.CT: no visible global function definition for 'box'
Undefined global functions or variables:
  Fluor Identifier Type aggregate.data.frame arrows barplot box
  read.csv sd tr_gene_name
Consider adding
  importFrom("graphics", "arrows", "barplot", "box")
  importFrom("stats", "aggregate.data.frame", "sd")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    data  11.8Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
ci.length: no visible global function definition for 'qexp'
detectable.bc: no visible global function definition for 'uniroot'
detectable.f2: no visible global function definition for 'uniroot'
detectable.ri: no visible global function definition for 'uniroot'
nu: no visible global function definition for 'pnorm'
nullinfo: no visible global function definition for 'qnorm'
nullinfo: no visible global function definition for 'dnorm'
optselection.bc: no visible global function definition for 'optimize'
optselection.f2: no visible global function definition for 'optimize'
optspacing.bc: no visible global function definition for 'optim'
optspacing.bc: no visible global function definition for 'optimize'
optspacing.f2: no visible global function definition for 'optim'
optspacing.f2: no visible global function definition for 'optimize'
powercalc.bc: no visible global function definition for 'pchisq'
powercalc.f2: no visible global function definition for 'pchisq'
samplesize.bc: no visible global function definition for 'uniroot'
samplesize.f2: no visible global function definition for 'uniroot'
samplesize.ri: no visible global function definition for 'uniroot'
tailprob: no visible global function definition for 'pchisq'
thresh: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  dnorm optim optimize pchisq pnorm qexp qnorm uniroot
Consider adding
  importFrom("stats", "dnorm", "optim", "optimize", "pchisq", "pnorm",
             "qexp", "qnorm", "uniroot")
to your NAMESPACE file.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.6Mb
    doc       2.9Mb
Package required but not available: 'qtbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' call to 'Rmpfr' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
adjacencyMatrix: no visible global function definition for 'as'
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
quadp: no visible global function definition for 'var'
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
Found the following significant warnings:
  bounded_reg.cpp:87:14: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
  elastic_net.cpp:86:14: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
  elastic_net.cpp:153:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  quadratic.cpp:106:21: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  utils.cpp:70:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  utils.cpp:102:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  utils.cpp:124:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  utils.cpp:191:23: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  utils.cpp:222:23: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/quadrupen.Rcheck/00install.out' for details.
alphaf: no visible global function definition for 'pchisq'
alphaf: no visible global function definition for 'dbinom'
conout: no visible global function definition for 'sd'
ibgaout: no visible global function definition for 'qnorm'
ibgaout: no visible global function definition for 'pnorm'
plot.qualint: no visible global function definition for 'qnorm'
powerval: no visible global function definition for 'rnorm'
powerval: no visible global function definition for 'qnorm'
powerval: no visible global function definition for 'pnorm'
print.expplot: no visible global function definition for 'gray'
print.expplot: no visible binding for global variable 'coef'
print.outplot: no visible global function definition for 'gray'
print.outplot: no visible binding for global variable 'coef'
qualint: no visible global function definition for 'qnorm'
qualint: no visible global function definition for 'plot'
qualval: no visible global function definition for 'qnorm'
qualval: no visible global function definition for 'plot'
surout: no visible global function definition for 'tail'
surout: no visible global function definition for 'coef'
Undefined global functions or variables:
  coef dbinom gray pchisq plot pnorm qnorm rnorm sd tail
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "plot")
  importFrom("stats", "coef", "dbinom", "pchisq", "pnorm", "qnorm",
             "rnorm", "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
Running examples in 'quantable-Ex.R' failed
The error most likely occurred in:

> ### Name: determineCut
> ### Title: determine best Accuracy cuttoff
> ### Aliases: determineCut
> 
> ### ** Examples
> 
> library(pROC)
Type 'citation("pROC")' for a citation.

Attaching package: 'pROC'

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

    cov, smooth, var

> cases <- rnorm(100,-1,1.1)
> controls <- rnorm(500,1,1.1)
> cut <- determineCut(cases,controls)
Error: `data` and `reference` should be factors with the same levels.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   3.0Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   2.1Mb
File 'QUIC/libs/i386/QUIC.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'QUIC.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'QUIC.o'
File 'QUIC/libs/x64/QUIC.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'QUIC.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'QUIC.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor 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/i386/qVarSel.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'qVarSelH.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'qVarSelH.o'
File 'qVarSel/libs/x64/qVarSel.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'qVarSelH.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'qVarSelH.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
S3 methods shown with full name in documentation object 'summary_table':
  'cbind.qwraps2_summary_table'

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.
mutualCoherence : .setOneMutualP: no visible global function definition
  for 'combn'
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
conf2d.default: no visible global function definition for 'polygon'
conf2d_int: no visible global function definition for 'contourLines'
Undefined global functions or variables:
  contourLines polygon
Consider adding
  importFrom("grDevices", "contourLines")
  importFrom("graphics", "polygon")
to your NAMESPACE file.
'library' or 'require' call to 'rgdal' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'matrixStats' 'rgdal' 'sp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    Output   2.2Mb
    bin      9.3Mb
Packages suggested but not available for checking: 'rcom' 'RDCOMClient'
'library' or 'require' calls in package code:
  'RDCOMClient' 'rcom'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
PPT.AddBlankSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddDataFrame: no visible global function definition for
  'comIsValidHandle'
PPT.AddDataFrame: no visible global function definition for
  'write.table'
PPT.AddDataFrame: no visible global function definition for 'write.csv'
PPT.AddGraphicstoSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddGraphicstoSlide: no visible global function definition for
  'dev.cur'
PPT.AddGraphicstoSlide: no visible global function definition for
  'dev.list'
PPT.AddGraphicstoSlide: no visible global function definition for
  'savePlot'
PPT.AddTextSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTitleOnlySlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTitleSlide: no visible global function definition for
  'comIsValidHandle'
PPT.ApplyTemplate: no visible global function definition for
  'comIsValidHandle'
PPT.Close: no visible global function definition for 'comIsValidHandle'
PPT.Init: no visible global function definition for 'comCreateObject'
PPT.Init: no visible global function definition for 'comIsValidHandle'
PPT.Init: no visible global function definition for 'COMCreate'
PPT.Present: no visible global function definition for
  'comIsValidHandle'
PPT.SaveAs: no visible global function definition for
  'comIsValidHandle'
PPT.getAbsolutePath : PPT.filePath: no visible global function
  definition for 'readWindowsShortcut'
Undefined global functions or variables:
  COMCreate comCreateObject comIsValidHandle dev.cur dev.list
  readWindowsShortcut savePlot write.csv write.table
Consider adding
  importFrom("grDevices", "dev.cur", "dev.list", "savePlot")
  importFrom("utils", "write.csv", "write.table")
to your NAMESPACE file.
r2stl: no visible global function definition for 'persp'
Undefined global functions or variables:
  persp
Consider adding
  importFrom("graphics", "persp")
to your NAMESPACE file.
'library' or 'require' call to 'rgl' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'lattice' 'leaps' 'rgl' 's20x'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: 'rpvm'
'library' or 'require' call to 'rpvm' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
race : killSlaves.exit: no visible global function definition for
  '.PVM.initsend'
race : killSlaves.exit: no visible global function definition for
  '.PVM.send'
race : killSlaves.exit: no visible global function definition for
  '.PVM.exit'
race: no visible global function definition for '.PVM.mytid'
race: no visible global function definition for '.PVM.spawn'
race: no visible global function definition for '.PVM.initsend'
race: no visible global function definition for '.PVM.pkstrvec'
race: no visible global function definition for '.PVM.send'
race: no visible global function definition for '.PVM.recv'
race: no visible global function definition for '.PVM.bufinfo'
race: no visible global function definition for '.PVM.upkstrvec'
race : job.start: no visible global function definition for
  '.PVM.initsend'
race : job.start: no visible global function definition for
  '.PVM.pkint'
race : job.start: no visible global function definition for '.PVM.send'
race : job.wait: no visible global function definition for '.PVM.recv'
race : job.wait: no visible global function definition for
  '.PVM.bufinfo'
race : job.wait: no visible global function definition for
  '.PVM.upkint'
race : job.wait: no visible global function definition for
  '.PVM.upkdblvec'
race : aux2.friedman: no visible global function definition for
  'pchisq'
race : aux2.friedman: no visible global function definition for 'qt'
race : aux.friedman: no visible global function definition for
  'wilcox.test'
race : aux.ttest: no visible global function definition for 't.test'
race : aux.ttest: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  .PVM.bufinfo .PVM.exit .PVM.initsend .PVM.mytid .PVM.pkint
  .PVM.pkstrvec .PVM.recv .PVM.send .PVM.spawn .PVM.upkdblvec
  .PVM.upkint .PVM.upkstrvec p.adjust pchisq qt t.test wilcox.test
Consider adding
  importFrom("stats", "p.adjust", "pchisq", "qt", "t.test",
             "wilcox.test")
to your NAMESPACE file.
getsonde: no visible global function definition for 'read.table'
plotsonde: no visible global function definition for 'par'
plotwind: no visible global function definition for 'plot'
plotwind: no visible global function definition for 'mtext'
plotwind: no visible global function definition for 'abline'
skewt.axis: no visible global function definition for 'par'
skewt.axis: no visible global function definition for 'plot'
skewt.axis: no visible global function definition for 'axis'
skewt.axis: no visible global function definition for 'mtext'
skewt.axis: no visible global function definition for 'segments'
skewt.axis: no visible global function definition for 'text'
skewt.axis: no visible global function definition for 'lines'
skewt.lines: no visible global function definition for 'lines'
skewt.points: no visible global function definition for 'points'
station.symbol: no visible global function definition for 'sd'
station.symbol: no visible global function definition for 'par'
station.symbol: no visible global function definition for 'lines'
station.symbol: no visible global function definition for 'polygon'
station.symbol: no visible global function definition for 'text'
station.symbol: no visible global function definition for 'segments'
Undefined global functions or variables:
  abline axis lines mtext par plot points polygon read.table sd
  segments text
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "mtext", "par",
             "plot", "points", "polygon", "segments", "text")
  importFrom("stats", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
RnDif.het: no visible global function definition for 'runif'
RnDif.hom: no visible global function definition for 'runif'
RnDifAdv.hom: no visible global function definition for 'runif'
SoilAdv.hom: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
cpc_get_rawdata: no visible global function definition for
  'download.file'
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
plot.rsm: no visible global function definition for 'par'
plot.rsm: no visible global function definition for 'abline'
plot.rsm: no visible global function definition for 'barplot'
Undefined global functions or variables:
  abline barplot par
Consider adding
  importFrom("graphics", "abline", "barplot", "par")
to your NAMESPACE file.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    htmlwidgets   6.0Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/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'.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs   2.8Mb
.disableThreads: no visible global function definition for
  'stopCluster'
.enableThreads: no visible global function definition for 'detectCores'
.enableThreads: no visible global function definition for
  'makePSOCKcluster'
.enableThreads: no visible global function definition for
  'clusterExport'
.enableThreads: no visible global function definition for 'clusterCall'
.forwardSelection: no visible binding for global variable 'var'
.forwardSelection: no visible global function definition for 'glm'
.forwardSelection: no visible global function definition for 'formula'
.forwardSelection: no visible global function definition for 'binomial'
.forwardSelection: no visible global function definition for 'lm'
.forwardSelection: no visible global function definition for 'predict'
.predict.internal: no visible global function definition for 'predict'
randomGLM: no visible binding for global variable 'cor'
randomGLM: no visible binding for global variable 'sd'
randomGLM: no visible global function definition for 'var'
thinRandomGLM: no visible global function definition for 'glm'
thinRandomGLM: no visible global function definition for 'binomial'
thinRandomGLM: no visible global function definition for 'lm'
Undefined global functions or variables:
  binomial clusterCall clusterExport cor detectCores formula glm lm
  makePSOCKcluster predict sd stopCluster var
Consider adding
  importFrom("stats", "binomial", "cor", "formula", "glm", "lm",
             "predict", "sd", "var")
to your NAMESPACE file.
anovaF: no visible global function definition for 'anova'
anovaF: no visible global function definition for 'lm'
randInterval: no visible global function definition for 'quantile'
randInterval : <anonymous>: no visible global function definition for
  'quantile'
randPlot: no visible global function definition for 'par'
randPlot: no visible global function definition for 'hist'
randPlot: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline anova hist lm par quantile
Consider adding
  importFrom("graphics", "abline", "hist", "par")
  importFrom("stats", "anova", "lm", "quantile")
to your NAMESPACE file.
bartels.rank.test: no visible global function definition for 'na.omit'
bartels.rank.test: no visible global function definition for 'pbeta'
bartels.rank.test: no visible global function definition for 'pnorm'
cox.stuart.test: no visible global function definition for 'pbinom'
difference.sign.test: no visible global function definition for
  'na.omit'
difference.sign.test: no visible global function definition for 'pnorm'
rank.test: no visible global function definition for 'na.omit'
rank.test: no visible global function definition for 'pnorm'
rruns: no visible global function definition for 'runif'
runs.test: no visible global function definition for 'median'
runs.test: no visible global function definition for 'na.omit'
runs.test: no visible global function definition for 'points'
runs.test: no visible global function definition for 'abline'
runs.test: no visible global function definition for 'gray'
runs.test: no visible global function definition for 'pnorm'
turning.point.test: no visible global function definition for 'embed'
turning.point.test: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  abline embed gray median na.omit pbeta pbinom pnorm points runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "points")
  importFrom("stats", "embed", "median", "na.omit", "pbeta", "pbinom",
             "pnorm", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  congruRand.c:180:3: warning: ISO C does not support the 'I64' ms_scanf length modifier [-Wformat=]
  congruRand.c:187:2: warning: ISO C does not support the 'I64' ms_scanf length modifier [-Wformat=]
  congruRand.c:188:2: warning: ISO C does not support the 'I64' ms_scanf length modifier [-Wformat=]
  congruRand.c:189:2: warning: ISO C does not support the 'I64' ms_scanf length modifier [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/3.5/randtoolbox.Rcheck/00install.out' for details.
rank.L2R: no visible global function definition for 'kmeans'
rank.L2R: no visible global function definition for 'pnorm'
rank.LN: no visible global function definition for 'kmeans'
rank.LN: no visible global function definition for 'pnorm'
rank.gs: no visible global function definition for 'qnorm'
rank.wald: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  kmeans pnorm qnorm
Consider adding
  importFrom("stats", "kmeans", "pnorm", "qnorm")
to your NAMESPACE file.
CropSpatialPolygonsDataFrame: no visible global function definition for
  'bbox'
CropSpatialPolygonsDataFrame: no visible global function definition for
  'clipPolys'
DiagnoseFailure: no visible global function definition for 'points'
Undefined global functions or variables:
  bbox clipPolys points
Consider adding
  importFrom("graphics", "points")
to your NAMESPACE file.
'library' or 'require' call to 'BSgenome.Hsapiens.UCSC.hg19' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
freq: no visible global function definition for 'xtabs'
freq: no visible binding for global variable 'na.pass'
freq: no visible global function definition for 'melt'
freq: no visible global function definition for 'complete.cases'
freq: no visible global function definition for 'tail'
kurtosis: no visible global function definition for 'na.omit'
label: no visible global function definition for 'tail'
name: no visible global function definition for 'tail'
nvalid : <anonymous>: no visible global function definition for
  'na.omit'
rp.desc: no visible global function definition for 'melt.data.frame'
rp.desc: no visible global function definition for 'cast'
rp.desc: no visible global function definition for 'na.omit'
rp.desc : <anonymous>: no visible global function definition for 'tail'
rp.desc : <anonymous>: no visible global function definition for 'head'
rp.freq: no visible global function definition for 'xtabs'
rp.freq: no visible binding for global variable 'na.pass'
rp.freq: no visible global function definition for 'melt'
rp.freq: no visible global function definition for 'complete.cases'
rp.freq: no visible global function definition for 'tail'
rp.label: no visible global function definition for 'tail'
rp.name: no visible global function definition for 'tail'
rp.outlier : lundcrit: no visible global function definition for 'qf'
rp.outlier: no visible global function definition for 'lm'
rp.outlier: no visible global function definition for 'rstandard'
rp.valid : <anonymous>: no visible global function definition for
  'na.omit'
skewness: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  cast complete.cases head lm melt melt.data.frame na.omit na.pass qf
  rstandard tail xtabs
Consider adding
  importFrom("stats", "complete.cases", "lm", "na.omit", "na.pass", "qf",
             "rstandard", "xtabs")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
fnRAP: no visible global function definition for 'chisq.test'
fnRAP: no visible global function definition for 'combn'
Undefined global functions or variables:
  chisq.test combn
Consider adding
  importFrom("stats", "chisq.test")
  importFrom("utils", "combn")
to your NAMESPACE file.
Packages suggested but not available for checking: 'gurobi' 'rgurobi'
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs   2.3Mb
plotarc: no visible global function definition for 'par'
plotarc: no visible global function definition for 'plot'
plotarc: no visible global function definition for 'lines'
plotpoly: no visible global function definition for 'par'
plotpoly: no visible global function definition for 'plot'
plotpoly: no visible global function definition for 'polygon'
Undefined global functions or variables:
  lines par plot polygon
Consider adding
  importFrom("graphics", "lines", "par", "plot", "polygon")
to your NAMESPACE file.
INT_FIX: no visible global function definition for 'rbinom'
INT_FIX: no visible global function definition for 'glm'
INT_FIX: no visible global function definition for 'as.formula'
INT_FIX: no visible global function definition for 'residuals'
INT_FIX: no visible global function definition for 'var'
INT_RAN: no visible global function definition for 'rbinom'
INT_RAN: no visible global function definition for 'as.formula'
INT_RAN: no visible global function definition for 'predict'
JOINT: no visible global function definition for 'rbinom'
JOINT: no visible global function definition for 'glm'
JOINT: no visible global function definition for 'as.formula'
JOINT: no visible global function definition for 'var'
JOINT: no visible global function definition for 'residuals'
pKuonen: no visible global function definition for 'pchisq'
pKuonen: no visible global function definition for 'uniroot'
pKuonen: no visible global function definition for 'pnorm'
rareGE: no visible global function definition for 'rbinom'
rareGE: no visible global function definition for 'as.formula'
rareGE: no visible global function definition for 'predict'
rareGE: no visible global function definition for 'glm'
rareGE: no visible global function definition for 'residuals'
rareGE: no visible global function definition for 'var'
rareGE_joint_mc: no visible global function definition for 'pchisq'
rareGE_joint_mc: no visible global function definition for 'qchisq'
wuweights: no visible global function definition for 'dbeta'
Undefined global functions or variables:
  as.formula dbeta glm pchisq pnorm predict qchisq rbinom residuals
  uniroot var
Consider adding
  importFrom("stats", "as.formula", "dbeta", "glm", "pchisq", "pnorm",
             "predict", "qchisq", "rbinom", "residuals", "uniroot",
             "var")
to your NAMESPACE file.
BiogTest.individual: no visible global function definition for 'combn'
BiogTest.individual: no visible global function definition for 'runif'
BiogTest.individual: no visible global function definition for 'rlnorm'
BiogTest.individual: no visible global function definition for
  'rnbinom'
BiogTest.sample: no visible global function definition for 'combn'
BiogTest.sample: no visible global function definition for 'runif'
BiogTest.sample: no visible global function definition for 'rlnorm'
BiogTest.sample: no visible global function definition for 'rnbinom'
BiogTest.sample: no visible global function definition for 'aggregate'
EcoTest.individual: no visible global function definition for 'xtabs'
plot.BiogTest: no visible global function definition for 'quantile'
plot.BiogTest: no visible global function definition for 'combn'
plot.EcoTest: no visible global function definition for 'quantile'
Undefined global functions or variables:
  aggregate combn quantile rlnorm rnbinom runif xtabs
Consider adding
  importFrom("stats", "aggregate", "quantile", "rlnorm", "rnbinom",
             "runif", "xtabs")
  importFrom("utils", "combn")
to your NAMESPACE file.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs   1.8Mb
rateratio.test: no visible global function definition for
  'complete.cases'
rateratio.test: no visible global function definition for 'pbinom'
rateratio.test : p.L: no visible global function definition for 'qbeta'
rateratio.test : p.U: no visible global function definition for 'qbeta'
Undefined global functions or variables:
  complete.cases pbinom qbeta
Consider adding
  importFrom("stats", "complete.cases", "pbinom", "qbeta")
to your NAMESPACE file.
concordance: no visible global function definition for 'quantile'
concordance : Normal: no visible global function definition for 'qnorm'
concordance : Normal: no visible global function definition for 'pnorm'
concordance : MC: no visible global function definition for 'rmultinom'
concordance : MC: no visible global function definition for 'quantile'
concordance: no visible global function definition for 'qnorm'
concordance: no visible global function definition for 'pnorm'
concordance : Chisq: no visible global function definition for 'qchisq'
concordance : Chisq: no visible global function definition for 'pchisq'
concordance : Normal2: no visible global function definition for
  'qnorm'
concordance : Normal2: no visible global function definition for
  'pnorm'
concordance : MC2: no visible global function definition for
  'rmultinom'
concordance : MC2: no visible global function definition for 'quantile'
wlin.conc: no visible global function definition for 'quantile'
wlin.conc : MC: no visible global function definition for 'rmultinom'
wlin.conc : MC: no visible global function definition for 'quantile'
wquad.conc: no visible global function definition for 'quantile'
wquad.conc : MC: no visible global function definition for 'rmultinom'
wquad.conc : MC: no visible global function definition for 'quantile'
Undefined global functions or variables:
  pchisq pnorm qchisq qnorm quantile rmultinom
Consider adding
  importFrom("stats", "pchisq", "pnorm", "qchisq", "qnorm", "quantile",
             "rmultinom")
to your NAMESPACE file.
.GCD: no visible global function definition for 'as.polynomial'
.LCM: no visible global function definition for 'as.polynomial'
.is_zero_polynomial: no visible global function definition for 'coef'
.poly2expr: no visible global function definition for 'coef'
integral.rationalfun: no visible global function definition for 'coef'
integraterf.transcendent: no visible global function definition for
  'coef'
rationalfun: no visible global function definition for 'polynomial'
rationalfun.poly: no visible global function definition for
  'polynomial'
rationalfun.poly: no visible global function definition for
  'is.polynomial'
rfun: no visible global function definition for 'polynomial'
rfun.poly: no visible global function definition for 'polynomial'
rfun.poly: no visible global function definition for 'is.polynomial'
simplify: no visible global function definition for 'coef'
simplify: no visible global function definition for 'polynomial'
Undefined global functions or variables:
  as.polynomial coef is.polynomial polynomial
Consider adding
  importFrom("stats", "coef")
to your NAMESPACE file.
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 [Â°deg]')
> sun=suncalc(t0[['yday']],UTC=TRUE)
Error in FUN(X[[i]], ...) : subscript out of bounds
Calls: suncalc -> [[ -> [[.POSIXlt -> .POSIXlt -> lapply
Execution halted
.avisApiBusAvanzada: no visible global function definition for
  'read.csv'
.avisRenderMapAdmin: no visible global function definition for 'points'
.avisRenderMapAdmin: no visible global function definition for 'rect'
.avisRenderMapPhysical: no visible global function definition for
  'points'
avisMap: no visible global function definition for 'par'
avisMap: no visible global function definition for 'layout'
Undefined global functions or variables:
  layout par points read.csv rect
Consider adding
  importFrom("graphics", "layout", "par", "points", "rect")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
GetHistoricTradeData: no visible global function definition for
  'read.csv'
Undefined global functions or variables:
  read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
bn2nbn: no visible binding for global variable 'bn.fit'
chain4chain: no visible binding for global variable 'head'
chain4chain: no visible binding for global variable 'tail'
estimate8arcs: no visible global function definition for 'lm'
estimate8arcs: no visible global function definition for 'coefficients'
estimate8nbn: no visible global function definition for 'lm'
estimate8nbn: no visible global function definition for 'as.formula'
estimate8nbn: no visible global function definition for 'anova'
estimate8nbn: no visible global function definition for 'coefficients'
generate8chain: no visible global function definition for 'runif'
generate8chain: no visible global function definition for 'rbinom'
generate8nbn: no visible global function definition for 'runif'
generate8nbn: no visible global function definition for 'rbinom'
nbn2bnfit: no visible global function definition for 'model2network'
nbn2bnfit: no visible global function definition for 'custom.fit'
simulate8gema: no visible global function definition for 'rnorm'
simulate8mn: no visible global function definition for 'mvrnorm'
simulate8nbn: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  anova as.formula bn.fit coefficients custom.fit head lm model2network
  mvrnorm rbinom rnorm runif tail
Consider adding
  importFrom("stats", "anova", "as.formula", "coefficients", "lm",
             "rbinom", "rnorm", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
SumTestSens: no visible global function definition for 'pnorm'
binarysens: no visible global function definition for 'dbinom'
hlsens: no visible global function definition for 'wilcox.test'
iv_sens: no visible global function definition for 'pnorm'
mcontrol: no visible global function definition for 'pnorm'
psens: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dbinom pnorm wilcox.test
Consider adding
  importFrom("stats", "dbinom", "pnorm", "wilcox.test")
to your NAMESPACE file.
':::' call which should be '::': 'tools:::file_path_as_absolute'
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: 'tools:::file_test'
  See the note in ?`:::` about the use of this operator.
genBugsScript: no visible global function definition for 'runif'
getBugsOutput: no visible global function definition for 'read.table'
rbugs2coda: no visible global function definition for 'as.mcmc'
rbugs2coda: no visible global function definition for 'mcmc'
rbugs2coda: no visible global function definition for 'as.mcmc.list'
Undefined global functions or variables:
  as.mcmc as.mcmc.list mcmc read.table runif
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "read.table")
to your NAMESPACE file.
find_available_versions: no visible global function definition for
  'contrib.url'
find_available_versions: no visible global function definition for
  'available.packages'
install_version: no visible global function definition for
  'contrib.url'
install_version: no visible global function definition for
  'available.packages'
install_version: no visible global function definition for
  'install_url'
load_available_packages: no visible global function definition for
  'contrib.url'
validate_installed_package: no visible global function definition for
  'installed.packages'
Undefined global functions or variables:
  available.packages contrib.url install_url installed.packages
Consider adding
  importFrom("utils", "available.packages", "contrib.url",
             "installed.packages")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'RColorBrewer' 'classInt' 'maptools'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'RColorBrewer' 'classInt' 'maptools'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
RC.read.table: no visible global function definition for 'type.convert'
Undefined global functions or variables:
  type.convert
Consider adding
  importFrom("utils", "type.convert")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/rCBA.Rcheck/00install.out' for details.
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    cont  23.3Mb
.onAttach: no visible global function definition for
  'packageDescription'
rselect.list: no visible global function definition for 'select.list'
Undefined global functions or variables:
  packageDescription select.list
Consider adding
  importFrom("utils", "packageDescription", "select.list")
to your NAMESPACE file.
climdex.data.frame: no visible global function definition for
  'as.PCICt'
Undefined global functions or variables:
  as.PCICt
get_ClinicalCodes: no visible global function definition for 'read.csv'
get_ClinicalCodes : <anonymous>: no visible global function definition
  for 'read.csv'
Undefined global functions or variables:
  read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
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.
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.
cmaOptimDP: no visible global function definition for 'flush.console'
Undefined global functions or variables:
  flush.console
Consider adding
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: replacing previous import 'Rcmdr::Confint' by 'car::Confint' when loading 'RcmdrPlugin.BCA'
See 'd:/Rcompile/CRANpkg/local/3.5/RcmdrPlugin.BCA.Rcheck/00install.out' for details.
.onAttach: no visible global function definition for 'palette'
.onAttach: no visible global function definition for 'dev.off'
helpAboutBCA: no visible global function definition for 'help'
Undefined global functions or variables:
  dev.off help palette
Consider adding
  importFrom("grDevices", "dev.off", "palette")
  importFrom("utils", "help")
to your NAMESPACE file.
Depends: includes the non-default packages:
  'biclust' 'fabia' 'iBBiG' 'superbiclust' 'BcDiag' 'rqubic' 'BicARE'
  's4vd' 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
enterTableMHTest : onOK: no visible global function definition for
  'na.omit'
startStop: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Namespace with empty importFrom: 'tcltk'
'library' or 'require' calls to packages already attached by Depends:
  'depthTools' 'tcltk'
  Please remove these calls from your code.
computeMBD : OnOutput: no visible global function definition for
  'tkbutton'
computeMBD: no visible global function definition for 'tkbutton'
computeMBD : OnPlot: no visible global function definition for
  'tkcanvas'
computeMBD : OnPlot: no visible global function definition for
  'tkbutton'
computeTmean: no visible global function definition for 'tkcanvas'
computeTmean: no visible global function definition for 'tkbutton'
computeTmean : onOK: no visible global function definition for 'par'
plotCentralCurves: no visible global function definition for 'tkcanvas'
plotCentralCurves: no visible global function definition for 'tkbutton'
plotCentralCurves : onOK: no visible global function definition for
  'par'
Undefined global functions or variables:
  par tkbutton tkcanvas
Consider adding
  importFrom("graphics", "par")
to your NAMESPACE file.
'library' or 'require' call to 'FrF2.catlg128' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'Rcmdr' 'multcomp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Depends: includes the non-default packages:
  'Rcmdr' 'TeachingDemos' 'tseries' 'abind' 'MASS' 'xts' 'forecast'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'tseries'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'MASS' 'Rcmdr' 'TeachingDemos' 'abind' 'forecast' 'tseries' 'xts'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Missing link or links in documentation object 'Rcmdr.HH-package.Rd':
  '[car]{scatterplot.matrix}'

Missing link or links in documentation object 'scatterPlotMatrix.HH.Rd':
  '[car]{scatterplot.matrix}'

See section 'Cross-references' in the 'Writing R Extensions' manual.
'library' or 'require' calls in package code:
  'abind' 'e1071' 'qcc'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'ENmisc' 'Hmisc' 'Rcmdr' 'vcd'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.onAttach: no visible global function definition for 'getRcmdr'
.onAttach: no visible global function definition for 'closeCommander'
.onAttach: no visible global function definition for 'Commander'
mosaicMenuItem: no visible global function definition for
  'mosaicSelectDialog'
mosaicMenuItem: no visible global function definition for 'Message'
Undefined global functions or variables:
  Commander Message closeCommander getRcmdr mosaicSelectDialog
Packages in Depends field not imported from:
  'orloca' 'orloca.es'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rcmdr.new.loca.p: no visible binding for global variable 'top'
Rcmdr.new.loca.p: no visible binding for global variable 'buttonsFrame'
Rcmdr.orloca.norm: no visible binding for global variable 'top'
Rcmdr.orloca.norm : onOK: no visible binding for global variable
  'normaVariable'
Rcmdr.orloca.norm: no visible binding for global variable 'normaFrame'
Rcmdr.orloca.norm: no visible binding for global variable
  'buttonsFrame'
Rcmdr.rloca.p: no visible binding for global variable 'top'
Rcmdr.rloca.p: no visible binding for global variable 'buttonsFrame'
Rcmdr.zsum: no visible binding for global variable 'top'
Rcmdr.zsum: no visible binding for global variable 'buttonsFrame'
Rcmdr.zsummin: no visible binding for global variable 'top'
Rcmdr.zsummin : onOK: no visible binding for global variable
  'algorithmVariable'
Rcmdr.zsummin : onOK: no visible binding for global variable '.sol'
Rcmdr.zsummin: no visible binding for global variable 'algorithmFrame'
Rcmdr.zsummin: no visible binding for global variable 'buttonsFrame'
Undefined global functions or variables:
  .sol algorithmFrame algorithmVariable buttonsFrame normaFrame
  normaVariable top
BOXWP: no visible binding for global variable 'top'
BOXWP: no visible binding for global variable 'buttonsFrame'
HIST: no visible binding for global variable 'top'
HIST: no visible binding for global variable 'buttonsFrame'
QQN: no visible binding for global variable 'top'
QQN: no visible binding for global variable 'buttonsFrame'
Undefined global functions or variables:
  buttonsFrame top
Namespaces with empty importFrom:
  'stats' 'tcltk'
fncLRpROC: no visible global function definition for 'palette'
fncLRpROC : onOK : convert: no visible global function definition for
  'col2rgb'
fncLRpROC : onOK : convert: no visible global function definition for
  'rgb'
fncPairedpROC: no visible global function definition for 'palette'
fncPairedpROC : onOK : convert: no visible global function definition
  for 'col2rgb'
fncPairedpROC : onOK : convert: no visible global function definition
  for 'rgb'
fncUnpairedpROC: no visible global function definition for 'palette'
fncUnpairedpROC : onOK : convert: no visible global function definition
  for 'col2rgb'
fncUnpairedpROC : onOK : convert: no visible global function definition
  for 'rgb'
fncvpROC: no visible global function definition for 'palette'
fncvpROC : onOK : convert: no visible global function definition for
  'col2rgb'
fncvpROC : onOK : convert: no visible global function definition for
  'rgb'
Undefined global functions or variables:
  col2rgb palette rgb
Consider adding
  importFrom("grDevices", "col2rgb", "palette", "rgb")
to your NAMESPACE file.
SampleSizes: no visible global function definition for 'xtabs'
SampleSizes: no visible global function definition for 'weighted.mean'
SampleSizes: no visible global function definition for 'reshape'
stage1Sample.fn: no visible global function definition for 'runif'
stage2Sample.fn: no visible global function definition for 'runif'
strata.options : onOK: no visible global function definition for
  'packageDescription'
Undefined global functions or variables:
  packageDescription reshape runif weighted.mean xtabs
Consider adding
  importFrom("stats", "reshape", "runif", "weighted.mean", "xtabs")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
'library' or 'require' call to 'SLC' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'SLC'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Depends: includes the non-default packages:
  'Rcmdr' 'tcltk' 'car' 'RColorBrewer' 'colorspace' 'vcd'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' call to 'car' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'RColorBrewer' 'Rcmdr' 'car' 'colorspace' 'vcd'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rcmdr.steeptestDij : onOK: no visible binding for global variable
  'replications'
Rcmdr.steeptestPij : onOK: no visible binding for global variable
  'replications'
Undefined global functions or variables:
  replications
Consider adding
  importFrom("stats", "replications")
to your NAMESPACE file.
Package suggested but not available for checking: 'ROpenOffice'
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   2.7Mb
    po    2.1Mb
brewer.pal: no visible global function definition for 'rgb'
display.brewer.all: no visible global function definition for 'par'
display.brewer.all: no visible global function definition for 'plot'
display.brewer.all: no visible global function definition for 'rect'
display.brewer.all: no visible global function definition for 'text'
display.brewer.pal: no visible global function definition for 'image'
Undefined global functions or variables:
  image par plot rect rgb text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "image", "par", "plot", "rect", "text")
to your NAMESPACE file.
Running 'testthat.R' [100s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rcongresso)
  > 
  > test_check("rcongresso")
  -- 1. Failure: Dimensoes do dataframe (@test_votacoes.R#54)  -------------------
  dim(votos_pec241) not equal to c(478, 10).
  1/2 mismatches
  [1] 500 - 478 == 22
  
  == testthat results  ===========================================================
  OK: 66 SKIPPED: 0 FAILED: 1
  1. Failure: Dimensoes do dataframe (@test_votacoes.R#54) 
  
  Error: testthat unit tests failed
  Execution halted
addLine: no visible global function definition for 'abline'
ellipse: no visible global function definition for 'approx'
ellipse: no visible global function definition for 'tail'
Undefined global functions or variables:
  abline approx tail
Consider adding
  importFrom("graphics", "abline")
  importFrom("stats", "approx")
  importFrom("utils", "tail")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/Rcplex.Rcheck/00install.out' for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    include   5.5Mb
    libs      1.6Mb
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    include  25.3Mb
    libs      1.8Mb
File which contains pragma(s) suppressing diagnostics:
  'inst/include/RcppBlazeConfig.h'
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    include   7.7Mb
    libs      1.8Mb
Gauss: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    include   1.6Mb
    lib       3.9Mb
    libs      2.9Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      1.7Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    include   1.8Mb
    lib       8.9Mb
    libs      1.0Mb
installed size is 35.0Mb
  sub-directories of 1Mb or more:
    include   8.8Mb
    libs     26.1Mb
Files which contain pragma(s) suppressing diagnostics:
  'inst/include/ql/math/distributions/normaldistribution.hpp'
  'inst/include/ql/math/matrix.hpp'
  'inst/include/ql/math/optimization/levenbergmarquardt.hpp'
  'inst/include/ql/math/statistics/incrementalstatistics.hpp'
  'inst/include/ql/time/date.hpp' 'inst/include/ql/time/imm.hpp'
  'inst/include/ql/utilities/dataparsers.hpp'
  'inst/include/ql/utilities/null.hpp'
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    include   6.3Mb
    libs      2.0Mb
get_rollit_source: no visible global function definition for
  'file.edit'
Undefined global functions or variables:
  file.edit
Consider adding
  importFrom("utils", "file.edit")
to your NAMESPACE file.
Package suggested but not available for checking: 'Rcompression'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Packages in Depends field not imported from:
  'MASS' 'Matrix' 'lattice' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CUR: no visible global function definition for 'runif'
CUR: no visible global function definition for 'new'
plotLeverage,CURobj: no visible global function definition for 'plot'
plotLeverage,CURobj: no visible global function definition for 'points'
plotLeverage,CURobj: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline new plot points runif
Consider adding
  importFrom("graphics", "abline", "plot", "points")
  importFrom("methods", "new")
  importFrom("stats", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Drda1: no visible global function definition for 'model.matrix'
permute.rows: no visible global function definition for 'runif'
plot.rdacv: no visible global function definition for 'par'
rda.plotmat: no visible global function definition for 'par'
rda.plotmat: no visible global function definition for 'plot'
rda.plotmat: no visible global function definition for 'layout'
rda.plotmat: no visible global function definition for 'image'
rda.plotmat: no visible global function definition for 'terrain.colors'
rda.plotmat: no visible global function definition for 'axis'
rda.plotmat: no visible global function definition for 'points'
rda.plotmat: no visible global function definition for 'legend'
rda1: no visible global function definition for 'model.matrix'
Undefined global functions or variables:
  axis image layout legend model.matrix par plot points runif
  terrain.colors
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "axis", "image", "layout", "legend", "par",
             "plot", "points")
  importFrom("stats", "model.matrix", "runif")
to your NAMESPACE file.
get.datamarket.csv: no visible global function definition for
  'read.csv'
getUserAgent: no visible global function definition for 'sessionInfo'
Undefined global functions or variables:
  read.csv sessionInfo
Consider adding
  importFrom("utils", "read.csv", "sessionInfo")
to your NAMESPACE file.
distimage: no visible binding for global variable 'terrain.colors'
distimage: no visible global function definition for 'filled.contour'
distimage: no visible global function definition for 'title'
distimage: no visible global function definition for 'axis'
distimage: no visible global function definition for 'lines'
drawkpc: no visible global function definition for 'plot'
drawkpc: no visible global function definition for 'segments'
drawkpc: no visible global function definition for 'lines'
modelimage: no visible binding for global variable 'topo.colors'
modelimage: no visible global function definition for 'filled.contour'
modelimage: no visible global function definition for 'title'
modelimage: no visible global function definition for 'axis'
modelimage: no visible global function definition for 'lines'
sincdata: no visible global function definition for 'runif'
sincdata: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  axis filled.contour lines plot rnorm runif segments terrain.colors
  title topo.colors
Consider adding
  importFrom("grDevices", "terrain.colors", "topo.colors")
  importFrom("graphics", "axis", "filled.contour", "lines", "plot",
             "segments", "title")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
sumry_categorical: no visible global function definition for 'freq'
sumry_continous: no visible global function definition for 'quantile'
Undefined global functions or variables:
  freq quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/RDieHarder.Rcheck/00install.out' for details.
Running 'testthat.R' [159s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rdomains)
  > 
  > test_check("rdomains")
  -- 1. Error: dmoz cat (@test-dmoz-cat.R#5)  ------------------------------------
  HTTP error 503.
  1: get_dmoz_data() at testthat/test-dmoz-cat.R:5
  2: curl_download(paste0("https://github.com/themains/rdomains/blob/master/data-raw/dmoz/", 
         "dmoz_domain_category.zip?raw=TRUE"), tmp)
  
  Shallalist Data saved to the following destination: ./ 
  == testthat results  ===========================================================
  OK: 2 SKIPPED: 1 FAILED: 1
  1. Error: dmoz cat (@test-dmoz-cat.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
ip2coordinates: no visible global function definition for 'URLencode'
street2coordinates: no visible global function definition for
  'URLencode'
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
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.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   2.6Mb
Files which contain pragma(s) suppressing diagnostics:
  'inst/include/re2/prog.h' 'inst/include/re2/re2.h'
  'inst/include/re2/regexp.h' 'src/dfa.cc' 'src/onepass.cc'
File 'readr/libs/i386/readr.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_WriteConnection'
File 'readr/libs/x64/readr.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.
'library' or 'require' calls to packages already attached by Depends:
  'leaps' 'mgcv'
  Please remove these calls from your code.
xy: warning in assign(xname, X, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
xy: warning in assign(yname, y, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
bestmods: no visible global function definition for 'abline'
bestmods: no visible global function definition for 'axis'
bestmods: no visible global function definition for 'lines'
cic: no visible global function definition for 'lsfit'
cic: no visible global function definition for 'var'
cvic: no visible global function definition for 'lsfit'
cvic: no visible global function definition for 'lm'
eic: no visible global function definition for 'lsfit'
eic: no visible global function definition for 'lm'
ic.min: no visible global function definition for 'lsfit'
scoremods: no visible global function definition for 'lsfit'
scoremods: no visible global function definition for 'var'
xy: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  abline axis lines lm lsfit rnorm var
Consider adding
  importFrom("graphics", "abline", "axis", "lines")
  importFrom("stats", "lm", "lsfit", "rnorm", "var")
to your NAMESPACE file.
Package required but not available: 'Rmosek'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
ReCiPa: no visible global function definition for 'count.fields'
ReCiPa: no visible global function definition for 'read.table'
Undefined global functions or variables:
  count.fields read.table
Consider adding
  importFrom("utils", "count.fields", "read.table")
to your NAMESPACE file.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
mergeNamespace_roclet: no visible global function definition for
  'new_roclet'
Undefined global functions or variables:
  new_roclet
AutoCorrelationLRtest: no visible global function definition for
  'logLik'
AutoCorrelationLRtest: no visible global function definition for
  'pchisq'
REEMtree: no visible global function definition for 'terms'
REEMtree: no visible binding for global variable 'SubsetVector'
REEMtree: no visible global function definition for 'predict'
REEMtree: no visible global function definition for 'logLik'
fitted.REEMtree: no visible global function definition for 'fitted'
plot.REEMtree: no visible global function definition for 'plot'
predict.REEMtree: no visible global function definition for 'predict'
residuals.REEMtree: no visible global function definition for
  'residuals'
Undefined global functions or variables:
  SubsetVector fitted logLik pchisq plot predict residuals terms
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "fitted", "logLik", "pchisq", "predict",
             "residuals", "terms")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'fitted.REEMtree':
  'fitted.REEMtree'

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

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

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

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

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

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
cook.outliers: no visible global function definition for 'lm'
cook.outliers: no visible global function definition for
  'cooks.distance'
nonparRI: no visible global function definition for 'quantile'
plot.interval: no visible global function definition for 'par'
plot.interval: no visible global function definition for 'plot.new'
plot.interval: no visible global function definition for 'plot.window'
plot.interval: no visible global function definition for 'segments'
plot.interval: no visible global function definition for 'axis'
plot.interval: no visible global function definition for 'title'
plot.interval: no visible global function definition for 'legend'
plot.interval: no visible global function definition for 'box'
plot.interval: no visible global function definition for 'text'
robust: no visible global function definition for 'qt'
singleRefLimit: no visible global function definition for 'qnorm'
singleRefLimit: no visible global function definition for
  'shapiro.test'
singleRefLimit: no visible global function definition for 'ks.test'
Undefined global functions or variables:
  axis box cooks.distance ks.test legend lm par plot.new plot.window
  qnorm qt quantile segments shapiro.test text title
Consider adding
  importFrom("graphics", "axis", "box", "legend", "par", "plot.new",
             "plot.window", "segments", "text", "title")
  importFrom("stats", "cooks.distance", "ks.test", "lm", "qnorm", "qt",
             "quantile", "shapiro.test")
to your NAMESPACE file.
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.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/refund.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'.
Data2wd: no visible binding for global variable 'var'
getRsq: no visible global function definition for 'var'
plot.wcr: no visible global function definition for 'plot'
plot.wcr: no visible global function definition for 'image'
plot.wcr: no visible global function definition for 'par'
plot.wnet: no visible global function definition for 'plot'
plot.wnet: no visible global function definition for 'image'
plot.wnet: no visible global function definition for 'par'
waveletGetCV: no visible binding for global variable 'median'
waveletGetCV: no visible binding for global variable 'sd'
wcr: no visible binding for global variable 'var'
wcr: no visible global function definition for 'cov'
wcr: no visible global function definition for 'lm'
wcr: no visible global function definition for 'ginv'
wcr: no visible global function definition for 'glm'
wnet: no visible binding for global variable 'var'
wnet: no visible global function definition for 'predict'
Undefined global functions or variables:
  cov ginv glm image lm median par plot predict sd var
Consider adding
  importFrom("graphics", "image", "par", "plot")
  importFrom("stats", "cov", "glm", "lm", "median", "predict", "sd",
             "var")
to your NAMESPACE file.
cluster.reg: no visible global function definition for 'rnorm'
cluster.reg: no visible global function definition for 'runif'
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
.area.my: no visible global function definition for 'density'
optimalGT : <anonymous>: no visible global function definition for
  'median'
optimalGT: no visible global function definition for 'png'
optimalGT: no visible global function definition for 'dev.off'
permutation: no visible global function definition for 'flush.console'
plot.wls: no visible global function definition for 'par'
plot.wls: no visible global function definition for 'plot'
plot.wls: no visible global function definition for 'text'
plot.wls: no visible global function definition for 'abline'
reGenotyper: no visible global function definition for 'flush.console'
reGenotyper: no visible binding for global variable 'var'
reGenotyper: no visible global function definition for 'plot'
Undefined global functions or variables:
  abline density dev.off flush.console median par plot png text var
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "abline", "par", "plot", "text")
  importFrom("stats", "density", "median", "var")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
binregtest: no visible global function definition for 'str'
binregtest: no visible binding for global variable 'str'
binregtest: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif str
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "str")
to your NAMESPACE file.
Package which this enhances but not available for checking: 'Rcplex'
.onAttach: no visible global function definition for
  'packageDescription'
.relax.cv.elnet: no visible global function definition for 'predict'
.relax.cv.elnet: no visible binding for global variable 'weighted.mean'
.relax.cv.lognet: no visible global function definition for 'predict'
.relax.cv.lognet: no visible binding for global variable
  'weighted.mean'
.relax.cvcompute: no visible binding for global variable
  'weighted.mean'
.single.column: no visible global function definition for 'glm'
.single.column: no visible global function definition for 'coef'
cv.alpha.relaxnet: no visible global function definition for
  'mc.reset.stream'
cv.alpha.relaxnet: no visible global function definition for 'mclapply'
cv.relaxnet: no visible global function definition for 'predict'
cv.relaxnet: no visible global function definition for
  'mc.reset.stream'
cv.relaxnet: no visible global function definition for 'mclapply'
predict.cv.alpha.relaxnet: no visible global function definition for
  'predict'
predict.cv.relaxnet: no visible global function definition for
  'predict'
predict.relaxnet: no visible global function definition for 'predict'
Undefined global functions or variables:
  coef glm mc.reset.stream mclapply packageDescription predict
  weighted.mean
Consider adding
  importFrom("stats", "coef", "glm", "predict", "weighted.mean")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
'library' or 'require' call to 'lars' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'lars'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
relaxo: no visible global function definition for 'lars'
Undefined global functions or variables:
  lars
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/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.
print.summary.rem: no visible global function definition for
  'printCoefmat'
print.summary.rem: no visible global function definition for 'pnorm'
print.summary.rem: no visible binding for global variable 'quantile'
print.summary.rem: no visible global function definition for 'pchisq'
print.summary.rem.dyad: no visible global function definition for
  'printCoefmat'
print.summary.rem.dyad: no visible global function definition for
  'pnorm'
print.summary.rem.dyad: no visible global function definition for
  'pchisq'
rem: no visible global function definition for 'rnorm'
rem: no visible global function definition for 'dnorm'
rem: no visible global function definition for 'runif'
rem: no visible global function definition for 'rchisq'
rem: no visible global function definition for 'cov'
rem.dyad: no visible global function definition for 'rnorm'
rem.dyad: no visible global function definition for 'optim'
rem.dyad: no visible global function definition for 'rchisq'
rem.dyad: no visible global function definition for 'quantile'
rem.dyad: no visible global function definition for 'sd'
rem.dyad: no visible global function definition for 'var'
rem.dyad.lprior: no visible global function definition for 'dnorm'
rem.dyad.lprior: no visible global function definition for 'dt'
Undefined global functions or variables:
  cov dnorm dt optim pchisq pnorm printCoefmat quantile rchisq rnorm
  runif sd var
Consider adding
  importFrom("stats", "cov", "dnorm", "dt", "optim", "pchisq", "pnorm",
             "printCoefmat", "quantile", "rchisq", "rnorm", "runif",
             "sd", "var")
to your NAMESPACE file.
CapDistSlope: no visible global function definition for 'coef'
CapDistSlope: no visible global function definition for 'lm'
EnergyEntropyDecomp: no visible global function definition for 'legend'
FernholzDecomp: no visible global function definition for 'legend'
Invest: no visible global function definition for 'par'
Invest: no visible global function definition for 'legend'
SimMarketModel: no visible global function definition for 'rnorm'
plot.capdist: no visible global function definition for 'plot'
plot.capdist: no visible global function definition for 'abline'
plot.capdist: no visible global function definition for 'lm'
plot.toymkt: no visible global function definition for 'par'
plot.toymkt: no visible global function definition for 'plot'
plot.toymkt: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline coef legend lm par plot rnorm
Consider adding
  importFrom("graphics", "abline", "legend", "par", "plot")
  importFrom("stats", "coef", "lm", "rnorm")
to your NAMESPACE file.
RearrangeData: no visible global function definition for 'rainbow'
RearrangeData: no visible global function definition for 'hclust'
RearrangeData: no visible global function definition for
  'as.dendrogram'
RearrangeData: no visible global function definition for 'heatmap'
RearrangeData: no visible global function definition for 'pdf'
RearrangeData: no visible global function definition for
  'colorRampPalette'
RearrangeData: no visible global function definition for 'legend'
RearrangeData: no visible global function definition for 'dev.off'
RearrangeJoseph: no visible global function definition for
  'write.table'
RearrangeJoseph: no visible global function definition for
  'as.dendrogram'
RearrangeJoseph: no visible global function definition for
  'order.dendrogram'
colorDendClass : colLab: no visible global function definition for
  'is.leaf'
colorDendClass: no visible global function definition for 'dendrapply'
colorDendClass: no visible global function definition for 'plot'
testData1: no visible global function definition for 'runif'
testData1: no visible global function definition for 'image'
testData2: no visible global function definition for 'runif'
testData2: no visible global function definition for 'image'
Undefined global functions or variables:
  as.dendrogram colorRampPalette dendrapply dev.off hclust heatmap
  image is.leaf legend order.dendrogram pdf plot rainbow runif
  write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf",
             "rainbow")
  importFrom("graphics", "image", "legend", "plot")
  importFrom("stats", "as.dendrogram", "dendrapply", "hclust", "heatmap",
             "is.leaf", "order.dendrogram", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file.
GlobTestMissing: no visible global function definition for 'lme'
GlobTestMissing: no visible global function definition for 'anova'
TestStatSP: no visible global function definition for 'pf'
TestStatSimple: no visible global function definition for 'ginv'
TestStatSimple: no visible global function definition for 'pf'
Undefined global functions or variables:
  anova ginv lme pf
Consider adding
  importFrom("stats", "anova", "pf")
to your NAMESPACE file.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    java   5.8Mb
CA: no visible global function definition for 'readClipboard'
LL: no visible global function definition for 'readClipboard'
US: no visible global function definition for 'readClipboard'
delete: no visible global function definition for 'menu'
doc_temp: no visible global function definition for 'menu'
html5: no visible global function definition for 'na.omit'
install_pandoc: no visible global function definition for
  'download.file'
latexlist: no visible global function definition for 'readClipboard'
new_report: no visible global function definition for 'tail'
new_report: no visible global function definition for 'head'
new_report: no visible global function definition for 'menu'
presentation: no visible global function definition for 'head'
presentation: no visible global function definition for 'tail'
presentation: no visible global function definition for 'menu'
repo2github: no visible global function definition for 'download.file'
repo2github: no visible global function definition for 'unzip'
reveal.js: no visible global function definition for 'na.omit'
strWrap: no visible global function definition for 'readClipboard'
update_bib: no visible global function definition for 'tail'
update_bib: no visible global function definition for 'menu'
Undefined global functions or variables:
  download.file head menu na.omit readClipboard tail unzip
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "download.file", "head", "menu", "readClipboard",
             "tail", "unzip")
to your NAMESPACE file.
MBoxtest: no visible global function definition for 'var'
jrparams: no visible global function definition for 'prcomp'
jrparams: no visible global function definition for 'predict'
jrparams: no visible global function definition for 'qchisq'
jrparams: no visible global function definition for 'qf'
Undefined global functions or variables:
  prcomp predict qchisq qf var
Consider adding
  importFrom("stats", "prcomp", "predict", "qchisq", "qf", "var")
to your NAMESPACE file.
call.eqs: no visible global function definition for 'write.table'
read.eqs: no visible global function definition for 'read.fwf'
Undefined global functions or variables:
  read.fwf write.table
Consider adding
  importFrom("utils", "read.fwf", "write.table")
to your NAMESPACE file.
Found the following significant warnings:
  reReg.c:132:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/reReg.Rcheck/00install.out' for details.
.resampleMakeFunction: no visible global function definition for 'is'
.resampleSetSeed: no visible global function definition for 'runif'
CI.bca: no visible global function definition for 'is'
CI.bca: no visible global function definition for 'qnorm'
CI.bca: no visible global function definition for 'pnorm'
CI.t: no visible global function definition for 'qt'
ExpandProbs: no visible global function definition for 'pnorm'
ExpandProbs: no visible global function definition for 'qt'
colVars : f: no visible global function definition for 'var'
colVars: no visible global function definition for 'var'
hist.resample: no visible global function definition for 'density'
hist.resample: no visible global function definition for 'lines'
hist.resample: no visible global function definition for 'points'
hist.resample: no visible global function definition for 'approx'
hist.resample: no visible global function definition for 'segments'
resample: no visible global function definition for 'is'
samp.bootknife: no visible global function definition for 'runif'
samp.bootstrap: no visible global function definition for 'runif'
Undefined global functions or variables:
  approx density is lines pnorm points qnorm qt runif segments var
Consider adding
  importFrom("graphics", "lines", "points", "segments")
  importFrom("methods", "is")
  importFrom("stats", "approx", "density", "pnorm", "qnorm", "qt",
             "runif", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages in Depends field not imported from:
  'gWidgets' 'gWidgetsRGtk2' 'plyr' 'reshape2'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
reshapeGUI: no visible global function definition for 'gwindow'
reshapeGUI: no visible global function definition for 'gnotebook'
reshapeGUI: no visible global function definition for 'size<-'
reshapeGUI: no visible global function definition for 'ggroup'
reshapeGUI: no visible global function definition for 'gtable'
reshapeGUI: no visible global function definition for 'addSpring'
reshapeGUI: no visible global function definition for 'gbutton'
reshapeGUI: no visible global function definition for 'glabel'
reshapeGUI: no visible global function definition for 'gedit'
reshapeGUI: no visible global function definition for 'gcheckbox'
reshapeGUI: no visible global function definition for 'gdf'
reshapeGUI: no visible global function definition for 'visible<-'
reshapeGUI: no visible global function definition for
  'addHandlerClicked'
reshapeGUI : <anonymous>: no visible global function definition for
  'gmessage'
reshapeGUI : <anonymous>: no visible global function definition for
  'svalue'
reshapeGUI : <anonymous>: no visible global function definition for
  'svalue<-'
reshapeGUI : <anonymous>: no visible global function definition for
  'delete'
reshapeGUI : <anonymous>: no visible global function definition for
  'add'
reshapeGUI : <anonymous>: no visible global function definition for
  'gdf'
reshapeGUI : <anonymous>: no visible global function definition for
  'visible<-'
reshapeGUI: no visible global function definition for
  'addHandlerChanged'
updateMeltCodeBox: no visible global function definition for 'svalue<-'
Undefined global functions or variables:
  add addHandlerChanged addHandlerClicked addSpring delete gbutton
  gcheckbox gdf gedit ggroup glabel gmessage gnotebook gtable gwindow
  size<- svalue svalue<- visible<-
GUI_template : onHelp: no visible global function definition for 'help'
Undefined global functions or variables:
  help
Consider adding
  importFrom("utils", "help")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from 'retimes' for: 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
dexgauss: no visible global function definition for 'pnorm'
loglik: no visible global function definition for 'pnorm'
mexgauss: no visible global function definition for 'sd'
rexgauss: no visible global function definition for 'rnorm'
rexgauss: no visible global function definition for 'rexp'
timefit: no visible global function definition for 'optim'
timefit: no visible global function definition for 'sd'
timefit: no visible global function definition for 'par'
timefit: no visible global function definition for 'hist'
timefit: no visible global function definition for 'density'
timefit: no visible global function definition for 'curve'
timefit: no visible global function definition for 'new'
plot,timefit: no visible global function definition for 'density'
plot,timefit: no visible global function definition for 'par'
plot,timefit: no visible global function definition for 'curve'
Undefined global functions or variables:
  curve density hist new optim par pnorm rexp rnorm sd
Consider adding
  importFrom("graphics", "curve", "hist", "par")
  importFrom("methods", "new")
  importFrom("stats", "density", "optim", "pnorm", "rexp", "rnorm", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following significant warnings:
  simul.cpp:82:21: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/revealedPrefs.Rcheck/00install.out' for details.
'library' or 'require' call to 'pso' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.reweight: no visible global function definition for 'par'
plot.reweight: no visible global function definition for 'plot'
plot.reweight: no visible global function definition for 'density'
plot.reweight: no visible global function definition for 'rug'
reweight: no visible global function definition for 'aggregate'
search.best.h: no visible global function definition for 'quantile'
Undefined global functions or variables:
  aggregate density par plot quantile rug
Consider adding
  importFrom("graphics", "par", "plot", "rug")
  importFrom("stats", "aggregate", "density", "quantile")
to your NAMESPACE file.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
FDSNGetTimeSeries: no visible global function definition for
  'download.file'
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
fs_author_ids : <anonymous>: no visible global function definition for
  'select.list'
fs_download : <anonymous>: no visible global function definition for
  'download.file'
Undefined global functions or variables:
  download.file select.list
Consider adding
  importFrom("utils", "download.file", "select.list")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'XML' 'xts'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
quoteFXTsData : function.fx: no visible global function definition for
  'xmlValue'
quoteFundTsData : function.fund: no visible global function definition
  for 'xmlValue'
quoteStockTsData : function.stock: no visible global function
  definition for 'xmlSize'
quoteStockTsData : function.stock: no visible global function
  definition for 'xmlValue'
quoteTsData: no visible global function definition for 'xmlRoot'
quoteTsData: no visible global function definition for 'htmlTreeParse'
quoteTsData: no visible global function definition for
  'xmlErrorCumulator'
quoteTsData: no visible global function definition for 'xmlSize'
toXts: no visible global function definition for 'as.xts'
Undefined global functions or variables:
  as.xts htmlTreeParse xmlErrorCumulator xmlRoot xmlSize xmlValue
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    java   5.2Mb
.testLTS: no visible binding for global variable 'stackloss'
Undefined global functions or variables:
  stackloss
Consider adding
  importFrom("datasets", "stackloss")
to your NAMESPACE file.
gabriel.plot: no visible global function definition for 'barplot'
gabriel.plot: no visible global function definition for 'arrows'
rgabriel: no visible binding for global variable 'sd'
rgabriel : psmm_x: no visible global function definition for 'pnorm'
rgabriel : psmm: no visible global function definition for 'integrate'
rgabriel : qsmm: no visible global function definition for 'qnorm'
rgabriel : qsmm: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  arrows barplot integrate pnorm qnorm sd uniroot
Consider adding
  importFrom("graphics", "arrows", "barplot")
  importFrom("stats", "integrate", "pnorm", "qnorm", "sd", "uniroot")
to your NAMESPACE file.
Package in Depends field not imported from: 'gsl'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
gammaIntegral: no visible global function definition for 'integrate'
gammaIntegral : <anonymous>: no visible global function definition for
  'hyperg_1F1'
gammaMLE: no visible global function definition for 'weighted.mean'
gammaMME: no visible binding for global variable 'sd'
gammaMME: no visible binding for global variable 'var'
Undefined global functions or variables:
  hyperg_1F1 integrate sd var weighted.mean
Consider adding
  importFrom("stats", "integrate", "sd", "var", "weighted.mean")
to your NAMESPACE file.
installed size is 80.2Mb
  sub-directories of 1Mb or more:
    gdal       3.9Mb
    libs      68.7Mb
    pictures   1.2Mb
    proj       5.0Mb
Found the following significant warnings:
  evaluate.cpp:787:18: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  evaluate.cpp:1097:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  evaluate.cpp:1207:19: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  evaluate.cpp:3172:18: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  print_format.cpp:57:18: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  print_format.cpp:71:18: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/rgenoud.Rcheck/00install.out' for details.
genoud: multiple local function definitions for 'fn1.bfgs' with
  different formal arguments
genoud: multiple local function definitions for 'gr1' with different
  formal arguments
genoud: multiple local function definitions for 'hess.fn' with
  different formal arguments
genoud_transform: multiple local function definitions for 'fn1.bfgs'
  with different formal arguments
genoud_transform: multiple local function definitions for 'gr1' with
  different formal arguments
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.7Mb
gexf.to.igraph: no visible global function definition for 'rgb'
igraph.to.gexf: no visible global function definition for 'col2rgb'
Undefined global functions or variables:
  col2rgb rgb
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
to your NAMESPACE file.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc     3.9Mb
    fonts   1.5Mb
    libs    2.0Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/RGoogleAnalytics.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
Running examples in 'RgoogleMaps-Ex.R' failed
The error most likely occurred in:

> ### Name: GetMap
> ### Title: download a static map from the Google server
> ### Aliases: GetMap
> 
> ### ** Examples
> 
>   lat = c(40.702147,40.718217,40.711614);
>   lon = c(-74.012318,-74.015794,-73.998284);
>   center = c(mean(lat), mean(lon));
>   zoom <- min(MaxZoom(range(lat), range(lon)));
>   #this overhead is taken care of implicitly by GetMap.bbox(); 
>   markers = paste0("&markers=color:blue|label:S|40.702147,-74.015794&markers=color:",
+                    "green|label:G|40.711614,-74.012318&markers=color:red|color:red|",
+                    "label:C|40.718217,-73.998284")
>   MyMap <- GetMap(center=center, zoom=zoom,markers=markers);
Warning in download.file(urlStr, destfile, mode = "wb", quiet = TRUE) :
  cannot open URL 'http://maps.google.com/maps/api/staticmap?center=40.7106593333333,-74.0087986666667&zoom=15&size=640x640&maptype=mobile&format=png32&sensor=true&markers=color:blue|label:S|40.702147,-74.015794&markers=color:green|label:G|40.711614,-74.012318&markers=color:red|color:red|label:C|40.718217,-73.998284': HTTP status was '403 Forbidden'
Error in download.file(urlStr, destfile, mode = "wb", quiet = TRUE) : 
  cannot open URL 'http://maps.google.com/maps/api/staticmap?center=40.7106593333333,-74.0087986666667&zoom=15&size=640x640&maptype=mobile&format=png32&sensor=true&markers=color:blue|label:S|40.702147,-74.015794&markers=color:green|label:G|40.711614,-74.012318&markers=color:red|color:red|label:C|40.718217,-73.998284'
Calls: GetMap -> download.file
Execution halted
Packages suggested but not available for checking: 'pmg' 'SVGAnnotation'
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extra   9.3Mb
'library' or 'require' call to 'gWidgetsRGtk2' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'RGtk2' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    R      3.6Mb
    help  10.6Mb
    libs   5.1Mb
File 'RGtk2/libs/i386/RGtk2.dll':
  Found non-API calls to R: 'R_new_custom_connection',
    'Rf_EncodeInteger', 'Rf_EncodeLogical', 'Rf_EncodeReal',
    'Rf_formatInteger', 'Rf_formatLogical', 'Rf_formatReal'
File 'RGtk2/libs/x64/RGtk2.dll':
  Found non-API calls to R: 'R_new_custom_connection',
    'Rf_EncodeInteger', 'Rf_EncodeLogical', 'Rf_EncodeReal',
    'Rf_formatInteger', 'Rf_formatLogical', 'Rf_formatReal'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc   9.8Mb
.quick_fetch: no visible global function definition for 'POST'
.quick_fetch: no visible global function definition for 'add_headers'
.quick_fetch: no visible global function definition for
  'stop_for_status'
.quick_fetch: no visible global function definition for 'content'
fetch_healthdata: no visible binding for global variable 'resources'
fetch_healthdata : <anonymous>: no visible binding for global variable
  'filters'
Undefined global functions or variables:
  POST add_headers content filters resources stop_for_status
Packages in Depends field not imported from:
  'RCurl' 'XML' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ECL: no visible global function definition for 'new'
ECLDataset: no visible global function definition for 'new'
ECLDedUp: no visible global function definition for 'new'
ECLDistribute: no visible global function definition for 'new'
ECLIterate: no visible global function definition for 'new'
ECLJoin: no visible global function definition for 'new'
ECLOutput: no visible global function definition for 'new'
ECLProject: no visible global function definition for 'new'
ECLRecord: no visible global function definition for 'new'
ECLRollUp: no visible global function definition for 'new'
ECLSort: no visible global function definition for 'new'
ECLTOPN: no visible global function definition for 'new'
ECLTable: no visible global function definition for 'new'
ECLTransform: no visible global function definition for 'new'
eclDirectCall: no visible global function definition for 'postForm'
parseResults: no visible global function definition for 'xmlRoot'
parseResults: no visible global function definition for 'xmlTreeParse'
parseResults: no visible global function definition for 'getNodeSet'
parseResults: no visible global function definition for 'xmlGetAttr'
parseResults: no visible global function definition for 'xmlValue'
parseResults: no visible global function definition for 'write.table'
Undefined global functions or variables:
  getNodeSet new postForm write.table xmlGetAttr xmlRoot xmlTreeParse
  xmlValue
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
RHT.2samp : my.HotellingT2 : my.InvCov2: no visible global function
  definition for 'cov'
RHT.2samp : get.lambda : get.para: no visible global function
  definition for 'optimize'
RHT.2samp : get.lambda : gg: no visible global function definition for
  'qchisq'
RHT.2samp : get.lambda : ggl: no visible global function definition for
  'qnorm'
RHT.2samp : <anonymous>: no visible global function definition for
  'cov'
RHT.fun : my.HotellingT : my.InvCov: no visible global function
  definition for 'cov'
RHT.fun : get.lambda : get.para: no visible global function definition
  for 'optimize'
RHT.fun : get.lambda : gg: no visible global function definition for
  'qchisq'
RHT.fun : get.lambda : ggl: no visible global function definition for
  'qnorm'
RHT.fun : <anonymous>: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov optimize qchisq qnorm
Consider adding
  importFrom("stats", "cov", "optimize", "qchisq", "qnorm")
to your NAMESPACE file.
FusedQDA : <anonymous>: no visible global function definition for 'cov'
RidgeFused: no visible binding for global variable 'cov2cor'
RidgeFusedCV : <anonymous>: no visible global function definition for
  'cov'
SSRidgeFused : <anonymous>: no visible global function definition for
  'cov'
Undefined global functions or variables:
  cov cov2cor
Consider adding
  importFrom("stats", "cov", "cov2cor")
to your NAMESPACE file.
ridit.raw: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
R2ngon: no visible global function definition for 'approx'
plotR2pre: no visible global function definition for 'plot'
plotR2pre: no visible global function definition for 'points'
plotR2pre: no visible global function definition for 'gray'
plotR2pre: no visible global function definition for 'legend'
plotR2pre: no visible global function definition for 'rainbow'
Undefined global functions or variables:
  approx gray legend plot points rainbow
Consider adding
  importFrom("grDevices", "gray", "rainbow")
  importFrom("graphics", "legend", "plot", "points")
  importFrom("stats", "approx")
to your NAMESPACE file.
plot.ijzip: no visible global function definition for 'plot'
plot.ijzip : <anonymous>: no visible global function definition for
  'plot'
plot.ijzip: no visible global function definition for 'axis'
read.ijzip: no visible global function definition for 'unzip'
Undefined global functions or variables:
  axis plot unzip
Consider adding
  importFrom("graphics", "axis", "plot")
  importFrom("utils", "unzip")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Quitting from lines 100-102 (rinatVignette.Rmd) 
Error: processing vignette 'rinatVignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
indexBytes: no visible global function definition for 'object.size'
rindexBytes: no visible global function definition for 'object.size'
Undefined global functions or variables:
  object.size
Consider adding
  importFrom("utils", "object.size")
to your NAMESPACE file.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    lib    3.5Mb
    libs   4.8Mb
File 'RInside/libs/i386/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/i386/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/i386/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/x64/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/i386/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/x64/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'library' or 'require' calls in package code:
  'doMC' 'doSNOW' 'e1071' 'fftw' 'foreach' 'jpeg' 'png' 'rggobi'
  'tkrplot'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'parallel' 'tcltk'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
desmat.sanitize: no visible global function definition for 'aggregate'
dispdist: no visible global function definition for 'quantile'
dispdist: no visible global function definition for 'hist'
dispdist: no visible global function definition for 'lines'
estate: no visible global function definition for 'weighted.mean'
estate: no visible global function definition for 'lm'
genperms: no visible global function definition for 'combn'
genprobexact: no visible global function definition for 'ave'
invert.ci: no visible global function definition for 'quantile'
invert.ci: no visible global function definition for 'uniroot'
omni.ate: no visible global function definition for 'hist'
omni.ate: no visible global function definition for 'lines'
omni.ate: no visible global function definition for 'quantile'
resresplot: no visible global function definition for 'lm'
resresplot: no visible global function definition for 'symbols'
resresplot: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline aggregate ave combn hist lines lm quantile symbols uniroot
  weighted.mean
Consider adding
  importFrom("graphics", "abline", "hist", "lines", "symbols")
  importFrom("stats", "aggregate", "ave", "lm", "quantile", "uniroot",
             "weighted.mean")
  importFrom("utils", "combn")
to your NAMESPACE file.
KM.plot: no visible global function definition for 'plot'
KM.plot: no visible global function definition for 'lines'
SchoenSmooth: no visible global function definition for 'lm'
llCoxReg: no visible binding for global variable 'time'
risksetAUC: no visible global function definition for 'abline'
risksetROC: no visible global function definition for 'abline'
weightedKM: no visible binding for global variable 'time'
Undefined global functions or variables:
  abline lines lm plot time
Consider adding
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "lm", "time")
to your NAMESPACE file.
Alg2: no visible global function definition for 'uniroot'
Alg3: no visible global function definition for 'optim'
NVCopula: no visible global function definition for 'rnorm'
NVCopula: no visible global function definition for 'rgamma'
NVCopula: no visible global function definition for 'var'
NVCopula: no visible global function definition for 'cov'
NVCopula: no visible global function definition for 'qnorm'
NVCopulaMT: no visible global function definition for 'rnorm'
NVCopulaMT: no visible global function definition for 'rgamma'
NVCopulaMT: no visible global function definition for 'var'
NVCopulaMT: no visible global function definition for 'cov'
NVCopulaMT: no visible global function definition for 'qnorm'
R2X: no visible global function definition for 'write.table'
ReturnCopula: no visible global function definition for 'qt'
ReturnCopula: no visible global function definition for 'pt'
SISCopula: no visible global function definition for 'runif'
SISCopula: no visible global function definition for 'qnorm'
SISCopula: no visible global function definition for 'rnorm'
SISCopula: no visible global function definition for 'qgamma'
SISCopula: no visible global function definition for 'var'
SISCopula: no visible global function definition for 'cov'
SISCopulaMT: no visible global function definition for 'runif'
SISCopulaMT: no visible global function definition for 'qnorm'
SISCopulaMT: no visible global function definition for 'rnorm'
SISCopulaMT: no visible global function definition for 'qgamma'
SISCopulaMT: no visible global function definition for 'var'
SISCopulaMT: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov optim pt qgamma qnorm qt rgamma rnorm runif uniroot var
  write.table
Consider adding
  importFrom("stats", "cov", "optim", "pt", "qgamma", "qnorm", "qt",
             "rgamma", "rnorm", "runif", "uniroot", "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
rite : exitWiz: no visible global function definition for 'bringToTop'
rite : loadHistory: no visible global function definition for
  'savehistory'
rite : saveGist: no visible global function definition for 'browseURL'
rite : uploadToRPubs : processEntry: no visible global function
  definition for 'browseURL'
rite : runCode: no visible global function definition for 'savehistory'
rite : runCode: no visible global function definition for 'loadhistory'
rite : knittxt: no visible global function definition for 'Sweave'
rite : knittxt: no visible global function definition for 'browseURL'
rite : addHighlighting : addHighlight: no visible global function
  definition for 'packageDescription'
rite : addHighlighting : addHighlight: no visible global function
  definition for 'na.omit'
rite : about : <anonymous>: no visible global function definition for
  'browseURL'
rite : <anonymous>: no visible global function definition for
  'capture.output'
rite : <anonymous>: no visible global function definition for
  'update.packages'
rite : <anonymous>: no visible global function definition for 'help'
rite : f1: no visible global function definition for 'help'
rite : f1: no visible global function definition for 'help.search'
rite : commandCompletion: no visible global function definition for
  'apropos'
rite : findreplace : <anonymous>: no visible global function definition
  for 'browseURL'
Undefined global functions or variables:
  Sweave apropos bringToTop browseURL capture.output help help.search
  loadhistory na.omit packageDescription savehistory update.packages
Consider adding
  importFrom("grDevices", "bringToTop")
  importFrom("stats", "na.omit")
  importFrom("utils", "Sweave", "apropos", "browseURL", "capture.output",
             "help", "help.search", "loadhistory", "packageDescription",
             "savehistory", "update.packages")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'compiler' 'signal'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
NumConv: no visible global function definition for 'pchip'
NumConv: no visible global function definition for 'cmpfun'
NumDeconv: no visible global function definition for 'pchip'
NumDeconv : error_function: no visible global function definition for
  'pchip'
NumDeconv: no visible global function definition for 'cmpfun'
NumDeconv: no visible global function definition for 'optim'
RivivcA: no visible global function definition for 'lm'
Undefined global functions or variables:
  cmpfun lm optim pchip
Consider adding
  importFrom("stats", "lm", "optim")
to your NAMESPACE file.
Tbsb : ksiint: no visible global function definition for 'pgamma'
Tbsb: no visible global function definition for 'pchisq'
Tbsc: no visible global function definition for 'qchisq'
riv_classical: no visible global function definition for 'cov'
riv_classical: no visible global function definition for 'pt'
riv_sest: no visible global function definition for 'pt'
riv_sest: no visible global function definition for 'mad'
riv_sest: no visible global function definition for 'mahalanobis'
riv_withDummies: no visible global function definition for 'coef'
riv_withDummies : <anonymous>: no visible global function definition
  for 'coef'
Undefined global functions or variables:
  coef cov mad mahalanobis pchisq pgamma pt qchisq
Consider adding
  importFrom("stats", "coef", "cov", "mad", "mahalanobis", "pchisq",
             "pgamma", "pt", "qchisq")
to your NAMESPACE file.
Found the following significant warnings:
  jri.h:21:20: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  jri.c:308:27: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  jri_glue.c:24:15: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.5/rJava.Rcheck/00install.out' for details.
Found the following possibly unsafe calls:
File 'rJava/R/import.R':
  unlockBinding(IMPORTER, env = env)
  assignInNamespace(IMPORTER, importer, envir = env)
File 'rJava/R/jinit.R':
  unlockBinding(x, .env)
  unlockBinding(x, pe)
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.5/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.
Undocumented S4 methods:
  generic 'dbExistsTable' and siglist 'JDBCConnection,ANY'
  generic 'dbListFields' and siglist 'JDBCConnection,ANY'
  generic 'dbRemoveTable' and siglist 'JDBCConnection,ANY'
  generic 'dbWriteTable' and siglist 'JDBCConnection,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
cubeHelix : <anonymous>: no visible global function definition for
  'rgb'
rdirichlet: no visible global function definition for 'rgamma'
Undefined global functions or variables:
  rgamma rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "rgamma")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/rJPSGCS.Rcheck/00install.out' for details.
getStatsData: no visible global function definition for 'xmlRoot'
getStatsData: no visible global function definition for 'xmlTreeParse'
getStatsData: no visible global function definition for 'xmlValue'
getStatsData: no visible global function definition for 'getNodeSet'
getStatsData: no visible global function definition for 'xmlSApply'
getStatsData: no visible binding for global variable 'xmlGetAttr'
getStatsData: no visible binding for global variable 'xmlValue'
getStatsData: no visible global function definition for 'new'
getStatsList: no visible global function definition for 'xmlRoot'
getStatsList: no visible global function definition for 'xmlTreeParse'
getStatsList: no visible global function definition for 'xmlValue'
getStatsList: no visible binding for global variable 'xmlGetAttr'
getStatsList : <anonymous>: no visible global function definition for
  'xmlValue'
getStatsList : <anonymous>: no visible global function definition for
  'xmlGetAttr'
print.jpstat: no visible global function definition for 'head'
Undefined global functions or variables:
  getNodeSet head new xmlGetAttr xmlRoot xmlSApply xmlTreeParse
  xmlValue
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "head")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following significant warnings:
  libjson/Source/JSONGlobals.h:43:50: warning: invoking macro json_global_decl argument 3: empty macro arguments are undefined in ISO C90 and ISO C++98
  libjson/Source/JSONGlobals.h:44:49: warning: invoking macro json_global_decl argument 3: empty macro arguments are undefined in ISO C90 and ISO C++98
  libjson/Source/JSONSharedString.h:297:17: warning: 'json_shared_string::len' will be initialized after [-Wreorder]
  libjson/Source/JSONSharedString.h:295:40: warning:   'json_shared_string::json_shared_string_internal* json_shared_string::_str' [-Wreorder]
  libjson/Source/JSONSharedString.h:180:9: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONSharedString.h:182:9: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONStream.h:79:7: warning: 'JSONStream::state' will be initialized after [-Wreorder]
  libjson/Source/JSONStream.h:76:28: warning:   'void (* JSONStream::call)(void*, void*)' [-Wreorder]
  JSONStream.cpp:8:1: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONStream.h:77:27: warning: 'JSONStream::err_call' will be initialized after [-Wreorder]
  libjson/Source/JSONStream.h:75:17: warning:   'json_string JSONStream::buffer' [-Wreorder]
  JSONStream.cpp:12:1: warning:   when initialized here [-Wreorder]
  JSONValidator.cpp:394:105: warning: invoking macro JSON_ASSERT_SAFE argument 3: empty macro arguments are undefined in ISO C90 and ISO C++98
  JSONValidator.cpp:397:104: warning: invoking macro JSON_ASSERT_SAFE argument 3: empty macro arguments are undefined in ISO C90 and ISO C++98
  libjson/Source/internalJSONNode.h:257:18: warning: 'internalJSONNode::_name_encoded' will be initialized after [-Wreorder]
  libjson/Source/internalJSONNode.h:256:17: warning:   'json_string internalJSONNode::_name' [-Wreorder]
  internalJSONNode.cpp:78:1: warning:   when initialized here [-Wreorder]
See 'd:/Rcompile/CRANpkg/local/3.5/RJSONIO.Rcheck/00install.out' for details.
'library' or 'require' call to 'rJava' which was already attached by Depends.
  Please remove these calls from your code.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
cv.coef: no visible global function definition for 'sd'
normalize.softmax: no visible global function definition for 'plogis'
plot.rknnBeg: no visible global function definition for 'plot'
plot.rknnBel: no visible global function definition for 'plot'
plot.rknnSupport: no visible global function definition for 'dotchart'
predicted: no visible global function definition for 'influence'
predicted: no visible global function definition for 'fitted'
predicted: no visible global function definition for 'resid'
pressresid: no visible global function definition for 'influence'
pressresid: no visible global function definition for 'resid'
Undefined global functions or variables:
  dotchart fitted influence plogis plot resid sd
Consider adding
  importFrom("graphics", "dotchart", "plot")
  importFrom("stats", "fitted", "influence", "plogis", "resid", "sd")
to your NAMESPACE file.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
':::' calls which should be '::':
  'stats:::dexp' 'stats:::dgamma' 'stats:::dweibull' 'stats:::pexp'
  'stats:::pgamma' 'stats:::pweibull' 'stats:::qexp' 'stats:::qgamma'
  'stats:::qweibull' 'stats:::rexp' 'stats:::rgamma' 'stats:::rweibull'
  See the note in ?`:::` about the use of this operator.
Found the following significant warnings:
  PresenceAndAbsence.cpp:536:14: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  PresenceAndAbsence.cpp:537:14: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/Rlda.Rcheck/00install.out' for details.
Found the following Makefile(s) without a final LF:
  src/Makevars.in
Some 'make' programs ignore lines not ending in LF.
Package in Depends field not imported from: 'msm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'EMSRb_internal' 'EM_internal' 'PD_internal'
EMSRb_internal: no visible global function definition for 'qnorm'
EM_internal: no visible global function definition for 'dnorm'
EM_internal: no visible global function definition for 'pnorm'
PD_internal: no visible global function definition for 'qtnorm'
PD_internal: no visible global function definition for 'sd'
Undefined global functions or variables:
  dnorm pnorm qnorm qtnorm sd
Consider adding
  importFrom("stats", "dnorm", "pnorm", "qnorm", "sd")
to your NAMESPACE file.
ma.filter: no visible global function definition for 'par'
ma.filter: no visible global function definition for 'lines'
ma.filter: no visible global function definition for 'abline'
qn: no visible global function definition for 'lm'
qn: no visible global function definition for 'var'
qn: no visible global function definition for 'resid'
ss.filter: no visible global function definition for 'smooth.spline'
ss.filter: no visible global function definition for 'par'
ss.filter: no visible global function definition for 'lines'
ss.filter: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline lines lm par resid smooth.spline var
Consider adding
  importFrom("graphics", "abline", "lines", "par")
  importFrom("stats", "lm", "resid", "smooth.spline", "var")
to your NAMESPACE file.
Mallows: no visible global function definition for 'runif'
Mallows: no visible global function definition for 'x11'
Mallows: no visible global function definition for 'plot'
Mallows: no visible global function definition for 'dev.off'
UpdateLambda: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  dev.off plot runif uniroot x11
Consider adding
  importFrom("grDevices", "dev.off", "x11")
  importFrom("graphics", "plot")
  importFrom("stats", "runif", "uniroot")
to your NAMESPACE file.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    rmd   5.9Mb
.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/i386/RMC.dll':
  Found '_ZSt4cout', possibly from 'std::cout' (C++)
    Objects: 'RMC.o', 'predict.o'
  Found 'rand', possibly from 'rand' (C)
    Object: 'ap.o'
File 'RMC/libs/x64/RMC.dll':
  Found '_ZSt4cout', possibly from 'std::cout' (C++)
    Objects: 'RMC.o', 'predict.o'
  Found 'rand', possibly from 'rand' (C)
    Object: 'ap.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor 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:
    R      2.0Mb
    libs   2.1Mb
CI: no visible global function definition for 'sd'
CI: no visible global function definition for 'qt'
L: no visible global function definition for 'sd'
L: no visible global function definition for 'residuals'
Qa: no visible global function definition for 'logLik'
Qb: no visible global function definition for 'residuals'
Qc: no visible global function definition for 'residuals'
Qc: no visible global function definition for 'logLik'
STDERR: no visible global function definition for 'sd'
group.UCL: no visible global function definition for 'aggregate'
lr.glover: no visible binding for global variable 'logLik'
lr.glover: no visible binding for global variable 'update'
lr.glover : nobs0: no visible binding for global variable 'nobs'
lr.glover : nobs0 : nobs2: no visible global function definition for
  'residuals'
lr.glover : tlab: no visible global function definition for 'terms'
lr.glover : name: no visible global function definition for 'formula'
lr.glover : modelUpdate: no visible global function definition for
  'as.formula'
lr.glover: no visible global function definition for 'model.frame'
lr.glover: no visible binding for global variable 'AIC'
lr.glover: no visible binding for global variable 'BIC'
summarySE : <anonymous>: no visible global function definition for 'sd'
summarySE: no visible global function definition for 'qt'
Undefined global functions or variables:
  AIC BIC aggregate as.formula formula logLik model.frame nobs qt
  residuals sd terms update
Consider adding
  importFrom("stats", "AIC", "BIC", "aggregate", "as.formula", "formula",
             "logLik", "model.frame", "nobs", "qt", "residuals", "sd",
             "terms", "update")
to your NAMESPACE file.
Combi: no visible global function definition for 'new'
barplotMixCluster: no visible global function definition for 'is'
barplotMixCluster: no visible global function definition for 'par'
barplotMixCluster: no visible global function definition for 'lines'
barplotMixCluster: no visible global function definition for 'text'
barplotMixCluster: no visible global function definition for 'title'
barplotMixCluster: no visible global function definition for 'mtext'
histMixCluster: no visible global function definition for 'is'
histMixCluster: no visible global function definition for 'par'
histMixCluster: no visible global function definition for 'dnorm'
histMixCluster: no visible global function definition for 'lines'
mixmodEntPlot: no visible global function definition for 'par'
mixmodEntPlot: no visible global function definition for 'lines'
mixmodEntPlot: no visible global function definition for 'axis'
mixmodEntPlot: no visible global function definition for 'title'
mixmodEntPlot: no visible binding for global variable 'par'
plot,MixmodCombi: no visible global function definition for 'par'
plot,MixmodCombi: no visible global function definition for 'plot.new'
plot,MixmodCombi: no visible global function definition for 'title'
Undefined global functions or variables:
  axis dnorm is lines mtext new par plot.new text title
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "par", "plot.new",
             "text", "title")
  importFrom("methods", "is", "new")
  importFrom("stats", "dnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
.pLGP_qvec: no visible global function definition for 'ppois'
.qLGP_pvec: no visible global function definition for 'qpois'
.rLGP.failsafe: no visible global function definition for 'runif'
.subdmg: no visible global function definition for 'dbinom'
dnegbin: no visible global function definition for 'dnbinom'
pLGP: no visible global function definition for 'ppois'
qLGP: no visible global function definition for 'qpois'
rLGP: no visible global function definition for 'rpois'
rLGP: no visible global function definition for 'rnorm'
rLGP: no visible global function definition for 'runif'
rbinegbin: no visible global function definition for 'rnbinom'
rmanaclash: no visible global function definition for 'rbinom'
rmanaclash: no visible global function definition for 'runif'
Undefined global functions or variables:
  dbinom dnbinom ppois qpois rbinom rnbinom rnorm rpois runif
Consider adding
  importFrom("stats", "dbinom", "dnbinom", "ppois", "qpois", "rbinom",
             "rnbinom", "rnorm", "rpois", "runif")
to your NAMESPACE file.
predict.MOA_trainedmodel: no visible global function definition for
  'delete.response'
predict.MOA_trainedmodel: no visible global function definition for
  'model.frame'
trainMOA: no visible binding for global variable 'na.exclude'
Undefined global functions or variables:
  delete.response model.frame na.exclude
Consider adding
  importFrom("stats", "delete.response", "model.frame", "na.exclude")
to your NAMESPACE file.
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/Rmosek.Rcheck/00install.out' for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/Rmpi.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:
  npmpois.c:246:38: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  rmg.c:335:38: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/rmp.Rcheck/00install.out' for details.
CoeffYWeq: no visible global function definition for 'index'
fitdistrForPrecipitation: no visible global function definition for
  'fitdistr'
generate.CCGammaObject: no visible binding for global variable 'rnorm'
generate.CCGammaObject: no visible global function definition for
  'pnorm'
generate.YuleWalkerCoefficientBlockmatrices: no visible binding for
  global variable 'rnorm'
generate.YuleWalkerCoefficientBlockmatricesPerEachMonth: no visible
  binding for global variable 'rnorm'
generatePrecipitationAmount: no visible global function definition for
  'str'
omega_inv: no visible global function definition for 'uniroot'
qqfit: no visible binding for global variable 'qexp'
qqfit: no visible global function definition for 'ecdf'
Undefined global functions or variables:
  ecdf fitdistr index pnorm qexp rnorm str uniroot
Consider adding
  importFrom("stats", "ecdf", "pnorm", "qexp", "rnorm", "uniroot")
  importFrom("utils", "str")
to your NAMESPACE file.
rms.pval: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
dWishartSpike: no visible global function definition for 'dnorm'
pWishartSpike: no visible global function definition for 'pnorm'
qWishartSpike: no visible global function definition for 'qnorm'
rWishartSpike: no visible global function definition for 'qnorm'
rmp: no visible global function definition for 'runif'
rtw: no visible global function definition for 'runif'
Undefined global functions or variables:
  dnorm pnorm qnorm runif
Consider adding
  importFrom("stats", "dnorm", "pnorm", "qnorm", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/RM.weights.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
'library' or 'require' calls in package code:
  'DESeq' 'seqinr' 'topGO'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: 'rnaturalearthhires'
.isPath: no visible global function definition for 'tail'
.isPath: no visible global function definition for 'head'
navGraph : <anonymous>: no visible global function definition for
  'tail'
navGraph : <anonymous>: no visible global function definition for 'sd'
navGraph: no visible global function definition for 'colors'
ng_image_array_gray : <anonymous>: no visible global function
  definition for 'grey'
scagGraph: no visible global function definition for 'quantile'
closeViz,NG_Viz2DAxis: no visible global function definition for
  'dev.off'
initializeViz,NG_Viz2DAxis: no visible global function definition for
  'dev.new'
initializeViz,NG_Viz2DAxis: no visible global function definition for
  'dev.cur'
plot,NG_graph-ANY: no visible global function definition for 'box'
plot,NG_graph-ANY: no visible global function definition for 'axis'
plot,NG_graph-ANY: no visible global function definition for 'points'
plot,NG_graph-ANY: no visible global function definition for 'text'
plot,NG_graph-ANY: no visible global function definition for 'segments'
updateViz,NG_Viz2DAxis: no visible global function definition for
  'dev.set'
Undefined global functions or variables:
  axis box colors dev.cur dev.new dev.off dev.set grey head points
  quantile sd segments tail text
Consider adding
  importFrom("grDevices", "colors", "dev.cur", "dev.new", "dev.off",
             "dev.set", "grey")
  importFrom("graphics", "axis", "box", "points", "segments", "text")
  importFrom("stats", "quantile", "sd")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.5/progress/include/RProgress.h:172:27: warning: ISO C++ forbids variable length array 'bar' [-Wvla]
  d:/RCompile/CRANpkg/lib/3.5/progress/include/RProgress.h:220:26: warning: ISO C++ forbids variable length array 'spaces' [-Wvla]
See 'd:/Rcompile/CRANpkg/local/3.5/rncl.Rcheck/00install.out' for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Packages suggested but not available for checking: 'rrdf' 'Sxslt'
.collapse: no visible global function definition for 'head'
RNGinfo: no visible global function definition for 'setNames'
RNGlibs: no visible global function definition for 'tail'
RNGseq : <anonymous>: no visible global function definition for
  'nextRNGStream'
RNGseq: no visible global function definition for 'nextRNGStream'
RNGseq_seed: no visible global function definition for 'runif'
RNGseq_seed: no visible global function definition for 'nextRNGStream'
checkRNG: no visible global function definition for 'checkTrue'
nextRNG: no visible global function definition for 'runif'
.setRNG,numeric: no visible global function definition for 'runif'
Undefined global functions or variables:
  checkTrue head nextRNGStream runif setNames tail
Consider adding
  importFrom("stats", "runif", "setNames")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
well19937.validate: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      5.5Mb
Nnls.trimW : fun1: no visible global function definition for 'runif'
initM: no visible global function definition for 'runif'
rnmf: no visible global function definition for 'txtProgressBar'
rnmf: no visible global function definition for 'setTxtProgressBar'
see: no visible global function definition for 'heat.colors'
see: no visible global function definition for 'colorRampPalette'
see: no visible global function definition for 'grey'
see: no visible global function definition for 'par'
see: no visible global function definition for 'image'
see: no visible global function definition for 'mtext'
simtum: no visible global function definition for 'runif'
simtum: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  colorRampPalette grey heat.colors image mtext par rnorm runif
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("grDevices", "colorRampPalette", "grey", "heat.colors")
  importFrom("graphics", "image", "mtext", "par")
  importFrom("stats", "rnorm", "runif")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Error : Oops, API did not return json after calling '§dldl  ':
        check your query - or api.oadoi.org may experience problems
Quitting from lines 177-178 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
Oops, API did not return json after calling '10.7705/biomedica.v34i3.2134':
        check your query - or api.oadoi.org may experience problems
Execution halted
'library' or 'require' calls in package code:
  'robustbase' 'sfsmisc'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.BuildPartial: no visible global function definition for 'as.formula'
.BuildPartial: no visible global function definition for 'residuals'
.PairwiseCorrelation : .Standardize : <anonymous>: no visible global
  function definition for 'na.omit'
.PairwiseCorrelation : .Standardize: no visible binding for global
  variable 'median'
.PairwiseCorrelation: no visible global function definition for
  'complete.cases'
.yw: no visible global function definition for 'toeplitz'
FastQn: no visible global function definition for 'median'
FastQn: no visible global function definition for 'mad'
fqn: no visible global function definition for 'median'
fqn: no visible global function definition for 'mad'
psdcor: no visible global function definition for 'posdefify'
psdcor: no visible global function definition for 'nearcor'
robar: no visible global function definition for 'frequency'
robcor: no visible global function definition for 'covMcd'
s_FastQn: no visible global function definition for 'median'
Undefined global functions or variables:
  as.formula complete.cases covMcd frequency mad median na.omit nearcor
  posdefify residuals toeplitz
Consider adding
  importFrom("stats", "as.formula", "complete.cases", "frequency", "mad",
             "median", "na.omit", "residuals", "toeplitz")
to your NAMESPACE file.
QD2coef.f: no visible global function definition for 'ppoints'
QD2coef.f: no visible global function definition for 'lsfit'
QD2funC.f: no visible global function definition for 'ppoints'
QD2funC.f: no visible global function definition for 'lsfit'
gminit: no visible global function definition for 'var'
lywalg: no visible global function definition for 'median'
qloggamma: no visible global function definition for 'qgamma'
qloggamma: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  lsfit median ppoints qgamma qnorm var
Consider adding
  importFrom("stats", "lsfit", "median", "ppoints", "qgamma", "qnorm",
             "var")
to your NAMESPACE file.
Package in Depends field not imported from: 'ROptRegTS'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
RobRSVD: no visible global function definition for 'median'
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
Package suggested but not available for checking: 'SSOAP'
'LinkingTo' for
  'mgcv' 'robustbase'
are unused as they have no 'include' directory
Packages in Depends field not imported from:
  'Rcpp' 'RcppArmadillo' 'mgcv' 'robustbase'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GIC: no visible global function definition for 'integrate'
QM.poisson: no visible global function definition for 'ppois'
QM.poisson: no visible global function definition for 'dpois'
cplot.robustgam: no visible global function definition for 'plot'
expect.poisson: no visible global function definition for 'dpois'
expect.poisson: no visible global function definition for 'ppois'
pred.robustgam: no visible global function definition for
  'Predict.matrix'
robust.sigma: no visible global function definition for 'median'
robustgam: no visible global function definition for 's'
robustgam: no visible global function definition for
  'smooth.construct.tp.smooth.spec'
robustgam: no visible global function definition for
  'smooth.construct.cr.smooth.spec'
robustgam: no visible global function definition for
  'smooth.construct.ps.smooth.spec'
robustgam : w.fun: no visible global function definition for 'covMcd'
robustgam.GIC.optim: no visible global function definition for 'optim'
robustgam.crossval : w.fun: no visible global function definition for
  'covMcd'
robustgam.crossval: no visible global function definition for
  'integrate'
smooth.construct.tr.smooth.spec: no visible global function definition
  for 'quantile'
w.binomial: no visible global function definition for 'pbinom'
w.poisson: no visible global function definition for 'ppois'
Undefined global functions or variables:
  Predict.matrix covMcd dpois integrate median optim pbinom plot ppois
  quantile s smooth.construct.cr.smooth.spec
  smooth.construct.ps.smooth.spec smooth.construct.tp.smooth.spec
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dpois", "integrate", "median", "optim", "pbinom",
             "ppois", "quantile")
to your NAMESPACE file.
aggregateRanks: no visible binding for global variable 'median'
aggregateRanks: no visible global function definition for 'pnorm'
betaScores: no visible global function definition for 'pbeta'
correctBetaPvaluesExact: no visible binding for global variable 'qbeta'
thresholdBetaScore: no visible global function definition for 'pbeta'
Undefined global functions or variables:
  median pbeta pnorm qbeta
Consider adding
  importFrom("stats", "median", "pbeta", "pnorm", "qbeta")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'penalized' 'splines' 'survival' 'survivalROC'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
boot.ROC: no visible global function definition for 'qnorm'
boot.ROC: no visible global function definition for 'penalized'
boot.ROC: no visible global function definition for 'coefficients'
boot.ROC: no visible global function definition for 'sd'
boot.ROC: no visible global function definition for 'optL1'
boot.ROCt: no visible global function definition for 'qnorm'
boot.ROCt: no visible global function definition for 'penalized'
boot.ROCt: no visible global function definition for 'Surv'
boot.ROCt: no visible global function definition for 'coefficients'
boot.ROCt: no visible global function definition for 'sd'
boot.ROCt: no visible global function definition for 'survivalROC'
boot.ROCt: no visible global function definition for 'optL1'
Undefined global functions or variables:
  Surv coefficients optL1 penalized qnorm sd survivalROC
Consider adding
  importFrom("stats", "coefficients", "qnorm", "sd")
to your NAMESPACE file.
'library' or 'require' call to 'ROCR' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'ROCR'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
o.rocc: warning in factor(pr, level = c(0, 1)): partial argument match
  of 'level' to 'levels'
p.rocc: warning in factor(pr, level = c(0, 1)): partial argument match
  of 'level' to 'levels'
o.rocc: no visible global function definition for 'prediction'
o.rocc: no visible global function definition for 'performance'
o.rocc: no visible global function definition for 'binom.test'
tr.rocc: no visible global function definition for 'prediction'
tr.rocc: no visible global function definition for 'performance'
Undefined global functions or variables:
  binom.test performance prediction
Consider adding
  importFrom("stats", "binom.test")
to your NAMESPACE file.
NPROCwoGS: no visible global function definition for 'quantile'
NPROCwoGS : rdirichlet: no visible global function definition for
  'rgamma'
NPROCwoGS: no visible global function definition for 'rbinom'
NPROCwoGS: no visible global function definition for 'rbeta'
NPROCwoGS: no visible binding for global variable 'quantile'
Undefined global functions or variables:
  quantile rbeta rbinom rgamma
Consider adding
  importFrom("stats", "quantile", "rbeta", "rbinom", "rgamma")
to your NAMESPACE file.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'RODBC'
A package should be listed in only one of these fields.
'library' or 'require' call to 'RODBC' which was already attached by Depends.
  Please remove these calls from your code.
Package required but not available: 'Rcplex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package which this enhances but not available for checking: 'ROI.plugin.cplex'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/ROracle.Rcheck/00install.out' for details.
ROSE.eval: no visible global function definition for 'methods'
ROSE.eval: no visible binding for global variable 'model.frame'
ROSE.eval: no visible binding for global variable 'predict'
adj.formula: no visible global function definition for 'terms'
adj.formula: no visible global function definition for 'as.formula'
omnibus.balancing: no visible binding for global variable 'model.frame'
ou.sampl: no visible global function definition for 'rbinom'
over.sampl: no visible global function definition for 'rbinom'
plot.roc.inner: no visible global function definition for 'plot'
roc.curve: no visible global function definition for 'lines'
roc.curve: no visible global function definition for 'abline'
rose.real: no visible binding for global variable 'sd'
rose.real: no visible global function definition for 'sd'
rose.real: no visible global function definition for 'rnorm'
rose.sampl: no visible global function definition for 'rbinom'
under.sampl: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  abline as.formula lines methods model.frame plot predict rbinom rnorm
  sd terms
Consider adding
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "as.formula", "model.frame", "predict", "rbinom",
             "rnorm", "sd", "terms")
  importFrom("utils", "methods")
to your NAMESPACE file.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.3Mb
    libs   2.2Mb
bestFM: no visible global function definition for 'data'
gaRoth: no visible global function definition for 'data'
ros: no visible global function definition for 'na.omit'
rosunc: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  data na.omit rnorm
Consider adding
  importFrom("stats", "na.omit", "rnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
mfix : m4m: no visible global function definition for 'median'
rrfa: no visible global function definition for 'predict'
rrfb: no visible global function definition for 'predict'
rrfc1: no visible global function definition for 'predict'
rrfc2: no visible global function definition for 'predict'
rrfc3: no visible global function definition for 'predict'
rrfc4: no visible global function definition for 'predict'
rrfc5 : regdat: no visible global function definition for 'predict'
rrfc5 : regdat: no visible global function definition for 'glm'
rrfc5: no visible global function definition for 'predict'
rrfc6: no visible global function definition for 'predict'
rrfc7: no visible global function definition for 'predict'
rrfd: no visible global function definition for 'predict'
rrfe : rdms: no visible global function definition for 'rbinom'
rrfe: no visible global function definition for 'predict'
Undefined global functions or variables:
  glm median predict rbinom
Consider adding
  importFrom("stats", "glm", "median", "predict", "rbinom")
to your NAMESPACE file.
.computeValueReduct: no visible global function definition for 'combn'
.findAllReductsFromCore: no visible global function definition for
  'combn'
.findFirstReductsFromCore: no visible global function definition for
  'combn'
.findSmallestReductFamilyFromCore: no visible global function
  definition for 'combn'
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'cbind.fill':
  'cbind.fill'

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.
royston.test: no visible global function definition for 'shapiro.test'
royston.test: no visible global function definition for 'cor'
royston.test: no visible global function definition for 'qnorm'
royston.test: no visible global function definition for 'pnorm'
royston.test: no visible global function definition for 'cov'
royston.test: no visible global function definition for 'mahalanobis'
royston.test: no visible global function definition for 'qqplot'
royston.test: no visible global function definition for 'qchisq'
royston.test: no visible global function definition for 'ppoints'
royston.test: no visible global function definition for 'abline'
royston.test: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  abline cor cov mahalanobis pchisq pnorm ppoints qchisq qnorm qqplot
  shapiro.test
Consider adding
  importFrom("graphics", "abline")
  importFrom("stats", "cor", "cov", "mahalanobis", "pchisq", "pnorm",
             "ppoints", "qchisq", "qnorm", "qqplot", "shapiro.test")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'MASS' 'RandomFields' 'akima' 'denstrip' 'geoR' 'lattice' 'maps'
  'mgcv' 'rgl' 'sm' 'tkrplot'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'tcltk'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package in Depends field not imported from: 'hash'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
P: no visible global function definition for 'has.key'
get_rand_int: no visible global function definition for 'runif'
last: no visible global function definition for 'tail'
rand_partitions: no visible global function definition for 'hash'
Undefined global functions or variables:
  has.key hash runif tail
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "tail")
to your NAMESPACE file.
evalMedian: no visible global function definition for 'xtabs'
evalMode: no visible global function definition for 'xtabs'
rpartScore: no visible global function definition for 'model.extract'
rpartScore: no visible global function definition for 'var'
rpartScore: no visible binding for global variable 'var'
splitAbs: no visible global function definition for 'xtabs'
Undefined global functions or variables:
  model.extract var xtabs
Consider adding
  importFrom("stats", "model.extract", "var", "xtabs")
to your NAMESPACE file.
'library' or 'require' call to 'RODBC' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
rpart.rules.push: no visible global function definition for 'sqlSave'
rpart.rules.table : <anonymous>: no visible global function definition
  for 'setNames'
rpart.subrules.table : <anonymous>: no visible global function
  definition for 'setNames'
Undefined global functions or variables:
  setNames sqlSave
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'survival'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'MASS' 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GenerateData: no visible global function definition for 'mvrnorm'
GetVarImp : FitPenalizedModel: no visible global function definition
  for 'clogit'
Undefined global functions or variables:
  clogit mvrnorm
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      2.8Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    extdata  12.1Mb
but_last: no visible global function definition for 'head'
first: no visible global function definition for 'head'
last: no visible global function definition for 'tail'
preview_frames: no visible global function definition for 'str'
print.EprimeFrame: no visible global function definition for 'str'
print.FrameList: no visible global function definition for 'str'
Undefined global functions or variables:
  head str tail
Consider adding
  importFrom("utils", "head", "str", "tail")
to your NAMESPACE file.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.4Mb
rpygeo.geoprocessor: warning in system(py.call, invisible = TRUE,
  minimize = TRUE, wait = wait): partial argument match of 'minimize'
  to 'minimized'
Package which this enhances but not available for checking: 'rjpod'
rrBlupM6: no visible global function definition for 'optimize'
Undefined global functions or variables:
  optimize
Consider adding
  importFrom("stats", "optimize")
to your NAMESPACE file.
Found the following significant warnings:
  regTree.c:242:19: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/RRF.Rcheck/00install.out' for details.
Packages in Depends field not imported from:
  'glasso' 'matrixcalc' 'mvoutlier' 'pcaPP'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
rrest: no visible binding for global variable 'glasso'
rrest: no visible global function definition for 'pcout'
rrest: no visible global function definition for 'var'
rrest: no visible global function definition for 'mahalanobis'
rrlda : centerObservations: no visible global function definition for
  'l1median_NLM'
rrlda : df.L2glasso: no visible global function definition for
  'duplication.matrix'
rrlda : alt.df.L2glasso: no visible global function definition for
  'lower.triangle'
Undefined global functions or variables:
  duplication.matrix glasso l1median_NLM lower.triangle mahalanobis
  pcout var
Consider adding
  importFrom("stats", "mahalanobis", "var")
to your NAMESPACE file.
'library' or 'require' call to 'robustbase' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.computekappa: no visible global function definition for 'pnorm'
.computekappa: no visible global function definition for 'dnorm'
.initmethod : <anonymous>: no visible global function definition for
  'median'
.initmethod: no visible global function definition for 'model.matrix'
.mspe: no visible global function definition for 'rnorm'
.mspe : <anonymous>: no visible global function definition for 'rnorm'
makedata: no visible global function definition for 'rnorm'
makedata : addraneff: no visible global function definition for 'rnorm'
plot.meanssaemodel: no visible global function definition for 'par'
plot.meanssaemodel: no visible global function definition for 'plot'
plot.meanssaemodel: no visible global function definition for 'lines'
plot.meanssaemodel: no visible global function definition for 'axis'
plot.meanssaemodel: no visible global function definition for 'grid'
plot.meanssaemodel: no visible global function definition for 'box'
plot.meanssaemodel: no visible global function definition for 'legend'
plot.meanssaemodel: no visible global function definition for 'arrows'
saemodel: no visible global function definition for 'model.frame'
saemodel: no visible global function definition for 'model.response'
saemodel: no visible global function definition for 'model.matrix'
summary.fitsaemodel: no visible global function definition for 'pt'
summary.fitsaemodel: no visible global function definition for
  'printCoefmat'
Undefined global functions or variables:
  arrows axis box dnorm grid legend lines median model.frame
  model.matrix model.response par plot pnorm printCoefmat pt rnorm
Consider adding
  importFrom("graphics", "arrows", "axis", "box", "grid", "legend",
             "lines", "par", "plot")
  importFrom("stats", "dnorm", "median", "model.frame", "model.matrix",
             "model.response", "pnorm", "printCoefmat", "pt", "rnorm")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/RSAP.Rcheck/00install.out' for details.
Files named as vignettes but with no recognized vignette engine:
   'vignettes/Untitled.Rnw'
(Is a VignetteBuilder field missing?)
stripslash: no visible global function definition for 'tail'
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
convexhull: no visible global function definition for 'chull'
convexhull: no visible global function definition for 'rnorm'
drawcompletegraph: no visible global function definition for 'plot'
drawcompletegraph: no visible global function definition for 'segments'
getbag: no visible global function definition for 'plot'
getbag: no visible global function definition for 'chull'
getbag: no visible global function definition for 'polygon'
getbag: no visible global function definition for 'points'
inflate: no visible global function definition for 'rnorm'
rsmed: no visible global function definition for 'runif'
rsplot: no visible global function definition for 'plot'
rsplot: no visible global function definition for 'chull'
rsplot: no visible global function definition for 'polygon'
rsplot: no visible global function definition for 'points'
rsrings: no visible global function definition for 'plot'
rsrings: no visible global function definition for 'chull'
rsrings: no visible global function definition for 'polygon'
rsrings: no visible global function definition for 'points'
rstinterval: no visible global function definition for 'plot'
rstinterval: no visible global function definition for 'runif'
rstinterval: no visible global function definition for 'rnorm'
rstinterval: no visible global function definition for 'chull'
rstinterval: no visible global function definition for 'polygon'
Undefined global functions or variables:
  chull plot points polygon rnorm runif segments
Consider adding
  importFrom("grDevices", "chull")
  importFrom("graphics", "plot", "points", "polygon", "segments")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/RSEIS.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
rsem: no visible global function definition for 'write.table'
rsem.Ascov: no visible global function definition for 'qchisq'
rsem.Ascov: no visible global function definition for 'pchisq'
rsem.emmusig: no visible global function definition for 'na.omit'
rsem.emmusig: no visible global function definition for 'qchisq'
rsem.emmusig: no visible global function definition for 'pchisq'
rsem.fit: no visible global function definition for 'pchisq'
rsem.fit: no visible global function definition for 'pf'
rsem.print : print.estimate: no visible global function definition for
  'pnorm'
rsem.weight: no visible global function definition for 'qchisq'
rsem.weight: no visible global function definition for 'pchisq'
semdiag.call.eqs: no visible global function definition for
  'write.table'
semdiag.read.eqs: no visible global function definition for 'read.fwf'
Undefined global functions or variables:
  na.omit pchisq pf pnorm qchisq read.fwf write.table
Consider adding
  importFrom("stats", "na.omit", "pchisq", "pf", "pnorm", "qchisq")
  importFrom("utils", "read.fwf", "write.table")
to your NAMESPACE file.
Found the following significant warnings:
   #warning Please include winsock2.h before windows.h
  qap_decode.c:200:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:200:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:55: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:60: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.5/Rserve.Rcheck/00install.out' for details.
Rserve: no visible global function definition for 'shortPathName'
Undefined global functions or variables:
  shortPathName
Consider adding
  importFrom("utils", "shortPathName")
to your NAMESPACE file.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.5/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.
addNoisyCopies: no visible global function definition for 'rnorm'
eta: no visible global function definition for 'var'
gaussClassifier: no visible global function definition for 'runif'
getSigma: no visible global function definition for 'sd'
getSigma: no visible binding for global variable 'sd'
sfaClassify: no visible global function definition for 'rainbow'
sfaClassify: no visible global function definition for 'par'
sfaClassify: no visible global function definition for 'plot'
sfaClassify: no visible global function definition for 'points'
sfaClassify: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines par plot points rainbow rnorm runif sd var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "lines", "par", "plot", "points")
  importFrom("stats", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
Depends: includes the non-default packages:
  'biwt' 'cairoDevice' 'fBasics' 'gplots' 'gWidgets' 'gWidgetsRGtk2'
  'minerva' 'parmigene' 'stringr' 'snowfall'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' calls to packages already attached by Depends:
  'grDevices' 'snowfall'
  Please remove these calls from your code.
'library' or 'require' call to 'ctc' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'biwt' 'cairoDevice' 'fBasics' 'gWidgets' 'gWidgetsRGtk2' 'gplots'
  'minerva' 'parmigene' 'snowfall' 'stringr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
Running examples in 'RSMET-Ex.R' failed
The error most likely occurred in:

> ### Name: meteofrance
> ### Title: Snow Weather Data in France
> ### Aliases: meteofrance
> 
> ### ** Examples
> 
>  
> 
> library(ggmap)
Loading required package: ggplot2
> data(meteofrance)
> 
> dates <- as.Date(meteofrance$timestamp)
> 
> data=meteofrance[dates==dates[1],]
> 
> 
> 
> map <- get_map(location ="France", zoom = 6)
Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=France&zoom=6&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false
Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=France&sensor=false
Warning: geocode failed with status OVER_QUERY_LIMIT, location = "France"
Error in data.frame(ll.lat = ll[1], ll.lon = ll[2], ur.lat = ur[1], ur.lon = ur[2]) : 
  arguments imply differing number of rows: 0, 1
Calls: get_map -> get_googlemap -> data.frame
Execution halted
Running 'testthat.R' [17s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rsoi)
  > 
  > test_check("rsoi")
  -- 1. Error: Test whether SOI values have not changed from February 2017 (@test_
  Recv failure: Connection was reset
  1: download_enso() at testthat/test_download_enso.R:11
  2: rsoi::download_oni()
  3: readr::read_table("http://www.cpc.ncep.noaa.gov/products/analysis_monitoring/ensostuff/detrend.nino34.ascii.txt", 
         skip = 1, col_names = c("Year", "Month", "TOTAL", "ClimAdjust", "dSST3.4"))
  4: datasource(file, skip = skip)
  5: datasource_connection(file, skip, comment)
  6: datasource_raw(read_connection(path), skip, comment = comment)
  7: new_datasource("raw", text, skip = skip, comment = comment)
  8: structure(list(x, skip = skip, comment = comment, ...), class = c(paste0("source_", 
         type), "source"))
  9: read_connection(path)
  10: open(con, "rb")
  11: open.connection(con, "rb")
  
  == testthat results  ===========================================================
  OK: 4 SKIPPED: 1 FAILED: 1
  1. Error: Test whether SOI values have not changed from February 2017 (@test_download_enso.R#11) 
  
  Error: testthat unit tests failed
  Execution halted
negbin.pow : negbin.disp: no visible global function definition for
  'rpois'
negbin.pow : negbin.disp: no visible global function definition for
  'rnbinom'
negbin.pow : inner.fcn: no visible global function definition for
  'na.omit'
negbin.pow : inner.fcn: no visible global function definition for
  'quantile'
negbin.pow: no visible global function definition for 'txtProgressBar'
negbin.pow: no visible global function definition for
  'setTxtProgressBar'
poiss.pow : inner.fcn: no visible global function definition for
  'rpois'
poiss.pow : inner.fcn: no visible global function definition for
  'quantile'
poiss.pow: no visible global function definition for 'txtProgressBar'
poiss.pow: no visible global function definition for
  'setTxtProgressBar'
Undefined global functions or variables:
  na.omit quantile rnbinom rpois setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit", "quantile", "rnbinom", "rpois")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    2.4Mb
    libs  17.3Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
rbing.O2: no visible global function definition for 'runif'
rbing.O2: no visible global function definition for 'rbeta'
rbing.O2: no visible global function definition for 'rbinom'
rbing.Op: no visible global function definition for 'rnorm'
rbing.Op: no visible global function definition for 'rbinom'
rbing.Op: no visible global function definition for 'runif'
rbmf.O2: no visible global function definition for 'runif'
rmf.matrix: no visible global function definition for 'runif'
rmf.vector: no visible global function definition for 'rnorm'
rmf.vector: no visible global function definition for 'rbinom'
rustiefel: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rbeta rbinom rnorm runif
Consider adding
  importFrom("stats", "rbeta", "rbinom", "rnorm", "runif")
to your NAMESPACE file.
Package in Depends field not imported from: 'plyr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
RStorm: no visible global function definition for 'alply'
Undefined global functions or variables:
  alply
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/rsunlight.Rcheck/00install.out' for details.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/RSurvey.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 17.5Mb
  sub-directories of 1Mb or more:
    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  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    Lib  11.5Mb
Math.Sym: no visible binding for global variable 'transtab'
jythonStart: no visible global function definition for '.jinit'
jythonStart: no visible global function definition for '.jnew'
jythonStart: no visible binding for global variable '.Jython'
sympy: no visible binding for global variable '.Jython'
sympy: no visible global function definition for '.jstrVal'
sympyStart: no visible binding for global variable '.Jython'
Undefined global functions or variables:
  .Jython .jinit .jnew .jstrVal transtab
barplot.rtconnect: no visible global function definition for 'rainbow'
barplot.rtconnect: no visible global function definition for 'text'
plot.rtconnect: no visible global function definition for 'par'
plot.rtconnect: no visible global function definition for 'plot'
plot.rtconnect: no visible global function definition for 'axis.Date'
rtconnect: no visible global function definition for 'read.table'
Undefined global functions or variables:
  axis.Date par plot rainbow read.table text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis.Date", "par", "plot", "text")
  importFrom("utils", "read.table")
to your NAMESPACE file.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
classify_model: no visible global function definition for 'predict'
cross_validate: no visible global function definition for 'predict'
read_data: no visible global function definition for 'read.csv'
read_data: no visible global function definition for 'read.delim'
Undefined global functions or variables:
  predict read.csv read.delim
Consider adding
  importFrom("stats", "predict")
  importFrom("utils", "read.csv", "read.delim")
to your NAMESPACE file.
plotGLCM: no visible global function definition for 'plot'
plotGLCM: no visible global function definition for 'points'
Undefined global functions or variables:
  plot points
Consider adding
  importFrom("graphics", "plot", "points")
to your NAMESPACE file.
.forest.plot: no visible global function definition for 'par'
.forest.plot: no visible global function definition for 'plot'
.forest.plot: no visible global function definition for 'abline'
.forest.plot: no visible global function definition for 'arrows'
.forest.plot: no visible global function definition for 'points'
.forest.plot.scale: no visible global function definition for 'par'
.forest.plot.scale: no visible global function definition for 'plot'
.forest.plot.scale: no visible global function definition for 'axTicks'
.forest.plot.scale : <anonymous>: no visible global function definition
  for 'lines'
.forest.plot.scale: no visible global function definition for 'lines'
.forest.plot.scale: no visible global function definition for 'text'
.rtf.plot: no visible global function definition for 'png'
.rtf.plot: no visible global function definition for 'dev.off'
.rtf.trellis.object: no visible global function definition for 'png'
.rtf.trellis.object: no visible global function definition for
  'dev.off'
addSessionInfo.RTF: no visible global function definition for
  'sessionInfo'
Undefined global functions or variables:
  abline arrows axTicks dev.off lines par plot png points sessionInfo
  text
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "abline", "arrows", "axTicks", "lines", "par",
             "plot", "points", "text")
  importFrom("utils", "sessionInfo")
to your NAMESPACE file.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc        1.0Mb
    libs       1.7Mb
    projects   2.5Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   2.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
HapMendlianCheck: no visible global function definition for
  'write.table'
rvPDT.test.sub: no visible global function definition for 'pnorm'
whap.prehap: no visible global function definition for 'write.table'
whap.prehap: no visible global function definition for 'read.table'
Undefined global functions or variables:
  pnorm read.table write.table
Consider adding
  importFrom("stats", "pnorm")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
'library' or 'require' call to 'pixmap' which was already attached by Depends.
  Please remove these calls from your code.
rvideopoker: warning in rp.radiogroup(mypanel, var =
  state$penny.nickel.quarter.dollar, initval = 1, values = c(1, 5, 25,
  100), title = "Bet (in Cents)", action = setbet): partial argument
  match of 'var' to 'variable'
rvideopoker: warning in rp.slider(mypanel, var = state$no.of.credits,
  from = 1, to = 5, initval = 1, title = "How many Credits?",
  resolution = 1, action = creditset, showvalue = TRUE): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC1, action = card1check, title = "Keep Card 1?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC2, action = card2check, title = "Keep Card 2?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC3, action = card3check, title = "Keep Card 3?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC4, action = card4check, title = "Keep Card 4?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC5, action = card5check, title = "Keep Card 5?"): partial
  argument match of 'var' to 'variable'
rvideopoker : plotFrame: no visible global function definition for
  'par'
rvideopoker : showBack: no visible global function definition for
  'title'
rvideopoker : showCardsInitially: no visible global function definition
  for 'title'
Undefined global functions or variables:
  par title
Consider adding
  importFrom("graphics", "par", "title")
to your NAMESPACE file.
Package suggested but not available for checking: 'gpuR'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    include   5.2Mb
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.
lc_TDT: no visible global function definition for 'pchisq'
rvTDT: no visible global function definition for 'dbeta'
Undefined global functions or variables:
  dbeta pchisq
Consider adding
  importFrom("stats", "dbeta", "pchisq")
to your NAMESPACE file.
LASSO: no visible global function definition for 'lm'
LASSO: no visible global function definition for 'anova'
LASSO: no visible global function definition for 'glm'
LASSO: no visible global function definition for 'pchisq'
LASSO : <anonymous>: no visible global function definition for
  'extractAIC'
PCR : <anonymous>: no visible global function definition for 'cor'
PLS : <anonymous>: no visible global function definition for 'cor'
RR : RRscore: no visible binding for global variable 'sd'
SPLS: no visible global function definition for 'lm'
SPLS: no visible global function definition for 'anova'
SPLS : <anonymous>: no visible global function definition for
  'extractAIC'
VTWOD : getScores: no visible global function definition for 'sd'
VTWOD : getScores: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  anova cor extractAIC glm lm pchisq pnorm sd
Consider adding
  importFrom("stats", "anova", "cor", "extractAIC", "glm", "lm",
             "pchisq", "pnorm", "sd")
to your NAMESPACE file.
check_ISO_code: no visible binding for global variable 'NoAm_country'
check_ISO_code: no visible binding for global variable 'SoAm_country'
check_ISO_code: no visible binding for global variable 'Oceana_country'
check_ISO_code: no visible binding for global variable 'Africa_country'
check_ISO_code: no visible binding for global variable 'Asia_country'
check_ISO_code: no visible binding for global variable 'Eur_country'
climate_map: no visible binding for global variable 'data'
date_correct: no visible global function definition for 'tail'
Undefined global functions or variables:
  Africa_country Asia_country Eur_country NoAm_country Oceana_country
  SoAm_country data tail
Consider adding
  importFrom("utils", "data", "tail")
to your NAMESPACE file.
RWBP.default: no visible global function definition for 'na.omit'
RWBP.default: no visible global function definition for 'kmeans'
RWBP.formula: no visible global function definition for 'model.extract'
plot.RWBP: no visible global function definition for 'plot'
predict.RWBP: no visible global function definition for 'head'
Undefined global functions or variables:
  head kmeans model.extract na.omit plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "kmeans", "model.extract", "na.omit")
  importFrom("utils", "head")
to your NAMESPACE file.
weblogo: no visible global function definition for 'browseURL'
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    java  10.6Mb
File 'RWinEdt/R/zzz.R':
  .onAttach calls:
    writeLines(edtFile, con = send2RedtLoc)
    writeLines(edtFile, con = send2RedtLoc)

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
getcolors: no visible global function definition for 'rainbow'
lines.rief: no visible global function definition for 'lines.default'
lines.riif: no visible global function definition for 'lines.default'
lines.rirf: no visible global function definition for 'lines.default'
plot.ifile: no visible global function definition for 'plot'
plot.rief: no visible global function definition for 'plot.default'
plot.rief: no visible global function definition for 'lines'
plot.riif: no visible global function definition for 'plot.default'
plot.riif: no visible global function definition for 'lines'
plot.rirf: no visible global function definition for 'plot.default'
plot.rirf: no visible global function definition for 'lines'
plot.rtef: no visible global function definition for 'plot.default'
plot.rtif: no visible global function definition for 'plot.default'
plot.rtrf: no visible global function definition for 'plot.default'
read.ifile: no visible global function definition for 'read.table'
read.pfile: no visible global function definition for 'read.table'
write.wdat: no visible global function definition for 'write.table'
Undefined global functions or variables:
  lines lines.default plot plot.default rainbow read.table write.table
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "lines", "lines.default", "plot",
             "plot.default")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
.dwt: no visible global function definition for 'median'
.udwt: no visible global function definition for 'median'
plotSignalTransformation: no visible global function definition for
  'plot'
plotSignalTransformation: no visible global function definition for
  'box'
plotSignalTransformation: no visible global function definition for
  'axis'
plotSignalTransformation: no visible global function definition for
  'lines'
plotSignalTransformation: no visible global function definition for
  'legend'
Undefined global functions or variables:
  axis box legend lines median plot
Consider adding
  importFrom("graphics", "axis", "box", "legend", "lines", "plot")
  importFrom("stats", "median")
to your NAMESPACE file.
Missing or unexported object: 'countrycode::countrycode_data'
Running examples in 'rwunderground-Ex.R' failed
The error most likely occurred in:

> ### Name: set_location
> ### Title: Specifies location of request
> ### Aliases: set_location
> 
> ### ** Examples
> 
> set_location(zip_code = "90210")
[1] "90210"
> set_location(territory = "Hawaii", city = "Honolulu")
Error: 'countrycode_data' is not an exported object from 'namespace:countrycode'
Execution halted
Analyze: no visible global function definition for 'runif'
Analyze: no visible global function definition for 'mcmc'
Analyze: no visible global function definition for 'varnames<-'
AnalyzeWithExitPoll: no visible global function definition for 'runif'
AnalyzeWithExitPoll: no visible global function definition for 'mcmc'
AnalyzeWithExitPoll: no visible global function definition for
  'varnames<-'
Tune: no visible global function definition for 'runif'
TuneWithExitPoll: no visible global function definition for 'runif'
form.mcmc.object: no visible global function definition for
  'varnames<-'
gendata.ep : rdirichlet: no visible global function definition for
  'rgamma'
gendata.ep : rwish: no visible global function definition for 'rchisq'
gendata.ep : rwish: no visible global function definition for 'rnorm'
gendata.ep: no visible global function definition for 'rpois'
gendata.ep: no visible global function definition for 'runif'
gendata.ep: no visible global function definition for 'rmultinom'
gendata.ep: no visible global function definition for 'cov2cor'
gq.summary: no visible global function definition for 'mcmc.list'
gq.summary: no visible global function definition for 'mcmc'
gq_diagnostics: no visible global function definition for 'mcmc.list'
gq_diagnostics: no visible global function definition for 'mcmc'
gq_diagnostics: no visible global function definition for 'gelman.diag'
gq_diagnostics: no visible global function definition for 'geweke.diag'
gq_diagnostics: no visible global function definition for 'heidel.diag'
gq_diagnostics: no visible global function definition for
  'autocorr.diag'
Undefined global functions or variables:
  autocorr.diag cov2cor gelman.diag geweke.diag heidel.diag mcmc
  mcmc.list rchisq rgamma rmultinom rnorm rpois runif varnames<-
Consider adding
  importFrom("stats", "cov2cor", "rchisq", "rgamma", "rmultinom",
             "rnorm", "rpois", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: 'SnakeCharmR'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/Ryacas.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    sample_data   3.0Mb
Found the following significant warnings:
  Rcpp_s2cell.cpp:20:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  Rcpp_s2cell.cpp:163:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/s2.Rcheck/00install.out' for details.
calculate.summary: no visible global function definition for 'sd'
detect.saccades: no visible global function definition for 'median'
diagnostic.plot: no visible global function definition for 'dev.new'
diagnostic.plot: no visible global function definition for 'par'
diagnostic.plot: no visible global function definition for 'recordPlot'
diagnostic.plot: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  dev.new dev.off median par recordPlot sd
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "recordPlot")
  importFrom("graphics", "par")
  importFrom("stats", "median", "sd")
to your NAMESPACE file.
eblupDyn: no visible global function definition for 'model.frame'
eblupDyn: no visible global function definition for 'model.matrix'
eblupDyn: no visible global function definition for 'pnorm'
eblupRY: no visible global function definition for 'model.frame'
eblupRY: no visible global function definition for 'model.matrix'
eblupRY: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  model.frame model.matrix pnorm
Consider adding
  importFrom("stats", "model.frame", "model.matrix", "pnorm")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/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.
fit.saery.AR1: no visible global function definition for 'qnorm'
fit.saery.MA1: no visible global function definition for 'qnorm'
fit.saery.indep: no visible global function definition for 'qnorm'
mse.saery.boot.AR1.typeI: no visible global function definition for
  'rnorm'
mse.saery.boot.AR1.typeI: no visible global function definition for
  'write.table'
mse.saery.boot.AR1.typeII: no visible global function definition for
  'rnorm'
mse.saery.boot.AR1.typeII: no visible global function definition for
  'write.table'
mse.saery.boot.MA1.typeI: no visible global function definition for
  'rnorm'
mse.saery.boot.MA1.typeI: no visible global function definition for
  'write.table'
mse.saery.boot.MA1.typeII: no visible global function definition for
  'rnorm'
mse.saery.boot.MA1.typeII: no visible global function definition for
  'write.table'
plot.saery: no visible global function definition for 'devAskNewPage'
plot.saery: no visible global function definition for 'par'
plot.saery: no visible global function definition for 'plot'
plot.saery: no visible global function definition for 'abline'
plot.saery: no visible global function definition for 'title'
plot.saery: no visible global function definition for 'axis'
plot.saery: no visible global function definition for 'lines'
plot.saery: no visible global function definition for 'legend'
pvalue: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  abline axis devAskNewPage legend lines par plot pnorm qnorm rnorm
  title write.table
Consider adding
  importFrom("grDevices", "devAskNewPage")
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "plot", "title")
  importFrom("stats", "pnorm", "qnorm", "rnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Package in Depends field not imported from: 'lpSolveAPI'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
glm: no visible binding for global variable 'gaussian'
glm: no visible global function definition for 'glm.control'
glm: no visible global function definition for 'model.response'
glm: no visible global function definition for 'is.empty.model'
glm: no visible global function definition for 'model.matrix'
glm: no visible global function definition for 'model.weights'
glm: no visible global function definition for 'model.offset'
glm: no visible global function definition for 'model.extract'
glm: no visible global function definition for 'glm.fit'
glm: no visible global function definition for '.getXlevels'
separator: no visible global function definition for 'make.lp'
separator: no visible global function definition for 'set.column'
separator: no visible global function definition for 'set.rhs'
separator: no visible global function definition for 'set.constr.type'
separator: no visible global function definition for 'set.objfn'
separator: no visible global function definition for 'set.bounds'
separator: no visible global function definition for 'lp.control'
separator: no visible global function definition for 'get.variables'
separator: no visible global function definition for 'set.basis'
separator: no visible global function definition for
  'get.dual.solution'
Undefined global functions or variables:
  .getXlevels gaussian get.dual.solution get.variables glm.control
  glm.fit is.empty.model lp.control make.lp model.extract model.matrix
  model.offset model.response model.weights set.basis set.bounds
  set.column set.constr.type set.objfn set.rhs
Consider adding
  importFrom("stats", ".getXlevels", "gaussian", "glm.control",
             "glm.fit", "is.empty.model", "model.extract",
             "model.matrix", "model.offset", "model.response",
             "model.weights")
to your NAMESPACE file.
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.
propdiff.acc: no visible global function definition for 'rbeta'
propdiff.acc: no visible global function definition for 'rbinom'
propdiff.acc: no visible global function definition for 'pbeta'
propdiff.alc: no visible global function definition for 'rbeta'
propdiff.alc: no visible global function definition for 'rbinom'
propdiff.alc: no visible global function definition for 'qbeta'
propdiff.freq: no visible global function definition for 'qnorm'
propdiff.mblacc: no visible global function definition for 'rbeta'
propdiff.mblacc: no visible global function definition for 'rbinom'
propdiff.mblacc: no visible global function definition for 'pbeta'
propdiff.mblalc: no visible global function definition for 'rbeta'
propdiff.mblalc: no visible global function definition for 'rbinom'
propdiff.mblalc: no visible global function definition for 'qbeta'
propdiff.mblmodwoc: no visible global function definition for 'qchisq'
propdiff.mblmodwoc: no visible global function definition for 'pbeta'
propdiff.mblwoc: no visible global function definition for 'pbeta'
propdiff.modwoc: no visible global function definition for 'qchisq'
propdiff.modwoc: no visible global function definition for 'pbeta'
propdiff.woc: no visible global function definition for 'pbeta'
Undefined global functions or variables:
  pbeta qbeta qchisq qnorm rbeta rbinom
Consider adding
  importFrom("stats", "pbeta", "qbeta", "qchisq", "qnorm", "rbeta",
             "rbinom")
to your NAMESPACE file.
plot.samEL: no visible global function definition for 'matplot'
plot.samHL: no visible global function definition for 'matplot'
plot.samLL: no visible global function definition for 'matplot'
plot.samQL: no visible global function definition for 'matplot'
predict.samEL: no visible global function definition for 'ns'
predict.samHL: no visible global function definition for 'ns'
predict.samLL: no visible global function definition for 'ns'
predict.samQL: no visible global function definition for 'ns'
samEL: no visible global function definition for 'ns'
samHL: no visible global function definition for 'ns'
samHL: no visible binding for global variable 'median'
samLL: no visible global function definition for 'ns'
samQL: no visible global function definition for 'ns'
Undefined global functions or variables:
  matplot median ns
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "median")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'impute' 'matrixStats'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'impute' 'matrixStats'
  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 'samr-internal':
  'plot.SAMoutput' 'print.SAMoutput'

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.
GraphBinaryForestPlot: no visible global function definition for
  'abline'
GraphBinaryForestPlot: no visible global function definition for 'text'
GraphContinuousForestPlot: no visible global function definition for
  'abline'
GraphContinuousForestPlot: no visible global function definition for
  'text'
ImputeBinaryEvents: no visible global function definition for 'rbinom'
ImputeSMD: no visible global function definition for 'rnorm'
funnelplot: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline rbinom rnorm text
Consider adding
  importFrom("graphics", "abline", "text")
  importFrom("stats", "rbinom", "rnorm")
to your NAMESPACE file.
generate.sample.core: no visible global function definition for
  'predict'
mdh: no visible global function definition for 'model.frame'
mdh: no visible binding for global variable 'na.fail'
mdh: no visible global function definition for '.getXlevels'
mdh: no visible global function definition for 'quantile'
mdh: no visible global function definition for 'hist'
predict.mdh: no visible global function definition for 'model.frame'
samur: no visible global function definition for 'predict'
Undefined global functions or variables:
  .getXlevels hist model.frame na.fail predict quantile
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", ".getXlevels", "model.frame", "na.fail", "predict",
             "quantile")
to your NAMESPACE file.
download.sas7bdat.sources : <anonymous>: no visible global function
  definition for 'download.file'
generate.sas7bdat.source: no visible global function definition for
  'download.file'
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
parse.SAScii: no visible binding for global variable 'end'
parse.SAScii: no visible binding for global variable 'start'
read.SAScii: no visible global function definition for 'download.file'
read.SAScii: no visible global function definition for 'unzip'
read.SAScii: no visible global function definition for 'read.fwf'
read.SAScii: no visible global function definition for 'capture.output'
Undefined global functions or variables:
  capture.output download.file end read.fwf start unzip
Consider adding
  importFrom("stats", "end", "start")
  importFrom("utils", "capture.output", "download.file", "read.fwf",
             "unzip")
to your NAMESPACE file.
SASPECT: no visible global function definition for 'dbinom'
my.SOnePro: missing arguments not allowed in calls to 'c'
my.ttest: no visible global function definition for 'var'
Undefined global functions or variables:
  dbinom var
Consider adding
  importFrom("stats", "dbinom", "var")
to your NAMESPACE file.
loads: no visible global function definition for 'untar'
saves: no visible global function definition for 'tar'
Undefined global functions or variables:
  tar untar
Consider adding
  importFrom("utils", "tar", "untar")
to your NAMESPACE file.
clogistCalc: no visible global function definition for 'model.matrix'
clogistCalc: no visible global function definition for 'glm.fit'
clogistCalc: no visible global function definition for 'binomial'
clogistInfo : all.not.equal: no visible global function definition for
  'var'
geeUOmega: no visible global function definition for 'model.extract'
geeUOmega: no visible global function definition for 'model.matrix'
geeUOmega: no visible binding for global variable 'contrasts'
mgee: no visible binding for global variable 'gaussian'
sawsCalc: no visible global function definition for 'pf'
sawsCalc: no visible global function definition for 'qt'
Undefined global functions or variables:
  binomial contrasts gaussian glm.fit model.extract model.matrix pf qt
  var
Consider adding
  importFrom("stats", "binomial", "contrasts", "gaussian", "glm.fit",
             "model.extract", "model.matrix", "pf", "qt", "var")
to your NAMESPACE file.
File which contains pragma(s) suppressing important diagnostics:
  'src/Eigen/src/Core/arch/SSE/Complex.h'
File which contains pragma(s) suppressing diagnostics:
  'src/Eigen/src/Core/util/DisableStupidWarnings.h'
K: no visible global function definition for 'dnorm'
sBF: no visible global function definition for 'density'
sBF: no visible global function definition for 'txtProgressBar'
sBF: no visible global function definition for 'setTxtProgressBar'
Undefined global functions or variables:
  density dnorm setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "density", "dnorm")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
plot.psgc: no visible global function definition for 'par'
plot.psgc: no visible global function definition for 'barplot'
plot.psgc: no visible global function definition for 'hist'
plotci.sA: no visible global function definition for 'par'
plotci.sA: no visible global function definition for 'plot'
plotci.sA: no visible global function definition for 'points'
plotci.sA: no visible global function definition for 'segments'
plotci.sA: no visible global function definition for 'abline'
plotci.sA: no visible global function definition for 'axis'
qM.sM: no visible binding for global variable 'quantile'
rwish: no visible global function definition for 'rnorm'
sbgcop.mcmc: no visible global function definition for 'qnorm'
sbgcop.mcmc: no visible global function definition for 'rnorm'
sbgcop.mcmc: no visible global function definition for 'cov'
sbgcop.mcmc: no visible global function definition for 'runif'
sbgcop.mcmc: no visible global function definition for 'pnorm'
sbgcop.mcmc: no visible global function definition for 'quantile'
summary.psgc: no visible global function definition for 'acf'
Undefined global functions or variables:
  abline acf axis barplot cov hist par plot pnorm points qnorm quantile
  rnorm runif segments
Consider adding
  importFrom("graphics", "abline", "axis", "barplot", "hist", "par",
             "plot", "points", "segments")
  importFrom("stats", "acf", "cov", "pnorm", "qnorm", "quantile",
             "rnorm", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  d:/Compiler/gcc-4.9.3/local330/include/gmp-x64.h:140:23: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/Compiler/gcc-4.9.3/local330/include/gmp-x64.h:141:14: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.5/sbrl.Rcheck/00install.out' for details.
fitSBSA: no visible binding for global variable 'var'
fitSBSA: no visible global function definition for 'var'
fitSBSA: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  qnorm var
Consider adding
  importFrom("stats", "qnorm", "var")
to your NAMESPACE file.
ChooseBest: no visible global function definition for 'head'
GetScores: no visible global function definition for 'write.table'
ReportTable: no visible binding for global variable 'sd'
ReportTable: no visible global function definition for 'write.table'
Undefined global functions or variables:
  head sd write.table
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "head", "write.table")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'MASS' 'lars'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
lse: no visible global function definition for 'lm'
predict.scalreg: no visible global function definition for 'fitted'
slassoEst: no visible global function definition for 'qnorm'
slassoEst: no visible global function definition for 'lars'
slassoEst: no visible global function definition for 'predict.lars'
Undefined global functions or variables:
  fitted lars lm predict.lars qnorm
Consider adding
  importFrom("stats", "fitted", "lm", "qnorm")
to your NAMESPACE file.
plot.scair: no visible global function definition for 'par'
plot.scair: no visible global function definition for 'plot'
plot.scair: no visible global function definition for 'points'
plot.scar: no visible global function definition for 'par'
plot.scar: no visible global function definition for 'plot'
plot.scar: no visible global function definition for 'points'
predict.scair: no visible global function definition for 'approx'
predict.scar: no visible global function definition for 'approx'
scair: no visible global function definition for 'gaussian'
scair: no visible global function definition for 'runif'
scair: no visible global function definition for 'rnorm'
scar: no visible global function definition for 'gaussian'
scar: no visible global function definition for 'glm.fit'
scar: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx gaussian glm.fit par plot points rnorm runif
Consider adding
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "approx", "gaussian", "glm.fit", "rnorm", "runif")
to your NAMESPACE file.
prime.factor: no visible global function definition for 'data'
prime.factor: no visible binding for global variable 'primlist'
Undefined global functions or variables:
  data primlist
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
'library' or 'require' call to 'QUIC' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
scio.cv: no visible global function definition for 'cov'
scio.refit: no visible global function definition for 'QUIC'
Undefined global functions or variables:
  QUIC cov
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
score.GGUM: no visible global function definition for 'dnorm'
score.GGUM: no visible global function definition for 'hist'
score.GGUM: no visible global function definition for 'write.table'
Undefined global functions or variables:
  dnorm hist write.table
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "dnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file.
CreatePssm: no visible binding for global variable 'training'
Undefined global functions or variables:
  training
plot.SK: no visible global function definition for 'plot'
plot.SK: no visible global function definition for 'segments'
plot.SK: no visible global function definition for 'axis'
plot.SK: no visible global function definition for 'mtext'
Undefined global functions or variables:
  axis mtext plot segments
Consider adding
  importFrom("graphics", "axis", "mtext", "plot", "segments")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'RCurl' 'XML'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'RCurl' 'XML'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
scrape: no visible global function definition for 'getURLAsynchronous'
scrape: no visible global function definition for 'runif'
scrape: no visible global function definition for 'capture.output'
scrape: no visible binding for global variable 'xmlParse'
scrape: no visible binding for global variable 'htmlParse'
Undefined global functions or variables:
  capture.output getURLAsynchronous htmlParse runif xmlParse
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'MASS' 'oligoClasses'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Files which contain pragma(s) suppressing diagnostics:
  'src/scrm/macros.h' 'src/scrm/model.h'
lahiri.design: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Running examples in 'sdcMicro-Ex.R' failed
The error most likely occurred in:

> ### Name: shuffle
> ### Title: Shuffling and EGADP
> ### Aliases: shuffle
> ### Keywords: manip
> 
> ### ** Examples
> 
> data(Prestige,package="car")
Warning in data(Prestige, package = "car") :
  data set 'Prestige' not found
> form <- formula(income + education ~ women + prestige + type, data=Prestige)
> sh <- shuffle(obj=Prestige,form)
Error in shuffleX(obj = obj, form = form, method = method, weights = weights,  : 
  object 'Prestige' not found
Calls: shuffle -> shuffleX
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   3.5Mb
estimateTimeToComputeTargetDefinition: no visible global function
  definition for 'flush.console'
estimateTimeToComputeTargetDefinition: no visible global function
  definition for 'combn'
initialize,sdcTargetDefinitionClass: no visible global function
  definition for 'flush.console'
initialize,sdcTargetDefinitionClass: no visible global function
  definition for 'combn'
initialize,sdcTargetDefinitionClass: no visible global function
  definition for 'quantile'
initialize,sdcTargetMatrixClass: no visible global function definition
  for 'flush.console'
Undefined global functions or variables:
  combn flush.console quantile
Consider adding
  importFrom("stats", "quantile")
  importFrom("utils", "combn", "flush.console")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'raster' 'sp'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'lars'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
sealasso: no visible global function definition for 'lars'
weight.calc: no visible global function definition for 'lars'
Undefined global functions or variables:
  lars
adx: no visible global function definition for 'abline'
adx: no visible global function definition for 'legend'
dx: no visible global function definition for 'abline'
dx: no visible global function definition for 'legend'
maxd: no visible global function definition for 'abline'
maxd: no visible global function definition for 'legend'
pc: no visible global function definition for 'rainbow'
pc: no visible global function definition for 'plot'
pc: no visible global function definition for 'abline'
pc: no visible global function definition for 'legend'
pc: no visible global function definition for 'points'
pcu: no visible global function definition for 'rainbow'
pcu: no visible global function definition for 'plot'
pcu: no visible global function definition for 'abline'
pcu: no visible global function definition for 'legend'
pcu: no visible global function definition for 'points'
rmsd: no visible global function definition for 'abline'
rmsd: no visible global function definition for 'legend'
rsd: no visible global function definition for 'abline'
rsd: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline legend plot points rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "legend", "plot", "points")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'NADA' 'lubridate' 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package in Depends field not imported from: 'JM'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SEchart: no visible global function definition for 'plot'
SEchart: no visible global function definition for 'rect'
SEchart: no visible global function definition for 'par'
SEchart: no visible global function definition for 'grid'
SEchart: no visible global function definition for 'axis'
SEchart: no visible global function definition for 'text'
SEchart: no visible global function definition for 'lines'
SEchart: no visible global function definition for 'heat.colors'
SEchart: no visible global function definition for 'topo.colors'
SEchart: no visible global function definition for 'cm.colors'
SEchart: no visible global function definition for 'terrain.colors'
SEchart: no visible global function definition for 'gray.colors'
SEchart: no visible global function definition for 'rainbow'
SEchart: no visible global function definition for 'points'
SEchart: no visible global function definition for 'legend'
Undefined global functions or variables:
  axis cm.colors gray.colors grid heat.colors legend lines par plot
  points rainbow rect terrain.colors text topo.colors
Consider adding
  importFrom("grDevices", "cm.colors", "gray.colors", "heat.colors",
             "rainbow", "terrain.colors", "topo.colors")
  importFrom("graphics", "axis", "grid", "legend", "lines", "par",
             "plot", "points", "rect", "text")
to your NAMESPACE file.
fdc2s: no visible global function definition for 'lm'
fdc3s: no visible global function definition for 'lm'
fds2s: no visible global function definition for 'lm'
fds3s: no visible global function definition for 'lm'
Undefined global functions or variables:
  lm
Consider adding
  importFrom("stats", "lm")
to your NAMESPACE file.
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 secr 3.1.5. For overview type ?secr
No errors found :-)
Quitting from lines 239-241 (secr-datainput.Rmd) 
Error: processing vignette 'secr-datainput.Rmd' failed with diagnostics:
cannot open URL 'http://www.otago.ac.nz/density/examples/stoat.xlsx'
Execution halted
.read.SeerStatTXT: no visible global function definition for
  'read.table'
.write.SeerStatTXT: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.5Mb
'library' or 'require' calls in package code:
  'rgdal' 'spdep' 'spgrass6'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.use.spgrass6: no visible global function definition for 'listw2mat'
.use.spgrass6: no visible global function definition for 'sn2listw'
conprof: no visible global function definition for 'axis'
conprof: no visible global function definition for 'lines'
isp: no visible global function definition for 'combn'
points.SegLocal: no visible global function definition for 'points'
Undefined global functions or variables:
  axis combn lines listw2mat points sn2listw
Consider adding
  importFrom("graphics", "axis", "lines", "points")
  importFrom("utils", "combn")
to your NAMESPACE file.
get.infectiousness: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  qchisq
Consider adding
  importFrom("stats", "qchisq")
to your NAMESPACE file.
get_statistics_from_file: no visible global function definition for
  'read.csv'
glm_anova: no visible global function definition for 'aov'
glm_anova: no visible global function definition for 'glm'
glm_anova: no visible global function definition for 'gaussian'
glm_anova: no visible global function definition for 'anova'
glm_anova: no visible global function definition for 'quasipoisson'
glm_anova: no visible global function definition for 'sd'
glm_anova: no visible global function definition for 'p.adjust'
ttest_cohens_d: no visible global function definition for 't.test'
ttest_cohens_d: no visible global function definition for 'sd'
Undefined global functions or variables:
  anova aov gaussian glm p.adjust quasipoisson read.csv sd t.test
Consider adding
  importFrom("stats", "anova", "aov", "gaussian", "glm", "p.adjust",
             "quasipoisson", "sd", "t.test")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
predict.SEL: warning in splineDesign(newdata, knots = knts, ord =
  object$nord, deriv = rep(deriv, length(newdata)), outer.ok = TRUE):
  partial argument match of 'deriv' to 'derivs'
getbinPost: no visible binding for global variable 'dbeta'
getbinPost: no visible binding for global variable 'pbeta'
getbinPost : fu: no visible global function definition for 'dbinom'
getbinPost : fu: no visible global function definition for 'predict'
getbinPost: no visible global function definition for 'integrate'
getbinPost: no visible global function definition for 'splinefun'
int.funct: no visible global function definition for 'integrate'
int.funct2: no visible global function definition for 'integrate'
min.abs: no visible global function definition for 'uniroot'
plot.SEL: no visible global function definition for 'plot'
print.SEL: no visible global function definition for 'integrate'
print.summary.SEL : foo1: no visible global function definition for
  'predict'
print.summary.SEL : foo2: no visible global function definition for
  'predict'
print.summary.SEL: no visible global function definition for
  'integrate'
quantSEL: no visible global function definition for 'predict'
quantSEL: no visible global function definition for 'splinefun'
rvSEL: no visible global function definition for 'runif'
Undefined global functions or variables:
  dbeta dbinom integrate pbeta plot predict runif splinefun uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dbeta", "dbinom", "integrate", "pbeta", "predict",
             "runif", "splinefun", "uniroot")
to your NAMESPACE file.
Package in Depends field not imported from: 'sem'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
ChiSquaredLRTest: no visible global function definition for 'na.omit'
ChiSquaredLRTest: no visible global function definition for 'cov'
ChiSquaredLRTest: no visible global function definition for 'dmvnorm'
ChiSquaredLRTest: no visible global function definition for 'pchisq'
NormalTheoryLRTest: no visible global function definition for 'na.omit'
NormalTheoryLRTest: no visible global function definition for 'cov'
NormalTheoryLRTest: no visible global function definition for 'dmvnorm'
NormalTheoryLRTest: no visible global function definition for 'sd'
NormalTheoryLRTest: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  cov dmvnorm na.omit pchisq pnorm sd
Consider adding
  importFrom("stats", "cov", "na.omit", "pchisq", "pnorm", "sd")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'XML' 'boot' 'sem'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  'boot:::const' 'stats:::AIC.logLik' 'stats:::BIC.logLik'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'addPath.plsm' 'endogenous' 'predecessors' 'qSquared' 'reorder'
  'resempls' 'residuals.sempls'
efficiencies.semsfa: no visible global function definition for 'dnorm'
efficiencies.semsfa: no visible global function definition for 'pnorm'
fan: no visible global function definition for 'pnorm'
plot.semsfa: no visible global function definition for 'hist'
plot.semsfa: no visible global function definition for 'plot'
plot.semsfa: no visible global function definition for 'density'
semsfa: no visible global function definition for 'residuals'
semsfa: no visible global function definition for 'loess'
semsfa: no visible global function definition for 'optimize'
semsfa: no visible global function definition for 'pnorm'
semsfa: no visible binding for global variable 'sd'
summary.semsfa: no visible global function definition for 'pt'
summary.semsfa: no visible global function definition for
  'printCoefmat'
Undefined global functions or variables:
  density dnorm hist loess optimize plot pnorm printCoefmat pt
  residuals sd
Consider adding
  importFrom("graphics", "hist", "plot")
  importFrom("stats", "density", "dnorm", "loess", "optimize", "pnorm",
             "printCoefmat", "pt", "residuals", "sd")
to your NAMESPACE file.
.plot_attachment: no visible global function definition for 'dev.off'
.update_list: no visible global function definition for 'modifyList'
mime_part.data.frame: no visible global function definition for
  'write.table'
mime_part.ggplot: no visible binding for global variable 'pdf'
mime_part.matrix: no visible global function definition for
  'write.table'
mime_part.trellis: no visible binding for global variable 'pdf'
Undefined global functions or variables:
  dev.off modifyList pdf write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("utils", "modifyList", "write.table")
to your NAMESPACE file.
'library' or 'require' call to 'rtiff' which was already attached by Depends.
  Please remove these calls from your code.
gconv: no visible global function definition for 'convolve'
sens.analysis.aberrant.rank: no visible global function definition for
  'pnorm'
sens.analysis.mh: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  convolve pnorm
Consider adding
  importFrom("stats", "convolve", "pnorm")
to your NAMESPACE file.
mscorev: no visible global function definition for 'quantile'
senmwCI : funcCI: no visible global function definition for 'qnorm'
senmwCI : funcCI2: no visible global function definition for 'qnorm'
separable1k: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm qnorm quantile
Consider adding
  importFrom("stats", "pnorm", "qnorm", "quantile")
to your NAMESPACE file.
plot.sensitivity.2.0d: no visible global function definition for 'gray'
sensitivitySGD: no visible global function definition for 'tail'
sensitivitySGL: no visible global function definition for 'tail'
Undefined global functions or variables:
  gray tail
Consider adding
  importFrom("grDevices", "gray")
  importFrom("utils", "tail")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/sensors4plumes.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'.
S3 methods shown with full name in documentation object 'cbind.Simulations':
  'cbind.Simulations'

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.
separationplot: no visible global function definition for 'dev.new'
separationplot: no visible global function definition for 'pdf'
separationplot: no visible global function definition for 'par'
separationplot: no visible global function definition for 'plot'
separationplot: no visible global function definition for 'title'
separationplot: no visible global function definition for 'segments'
separationplot: no visible global function definition for 'rect'
separationplot: no visible global function definition for 'points'
separationplot: no visible global function definition for 'lines'
separationplot: no visible global function definition for
  'colorRampPalette'
separationplot: no visible global function definition for 'layout'
separationplot: no visible global function definition for 'plot.new'
separationplot: no visible global function definition for 'legend'
separationplot: no visible global function definition for 'dev.off'
separationplot: no visible global function definition for 'locator'
sp.categorical: no visible global function definition for 'dev.new'
sp.categorical: no visible global function definition for 'pdf'
sp.categorical: no visible global function definition for 'par'
sp.categorical: no visible global function definition for 'layout'
sp.categorical: no visible global function definition for 'plot'
sp.categorical: no visible global function definition for 'text'
sp.categorical: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  colorRampPalette dev.new dev.off layout legend lines locator par pdf
  plot plot.new points rect segments text title
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.new", "dev.off",
             "pdf")
  importFrom("graphics", "layout", "legend", "lines", "locator", "par",
             "plot", "plot.new", "points", "rect", "segments", "text",
             "title")
to your NAMESPACE file.
GammaDist: no visible binding for global variable 'rgamma'
VEpowerPP: no visible global function definition for 'qnorm'
applyStopRules: no visible global function definition for 'qnorm'
finalLogRankTest: no visible global function definition for 'qnorm'
finalLogRankTest: no visible global function definition for 'pchisq'
generateDropout: no visible global function definition for 'rexp'
generateEnrollment: no visible global function definition for 'rpois'
generateEnrollment: no visible global function definition for 'runif'
generateInfection: no visible global function definition for 'rexp'
generateInfection : <anonymous>: no visible global function definition
  for 'rexp'
getAlphaPerTest: no visible global function definition for 'uniroot'
getHarmBound: no visible global function definition for 'dbinom'
getHarmBound: no visible global function definition for 'write.csv'
getTreatmentAssignment : <anonymous>: no visible global function
  definition for 'runif'
getTreatmentAssignment: no visible global function definition for
  'runif'
simTrial: no visible global function definition for 'runif'
sumTrialOneTrtArm: no visible global function definition for 'quantile'
testVE: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  dbinom pchisq qnorm quantile rexp rgamma rpois runif uniroot
  write.csv
Consider adding
  importFrom("stats", "dbinom", "pchisq", "qnorm", "quantile", "rexp",
             "rgamma", "rpois", "runif", "uniroot")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    6.0Mb
    libs   2.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
plotenz : addmark: no visible global function definition for 'par'
plotenz : addmark: no visible global function definition for 'plot'
plotenz : addmark: no visible global function definition for 'text'
plotenz : addmark: no visible global function definition for 'segments'
plotenz : addband: no visible global function definition for 'segments'
plotenz : addband: no visible global function definition for 'text'
plotenz: no visible global function definition for 'layout'
plotenz: no visible global function definition for 'text'
plotenz: no visible global function definition for 'dev.new'
Undefined global functions or variables:
  dev.new layout par plot segments text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "layout", "par", "plot", "segments", "text")
to your NAMESPACE file.
Running examples in 'SequenceAnalysis-Ex.R' failed
The error most likely occurred in:

> ### Name: SequenceAnalysis.Complement
> ### Title: SequenceAnalysis.Complement
> ### Aliases: SequenceAnalysis.Complement
> 
> ### ** Examples
> 
> SequenceAnalysis.Complement("actagtcacgatcag")
       Complement 
"TGATCAGTGCTAGTC" 
> SequenceAnalysis.Complement(UniprotKB="O15131")
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Complement 
     "N/A" 
> SequenceAnalysis.Complement(UniprotKB="O15131",CDS=TRUE)
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in Nucleotide_Sequence[[3]] : subscript out of bounds
Calls: SequenceAnalysis.Complement
Execution halted
capture: no visible binding for global variable 'resultText'
restore.session: no visible binding for global variable
  '.save.session.packages'
restore.session: no visible binding for global variable
  '.save.session.search'
save.session: no visible global function definition for 'dev.list'
save.session: no visible binding for '<<-' assignment to
  '.save.session.search'
save.session: no visible binding for '<<-' assignment to
  '.save.session.packages'
Undefined global functions or variables:
  .save.session.packages .save.session.search dev.list resultText
Consider adding
  importFrom("grDevices", "dev.list")
to your NAMESPACE file.
setpath: no visible global function definition for 'cov'
setpath: no visible global function definition for 'median'
setpath: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  cov median pchisq
Consider adding
  importFrom("stats", "cov", "median", "pchisq")
to your NAMESPACE file.
random.number.test: no visible global function definition for 'runif'
random.number.test: no visible global function definition for 'rnorm'
setRNG: no visible global function definition for 'runif'
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
'library' or 'require' call to 'graphics' which was already attached by Depends.
  Please remove these calls from your code.
severity: no visible global function definition for 'qnorm'
severity: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
L_exp: no visible global function definition for 'pnorm'
L_hNV: no visible global function definition for 'pnorm'
L_trunc: no visible global function definition for 'pnorm'
L_trunc_mufest: no visible global function definition for 'pnorm'
dgp: no visible global function definition for 'runif'
dgp: no visible global function definition for 'rnorm'
eff.sfa: no visible global function definition for 'predict'
fitted.sfa: no visible global function definition for 'predict'
predict.sfa: no visible global function definition for 'coef'
print.sfa: no visible global function definition for 'coef'
residuals.sfa: no visible global function definition for 'fitted'
sfa: no visible global function definition for 'model.frame'
sfa: no visible global function definition for 'model.response'
sfa.fit: no visible global function definition for 'lm'
sfa.fit: no visible global function definition for 'resid'
sfa.fit: no visible global function definition for 'var'
sfa.fit: no visible global function definition for 'optim'
summary.sfa: no visible global function definition for 'logLik'
summary.sfa: no visible global function definition for 'pchisq'
te.eff.sfa: no visible global function definition for 'residuals'
te.eff.sfa: no visible global function definition for 'pnorm'
u.sfa: no visible global function definition for 'residuals'
u.sfa: no visible global function definition for 'dnorm'
u.sfa: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  coef dnorm fitted lm logLik model.frame model.response optim pchisq
  pnorm predict resid residuals rnorm runif var
Consider adding
  importFrom("stats", "coef", "dnorm", "fitted", "lm", "logLik",
             "model.frame", "model.response", "optim", "pchisq", "pnorm",
             "predict", "resid", "residuals", "rnorm", "runif", "var")
to your NAMESPACE file.
installed size is 93.5Mb
  sub-directories of 1Mb or more:
    doc     10.7Mb
    gdal     3.9Mb
    libs    69.9Mb
    proj     5.0Mb
    sqlite   1.5Mb
coxCrossVal: no visible binding for global variable 'sd'
error.bars: no visible global function definition for 'segments'
linCrossVal: no visible binding for global variable 'sd'
logitCrossVal: no visible binding for global variable 'sd'
plot.cv.SGL: no visible global function definition for 'points'
Undefined global functions or variables:
  points sd segments
Consider adding
  importFrom("graphics", "points", "segments")
  importFrom("stats", "sd")
to your NAMESPACE file.
.computePStar: no visible global function definition for 'uniroot'
plotBoundary: no visible global function definition for
  'scale_y_continuous'
Undefined global functions or variables:
  scale_y_continuous uniroot
Consider adding
  importFrom("stats", "uniroot")
to your NAMESPACE file.
amse: no visible global function definition for 'na.omit'
arb: no visible global function definition for 'na.omit'
rdatagen: no visible global function definition for 'qnorm'
rdatagen: no visible global function definition for 'pbinom'
rdatagen: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  na.omit pbinom pnorm qnorm
Consider adding
  importFrom("stats", "na.omit", "pbinom", "pnorm", "qnorm")
to your NAMESPACE file.
UQnormalize.count: no visible binding for global variable 'quantile'
plotNScores: no visible global function definition for 'par'
plotNScores: no visible global function definition for 'hist'
plotNScores: no visible global function definition for 'title'
plotScores: no visible global function definition for 'par'
plotScores: no visible global function definition for 'hist'
plotScores: no visible global function definition for 'title'
sgRSEA: no visible binding for global variable 'sd'
sgRSEA: no visible global function definition for 'p.adjust'
sgRSEA.mean: no visible binding for global variable 'sd'
sgRSEA.mean: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  hist p.adjust par quantile sd title
Consider adding
  importFrom("graphics", "hist", "par", "title")
  importFrom("stats", "p.adjust", "quantile", "sd")
to your NAMESPACE file.
'library' or 'require' call to 'foreign' which was already attached by Depends.
  Please remove these calls from your code.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    www   9.4Mb
popify: no visible global function definition for 'runif'
tipify: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    www   6.3Mb
get_selected_names: no visible global function definition for 'tail'
get_selected_names: no visible global function definition for 'head'
Undefined global functions or variables:
  head tail
Consider adding
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
shrink.estim: no visible global function definition for 'cov'
shrink.estim: no visible global function definition for 'cor'
shrink.estim: no visible global function definition for 'cov2cor'
targetCor: no visible global function definition for 'cor.test'
targetCor: no visible global function definition for 'cor'
targetCor: no visible global function definition for 'sd'
targetCor: no visible global function definition for 'cov'
targetD: no visible binding for global variable 'var'
targetF: no visible global function definition for 'cov'
targetF: no visible global function definition for 'cor'
targetG: no visible global function definition for 'cor'
targetG: no visible global function definition for 'sd'
targetG: no visible global function definition for 'cov'
targetGpos: no visible global function definition for 'cor'
targetGpos: no visible global function definition for 'sd'
targetGpos: no visible global function definition for 'cov'
targetGstar: no visible global function definition for 'cor'
targetGstar: no visible global function definition for 'sd'
targetGstar: no visible global function definition for 'cov'
Undefined global functions or variables:
  cor cor.test cov cov2cor sd var
Consider adding
  importFrom("stats", "cor", "cor.test", "cov", "cov2cor", "sd", "var")
to your NAMESPACE file.
.params: no visible binding for global variable 'URLencode'
.params: no visible global function definition for 'URLencode'
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
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.
Packages in Depends field not imported from:
  'MASS' 'bayesm' 'coda' 'hdrcde' 'mnormt' 'spatstat'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages in Depends field not imported from:
  'ade4' 'corpcor'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
filter.PCA.default: no visible global function definition for
  'princomp'
filter.mRMR.default: no visible global function definition for
  'discretize'
gaussian.default: no visible global function definition for 'cov'
gaussian.default: no visible global function definition for
  'cov.shrink'
plot.verify.cv: no visible global function definition for 'plot'
plot.verify.cv: no visible global function definition for 'points'
plot.verify.ho: no visible global function definition for 'plot'
plot.verify.ho: no visible global function definition for 'points'
plot.verify.loo: no visible global function definition for 'plot'
plot.verify.loo: no visible global function definition for 'points'
predict.dpa1: no visible global function definition for 'cor'
predict.filter.PCA: no visible global function definition for 'predict'
predict.filter.RegressionTreeFilter: no visible global function
  definition for 'is.struct'
predict.filter.RegressionTreeFilter: no visible global function
  definition for 'var'
simulator.Simple1: no visible global function definition for 'rnorm'
verify.ho.default: no visible global function definition for 'predict'
verify.loo.default: no visible global function definition for 'predict'
Undefined global functions or variables:
  cor cov cov.shrink discretize is.struct plot points predict princomp
  rnorm var
Consider adding
  importFrom("graphics", "plot", "points")
  importFrom("stats", "cor", "cov", "predict", "princomp", "rnorm",
             "var")
to your NAMESPACE file.
dSepAdji: no visible global function definition for 'as'
dag2cpdagAdj: no visible global function definition for 'as'
randomDAG: no visible global function definition for 'rbinom'
structIntervDist: no visible global function definition for 'as'
Undefined global functions or variables:
  as rbinom
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "rbinom")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
plot.std: no visible global function definition for 'rainbow'
plot.std: no visible global function definition for 'legend'
read.std: no visible global function definition for 'read.table'
std: no visible global function definition for 'na.exclude'
Undefined global functions or variables:
  legend na.exclude rainbow read.table
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend")
  importFrom("stats", "na.exclude")
  importFrom("utils", "read.table")
to your NAMESPACE file.
.cluster: no visible global function definition for 'kmeans'
.plot.sigclust: no visible global function definition for 'par'
.plot.sigclust: no visible global function definition for 'density'
.plot.sigclust: no visible global function definition for 'runif'
.plot.sigclust: no visible global function definition for 'dnorm'
.plot.sigclust: no visible global function definition for 'lines'
.plot.sigclust: no visible global function definition for 'points'
.plot.sigclust: no visible global function definition for 'title'
.plot.sigclust: no visible global function definition for 'text'
.plot.sigclust: no visible global function definition for 'qnorm'
.plot.sigclust: no visible global function definition for 'abline'
.plot.sigclust: no visible global function definition for 'quantile'
.plot.sigclust: no visible global function definition for 'legend'
.simnull: no visible global function definition for 'rnorm'
.vareigen: no visible global function definition for 'mad'
.vareigen: no visible global function definition for 'cov'
sigclust: no visible global function definition for 'sd'
sigclust: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  abline cov density dnorm kmeans legend lines mad par pnorm points
  qnorm quantile rnorm runif sd text title
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "points",
             "text", "title")
  importFrom("stats", "cov", "density", "dnorm", "kmeans", "mad",
             "pnorm", "qnorm", "quantile", "rnorm", "runif", "sd")
to your NAMESPACE file.
Sight.Est: no visible global function definition for 'glm'
Sight.Est: no visible global function definition for 'binomial'
Sight.Est: no visible global function definition for 'coef'
Sight.Est: no visible global function definition for 'terms'
Sight.Est: no visible binding for global variable 'binomial'
covtheta: no visible global function definition for 'cov'
print.sightest: no visible global function definition for 'qnorm'
summary.sightest: no visible global function definition for 'qnorm'
vardiff: no visible global function definition for 'vcov'
vardiff: no visible global function definition for 'coef'
vardiff: no visible global function definition for 'terms'
varlog.lam: no visible global function definition for 'vcov'
varlog.lam: no visible global function definition for 'coef'
varlog.lam: no visible global function definition for 'terms'
Undefined global functions or variables:
  binomial coef cov glm qnorm terms vcov
Consider adding
  importFrom("stats", "binomial", "coef", "cov", "glm", "qnorm", "terms",
             "vcov")
to your NAMESPACE file.
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.
signmedian.test: no visible global function definition for 'median'
signmedian.test: no visible global function definition for 'binom.test'
signmedian.test: no visible global function definition for 'pbinom'
signmedian.test: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  binom.test median pbinom pnorm
Consider adding
  importFrom("stats", "binom.test", "median", "pbinom", "pnorm")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'gdata' 'splines'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.SII: no visible global function definition for 'plot'
plot.SII: no visible global function definition for 'lines'
plot.SII: no visible global function definition for 'abline'
plot.SII: no visible global function definition for 'legend'
sii : approx.l: no visible global function definition for 'approx'
sii.excel: no visible global function definition for 'predict'
sii.excel : approx.l: no visible global function definition for
  'approx'
Undefined global functions or variables:
  abline approx legend lines plot predict
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "plot")
  importFrom("stats", "approx", "predict")
to your NAMESPACE file.
linearextrapolation: no visible global function definition for 'coef'
linearextrapolation: no visible global function definition for 'lm'
plotsimexaft: no visible global function definition for 'plot'
plotsimexaft: no visible global function definition for 'lm'
plotsimexaft: no visible global function definition for 'predict'
plotsimexaft: no visible global function definition for 'lines'
plotsimexaft: no visible global function definition for 'points'
plotsimexaft: no visible global function definition for 'legend'
print.simexaft: no visible global function definition for 'coef'
quadraticextrapolation: no visible global function definition for
  'coef'
quadraticextrapolation: no visible global function definition for 'lm'
simexaft: no visible global function definition for 'terms'
simexaft: no visible global function definition for 'rnorm'
simexaft: no visible binding for global variable 'var'
simexaft: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  coef legend lines lm plot pnorm points predict rnorm terms var
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points")
  importFrom("stats", "coef", "lm", "pnorm", "predict", "rnorm", "terms",
             "var")
to your NAMESPACE file.
getFormula: no visible global function definition for 'as.formula'
internalSimXyplot : f: no visible global function definition for
  'median'
runSimulation: no visible global function definition for 'runif'
setup: no visible global function definition for 'runif'
clusterSetup,ANY-data.frame-SampleControl: no visible binding for
  global variable 'cnam'
clusterSetup,ANY-data.frame-TwoStageControl: no visible binding for
  global variable 'cnam'
initialize,DCARContControl: no visible binding for global variable
  'rnorm'
initialize,DataControl: no visible binding for global variable 'rnorm'
Undefined global functions or variables:
  as.formula cnam median rnorm runif
Consider adding
  importFrom("stats", "as.formula", "median", "rnorm", "runif")
to your NAMESPACE file.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
cumallcausehr: no visible global function definition for 'integrate'
plotbe: no visible global function definition for 'plot'
plotbe: no visible global function definition for 'lines'
plotbe: no visible global function definition for 'legend'
plotcph: no visible global function definition for 'confint'
plotcph: no visible global function definition for 'plot'
plotcph: no visible global function definition for 'abline'
plotcph: no visible global function definition for 'axis'
plotcph: no visible global function definition for 'polygon'
plotcph: no visible global function definition for 'lines'
plotnae: no visible global function definition for 'plot'
simCR: no visible global function definition for 'rnorm'
simEBMT: no visible global function definition for 'model.matrix'
simexit: no visible global function definition for 'runif'
simexitinner: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  abline axis confint integrate legend lines model.matrix plot polygon
  rnorm runif uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "plot",
             "polygon")
  importFrom("stats", "confint", "integrate", "model.matrix", "rnorm",
             "runif", "uniroot")
to your NAMESPACE file.
'library' or 'require' call to 'boot' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'boot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File 'simpleboot/R/zzz.R':
  .onLoad calls:
    require(boot)

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

lo.boot.resample: warning in sample(1:nrow(orig.data), rep = TRUE, prob
  = weights): partial argument match of 'rep' to 'replace'
lo.boot.resample: warning in sample(res, rep = TRUE, prob = weights):
  partial argument match of 'rep' to 'replace'
S3 methods shown with full name in documentation object 'pairs.boot':
  'pairs.boot'

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.
randInitializeWeights: no visible global function definition for
  'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Package in Depends field not imported from: 'mclust'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Simpsons: no visible global function definition for 'Mclust'
Simpsons: no visible global function definition for 'lm'
Simpsons: no visible global function definition for 'plot'
Simpsons: no visible global function definition for 'abline'
Simpsons: no visible global function definition for 'par'
Simpsons: no visible global function definition for 'legend'
Simpsons: no visible global function definition for 'txtProgressBar'
Simpsons: no visible global function definition for 'setTxtProgressBar'
Simpsons: no visible global function definition for 'quantile'
plot.Simpson: no visible global function definition for 'plot'
plot.Simpson: no visible global function definition for 'lm'
plot.Simpson: no visible global function definition for 'abline'
plot.Simpson: no visible global function definition for 'par'
plot.Simpson: no visible global function definition for 'legend'
Undefined global functions or variables:
  Mclust abline legend lm par plot quantile setTxtProgressBar
  txtProgressBar
Consider adding
  importFrom("graphics", "abline", "legend", "par", "plot")
  importFrom("stats", "lm", "quantile")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
simrel: no visible global function definition for 'runif'
simrel: no visible global function definition for 'rnorm'
simrelplot: no visible global function definition for 'par'
simrelplot: no visible global function definition for 'layout'
simrelplot: no visible global function definition for 'devAskNewPage'
simrelplot: no visible global function definition for 'dev.hold'
simrelplot: no visible global function definition for 'plot'
simrelplot: no visible global function definition for 'abline'
simrelplot: no visible global function definition for 'dev.flush'
simrelplot: no visible global function definition for 'points'
simrelplot: no visible global function definition for 'axis'
simrelplot: no visible global function definition for 'mtext'
simrelplot: no visible global function definition for 'box'
simrelplot: no visible global function definition for 'cov'
Undefined global functions or variables:
  abline axis box cov dev.flush dev.hold devAskNewPage layout mtext par
  plot points rnorm runif
Consider adding
  importFrom("grDevices", "dev.flush", "dev.hold", "devAskNewPage")
  importFrom("graphics", "abline", "axis", "box", "layout", "mtext",
             "par", "plot", "points")
  importFrom("stats", "cov", "rnorm", "runif")
to your NAMESPACE file.
Found the following hidden files and directories:
  vignettes/.Rhistory
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'abind' 'svUnit'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
simSummary: no visible global function definition for 'abind'
simSummary_unitTests: no visible global function definition for
  'clearLog'
simSummary_unitTests: no visible global function definition for
  'runTest'
simSummary_unitTests: no visible global function definition for
  'svSuite'
simSummary_unitTests: no visible global function definition for 'Log'
simSummary_unitTests: no visible global function definition for 'stats'
simSummary_unitTests: no visible global function definition for
  'metadata'
simSummary_unitTests: no visible global function definition for
  'errorLog'
Undefined global functions or variables:
  Log abind clearLog errorLog metadata runTest stats svSuite
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  5.9Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   2.3Mb
Running examples in 'sisus-Ex.R' failed
The error most likely occurred in:

> ### Name: sisus.run
> ### Title: driver program for SISUS
> ### Aliases: sisus.run
> 
> ### ** Examples
> 
> # set working directory for many output files with setwd()
> # see http://statacumen.com/sisus for workbook
> filename = "http://statacumen.com/sw/sisus/examples/SISUS_v0_09_template.xls";
> sisus.run(filename)
trying URL 'http://statacumen.com/sw/sisus/examples/SISUS_v0_09_template.xls'
Warning in download.file(xls, tf, mode = "wb") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in download.file(xls, tf, mode = "wb") : 
  cannot open URL 'http://statacumen.com/sw/sisus/examples/SISUS_v0_09_template.xls'
Calls: sisus.run ... as.matrix -> <Anonymous> -> xls2sep -> download.file
Error in file.exists(tfn) : invalid 'file' argument
Calls: sisus.run ... get.data -> as.matrix -> <Anonymous> -> file.exists
Execution halted
cvskda: no visible global function definition for 'detectCores'
cvskda: no visible global function definition for 'makeCluster'
cvskda: no visible global function definition for 'clusterApplyLB'
cvskda: no visible global function definition for 'mclapply'
cvskda: no visible global function definition for 'stopCluster'
Undefined global functions or variables:
  clusterApplyLB detectCores makeCluster mclapply stopCluster
dskt: no visible global function definition for 'dt'
pskt: no visible global function definition for 'pt'
qskt: no visible global function definition for 'qt'
rskt: no visible global function definition for 'runif'
Undefined global functions or variables:
  dt pt qt runif
Consider adding
  importFrom("stats", "dt", "pt", "qt", "runif")
to your NAMESPACE file.
Package which this enhances but not available for checking: 'kmndirs'
Unavailable namespace imported from by a ':::' call: 'kmndirs'
  See the note in ?`:::` about the use of this operator.
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tthread/tinythread.h:632:14: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tbb_stddef.h:470:37: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/atomic.h:29:30: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:42:14: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:43:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:75:21: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:102:10: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:80:37: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:127:30: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.5/skm.Rcheck/00install.out' for details.
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.
slcestimates: no visible global function definition for 'par'
slcestimates: no visible global function definition for 'plot'
slcestimates: no visible global function definition for 'abline'
slcestimates: no visible global function definition for 'lines'
slcestimates: no visible global function definition for 'axis'
slcestimates: no visible global function definition for 'points'
slcestimates: no visible global function definition for 'title'
Undefined global functions or variables:
  abline axis lines par plot points title
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "par", "plot",
             "points", "title")
to your NAMESPACE file.
cvsmac: no visible global function definition for 'predict'
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
File 'smco/R/smco.R':
  .onAttach calls:
    cat(paste("This is smco package", version, "\n"))

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

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

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

.MHUpdateFuncGen.PF : MHUpdateFunc: no visible global function
  definition for 'runif'
MarkovSwitchingFuncGenerator : generateNextStreamsFunc: no visible
  global function definition for 'runif'
MarkovSwitchingFuncGenerator: no visible global function definition for
  'rnorm'
MarkovSwitchingFuncGenerator: no visible global function definition for
  'runif'
MarkovSwitchingFuncGenerator : logObsDensFunc: no visible global
  function definition for 'dnorm'
MarkovSwitchingFuncGenerator : propagateFunc: no visible global
  function definition for 'dnorm'
MarkovSwitchingFuncGenerator : propagateFunc: no visible global
  function definition for 'runif'
Undefined global functions or variables:
  dnorm rnorm runif
Consider adding
  importFrom("stats", "dnorm", "rnorm", "runif")
to your NAMESPACE file.
em: no visible global function definition for 'coxph'
em: no visible global function definition for 'optim'
plotpredictsmcure: no visible global function definition for 'plot'
plotpredictsmcure: no visible global function definition for 'matplot'
plotpredictsmcure: no visible global function definition for 'lines'
smcure: no visible binding for global variable 'na.omit'
smcure: no visible global function definition for 'model.frame'
smcure: no visible global function definition for 'model.extract'
smcure: no visible global function definition for 'model.matrix'
smcure: no visible global function definition for 'coxph'
smcure: no visible global function definition for 'survreg'
smcure: no visible binding for global variable 'var'
smcure: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  coxph lines matplot model.extract model.frame model.matrix na.omit
  optim plot pnorm survreg var
Consider adding
  importFrom("graphics", "lines", "matplot", "plot")
  importFrom("stats", "model.extract", "model.frame", "model.matrix",
             "na.omit", "optim", "pnorm", "var")
to your NAMESPACE file.
branching.resample: no visible global function definition for 'rbinom'
cov.weights: no visible global function definition for 'var'
inverse.cdf.weights: no visible global function definition for 'runif'
multinomial.resample: no visible global function definition for 'runif'
stratified.resample: no visible global function definition for 'runif'
systematic.resample: no visible global function definition for 'runif'
Undefined global functions or variables:
  rbinom runif var
Consider adding
  importFrom("stats", "rbinom", "runif", "var")
to your NAMESPACE file.
'library' or 'require' call to 'proxy' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'proxy' 'tm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
normalize: no visible binding for global variable 'sd'
simDic: no visible global function definition for 'simil'
simDoc: no visible global function definition for 'simil'
Undefined global functions or variables:
  sd simil
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Grad.sph: no visible global function definition for 'dist'
IMDS: no visible global function definition for 'cmdscale'
IMDS: no visible global function definition for 'as.dist'
IMDS: no visible global function definition for 'runif'
IMDS: no visible global function definition for 'optim'
idistSph: no visible global function definition for 'dist'
obj.sph: no visible global function definition for 'dist'
plot.imds: no visible binding for global variable 'lines'
plot.imds: no visible global function definition for 'plot'
plot.imds: no visible global function definition for 'text'
plot.imds: no visible global function definition for 'rect'
Undefined global functions or variables:
  as.dist cmdscale dist lines optim plot rect runif text
Consider adding
  importFrom("graphics", "lines", "plot", "rect", "text")
  importFrom("stats", "as.dist", "cmdscale", "dist", "optim", "runif")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'ggplot2' 'reshape'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'corpcor' 'ggplot2' 'reshape'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' calls in package code:
  'MASS' 'survival'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
lines.SmithWilsonYieldCurve: no visible global function definition for
  'lines'
plot.SmithWilsonYieldCurve: no visible global function definition for
  'plot'
points.SmithWilsonYieldCurve: no visible global function definition for
  'points'
Undefined global functions or variables:
  lines plot points
Consider adding
  importFrom("graphics", "lines", "plot", "points")
to your NAMESPACE file.
Fourier2d: no visible global function definition for 'fft'
kernel2dsmooth: no visible global function definition for 'fft'
Undefined global functions or variables:
  fft
Consider adding
  importFrom("stats", "fft")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/sm.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
'library' or 'require' calls in package code:
  'akima' 'misc3d' 'rgl' 'rpanel' 'tkrplot'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
dNMR: no visible global function definition for 'pnorm'
dNMR: no visible global function definition for 'dnorm'
pNMR: no visible global function definition for 'pnorm'
pNMR: no visible global function definition for 'dnorm'
rMR: no visible global function definition for 'rnorm'
rMR: no visible global function definition for 'rchisq'
Undefined global functions or variables:
  dnorm pnorm rchisq rnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm", "rchisq", "rnorm")
to your NAMESPACE file.
SMVar.paired : <anonymous>: no visible global function definition for
  'var'
SMVar.paired: no visible global function definition for 'var'
SMVar.paired: no visible global function definition for 'pt'
SMVar.paired: no visible global function definition for 'p.adjust'
SMVar.paired: no visible global function definition for 'write.table'
SMVar.unpaired : <anonymous>: no visible global function definition for
  'var'
SMVar.unpaired: no visible global function definition for 'var'
SMVar.unpaired: no visible global function definition for 'pt'
SMVar.unpaired: no visible global function definition for 'p.adjust'
SMVar.unpaired: no visible global function definition for 'write.table'
Undefined global functions or variables:
  p.adjust pt var write.table
Consider adding
  importFrom("stats", "p.adjust", "pt", "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
sclust: no visible global function definition for 'var'
snipEM: no visible global function definition for 'cov'
stEM: no visible global function definition for 'cov'
stEM: no visible global function definition for 'quantile'
Undefined global functions or variables:
  cov quantile var
Consider adding
  importFrom("stats", "cov", "quantile", "var")
to your NAMESPACE file.
Package in Depends field not imported from: 'snow'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
KS.test: no visible global function definition for 'quantile'
KS.test : Fgaus: no visible global function definition for 'pnorm'
KS.test: no visible global function definition for 'setNames'
cs.test: no visible global function definition for 'pbinom'
cs.test: no visible global function definition for 'pnorm'
cs.test: no visible global function definition for 'setNames'
kde: no visible global function definition for 'quantile'
kde : Fgaus: no visible global function definition for 'pnorm'
kde: no visible global function definition for 'par'
kre: no visible global function definition for 'quantile'
kre: no visible global function definition for 'lines'
ns.test: no visible global function definition for 'complete.cases'
ns.test: no visible global function definition for 'qnorm'
ns.test: no visible global function definition for 'pnorm'
ns.test: no visible global function definition for 'pchisq'
ns.test: no visible global function definition for 'setNames'
ns.test: no visible global function definition for 'qt'
quant.test: no visible global function definition for 'complete.cases'
quant.test: no visible global function definition for 'pbinom'
quant.test: no visible global function definition for 'pnorm'
quant.test: no visible global function definition for 'setNames'
quant.test: no visible global function definition for 'quantile'
quant.test: no visible global function definition for 'phyper'
runs.test: no visible global function definition for 'median'
runs.test: no visible global function definition for 'setNames'
runs.test: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  complete.cases lines median par pbinom pchisq phyper pnorm qnorm qt
  quantile setNames
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "complete.cases", "median", "pbinom", "pchisq",
             "phyper", "pnorm", "qnorm", "qt", "quantile", "setNames")
to your NAMESPACE file.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'mvtnorm' 'combinat'
A package should be listed in only one of these fields.
chisq.test.a: no visible global function definition for 'chisq.test'
maxsel: no visible global function definition for 'complete.cases'
maxsel.asymp.test: no visible global function definition for
  'complete.cases'
Undefined global functions or variables:
  chisq.test complete.cases
Consider adding
  importFrom("stats", "chisq.test", "complete.cases")
to your NAMESPACE file.
MDSplot: no visible global function definition for 'par'
MDSplot: no visible global function definition for 'rainbow'
MDSplot: no visible global function definition for 'plot'
MDSplot: no visible global function definition for 'pairs'
classCenter : <anonymous>: no visible binding for global variable
  'median'
grow.snpRF: no visible global function definition for 'update'
na.roughfix.data.frame : roughfix: no visible global function
  definition for 'median'
na.roughfix.default: no visible global function definition for 'median'
outlier.default: no visible global function definition for 'median'
outlier.default: no visible global function definition for 'mad'
plot.margin: no visible global function definition for
  'installed.packages'
plot.margin: no visible global function definition for 'rainbow'
plot.margin: no visible global function definition for 'plot.default'
plot.snpRF: no visible global function definition for 'matplot'
tuneSnpRF: no visible global function definition for 'axis'
varImpPlot: no visible global function definition for 'par'
varImpPlot: no visible global function definition for 'dotchart'
varImpPlot: no visible global function definition for 'mtext'
Undefined global functions or variables:
  axis dotchart installed.packages mad matplot median mtext pairs par
  plot plot.default rainbow update
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "dotchart", "matplot", "mtext", "pairs",
             "par", "plot", "plot.default")
  importFrom("stats", "mad", "median", "update")
  importFrom("utils", "installed.packages")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'Biostrings' 'GenomicRanges' 'IRanges' 'Rsamtools'
  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:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/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'.
calculate.areas: no visible global function definition for 'runif'
calculate.gradedareas: no visible global function definition for
  'rnorm'
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from 'SoDA' for: 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Missing or unexported object: 'base::WHAT'
Packages in Depends field not imported from:
  'MASS' 'magic' 'ppls' 'psych'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
get.hnx.B.initialW: no visible global function definition for
  'normalize.vector'
get.hnx.B.initialW: no visible global function definition for 'adiag'
hclust.wrap: no visible global function definition for 'hclust'
hclust.wrap: no visible global function definition for 'dist'
hclust.wrap: no visible global function definition for 'cutree'
my.normdata.gen: no visible global function definition for 'mvrnorm'
my.normdata.gen: no visible global function definition for 'rnorm'
odc.clust: no visible binding for global variable 'kmeans'
odc.cv: no visible global function definition for 'ginv'
odc.optimallambda2: no visible global function definition for 'tr'
odc.optimallambda2: no visible global function definition for 'ginv'
odc.optimallambda2: no visible binding for global variable 'sd'
sodc.clust: no visible binding for global variable 'kmeans'
Undefined global functions or variables:
  adiag cutree dist ginv hclust kmeans mvrnorm normalize.vector rnorm
  sd tr
Consider adding
  importFrom("stats", "cutree", "dist", "hclust", "kmeans", "rnorm",
             "sd")
to your NAMESPACE file.
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.
HardKMeansDemo: no visible global function definition for
  'graphics.off'
HardKMeansDemo: no visible global function definition for 'plot'
HardKMeansDemo: no visible global function definition for 'points'
initializeMeansMatrix: no visible global function definition for
  'runif'
initializeMeansMatrix: no visible global function definition for 'dist'
normalizeMatrix: no visible global function definition for 'sd'
plotRoughKMeans: no visible global function definition for
  'graphics.off'
plotRoughKMeans: no visible global function definition for 'plot'
plotRoughKMeans: no visible global function definition for 'points'
Undefined global functions or variables:
  dist graphics.off plot points runif sd
Consider adding
  importFrom("grDevices", "graphics.off")
  importFrom("graphics", "plot", "points")
  importFrom("stats", "dist", "runif", "sd")
to your NAMESPACE file.
Ssimpute.als: no visible global function definition for 'rnorm'
Ssvd.als: no visible global function definition for 'rnorm'
cs.default: no visible binding for global variable 'weighted.mean'
simpute.als: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm weighted.mean
Consider adding
  importFrom("stats", "rnorm", "weighted.mean")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'aqp' 'lattice' 'methods' 'munsell' 'splancs'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' calls in package code:
  'chemometrics' 'spatstat'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.soma: no visible global function definition for 'plot'
soma: no visible global function definition for 'runif'
Undefined global functions or variables:
  plot runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
to your NAMESPACE file.
bm: no visible global function definition for 'rnorm'
bm: no visible global function definition for 'ts'
fbm: no visible global function definition for 'fft'
fbm: no visible global function definition for 'rnorm'
fbm: no visible global function definition for 'ts'
gbm: no visible global function definition for 'rnorm'
gbm: no visible global function definition for 'ts'
Undefined global functions or variables:
  fft rnorm ts
Consider adding
  importFrom("stats", "fft", "rnorm", "ts")
to your NAMESPACE file.
getAlpha: no visible global function definition for 'pbinom'
kfweOrd: no visible global function definition for 'qnbinom'
Undefined global functions or variables:
  pbinom qnbinom
Consider adding
  importFrom("stats", "pbinom", "qnbinom")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from 'someMTP' for: 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
'library' or 'require' call to 'hexbin' which was already attached by Depends.
  Please remove these calls from your code.
hexbinpie: no visible global function definition for 'quantile'
hexbinpie: no visible global function definition for 'polygon'
hexbinpie: no visible global function definition for 'text'
makehexbinplot: no visible global function definition for 'rainbow'
makehexbinplot: no visible global function definition for 'col2rgb'
makehexbinplot: no visible global function definition for 'edit'
makehexbinplot: no visible global function definition for 'dev.new'
makehexbinplot: no visible global function definition for 'plot.new'
makehexbinplot: no visible global function definition for 'plot.window'
makehexbinplot: no visible global function definition for 'box'
makehexbinplot: no visible global function definition for 'axis'
makehexbinplot: no visible global function definition for 'legend'
som.plot: no visible global function definition for 'read.table'
Undefined global functions or variables:
  axis box col2rgb dev.new edit legend plot.new plot.window polygon
  quantile rainbow read.table text
Consider adding
  importFrom("grDevices", "col2rgb", "dev.new", "rainbow")
  importFrom("graphics", "axis", "box", "legend", "plot.new",
             "plot.window", "polygon", "text")
  importFrom("stats", "quantile")
  importFrom("utils", "edit", "read.table")
to your NAMESPACE file.
dfrag: no visible global function definition for 'qgeom'
dfrag: no visible global function definition for 'plogis'
dfrag: no visible global function definition for 'dgeom'
estAbund: no visible global function definition for 'xtabs'
mmN : <anonymous>: no visible global function definition for 'uniroot'
pfrag: no visible global function definition for 'qgeom'
phi.deriv.default: no visible global function definition for
  'model.matrix'
phi.deriv.default: no visible binding for global variable 'sd'
phi.update.default: no visible global function definition for 'glm'
phi.update.default: no visible binding for global variable
  'quasipoisson'
phi.update.default: no visible global function definition for 'predict'
phi.update.lframe: no visible global function definition for 'glm'
phi.update.lframe: no visible binding for global variable
  'quasipoisson'
phi.update.lframe: no visible global function definition for 'predict'
pr.y.given.x : <anonymous>: no visible global function definition for
  'dpois'
pr.y.given.x : <anonymous> : <anonymous>: no visible global function
  definition for 'dpois'
pr.y.given.x : <anonymous>: no visible global function definition for
  'convolve'
qfrag: no visible global function definition for 'qgeom'
rfrag: no visible global function definition for 'qgeom'
simSonic: no visible global function definition for 'rpois'
Undefined global functions or variables:
  convolve dgeom dpois glm model.matrix plogis predict qgeom
  quasipoisson rpois sd uniroot xtabs
Consider adding
  importFrom("stats", "convolve", "dgeom", "dpois", "glm",
             "model.matrix", "plogis", "predict", "qgeom",
             "quasipoisson", "rpois", "sd", "uniroot", "xtabs")
to your NAMESPACE file.
plot.soo_function: no visible global function definition for
  'terrain.colors'
plot.soo_function: no visible binding for global variable 'image'
plot.soo_function: no visible binding for global variable 'contour'
plot3d: no visible global function definition for 'persp3d'
plot3d: no visible global function definition for 'terrain.colors'
random_parameters.soo_function: no visible global function definition
  for 'runif'
random_rotation_matrix: no visible global function definition for
  'runif'
Undefined global functions or variables:
  contour image persp3d runif terrain.colors
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "contour", "image")
  importFrom("stats", "runif")
to your NAMESPACE file.
simdata_contaminated : <anonymous>: no visible global function
  definition for 'rbinom'
simdata_uniform : multivariate_uniform : <anonymous>: no visible global
  function definition for 'runif'
which_min: no visible global function definition for 'head'
which_min: no visible global function definition for 'tail'
Undefined global functions or variables:
  head rbinom runif tail
Consider adding
  importFrom("stats", "rbinom", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
convert_municipality_names: no visible global function definition for
  'read.csv'
regression_plot: no visible binding for global variable 'loess'
regression_plot: no visible global function definition for
  'colorRampPalette'
regression_plot: no visible global function definition for
  'loess.control'
regression_plot: no visible global function definition for 'predict'
regression_plot : <anonymous>: no visible global function definition
  for 'quantile'
regression_plot : <anonymous>: no visible global function definition
  for 'pnorm'
regression_plot: no visible global function definition for
  'flush.console'
regression_plot: no visible global function definition for 'density'
Undefined global functions or variables:
  colorRampPalette density flush.console loess loess.control pnorm
  predict quantile read.csv
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "density", "loess", "loess.control", "pnorm",
             "predict", "quantile")
  importFrom("utils", "flush.console", "read.csv")
to your NAMESPACE file.
'library' or 'require' call to 'rgdal' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: 'r2cytoscape'
analyzeSP23Design: no visible global function definition for 'plot'
exploreSP23Design: no visible global function definition for
  'txtProgressBar'
exploreSP23Design: no visible global function definition for
  'setTxtProgressBar'
generateClinicalTrialData : <anonymous>: no visible global function
  definition for 'runif'
generateClinicalTrialData: no visible global function definition for
  'rbinom'
generateClinicalTrialData: no visible global function definition for
  'rexp'
mHP.b : crossingProbDiff: no visible global function definition for
  'pnorm'
mHP.b : crossingProbDiff: no visible global function definition for
  'Miwa'
mHP.b: no visible global function definition for 'qnorm'
mHP.b: no visible global function definition for 'uniroot'
mHP.c : crossingProbDiff: no visible global function definition for
  'Miwa'
mHP.c: no visible global function definition for 'uniroot'
mHP.c: no visible global function definition for 'qnorm'
performInterimLook: no visible global function definition for 'optim'
performInterimLook: no visible global function definition for
  'constrOptim'
performInterimLook: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  Miwa constrOptim optim plot pnorm qnorm rbinom rexp runif
  setTxtProgressBar txtProgressBar uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "constrOptim", "optim", "pnorm", "qnorm", "rbinom",
             "rexp", "runif", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
SPA: no visible global function definition for 'var'
Score.Test.Interact: no visible global function definition for 'pchisq'
Score.Test.Overall: no visible global function definition for 'var'
Score.Test.Overall: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  pchisq var
Consider adding
  importFrom("stats", "pchisq", "var")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/spaceExt.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
Packages in Depends field not imported from:
  'glasso' 'limSolve'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
glasso.miss: no visible global function definition for 'cov'
glasso.miss: no visible global function definition for 'glasso'
glasso.miss: no visible global function definition for 'Solve'
space.miss: no visible global function definition for 'Solve'
Undefined global functions or variables:
  Solve cov glasso
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
'library' or 'require' call to 'Matrix' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'Matrix' 'igraph' 'splines'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GenPar: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'Rcpp' 'colorspace' 'picante'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
hausman: no visible global function definition for 'pchisq'
span.formula: no visible global function definition for 'model.frame'
span.formula: no visible global function definition for 'model.matrix'
span.formula: no visible global function definition for
  'model.response'
spbe: no visible global function definition for 'cor'
spbe: no visible global function definition for 'pt'
spfe: no visible global function definition for 'cor'
spfe: no visible global function definition for 'pt'
sprandom: no visible global function definition for 'cor'
sprandom: no visible global function definition for 'pt'
summary.span: no visible global function definition for 'printCoefmat'
Undefined global functions or variables:
  cor model.frame model.matrix model.response pchisq printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.frame", "model.matrix",
             "model.response", "pchisq", "printCoefmat", "pt")
to your NAMESPACE file.
plot.spa: no visible global function definition for 'plot'
plot.spa: no visible global function definition for 'lines'
plot.spa: no visible global function definition for 'points'
plot.spa: no visible global function definition for 'gray'
plot.spa: no visible global function definition for 'box'
predict.spa: no visible global function definition for 'fitted'
predict.spa: no visible global function definition for 'coef'
spa.gcv: no visible global function definition for 'density'
spa.gcv: no visible global function definition for 'quantile'
spa.sim: no visible global function definition for 'runif'
spa.sim: no visible global function definition for 'rnorm'
spa.sim: no visible global function definition for 'rbinom'
update.spa: no visible global function definition for 'quantile'
Undefined global functions or variables:
  box coef density fitted gray lines plot points quantile rbinom rnorm
  runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "box", "lines", "plot", "points")
  importFrom("stats", "coef", "density", "fitted", "quantile", "rbinom",
             "rnorm", "runif")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'RCurl' 'XML'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SPARQL : <anonymous>: no visible global function definition for
  'URLencode'
SPARQL: no visible binding for global variable 'getURL'
SPARQL: no visible global function definition for 'URLencode'
SPARQL: no visible binding for global variable 'xmlParse'
SPARQL: no visible global function definition for 'getNodeSet'
SPARQL: no visible global function definition for 'xpathApply'
SPARQL: no visible binding for global variable 'postForm'
get_attr: no visible global function definition for 'getNodeSet'
get_attr : <anonymous> : <anonymous>: no visible global function
  definition for 'getNodeSet'
get_attr : <anonymous> : <anonymous>: no visible global function
  definition for 'xmlDoc'
get_value: no visible global function definition for 'xmlDoc'
get_value: no visible global function definition for 'xpathSApply'
get_value: no visible binding for global variable 'xmlValue'
get_value: no visible global function definition for 'xpathApply'
get_value: no visible binding for global variable 'xmlGetAttr'
readCSVstring: no visible global function definition for 'read.csv'
readTSVstring: no visible global function definition for 'read.delim'
Undefined global functions or variables:
  URLencode getNodeSet getURL postForm read.csv read.delim xmlDoc
  xmlGetAttr xmlParse xmlValue xpathApply xpathSApply
Consider adding
  importFrom("utils", "URLencode", "read.csv", "read.delim")
to your NAMESPACE file.
f.I2.cont: no visible global function definition for 'combn'
f.I2.dich: no visible global function definition for 'combn'
f.pstar.cont: no visible global function definition for 'combn'
f.pstar.dich: no visible global function definition for 'combn'
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
image.matrixBC: no visible global function definition for 'dev.new'
image.matrixBC: no visible global function definition for 'image'
image.matrixBC: no visible global function definition for 'heat.colors'
image.matrixBC: no visible global function definition for 'axis'
image.matrixBC: no visible global function definition for 'title'
image.sparseBC: no visible global function definition for 'dev.new'
image.sparseBC: no visible global function definition for 'image'
image.sparseBC: no visible global function definition for 'heat.colors'
image.sparseBC: no visible global function definition for 'axis'
image.sparseBC: no visible global function definition for 'tail'
image.sparseBC: no visible global function definition for 'title'
matrixBC: no visible global function definition for 'kmeans'
sparseBC: no visible global function definition for 'kmeans'
sparseBC.choosekr: no visible global function definition for 'kmeans'
sparseBC.choosekr: no visible binding for global variable 'sd'
Undefined global functions or variables:
  axis dev.new heat.colors image kmeans sd tail title
Consider adding
  importFrom("grDevices", "dev.new", "heat.colors")
  importFrom("graphics", "axis", "image", "title")
  importFrom("stats", "kmeans", "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
Found the following significant warnings:
  sparseSVM.c:367:30: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/sparseSVM.Rcheck/00install.out' for details.
gev.impute: no visible global function definition for 'rnorm'
gev.init: no visible global function definition for 'rbinom'
gev.init: no visible global function definition for 'var'
gev.init: no visible global function definition for 'optimize'
gev.logscore: no visible global function definition for 'density'
gev.logscore: no visible global function definition for 'splinefun'
gev.update.M: no visible global function definition for 'runif'
gev.update.hyper: no visible global function definition for 'rgamma'
gev.update.lambda: no visible global function definition for 'rnorm'
gev.update.lambda: no visible global function definition for 'dgamma'
gev.update.lambda: no visible global function definition for 'dnorm'
gev.update.lambda: no visible global function definition for 'runif'
gev.update.tau.kappa: no visible global function definition for 'rnorm'
gev.update.tau.kappa: no visible global function definition for 'dnorm'
gev.update.tau.kappa: no visible global function definition for 'runif'
gev.update.tau.mu: no visible global function definition for 'rnorm'
gev.update.tau.mu: no visible global function definition for 'dnorm'
gev.update.tau.mu: no visible global function definition for 'runif'
gev.update.tau.xi: no visible global function definition for 'rnorm'
gev.update.tau.xi: no visible global function definition for 'dnorm'
gev.update.tau.xi: no visible global function definition for 'runif'
gev.update.theta: no visible global function definition for 'rnorm'
gp.like.lambda: no visible global function definition for 'dgamma'
Undefined global functions or variables:
  density dgamma dnorm optimize rbinom rgamma rnorm runif splinefun var
Consider adding
  importFrom("stats", "density", "dgamma", "dnorm", "optimize", "rbinom",
             "rgamma", "rnorm", "runif", "splinefun", "var")
to your NAMESPACE file.
I2BR: no visible global function definition for 'pnorm'
I2SmD2: no visible global function definition for 'pnorm'
IBR: no visible global function definition for 'pnorm'
ISmD2: no visible global function definition for 'pnorm'
MestimatorBR: no visible global function definition for 'optim'
MestimatorSmith: no visible global function definition for 'optim'
psidotBR: no visible global function definition for 'dnorm'
psidotBR: no visible global function definition for 'pnorm'
psidotSmD2: no visible global function definition for 'dnorm'
psidotSmD2: no visible global function definition for 'pnorm'
tailBRInt: no visible global function definition for 'pnorm'
tailSmithInt: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dnorm optim pnorm
Consider adding
  importFrom("stats", "dnorm", "optim", "pnorm")
to your NAMESPACE file.
bbox_to_SpatialPolygons: no visible global function definition for
  'CRS'
bbox_to_SpatialPolygons: no visible global function definition for
  'Polygon'
bbox_to_SpatialPolygons: no visible global function definition for
  'Polygons'
bbox_to_SpatialPolygons: no visible global function definition for
  'SpatialPolygons'
list.raster.files: no visible global function definition for 'CRS'
list.raster.files: no visible global function definition for
  'spTransform'
list.raster.files: no visible global function definition for
  'SpatialPolygonsDataFrame'
list.raster.files: no visible global function definition for 'spChFIDs'
predict_rasterEngine : predict.rasterEngine_function: no visible global
  function definition for 'complete.cases'
projectRaster_rigorous : chunk_function: no visible global function
  definition for 'spTransform'
projectRaster_rigorous : chunk_function: no visible global function
  definition for 'CRS'
spatial_sync_raster: no visible global function definition for 'bbox'
spatial_sync_vector: no visible global function definition for
  'spTransform'
spatial_sync_vector: no visible global function definition for 'CRS'
Undefined global functions or variables:
  CRS Polygon Polygons SpatialPolygons SpatialPolygonsDataFrame bbox
  complete.cases spChFIDs spTransform
Consider adding
  importFrom("stats", "complete.cases")
to your NAMESPACE file.
Missing link or links in documentation object 'FeatureAxis.Rd':
  'bounding.box'

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

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

See section 'Cross-references' in the 'Writing R Extensions' manual.
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    R      5.0Mb
    doc    4.7Mb
    help   5.0Mb
    libs   1.2Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.5Mb
GenerateCliquesCovariance: no visible global function definition for
  'rnorm'
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Package suggested but not available for checking: 'spDataLarge'
Found the following significant warnings:
  loglog_lnl.cpp:34:15: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
  loglog_lnl.cpp:43:15: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  sploglog_lnl.cpp:40:15: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
  sploglog_lnl.cpp:49:15: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  spweib_lnl.cpp:40:15: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
  spweib_lnl.cpp:49:15: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  weib_lnl.cpp:34:14: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
  weib_lnl.cpp:43:14: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/spduration.Rcheck/00install.out' for details.
bartlett: no visible global function definition for 'pchisq'
local.rbfdot: no visible binding for global variable 'sd'
local.rbfdot: no visible global function definition for 'dist'
local.rbfdot : <anonymous>: no visible global function definition for
  'median'
speccalt: no visible global function definition for 'kmeans'
Undefined global functions or variables:
  dist kmeans median pchisq sd
Consider adding
  importFrom("stats", "dist", "kmeans", "median", "pchisq", "sd")
to your NAMESPACE file.
ChaoBunge: no visible global function definition for 'qnorm'
ChaoLee1992: no visible global function definition for 'qnorm'
Pmix: no visible global function definition for 'dpois'
PmixSCon: no visible global function definition for 'dbeta'
bootPCG: no visible global function definition for 'flush.console'
bootPCG: no visible global function definition for 'quantile'
bootPnpmle: no visible global function definition for 'flush.console'
bootPnpmle: no visible global function definition for 'quantile'
bootUnpmle: no visible global function definition for 'flush.console'
bootUnpmle: no visible global function definition for 'quantile'
chao1984: no visible global function definition for 'qnorm'
jackknife: no visible global function definition for 'dbinom'
jackknife: no visible global function definition for 'qnorm'
pcg: no visible global function definition for 'flush.console'
unpmle: no visible global function definition for 'flush.console'
untrunPmix: no visible global function definition for 'dpois'
Undefined global functions or variables:
  dbeta dbinom dpois flush.console qnorm quantile
Consider adding
  importFrom("stats", "dbeta", "dbinom", "dpois", "qnorm", "quantile")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
randomCorrelations: no visible global function definition for 'cor'
specGlm : <anonymous>: no visible global function definition for 'coef'
specLm : <anonymous>: no visible global function definition for 'coef'
Undefined global functions or variables:
  coef cor
Consider adding
  importFrom("stats", "coef", "cor")
to your NAMESPACE file.
'library' or 'require' call to 'leaps' which was already attached by Depends.
  Please remove these calls from your code.
modSearch: no visible global function definition for 'glm'
modSearch: no visible binding for global variable 'binomial'
modSearch: no visible global function definition for 'na.omit'
modSearch: no visible global function definition for 'as.formula'
speff: no visible binding for global variable 'na.pass'
speff: no visible global function definition for 'model.matrix'
speff: no visible global function definition for 'terms'
speff: no visible global function definition for 'model.response'
speff: no visible global function definition for 'as.formula'
speff: no visible global function definition for 'predict'
speff: no visible global function definition for 'na.omit'
speff: no visible global function definition for 'glm'
speff: no visible binding for global variable 'na.omit'
speffSurv: no visible global function definition for 'model.matrix'
speffSurv: no visible global function definition for 'terms'
speffSurv: no visible global function definition for 'model.response'
speffSurv: no visible global function definition for 'as.formula'
speffSurv: no visible global function definition for 'uniroot'
summary.speff: no visible global function definition for 'qnorm'
summary.speff: no visible global function definition for 'pnorm'
summary.speffSurv: no visible global function definition for 'qnorm'
summary.speffSurv: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  as.formula binomial glm model.matrix model.response na.omit na.pass
  pnorm predict qnorm terms uniroot
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "model.matrix",
             "model.response", "na.omit", "na.pass", "pnorm", "predict",
             "qnorm", "terms", "uniroot")
to your NAMESPACE file.
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nr' to 'nrow'
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nc' to 'ncol'
spe: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Package in Depends field not imported from: 'rgl'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
pointsphere: no visible global function definition for 'runif'
rgl.sphMW: no visible global function definition for 'plot3d'
rgl.sphcirc: no visible global function definition for 'rotate3d'
rgl.sphcirc: no visible global function definition for 'lines3d'
rgl.sphgrid: no visible global function definition for 'open3d'
rgl.sphgrid: no visible global function definition for 'plot3d'
rgl.sphgrid: no visible global function definition for 'lines3d'
rgl.sphgrid: no visible global function definition for 'text3d'
rgl.sphpoints: no visible global function definition for 'points3d'
rgl.sphsun: no visible global function definition for 'plot3d'
rgl.sphtext: no visible global function definition for 'text3d'
Undefined global functions or variables:
  lines3d open3d plot3d points3d rotate3d runif text3d
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'lars' 'parallel' 'randomForest'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' call to 'quadprog' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'quadprog'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SPIn: no visible global function definition for 'density'
SPIn: no visible global function definition for 'quantile'
SPIn: no visible global function definition for 'solve.QP'
bootSPIn: no visible global function definition for 'runif'
plot.SPIn: no visible global function definition for 'hist'
plot.SPIn: no visible global function definition for 'lines'
plot.SPIn: no visible global function definition for 'text'
plot.SPIn: no visible global function definition for 'quantile'
plot.SPIn: no visible global function definition for 'legend'
Undefined global functions or variables:
  density hist legend lines quantile runif solve.QP text
Consider adding
  importFrom("graphics", "hist", "legend", "lines", "text")
  importFrom("stats", "density", "quantile", "runif")
to your NAMESPACE file.
spi: no visible global function definition for 'read.table'
spi: no visible global function definition for 'ecdf'
spi: no visible global function definition for 'qnorm'
spi: no visible global function definition for 'colorRampPalette'
spi: no visible global function definition for 'filled.contour'
spi: no visible global function definition for 'axis'
Undefined global functions or variables:
  axis colorRampPalette ecdf filled.contour qnorm read.table
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "filled.contour")
  importFrom("stats", "ecdf", "qnorm")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following significant warnings:
  timeFuns.c:1084:34: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/splusTimeDate.Rcheck/00install.out' for details.
R2.global: no visible global function definition for 'var'
calculer.var.exp: no visible global function definition for 'var'
creer.noeud: no visible global function definition for 'var'
ponderer.classe: no visible global function definition for 'var'
ponderer.classe: no visible global function definition for 'cov'
spodt: no visible global function definition for 'model.frame'
spodt.tree: no visible global function definition for 'plot.new'
spodt.tree: no visible global function definition for 'par'
spodt.tree: no visible global function definition for 'plot.window'
spodt.tree: no visible global function definition for 'text'
spodt.tree: no visible global function definition for 'segments'
test.spodt: no visible global function definition for 'model.frame'
test.spodt: no visible global function definition for 'hist'
test.spodt: no visible global function definition for 'abline'
tracer.noeud: no visible global function definition for 'text'
tracer.noeud: no visible global function definition for 'segments'
Undefined global functions or variables:
  abline cov hist model.frame par plot.new plot.window segments text
  var
Consider adding
  importFrom("graphics", "abline", "hist", "par", "plot.new",
             "plot.window", "segments", "text")
  importFrom("stats", "cov", "model.frame", "var")
to your NAMESPACE file.
Ell.Theta: no visible global function definition for 'ell.theta'
confid.int.theta: no visible global function definition for 'qchisq'
confid.int.theta : sim.c: no visible global function definition for
  'runif'
confid.int.theta: no visible global function definition for 'quantile'
dd.est: no visible global function definition for 'ecdf'
ks.sporm : Simul: no visible global function definition for 'runif'
ks.stat: no visible global function definition for 'ecdf'
plotor: no visible global function definition for 'ecdf'
plotor: no visible global function definition for 'plot'
test.theta: no visible global function definition for 'ecdf'
test.theta : sim: no visible global function definition for 'runif'
Undefined global functions or variables:
  ecdf ell.theta plot qchisq quantile runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "ecdf", "qchisq", "quantile", "runif")
to your NAMESPACE file.
fetch_NBAPlayerStatistics: no visible global function definition for
  'read.table'
Undefined global functions or variables:
  read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   2.6Mb
plot.SPRT: no visible global function definition for 'par'
plot.SPRT: no visible global function definition for 'plot'
plot.SPRT: no visible global function definition for 'abline'
print.SPRT: no visible global function definition for 'head'
Undefined global functions or variables:
  abline head par plot
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("utils", "head")
to your NAMESPACE file.
fssa20: no visible global function definition for 'runif'
fssa2d: no visible global function definition for 'runif'
fssa30: no visible global function definition for 'runif'
fssa3d: no visible global function definition for 'runif'
ssa20: no visible global function definition for 'runif'
ssa2d: no visible global function definition for 'runif'
ssa30: no visible global function definition for 'runif'
ssa3d: no visible global function definition for 'runif'
ssi20: no visible global function definition for 'runif'
ssi2d: no visible global function definition for 'runif'
ssi30: no visible global function definition for 'runif'
ssi3d: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs   1.9Mb
plotThin: no visible global function definition for 'par'
plotThin: no visible global function definition for 'dev.interactive'
plotThin: no visible global function definition for 'plot'
plotThin: no visible global function definition for 'hist'
thin: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  dev.interactive hist par plot write.csv
Consider adding
  importFrom("grDevices", "dev.interactive")
  importFrom("graphics", "hist", "par", "plot")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
.GameSPT: no visible global function definition for 'runif'
.GameSPT: no visible global function definition for 'points'
.GameST: no visible global function definition for 'runif'
.GameST: no visible global function definition for 'points'
.arc: no visible global function definition for 'lines'
.ptpedal: no visible global function definition for 'polygon'
.sptpedal2: no visible global function definition for 'segments'
.sptpedal3: no visible global function definition for 'polygon'
.sptpedal4: no visible global function definition for 'polygon'
chaos.spt: no visible global function definition for 'plot'
chaos.spt: no visible global function definition for 'polygon'
chaos.spt: no visible global function definition for 'runif'
chaos.spt: no visible global function definition for 'points'
chaos.st: no visible global function definition for 'plot'
chaos.st: no visible global function definition for 'polygon'
chaos.st: no visible global function definition for 'runif'
chaos.st: no visible global function definition for 'points'
plot.spt: no visible global function definition for 'plot'
plot.spt: no visible global function definition for 'polygon'
plot.st: no visible global function definition for 'plot'
plot.st: no visible global function definition for 'polygon'
Undefined global functions or variables:
  lines plot points polygon runif segments
Consider adding
  importFrom("graphics", "lines", "plot", "points", "polygon",
             "segments")
  importFrom("stats", "runif")
to your NAMESPACE file.
sGda : <anonymous>: no visible global function definition for 'cov'
sortgene: no visible global function definition for 'model.matrix'
Undefined global functions or variables:
  cov model.matrix
Consider adding
  importFrom("stats", "cov", "model.matrix")
to your NAMESPACE file.
Running 'testthat.R' [15s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(sqlscore)
  > 
  > test_check("sqlscore")
  -- 1. Failure: cv.glmnet objects are handled correctly (@test-linpred.R#191)  --
  rec_round(linpred(mod1)) not equal to rec_round(res).
  target, current do not match when deparsed
  
  -- 2. Failure: cv.glmnet is handled correctly (@test-score_expression.R#177)  --
  rec_round(score_expression(mod1)) not equal to rec_round(res).
  target, current do not match when deparsed
  
  -- 3. Failure: cv.glmnet is handled correctly (@test-score_expression.R#187)  --
  rec_round(score_expression(mod2)) not equal to rec_round(res).
  target, current do not match when deparsed
  
  == testthat results  ===========================================================
  OK: 94 SKIPPED: 0 FAILED: 3
  1. Failure: cv.glmnet objects are handled correctly (@test-linpred.R#191) 
  2. Failure: cv.glmnet is handled correctly (@test-score_expression.R#177) 
  3. Failure: cv.glmnet is handled correctly (@test-score_expression.R#187) 
  
  Error: testthat unit tests failed
  Execution halted
'library' or 'require' calls in package code:
  'RJDBC' 'RMySQL' 'RODBC' 'RPostgreSQL' 'RSQLite' 'tcltk'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
cacheQuery: no visible global function definition for 'read.csv'
cacheQuery: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  read.csv write.csv
Consider adding
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
SQN: no visible binding for global variable 'median'
SQN: no visible global function definition for 'quantile'
SQN.demo.data: no visible global function definition for 'rnorm'
mix.qn: no visible global function definition for 'ecdf'
mix.qn: no visible global function definition for 'quantile'
Undefined global functions or variables:
  ecdf median quantile rnorm
Consider adding
  importFrom("stats", "ecdf", "median", "quantile", "rnorm")
to your NAMESPACE file.
plot.srafit: no visible global function definition for 'layout'
plot.srafit: no visible global function definition for 'par'
sraData : vartruncGauss : ff: no visible global function definition for
  'dnorm'
sraData : vartruncGauss : ff: no visible global function definition for
  'pnorm'
sraData : vartruncGauss: no visible global function definition for
  'uniroot'
sraPlotMean: no visible global function definition for 'axis'
sraPlotMean: no visible global function definition for 'points'
sraPlotMean: no visible global function definition for 'lines'
sraPlotMeanResid: no visible global function definition for 'axis'
sraPlotMeanResid: no visible global function definition for 'abline'
sraPlotMeanResid: no visible global function definition for 'points'
sraPlotVar: no visible global function definition for 'axis'
sraPlotVar: no visible global function definition for 'points'
sraPlotVar: no visible global function definition for 'lines'
sraPlotVarResid: no visible global function definition for 'axis'
sraPlotVarResid: no visible global function definition for 'abline'
sraPlotVarResid: no visible global function definition for 'points'
sraPlotlegend: no visible global function definition for 'legend'
sraStartingvalues : sraStartingvalues.mu0: no visible global function
  definition for 'rnorm'
sraStartingvalues : sraStartingvalues.logvarA0: no visible global
  function definition for 'rnorm'
sraStartingvalues : sraStartingvalues.logvarE0: no visible global
  function definition for 'rnorm'
sraStartingvalues: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  abline axis dnorm layout legend lines par pnorm points rnorm uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "layout", "legend", "lines",
             "par", "points")
  importFrom("stats", "dnorm", "pnorm", "rnorm", "uniroot")
to your NAMESPACE file.
Found the following hidden files and directories:
  .Rapp.history
  inst/script/.Rapp.history
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
File 'sROC/R/onload.R':
  .onLoad calls:
    packageStartupMessage("sROC 0.1-2 loaded")

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

AUC : TrapezInt: no visible global function definition for 'approx'
AUC : SimpsonInt: no visible global function definition for 'approx'
CI.CDF: no visible global function definition for 'qnorm'
bw.CDF: no visible global function definition for 'sd'
bw.CDF: no visible global function definition for 'IQR'
bw.CDF.pi: no visible global function definition for 'sd'
bw.CDF.pi: no visible global function definition for 'bw.nrd0'
bw.CDF.pi: no visible global function definition for 'bw.nrd'
bw.CDF.pi: no visible global function definition for 'bw.ucv'
bw.CDF.pi: no visible global function definition for 'bw.bcv'
bw.CDF.pi: no visible global function definition for 'bw.SJ'
bw.CDF.pi: no visible global function definition for 'IQR'
plot.CDF: no visible global function definition for 'plot.default'
plot.CDF: no visible global function definition for 'lines'
plot.CDF: no visible global function definition for 'polygon'
plot.ROC: no visible global function definition for 'plot.default'
plot.ROC: no visible global function definition for 'abline'
Undefined global functions or variables:
  IQR abline approx bw.SJ bw.bcv bw.nrd bw.nrd0 bw.ucv lines
  plot.default polygon qnorm sd
Consider adding
  importFrom("graphics", "abline", "lines", "plot.default", "polygon")
  importFrom("stats", "IQR", "approx", "bw.SJ", "bw.bcv", "bw.nrd",
             "bw.nrd0", "bw.ucv", "qnorm", "sd")
to your NAMESPACE file.
ssd : correction_method_D: no visible global function definition for
  'rnorm'
ssd : generate_bootstrap: no visible global function definition for
  'rmultinom'
ssd : bootstrap_method: no visible global function definition for
  'median'
ssd : bootstrap_method: no visible global function definition for
  'quantile'
ssd : unbalanced_generate_bootstrap: no visible global function
  definition for 'rmultinom'
ssd : unbalanced_bootstrap_method: no visible global function
  definition for 'median'
ssd : unbalanced_bootstrap_method: no visible global function
  definition for 'quantile'
ssd: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  median qchisq quantile rmultinom rnorm
Consider adding
  importFrom("stats", "median", "qchisq", "quantile", "rmultinom",
             "rnorm")
to your NAMESPACE file.
L_hNV: no visible global function definition for 'pnorm'
L_hNV_rho: no visible global function definition for 'pnorm'
eff.ssfa: no visible global function definition for 'pnorm'
plot_fitted: no visible global function definition for 'lines'
plot_moran: no visible global function definition for 'residuals'
print.summary.ssfa: no visible global function definition for
  'printCoefmat'
ssfa: no visible global function definition for 'model.frame'
ssfa: no visible global function definition for 'model.response'
ssfa.fit: no visible global function definition for 'lm'
ssfa.fit: no visible global function definition for 'var'
ssfa.fit: no visible global function definition for 'logLik'
summary.ssfa: no visible global function definition for 'pnorm'
summary.ssfa: no visible global function definition for 'logLik'
summary.ssfa: no visible global function definition for 'pchisq'
summary.ssfa: no visible binding for global variable 'df'
u.ssfa: no visible global function definition for 'dnorm'
u.ssfa: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  df dnorm lines lm logLik model.frame model.response pchisq pnorm
  printCoefmat residuals var
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "df", "dnorm", "lm", "logLik", "model.frame",
             "model.response", "pchisq", "pnorm", "printCoefmat",
             "residuals", "var")
to your NAMESPACE file.
Package in Depends field not imported from: 'survey'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fit.model: no visible global function definition for 'hadamard'
Undefined global functions or variables:
  hadamard
sslCoTrain: no visible global function definition for 'predict'
sslSelfTrain: no visible global function definition for 'predict'
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
map.world: no visible global function definition for 'par'
map.world: no visible global function definition for 'plot.new'
map.world: no visible global function definition for 'plot.window'
map.world: no visible global function definition for 'lines'
map.world: no visible global function definition for 'title'
map.world: no visible global function definition for 'axis'
map.world: no visible global function definition for 'box'
plot.smooth.sspline: no visible global function definition for
  'predict'
plot.smooth.sspline: no visible global function definition for
  'filled.contour'
plot.smooth.sspline: no visible binding for global variable
  'terrain.colors'
plot.smooth.sspline: no visible global function definition for 'title'
plot.smooth.sspline: no visible global function definition for 'axis'
station: no visible binding for global variable 'WTdiff'
station: no visible global function definition for 'points'
Undefined global functions or variables:
  WTdiff axis box filled.contour lines par plot.new plot.window points
  predict terrain.colors title
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "axis", "box", "filled.contour", "lines", "par",
             "plot.new", "plot.window", "points", "title")
  importFrom("stats", "predict")
to your NAMESPACE file.
SS.ID: no visible global function definition for 'var'
SS.sim.chol: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm var
Consider adding
  importFrom("stats", "rnorm", "var")
to your NAMESPACE file.
error.est : <anonymous>: no visible global function definition for
  'median'
holm.robust: no visible global function definition for 'pnorm'
holm.robust: no visible global function definition for 'median'
holm.robust: no visible global function definition for 'mad'
huberize: no visible global function definition for 'quantile'
ssvd.initial: no visible global function definition for 'mad'
ssvd.iter.thresh: no visible global function definition for 'mad'
Undefined global functions or variables:
  mad median pnorm quantile
Consider adding
  importFrom("stats", "mad", "median", "pnorm", "quantile")
to your NAMESPACE file.
.ls.objects: no visible binding for global variable 'object.size'
Undefined global functions or variables:
  object.size
Consider adding
  importFrom("utils", "object.size")
to your NAMESPACE file.
.expandLevels: no visible global function definition for 'na.omit'
.ffStack: no visible global function definition for 'na.omit'
.ffffStack: no visible global function definition for 'na.omit'
Stack : <anonymous>: no visible global function definition for
  'na.omit'
ffStack,ffdf-data.frame: no visible global function definition for
  'na.omit'
ffStack,ffdf-ffdf: no visible global function definition for 'na.omit'
ffStack,ffdf-list: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
genericPlot: no visible global function definition for 'dev.new'
genericPlot: no visible global function definition for 'par'
genericPlot: no visible global function definition for 'rainbow'
genericPlot: no visible global function definition for 'plot'
genericPlot: no visible global function definition for 'lines'
genericPlot: no visible global function definition for 'legend'
genericPlot: no visible global function definition for 'dev.copy2pdf'
genericPlot: no visible global function definition for 'dev.copy2eps'
genericPlot: no visible global function definition for 'dev.print'
genericPlot: no visible binding for global variable 'png'
genericPlot: no visible binding for global variable 'tiff'
plotStrains: no visible global function definition for 'rainbow'
plotStrains: no visible global function definition for 'dev.new'
plotStrains: no visible global function definition for 'par'
plotStrains: no visible global function definition for 'plot'
plotStrains: no visible global function definition for 'lines'
plotStrains: no visible global function definition for 'legend'
plotStrains: no visible global function definition for 'dev.copy2pdf'
plotStrains: no visible global function definition for 'dev.copy2eps'
plotStrains: no visible global function definition for 'dev.print'
plotStrains: no visible binding for global variable 'png'
plotStrains: no visible binding for global variable 'tiff'
Undefined global functions or variables:
  dev.copy2eps dev.copy2pdf dev.new dev.print legend lines par plot png
  rainbow tiff
Consider adding
  importFrom("grDevices", "dev.copy2eps", "dev.copy2pdf", "dev.new",
             "dev.print", "png", "rainbow", "tiff")
  importFrom("graphics", "legend", "lines", "par", "plot")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'np' 'sp'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'np' 'sp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
stkde: no visible global function definition for 'npudensbw'
stkde: no visible global function definition for 'npudens'
stkde: no visible global function definition for 'quantile'
stkde: no visible global function definition for 'heat.colors'
stkde: no visible global function definition for 'par'
stkde: no visible global function definition for 'image'
stkde: no visible global function definition for 'contour'
stkde.base: no visible global function definition for 'npudensbw'
stkde.base: no visible global function definition for 'npudens'
stkde.sig: no visible global function definition for 'SpatialPoints'
stkde.sig: no visible global function definition for 'spsample'
stkde.sig: no visible global function definition for 'bbox'
stkde.sig: no visible global function definition for 'quantile'
stkde.sig: no visible global function definition for 'heat.colors'
stkde.sig: no visible global function definition for 'par'
stkde.sig: no visible global function definition for 'image'
stkde.sig: no visible global function definition for 'contour'
Undefined global functions or variables:
  SpatialPoints bbox contour heat.colors image npudens npudensbw par
  quantile spsample
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "contour", "image", "par")
  importFrom("stats", "quantile")
to your NAMESPACE file.
find.names: no visible global function definition for 'na.omit'
generate.names: no visible global function definition for 'na.omit'
standardize.countrynames: no visible global function definition for
  'data'
standardize.names: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    include   7.8Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   5.0Mb
'library' or 'require' call to 'codetools' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'codetools' 'gss'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following hidden files and directories:
  inst/.Renviron.d
  inst/.Rprofile.d
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
actvspred: no visible global function definition for 'quantile'
actvspred: no visible global function definition for 'aggregate'
actvspred: no visible global function definition for 'par'
actvspred: no visible global function definition for 'plot'
actvspred: no visible global function definition for 'lines'
auc: no visible global function definition for 'par'
auc: no visible global function definition for 'plot'
decile: no visible global function definition for 'quantile'
dqcontinuous : numoutliers: no visible global function definition for
  'quantile'
dqcontinuous : <anonymous>: no visible global function definition for
  'sd'
dqcontinuous : <anonymous>: no visible global function definition for
  'quantile'
gini: no visible global function definition for 'par'
gini: no visible global function definition for 'plot'
gini: no visible global function definition for 'abline'
iv: no visible global function definition for 'quantile'
iv: no visible global function definition for 'aggregate'
ks: no visible global function definition for 'aggregate'
ks: no visible global function definition for 'par'
ks: no visible global function definition for 'plot'
ks: no visible global function definition for 'lines'
outliers: no visible global function definition for 'quantile'
outliers: no visible global function definition for 'na.omit'
pentile: no visible global function definition for 'quantile'
Undefined global functions or variables:
  abline aggregate lines na.omit par plot quantile sd
Consider adding
  importFrom("graphics", "abline", "lines", "par", "plot")
  importFrom("stats", "aggregate", "na.omit", "quantile", "sd")
to your NAMESPACE file.
inspect: no visible global function definition for 'par'
inspect: no visible global function definition for 'abline'
inspect: no visible global function definition for 'lines'
inspect: no visible global function definition for 'points'
plotfit: no visible global function definition for 'dev.off'
plotfit: no visible global function definition for 'par'
plotfit: no visible global function definition for 'lines'
plotfit: no visible global function definition for 'points'
plotfit: no visible global function definition for 'legend'
plothill: no visible global function definition for 'par'
plothill: no visible global function definition for 'abline'
plothill: no visible global function definition for 'points'
plotmultifit: no visible global function definition for 'par'
plotmultifit: no visible global function definition for 'lines'
plotmultifit: no visible global function definition for 'points'
plotmultifit: no visible global function definition for 'pexp'
plotmultifit: no visible global function definition for 'plnorm'
plotmultifit: no visible global function definition for 'ppois'
plotmultifit: no visible global function definition for 'legend'
plotols: no visible global function definition for 'dev.off'
plotols: no visible global function definition for 'lm'
plotols: no visible global function definition for 'par'
plotols: no visible global function definition for 'abline'
plotols: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline dev.off legend lines lm par pexp plnorm points ppois
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("graphics", "abline", "legend", "lines", "par", "points")
  importFrom("stats", "lm", "pexp", "plnorm", "ppois")
to your NAMESPACE file.
getStp: no visible global function definition for 'lm'
plot.steeptest: no visible global function definition for 'plot'
plot.steeptest: no visible global function definition for 'axis'
plot.steeptest: no visible global function definition for 'box'
plot.steeptest: no visible global function definition for 'lm'
plot.steeptest: no visible global function definition for 'abline'
plot.steeptest: no visible global function definition for 'legend'
plot.steeptest: no visible global function definition for
  'as.graphicsAnnot'
steeptest: no visible global function definition for 'lm'
summary.steeptest: no visible global function definition for 'var'
summary.steeptest: no visible global function definition for 'quantile'
Undefined global functions or variables:
  abline as.graphicsAnnot axis box legend lm plot quantile var
Consider adding
  importFrom("grDevices", "as.graphicsAnnot")
  importFrom("graphics", "abline", "axis", "box", "legend", "plot")
  importFrom("stats", "lm", "quantile", "var")
to your NAMESPACE file.
Stem.Bootstrap: no visible global function definition for 'runif'
filtering: no visible global function definition for 'is.ts'
filtering: no visible global function definition for 'ts'
filtering: no visible global function definition for 'start'
filtering: no visible global function definition for 'end'
filtering: no visible global function definition for 'frequency'
kalman: no visible global function definition for 'ts'
smoothing: no visible global function definition for 'is.ts'
smoothing: no visible global function definition for 'ts'
smoothing: no visible global function definition for 'start'
smoothing: no visible global function definition for 'end'
smoothing: no visible global function definition for 'frequency'
Undefined global functions or variables:
  end frequency is.ts runif start ts
Consider adding
  importFrom("stats", "end", "frequency", "is.ts", "runif", "start",
             "ts")
to your NAMESPACE file.
Found the following significant warnings:
  ChangePointAnalyzeNorm.cpp:49:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  ChangePointAnalyzePoiss.cpp:42:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/StepSignalMargiLike.Rcheck/00install.out' for details.
d1spectrum: no visible global function definition for 'fft'
d2spectrum: no visible global function definition for 'fft'
plot.d1nat: no visible global function definition for 'plot'
plot.d1nat: no visible global function definition for 'lines'
plot.d1nat: no visible global function definition for 'legend'
plot.d1nat: no visible global function definition for 'title'
plot.d1spec: no visible global function definition for 'plot'
plot.d1spec: no visible global function definition for 'lines'
plot.d1spec: no visible global function definition for 'legend'
plot.d1spec: no visible global function definition for 'title'
plot.d2spec: no visible global function definition for 'plot'
plot.d2spec: no visible global function definition for 'lines'
plot.d2spec: no visible global function definition for 'legend'
plot.d2spec: no visible global function definition for 'title'
plot.pvalign: no visible global function definition for 'plot'
plot.pvalign: no visible global function definition for 'lines'
plot.pvalign: no visible global function definition for 'legend'
plot.pvalign: no visible global function definition for 'title'
print.d1nat: no visible global function definition for 'plot'
print.d1spec: no visible global function definition for 'plot'
print.d2spec: no visible global function definition for 'plot'
print.pvalign: no visible global function definition for 'plot'
utild1bin: no visible global function definition for 'median'
utild1bin: no visible global function definition for 'sd'
utild1clean: no visible global function definition for 'sd'
utild1filt: no visible global function definition for 'convolve'
Undefined global functions or variables:
  convolve fft legend lines median plot sd title
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "title")
  importFrom("stats", "convolve", "fft", "median", "sd")
to your NAMESPACE file.
na.stinterp.default: no visible global function definition for 'time'
na.stinterp.default: no visible global function definition for
  'na.omit'
Undefined global functions or variables:
  na.omit time
Consider adding
  importFrom("stats", "na.omit", "time")
to your NAMESPACE file.
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tthread/tinythread.h:632:14: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.5/StMoSim.Rcheck/00install.out' for details.
myQQNorm: no visible global function definition for 'mad'
myQQNorm: no visible global function definition for 'qnorm'
myQQNorm: no visible global function definition for 'plot'
myQQNorm: no visible global function definition for 'matlines'
myQQNorm: no visible global function definition for 'points'
myQQNorm: no visible global function definition for 'qqline'
myQQNorm: no visible global function definition for 'box'
qqnormSim,lm: no visible global function definition for 'resid'
Undefined global functions or variables:
  box mad matlines plot points qnorm qqline resid
Consider adding
  importFrom("graphics", "box", "matlines", "plot", "points")
  importFrom("stats", "mad", "qnorm", "qqline", "resid")
to your NAMESPACE file.
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'gridExtra'

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

    combine

Warning in download.file(url, destfile = tmp, quiet = !messaging, mode = "wb") :
  cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=georgia&zoom=5&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false': HTTP status was '403 Forbidden'
Quitting from lines 220-233 (Details.Rmd) 
Error: processing vignette 'Details.Rmd' failed with diagnostics:
cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=georgia&zoom=5&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false'
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R          2.0Mb
    datasets   2.6Mb
Namespace with empty importFrom: 'tcltk2'
DetailOpLines: no visible global function definition for
  'tkProgressBar'
DetailOpLines: no visible global function definition for
  'setTkProgressBar'
MultiTrainWithInventory: no visible global function definition for
  'tkProgressBar'
MultiTrainWithInventory: no visible global function definition for
  'setTkProgressBar'
SimHistory: no visible global function definition for 'tkProgressBar'
SimHistory: no visible global function definition for
  'setTkProgressBar'
Undefined global functions or variables:
  setTkProgressBar tkProgressBar
Error in re-building vignettes:
  ...
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "VignetteforSTPGA.ltx" --max-iterations=20 -I "D:/RCompile/recent/R/share/texmf/tex/latex" -I "D:/RCompile/recent/R/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'VignetteforSTPGA.ltx' failed with diagnostics:
running 'texi2dvi' on 'VignetteforSTPGA.ltx' failed

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

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

Execution halted
Packages in Depends field not imported from:
  'cubature' 'deldir' 'splancs'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
StratPhyloCongruence: no visible global function definition for 'runif'
StratPhyloCongruence: no visible global function definition for
  'txtProgressBar'
StratPhyloCongruence: no visible global function definition for
  'setTxtProgressBar'
StratPhyloCongruence: no visible global function definition for 'pnorm'
StratPhyloCongruence: no visible global function definition for 'sd'
geoscalePhylo: no visible global function definition for 'data'
geoscalePhylo: no visible global function definition for 'par'
geoscalePhylo: no visible global function definition for 'text'
geoscalePhylo: no visible global function definition for 'segments'
geoscalePhylo: no visible global function definition for 'rect'
geoscalePhylo: no visible global function definition for 'rgb'
Undefined global functions or variables:
  data par pnorm rect rgb runif sd segments setTxtProgressBar text
  txtProgressBar
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "par", "rect", "segments", "text")
  importFrom("stats", "pnorm", "runif", "sd")
  importFrom("utils", "data", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
HRatio: no visible global function definition for 'qnorm'
icweib: no visible global function definition for 'model.frame'
icweib: no visible binding for global variable 'na.pass'
icweib: no visible global function definition for 'complete.cases'
icweib: no visible global function definition for 'model.matrix'
icweib: no visible global function definition for 'optim'
icweib: no visible global function definition for 'pchisq'
icweib: no visible global function definition for 'pnorm'
plot.icweib : getstat: no visible global function definition for
  'qnorm'
plot.icweib: no visible global function definition for 'plot'
plot.icweib: no visible global function definition for 'lines'
plot.icweib: no visible global function definition for 'legend'
print.icweib: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  complete.cases legend lines model.frame model.matrix na.pass optim
  pchisq plot pnorm qnorm
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "complete.cases", "model.frame", "model.matrix",
             "na.pass", "optim", "pchisq", "pnorm", "qnorm")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/streamR.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
'library' or 'require' call to 'ROAuth' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  icu55/common/cstring.h:38:63: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  icu55/i18n/windtfmt.cpp:303:96: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/stringi.Rcheck/00install.out' for details.
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    libs  33.4Mb
breakpoints.formula: no visible global function definition for
  '%dopar%'
breakpoints.formula: no visible binding for global variable 'i'
efpFunctional: multiple local function definitions for 'plotProcess'
  with different formal arguments
mefp.efp: multiple local function definitions for 'computeEmpProc' with
  different formal arguments
sctest.default: no visible global function definition for 'tail'
Undefined global functions or variables:
  %dopar% i tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
PlotHypTree: no visible global function definition for 'browseURL'
treePValues: no visible global function definition for 'lm'
treePValues: no visible global function definition for 'pf'
plot,GBH-ANY: no visible binding for global variable 'sorted.hyp'
plot,GBH-ANY: no visible binding for global variable 'pval'
plot,GBH-ANY: no visible binding for global variable 'group'
plot,GBH-ANY: no visible binding for global variable 'type'
Undefined global functions or variables:
  browseURL group lm pf pval sorted.hyp type
Consider adding
  importFrom("stats", "lm", "pf")
  importFrom("utils", "browseURL")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from 'stsm.class' for: 'show'

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

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

plot.survAUC: no visible global function definition for 'plot'
plot.survAUC: no visible global function definition for 'lines'
plot.survErr: no visible global function definition for 'plot'
plot.survErr: no visible global function definition for 'lines'
schemper: no visible global function definition for 'predict'
schemper: no visible global function definition for 'survfit'
schemper: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx lines plot predict survfit
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "approx", "predict")
to your NAMESPACE file.
Est.PH: no visible global function definition for 'coxph'
Inf.Cval: no visible global function definition for 'rexp'
Inf.Cval: no visible global function definition for 'var'
Inf.Cval.Delta: no visible global function definition for 'rexp'
Inf.Cval.Delta: no visible global function definition for 'var'
cvC: no visible global function definition for 'coxph'
cvC: no visible global function definition for 'weighted.mean'
Undefined global functions or variables:
  coxph rexp var weighted.mean
Consider adding
  importFrom("stats", "rexp", "var", "weighted.mean")
to your NAMESPACE file.
Files named as vignettes but with no recognized vignette engine:
   'vignettes/survClip.Rnw'
(Is a VignetteBuilder field missing?)
pearson: no visible global function definition for 'cor'
plot.survcorr: no visible global function definition for 'pnorm'
plot.survcorr: no visible global function definition for 'par'
plot.survcorr: no visible global function definition for 'plot'
plot.survcorr: no visible global function definition for 'points'
survcorr: no visible global function definition for 'model.frame'
survcorr: no visible global function definition for 'qnorm'
survcorr: no visible global function definition for 'runif'
survcorr: no visible global function definition for 'pnorm'
survcorr: no visible global function definition for 'var'
survcorr: no visible global function definition for 'qt'
Undefined global functions or variables:
  cor model.frame par plot pnorm points qnorm qt runif var
Consider adding
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "cor", "model.frame", "pnorm", "qnorm", "qt",
             "runif", "var")
to your NAMESPACE file.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.3Mb
    help   1.0Mb
    libs   1.7Mb
'library' or 'require' call to 'survival' which was already attached by Depends.
  Please remove these calls from your code.
Survgini: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/math/special_functions/detail/bernoulli_details.hpp:72:36: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/math/special_functions/detail/bernoulli_details.hpp:96:9: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.5/survHE.Rcheck/00install.out' for details.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
Packages in Depends field not imported from:
  'survC1' 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Est.HR.FUN: no visible global function definition for 'coxph'
Est.HR.FUN: no visible global function definition for 'basehaz'
Est.HR.FUN: no visible global function definition for 'approx'
Ghat.FUN: no visible global function definition for 'survfit'
IDI.INF: no visible global function definition for 'kmcens'
IDI.INF: no visible global function definition for 'quantile'
IDI.INF.GRAPH: no visible global function definition for 'plot'
IDI.INF.GRAPH: no visible global function definition for 'lines'
IDI.INF.GRAPH: no visible global function definition for 'abline'
IDI.INF.GRAPH: no visible global function definition for 'points'
IDI.INF.GRAPH: no visible global function definition for 'title'
PTB.IDI.FUN: no visible global function definition for 'rexp'
shade: no visible global function definition for 'polygon'
Undefined global functions or variables:
  abline approx basehaz coxph kmcens lines plot points polygon quantile
  rexp survfit title
Consider adding
  importFrom("graphics", "abline", "lines", "plot", "points", "polygon",
             "title")
  importFrom("stats", "approx", "quantile", "rexp")
to your NAMESPACE file.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.6Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
betaEst: no visible global function definition for 'is'
fullKernel: no visible global function definition for 'is'
halfKernel: no visible global function definition for 'is'
kernelAuto: no visible global function definition for 'quantile'
kernelAuto: no visible global function definition for 'lm'
kernelAuto: no visible global function definition for 'pnorm'
kernelFixed: no visible global function definition for 'pnorm'
lastValue: no visible global function definition for 'pnorm'
nearValue: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  is lm pnorm quantile
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "lm", "pnorm", "quantile")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Running examples in 'survtmle-Ex.R' failed
The error most likely occurred in:

> ### Name: plot.tp.survtmle
> ### Title: Plot Results of Cumulative Incidence Estimates
> ### Aliases: plot.tp.survtmle
> 
> ### ** Examples
> 
> library(survtmle)
> set.seed(341796)
> n <- 100
> t_0 <- 10
> W <- data.frame(W1 = runif(n), W2 = rbinom(n, 1, 0.5))
> A <- rbinom(n, 1, 0.5)
> T <- rgeom(n,plogis(-4 + W$W1 * W$W2 - A)) + 1
> C <- rgeom(n, plogis(-6 + W$W1)) + 1
> ftime <- pmin(T, C)
> ftype <- as.numeric(ftime == T)
> suppressWarnings(
+   fit <- survtmle(ftime = ftime, ftype = ftype,
+                   adjustVars = W, glm.ftime = "I(W1*W2) + trt + t",
+                   trt = A, glm.ctime = "W1 + t", method = "hazard",
+                   verbose = TRUE,  t0 = t_0, maxIter = 2)
+ )
> tpfit <- timepoints(fit, times = seq_len(t_0))
> plot(tpfit)
Error in names(x) <- value : 
  'names' attribute [3] must be the same length as the vector [2]
Calls: plot -> plot.tp.survtmle -> colnames<-
Execution halted
fitModel: no visible global function definition for 'var'
fitModel: no visible global function definition for 'cov'
svpls: no visible global function definition for 'pt'
Undefined global functions or variables:
  cov pt var
Consider adding
  importFrom("stats", "cov", "pt", "var")
to your NAMESPACE file.
dlgMessage.tcltkGUI: no visible global function definition for 'alarm'
dlgMessage.tcltkGUI: no visible global function definition for
  'bringToTop'
Undefined global functions or variables:
  alarm bringToTop
Consider adding
  importFrom("grDevices", "bringToTop")
  importFrom("utils", "alarm")
to your NAMESPACE file.
svd3dplot: no visible global function definition for 'wireframe'
svd3dplot: no visible global function definition for 'levelplot'
Undefined global functions or variables:
  levelplot wireframe
startHttpServer : <anonymous> : Rjsonp: no visible global function
  definition for 'localeToCharset'
Undefined global functions or variables:
  localeToCharset
Consider adding
  importFrom("utils", "localeToCharset")
to your NAMESPACE file.
.onAttach : svBrowser: no visible global function definition for
  'browseURL'
.onAttach: no visible global function definition for 'loadhistory'
Undefined global functions or variables:
  browseURL loadhistory
Consider adding
  importFrom("utils", "browseURL", "loadhistory")
to your NAMESPACE file.
File 'svmpath/libs/i386/svmpath.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'mi10unix.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'mi10unix.o'
File 'svmpath/libs/x64/svmpath.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'mi10unix.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'mi10unix.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
processSocket: no visible global function definition for 'URLdecode'
Undefined global functions or variables:
  URLdecode
Consider adding
  importFrom("utils", "URLdecode")
to your NAMESPACE file.
completeCol: no visible global function definition for 'colors'
completeCol: no visible global function definition for 'col2rgb'
completeCol: no visible global function definition for 'palette'
Undefined global functions or variables:
  col2rgb colors palette
Consider adding
  importFrom("grDevices", "col2rgb", "colors", "palette")
to your NAMESPACE file.
.formatResult : capture.str: no visible global function definition for
  'str'
createLog: no visible global function definition for 'sessionInfo'
protocol_junit.svSuiteData: no visible global function definition for
  'xmlNode'
protocol_junit.svSuiteData: no visible global function definition for
  'addChildren'
protocol_junit.svSuiteData: no visible global function definition for
  'saveXML'
protocol_junit.svTestData: no visible global function definition for
  'xmlNode'
protocol_junit.svTestData: no visible global function definition for
  'addChildren'
Undefined global functions or variables:
  addChildren saveXML sessionInfo str xmlNode
Consider adding
  importFrom("utils", "sessionInfo", "str")
to your NAMESPACE file.
svycox.calibrate: no visible global function definition for 'quantile'
svycox.calibrate: no visible binding for global variable 'median'
svycox.calibrate: no visible global function definition for
  'as.formula'
svycox.calibrate: no visible global function definition for 'plot'
svycox.calibrate: no visible global function definition for 'arrows'
svycox.calibrate: no visible global function definition for 'abline'
svycox.nomogram: no visible global function definition for 'predict'
svycox.nomogram: no visible global function definition for 'as.formula'
svycox.validate : internal.validate.func: no visible global function
  definition for 'as.formula'
svycox.validate : internal.validate.func: no visible global function
  definition for 'formula'
Undefined global functions or variables:
  abline arrows as.formula formula median plot predict quantile
Consider adding
  importFrom("graphics", "abline", "arrows", "plot")
  importFrom("stats", "as.formula", "formula", "median", "predict",
             "quantile")
to your NAMESPACE file.
additional_comp: no visible global function definition for 'aggregate'
additional_compPV : <anonymous>: no visible global function definition
  for 'aggregate'
cor.aux.func : <anonymous>: no visible global function definition for
  'cov.wt'
eta.func : <anonymous>: no visible global function definition for 'lm'
eta.func : <anonymous>: no visible global function definition for
  'anova'
glm.dummy.no.std: no visible global function definition for
  'as.formula'
pv_by: no visible binding for global variable 'var'
pv_perc: no visible binding for global variable 'var'
pv_quantile: no visible binding for global variable 'var'
svyPVcor: no visible global function definition for 'update'
svyPVcor: no visible global function definition for 'var'
svyPVeta: no visible global function definition for 'update'
svyPVeta: no visible global function definition for 'var'
svyPVglm: no visible global function definition for 'gaussian'
svyPVglm: no visible binding for global variable 'as.formula'
svyPVglm: no visible binding for global variable 'var'
svyPVglm: no visible global function definition for 'pt'
svyPVttest: no visible binding for global variable 'as.formula'
svyPVttest: no visible global function definition for 'var'
svyPVttest: no visible global function definition for 'pt'
svyPVttest: no visible binding for global variable 'var'
t.test.aux: no visible global function definition for 'as.formula'
t.test.aux: no visible global function definition for 'complete.cases'
Undefined global functions or variables:
  aggregate anova as.formula complete.cases cov.wt gaussian lm pt
  update var
Consider adding
  importFrom("stats", "aggregate", "anova", "as.formula",
             "complete.cases", "cov.wt", "gaussian", "lm", "pt",
             "update", "var")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: GNU Extension: Different type kinds at (1)
  Warning: GNU Extension: initialization of common block variable 'iset' in DATA statement at (1)
  Warning: GNU Extension: Variable 'iset' at (1) is in COMMON but only in BLOCK DATA initialization is allowed
  Warning: GNU Extension: Missing comma at (1)
See 'd:/Rcompile/CRANpkg/local/3.5/SWATmodel.Rcheck/00install.out' for details.
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    libs  25.5Mb
readSWAT: no visible global function definition for 'read.fortran'
runSWAT2005: no visible global function definition for 'read.fortran'
runSWAT2009: no visible global function definition for 'read.fortran'
runSWAT2012: no visible global function definition for 'read.fortran'
Undefined global functions or variables:
  read.fortran
Consider adding
  importFrom("utils", "read.fortran")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'MASS' 'fda' 'splines'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fj_pl: no visible global function definition for 'getbasismatrix'
fj_pl: no visible global function definition for 'create.bspline.basis'
fj_pl: no visible global function definition for 'getbasispenalty'
forward_backward.quantities : <anonymous>: no visible global function
  definition for 'dnorm'
function_cases1AND2: no visible global function definition for 'dnorm'
function_cases3AND4: no visible global function definition for 'dnorm'
pij_iid: no visible global function definition for 'dnorm'
pilj: no visible global function definition for 'dnorm'
updateLambda: no visible global function definition for 'optimize'
Undefined global functions or variables:
  create.bspline.basis dnorm getbasismatrix getbasispenalty optimize
Consider adding
  importFrom("stats", "dnorm", "optimize")
to your NAMESPACE file.
calc_MW: no visible global function definition for 'read.table'
cfba_moment: no visible global function definition for 'median'
cfba_moment: no visible global function definition for 'write.csv'
cfba_moment_mr: no visible global function definition for 'median'
cfba_moment_mr: no visible global function definition for 'write.csv'
cfba_moment_pw: no visible global function definition for 'median'
cfba_moment_pw: no visible global function definition for 'write.csv'
readmodel: no visible global function definition for 'as'
Undefined global functions or variables:
  as median read.table write.csv
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "median")
  importFrom("utils", "read.table", "write.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/sybilEFBA.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
FECorr: no visible global function definition for 'is'
FECorr: no visible global function definition for 'write.csv'
FECorr: no visible global function definition for 'aggregate'
FECorr: no visible global function definition for 'lm'
FECorr: no visible global function definition for 'nlm'
eFBA_gene: no visible global function definition for 'is'
eFBA_gene: no visible global function definition for 'as'
eFBA_rxn : adjustTol: no visible global function definition for 'is'
eFBA_rxn: no visible global function definition for 'is'
eFBA_rxn: no visible global function definition for 'as'
findFluxGeneExpr: no visible global function definition for 'as'
findMDCFlux: no visible global function definition for 'is'
findMDCFlux: no visible global function definition for 'as'
gene2Rule: no visible global function definition for 'is'
Undefined global functions or variables:
  aggregate as is lm nlm write.csv
Consider adding
  importFrom("methods", "as", "is")
  importFrom("stats", "aggregate", "lm", "nlm")
  importFrom("utils", "write.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Packages suggested but not available for checking: 'sylly.de' 'sylly.es'
symbol: no visible global function definition for 'plot.new'
symbol: no visible global function definition for 'plot.window'
symbol: no visible global function definition for 'axis'
symbol: no visible global function definition for 'box'
symbol: no visible global function definition for 'title'
symbol: no visible global function definition for 'rainbow'
symbol: no visible global function definition for 'hsv'
symbol: no visible global function definition for 'rect'
symbol: no visible global function definition for 'polygon'
symbol: no visible global function definition for 'lines'
symbol: no visible global function definition for 'text'
Undefined global functions or variables:
  axis box hsv lines plot.new plot.window polygon rainbow rect text
  title
Consider adding
  importFrom("grDevices", "hsv", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "polygon", "rect", "text", "title")
to your NAMESPACE file.
integrate.polynomial : f: no visible global function definition for
  'dmvnorm'
Undefined global functions or variables:
  dmvnorm
Package in Depends field not imported from: 'fields'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cwt_fw: no visible global function definition for 'fft'
cwt_iw: no visible global function definition for 'fft'
est_riskshrink_thresh: no visible global function definition for
  'median'
Undefined global functions or variables:
  fft median
Consider adding
  importFrom("stats", "fft", "median")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/SynergizeR.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
Packages in Depends field not imported from:
  'RCurl' 'RJSONIO'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' calls to packages already attached by Depends:
  'tcltk' 'tkrplot'
  Please remove these calls from your code.
Namespaces with empty importFrom:
  'Rcpp' 'methods'
mainNetFunction: no visible global function definition for 'png'
mainNetFunction: no visible global function definition for 'plot'
mainNetFunction: no visible global function definition for 'lines'
mainNetFunction: no visible global function definition for 'legend'
mainNetFunction: no visible global function definition for 'dev.off'
plotPR: no visible global function definition for 'plot'
plotROC: no visible global function definition for 'plot'
plotROC: no visible global function definition for 'lines'
simulatedData: no visible global function definition for 'rpois'
simulatedData : <anonymous>: no visible global function definition for
  'rpois'
simulatedData : rlognormpois: no visible global function definition for
  'rnorm'
simulatedData : rlognormpois: no visible global function definition for
  'rpois'
Undefined global functions or variables:
  dev.off legend lines plot png rnorm rpois
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "rnorm", "rpois")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'LowRankQP' 'rgenoud'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
fn.V: no visible global function definition for 'LowRankQP'
gaps.plot: no visible global function definition for 'abline'
path.plot: no visible global function definition for 'lines'
path.plot: no visible global function definition for 'abline'
path.plot: no visible global function definition for 'legend'
synth: no visible binding for global variable 'sd'
synth: no visible binding for global variable 'var'
synth: no visible global function definition for 'LowRankQP'
Undefined global functions or variables:
  LowRankQP abline legend lines sd var
Consider adding
  importFrom("graphics", "abline", "legend", "lines")
  importFrom("stats", "sd", "var")
to your NAMESPACE file.
Package unavailable to check Rd xrefs: 'unix'
.checkDimAndTest: no visible global function definition for
  'chisq.test'
.checkDimAndTest: no visible global function definition for
  'fisher.test'
plotTable1Heatmap: no visible global function definition for 'par'
plotTable1Heatmap: no visible global function definition for 'image'
plotTable1Heatmap: no visible global function definition for 'abline'
plotTable1Heatmap: no visible global function definition for 'axis'
plotTable1Heatmap: no visible global function definition for 'text'
plotTable1Heatmap: no visible global function definition for 'legend'
plotTable1Heatmap: no visible global function definition for 'box'
Undefined global functions or variables:
  abline axis box chisq.test fisher.test image legend par text
Consider adding
  importFrom("graphics", "abline", "axis", "box", "image", "legend",
             "par", "text")
  importFrom("stats", "chisq.test", "fisher.test")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'rbind.tableList':
  'rbind.tableList'

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

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
cluster_cutoff_at_first_empty_bin: no visible global function
  definition for 'hist'
mapper1D: no visible global function definition for 'dist'
mapper1D: no visible global function definition for 'as.dist'
mapper1D: no visible global function definition for 'hclust'
mapper1D: no visible global function definition for 'cutree'
mapper2D: no visible global function definition for 'dist'
mapper2D: no visible global function definition for 'as.dist'
mapper2D: no visible global function definition for 'hclust'
mapper2D: no visible global function definition for 'cutree'
Undefined global functions or variables:
  as.dist cutree dist hclust hist
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "as.dist", "cutree", "dist", "hclust")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'RSEIS' 'pracma' 'signal'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
tdt.quad: no visible global function definition for 'runif'
tdt.rr: no visible global function definition for 'pf'
tdt.rr: no visible global function definition for 'qbeta'
Undefined global functions or variables:
  pf qbeta runif
Consider adding
  importFrom("stats", "pf", "qbeta", "runif")
to your NAMESPACE file.
E.2SI: no visible binding for global variable 'var'
E.2SI: no visible global function definition for 'var'
E.BE: no visible global function definition for 'var'
E.Beta: no visible global function definition for 'var'
E.PO: no visible global function definition for 'var'
E.PPS: no visible global function definition for 'var'
E.SI: no visible global function definition for 'var'
E.STPPS: no visible global function definition for 'var'
E.STSI: no visible global function definition for 'var'
E.STpiPS: no visible global function definition for 'var'
E.SY: no visible global function definition for 'var'
E.WR: no visible global function definition for 'var'
E.piPS: no visible global function definition for 'var'
GREG.SI: no visible global function definition for 'var'
S.BE: no visible global function definition for 'runif'
S.PO: no visible global function definition for 'runif'
S.PPS: no visible global function definition for 'runif'
S.SI: no visible global function definition for 'runif'
S.STPPS: no visible global function definition for 'runif'
S.WR: no visible global function definition for 'rbinom'
S.piPS: no visible global function definition for 'runif'
p.WR: no visible global function definition for 'dmultinom'
Undefined global functions or variables:
  dmultinom rbinom runif var
Consider adding
  importFrom("stats", "dmultinom", "rbinom", "runif", "var")
to your NAMESPACE file.
TeachNet: no visible global function definition for 'predict'
createWeights1: no visible global function definition for 'rnorm'
createWeights2: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  predict rnorm
Consider adding
  importFrom("stats", "predict", "rnorm")
to your NAMESPACE file.
aniplotevents: no visible global function definition for 'plot'
aniplotevents: no visible global function definition for 'lines'
cbfs: no visible global function definition for 'rnorm'
cbfs: no visible global function definition for 'runif'
cbfs_red: no visible global function definition for 'arima.sim'
cbfs_red: no visible global function definition for 'runif'
eventCluster: no visible global function definition for 'princomp'
eventCluster: no visible global function definition for 'kmeans'
measures: no visible global function definition for 'sd'
measures: no visible global function definition for 'var'
measures: no visible global function definition for 'PP.test'
noiseTests: no visible global function definition for 'Box.test'
noiseTests: no visible global function definition for 'PP.test'
noiseTests: no visible global function definition for 'ar'
plotevents: no visible global function definition for 'plot'
plotevents: no visible global function definition for 'lines'
ur.za.fast : roll: no visible global function definition for 'coef'
ur.za.fast : roll: no visible global function definition for 'lm'
Undefined global functions or variables:
  Box.test PP.test ar arima.sim coef kmeans lines lm plot princomp
  rnorm runif sd var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "Box.test", "PP.test", "ar", "arima.sim", "coef",
             "kmeans", "lm", "princomp", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
S3 methods shown with full name in documentation object 'mean.tensor':
  'mean.tensor'

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/tensorBF.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
TER.deesc.1.B : A1.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.1.B : A1.f: no visible binding for global variable 'ID'
TER.deesc.1.B : A2.n.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.1.B : A2.n.f: no visible binding for global variable 'ID'
TER.deesc.1.B: no visible binding for '<<-' assignment to 'ID'
TER.deesc.1.B: no visible binding for global variable 'ID'
TER.deesc.A.B : A1.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : A1.f: no visible binding for global variable 'ID'
TER.deesc.A.B : A3.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : A3.f: no visible binding for global variable 'ID'
TER.deesc.A.B : A2.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : A2.f: no visible binding for global variable 'ID'
TER.deesc.A.B : B1.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : B1.f: no visible binding for global variable 'ID'
TER.deesc.A.B: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B: no visible binding for global variable 'ID'
Undefined global functions or variables:
  ID
Depends: includes the non-default packages:
  'grid' 'quadprog' 'maps' 'maptools' 'mapdata' 'dichromat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  'dichromat' 'grid' 'mapdata' 'maps' 'maptools' 'quadprog'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 35.0Mb
  sub-directories of 1Mb or more:
    libs      13.2Mb
    tessdata  20.9Mb
File which contains pragma(s) suppressing diagnostics:
  'inst/include/testthat/vendor/catch.h'
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    3.6Mb
    libs   2.1Mb
phyper_right: no visible global function definition for 'dhyper'
progression: no visible global function definition for 'density'
progression: no visible global function definition for 'plot'
progression: no visible global function definition for 'points'
progression: no visible global function definition for 'legend'
progression: no visible global function definition for 'text'
specificities.distribution.plot: no visible global function definition
  for 'dhyper'
specificities.distribution.plot: no visible global function definition
  for 'plot'
specificities.distribution.plot: no visible global function definition
  for 'Axis'
specificities.distribution.plot: no visible global function definition
  for 'arrows'
specificities.distribution.plot: no visible global function definition
  for 'text'
specificities.distribution.plot: no visible global function definition
  for 'title'
specificities.probabilities.vector: no visible global function
  definition for 'phyper'
Undefined global functions or variables:
  Axis arrows density dhyper legend phyper plot points text title
Consider adding
  importFrom("graphics", "Axis", "arrows", "legend", "plot", "points",
             "text", "title")
  importFrom("stats", "density", "dhyper", "phyper")
to your NAMESPACE file.
.dea_create_model: no visible global function definition for
  'getSrcFilename'
.wMean: no visible global function definition for 'weighted.mean'
Undefined global functions or variables:
  getSrcFilename weighted.mean
Consider adding
  importFrom("stats", "weighted.mean")
  importFrom("utils", "getSrcFilename")
to your NAMESPACE file.
transfer: no visible global function definition for 'rgamma'
transfer: no visible global function definition for 'rnorm'
transfer: no visible global function definition for 'rnbinom'
transfer: no visible global function definition for 'rpois'
transfer: no visible global function definition for 'rbinom'
transfer: no visible global function definition for 'runif'
plot,transfer: no visible global function definition for 'barplot'
plot,transfer: no visible global function definition for 'axis'
plot,transfer: no visible global function definition for 'par'
plot,transfer: no visible global function definition for 'hist'
Undefined global functions or variables:
  axis barplot hist par rbinom rgamma rnbinom rnorm rpois runif
Consider adding
  importFrom("graphics", "axis", "barplot", "hist", "par")
  importFrom("stats", "rbinom", "rgamma", "rnbinom", "rnorm", "rpois",
             "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Matrix.h:27:18: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.5/TFMPvalue.Rcheck/00install.out' for details.
ParseTrueFX: no visible global function definition for 'read.csv'
TrueFXRef: no visible global function definition for 'download.file'
TrueFXRef: no visible global function definition for 'browseURL'
Undefined global functions or variables:
  browseURL download.file read.csv
Consider adding
  importFrom("utils", "browseURL", "download.file", "read.csv")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    rda    3.8Mb
Thinknum: no visible global function definition for 'URLencode'
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
coef_traceplot: no visible global function definition for 'rainbow'
coef_traceplot: no visible global function definition for 'plot'
coef_traceplot: no visible global function definition for 'abline'
coef_traceplot : <anonymous>: no visible global function definition for
  'lines'
coef_traceplot: no visible global function definition for 'text'
ee.GEE.aux : <anonymous>: no visible global function definition for
  'combn'
Undefined global functions or variables:
  abline combn lines plot rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "plot", "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
summary.tsls: no visible global function definition for 'printCoefmat'
threesls: no visible global function definition for 'cor'
threesls: no visible global function definition for 'pt'
tsls.formula: no visible global function definition for 'model.matrix'
tsls.formula: no visible global function definition for
  'model.response'
Undefined global functions or variables:
  cor model.matrix model.response printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.matrix", "model.response",
             "printCoefmat", "pt")
to your NAMESPACE file.
.LoadTickDataHK: no visible global function definition for 'read.csv'
.LoadTickDataSHSZ: no visible global function definition for 'read.csv'
DrawDown: no visible global function definition for 'na.omit'
PerformanceReport: no visible global function definition for
  'aggregate'
PerformanceReport: no visible global function definition for 'sd'
Undefined global functions or variables:
  aggregate na.omit read.csv sd
Consider adding
  importFrom("stats", "aggregate", "na.omit", "sd")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
newTiddler: no visible global function definition for 'new'
twImage: no visible global function definition for 'new'
twLink: no visible global function definition for 'new'
twList: no visible global function definition for 'new'
twTable: no visible global function definition for 'new'
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidyinftheo)
  > 
  > test_check("tidyinftheo")
  -- 1. Error: right number of columns given (@test-errors.R#10)  ----------------
  argument "expr" is missing, with no default
  1: expect_length(tab %>% select(vs) %>% shannon_entropy(), 1) at testthat/test-errors.R:10
  2: quasi_label(enquo(object))
  3: eval_bare(get_expr(quo), get_env(quo))
  4: tab %>% select(vs) %>% shannon_entropy()
  5: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  6: eval(quote(`_fseq`(`_lhs`)), env, env)
  7: eval(quote(`_fseq`(`_lhs`)), env, env)
  8: `_fseq`(`_lhs`)
  9: freduce(value, `_function_list`)
  10: withVisible(function_list[[k]](value))
  11: function_list[[k]](value)
  12: shannon_entropy(.)
  13: reduce_data(.data, !!enquo(X), numvars = 1, na.rm = na.rm)
  14: tidyselect::vars_select(names(reduced_tab), !!!quos(...))
  15: vars_select_eval(.vars, quos)
  16: map_lgl(quos, quo_is_helper)
  17: .f(.x[[i]], ...)
  18: extract_expr(quo)
  19: is_call(expr, paren_sym)
  
  == testthat results  ===========================================================
  OK: 37 SKIPPED: 0 FAILED: 1
  1. Error: right number of columns given (@test-errors.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
plot.tight.clust: no visible global function definition for 'hclust'
plot.tight.clust: no visible global function definition for 'dist'
plot.tight.clust: no visible global function definition for 'image'
plot.tight.clust: no visible global function definition for
  'colorRampPalette'
plot.tight.clust: no visible global function definition for 'axis'
plot.tight.clust: no visible global function definition for 'lines'
tight.clust : find.candidates : kmeans.classify: no visible global
  function definition for 'kmeans'
write.tight.clust: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  axis colorRampPalette dist hclust image kmeans lines write.table
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "image", "lines")
  importFrom("stats", "dist", "hclust", "kmeans")
  importFrom("utils", "write.table")
to your NAMESPACE file.
'library' or 'require' call to 'shiny' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'ggplot2'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
timeline: no visible global function definition for 'ggplot'
timeline: no visible global function definition for 'geom_segment'
timeline: no visible global function definition for 'aes_string'
timeline: no visible global function definition for 'geom_rect'
timeline: no visible global function definition for 'geom_text'
timeline: no visible global function definition for 'theme'
timeline: no visible global function definition for 'element_blank'
timeline: no visible global function definition for 'xlab'
timeline: no visible global function definition for 'ylab'
timeline: no visible global function definition for 'xlim'
timeline: no visible global function definition for
  'scale_y_continuous'
timeline: no visible global function definition for 'geom_point'
timeline: no visible global function definition for 'scale_color_grey'
timeline: no visible global function definition for 'geom_hline'
Undefined global functions or variables:
  aes_string element_blank geom_hline geom_point geom_rect geom_segment
  geom_text ggplot scale_color_grey scale_y_continuous theme xlab xlim
  ylab
density.tm: no visible global function definition for 'density'
mu.mle: no visible global function definition for 'optimize'
pophistory.tm: no visible binding for global variable 'quantile'
quantile.tm: no visible global function definition for 'quantile'
sample.pop: no visible global function definition for 'runif'
summary.tm: no visible global function definition for 'quantile'
Undefined global functions or variables:
  density optimize quantile runif
Consider adding
  importFrom("stats", "density", "optimize", "quantile", "runif")
to your NAMESPACE file.
generatelatencies: no visible binding for global variable 'allNames'
generatetimedeltas: no visible global function definition for 'head'
generatetimedeltas: no visible global function definition for 'tail'
generatevertexedgelist : <anonymous>: no visible global function
  definition for 'head'
generatevertexedgelist : <anonymous>: no visible global function
  definition for 'tail'
plotnetworkslices: no visible global function definition for 'par'
plotnetworkslices: no visible global function definition for 'text'
plottanet: no visible global function definition for 'plot'
plottonet: no visible global function definition for 'plot'
shortesttimepath : <anonymous>: no visible global function definition
  for 'tail'
Undefined global functions or variables:
  allNames head par plot tail text
Consider adding
  importFrom("graphics", "par", "plot", "text")
  importFrom("methods", "allNames")
  importFrom("utils", "head", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' calls in package code:
  'ggplot2' 'plyr'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'Matrix' 'lubridate' 'timeDate'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
is.Bizday: no visible global function definition for 'isWeekday'
plotCalendarHeatmap: no visible global function definition for 'ddply'
plotCalendarHeatmap: no visible global function definition for '.'
plotCalendarHeatmap: no visible binding for global variable 'year'
plotCalendarHeatmap: no visible binding for global variable 'month'
plotCalendarHeatmap: no visible binding for global variable 'week'
plotCalendarHeatmap: no visible global function definition for 'ggplot'
plotCalendarHeatmap: no visible global function definition for 'aes'
plotCalendarHeatmap: no visible binding for global variable 'monthweek'
plotCalendarHeatmap: no visible binding for global variable 'weekday'
plotCalendarHeatmap: no visible global function definition for
  'geom_tile'
plotCalendarHeatmap: no visible global function definition for
  'facet_grid'
plotCalendarHeatmap: no visible global function definition for
  'scale_fill_gradientn'
projectDate: no visible global function definition for 'holidayNYSE'
projectDate: no visible global function definition for
  'sparse.model.matrix'
Undefined global functions or variables:
  . aes ddply facet_grid geom_tile ggplot holidayNYSE isWeekday month
  monthweek scale_fill_gradientn sparse.model.matrix week weekday year
boot_autocov: no visible global function definition for 'is.ts'
boot_autocov: no visible global function definition for 'tsboot'
boot_autocov: no visible global function definition for 'quantile'
boot_autocov: no visible global function definition for 'par'
boot_autocov: no visible global function definition for 'frequency'
boot_autocov: no visible global function definition for 'polygon'
boot_autocov: no visible global function definition for 'lines'
boot_autocov: no visible global function definition for 'abline'
boot_autocov: no visible global function definition for 'acf'
boot_spec: no visible global function definition for 'is.ts'
boot_spec: no visible global function definition for 'tsboot'
boot_spec: no visible global function definition for 'spec.pgram'
boot_spec: no visible global function definition for 'quantile'
boot_spec: no visible global function definition for 'polygon'
boot_spec: no visible global function definition for 'lines'
redraw: no visible global function definition for 'spec.pgram'
statistic: no visible global function definition for 'acf'
Undefined global functions or variables:
  abline acf frequency is.ts lines par polygon quantile spec.pgram
  tsboot
Consider adding
  importFrom("graphics", "abline", "lines", "par", "polygon")
  importFrom("stats", "acf", "frequency", "is.ts", "quantile",
             "spec.pgram")
to your NAMESPACE file.
createHstore.ts: no visible global function definition for 'time'
exploreDb : <anonymous>: no visible global function definition for
  'plot'
exportTsList : <anonymous>: no visible global function definition for
  'time'
exportTsList: no visible global function definition for 'write.csv2'
importTsList: no visible global function definition for 'read.csv2'
importTsList : <anonymous>: no visible global function definition for
  'as.ts'
plot.tslist: no visible global function definition for 'plot'
plot.tslist : <anonymous>: no visible global function definition for
  'time'
plot.tslist: no visible global function definition for 'par'
plot.tslist: no visible global function definition for 'legend'
readTimeSeries : <anonymous>: no visible global function definition for
  'ts'
resolveOverlap: no visible global function definition for 'is.ts'
resolveOverlap: no visible global function definition for 'frequency'
resolveOverlap: no visible global function definition for 'time'
resolveOverlap: no visible global function definition for 'ts'
storeTimeSeries: no visible binding for global variable 'frequency'
zooLikeDateConvert: no visible global function definition for 'time'
zooLikeDateConvert: no visible global function definition for
  'frequency'
zooLikeDateConvert: no visible global function definition for 'cycle'
Undefined global functions or variables:
  as.ts cycle frequency is.ts legend par plot read.csv2 time ts
  write.csv2
Consider adding
  importFrom("graphics", "legend", "par", "plot")
  importFrom("stats", "as.ts", "cycle", "frequency", "is.ts", "time",
             "ts")
  importFrom("utils", "read.csv2", "write.csv2")
to your NAMESPACE file.
author.search: no visible binding for global variable 'na.omit'
reference.list: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
drawGraph: no visible global function definition for 'pdf'
drawGraph: no visible global function definition for 'par'
drawGraph: no visible global function definition for 'plot'
drawGraph: no visible global function definition for 'segments'
drawGraph: no visible global function definition for 'lines'
drawGraph: no visible global function definition for 'text'
drawGraph: no visible global function definition for 'dev.off'
drugRank: no visible global function definition for 'aggregate'
floating2: no visible global function definition for 'cor'
timma: no visible global function definition for 'median'
timma: no visible global function definition for 'write.table'
Undefined global functions or variables:
  aggregate cor dev.off lines median par pdf plot segments text
  write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "plot", "segments", "text")
  importFrom("stats", "aggregate", "cor", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'ExPosition' 'InPosition' 'TExPosition' 'prettyGraphs'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc         3.7Mb
    rmarkdown   1.3Mb
tipom.car: no visible global function definition for 'abline'
tipom.car: no visible global function definition for 'axis'
tipom.heat: no visible global function definition for 'image'
tipom.heat: no visible global function definition for 'gray'
tipom.lw: no visible global function definition for 'plot'
tipom.lw: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline axis gray image plot
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "image", "plot")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'boot' 'lattice' 'splines' 'tcltk'
  Please remove these calls from your code.
ls.tree: no visible global function definition for 'lm'
ls.tree: no visible global function definition for 'coef'
Undefined global functions or variables:
  coef lm
Consider adding
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'rgl' 'tcltk'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.my.tkdev: no visible global function definition for 'win.metafile'
tkpersp : draw: no visible global function definition for 'par'
tkpersp : draw: no visible global function definition for 'persp'
Undefined global functions or variables:
  par persp win.metafile
Consider adding
  importFrom("grDevices", "win.metafile")
  importFrom("graphics", "par", "persp")
to your NAMESPACE file.
FLXmclust.Density: no visible global function definition for 'dmvnorm'
FLXmclust.Estimate: no visible global function definition for 'flexmix'
FLXmclust.Estimate: no visible global function definition for
  'FLXmclust'
coefmclust: no visible global function definition for 'parameters'
flexmix.Density: no visible global function definition for
  'model.matrix'
flexmix.Density: no visible global function definition for
  'model.response'
flexmix.Density: no visible global function definition for
  'model.frame'
flexmix.Density: no visible global function definition for 'dnorm'
flexmix.Density: no visible global function definition for 'dpois'
flexmix.Density: no visible global function definition for 'dbinom'
flexmix.Estimate: no visible global function definition for 'flexmix'
flexmix.Estimate: no visible global function definition for 'FLXglm'
tleplot,TLE-data.frame: no visible global function definition for
  'legend'
Undefined global functions or variables:
  FLXglm FLXmclust dbinom dmvnorm dnorm dpois flexmix legend
  model.frame model.matrix model.response parameters
Consider adding
  importFrom("graphics", "legend")
  importFrom("stats", "dbinom", "dnorm", "dpois", "model.frame",
             "model.matrix", "model.response")
to your NAMESPACE file.
'library' or 'require' call to 'mvtnorm' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'mvtnorm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
EMN: no visible global function definition for 'dmvnorm'
EMN: no visible global function definition for 'pmvnorm'
EMT: no visible global function definition for 'GenzBretz'
EMT: no visible global function definition for 'dmvt'
EMT: no visible global function definition for 'pmvt'
MomemNT: no visible global function definition for 'pnorm'
MomemNT: no visible global function definition for 'dnorm'
MomemNT: no visible global function definition for 'pmvnorm'
MomemNT: no visible global function definition for 'dmvnorm'
TT.moment: no visible global function definition for 'GenzBretz'
TT.moment: no visible global function definition for 'pmvt'
TT.moment: no visible global function definition for 'dt'
TT.moment: no visible global function definition for 'pt'
TT.moment: no visible global function definition for 'dmvt'
cdfNI: no visible global function definition for 'pnorm'
cdfNI: no visible global function definition for 'pt'
inits: no visible global function definition for 'lm'
Undefined global functions or variables:
  GenzBretz dmvnorm dmvt dnorm dt lm pmvnorm pmvt pnorm pt
Consider adding
  importFrom("stats", "dnorm", "dt", "lm", "pnorm", "pt")
to your NAMESPACE file.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.3Mb
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    examples  19.2Mb
    include    2.9Mb
search_collection: no visible global function definition for
  'URLencode'
search_company: no visible global function definition for 'URLencode'
search_keyword: no visible global function definition for 'URLencode'
search_list: no visible global function definition for 'URLencode'
search_movie: no visible global function definition for 'URLencode'
search_multi: no visible global function definition for 'URLencode'
search_person: no visible global function definition for 'URLencode'
search_tv: no visible global function definition for 'URLencode'
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
extractContentDOM: no visible global function definition for
  'capture.output'
extractHTMLStrip: no visible global function definition for
  'capture.output'
Undefined global functions or variables:
  capture.output
Consider adding
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'Rcampdf' 'Rpoppler' 'tm.lexicon.GeneralInquirer'
Package unavailable to check Rd xrefs: 'Rpoppler'
Package suggested but not available for checking: 'corpus.JSS.papers'
Tosls.formula: no visible global function definition for 'model.matrix'
Tosls.formula: no visible global function definition for
  'model.response'
summary: no visible global function definition for 'coef'
summary: no visible global function definition for 'pt'
Undefined global functions or variables:
  coef model.matrix model.response pt
Consider adding
  importFrom("stats", "coef", "model.matrix", "model.response", "pt")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'Cairo' 'RGtk2' 'colorspace' 'gWidgets' 'tourr'
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'TeachingDemos' 'ash'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'Cairo' 'RGtk2' 'colorspace' 'gWidgets' 'tourr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: 'rmongodb'
ConfA: no visible global function definition for 'qf'
EstM2Sn: no visible global function definition for 'nlm'
EstM2Sn: no visible global function definition for 'qnorm'
TV.model: no visible global function definition for 'dev.new'
TV.model: no visible global function definition for 'points'
betaBino: no visible global function definition for 'pbinom'
doseD: no visible global function definition for 'lm'
doseD: no visible global function definition for 'dev.new'
doseD: no visible global function definition for 'par'
doseD: no visible global function definition for 'plot'
doseD: no visible global function definition for 'axTicks'
doseD: no visible global function definition for 'axis'
doseD: no visible global function definition for 'lines'
doseD: no visible global function definition for 'abline'
doseD: no visible global function definition for 'legend'
setD: no visible global function definition for 'dev.new'
setD: no visible global function definition for 'par'
setD: no visible global function definition for 'pbinom'
setD: no visible global function definition for 'abline'
setD: no visible global function definition for 'axis'
setD: no visible global function definition for 'rect'
setD: no visible global function definition for 'lines'
setD: no visible global function definition for 'text'
setD: no visible global function definition for 'axTicks'
setD: no visible global function definition for 'legend'
spoD : spoD_A: no visible global function definition for 'chisq.test'
Undefined global functions or variables:
  abline axTicks axis chisq.test dev.new legend lines lm nlm par pbinom
  plot points qf qnorm rect text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axTicks", "axis", "legend", "lines",
             "par", "plot", "points", "rect", "text")
  importFrom("stats", "chisq.test", "lm", "nlm", "pbinom", "qf", "qnorm")
to your NAMESPACE file.
align1d : obj: no visible global function definition for 'dist'
align2d : obj: no visible global function definition for 'dist'
align2d : pen: no visible global function definition for 'dist'
align2d: no visible global function definition for 'dist'
sumt: no visible global function definition for 'optim'
tpe1d: no visible global function definition for 'hclust'
tpe2d: no visible global function definition for 'hclust'
tpe2d: no visible global function definition for 'cmdscale'
Undefined global functions or variables:
  cmdscale dist hclust optim
Consider adding
  importFrom("stats", "cmdscale", "dist", "hclust", "optim")
to your NAMESPACE file.
Package in Depends field not imported from: 'lgtdl'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ci.plot: no visible global function definition for 'gaussian'
ci.plot: no visible global function definition for 'qnorm'
ci.plot: no visible global function definition for 'plot'
ci.plot: no visible global function definition for 'lines'
cst.fit.ff: no visible global function definition for 'pnorm'
cstfit.1: no visible global function definition for 'var'
gof.test.boots.pf: no visible binding for global variable 'sd'
gof.test.int.1.ff: no visible global function definition for 'quantile'
gof.test.int.1.ff: no visible global function definition for 'var'
gof.test.int.ff: no visible global function definition for 'pnorm'
gofTest: no visible binding for global variable 'sd'
plotGof: no visible global function definition for 'plot'
plotGof : <anonymous>: no visible global function definition for
  'lines'
plotGof: no visible global function definition for 'lines'
sig.test.int.1.ff: no visible global function definition for 'quantile'
sig.test.int.1.ff: no visible global function definition for 'var'
sig.test.int.ff: no visible global function definition for 'pnorm'
test.boots.1: no visible binding for global variable 'sd'
tpr: no visible global function definition for 'poisson'
tpr: no visible global function definition for 'glm.fit'
tpr: no visible global function definition for 'coef'
tpr: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx coef gaussian glm.fit lines plot pnorm poisson qnorm quantile
  sd var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "approx", "coef", "gaussian", "glm.fit", "pnorm",
             "poisson", "qnorm", "quantile", "sd", "var")
to your NAMESPACE file.
File 'tpr/libs/i386/tpr.dll':
  Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
    Object: 'utils.o'
File 'tpr/libs/x64/tpr.dll':
  Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
    Object: 'utils.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
DeadReckoning: no visible global function definition for 'filter'
DeadReckoning: no visible global function definition for 'approx'
DeadReckoning: no visible global function definition for 'lm'
Mapper: no visible global function definition for 'colorRampPalette'
Mapper: no visible global function definition for 'terrain.colors'
Mapper: no visible global function definition for 'points'
Mapper: no visible global function definition for 'axis'
Standardize: no visible global function definition for 'lm'
Undefined global functions or variables:
  approx axis colorRampPalette filter lm points terrain.colors
Consider adding
  importFrom("grDevices", "colorRampPalette", "terrain.colors")
  importFrom("graphics", "axis", "points")
  importFrom("stats", "approx", "filter", "lm")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/TrajDataMining.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'.
microsoftTranslate: no visible global function definition for
  'URLencode'
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
Found the following significant warnings:
  getKendall.c:37:30: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  getKendall.c:39:64: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/tranSurv.Rcheck/00install.out' for details.
rtrapezoid: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Build_JTree: no visible global function definition for 'flush.console'
Run_JTree: no visible global function definition for 'cov2cor'
Undefined global functions or variables:
  cov2cor flush.console
Consider adding
  importFrom("stats", "cov2cor")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
LikAge: no visible global function definition for 'read.table'
bd.ME.optim: no visible global function definition for 'optim'
bd.ME.optim.rho: no visible global function definition for 'optim'
bd.ME.optim.rho.all: no visible global function definition for 'optim'
bd.MEyule.optim: no visible global function definition for 'optimize'
bd.MEyule.optim: no visible global function definition for 'optim'
bd.age.optim.matlab: no visible global function definition for
  'read.table'
bd.groups.conf: no visible global function definition for 'uniroot'
bd.shifts.plot: no visible global function definition for 'plot'
bd.shifts.plot: no visible global function definition for 'lines'
bdsky.stt.optim: no visible global function definition for 'optim'
create.mat: no visible global function definition for 'write.table'
Undefined global functions or variables:
  lines optim optimize plot read.table uniroot write.table
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "optim", "optimize", "uniroot")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
plot.treeperm: no visible global function definition for 'hist'
plot.treeperm: no visible global function definition for 'points'
plot.treeperm: no visible global function definition for 'text'
treeperm.formula: no visible global function definition for
  'model.frame'
treeperm.formula: no visible global function definition for
  'model.response'
Undefined global functions or variables:
  hist model.frame model.response points text
Consider adding
  importFrom("graphics", "hist", "points", "text")
  importFrom("stats", "model.frame", "model.response")
to your NAMESPACE file.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.4Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
plot.trifield: no visible global function definition for 'topo.colors'
plot.trifield: no visible global function definition for 'plot'
plot.trifield: no visible global function definition for 'image'
plot.trifield: no visible global function definition for 'contour'
plot.trifield: no visible global function definition for 'text'
ternary.legend: no visible global function definition for 'arrows'
ternary.legend: no visible global function definition for 'text'
triaxes: no visible global function definition for 'lines'
tribox: no visible global function definition for 'polygon'
Undefined global functions or variables:
  arrows contour image lines plot polygon text topo.colors
Consider adding
  importFrom("grDevices", "topo.colors")
  importFrom("graphics", "arrows", "contour", "image", "lines", "plot",
             "polygon", "text")
to your NAMESPACE file.
'library' or 'require' call to 'fpc' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.tkm: no visible global function definition for 'plotcluster'
plot.tkm: no visible global function definition for 'plot'
plot.tkm: no visible global function definition for 'points'
plot.tkm: no visible global function definition for 'lines'
plot.tkm: no visible global function definition for 'discrcoord'
Undefined global functions or variables:
  discrcoord lines plot plotcluster points
Consider adding
  importFrom("graphics", "lines", "plot", "points")
to your NAMESPACE file.
cinbag: no visible global function definition for 'var'
trimTrees: no visible global function definition for 'predict'
Undefined global functions or variables:
  predict var
Consider adding
  importFrom("stats", "predict", "var")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'gtools' 'mgcv'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'gtools' 'mgcv' 'msm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
HtoGp: no visible global function definition for 'odd'
HtoGp: no visible global function definition for 'even'
plot.pirls.gam: no visible global function definition for 'par'
plot.pirls.gam: no visible global function definition for 'plot'
plot.pirls.gam: no visible global function definition for 'title'
plot.pirls.gam: no visible global function definition for 'lines'
plot.pirls.gam: no visible global function definition for 'rug'
plot.pirls.gam: no visible global function definition for 'mtext'
test.trioGxE: no visible global function definition for 'write.table'
trioGxE: no visible global function definition for 'quantile'
trioGxE: no visible global function definition for 'qtnorm'
trioplot: no visible global function definition for 'quantile'
trioplot: no visible global function definition for 'formula'
trioplot: no visible global function definition for 'gam'
trioplot: no visible global function definition for 'binomial'
Undefined global functions or variables:
  binomial even formula gam lines mtext odd par plot qtnorm quantile
  rug title write.table
Consider adding
  importFrom("graphics", "lines", "mtext", "par", "plot", "rug", "title")
  importFrom("stats", "binomial", "formula", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
DrawMargin: no visible global function definition for 'qnorm'
DrawProbability: no visible global function definition for 'pnorm'
Factor: no visible global function definition for 'new'
Gaussian: no visible global function definition for 'new'
LikelihoodFactor: no visible global function definition for 'new'
Parameters: no visible global function definition for 'new'
Player: no visible global function definition for 'new'
PriorFactor: no visible global function definition for 'new'
SumFactor: no visible global function definition for 'new'
TruncateFactor: no visible global function definition for 'new'
Variable: no visible global function definition for 'new'
Vdraw: no visible global function definition for 'dnorm'
Vdraw: no visible global function definition for 'pnorm'
Vwin: no visible global function definition for 'dnorm'
Vwin: no visible global function definition for 'pnorm'
Wdraw: no visible global function definition for 'dnorm'
Wdraw: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dnorm new pnorm qnorm
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "dnorm", "pnorm", "qnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
cdens: no visible global function definition for 'head'
dplot: no visible global function definition for 'knots'
dplot: no visible global function definition for 'median'
dplot: no visible global function definition for 'par'
dplot: no visible global function definition for 'plot.stepfun'
dplot: no visible global function definition for 'abline'
edf: no visible global function definition for 'approxfun'
mctest : rdist: no visible global function definition for 'runif'
mctest : S: no visible global function definition for 'optim'
qplot: no visible global function definition for 'plot'
qplot: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline approxfun head knots median optim par plot plot.stepfun runif
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("stats", "approxfun", "knots", "median", "optim",
             "plot.stepfun", "runif")
  importFrom("utils", "head")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'leaps' 'locfit' 'mgcv'
  Please remove these calls from your code.
':::' calls which should be '::':
  'stats:::ARMAacf' 'stats:::acf' 'stats:::arima'
  See the note in ?`:::` about the use of this operator.
dmvnb: no visible global function definition for 'dbinom'
drvts: no visible global function definition for 'dnorm'
drvts: no visible global function definition for 'dbinom'
dsvts: no visible global function definition for 'dnorm'
rescale: no visible global function definition for 'qlogis'
rescale: no visible global function definition for 'plogis'
tslogl: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dbinom dnorm plogis qlogis
Consider adding
  importFrom("stats", "dbinom", "dnorm", "plogis", "qlogis")
to your NAMESPACE file.
tfDetails: no visible global function definition for 'start'
tfDetails: no visible global function definition for 'end'
Undefined global functions or variables:
  end start
Consider adding
  importFrom("stats", "end", "start")
to your NAMESPACE file.
Qhat: no visible global function definition for 'pnorm'
plrt: no visible global function definition for 'uniroot'
plrt: no visible global function definition for 'optimize'
simulatedata: no visible global function definition for 'rnorm'
tsc.test: no visible global function definition for 'shapiro.test'
tsc.test: no visible global function definition for 'p.adjust'
tsc.test: no visible global function definition for 'glm'
tsc.test : f: no visible global function definition for 'pnorm'
tsc.test: no visible global function definition for 'uniroot'
tsc.test: no visible global function definition for 'optimize'
variance: no visible global function definition for 'density'
variance: no visible global function definition for 'ecdf'
Undefined global functions or variables:
  density ecdf glm optimize p.adjust pnorm rnorm shapiro.test uniroot
Consider adding
  importFrom("stats", "density", "ecdf", "glm", "optimize", "p.adjust",
             "pnorm", "rnorm", "shapiro.test", "uniroot")
to your NAMESPACE file.
Package in Depends field not imported from: 'deSolve'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in 'tseries-Ex.R' failed
The error most likely occurred in:

> ### Name: get.hist.quote
> ### Title: Download Historical Finance Data
> ### Aliases: get.hist.quote
> ### Keywords: ts
> 
> ### ** Examples
> 
> con <- url("https://finance.yahoo.com")
> if(!inherits(try(open(con), silent = TRUE), "try-error")) {
+   close(con)
+   x <- get.hist.quote(instrument = "^gspc", start = "1998-01-01",
+                       quote = "Close")
+   plot(x)
+ 
+   x <- get.hist.quote(instrument = "ibm", quote = c("Cl", "Vol"))
+   plot(x, main = "International Business Machines Corp")
+ 
+   spc <- get.hist.quote(instrument = "^gspc", start = "1998-01-01",
+          quote = "Close")
+   ibm <- get.hist.quote(instrument = "ibm",  start = "1998-01-01",
+          quote = "Adj")
+   require("zoo")		# For merge() method.
+   x <- merge(spc, ibm)
+   plot(x, main = "IBM vs S&P 500")
+ }
'getSymbols' currently uses auto.assign=TRUE by default, but will
use auto.assign=FALSE in 0.5-0. You will still be able to use
'loadSymbols' to automatically load data. getOption("getSymbols.env")
and getOption("getSymbols.auto.assign") will still be checked for
alternate defaults.

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

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

This message is shown once per session and may be disabled by setting
options("getSymbols.yahoo.warning"=FALSE).
Error in curl::curl_download(cu, tmp, handle = h) : 
  Timeout was reached: Operation timed out after 10015 milliseconds with 0 out of 0 bytes received
Calls: get.hist.quote ... getSymbols.yahoo -> .getHandle -> new.session -> <Anonymous>
Execution halted
vintageMap: no visible global function definition for 'read.table'
TSget,character-TSfameLocalConnection: no visible global function
  definition for 'as.ts'
TSget,character-TSfameLocalConnection: no visible global function
  definition for 'zoo'
TSget,character-TSfameLocalConnection: no visible global function
  definition for 'frequency'
TSget,character-TSfameServerConnection: no visible global function
  definition for 'as.ts'
TSget,character-TSfameServerConnection: no visible global function
  definition for 'zoo'
TSget,character-TSfameServerConnection: no visible global function
  definition for 'frequency'
Undefined global functions or variables:
  as.ts frequency read.table zoo
Consider adding
  importFrom("stats", "as.ts", "frequency")
  importFrom("utils", "read.table")
to your NAMESPACE file.
DstandardizedLoadings.TSFmodel: no visible global function definition
  for 'cov'
FAfitStats.TSFmodel: no visible global function definition for 'cov'
FAfitStats.default: no visible global function definition for 'cor'
FAfitStats.default: no visible global function definition for
  'factanal'
FAfitStats.default: no visible global function definition for 'pchisq'
FAmodelFitStats: no visible global function definition for 'pchisq'
checkResiduals.TSFmodel: no visible global function definition for
  'cov'
distribution.factorsEstEval: no visible global function definition for
  'par'
distribution.factorsEstEval: no visible binding for global variable
  'par'
distribution.factorsEstEval: no visible global function definition for
  'density'
distribution.factorsEstEval: no visible global function definition for
  'matplot'
distribution.factorsEstEval: no visible global function definition for
  'title'
summary.TSFmodel: no visible global function definition for 'start'
summary.TSFmodel: no visible global function definition for 'end'
Undefined global functions or variables:
  cor cov density end factanal matplot par pchisq start title
Consider adding
  importFrom("graphics", "matplot", "par", "title")
  importFrom("stats", "cor", "cov", "density", "end", "factanal",
             "pchisq", "start")
to your NAMESPACE file.
Func.SAX: no visible global function definition for 'sd'
Func.SAX: no visible global function definition for 'qnorm'
Func.matrix: no visible global function definition for 'qnorm'
Func.motif: no visible global function definition for 'sd'
Func.motif: no visible global function definition for 'na.omit'
Func.motif: no visible global function definition for 'combn'
Func.motif.multivariate: no visible global function definition for
  'txtProgressBar'
Func.motif.multivariate: no visible global function definition for
  'setTxtProgressBar'
Undefined global functions or variables:
  combn na.omit qnorm sd setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit", "qnorm", "sd")
  importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
dLag : dlag.f: no visible global function definition for
  'complete.cases'
distmat: no visible global function definition for 'dist'
fitCity: no visible global function definition for 'glm.control'
fitCity: no visible global function definition for 'terms'
ldmvnorm: no visible global function definition for 'mahalanobis'
lspline: no visible global function definition for 'quantile'
plot.tsdecomp: no visible global function definition for 'par'
plot.tsdecomp: no visible global function definition for 'plot'
setupFormula: no visible global function definition for 'as.formula'
spatialgibbs: no visible global function definition for 'rnorm'
spatialgibbs: no visible global function definition for 'rgamma'
spatialgibbs: no visible global function definition for 'runif'
tsdecomp: no visible global function definition for 'fft'
Undefined global functions or variables:
  as.formula complete.cases dist fft glm.control mahalanobis par plot
  quantile rgamma rnorm runif terms
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "as.formula", "complete.cases", "dist", "fft",
             "glm.control", "mahalanobis", "quantile", "rgamma", "rnorm",
             "runif", "terms")
to your NAMESPACE file.
covTranspose11: warning in glasso(sc, 2 * rhoc/n, wi.init = gc$wi,
  w.init = gc$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
covTranspose11: warning in glasso(sr, 2 * rhor/p, wi.init = gr$wi,
  w.init = gr$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
.help.ESS: no visible global function definition for 'index.search'
TransSphere : ttin: no visible global function definition for 't.test'
TransSphere: no visible global function definition for 'sd'
TransSphere: no visible global function definition for 'quantile'
TransSphere: no visible global function definition for 'pt'
Undefined global functions or variables:
  index.search pt quantile sd t.test
Consider adding
  importFrom("stats", "pt", "quantile", "sd", "t.test")
to your NAMESPACE file.
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > 
  > library("TSP")
  > test_check("TSP")
  -- 1. Failure: (unknown) (@test-solve_TSP.R#56)  -------------------------------
  all(sapply(tours1, attr, "tour_length") == 0) isn't true.
  
  == testthat results  ===========================================================
  OK: 21 SKIPPED: 0 FAILED: 1
  1. Failure: (unknown) (@test-solve_TSP.R#56) 
  
  Error: testthat unit tests failed
  Execution halted
TT.GS : TT.GS.sp: no visible global function definition for 'qt'
TT.GS : TT.GS.sp: no visible global function definition for 'runif'
TT.GS : TT.GS.sp: no visible global function definition for 'pt'
TT.moment: no visible global function definition for 'dt'
TT.moment: no visible global function definition for 'pt'
Undefined global functions or variables:
  dt pt qt runif
Consider adding
  importFrom("stats", "dt", "pt", "qt", "runif")
to your NAMESPACE file.
Running examples in 'TTR-Ex.R' failed
The error most likely occurred in:

> ### Name: TTR
> ### Title: Functions to create Technical Trading Rules (TTR)
> ### Aliases: TTR TTR-package
> ### Keywords: package
> 
> ### ** Examples
> 
> 
> data(ttrc)
> 
> # Bollinger Bands
> bbands <- BBands( ttrc[,c("High","Low","Close")] )
> 
> # Directional Movement Index
> adx <- ADX(ttrc[,c("High","Low","Close")])
> 
> # Moving Averages
> ema <- EMA(ttrc[,"Close"], n=20)
> sma <- SMA(ttrc[,"Close"], n=20)
> 
> # MACD
> macd <- MACD( ttrc[,"Close"] )
> 
> # RSI
> rsi <- RSI(ttrc[,"Close"])
> 
> # Stochastics
> stochOsc <- stoch(ttrc[,c("High","Low","Close")])
> 
> ### Note: you must have a working internet connection
> ### for the examples below to work!
> 
> # Fetch U.S. symbols from the internet
> nyseSymbols <- stockSymbols("NYSE")
Fetching NYSE symbols...
Warning in file(file, "rt") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in file(file, "rt") : cannot open the connection
Calls: stockSymbols -> read.csv -> read.table -> file
Execution halted
ttScreening: no visible global function definition for 'gaussian'
ttScreening: no visible global function definition for 'glm.control'
ttScreening: no visible global function definition for 'model.response'
ttScreening: no visible global function definition for 'is.empty.model'
ttScreening: no visible global function definition for 'model.matrix'
ttScreening: no visible global function definition for 'na.omit'
ttScreening: no visible global function definition for 'terms'
ttScreening: no visible global function definition for 'capture.output'
ttScreening: no visible global function definition for 'glm'
ttScreening: no visible binding for global variable 'gaussian'
ttScreening: no visible global function definition for 'pt'
ttScreening: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  capture.output gaussian glm glm.control is.empty.model model.matrix
  model.response na.omit p.adjust pt terms
Consider adding
  importFrom("stats", "gaussian", "glm", "glm.control", "is.empty.model",
             "model.matrix", "model.response", "na.omit", "p.adjust",
             "pt", "terms")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
.saveDevice: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  dev.off
Consider adding
  importFrom("grDevices", "dev.off")
to your NAMESPACE file.
ttwa: no visible global function definition for 'aggregate'
ttwa: no visible global function definition for 'txtProgressBar'
ttwa: no visible global function definition for 'setTxtProgressBar'
Undefined global functions or variables:
  aggregate setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "aggregate")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
http.connection: no visible global function definition for 'setNames'
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'gsl' 'igraph' 'snowfall'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/turboEM.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'.
accelerate: no visible global function definition for 'modifyList'
boxplot.turbosim: no visible global function definition for 'par'
boxplot.turbosim: no visible global function definition for 'axis'
boxplot.turbosim: no visible global function definition for 'mtext'
dataprof.turbosim: no visible global function definition for 'quantile'
dataprof.turbosim: no visible global function definition for 'par'
dataprof.turbosim: no visible global function definition for 'plot'
dataprof.turbosim: no visible global function definition for 'lines'
dataprof.turbosim: no visible global function definition for 'segments'
dataprof.turbosim: no visible global function definition for 'legend'
line.search: no visible global function definition for 'optimize'
pairs.turbosim: no visible global function definition for 'par'
pairs.turbosim: no visible global function definition for 'plot'
pairs.turbosim: no visible global function definition for 'legend'
pairs.turbosim: no visible global function definition for 'axis'
pairs.turbosim: no visible global function definition for 'title'
pairs.turbosim: no visible global function definition for 'coef'
pairs.turbosim: no visible global function definition for 'abline'
pairs.turbosim: no visible global function definition for 'text'
plot.turbo: no visible global function definition for 'plot'
plot.turbo: no visible global function definition for 'lines'
plot.turbo: no visible global function definition for 'legend'
turboSim: no visible binding for global variable 'par'
turboem: no visible global function definition for 'modifyList'
Undefined global functions or variables:
  abline axis coef legend lines modifyList mtext optimize par plot
  quantile segments text title
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "mtext",
             "par", "plot", "segments", "text", "title")
  importFrom("stats", "coef", "optimize", "quantile")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
turf: no visible global function definition for 'read.table'
turf: no visible global function definition for 'flush.console'
turf.combos: no visible global function definition for 'combn'
Undefined global functions or variables:
  combn flush.console read.table
Consider adding
  importFrom("utils", "combn", "flush.console", "read.table")
to your NAMESPACE file.
TwoCop: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
condnorm: no visible global function definition for 'pnorm'
condnorm: no visible global function definition for 'dnorm'
find.p.joint: no visible global function definition for 'integrate'
find.p.joint.alt: no visible global function definition for 'integrate'
termsInt: no visible global function definition for 'pnorm'
termsInt.alt: no visible global function definition for 'pnorm'
twoStageNull: no visible global function definition for 'qnorm'
twoStageNull: no visible global function definition for 'optimize'
twoStagePower: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dnorm integrate optimize pnorm qnorm
Consider adding
  importFrom("stats", "dnorm", "integrate", "optimize", "pnorm", "qnorm")
to your NAMESPACE file.
txtacf: no visible binding for global variable 'na.fail'
txtacf: no visible global function definition for 'acf'
txtboxplot : <anonymous>: no visible global function definition for
  'boxplot.stats'
txtboxplot: no visible global function definition for 'boxplot.stats'
txtdensity: no visible global function definition for 'density'
Undefined global functions or variables:
  acf boxplot.stats density na.fail
Consider adding
  importFrom("grDevices", "boxplot.stats")
  importFrom("stats", "acf", "density", "na.fail")
to your NAMESPACE file.
Crm: no visible global function definition for 'integrate'
Crm : <anonymous>: no visible global function definition for
  'integrate'
Crm: no visible global function definition for 'optimize'
ail1: no visible global function definition for 'uniroot'
ail2 : fu : <anonymous>: no visible global function definition for
  'integrate'
ail2: no visible global function definition for 'uniroot'
aip : fu : <anonymous>: no visible global function definition for
  'integrate'
aip: no visible global function definition for 'uniroot'
ait1: no visible global function definition for 'uniroot'
ait2 : fu : <anonymous>: no visible global function definition for
  'integrate'
ait2: no visible global function definition for 'uniroot'
sim3p3: no visible global function definition for 'rbinom'
simCrm: no visible global function definition for 'rbinom'
simCrm: no visible global function definition for 'palette'
simCrm: no visible global function definition for 'gray'
simCrm: no visible global function definition for 'plot'
simCrm: no visible global function definition for 'abline'
simCrm: no visible global function definition for 'lines'
ssim3p3: no visible global function definition for 'txtProgressBar'
ssim3p3: no visible global function definition for 'setTxtProgressBar'
ssimCrm: no visible global function definition for 'txtProgressBar'
ssimCrm: no visible global function definition for 'setTxtProgressBar'
Undefined global functions or variables:
  abline gray integrate lines optimize palette plot rbinom
  setTxtProgressBar txtProgressBar uniroot
Consider adding
  importFrom("grDevices", "gray", "palette")
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "integrate", "optimize", "rbinom", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
rmd2pdf: no visible global function definition for 'tail'
rnw2pdf: no visible global function definition for 'tail'
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    doc         5.3Mb
    dummydata   1.4Mb
    libs        4.1Mb
ubRacing : predCandidate: no visible global function definition for
  'predict'
ubRacing : aux2.friedman.edit: no visible global function definition
  for 'pchisq'
ubRacing : aux2.friedman.edit: no visible global function definition
  for 'qt'
ubRacing : aux.friedman.edit: no visible global function definition for
  'wilcox.test'
ubRacing : aux.ttest.edit: no visible global function definition for
  't.test'
ubRacing : aux.ttest.edit: no visible global function definition for
  'p.adjust'
ubRacing : idFolds: no visible global function definition for
  'quantile'
ubRacing: no visible binding for global variable 'sd'
ubSmoteExs: no visible global function definition for 'runif'
Undefined global functions or variables:
  p.adjust pchisq predict qt quantile runif sd t.test wilcox.test
Consider adding
  importFrom("stats", "p.adjust", "pchisq", "predict", "qt", "quantile",
             "runif", "sd", "t.test", "wilcox.test")
to your NAMESPACE file.
med: no visible global function definition for 'quantile'
uh: no visible global function definition for 'mad'
uh.bu: no visible global function definition for 'mad'
Undefined global functions or variables:
  mad quantile
Consider adding
  importFrom("stats", "mad", "quantile")
to your NAMESPACE file.
permute.rows: no visible global function definition for 'runif'
uniCox: no visible global function definition for 'quantile'
uniCoxCV: no visible global function definition for 'quantile'
uniCoxCV: no visible global function definition for 'coxph'
uniCoxCV: no visible binding for global variable 'var'
Undefined global functions or variables:
  coxph quantile runif var
Consider adding
  importFrom("stats", "quantile", "runif", "var")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'predict.uniCox':
  'predict.uniCox'

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
dudewicz.unif.test: no visible global function definition for 'runif'
frosini.unif.test: no visible global function definition for 'runif'
hegazy.unif.test: no visible global function definition for 'runif'
kolmogorov.unif.test: no visible global function definition for 'runif'
kuiper.unif.test: no visible global function definition for 'runif'
neyman.unif.test: no visible global function definition for 'runif'
quesenberry.unif.test: no visible global function definition for
  'runif'
sarkadi.unif.test: no visible global function definition for 'runif'
sherman.unif.test: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
cumcount: no visible global function definition for 'setNames'
uniqtag: no visible global function definition for 'setNames'
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    1.6Mb
    libs   1.7Mb
plot.upclassfit: no visible global function definition for 'frame'
plot.upclassfit: no visible global function definition for 'par'
plot.upclassfit: no visible global function definition for 'axis'
plot.upclassfit: no visible global function definition for 'matplot'
plot.upclassfit: no visible global function definition for 'legend'
plot.upclassfit: no visible global function definition for 'title'
Undefined global functions or variables:
  axis frame legend matplot par title
Consider adding
  importFrom("graphics", "axis", "frame", "legend", "matplot", "par",
             "title")
to your NAMESPACE file.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(upwaver)
  > 
  > test_check("upwaver")
  -- 1. Failure: board_details() works (@test-upwaver.R#47)  ---------------------
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 12 - 11 == 1
  
  == testthat results  ===========================================================
  OK: 22 SKIPPED: 1 FAILED: 1
  1. Failure: board_details() works (@test-upwaver.R#47) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: 'USAboundariesData'
readSEER: no visible global function definition for 'read.fwf'
Undefined global functions or variables:
  read.fwf
Consider adding
  importFrom("utils", "read.fwf")
to your NAMESPACE file.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'UScensus2000cdp/R/zzz.R':
  .First.lib calls:
    cat(paste("'", ehelp[4], "'\n", "Version ", ehelp[2], " created on ",     ehelp[3], ".\n", sep = ""))
    cat(paste(substring(ehelp[3], first = 16), "\n", "Version ",     substring(ehelp[4], first = 16), " created on ", substring(ehelp[5],         first = 16), ".\n", sep = ""))
    cat(paste("copyright (c) 2009, Zack W. Almquist, University of California-Irvine\n",     sep = ""))
    cat("For citation information, type citation(\"UScensus2000cdp\").\n")
    cat("Type help(package=\"UScensus2000cdp\") to get started.\n")

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

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
'library' or 'require' call to 'rgdal' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'foreign' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Missing link or links in documentation object 'fanova.Rd':
  'car'

Missing link or links in documentation object 'ggqq.Rd':
  'car'

Missing link or links in documentation object 'oneway.Rd':
  'car'

Missing link or links in documentation object 'userfriendlyscience-package.Rd':
  'car'

See section 'Cross-references' in the 'Writing R Extensions' manual.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    extdata   6.2Mb
File 'uuid/libs/i386/uuid.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'gen_uuid.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'gen_uuid.o'
File 'uuid/libs/x64/uuid.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'gen_uuid.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'gen_uuid.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
histw: no visible global function definition for 'plot.new'
histw: no visible global function definition for 'plot.window'
histw: no visible global function definition for 'axis'
histw: no visible global function definition for 'rect'
histw: no visible global function definition for 'lines'
uwham.boot: no visible binding for global variable 'var'
Undefined global functions or variables:
  axis lines plot.new plot.window rect var
Consider adding
  importFrom("graphics", "axis", "lines", "plot.new", "plot.window",
             "rect")
  importFrom("stats", "var")
to your NAMESPACE file.
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
Packages suggested but not available for checking: 'vaers' 'vaersND'
Mammen: no visible global function definition for 'runif'
PR2: no visible global function definition for 'ar.burg'
PR2: no visible global function definition for 'pt'
PR2: no visible global function definition for 'pf'
PR3: no visible global function definition for 'ar.burg'
PR3: no visible global function definition for 'pt'
PR3: no visible global function definition for 'pf'
VAR.FOR: no visible global function definition for 'qnorm'
VAR.ForeB: no visible global function definition for 'runif'
VAR.LRtest: no visible global function definition for 'pchisq'
VAR.LRtest: no visible global function definition for 'pf'
VAR.PI: no visible global function definition for 'quantile'
VAR.Waldtest: no visible global function definition for 'pf'
VAR.irf: no visible global function definition for 'par'
VAR.irf: no visible global function definition for 'plot'
VAR.irf: no visible global function definition for 'abline'
VAR1.sim: no visible global function definition for 'rnorm'
resamp: no visible global function definition for 'runif'
Undefined global functions or variables:
  abline ar.burg par pchisq pf plot pt qnorm quantile rnorm runif
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("stats", "ar.burg", "pchisq", "pf", "pt", "qnorm",
             "quantile", "rnorm", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/VarReg.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' 'strucchange'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
black_scholes: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
burdenPlot: no visible global function definition for 'density'
burdenPlot: no visible global function definition for 'axis'
burdenPlot: no visible global function definition for 'points'
burdenPlot: no visible global function definition for 'lines'
burdenPlot: no visible global function definition for 'abline'
burdenPlot: no visible global function definition for 'text'
burdenPlot: no visible global function definition for 'sd'
burdenPlot: no visible global function definition for 'segments'
vbdm: no visible global function definition for 'var'
vbdm: no visible global function definition for 'pchisq'
vbdmR : run_discrete_mixture_vanilla: no visible global function
  definition for 'var'
vbdmR: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  abline axis density lines pchisq points sd segments text var
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "points", "segments",
             "text")
  importFrom("stats", "density", "pchisq", "sd", "var")
to your NAMESPACE file.
compute_KL : rtnorm: no visible global function definition for 'runif'
compute_KL : rtnorm: no visible global function definition for 'dnorm'
compute_KL: no visible global function definition for 'qnorm'
compute_KL: no visible global function definition for 'dnorm'
compute_KL: no visible global function definition for 'pnorm'
compute_KL: no visible global function definition for 'var'
compute_KL: no visible global function definition for 'rbinom'
compute_KL: no visible global function definition for 'rnorm'
compute_KL: no visible global function definition for 'sd'
vbsr: no visible global function definition for 'qchisq'
vbsr: no visible global function definition for 'var'
vbsr: no visible global function definition for 'pchisq'
vbsr: no visible global function definition for 'sd'
vbsr: no visible binding for global variable 'sd'
Undefined global functions or variables:
  dnorm pchisq pnorm qchisq qnorm rbinom rnorm runif sd var
Consider adding
  importFrom("stats", "dnorm", "pchisq", "pnorm", "qchisq", "qnorm",
             "rbinom", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
Found the following significant warnings:
  read_vcfR.cpp:94:18: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/vcfR.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'.
cv.vda.le.default: no visible global function definition for 'predict'
cv.vda.r.default: no visible global function definition for 'predict'
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
Compare2FDS: no visible global function definition for 'runif'
Compare2FDS: no visible global function definition for 'lm'
Compare2FDS: no visible global function definition for 'model.matrix'
Compare2FDS: no visible global function definition for 'plot'
Compare2FDS: no visible global function definition for 'abline'
Compare2FDS: no visible global function definition for 'lines'
Compare2FDS: no visible global function definition for 'text'
Compare2Vdg: no visible global function definition for 'par'
Compare2Vdg: no visible global function definition for 'plot'
Compare2Vdg: no visible global function definition for 'lines'
Compare2Vdg: no visible global function definition for 'legend'
FDSPlot: no visible global function definition for 'runif'
FDSPlot: no visible global function definition for 'lm'
FDSPlot: no visible global function definition for 'model.matrix'
FDSPlot: no visible global function definition for 'plot'
FDSPlot: no visible global function definition for 'abline'
Vdgraph: no visible global function definition for 'par'
Vdgraph: no visible global function definition for 'plot'
Vdgraph: no visible global function definition for 'lines'
Vdgraph: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline legend lines lm model.matrix par plot runif text
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "plot",
             "text")
  importFrom("stats", "lm", "model.matrix", "runif")
to your NAMESPACE file.
calculateParameters,AffineTransformation: no visible global function
  definition for 'lm'
calculateParameters,AffineTransformation: no visible global function
  definition for 'coef'
calculateParameters,SimilarityTransformation: no visible global
  function definition for 'lm'
calculateParameters,SimilarityTransformation: no visible global
  function definition for 'coef'
plotGridTransformation,Cartesian2DCoordinateTransformation: no visible
  global function definition for 'points'
plotGridTransformation,Cartesian2DCoordinateTransformation: no visible
  global function definition for 'legend'
Undefined global functions or variables:
  coef legend lm points
Consider adding
  importFrom("graphics", "legend", "points")
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
DrawDensity3D: no visible global function definition for 'colorRamp'
DrawDensity3D: no visible global function definition for 'rgb'
ReadFromFile3D: no visible global function definition for 'read.table'
Undefined global functions or variables:
  colorRamp read.table rgb
Consider adding
  importFrom("grDevices", "colorRamp", "rgb")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Running examples in 'vegalite-Ex.R' failed
The error most likely occurred in:

> ### Name: from_spec
> ### Title: Take a JSON Vega-Lite Spec and render as an htmlwidget
> ### Aliases: from_spec
> 
> ### ** Examples
> 
> from_spec("http://rud.is/dl/embedded.json")
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in file(con, "r") : cannot open the connection
Calls: from_spec -> readLines -> file
Execution halted
'library' or 'require' call to 'stats' which was already attached by Depends.
  Please remove these calls from your code.
plot.VennDiagram : <anonymous>: no visible global function definition
  for 'hcl'
plot.VennDiagram: no visible global function definition for 'plot.new'
plot.VennDiagram: no visible global function definition for
  'plot.window'
plot.VennDiagram: no visible global function definition for 'col2rgb'
plot.VennDiagram: no visible global function definition for 'rgb'
plot.VennDiagram: no visible global function definition for 'polygon'
plot.VennDiagram: no visible global function definition for 'text'
plot.VennDiagram: no visible global function definition for 'title'
Undefined global functions or variables:
  col2rgb hcl plot.new plot.window polygon rgb text title
Consider adding
  importFrom("grDevices", "col2rgb", "hcl", "rgb")
  importFrom("graphics", "plot.new", "plot.window", "polygon", "text",
             "title")
to your NAMESPACE file.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      3.4Mb
    doc    1.2Mb
    help   2.7Mb
    libs   1.3Mb
vif: no visible global function definition for 'sd'
vif: no visible global function definition for 'lm'
vif: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  lm pnorm sd
Consider adding
  importFrom("stats", "lm", "pnorm", "sd")
to your NAMESPACE file.
hyperpara: no visible binding for global variable 'var'
hyperpara: no visible global function definition for 'hist'
Undefined global functions or variables:
  hist var
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "var")
to your NAMESPACE file.
panel.meansdplot : meansdplot.stats: no visible global function
  definition for 'sd'
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Package in Depends field not imported from: 'sm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
vioplot: no visible global function definition for 'quantile'
vioplot: no visible global function definition for 'median'
vioplot: no visible global function definition for 'plot.new'
vioplot: no visible global function definition for 'plot.window'
vioplot: no visible global function definition for 'axis'
vioplot: no visible global function definition for 'box'
vioplot: no visible global function definition for 'polygon'
vioplot: no visible global function definition for 'lines'
vioplot: no visible global function definition for 'rect'
vioplot: no visible global function definition for 'points'
Undefined global functions or variables:
  axis box lines median plot.new plot.window points polygon quantile
  rect
Consider adding
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "points", "polygon", "rect")
  importFrom("stats", "median", "quantile")
to your NAMESPACE file.
viopoints.default: no visible global function definition for 'par'
viopoints.default: no visible global function definition for 'plot.new'
viopoints.default: no visible global function definition for
  'plot.window'
viopoints.default: no visible global function definition for 'axis'
viopoints.default: no visible global function definition for 'arrows'
viopoints.default: no visible global function definition for
  'getFromNamespace'
viopoints.default: no visible global function definition for 'title'
viopoints.default: no visible global function definition for 'box'
Undefined global functions or variables:
  arrows axis box getFromNamespace par plot.new plot.window title
Consider adding
  importFrom("graphics", "arrows", "axis", "box", "par", "plot.new",
             "plot.window", "title")
  importFrom("utils", "getFromNamespace")
to your NAMESPACE file.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc           4.7Mb
    htmlwidgets   3.6Mb
Decile.Plot: no visible global function definition for 'barplot'
Decile.Plot: no visible global function definition for 'axis'
Sliding.Window: no visible global function definition for 'plot'
Sliding.Window: no visible global function definition for 'lines'
Sliding.Window: no visible global function definition for 'legend'
Undefined global functions or variables:
  axis barplot legend lines plot
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines", "plot")
to your NAMESPACE file.
RCplot: no visible global function definition for 'residuals'
RCplot: no visible global function definition for 'predict'
RCplot: no visible global function definition for 'par'
RCplot: no visible global function definition for 'plot.new'
RCplot: no visible global function definition for 'plot.window'
RCplot: no visible global function definition for 'strwidth'
RCplot: no visible global function definition for 'plot'
RCplot: no visible global function definition for 'abline'
RCplot: no visible global function definition for 'text'
RCplot: no visible global function definition for 'mtext'
fitted.vlmc: no visible global function definition for 'predict'
print.vlmc: no visible global function definition for 'AIC'
residuals.vlmc: no visible global function definition for 'predict'
simulate.vlmc: no visible global function definition for 'runif'
summary.vlmc: no visible global function definition for 'predict'
vlmc: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  AIC abline mtext par plot plot.new plot.window predict qchisq
  residuals runif strwidth text
Consider adding
  importFrom("graphics", "abline", "mtext", "par", "plot", "plot.new",
             "plot.window", "strwidth", "text")
  importFrom("stats", "AIC", "predict", "qchisq", "residuals", "runif")
to your NAMESPACE file.
voss1d: no visible global function definition for 'approx'
voss1d: no visible global function definition for 'rnorm'
voss1g: no visible global function definition for 'dchisq'
voss1g: no visible global function definition for 'approx'
voss1g: no visible global function definition for 'rnorm'
voss2d: no visible global function definition for 'rnorm'
voss2g: no visible global function definition for 'dchisq'
voss2g: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  approx dchisq rnorm
Consider adding
  importFrom("stats", "approx", "dchisq", "rnorm")
to your NAMESPACE file.
'library' or 'require' call to 'raster' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
level: no visible global function definition for 'quantile'
obj.rec: no visible global function definition for 'txtProgressBar'
obj.rec: no visible global function definition for 'setTxtProgressBar'
project: no visible global function definition for 'aggregate'
raster.proj: no visible global function definition for 'quantile'
raster.proj: no visible global function definition for 'rasterFromXYZ'
raster.proj: no visible global function definition for 'plot.new'
raster.proj: no visible global function definition for 'plot'
raster.proj: no visible global function definition for 'legend'
sub.obj: no visible global function definition for 'aggregate'
sub.obj: no visible global function definition for 'txtProgressBar'
sub.obj: no visible global function definition for 'setTxtProgressBar'
surface: no visible global function definition for 'quantile'
Undefined global functions or variables:
  aggregate legend plot plot.new quantile rasterFromXYZ
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "legend", "plot", "plot.new")
  importFrom("stats", "aggregate", "quantile")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
'library' or 'require' call to 'misc3d' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.vscc: no visible global function definition for 'rainbow'
plot.vscc: no visible global function definition for 'pairs'
Undefined global functions or variables:
  pairs rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "pairs")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'lattice' 'latticeExtra' 'stringdist'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ald: no visible global function definition for 'detectCores'
ald: no visible global function definition for 'mclapply'
coltheart.N: no visible global function definition for 'detectCores'
coltheart.N: no visible global function definition for 'mclapply'
hamming.distance: no visible global function definition for
  'stringdist'
ldknn: no visible global function definition for 'detectCores'
ldknn: no visible global function definition for 'mclapply'
ldknn.odds: no visible global function definition for 'glm'
ldknn.odds: no visible binding for global variable 'binomial'
ldknn.odds: no visible global function definition for 'coefficients'
levenshtein.damerau.distance: no visible global function definition for
  'stringdist'
levenshtein.distance: no visible global function definition for
  'stringdist'
plot.ldknn.run: no visible global function definition for 'histogram'
plot.ldknn.run: no visible global function definition for
  'theEconomist.theme'
plot.ldknn.run: no visible global function definition for 'xyplot'
plot.ldknn.run: no visible global function definition for 'as.layer'
Undefined global functions or variables:
  as.layer binomial coefficients detectCores glm histogram mclapply
  stringdist theEconomist.theme xyplot
Consider adding
  importFrom("stats", "binomial", "coefficients", "glm")
to your NAMESPACE file.
Package in Depends field not imported from: 'Rcpp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File 'waffect/libs/i386/waffect.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'waffect.o'
File 'waffect/libs/x64/waffect.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'waffect.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
summary.whc: no visible global function definition for 'printCoefmat'
wahc.fit: no visible global function definition for 'pt'
wahc.fit: no visible global function definition for 'cor'
whc: no visible global function definition for 'model.frame'
whc: no visible global function definition for 'model.matrix'
whc: no visible global function definition for 'model.response'
Undefined global functions or variables:
  cor model.frame model.matrix model.response printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.frame", "model.matrix",
             "model.response", "printCoefmat", "pt")
to your NAMESPACE file.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   7.3Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    doc  12.1Mb
plot.wb: no visible global function definition for 'plot'
plot.wb: no visible global function definition for 'lines'
power.sum: no visible global function definition for 'plot'
power.sum: no visible global function definition for 'lines'
test.data: no visible global function definition for 'var'
test.data: no visible global function definition for 'rnorm'
test.data: no visible global function definition for 'plot'
test.data: no visible global function definition for 'lines'
wave.band: no visible binding for global variable 'var'
wave.band: no visible global function definition for 'pnorm'
wave.band: no visible global function definition for 'qnorm'
wave.band: no visible global function definition for 'plot'
wave.band: no visible global function definition for 'lines'
wb.johnson.lims: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  lines plot pnorm qnorm rnorm var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "pnorm", "qnorm", "rnorm", "var")
to your NAMESPACE file.
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
Running examples in 'webuse-Ex.R' failed
The error most likely occurred in:

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

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

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

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Found the following significant warnings:
  weco.c:136:14: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
  weco.c:158:14: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
  weco.c:173:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  weco.c:196:13: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/weco.Rcheck/00install.out' for details.
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.
print.palette: no visible global function definition for 'par'
print.palette: no visible global function definition for 'image'
print.palette: no visible global function definition for 'rect'
print.palette: no visible global function definition for 'rgb'
print.palette: no visible global function definition for 'text'
wes_palette: no visible global function definition for
  'colorRampPalette'
Undefined global functions or variables:
  colorRampPalette image par rect rgb text
Consider adding
  importFrom("grDevices", "colorRampPalette", "rgb")
  importFrom("graphics", "image", "par", "rect", "text")
to your NAMESPACE file.
Package in Depends field not imported from: 'snpStats'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Z.value: no visible global function definition for 'sd'
Z.value: no visible global function definition for 'pnorm'
pairtest: no visible global function definition for 'is'
pairtest: no visible global function definition for 'new'
pairtest: no visible global function definition for 'rbind2'
pairtest: no visible global function definition for 'p.value'
pairtest: no visible global function definition for 'single.snp.tests'
scoretest: no visible global function definition for 'pchisq'
varplot : <anonymous>: no visible global function definition for 'var'
varplot: no visible global function definition for 'plot'
varplot: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline is new p.value pchisq plot pnorm rbind2 sd single.snp.tests
  var
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("methods", "is", "new", "rbind2")
  importFrom("stats", "pchisq", "pnorm", "sd", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' call to 'markdown' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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  5.3Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
'library' or 'require' call to 'tm' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'plyr' 'reshape2'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
wordmatch: no visible global function definition for 'llply'
wordmatch : <anonymous>: no visible global function definition for
  'llply'
wordmatch: no visible global function definition for 'melt'
wordmatch: no visible global function definition for 'count'
Undefined global functions or variables:
  count llply melt
pickList : <anonymous>: no visible global function definition for
  'na.omit'
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   6.5Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.6Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data  11.1Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.3Mb
simul.wsvm: no visible binding for global variable 'mixture.example'
wsvm.boost: no visible global function definition for 'plot'
Undefined global functions or variables:
  mixture.example plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
quadplot: no visible global function definition for 'median'
xgobi: no visible global function definition for 'write.table'
Undefined global functions or variables:
  median write.table
Consider adding
  importFrom("stats", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
XHWE: no visible global function definition for 'read.table'
result: no visible global function definition for 'pchisq'
result: no visible global function definition for 'rbinom'
result: no visible global function definition for 'rmultinom'
Undefined global functions or variables:
  pchisq rbinom read.table rmultinom
Consider adding
  importFrom("stats", "pchisq", "rbinom", "rmultinom")
  importFrom("utils", "read.table")
to your NAMESPACE file.
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    java  19.0Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    java   9.8Mb
.xssfcolor: no visible global function definition for 'col2rgb'
Undefined global functions or variables:
  col2rgb
Consider adding
  importFrom("grDevices", "col2rgb")
to your NAMESPACE file.
R5.value.default: no visible binding for global variable 'data.table'
R5.value.default: no visible global function definition for
  'as.data.table'
R5.value.parse: no visible binding for global variable 'data.table'
R5.value.parse: no visible global function definition for
  'is.data.table'
R5.value.parse: no visible global function definition for
  'as.data.table'
stampme: no visible global function definition for 'flush.console'
stampmsg: no visible global function definition for 'flush.console'
write.data.table: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  as.data.table data.table flush.console is.data.table write.table
Consider adding
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE file.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
File 'xml2/libs/i386/xml2.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_WriteConnection'
File 'xml2/libs/x64/xml2.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_WriteConnection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    exampleData   1.3Mb
    examples      4.5Mb
    libs          4.2Mb
newXMLDoc: no visible binding for global variable 'doc'
source: no visible binding for global variable 'use_file'
xmlFlatListTree : f: no visible binding for global variable 'nodeNames'
xmlFlatListTree : f: no visible binding for global variable 'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'nodeSet'
xmlFlatListTree : addNode: no visible binding for global variable
  'nodeSet'
xmlFlatListTree : addNode: no visible binding for global variable 'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'nodeNames'
xmlFlatListTree : addNode: no visible binding for global variable
  'nodeNames'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'parentCount'
xmlFlatListTree : addNode: no visible binding for global variable
  'parentCount'
xmlFlatListTree : <anonymous>: no visible binding for global variable
  'e'
xmlFlatTree : <anonymous>: no visible binding for global variable 'e'
Undefined global functions or variables:
  doc e idx nodeNames nodeSet parentCount use_file
LPGM: no visible global function definition for 'flush.console'
PGM: no visible global function definition for 'flush.console'
PGM.path.neighborhood: no visible global function definition for
  'runif'
PGMSim: no visible global function definition for 'rpois'
PGMSim: no visible global function definition for 'par'
WPGMSim: no visible global function definition for 'rpois'
XMRF.Sim: no visible global function definition for 'cov2cor'
XMRF.Sim: no visible global function definition for 'rbinom'
XMRF.Sim: no visible global function definition for 'rnorm'
glm.generic: no visible global function definition for 'flush.console'
mymult: no visible global function definition for 'rmultinom'
plot.GMS: no visible global function definition for 'pdf'
plot.GMS: no visible global function definition for 'dev.off'
plotNet: no visible global function definition for 'pdf'
plotNet: no visible global function definition for 'dev.off'
print.GMS: no visible global function definition for 'str'
processSeq: no visible binding for global variable 'quantile'
processSeq: no visible binding for global variable 'var'
processSeq: no visible global function definition for 'ks.test'
rmpois : <anonymous>: no visible global function definition for 'rpois'
Undefined global functions or variables:
  cov2cor dev.off flush.console ks.test par pdf quantile rbinom
  rmultinom rnorm rpois runif str var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par")
  importFrom("stats", "cov2cor", "ks.test", "quantile", "rbinom",
             "rmultinom", "rnorm", "rpois", "runif", "var")
  importFrom("utils", "flush.console", "str")
to your NAMESPACE file.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
big.read.table: no visible global function definition for 'read.table'
big.read.table: no visible global function definition for 'object.size'
sparkline: no visible global function definition for 'is.ts'
sparkline: no visible global function definition for 'time'
sparkline: no visible global function definition for 'boxplot'
Undefined global functions or variables:
  boxplot is.ts object.size read.table time
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "is.ts", "time")
  importFrom("utils", "object.size", "read.table")
to your NAMESPACE file.
bootstrapswapcurve: no visible global function definition for 'ts'
fitted: no visible global function definition for 'ts'
forwardrates: no visible global function definition for 'ts'
residuals: no visible global function definition for 'ts'
tZC_NS: no visible global function definition for 'cmpfun'
tZC_NS_extra: no visible global function definition for 'cmpfun'
tZC_SV: no visible global function definition for 'cmpfun'
tZC_SV_extra: no visible global function definition for 'cmpfun'
ycextra: no visible global function definition for 'new'
ycinter: no visible global function definition for 'new'
ycplot: no visible global function definition for 'par'
ycplot: no visible global function definition for 'points'
ycplot: no visible global function definition for 'abline'
ycplot: no visible global function definition for 'hist'
ycplot: no visible global function definition for 'lines'
ycplot: no visible global function definition for 'density'
ycplot: no visible global function definition for 'qqnorm'
ycplot: no visible global function definition for 'qqline'
ycsummary: no visible global function definition for 'shapiro.test'
ycsummary: no visible global function definition for 'pf'
Undefined global functions or variables:
  abline cmpfun density hist lines new par pf points qqline qqnorm
  shapiro.test ts
Consider adding
  importFrom("graphics", "abline", "hist", "lines", "par", "points")
  importFrom("methods", "new")
  importFrom("stats", "density", "pf", "qqline", "qqnorm",
             "shapiro.test", "ts")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
.NS.estimator: no visible global function definition for 'lm'
.NS.estimator: no visible global function definition for 'coef'
.NS.estimator: no visible global function definition for 'na.omit'
.NS.estimator: no visible global function definition for 'resid'
.NSS.estimator: no visible global function definition for 'lm'
.NSS.estimator: no visible global function definition for 'coef'
.NSS.estimator: no visible global function definition for 'na.omit'
.NSS.estimator: no visible global function definition for 'resid'
NSrates: no visible global function definition for 'time'
Nelson.Siegel: no visible global function definition for 'optimize'
Srates: no visible global function definition for 'time'
Svensson: no visible global function definition for 'median'
Svensson: no visible global function definition for 'optimize'
Undefined global functions or variables:
  coef lm median na.omit optimize resid time
Consider adding
  importFrom("stats", "coef", "lm", "median", "na.omit", "optimize",
             "resid", "time")
to your NAMESPACE file.
kmeansN: no visible global function definition for 'kmeans'
kmeansN: no visible global function definition for 'aggregate'
kmeansN2: no visible global function definition for 'aggregate'
kmeansN2: no visible binding for global variable 'sd'
Undefined global functions or variables:
  aggregate kmeans sd
Consider adding
  importFrom("stats", "aggregate", "kmeans", "sd")
to your NAMESPACE file.
Package suggested but not available for checking: 'zdat'
S3 methods shown with full name in documentation object 'merge':
  'cbind.zoocat'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
ztable.glm: no visible global function definition for 'confint'
ztable.glm: no visible global function definition for 'coef'
ztable.nls: no visible global function definition for 'formula'
Undefined global functions or variables:
  coef confint formula
Consider adding
  importFrom("stats", "coef", "confint", "formula")
to your NAMESPACE file.
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.
Package required but not available: ‘Rglpk’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'ABC.RAP.Rmd' failed with diagnostics:
there is no package called ‘markdown’
Execution halted
Package required but not available: ‘Cairo’

Package suggested but not available for checking: ‘INLA’

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/ACTCD.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: ‘imager’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error: processing vignette 'additivityTests-vignette.Rmd' failed with diagnostics:
shared object 'stringi.so' not found
Execution halted
row.names<-:
  function(x, make.names, value)
row.names<-.ktab:
  function(x, value)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Package required but not available: ‘Cairo’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'amigaDiskFiles.Rmd' failed with diagnostics:
shared object 'stringi.so' not found
Execution halted
Package suggested but not available for checking: ‘HiTC’
Package unavailable to check Rd xrefs: ‘HiTC’
Found the following significant warnings:
  ADM3.c:34:19: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:34:31: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:34:15: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:39:61: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:39:73: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:39:57: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:52:6: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:54:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:54:56: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:55:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:55:42: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:56:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:56:38: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ADM3.Rcheck/00install.out’ for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Running examples in ‘AFM-Ex.R’ failed
The error most likely occurred in:

> ### Name: evaluateVariogramModels
> ### Title: evaluateVariogramModels method to evaluate the basic variogram
> ###   models
> ### Aliases: evaluateVariogramModels
> ###   evaluateVariogramModels,AFMImageVariogramAnalysis-method
> 
> ### ** Examples
> 
> library(AFM)
> 
> data("AFMImageOfRegularPeaks")
> # take an extract of the image to fasten the calculation      
> AFMImage<-extractAFMImage(AFMImageOfRegularPeaks, 40, 40, 32)
[1] "40 40 31 40 71 40 71"
> # e.g. AFMImage@fullfilename<-"/users/ubuntu/AFMImageOfRegularPeaks-extract.txt"
> AFMImage@fullfilename<-paste(tempdir(), "AFMImageOfRegularPeaks-extract.txt", sep="/")
>  
> AFMImageAnalyser<-AFMImageAnalyser(AFMImage)
Warning in data.table(lib = c("AFM", "gstat", "fractaldim", "fftwtools"),  :
  Item 1 is of size 4 but maximum size is 5 (recycled leaving remainder of 1 items)
>  
>  # Variogram analysis 
> sampleFitPercentage<-3.43/100
> variogramAnalysis<-AFMImageVariogramAnalysis(sampleFitPercentage)
> variogramAnalysis@omnidirectionalVariogram<- 
+               AFM::calculateOmnidirectionalVariogram(AFMImage=AFMImage,
+                                                      AFMImageVariogramAnalysis=variogramAnalysis)
[1] "using automatic width of 1"
[1] "calculating omnidirectional variogram using width of 1 ..."
Error in CRS("+init") : no colon in init= string
Calls: <Anonymous> -> CRS
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 'afpt-aerodynamic-model.Rmd' failed with diagnostics:
shared object 'stringi.so' not found
Execution halted
Running examples in ‘agridat-Ex.R’ failed
The error most likely occurred in:

> ### Name: crossa.wheat
> ### Title: Multi-environment trial of wheat for 18 genotypes at 25
> ###   locations
> ### Aliases: crossa.wheat
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> data(crossa.wheat)
> dat <- crossa.wheat
> 
> # AMMI biplot.  Fig 3 of Crossa et al.
> if(require(agricolae)){
+   m1 <- with(dat, AMMI(E=loc, G=gen, R=1, Y=yield))
+   b1 <- m1$biplot[,1:4]
+   b1$PC1 <- -1 * b1$PC1 # Flip vertical
+   plot(b1$yield, b1$PC1, cex=0.0,
+        text(b1$yield, b1$PC1, cex=.5, labels=row.names(b1),col="brown"),
+        main="crossa.wheat AMMI biplot", xlab="Average yield", ylab="PC1", frame=TRUE)
+   mn <- mean(b1$yield)
+   abline(h=0, v=mn, col='wheat')
+ 
+   g1 <- subset(b1,type=="GEN")
+   text(g1$yield, g1$PC1, rownames(g1), col="darkgreen", cex=.5)
+ 
+   e1 <- subset(b1,type=="ENV")
+   arrows(mn, 0,
+          0.95*(e1$yield - mn) + mn, 0.95*e1$PC1,
+          col= "brown", lwd=1.8,length=0.1)
+ }
Loading required package: agricolae
> 
> # GGB example
> library(agridat)
> data(crossa.wheat)
> dat2 <- crossa.wheat
> 
> # FIXME: The loc grouping is now in the data
> 
> # Define mega-environment groups of locations
> dat2$eg <- ifelse(is.element(dat2$loc,
+                              c("KN","NB","PA","BJ","IL","TC",
+                                "JM","PI","AS","ID","SC","SS",
+                                "SJ","MS","MG","MM")), "Grp1", "Grp2")
> 
> library(gge)
Error: package or namespace load failed for ‘gge’ in library.dynam(lib, package, package.lib):
 shared object ‘stringi.so’ not found
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'agridat_examples.Rmd' failed with diagnostics:
shared object 'stringi.so' not found
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 66-67 (ahn.Rmd) 
Error: processing vignette 'ahn.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘Biostrings’
Packages unavailable to check Rd xrefs: ‘Biostrings’, ‘Starr’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 15-19 (ALA4R.Rmd) 
Error: processing vignette 'ALA4R.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
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.
Running examples in ‘AlphaVantageClient-Ex.R’ failed
The error most likely occurred in:

> ### Name: fetchSeries
> ### Title: Fetch time series data
> ### Aliases: fetchSeries
> 
> ### ** Examples
> 
> setAPIKey()
> example_prices <- fetchSeries(function_nm = "time_series_daily", symbol = "msft")
Warning in checkForRequiredAndOptionalArgs(given_list, function_nm) :
  All optional arguments not met, missing: outputsize, datatype
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: Resolving timed out after 10005 milliseconds
Calls: fetchSeries ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
Package suggested but not available for checking: ‘Biobase’
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:
  ...

Execution halted
Error in re-building vignettes:
  ...
Loading required package: network
network: Classes for Relational Data
Version 1.13.0 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 20.0Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/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’.
Error in re-building vignettes:
  ...
Warning 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
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/Anthropometry.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’.
Namespace in Imports field not imported from: ‘rhandsontable’
  All declared Imports should be used.
Running examples in ‘antiword-Ex.R’ failed
The error most likely occurred in:

> ### Name: antiword
> ### Title: Antiword
> ### Aliases: antiword
> 
> ### ** Examples
> 
> text <- antiword("https://jeroen.github.io/files/UDHR-english.doc")
trying URL 'https://jeroen.github.io/files/UDHR-english.doc'
Warning in utils::download.file(file, tmp, mode = "wb") :
  URL 'https://jeroen.github.io/files/UDHR-english.doc': status was 'Couldn't resolve host name'
Error in utils::download.file(file, tmp, mode = "wb") : 
  cannot open URL 'https://jeroen.github.io/files/UDHR-english.doc'
Calls: antiword -> <Anonymous>
Execution halted
Packages suggested but not available for checking: ‘Biostrings’ ‘kebabs’
Error in re-building vignettes:
  ...

Attaching package: 'apcluster'

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

    heatmap

Quitting from lines 293-307 (apcluster.Rnw) 
Error: processing vignette 'apcluster.Rnw' failed with diagnostics:
object 'apres1b' not found
Execution halted
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
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.
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’
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/aroma.affymetrix.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  5.3Mb
  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:
  ‘Cairo’ ‘GLAD’ ‘sfit’ ‘expectile’ ‘HaarSeg’ ‘mpcbs’
Package unavailable to check Rd xrefs: ‘GLAD’
Package suggested but not available for checking: ‘Cairo’
Error in re-building vignettes:
  ...

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

    filter, lag

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

    intersect, setdiff, setequal, union

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: car

Attaching package: 'car'

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

    recode

Quitting from lines 95-107 (art-contrasts.Rmd) 
Error: processing vignette 'art-contrasts.Rmd' failed with diagnostics:
there is no package called 'Cairo'
Execution halted
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/ARTP.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: ‘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.
Running ‘testthat.R’ [24s/42s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  14: curl::curl_fetch_memory(url, handle = handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2 SKIPPED: 0 FAILED: 3
  1. Error: basic usage of get_bucket for anonymous user (@test-public-bucket.R#4) 
  2. Error: usage of get_bucket with query args (@test-public-bucket.R#11) 
  3. Error: basic usage of get_object for anonymous user (@test-public-object.R#4) 
  
  Error: testthat unit tests failed
  In addition: Warning messages:
  1: In library(testthat) : package 'testthat' already present in search()
  2: In library(testthat) : package 'testthat' already present in search()
  3: In library(testthat) : package 'testthat' already present in search()
  4: In library(testthat) : package 'testthat' already present in search()
  Execution halted
File ‘aylmer/libs/aylmer.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘aylmer.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘aylmer.o’

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

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

Package suggested but not available for checking: ‘sybilSBML’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘pcalg’
Package unavailable to check Rd xrefs: ‘pcalg’
Package suggested but not available for checking: ‘mzR’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/bamboo.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/BANFF.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/BANOVA.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ArrayExpress’
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    2.3Mb
    libs   2.4Mb
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: survival
Quitting from lines 127-155 (hwbart.Rmd) 
Error: processing vignette 'hwbart.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.6Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
Package required but not available: ‘gridGraphics’

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.
Quitting from lines 46-49 (v01-introduction.Rmd) 
Error: processing vignette 'v01-introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘doMPI’
Package unavailable to check Rd xrefs: ‘Rmpi’
Package required but not available: ‘mritc’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    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.
Loading required package: orthopolynom
Loading required package: polynom
Loading required package: VGAM
Loading required package: stats4
Loading required package: splines
Error in readRDS(file) : error reading from connection

Execution halted
installed size is 56.9Mb
  sub-directories of 1Mb or more:
    libs  56.1Mb
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs  13.9Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R     1.7Mb
    doc   3.6Mb
File ‘BayesSAE/libs/BayesSAE.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘HBsae.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    ex-data   4.6Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Bayesthresh.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/BayesXsrc.Rcheck/00install.out’ for details.
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.
Error in re-building vignettes:
  ...
Warning 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 predictExtrapUp(alpha, lambda, beta, predictPositionsRescaled[depthIndRange],  :
  Unable to find suitable chronologies for top of core - truncated to date of extraction
Warning in predictExtrapUp(alpha, lambda, beta, predictPositionsRescaled[depthIndRange],  :
  Unable to find suitable chronologies for top of core - truncated to date of extraction
Warning in predictExtrapUp(alpha, lambda, beta, predictPositionsRescaled[depthIndRange],  :
  Unable to find suitable chronologies for top of core - truncated to date of extraction
Warning in predictExtrapUp(alpha, lambda, beta, predictPositionsRescaled[depthIndRange],  :
  Unable to find suitable chronologies for top of core - truncated to date of extraction
Warning in predictExtrapUp(alpha, lambda, beta, predictPositionsRescaled[depthIndRange],  :
  Unable to find suitable chronologies for top of core - truncated to date of extraction

Execution halted
Package suggested but not available for checking: ‘DNAcopy’
Package suggested but not available for checking: ‘BRugs’
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 52.1Mb
  sub-directories of 1Mb or more:
    libs  50.7Mb
package ‘TeachingDemos’ exists but was not installed under R >= 2.10.0 so xrefs cannot be checked
Running examples in ‘berryFunctions-Ex.R’ failed
The error most likely occurred in:

> ### Name: normalizePathCP
> ### Title: normalizePath Cross Platform
> ### Aliases: normalizePathCP
> ### Keywords: file
> 
> ### ** Examples
> 
> 
> normalizePath  ("doesnotexist.file", mustWork=FALSE) # on linux not full path
[1] "doesnotexist.file"
> normalizePathCP("doesnotexist.file") # full path on all platforms
[1] "doesnotexist.file"
> 
> checknp <- function(a,b=a,d=getwd()) 
+   {
+   aa <- normalizePathCP(a)
+   bb <- if(d=="") b else paste0(d,"/",b)
+   if(aa != bb) stop("'", a, "' -> '", aa, "', should be '",bb, "'.")
+   aa
+   }
> 
> checknp("notexist.file")
Error in checknp("notexist.file") : 
  'notexist.file' -> 'notexist.file', should be '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/berryFunctions.Rcheck/notexist.file'.
Execution halted
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    libs  25.1Mb
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 183-186 (BETS_basic_usage.Rmd) 
Error: processing vignette 'BETS_basic_usage.Rmd' failed with diagnostics:
invalid time series parameters specified
Execution halted
installed size is 141.1Mb
  sub-directories of 1Mb or more:
    include  141.0Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/biclust.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
'library' or 'require' call to ‘mvtnorm’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘bifactorial/libs/bifactorial.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘misc.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Objects: ‘krit.o’, ‘pv.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   5.4Mb
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    libs  27.8Mb
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Removed 199 rows containing non-finite values (stat_contour).
Warning in normalizePath(f2) :
  path[1]="./webshot1230d2fc69181.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot1230d2fc69181.png': No such file or directory
Quitting from lines 240-243 (analysis.Rmd) 
Error: processing vignette 'analysis.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/bigpca.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  15.1Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   6.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
Error in re-building vignettes:
  ...
Warning in engine$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:
cannot open the connection
Execution halted
Running ‘testthat.R’ [8s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
             stop("Function ", name, " not found in environment ", environmentName(env), 
                 ".", call. = FALSE)
         mock(name = name, env = env, new = eval(new_values[[qual_name]], eval_env, eval_env))
     })
  4: FUN(X[[i]], ...)
  5: stop("Can't mock functions in base packages (", pkg_name, ")", call. = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 28 SKIPPED: 0 FAILED: 3
  1. Error: canDownloadFiles (@test-download_files.R#9) 
  2. Error: canReturnEmptyDFWhenEmptyDownloadFiles (@test-download_files.R#27) 
  3. Error: canProcessYaml (@test-process_yaml.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘mzR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    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.
Quitting from lines 64-67 (BioCircos.Rmd) 
Error: processing vignette 'BioCircos.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘BiocStyle’
Running ‘test-all.R’ [6s/6s]
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
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/bioimagetools.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running ‘testthat.R’ [10s/38s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  trying URL 'ftp://ftp.sjtu.edu.cn/pub/CPAN/clpa//README'
  Content type 'unknown' length 107 bytes
  ==================================================
  trying URL 'ftp://ftp.sjtu.edu.cn/pub/CPAN/clpa//index.html'
  Content type 'unknown' length 3574 bytes
  ==================================================
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 61 SKIPPED: 0 FAILED: 4
  1. Error: install.github (@test_install.R#10) 
  2. Error: install.bioinfo (@test_install.R#57) 
  3. Error: dependence (@test_install_uilts.R#88) 
  4. Error: git.download (@test_install_uilts.R#102) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
trying URL 'https://raw.githubusercontent.com/Miachol/ftp/master/files/GRCh37_MT_ensGene.txt'
Content type 'text/plain; charset=utf-8' length 3131 bytes
==================================================
downloaded 3131 bytes

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

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

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

Quitting from lines 102-109 (BioInstaller.Rmd) 
Error: processing vignette 'BioInstaller.Rmd' failed with diagnostics:
Error in 'git2r_clone': SSL error: error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/BioPhysConnectoR.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
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.
Package suggested but not available for checking: ‘IHW’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Packages required but not available: ‘gWidgetsRGtk2’ ‘RGtk2’ ‘cairoDevice’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 31.5Mb
  sub-directories of 1Mb or more:
    libs  30.3Mb
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/BlockFeST.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 ‘sna’ exists but was not installed under R >= 2.10.0 so xrefs cannot be checked
installed size is 32.4Mb
  sub-directories of 1Mb or more:
    libs  32.2Mb
GibbsIteration: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  rbinom
Consider adding
  importFrom("stats", "rbinom")
to your NAMESPACE file.
File ‘BMN/libs/BMN.so’:
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
    Objects: ‘JunctionTree.o’, ‘pseudoLikelihood.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking:
  ‘graph’ ‘Rgraphviz’ ‘gRain’
Found the following significant warnings:
  conditional.least.squares.c:232:20: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  conditional.least.squares.c:233:20: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  conditional.least.squares.c:234:20: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/bnlearn.Rcheck/00install.out’ for details.
Running examples in ‘bnlearn-Ex.R’ failed
The error most likely occurred in:

> ### Name: compare
> ### Title: Compare two or more different Bayesian networks
> ### Aliases: compare all.equal.bn shd hamming graphviz.compare
> ### Keywords: graphs plots interfaces to other packages
> 
> ### ** Examples
> 
> data(learning.test)
> 
> e1 = model2network("[A][B][C|A:B][D|B][E|C][F|A:E]")
> e2 = model2network("[A][B][C|A:B][D|B][E|C:F][F|A]")
> shd(e2, e1, debug = TRUE)
* arcs between A and F do not match.
  > the learned network contains A - F.
  > the true network contains A -> F.
* arcs between E and F do not match.
  > the learned network contains F -> E.
  > the true network contains E -> F.
[1] 2
> unlist(compare(e1,e2))
tp fp fn 
 5  1  1 
> compare(target = e1, current = e2, arcs = TRUE)
$tp
     from to 
[1,] "A"  "C"
[2,] "B"  "C"
[3,] "B"  "D"
[4,] "C"  "E"
[5,] "A"  "F"

$fp
     from to 
[1,] "F"  "E"

$fn
     from to 
[1,] "E"  "F"

> graphviz.compare(e1, e2, diff = "none")
Loading required namespace: Rgraphviz
Failed with error:  ‘there is no package called ‘Rgraphviz’’
Error in check.and.load.package("Rgraphviz") : 
  this function requires the Rgraphviz package.
Calls: graphviz.compare -> check.and.load.package
Execution halted
Found the following significant warnings:
  ./sampling.h:84:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/BNSP.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/boclust.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Package suggested but not available for checking: ‘sangerseqR’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Boom.Rcheck/00install.out’ for details.
installed size is 37.2Mb
  sub-directories of 1Mb or more:
    libs  36.9Mb
Package required but not available: ‘gridGraphics’

Package suggested but not available for checking: ‘installr’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  rBGWM.cc:240:17: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  rBGWM.cc:599:18: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  rBGWM.cc:799:18: 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/Branching.Rcheck/00install.out’ for details.
installed size is 30.0Mb
  sub-directories of 1Mb or more:
    libs  29.8Mb
Error in re-building vignettes:
  ...
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:R2jags':

    traceplot

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

    traceplot

Warning 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: effective sample size cannot be calculated, has been replaced by number of samples.
Loading required package: Matrix
************
Welcome to BayesFactor 0.9.12-2. If you have questions, please contact Richard Morey (richarddmorey@gmail.com).

Type BFManual() to open the manual.
************

Execution halted
Running examples in ‘broom-Ex.R’ failed
The error most likely occurred in:

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

Error in 1:ncol(co) : argument of length 0
Calls: tidy -> tidy.lm -> tidy.summary.lm -> fix_data_frame
Execution halted
Running ‘test-all.R’ [21s/43s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
             row.names(value) <- row.names
         }
         value
     })(null.deviance = 83.2344746889857, `NA` = NULL, check.names = TRUE, fix.empty.names = TRUE, 
         stringsAsFactors = TRUE)
  8: stop(gettextf("arguments imply differing number of rows: %s", paste(unique(nrows), 
         collapse = ", ")), domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 680 SKIPPED: 12 FAILED: 2
  1. Error: tidy works on gam models (@test-gam.R#6) 
  2. Error: glance works on gam models (@test-gam.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
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 22.3Mb
  sub-directories of 1Mb or more:
    libs  21.0Mb
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.
make: *** [sde_ssm_template.o] Interrupt: 2

Execution halted
installed size is 42.8Mb
  sub-directories of 1Mb or more:
    libs  42.3Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    libs  17.1Mb
Running examples in ‘cablecuttr-Ex.R’ failed
The error most likely occurred in:

> ### Name: can_i_stream
> ### Title: Query CanIStream.It
> ### Aliases: can_i_stream can_i_stream_id can_i_stream_it
> 
> ### ** Examples
> 
> can_i_stream_id("4eb0173df5f8079d29000002", "purchase")
Error in as.POSIXlt.character(x, tz, ...) : 
  character string is not in a standard unambiguous format
Calls: can_i_stream_id ... as.POSIXct.default -> as.POSIXct -> as.POSIXlt -> as.POSIXlt.character
Execution halted
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.
Package which this enhances but not available for checking: ‘FastRWeb’
File ‘Cairo/libs/Cairo.so’:
  Found non-API calls to R: ‘R_InputHandlers’, ‘addInputHandler’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    5.7Mb
    libs   1.7Mb
File ‘camel/libs/camel.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘SFGen.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘SFGen.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: sp
rgdal: version: 1.2-16, (SVN revision 701)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.1.3, released 2017/20/01
 Path to GDAL shared files: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/rgdal/gdal
 GDAL binary built with GEOS: FALSE 
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/rgdal/proj
 Linking to sp version: 1.2-7 
Warning in engine$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
Packages suggested but not available for checking:
  ‘GenomicRanges’ ‘IRanges’ ‘S4Vectors’
Package unavailable to check Rd xrefs: ‘GenomicRanges’
Running examples in ‘CANSIM2R-Ex.R’ failed
The error most likely occurred in:

> ### Name: getCANSIM
> ### Title: getCANSIM
> ### Aliases: getCANSIM
> 
> ### ** Examples
> 
> getCANSIM(4010004, showLabels = FALSE)
Warning in open.connection(file, "rt") :
  cannot open zip file '/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//Rtmpq2ImMz/file16f9b199233ed'
Error in open.connection(file, "rt") : cannot open the connection
Calls: getCANSIM ... downloadCANSIM -> read.csv -> read.table -> open -> open.connection
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R        1.0Mb
    data     1.5Mb
    models   2.4Mb
Missing link or links in documentation object 'caretSBF.Rd':
  ‘[gam]{summary.gam}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
Package unavailable to check Rd xrefs: ‘limma’
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 940-945 (CaRpools.Rmd) 
Error: processing vignette 'CaRpools.Rmd' failed with diagnostics:
The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. Please report this to the mailing list.
Execution halted
Package required but not available: ‘OpenCL’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Found the following significant warnings:
  slpcovis.cpp:381:12: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/catlearn.Rcheck/00install.out’ for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
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.
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘rgdal’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   9.2Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.1Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/cem.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:
  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
Package suggested but not available for checking: ‘speaq’
Package suggested but not available for checking: ‘multtest’
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
Packages suggested but not available for checking: ‘graph’ ‘Rgraphviz’
Found the following significant warnings:
  Note: possible error in 'log.likelihood(list(latent.space.pos.prop, ': unused argument (edge.list.rows[[dd]]) 
  Note: possible error in 'log.likelihood(list(latent.space.pos.hold, ': unused argument (edge.list.rows[[dd]]) 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/CIDnetworks.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/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’.
Package suggested but not available for checking: ‘ComplexHeatmap’
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/CircStats.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Package required but not available: ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘FRAPO’
Package unavailable to check Rd xrefs: ‘FRAPO’
Package suggested but not available for checking: ‘rggobi’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Running ‘test-all.R’ [4s/10s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 31 SKIPPED: 0 FAILED: 11
  1. Error: clgeo_Clean (@test_Clean.R#49) 
  2. Error: Clean - 'bowtie' polygons (@test_Clean.R#69) 
  3. Error: Clean - 'bowtie' polygons with holes (@test_Clean.R#80) 
  4. Error: Clean - Inner ring with one edge sharing part of an edge of the outer ring (@test_Clean.R#117) 
  5. Error: Clean - Two adjacent inner rings (@test_Clean.R#126) 
  6. Error: Clean - Nested polygon (@test_Clean.R#135) 
  7. Error: Clean - Nested polygon (@test_Clean.R#145) 
  8. Error: Clean - Multiple nested polygon (@test_Clean.R#155) 
  9. Error: Clean - Dangling edge (@test_Clean.R#172) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 55-57 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
unable to find an inherited method for function 'row.names<-' for signature '"SpatialPolygons", "character"'
Execution halted
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/climatol.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/clpAPI.Rcheck/00install.out’ for details.
Packages required but not available: ‘rggobi’ ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/clustrd.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:
  ‘Biobase’ ‘annotate’ ‘GO.db’ ‘moe430a.db’
Package unavailable to check Rd xrefs: ‘Biobase’
Error in re-building vignettes:
  ...
Loading required package: cluster
Read 7 items
Loading required package: Biobase
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘Biobase’
Loading required package: RankAggreg
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'clValid.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file ./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
Package suggested but not available for checking: ‘limma’
Package unavailable to check Rd xrefs: ‘graph’
Running examples in ‘CodeDepends-Ex.R’ failed
The error most likely occurred in:

> ### Name: makeCallGraph
> ### Title: Create a graph representing which functions call other functions
> ### Aliases: makeCallGraph makeCallGraph,list-method
> ###   makeCallGraph,character-method
> ### Keywords: hplot programming
> 
> ### ** Examples
> 
> 
>   gg = makeCallGraph("package:CodeDepends")
Loading required package: graph
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘graph’
Error in getClass(Class, where = topenv(parent.frame())) : 
  “graphNEL” is not a defined class
Calls: makeCallGraph ... makeCallGraph -> makeCallGraph -> .local -> new -> getClass
Execution halted
Running ‘draw.R’ [1s/1s]
Running the tests in ‘tests/draw.R’ failed.
Complete output:
  > library(CodeDepends)
  > library(Rgraphviz)
  Error in library(Rgraphviz) : there is no package called 'Rgraphviz'
  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.
Failed with error:  'there is no package called 'graph''
Quitting from lines 144-150 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
Cannot make task graph without the graph package (available from the Bioconductor project).
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Combine.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages suggested but not available for checking:
  ‘inSilicoDb’ ‘mogene10sttranscriptcluster.db’
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/CompetingRisk.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  Utility.c:162:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:187:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:211:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:392:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:417:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:442:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/CompRandFld.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [4s/39s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > 
  > 
  > test_check("configr")
  trying URL 'https://raw.githubusercontent.com/JhuangLab/BioInstaller/master/inst/extdata/config/db/db_annovar.toml'
  ── 1. Error: fetch.config (@test_m_fetch.R#5)  ─────────────────────────────────
  cannot open URL 'https://raw.githubusercontent.com/JhuangLab/BioInstaller/master/inst/extdata/config/db/db_annovar.toml'
  1: fetch.config(links) at testthat/test_m_fetch.R:5
  2: download.file(link, config.download.tmp)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 272 SKIPPED: 0 FAILED: 1
  1. Error: fetch.config (@test_m_fetch.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
trying URL 'https://raw.githubusercontent.com/JhuangLab/BioInstaller/master/inst/extdata/config/db/db_annovar.toml'
Quitting from lines 88-93 (configr.Rmd) 
Error: processing vignette 'configr.Rmd' failed with diagnostics:
cannot open URL 'https://raw.githubusercontent.com/JhuangLab/BioInstaller/master/inst/extdata/config/db/db_annovar.toml'
Execution halted
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   6.5Mb
Error in re-building vignettes:
  ...
Warning in engine$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: copula
Warning 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 namespace: Runuran
Loading required package: bbmle
Loading required package: stats4
Loading required package: lattice
Loading required package: grid

Execution halted
Package required but not available: ‘CRF’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
h.inv: no visible global function definition for ‘pnorm’
h.inv: no visible global function definition for ‘qnorm’
hfunc: no visible global function definition for ‘pnorm’
hfunc: no visible global function definition for ‘qnorm’
modified.cvine.alg: no visible global function definition for ‘qpois’
modified.cvine.alg: no visible global function definition for ‘qnbinom’
modified.cvine.alg: no visible global function definition for ‘cor’
modified.cvine.alg.reg: no visible global function definition for
  ‘qpois’
modified.cvine.alg.reg: no visible global function definition for
  ‘qnbinom’
modified.cvine.alg.reg: no visible global function definition for ‘cor’
rcounts : mysampling: no visible global function definition for ‘runif’
rcounts : mysampling: no visible global function definition for ‘qpois’
rcounts : mysampling: no visible global function definition for
  ‘qnbinom’
rcounts.reg : mysampling: no visible global function definition for
  ‘runif’
rcounts.reg : mysampling: no visible global function definition for
  ‘qpois’
rcounts.reg : mysampling: no visible global function definition for
  ‘qnbinom’
unstructured: no visible global function definition for ‘runif’
Undefined global functions or variables:
  cor pnorm qnbinom qnorm qpois runif
Consider adding
  importFrom("stats", "cor", "pnorm", "qnbinom", "qnorm", "qpois",
             "runif")
to your NAMESPACE file.
Package suggested but not available for checking: ‘ProData’
Package required but not available: ‘xcms’

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/CorReg.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 in Depends field not imported from: ‘wavethresh’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.9Mb
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
Package suggested but not available for checking: ‘gridGraphics’
Found the following significant warnings:
  ./bdsmatrix_stub.h:44:11: warning: incompatible pointer to integer conversion returning 'int *' from a function with result type 'int'; dereference with * [-Wint-conversion]
  ./bdsmatrix_stub.h:53:11: warning: incompatible pointer to integer conversion returning 'int *' from a function with result type 'int'; dereference with * [-Wint-conversion]
  ./bdsmatrix_stub.h:100:11: warning: incompatible pointer types returning 'double *' from a function with result type 'double **' [-Wincompatible-pointer-types]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/coxme.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘qvalue’
installed size is 37.1Mb
  sub-directories of 1Mb or more:
    libs  36.9Mb
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.
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/cplm.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: ‘clusterProfiler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
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.

Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ctsem.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Error in re-building vignettes:
  ...

Begin fit attempt 2 of at maximum 16 tries

 Lowest minimum so far:  4203.31303320986

Solution found

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

> ### Name: ComputeMaxInfoGains
> ### Title: Max information gains
> ### Aliases: ComputeMaxInfoGains
> 
> ### ** Examples
> 
>   ComputeMaxInfoGains(data = madelon$data, decision = madelon$decision,
+     discretizations = 1, range = 0, divisions = 22, dimensions = 1)

 *** caught illegal operation ***
address 0x1045e1cb1, cause 'illegal opcode'

Traceback:
 1: ComputeMaxInfoGains(data = madelon$data, decision = madelon$decision,     discretizations = 1, range = 0, divisions = 22, dimensions = 1)
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/cudaBayesreg.Rcheck/00install.out’ for details.
Packages unavailable to check Rd xrefs: ‘DNAcopy’, ‘tilingArray’
Package which this enhances but not available for checking: ‘RGtk2’
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   4.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 177-179 (cycling_data_analysis.Rmd) 
Error: processing vignette 'cycling_data_analysis.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Cyclops.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$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 27-38 (Introduction.Rmd) 
Error: processing vignette 'Introduction.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/dartR.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’ ‘gWidgets2RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot1006c6eab9f1e.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot1006c6eab9f1e.png': No such file or directory
Quitting from lines 57-68 (dataexplorer-intro.Rmd) 
Error: processing vignette 'dataexplorer-intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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
installed size is 89.6Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  87.5Mb
Package suggested but not available for checking: ‘GenomicRanges’
Running ‘autoprint.R’ [1s/1s]
  Comparing ‘autoprint.Rout’ to ‘autoprint.Rout.save’ ... OK
  Running ‘knitr.R’ [1s/2s]
  Comparing ‘knitr.Rout’ to ‘knitr.Rout.save’ ... OK
  Running ‘main.R’ [148s/339s]
Running the tests in ‘tests/main.R’ failed.
Last 13 lines of output:
  4 h 6    TRUE 8   FALSE
  5 i 7    TRUE 5   FALSE
  6 j 9    TRUE 3   FALSE
  
  
  Running test id 1696     Test 1751 not run. If required call library(nanotime) first.
  
  Error in eval(exprs[i], envir) : 
    2 errors out of 5829 (lastID=1750, endian==little, sizeof(long double)==16, sizeof(pointer)==8) in inst/tests/tests.Rraw on Sun Mar 11 01:08:58 2018. Search tests.Rraw for test numbers: 1373, 1543.3.
  Calls: test.data.table -> sys.source -> eval -> eval
  In addition: Warning messages:
  1: S3 methods '.DollarNames.C++Object', '.DollarNames.Module', 'print.bytes', 'format.Rcpp_stack_trace', 'str.Rcpp_stack_trace', 'print.Rcpp_stack_trace' were declared in NAMESPACE but not found 
  2: S3 methods '.DollarNames.C++Object', '.DollarNames.Module', 'print.bytes', 'format.Rcpp_stack_trace', 'str.Rcpp_stack_trace', 'print.Rcpp_stack_trace' were declared in NAMESPACE but not found 
  3: S3 methods '.DollarNames.C++Object', '.DollarNames.Module', 'print.bytes', 'format.Rcpp_stack_trace', 'str.Rcpp_stack_trace', 'print.Rcpp_stack_trace' were declared in NAMESPACE but not found 
  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.
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]="./webshot4a505a3bb393.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot4a505a3bb393.png': No such file or directory
Quitting from lines 512-515 (data.tree.Rmd) 
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘gWidgetsRGtk2’
Package required but not available: ‘SDD’

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

> ### Name: copy_to.src_sql
> ### Title: Copy a local data frame to a DBI backend.
> ### Aliases: copy_to.src_sql
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: ‘dplyr’

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

    ident, sql

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

    filter, lag

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

    intersect, setdiff, setequal, union

> set.seed(1014)
> 
> mtcars$model <- rownames(mtcars)
> mtcars2 <- src_memdb() %>%
+   copy_to(mtcars, indexes = list("model"), overwrite = TRUE)
Error in library.dynam(lib, package, package.lib) : 
  shared object ‘RSQLite.so’ not found
Calls: %>% ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Running ‘testthat.R’ [6s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 344 SKIPPED: 24 FAILED: 76
  1. Error: two arranges equivalent to one (@test-arrange.r#4) 
  2. Error: collect equivalent to as.data.frame/as_tibble (@test-collect.R#4) 
  3. Error: explicit collection returns all data (@test-collect.R#13) 
  4. Error: tbl_dbi support colwise variants (@test-colwise.R#4) 
  5. Error: compute doesn't change representation (@test-compute.R#4) 
  6. Error: src_sql allows you to overwrite (@test-copy_to.R#19) 
  7. Error: distinct throws error if column is specified and .keep_all is TRUE (@test-distinct.R#27) 
  8. Error: ungrouped data collected first (@test-do.R#4) 
  9. Error: named argument become list columns (@test-do.R#9) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 61-63 (dbplyr.Rmd) 
Error: processing vignette 'dbplyr.Rmd' failed with diagnostics:
shared object 'RSQLite.so' not found
Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   5.1Mb
Running examples in ‘ddeploy-Ex.R’ failed
The error most likely occurred in:

> ### Name: duke_deploy
> ### Title: Deploy model using REST API
> ### Aliases: duke_deploy
> 
> ### ** Examples
> 
> duke_auth <- list(
+ user_name = "try_it",
+ api_key   = "db1542b66f16aba5768d8a19c27dec4facf9168a",
+ endpoint = "/api/v1.0"
+ )
> example_data <- as.data.frame(cbind(gl(3,50),rnorm(150)));names(example_data) <- c("x","y")
> example_fit  <- lm(y~x,data=example_data)
> duke_deploy(auth_details=duke_auth,model_object=example_fit)
Error: lexical error: invalid char in json text.
                                       <html>  <head><title>502 Bad Ga
                     (right here) ------^
Execution halted
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    libs  23.9Mb
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/deBInfer.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 
  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’.
Error in re-building vignettes:
  ...
Warning 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.
Note: found 83 marked Latin-1 strings
  Note: found 62 marked UTF-8 strings
Packages unavailable to check Rd xrefs: ‘WGCNA’, ‘moduleColor’
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
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
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.
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/derivmkts.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  6.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.7Mb
    help   1.4Mb
    libs   1.5Mb
Package required but not available: ‘Rglpk’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
Running ‘testthat.R’ [125s/234s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(detrendr)
  > 
  > test_check("detrendr")
  ── 1. Failure: cpp smoothing functions work (@test-smooth.R#12)  ───────────────
  `weighted_smooth(v, rep(1, 20))` threw an error with unexpected message.
  Expected match: "must be odd"
  Actual message: "c++ exception (unknown reason)"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 77 SKIPPED: 0 FAILED: 1
  1. Failure: cpp smoothing functions work (@test-smooth.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    libs  18.2Mb
Running ‘has-devel.R’ [1s/2s]
  Running ‘test-that.R’ [99s/198s]
Running the tests in ‘tests/test-that.R’ failed.
Last 13 lines of output:
      setup
  
  ── 1. Failure: remote_sha.github_remote returns expected value if remote does ex
  remote_sha(github_remote("hadley/devtools@v1.8.0")) not equal to "ad9aac7b9a522354e1ff363a86f389e32cec181b".
  1/1 mismatches
  x[1]: NA
  y[1]: "ad9aac7b9a522354e1ff363a86f389e32cec181b"
  
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 393 SKIPPED: 10 FAILED: 1
  1. Failure: remote_sha.github_remote returns expected value if remote does exist (@test-remotes.r#75) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   8.9Mb
Running examples in ‘dgmb-Ex.R’ failed
The error most likely occurred in:

> ### Name: dgmb-package
> ### Title: Simulating Data for PLS Mode B Structural Models
> ### Aliases: dgmb-package dgmb
> ### Keywords: package
> 
> ### ** Examples
> 
> dgmbGui()
 --------------------------------------------------
| Simulating Data for PLS Mode B Structural Models |
| Version: 1.2                                     |
| Depends: abind, tcltk, MASS                      |
| Licence: GPL >= 2                                |
| System Requirements: tktable, BWidget            |
 --------------------------------------------------
Warning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "ComboBox".
Calls: dgmbGui -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: rgl
Loading required namespace: rmarkdown
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 230-234 (DGVM3D.Rmd) 
Error: processing vignette 'DGVM3D.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/dhglm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Package suggested but not available for checking: ‘rsvg’
Packages required but not available: ‘missMethyl’ ‘methylumi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘run.R’ [2s/4s]
Running the tests in ‘tests/run.R’ failed.
Last 13 lines of output:
  +         "warning"
  +       ), collapse="|"
  +     )
  +   )
  +   with(
  +     as.data.frame(test.res), {
  +       fail <- sum(failed)
  +       err <- sum(error)
  +       if(fail != 0 || err) stop("Errors: ", err, " Failures: ", fail)
  +   })
  + })
  Error in `row.names<-.data.frame`(iris[c(1:5, 50:55, 100:105), ], NULL) : 
    argument "value" is missing, with no default
  Calls: local ... eval -> eval -> row.names<- -> row.names<-.data.frame
  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/diffusionMap.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
Error in re-building vignettes:
  ...
Warning 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 176-185 (Part_2_Transition_Densities.Rmd) 
Error: processing vignette 'Part_2_Transition_Densities.Rmd' failed with diagnostics:
package or namespace load failed for 'DiffusionRgqd' in library.dynam(lib, package, package.lib):
 shared object 'DiffusionRgqd.so' not found
Execution halted
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/di.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    include  19.2Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   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.
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’
Package unavailable to check Rd xrefs: ‘Cairo’
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    libs  14.6Mb
Running ‘testthat.R’ [15s/32s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  3: eval_bare(get_expr(quo), get_env(quo))
  4: summarise(gdf, out = 1:2)
  5: summarise.tbl_df(gdf, out = 1:2)
  6: summarise_impl(.data, dots)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2670 SKIPPED: 6 FAILED: 3
  1. Error: mutate() supports unquoted values (@test-mutate.r#721) 
  2. Failure: summarise() supports unquoted values (@test-summarise.r#980) 
  3. Error: summarise() supports unquoted values (@test-summarise.r#985) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  call dbDisconnect() when finished working with a connection 
  Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   3.3Mb
File ‘DPpackage/libs/DPpackage.so’:
  Found ‘__gfortran_st_close’, possibly from ‘close’ (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDBDPdensity.o’, ‘LDDPdensity.o’,
      ‘LDDPsurvival.o’, ‘LDPDdoublyintsba.o’, ‘LDTFPdensity.o’,
      ‘LDTFPglmmpois.o’, ‘LDTFPsurvival.o’, ‘PSgamgam.o’,
      ‘PSgamgauss.o’, ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’,
      ‘ToolsLDTFP.o’
  Found ‘__gfortran_st_open’, possibly from ‘open’ (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDBDPdensity.o’, ‘LDDPdensity.o’,
      ‘LDDPsurvival.o’, ‘LDPDdoublyintsba.o’, ‘LDTFPdensity.o’,
      ‘LDTFPglmmpois.o’, ‘LDTFPsurvival.o’, ‘PSgamgam.o’,
      ‘PSgamgauss.o’, ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’,
      ‘ToolsLDTFP.o’
  Found ‘__gfortran_st_read’, possibly from ‘read’ (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDDPdensity.o’, ‘LDDPsurvival.o’,
      ‘LDPDdoublyintsba.o’, ‘PSgamgam.o’, ‘PSgamgauss.o’,
      ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’, ‘ToolsLDTFP.o’
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDBDPdensity.o’, ‘LDDPdensity.o’,
      ‘LDDPsurvival.o’, ‘LDPDdoublyintsba.o’, ‘LDTFPdensity.o’,
      ‘LDTFPglmmpois.o’, ‘LDTFPsurvival.o’, ‘PSgamgam.o’,
      ‘PSgamgauss.o’, ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  compnoreggilks.cpp:31:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compnoreggilks.cpp:90:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:32:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:88:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:150:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:207:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:380:8: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/DPWeibull.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Super Learner
Version: 2.0-22
Package created on 2017-07-18

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

Error : 'predict.gam' is not an exported object from 'namespace:gam'
Error : 'predict.gam' is not an exported object from 'namespace:gam'
Error : 'predict.gam' is not an exported object from 'namespace:gam'
Error : 'predict.gam' is not an exported object from 'namespace:gam'
Error : 'predict.gam' is not an exported object from 'namespace:gam'
Error : 'predict.gam' is not an exported object from 'namespace:gam'
Error : 'predict.gam' is not an exported object from 'namespace:gam'
Error : 'predict.gam' is not an exported object from 'namespace:gam'
Error : 'predict.gam' is not an exported object from 'namespace:gam'
Error : 'predict.gam' is not an exported object from 'namespace:gam'
Quitting from lines 492-499 (using_drtmle.Rmd) 
Error: processing vignette 'using_drtmle.Rmd' failed with diagnostics:
matrix D in quadratic function is not positive definite!
Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   4.1Mb
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/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’.
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.2Mb
    libs  13.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Running examples in ‘EasyMx-Ex.R’ failed
The error most likely occurred in:

> ### Name: EasyMx-package
> ### Title: EasyMx: Easy modeling in OpenMx
> ### Aliases: EasyMx-package EasyMx
> 
> ### ** Examples
> 
> 
> # Make and run a one factor model
> require(EasyMx)
> 
> data(demoOneFactor)
> fmod <- list(G=names(demoOneFactor))
> fit1 <- emxFactorModel(fmod, demoOneFactor, run=TRUE)
Running Model with 15 parameters
Error in runHelper(model, frontendStart, intervals, silent, suppressWarnings,  : 
  c++ exception (unknown reason)
Calls: emxFactorModel -> mxRun -> runHelper
Execution halted
Package required but not available: ‘sdcTable’

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ecospat.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is 44.4Mb
  sub-directories of 1Mb or more:
    libs  44.1Mb
Package required but not available: ‘iCheck’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘elrm/libs/elrm.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Objects: ‘binomMCMC.o’, ‘functions.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘binomMCMC.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking: ‘hgu133plus2.db’ ‘lumi’
Namespaces in Imports field not imported from:
  ‘FNN’ ‘ggmap’ ‘simFrame’
  All declared Imports should be used.
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’ [80s/194s]
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
Package required but not available: ‘xcms’

Package suggested but not available for checking: ‘faahKO’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/EnvStats.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  input2.c:767:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/epanet2toolkit.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshote5d4335ad301.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshote5d4335ad301.png': No such file or directory
Quitting from lines 150-151 (epicontacts.Rmd) 
Error: processing vignette 'epicontacts.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘readr’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/EpiWeek.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Package required but not available: ‘rpanel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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/esmprep.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 24.1Mb
  sub-directories of 1Mb or more:
    libs  23.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Error in re-building vignettes:
  ...
==================================================
downloaded 4328 bytes

Table t2020_rk310 cached at /var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmpvVH477/eurostat/t2020_rk310_num_code_TF.rds

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

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

Table ten00081 cached at /var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmpvVH477/eurostat/ten00081_date_code_TF.rds
Quitting from lines 375-392 (eurostat_tutorial.Rmd) 
Error: processing vignette 'eurostat_tutorial.Rmd' failed with diagnostics:
there is no package called 'Cairo'
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’.
Functions or methods with usage in documentation object 'COMStop' but not in code:
  lapply sapply getItemClassName EnumValue createTypeVarName
Running examples in ‘excerptr-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_excerpts
> ### Title: Clone the Excerpts Code from <URL: github.com>
> ### Aliases: get_excerpts
> 
> ### ** Examples
> 
> path <- file.path(tempdir(), "excerpts")
> get_excerpts(directory = path, force = TRUE)
cloning into '/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmpNgExn7/excerpts'...
Error in git2r::clone(url = "https://github.com/fvafrCU/excerpts/", branch = branch,  : 
  Error in 'git2r_clone': SSL error: error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
Calls: get_excerpts -> <Anonymous> -> <Anonymous>
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > test_check("excerptr")
  cloning into '/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmpzCMAPS'...
  ── 1. Error: get (@test_basic.R#9)  ────────────────────────────────────────────
  SSL error: error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
  1: get_excerpts(directory = tempdir()) at testthat/test_basic.R:9
  2: git2r::clone(url = "https://github.com/fvafrCU/excerpts/", branch = branch, local_path = directory)
  3: git2r::clone(url = "https://github.com/fvafrCU/excerpts/", branch = branch, local_path = directory)
  
  3
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 4 SKIPPED: 0 FAILED: 1
  1. Error: get (@test_basic.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    exiftool  12.3Mb
Packages required but not available: ‘Rsamtools’ ‘GenomicAlignments’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: iteration 7 invokes undefined behavior [-Waggressive-loop-optimizations]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/expoRkit.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘pathClass’
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 16.6Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  15.2Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.2Mb
File ‘fastmatch/libs/fastmatch.so’:
  Found non-API call to R: ‘match5’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      4.7Mb
Found the following significant warnings:
  fasttext.cc:121:27: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
  fasttext.cc:137:27: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/fastTextR.Rcheck/00install.out’ for details.
Package required but not available: ‘glpkAPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  cgFbat.cpp:222:13: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  cgFbat.cpp:265:13: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  cgFbat.cpp:358:40: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  cgFbat.cpp:2210:14: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  rmatrix.cpp:23:8: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  rmatrix.cpp:23:23: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  rmatrix.cpp:33:8: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  rmatrix.cpp:33:23: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  rvector.cpp:23:8: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  rvector.cpp:34:8: 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/fbati.Rcheck/00install.out’ for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.9Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  32.3Mb
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    libs  21.9Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   5.3Mb
Running ‘test-as-dgCMatrix.R’ [3s/6s]
  Running ‘test-empty_array.R’ [3s/6s]
  Running ‘test-existence_collision.R’ [2s/5s]
  Running ‘test-hash.mapping.R’ [2s/5s]
  Running ‘test-hashing.R’ [3s/6s]
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
row.names<-:
  function(x, make.names, value)
row.names<-.ffdf:
  function(x, value)

row.names<-:
  function(x, make.names, value)
row.names<-.ffdf:
  function(x, value)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/fifer.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
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/FindIt.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 70-72 (lifeExpectancy.Rmd) 
Error: processing vignette 'lifeExpectancy.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/FisherEM.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages 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: ‘multipanelfigure’
Package required but not available: ‘flowWorkspace’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/frailtyHL.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
Found the following significant warnings:
  hcubature.c:923:12: warning: comparison of unsigned enum 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/frailtySurv.Rcheck/00install.out’ for details.
Found the following significant warnings:
  psplines.c:975:16: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  psplines.c:1087:15: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/freeknotsplines.Rcheck/00install.out’ for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    1.6Mb
Package suggested but not available for checking: ‘RTCGA.rnaseq’
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   8.4Mb
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    libs  17.8Mb
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
Package suggested but not available for checking: ‘WGCNA’
Package required but not available: ‘ROI.plugin.glpk’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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: strucchange
Loading required package: sandwich

Execution halted
Package suggested but not available for checking: ‘ArrayBin’
Package suggested but not available for checking: ‘DAAGbio’
GAMens: no visible global function definition for ‘predict.gam’
predict.GAMens: no visible global function definition for ‘predict.gam’
Undefined global functions or variables:
  predict.gam
Running examples in ‘GAMens-Ex.R’ failed
The error most likely occurred in:

> ### Name: GAMens
> ### Title: Applies the GAMbag, GAMrsm or GAMens ensemble classifier to a
> ###   data set
> ### Aliases: GAMens
> ### Keywords: models classif
> 
> ### ** Examples
> 
> 
> ## Load data (mlbench library should be loaded)
> library(mlbench)
> data(Ionosphere)
> 
> ## Train a GAMens ensemble,
> ## estimated using 4 nonparametric terms and 2 linear terms
> Ionosphere.GAMens <- GAMens(Class~s(V3,4)+s(V4,4)+s(V5,3)+s(V6,5)+V7+V8,
+ Ionosphere ,3 , autoform=FALSE, iter=10 )
Error in predict.gam(gam_model, oob_data, type = "response") : 
  could not find function "predict.gam"
Calls: GAMens
Execution halted
Package which this enhances but not available for checking: ‘doMPI’
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   5.9Mb
installed size is 62.1Mb
  sub-directories of 1Mb or more:
    libs  61.7Mb
installed size is 48.7Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     45.4Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  13.3Mb
Package in Depends field not imported from: ‘boot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.bincount: no visible global function definition for ‘sd’
.mom: no visible global function definition for ‘sd’
.mop: no visible global function definition for ‘quantile’
degld: no visible global function definition for ‘dbeta’
fit.egld: no visible global function definition for ‘sd’
fit.egld: no visible global function definition for ‘var’
fit.egld: no visible global function definition for ‘pchisq’
fit.gld: no visible global function definition for ‘sd’
fit.gld: no visible global function definition for ‘pchisq’
gboot: no visible global function definition for ‘boot’
lines.gld: no visible global function definition for ‘lines.default’
pegld: no visible global function definition for ‘pbeta’
plot.egld: no visible global function definition for ‘plot.default’
plot.egld: no visible global function definition for ‘abline’
plot.gld: no visible global function definition for ‘plot.default’
plot.gld: no visible global function definition for ‘abline’
qegld: no visible global function definition for ‘qbeta’
regld: no visible global function definition for ‘rbeta’
rrsgld: no visible global function definition for ‘runif’
Undefined global functions or variables:
  abline boot dbeta lines.default pbeta pchisq plot.default qbeta
  quantile rbeta runif sd var
Consider adding
  importFrom("graphics", "abline", "lines.default", "plot.default")
  importFrom("stats", "dbeta", "pbeta", "pchisq", "qbeta", "quantile",
             "rbeta", "runif", "sd", "var")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning in packageDescription("gputools") :
  no package 'gputools' was found
Error: processing vignette 'gcbd.Rnw' failed with diagnostics:
at gcbd.Rnw:860, subscript out of bounds
Execution halted
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘shinydashboard’
  All declared Imports should be used.
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.
Packages suggested but not available for checking: ‘qvalue’ ‘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  7.1Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.5Mb
Package required but not available: ‘ShortRead’

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/GeneFeST.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
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.
Unknown package ‘GeneticsDesign’ in Rd xrefs
Found the following significant warnings:
  mpi.c:3951:10: 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/GENLIB.Rcheck/00install.out’ for details.
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’ ‘AnnotationDbi’
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.1Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/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’.
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’.
Package suggested but not available for checking: ‘RGtk2’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 106-107 (IntroductionToGFD.Rmd) 
Error: processing vignette 'IntroductionToGFD.Rmd' failed with diagnostics:
there is no package called 'RGtk2'
Execution halted
Running examples in ‘GGEBiplotGUI-Ex.R’ failed
The error most likely occurred in:

> ### Name: GGEBiplot
> ### Title: GGEBiplotGUI: Interactive GGE Biplots in R
> ### Aliases: GGEBiplot
> 
> ### ** Examples
> 
> data(Ontario)
> GGEBiplot(Data = Ontario)
Warning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "ComboBox".
Calls: GGEBiplot -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Packages required but not available: ‘base2grob’ ‘gridGraphics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot61063259848a.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot61063259848a.png': No such file or directory
Quitting from lines 28-33 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'gglogo'

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

    fortify

Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Garamond"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Garamond"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Garamond"
Quitting from lines 46-52 (gglogo-alphabet.Rmd) 
Error: processing vignette 'gglogo-alphabet.Rmd' failed with diagnostics:
replacement has 1 row, data has 0
Execution halted
Error in re-building vignettes:
  ...
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Quitting from lines 142-143 (using_ggmcmc.Rmd) 
Error: processing vignette 'using_ggmcmc.Rmd' failed with diagnostics:
polygon edge not found
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.6Mb
Error in re-building vignettes:
  ...

Backtrace for this error:
#0  0x120b15579
#1  0x120b14945
#2  0x7fff93ac4529
sh: line 1: 71985 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//RtmpR5j1EM/x13116502cb2fa3a/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  0x125aa9579
#1  0x125aa8945
#2  0x7fff93ac4529
Quitting from lines 125-126 (ggsdc.Rmd) 
Error: processing vignette 'ggsdc.Rmd' failed with diagnostics:
X-13 has returned a non-zero exist status, which means that the current spec file cannot be processed for an unknown reason.
Execution halted
Running ‘test-all.R’ [1s/3s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  8: git2r::fetch(gitrepo, name = "github", credentials = credentials)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 9 SKIPPED: 0 FAILED: 8
  1. Error: Install a single package (@test_install.R#8) 
  2. Error: Install a single package, removing old install (@test_install.R#14) 
  3. Error: Install a single package w/o vignettes (@test_install.R#19) 
  4. Error: Install from a branch (@test_install.R#25) 
  5. Error: Install from a commit ref (@test_install.R#36) 
  6. Error: Install from a tag (@test_install.R#42) 
  7. Error: Install from a pull request (@test_install.R#49) 
  8. Error: (unknown) (@test_internal.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  openssl.c:420:31: warning: incompatible pointer types assigning to 'int (*)(EVP_CIPHER_CTX *, unsigned char *, const unsigned char *, unsigned int)' (aka 'int (*)(struct evp_cipher_ctx_st *, unsigned char *, const unsigned char *, unsigned int)') from 'int (EVP_CIPHER_CTX *, unsigned char *, const unsigned char *, size_t)' (aka 'int (struct evp_cipher_ctx_st *, unsigned char *, const unsigned char *, unsigned long)') [-Wincompatible-pointer-types]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/git2r.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
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  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is 40.0Mb
  sub-directories of 1Mb or more:
    libs  39.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Package which this enhances but not available for checking: ‘BRugs’
Running ‘bym.R’ [3s/8s]
Running the tests in ‘tests/bym.R’ failed.
Last 13 lines of output:
  + checkChain(kParams, c("intercept", "SDCountySpatial"))
  + dev.off()
  + 
  + kentucky = mergeBugsData(kentucky, kSummary)
  + 
  + if(require('sp', quietly=TRUE)) {
  +   pdf("spplotBym.pdf",height=4,width=8)
  +   print(spplot(kentucky, "FittedRateCounty.mean"))
  +   dev.off()
  + }
  + 
  + }
  Error in R2OpenBUGS::bugs(forBugs$ragged, inits = int2, model.file = "bym.txt",  : 
    Cannot find the OpenBUGS program
  Execution halted
installed size is 39.9Mb
  sub-directories of 1Mb or more:
    libs  39.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Execution halted
installed size is 58.1Mb
  sub-directories of 1Mb or more:
    libs  57.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/glpkAPI.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [2s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  5: RSQLite::SQLite
  6: getExportedValue(pkg, name)
  7: asNamespace(ns)
  8: getNamespace(ns)
  9: tryCatch(loadNamespace(name), error = function(e) stop(e))
  10: tryCatchList(expr, classes, parentenv, handlers)
  11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  12: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 132 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-sql.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘mutoss’
Running ‘testthat.R’ [7s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Loading required package: Gmisc
  Loading required package: Rcpp
  Loading required package: htmlTable
  ── 1. Error: (unknown) (@test-fig_caption.R#6)  ────────────────────────────────
  pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  1: rmarkdown::render(fn, output_file = file.path(td, "tmp.html")) at testthat/test-fig_caption.R:6
  2: pandoc_available(required_pandoc, error = TRUE)
  3: stop(paste(msg, collapse = " "), call. = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 311 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-fig_caption.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
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
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’.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/gpuR.Rcheck/00install.out’ for details.
Packages required but not available: ‘RGtk2’ ‘gWidgetsRGtk2’

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

Package suggested but not available for checking: ‘BiocStyle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Sxslt’
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Package unavailable to check Rd xrefs: ‘gRain’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/gridGraphics.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/GroupSeq.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Package suggested but not available for checking: ‘impute’
Error in re-building vignettes:
  ...
Warning 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:  1116 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//RtmpU0MCN3/x133e010f523d7/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  0x13006b579
#1  0x13006a945
#2  0x7fff93ac4529
Quitting from lines 33-34 (gunsales.Rmd) 
Error: processing vignette 'gunsales.Rmd' failed with diagnostics:
X-13 has returned a non-zero exist status, which means that the current spec file cannot be processed for an unknown reason.
Execution halted
Package required but not available: ‘RGtk2’

Package suggested but not available for checking: ‘cairoDevice’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/h5.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 122-128 (Basic_use.Rmd) 
Error: processing vignette 'Basic_use.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    libs  16.8Mb
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/hbmem.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: ‘rtracklayer’ ‘HiTC’

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

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

    filter

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

    layout

Loading required package: viridis
Loading required package: viridisLite

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

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

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

Quitting from lines 88-90 (heatmaply.Rmd) 
Error: processing vignette 'heatmaply.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘synbreed’
Packages suggested but not available for checking:
  ‘marray’ ‘affy’ ‘Biobase’ ‘limma’
Package required but not available: ‘ggimage’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Found the following significant warnings:
  Note: possible error in 'dgpd(x, xi = a, mu = 0, ': unused arguments (xi = a, mu = 0, beta = 1 - a) 
  Note: possible error in 'pgpd(q, xi = a, mu = 0, ': unused arguments (xi = a, mu = 0, beta = 1 - a) 
  Note: possible error in 'qgpd(p, xi = a, mu = 0, ': unused arguments (xi = a, mu = 0, beta = 1 - a) 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/HiDimMaxStable.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’.
build.clusters.spatial: no visible global function definition for
  ‘kmeans’
build.clusters.spatial: no visible global function definition for
  ‘points’
mubz.copula: no visible global function definition for ‘integrate’
perspcolor: no visible global function definition for ‘terrain.colors’
rCMS: no visible global function definition for ‘runif’
rSchlatherExcess: no visible global function definition for ‘runif’
simul.maxlik.maxstable: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  integrate kmeans points runif terrain.colors
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "points")
  importFrom("stats", "integrate", "kmeans", "runif")
to your NAMESPACE file.
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  6.7Mb
  sub-directories of 1Mb or more:
    highlight   1.0Mb
    libs        5.4Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   4.4Mb
Package suggested but not available for checking: ‘trackr’
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/HMMpa.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Package required but not available: ‘Rsamtools’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘RGtk2’ ‘cairoDevice’ ‘RGtk2Extras’
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R     1.9Mb
    doc   2.5Mb
File ‘hSDM/libs/hSDM.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘useful.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Objects: ‘hSDM.Nmixture.o’, ‘hSDM.Nmixture.iCAR.o’, ‘hSDM.ZIB.o’,
      ‘hSDM.ZIB.iCAR.alteration.o’, ‘hSDM.ZIB.iCAR.o’, ‘hSDM.ZIP.o’,
      ‘hSDM.ZIP.iCAR.alteration.o’, ‘hSDM.ZIP.iCAR.o’,
      ‘hSDM.binomial.o’, ‘hSDM.binomial.iCAR.o’, ‘hSDM.poisson.o’,
      ‘hSDM.poisson.iCAR.o’, ‘hSDM.siteocc.o’, ‘hSDM.siteocc.iCAR.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘HTSFilter’
Error in re-building vignettes:
  ...
  only letters, numbers, and delimiters '_' or '.', as these are safe characters
  for column names in R. [This is a message, not an warning or error]
  Note: levels of factors in the design contain characters other than
  letters, numbers, '_' and '.'. It is recommended (but not required) to use
  only letters, numbers, and delimiters '_' or '.', as these are safe characters
  for column names in R. [This is a message, not an warning or error]
  Note: levels of factors in the design contain characters other than
  letters, numbers, '_' and '.'. It is recommended (but not required) to use
  only letters, numbers, and delimiters '_' or '.', as these are safe characters
  for column names in R. [This is a message, not an warning or error]
converting counts to integer mode
  Note: levels of factors in the design contain characters other than
  letters, numbers, '_' and '.'. It is recommended (but not required) to use
  only letters, numbers, and delimiters '_' or '.', as these are safe characters
  for column names in R. [This is a message, not an warning or error]
  Note: levels of factors in the design contain characters other than
  letters, numbers, '_' and '.'. It is recommended (but not required) to use
  only letters, numbers, and delimiters '_' or '.', as these are safe characters
  for column names in R. [This is a message, not an warning or error]
  Note: levels of factors in the design contain characters other than
  letters, numbers, '_' and '.'. It is recommended (but not required) to use
  only letters, numbers, and delimiters '_' or '.', as these are safe characters
  for column names in R. [This is a message, not an warning or error]

Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    dict   1.3Mb
    libs   4.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
trying URL 'https://arxiv.org/e-print/1406.4806v1'
Content type 'application/x-eprint-tar' length 29273 bytes (28 KB)
==================================================
downloaded 28 KB

Quitting from lines 162-165 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   3.4Mb
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.
'library' or 'require' calls to packages already attached by Depends:
  ‘fastICA’ ‘mgcv’
  Please remove these calls from your code.
'library' or 'require' call to ‘wavethresh’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Package suggested but not available for checking: ‘Rglpk’
Running ‘testthat.R’ [5s/13s]
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 15.4Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   1.3Mb
    doc    3.2Mb
    libs   8.9Mb
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
Package suggested but not available for checking: ‘mixAK’
Running ‘testthat.R’ [3s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
         val
     })(Assessment.StockCode = "cod.27.47d20", Assessment.AssessmentYear = 2015L, Assessment.ContactPerson = "colin.millar@ices.dk", 
         Assessment.NameSystemProducedFile = "icesSAG R package version 1.3.2", Assessment.Fish_Data.Year = 2000L, 
         Assessment.Fish_Data.Year = 2001L, Assessment.Fish_Data.Year = 2002L, Assessment.Fish_Data.Year = 2003L, 
         Assessment.Fish_Data.Year = 2004L, Assessment.Fish_Data.Year = 2005L, Assessment.Fish_Data.Year = 2006L, 
         Assessment.Fish_Data.Year = 2007L, Assessment.Fish_Data.Year = 2008L, Assessment.Fish_Data.Year = 2009L, 
         Assessment.Fish_Data.Year = 2010L, Assessment.Fish_Data.Year = 2011L, Assessment.Fish_Data.Year = 2012L, 
         Assessment.Fish_Data.Year = 2013L, Assessment.Fish_Data.Year = 2014L, Assessment.Fish_Data.Year = 2015L)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1147 SKIPPED: 0 FAILED: 1
  1. Error: SAG upload (@test-test.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      1.7Mb
installed size is 40.1Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs  35.7Mb
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.
Warning in .local(object, ...) :
  some chains had errors; consider specifying chains = 1 to debug
Warning in .local(object, ...) :
  some chains had errors; consider specifying chains = 1 to debug
Quitting from lines 94-95 (Package_Introduction.Rmd) 
Error: processing vignette 'Package_Introduction.Rmd' failed with diagnostics:
Column `Rhats` must be a 1d atomic vector or a list
Execution halted
installed size is 26.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  24.5Mb
Package suggested but not available for checking: ‘PROcess’
Package unavailable to check Rd xrefs: ‘PROcess’
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/IDTurtle.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  12.2Mb
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//RtmplTxqUr/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’ [2s/4s]
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’
Package unavailable to check Rd xrefs: ‘minfi’
Running examples in ‘Inflation-Ex.R’ failed
The error most likely occurred in:

> ### Name: INFL.core_tf
> ### Title: Computes the triple filter core inflation
> ### Aliases: INFL.core_tf
> ### Keywords: core filter triple
> 
> ### ** Examples
> 
> ipca <- ipca_sub
> INFL.core_tf(subits.var=ipca$ipca_ts, weights = ipca$weights_ts)
sh: line 1: 15324 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//RtmpLWmcHe/x133852b6e78b0/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//RtmpLWmcHe/x133852b6e78b0/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  0x12e225579
#1  0x12e224945
#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
Missing link or links in documentation object 'ask.user.yn.question.Rd':
  ‘winDialog’

Missing link or links in documentation object 'check.for.updates.R.Rd':
  ‘winDialog’

Missing link or links in documentation object 'installr.Rd':
  ‘winDialog’

Missing link or links in documentation object 'os.manage.Rd':
  ‘winDialog’

Missing link or links in documentation object 'updateR.Rd':
  ‘winDialog’

See section 'Cross-references' in the 'Writing R Extensions' manual.
Packages suggested but not available for checking: ‘MLP’ ‘a4Base’
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’.
Error: package or namespace load failed for ‘ionicons’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/rsvg/libs/rsvg.so':
  dlopen(/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/rsvg/libs/rsvg.so, 6): Symbol not found: _OBJC_CLASS_$_NSAutoreleasePool
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/rsvg/libs/rsvg.so
  Expected in: flat namespace
 in /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/rsvg/libs/rsvg.so
Execution halted
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/rsvg/libs/rsvg.so':
  dlopen(/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/rsvg/libs/rsvg.so, 6): Symbol not found: _OBJC_CLASS_$_NSAutoreleasePool
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/rsvg/libs/rsvg.so
  Expected in: flat namespace
 in /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/rsvg/libs/rsvg.so
Calls: <Anonymous> ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
Execution halted

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.
Error: package or namespace load failed for ‘ionicons’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/rsvg/libs/rsvg.so':
  dlopen(/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/rsvg/libs/rsvg.so, 6): Symbol not found: _OBJC_CLASS_$_NSAutoreleasePool
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/rsvg/libs/rsvg.so
  Expected in: flat namespace
 in /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/rsvg/libs/rsvg.so
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps)
   }, error 
Execution halted
Package suggested but not available for checking: ‘rhdf5’
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   6.8Mb
Found the following significant warnings:
  Note: possible error in 'get.smiles(x, aromatic = T, ': unused arguments (aromatic = T, type = "generic") 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/iqspr.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  7.6Mb
  sub-directories of 1Mb or more:
    data   6.8Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘gridExtra’ ‘rBayesianOptimization’
  All declared Imports should be used.
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
Package suggested but not available for checking: ‘PMA’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   4.7Mb
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘GGally’ ‘GPArotation’ ‘PMCMR’ ‘R6’ ‘afex’ ‘car’
  ‘emmeans’ ‘ggridges’ ‘lavaan’ ‘multcomp’ ‘mvnormtest’ ‘psych’ ‘vcd’
  ‘vcdExtra’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   2.8Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  14.2Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘curl’ ‘utils’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
Namespace in Imports field not imported from: ‘stinepack’
  All declared Imports should be used.
Missing or unexported objects:
  ‘MVN::hzTest’ ‘MVN::mardiaTest’ ‘MVN::uniNorm’
Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘org.Hs.eg.db’
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/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  6.9Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   3.4Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.8Mb
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: 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
Package suggested but not available for checking: ‘Rgraphviz’
Error in re-building vignettes:
  ...

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: relations
Loading required package: sets
Loading required namespace: Rgraphviz
Failed with error:  ‘there is no package called ‘Rgraphviz’’
Loading required namespace: Rgraphviz
Failed with error:  ‘there is no package called ‘Rgraphviz’’
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'kst.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file ./kst-012.pdf): PDF inclusion: required page does
 not exist <0>
 ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  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 16.4Mb
  sub-directories of 1Mb or more:
    libs          11.4Mb
    testdata       1.8Mb
    vignettedata   2.0Mb
Running ‘testthat.R’ [6s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(lasvmR)
  lasvmR loaded.
  > 
  > test_check("lasvmR")
  ── 1. Failure: walltime works roughly as expected (@test_Parameter.R#37)  ──────
  mT[3] is not strictly less than 10. Difference: 1.11
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 4 SKIPPED: 0 FAILED: 1
  1. Failure: walltime works roughly as expected (@test_Parameter.R#37) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  tinycthread.c:302:43: warning: incompatible pointer types passing 'const struct _ttherad_timespec *' to parameter of type 'const struct timespec *' [-Wincompatible-pointer-types]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/later.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 40-43 (Intro_to_lavaanPlot.Rmd) 
Error: processing vignette 'Intro_to_lavaanPlot.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/lava.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'lazyeval-old.Rmd' failed with diagnostics:
there is no package called ‘markdown’
Execution halted
Running examples in ‘lcyanalysis-Ex.R’ failed
The error most likely occurred in:

> ### Name: bearpower
> ### Title: bear power technical analysis function
> ### Aliases: bearpower
> 
> ### ** Examples
> 
> library(quantmod)
Loading required package: xts
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

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

This message is shown once per session and may be disabled by setting 
options("getSymbols.warning4.0"=FALSE). See ?getSymbols for details.
Warning in download.file(paste(google.URL, "q=", Symbols.name, "&startdate=",  :
  cannot open URL 'http://finance.google.com/finance/historical?q=AAPL&startdate=Jan+01,+2007&enddate=Mar+25,+2018&output=csv': HTTP status was '403 Forbidden'
Error in download.file(paste(google.URL, "q=", Symbols.name, "&startdate=",  : 
  cannot open URL 'http://finance.google.com/finance/historical?q=AAPL&startdate=Jan+01,+2007&enddate=Mar+25,+2018&output=csv'
Calls: getSymbols -> do.call -> getSymbols.google -> download.file
Execution halted
Found the following significant warnings:
  partial_order.cpp:45:51: 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/ldat.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘rtracklayer’
Errors in running code in vignettes:
when running code in ‘addTracks.Rnw’
  ...
+     flip = TRUE)

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

> grid.newpage()

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 67-77 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
File ‘leaps/libs/leaps.so’:
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Object: ‘leaps.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘scales’ ‘tidyverse’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      2.9Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/libstableR.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘gWidgetsRGtk2’ ‘RGtk2’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 272-273 (Understanding_lime.Rmd) 
Error: processing vignette 'Understanding_lime.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   7.8Mb
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’.
installed size is 26.5Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    doc        1.5Mb
    libs      21.0Mb
    testdata   1.5Mb
Running ‘AAAtest-all.R’ [167s/354s]
Running the tests in ‘tests/AAAtest-all.R’ failed.
Last 13 lines of output:
  +     require(pkg, character.only=TRUE, quietly=TRUE)
  +     test_check(pkg)
  +     print(warnings()) # TODO? catch most of these by expect_warning(..)
  + } else {
  +     cat( "package 'testthat' not available, cannot run unit tests\n" )
  + }
  ── 1. Failure: missDataFun (@test-formulaEval.R#210)  ──────────────────────────
  system.time(g(X))["elapsed"] is not strictly less than 1. Difference: 0.082
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 726 SKIPPED: 0 FAILED: 1
  1. Failure: missDataFun (@test-formulaEval.R#210) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘LDheatmap’

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
'library' or 'require' calls in package code:
  ‘mclust’ ‘rgl’ ‘tkrplot’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  lsdall.c:2078:21: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2200:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2209:12: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2219:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2225:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/logspline.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  ‘graph’ ‘PairViz’ ‘Rgraphviz’ ‘RDRToolbox’
Error in re-building vignettes:
  ...
Warning 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: tcltk
Quitting from lines 686-690 (minorities.Rmd) 
Error: processing vignette 'minorities.Rmd' failed with diagnostics:
there is no package called 'PairViz'
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
Package suggested but not available for checking: ‘Rsymphony’
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/lqmm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 15-33 (README.Rmd) 
Error: processing vignette 'README.Rmd' failed with diagnostics:
object 'params' not found
Execution halted
installed size is 45.3Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  43.5Mb
Error in re-building vignettes:
  ...
Warning in engine$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 18-23 (lspline.Rmd) 
Error: processing vignette 'lspline.Rmd' failed with diagnostics:
object 'params' not found
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.9Mb
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
installed size is 25.0Mb
  sub-directories of 1Mb or more:
    libs  24.8Mb
Package suggested but not available for checking: ‘imager’
Found the following significant warnings:
  Warning: The post-install step did not complete successfully
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/magick.Rcheck/00install.out’ for details.
installed size is 23.2Mb
  sub-directories of 1Mb or more:
    doc    6.8Mb
    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/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 15.2Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
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]="./webshota2f8456f07ad.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshota2f8456f07ad.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  7.2Mb
  sub-directories of 1Mb or more:
    libs   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.
Warning in normalizePath(f2) :
  path[1]="./webshoteb2a363517c9.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshoteb2a363517c9.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 32.7Mb
  sub-directories of 1Mb or more:
    mapdata  32.6Mb
Package required but not available: ‘LPmerge’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  perspective.c:12:23: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/mapproj.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 95-100 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  mapclip.c:321:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/maps.Rcheck/00install.out’ for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   5.3Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   6.2Mb
Package suggested but not available for checking: ‘ASGSCA’
Package which this enhances but not available for checking: ‘graph’
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Found the following significant warnings:
  Note: possible error in 'writeLines(as.character(yy), ': unused argument (file = outfile) 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/matR.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: ‘kangar00’
Package unavailable to check Rd xrefs: ‘kangar00’
Packages required but not available: ‘Rglpk’ ‘glpkAPI’

Package suggested but not available for checking: ‘cplexAPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   5.4Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/mclcar.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:
    doc   2.7Mb
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    libs  23.2Mb
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/mdhglm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   3.9Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   6.7Mb
Package suggested but not available for checking: ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: GenABEL
Loading required package: MASS
Loading required package: GenABEL.data
Loading required package: SKAT
Loading required package: pedgene
Loading required package: Matrix
Loading required package: CompQuadForm
Loading required package: survey
Loading required package: grid
Loading required package: survival

Attaching package: 'survey'

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

    dotchart

Loading required package: kinship2
Loading required package: quadprog
Quitting from lines 694-696 (mega2rtutorial.Rmd) 
Error: processing vignette 'mega2rtutorial.Rmd' failed with diagnostics:
there is no package called 'TxDb.Hsapiens.UCSC.hg19.knownGene'
Execution halted
Package suggested but not available for checking: ‘ggimage’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 29-37 (meme.Rmd) 
Error: processing vignette 'meme.Rmd' failed with diagnostics:
there is no package called 'ggimage'
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  6.4Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   3.3Mb
Package required but not available: ‘rattle’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Quitting from lines 26-27 (MetaIntegrator.Rmd) 
Error: processing vignette 'MetaIntegrator.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
Execution halted
Packages suggested but not available for checking:
  ‘annaffy’ ‘hgu133plus2.db’ ‘hgu133a.db’ ‘hgu95av2.db’
Packages suggested but not available for checking:
  ‘GEOquery’ ‘affy’ ‘hgu133plus2.db’ ‘doSMP’ ‘impute’
Packages suggested but not available for checking:
  ‘HTSFilter’ ‘DESeq’ ‘DESeq2’
Errors in running code in vignettes:
when running code in ‘metaRNASeq.Rnw’
  ...

> options(width = 60)

> library(metaRNASeq)

> library(DESeq2)

  When sourcing ‘metaRNASeq.R’:
Error: there is no package called ‘DESeq2’
Execution halted
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
Running examples in ‘metaSEM-Ex.R’ failed
The error most likely occurred in:

> ### Name: indirectEffect
> ### Title: Estimate the asymptotic covariance matrix of standardized or
> ###   unstandardized indirect and direct effects
> ### Aliases: indirectEffect
> ### Keywords: compute effect sizes
> 
> ### ** Examples
> 
> ## A correlation matrix as input
> x <- matrix(c(1, 0.4, 0.2, 0.4, 1, 0.3, 0.2, 0.3, 1), ncol=3)
> dimnames(x) <- list( c("y", "m", "x"), c("y", "m", "x") )
> indirectEffect(x, n=300)
Error in runHelper(model, frontendStart, intervals, silent, suppressWarnings,  : 
  c++ exception (unknown reason)
Calls: indirectEffect -> mxRun -> runHelper
Execution halted
Found the following significant warnings:
  Warning: working directory was changed to ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/MetaSubtract.Rcheck/MetaSubtract/extdata’, resetting
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 47-49 (metaviz.Rmd) 
Error: processing vignette 'metaviz.Rmd' failed with diagnostics:
there is no package called 'Cairo'
Execution halted
Found the following significant warnings:
  binomial-twostage.cpp:78:4: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  binomial-twostage.cpp:280:4: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/mets.Rcheck/00install.out’ for details.
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  12.6Mb
    misc   1.1Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-13


Execution halted
package ‘survival’ exists but was not installed under R >= 2.10.0 so xrefs cannot be checked
Package suggested but not available for checking: ‘grasp2db’
Package suggested but not available for checking: ‘structSSI’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
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’ [14s/14s]
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’
Error in re-building vignettes:
  ...
Content type 'application/x-gzip' length 6249673 bytes (6.0 MB)
==================================================
downloaded 6.0 MB

Warning in fread("MilData/Musk/musk1norm.svm", header = FALSE) :
  Starting data input on line 2 and discarding line 1 because it has too few or too many items to be column names or data: # Generated by musk_2_svm(/pro/webagents/stu/mil//experiments/musk//data/clean1.data, /pro/webagents/stu/mil//experiments/musk//generate_data/clean1.svm)
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.

Execution halted
Packages suggested but not available for checking: ‘sybilSBML’ ‘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.
Quitting from lines 21-25 (MINVALintroduction.Rmd) 
Error: processing vignette 'MINVALintroduction.Rmd' failed with diagnostics:
there is no package called 'sybilSBML'
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   4.7Mb
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: comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:91:41: warning: comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:95:17: warning: 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.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/mixor.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
cband: no visible global function definition for ‘qnorm’
cband: no visible global function definition for ‘plot’
gfun: no visible global function definition for ‘dnorm’
init.rand: no visible global function definition for ‘lm’
init.rand: no visible global function definition for ‘coef’
init.rand: no visible global function definition for ‘rnorm’
mixreg: no visible global function definition for ‘lm’
mixreg: no visible global function definition for ‘coef’
mixreg: no visible global function definition for ‘fitted’
par.uin: no visible global function definition for ‘par’
plot.cband: no visible global function definition for ‘plot’
plot.cband: no visible global function definition for ‘points’
plot.cband: no visible global function definition for ‘lines’
plot.cband: no visible global function definition for ‘title’
plot.mresid: no visible global function definition for ‘plot’
plot.mresid: no visible global function definition for ‘polygon’
qq.mix: no visible global function definition for ‘qnorm’
qq.mix: no visible global function definition for ‘plot’
qq.mix: no visible global function definition for ‘polygon’
simmix: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  coef dnorm fitted lines lm par plot points polygon qnorm rnorm title
Consider adding
  importFrom("graphics", "lines", "par", "plot", "points", "polygon",
             "title")
  importFrom("stats", "coef", "dnorm", "fitted", "lm", "qnorm", "rnorm")
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
Error in re-building vignettes:
  ...
Warning 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 87-98 (pitch_plotting.Rmd) 
Error: processing vignette 'pitch_plotting.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
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’ ‘GEOquery’ ‘BiocStyle’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 27-28 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
Execution halted
Package suggested but not available for checking: ‘MM2Sdata’
Error in re-building vignettes:
  ...
Quitting from lines 80-84 (MM2S.Rnw) 
Error: processing vignette 'MM2S.Rnw' failed with diagnostics:
there is no package called 'MM2Sdata'
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.7Mb
    libs   2.7Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
Running ‘testthat.R’ [62s/147s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > test_check("MonetDBLite")
  Loading required package: MonetDBLite
  ── 1. Failure: we can read sql-specific types (@test_02_dbi.R#406)  ────────────
  res$d not equal to res$d1.
  Mean relative difference: 0.07219107
  
  [1] "E"
  [1] "H"
  [1] "M"
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 345 SKIPPED: 12 FAILED: 1
  1. Failure: we can read sql-specific types (@test_02_dbi.R#406) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    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/MortHump.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
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 39.5Mb
  sub-directories of 1Mb or more:
    libs  39.1Mb
Running examples in ‘mssqlR-Ex.R’ failed
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/mstR.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Namespaces in Imports field not imported from:
  ‘hms’ ‘methods’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is 56.9Mb
  sub-directories of 1Mb or more:
    libs  56.7Mb
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/MultiPhen.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
row.names<-:
  function(x, make.names, value)
row.names<-.model.selection:
  function(x, value)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.7Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Package unavailable to check Rd xrefs: ‘Biostrings’
Errors in running code in vignettes:
when running code in ‘test-vignette.ipynbmeta’
  ...

  When tangling ‘test-vignette.ipynbmeta’:
Error: Either IPython 3+ or Jupyter has to be installed, but neither could be called.
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'test-vignette.ipynbmeta' failed with diagnostics:
Either IPython 3+ or Jupyter has to be installed, but neither could be called.
Execution halted
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ncappc.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Package suggested but not available for checking: ‘BiocInstaller’
installed size is  6.2Mb
  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  7.9Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   4.3Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   4.3Mb
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.
AdjWGCNAFDR: no visible binding for global variable ‘cor’
Adjcor: no visible global function definition for ‘cor’
K: no visible global function definition for ‘integrate’
checkvar: no visible binding for global variable ‘var’
ipsen : K: no visible global function definition for ‘integrate’
ipsen : mydistfun: no visible global function definition for
  ‘integrate’
optimal_gamma: no visible global function definition for ‘uniroot’
optimal_gamma_dir: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  cor integrate uniroot var
Consider adding
  importFrom("stats", "cor", "integrate", "uniroot", "var")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘devtools’
  All declared Imports should be used.
Packages suggested but not available for checking:
  ‘BiocStyle’ ‘graphite’ ‘NFPdata’
Error in re-building vignettes:
  ...
Quitting from lines 10-11 (NFP.Rnw) 
Error: processing vignette 'NFP.Rnw' failed with diagnostics:
there is no package called 'BiocStyle'
Execution halted
Running ‘testthat.R’ [2s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── 1. Failure: attrnames finds the names of the attributes of a data frame (@tes
  attrnames(y) not equal to c("names", "row.names", "class").
  2/3 mismatches
  x[2]: "class"
  y[2]: "row.names"
  
  x[3]: "row.names"
  y[3]: "class"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 21 SKIPPED: 0 FAILED: 1
  1. Failure: attrnames finds the names of the attributes of a data frame (@test-attribute_names.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
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/nimble.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 34.1Mb
  sub-directories of 1Mb or more:
    CppCode        1.1Mb
    R              5.8Mb
    classic-bugs   1.5Mb
    include        5.6Mb
    libs          18.3Mb
    tests          1.2Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
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.
Error: processing vignette 'vignette_get_nltt_values.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 ‘nmslibR-Ex.R’ failed
The error most likely occurred in:

> ### Name: dgCMatrix_2scipy_sparse
> ### Title: conversion of an R dgCMatrix to a scipy sparse matrix
> ### Aliases: dgCMatrix_2scipy_sparse
> 
> ### ** Examples
> 
> 
> if (reticulate::py_available() && reticulate::py_module_available("scipy")) {
+ 
+   library(nmslibR)
+ 
+   data = c(1, 0, 2, 0, 0, 3, 4, 5, 6)
+ 
+   dgcM = Matrix::Matrix(data = data, nrow = 3,
+ 
+                         ncol = 3, byrow = TRUE,
+ 
+                         sparse = TRUE)
+ 
+   print(dim(dgcM))
+ 
+   res = dgCMatrix_2scipy_sparse(dgcM)
+ 
+   print(res$shape)
+ }
[1] 3 3
Error in py_call_impl(callable, dots$args, dots$keywords) : 
  TypeError: could not interpret data type

Detailed traceback: 
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/scipy/sparse/compressed.py", line 52, in __init__
    self.data = np.array(data, copy=copy, dtype=getdtype(dtype, data))
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/scipy/sparse/sputils.py", line 101, in getdtype
    raise TypeError("could not interpret data type")
Calls: dgCMatrix_2scipy_sparse -> <Anonymous> -> py_call_impl
Execution halted
Running ‘testthat.R’ [3s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/scipy/sparse/compressed.py", line 52, in __init__
      self.data = np.array(data, copy=copy, dtype=getdtype(dtype, data))
    File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/scipy/sparse/sputils.py", line 101, in getdtype
      raise TypeError("could not interpret data type")
  1: dgCMatrix_2scipy_sparse(dgcM) at testthat/test-nmslibR_pkg.R:115
  2: SCP$sparse$csc_matrix(reticulate::tuple(dgc_mat_object@x, dgc_mat_object@i, dgc_mat_object@p), 
         shape = reticulate::tuple(dgc_mat_object@Dim[1], dgc_mat_object@Dim[2]))
  3: py_call_impl(callable, dots$args, dots$keywords)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 3 SKIPPED: 11 FAILED: 1
  1. Error: the 'dgCMatrix_2scipy_sparse' returns the correct output (@test-nmslibR_pkg.R#115) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 197-201 (parameter-table.Rmd) 
Error: processing vignette 'parameter-table.Rmd' failed with diagnostics:
java.lang.NoClassDefFoundError: javax/xml/bind/JAXBException
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 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
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’.
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.
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/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’.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   7.2Mb
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]="./webshot808d37fb0bec.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot808d37fb0bec.png': No such file or directory
Quitting from lines 61-71 (nyc_taxi.Rmd) 
Error: processing vignette 'nyc_taxi.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
File ‘obliclus/libs/obliclus.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘random_cluster_C.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘random_cluster_C.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   2.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 75.3Mb
  sub-directories of 1Mb or more:
    libs  74.8Mb
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Expected match: "The length value"
  Actual message: "c++ exception (unknown reason)"
  
  ── 2. Failure: OLC encoding throws an error with odd-numbered requested lengths 
  `x` threw an error with unexpected message.
  Expected match: "The length value"
  Actual message: "c++ exception (unknown reason)"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 34 SKIPPED: 1 FAILED: 2
  1. Failure: OLC encoding throws an error with odd-numbered requested lengths below 8 (@test_encoding.R#20) 
  2. Failure: OLC encoding throws an error with odd-numbered requested lengths below 8 (@test_encoding.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘ROI.plugin.glpk’
Running examples in ‘ompr.roi-Ex.R’ failed
The error most likely occurred in:

> ### Name: with_ROI
> ### Title: Configures a solver based on 'ROI'
> ### Aliases: with_ROI
> 
> ### ** Examples
> 
> library(magrittr)
> library(ompr)
> library(ROI)
ROI.plugin.scs: R Optimization Infrastructure
Registered solver plugins: nlminb, alabama, deoptim, ecos, ipop, lpsolve, msbinlp, nloptr, optimx, quadprog, scs.
Default solver: auto.
> library(ROI.plugin.glpk)
Error in library(ROI.plugin.glpk) : 
  there is no package called ‘ROI.plugin.glpk’
Execution halted
Running ‘testthat.R’ [17s/36s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  Attaching package: 'magrittr'
  
  The following objects are masked from 'package:testthat':
  
      equals, is_less_than, not
  
  > library(ROI)
  ROI.plugin.scs: R Optimization Infrastructure
  Registered solver plugins: nlminb, alabama, deoptim, ecos, ipop, lpsolve, msbinlp, nloptr, optimx, quadprog, scs.
  Default solver: auto.
  > library(ROI.plugin.glpk)
  Error in library(ROI.plugin.glpk) : 
    there is no package called 'ROI.plugin.glpk'
  Execution halted
MLparameters: no visible global function definition for ‘optim’
comp.freq: no visible global function definition for ‘x11’
comp.freq: no visible global function definition for ‘par’
comp.freq: no visible global function definition for ‘plot’
Undefined global functions or variables:
  optim par plot x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "par", "plot")
  importFrom("stats", "optim")
to your NAMESPACE file.
Package suggested but not available for checking: ‘ontologyPlot’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 80-92 (intro-to-ontologyX.Rmd) 
Error: processing vignette 'intro-to-ontologyX.Rmd' failed with diagnostics:
there is no package called 'ontologyPlot'
Execution halted
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 113.2Mb
  sub-directories of 1Mb or more:
    R         2.4Mb
    libs    103.3Mb
    models    4.7Mb
Running examples in ‘OpenMx-Ex.R’ failed
The error most likely occurred in:

> ### Name: OpenMx
> ### Title: OpenMx: An package for Structural Equation Modeling and Matrix
> ###   Algebra Optimization
> ### Aliases: OpenMx OpenMx-package
> 
> ### ** Examples
> 
> library(OpenMx)
> data(demoOneFactor)
> # ===============================
> # = Make and run a 1-factor CFA =
> # ===============================
> 
> latents  = c("G") # the latent factor
> manifests = names(demoOneFactor) # manifest variables to be modeled
> # ====================
> # = Make the MxModel =
> # ====================
> m1 <- mxModel("One Factor", type = "RAM", 
+ 	manifestVars = manifests, latentVars = latents, 
+ 	mxPath(from = latents, to = manifests),
+ 	mxPath(from = manifests, arrows = 2),
+ 	mxPath(from = latents, arrows = 2, free = FALSE, values = 1.0),
+ 	mxData(cov(demoOneFactor), type = "cov", numObs = 500)
+ )
> 
> # ===============================
> # = mxRun it and get a summary! =
> # ===============================
> 
> m1 = mxRun(m1)
Running One Factor with 10 parameters
Error in runHelper(model, frontendStart, intervals, silent, suppressWarnings,  : 
  c++ exception (unknown reason)
Calls: mxRun -> runHelper
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/OpenRepGrid.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.3Mb
Running ‘testthat.R’ [19s/47s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  5: sapply(1:nSheets, function(i) isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]])))
  6: lapply(X = X, FUN = FUN, ...)
  7: FUN(X[[i]], ...)
  8: isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]]))
  9: all.equal(x$colWidths[[i]], y$colWidths[[i]])
  10: all.equal.list(x$colWidths[[i]], y$colWidths[[i]])
  11: attr.all.equal(target, current, ...)
  12: mode(current)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 505 SKIPPED: 2 FAILED: 1
  1. Error: loadWorkbook from different sources (@test-read_sources.R#49) 
  
  Error: testthat unit tests failed
  Execution halted
Packages suggested but not available for checking:
  ‘Biobase’ ‘annotate’ ‘GO.db’ ‘org.At.tair.db’
Package which this enhances but not available for checking: ‘CBPS’
Error in re-building vignettes:
  ...
sh: +RTS: command not found
Warning in system(command) : error in running command
Error: processing vignette 'optparse.Rrst' failed with diagnostics:
pandoc document conversion failed with error 127
Execution halted
Package required but not available: ‘ROracle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘IsoGene’
File ‘OriGen/libs/OriGen.so’:
  Found ‘__gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__gfortran_st_read’, possibly from ‘read’ (Fortran)
    Object: ‘OriGen.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  ccaRevolution.c:31:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:44:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:97:23: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:98:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:110:23: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:111:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/osc.Rcheck/00install.out’ for details.
Running examples in ‘osi-Ex.R’ failed
The error most likely occurred in:

> ### Name: extract_id
> ### Title: Extract components from OSI metadata
> ### Aliases: extract_id extract_keywords extract_name extract_superseded
> ###   extractors
> 
> ### ** Examples
> 
> 
> #Get the names of all licenses
> all_license_metadata <- license_list()
Error in curl::curl_fetch_memory(url, handle = handle) : 
  SSL certificate problem: Invalid certificate chain
Calls: license_list ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
Running ‘testthat.R’ [1s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  8: curl::curl_fetch_memory(url, handle = handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 8
  1. Error: All licenses can be retrieved (@test_connectors.R#6) 
  2. Error: Keyword retrieval works (@test_connectors.R#14) 
  3. Error: ID retrieval works (@test_connectors.R#22) 
  4. Error: Content retrieval works (@test_connectors.R#29) 
  5. Error: licenses IDs can be retrieved (@test_extractors.R#4) 
  6. Error: licenses names can be retrieved (@test_extractors.R#11) 
  7. Error: licenses superseded states can be retrieved (@test_extractors.R#18) 
  8. Error: licenses keywords can be retrieved (@test_extractors.R#25) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   3.7Mb
Package required but not available: ‘Rglpk’

Package suggested but not available for checking: ‘Rcplex’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   1.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$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
Info message:
Couldn't find 'pandoc'!
Pandoc version is set to '1.16', use `set_pandoc_version` to change the settings if necessary.
Running ‘testthat.R’ [12m/27m]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
  > ## GNU General Public License for more details.
  > ##
  > ## You should have received a copy of the GNU General Public License
  > ## along with parallelDist. If not, see <http://www.gnu.org/licenses/>.
  > 
  > library(testthat)
  > library(parallelDist)
  > # workaround for error "cannot open file 'startup.Rs': No such file or directory"
  > Sys.setenv("R_TESTS" = "")
  > test_check("parallelDist")
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 230139 SKIPPED: 0 FAILED: 0
  
  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.
Packages suggested but not available for checking: ‘pcalg’ ‘Rgraphviz’
Running examples in ‘ParallelPC-Ex.R’ failed
The error most likely occurred in:

> ### Name: IDA_parallel
> ### Title: Estimate Total Causal Effects using the IDA_parallel Algorithm
> ### Aliases: IDA_parallel
> 
> ### ** Examples
> 
> ##########################################
> ## Using IDA_parallel without mem.efficeient
> ##########################################
> library(bnlearn)

Attaching package: ‘bnlearn’

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

    sigma

> library(pcalg)
Error in library(pcalg) : there is no package called ‘pcalg’
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.
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]="./webshot1661cb2ef65e.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot1661cb2ef65e.png': No such file or directory
Quitting from lines 67-110 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package required but not available: ‘Rglpk’

Package suggested but not available for checking: ‘Rsymphony’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘parmigene/libs/parmigene.so’:
  Found ‘_rand_r’, possibly from ‘rand_r’ (C)
    Object: ‘points.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Error in re-building vignettes:
  ...
Quitting from lines 11-14 (patternplot-intro.Rmd) 
Error: processing vignette 'patternplot-intro.Rmd' failed with diagnostics:
there is no package called 'Cairo'
Execution halted
Packages required but not available: ‘pbdMPI’ ‘pbdSLAP’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘pbdPROF’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/pbdMPI.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/pbdPROF.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/pcaL1.Rcheck/00install.out’ for details.
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   2.1Mb
    libs   5.8Mb
Package required but not available: ‘strvalidator’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
pcse : extractLMvar: no visible global function definition for
  ‘model.frame’
pcse: no visible global function definition for ‘model.matrix’
pcse: no visible global function definition for ‘na.omit’
pcse: no visible global function definition for ‘resid’
pcse: no visible global function definition for ‘pt’
Undefined global functions or variables:
  model.frame model.matrix na.omit pt resid
Consider adding
  importFrom("stats", "model.frame", "model.matrix", "na.omit", "pt",
             "resid")
to your NAMESPACE file.
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    libs    5.6Mb
    share  11.9Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/pdolsms.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  spectrum.c:707:14: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:715:20: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1606:41: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1654:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1654:63: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Peaks.Rcheck/00install.out’ for details.
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’.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘devtools’ ‘ggplot2’ ‘haven’ ‘tidyverse’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/permGPU.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/phalen.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  LJMA_arms.c:297:11: warning: comparison of array 'env->p' equal to a null pointer is always false [-Wtautological-pointer-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PhaseType.Rcheck/00install.out’ for details.
File ‘PhaseType/libs/PhaseType.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘LJMA_arms.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  phreeqcpp/cvode.cpp:3783:8: warning: explicitly assigning value of variable of type 'realtype' (aka 'double') to itself [-Wself-assign]
  phreeqcpp/model.cpp:3047:7: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  phreeqcpp/model.cpp:3048:7: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:142:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:155:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:167:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:179:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:193:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:205:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/transport.cpp:630:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/phreeqc.Rcheck/00install.out’ for details.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
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 normalizePath(f2) :
  path[1]="./webshot62991a4e01b5.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot62991a4e01b5.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  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Error in re-building vignettes:
  ...
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.7.1 (2016-02-15) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.21.0 (2016-10-30) successfully loaded. See ?R.oo for help.

Attaching package: ‘R.oo’

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

    getClasses, getMethods

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

    attach, detach, gc, load, save

Loading required package: ape
Loading required package: compoisson
Loading required package: MASS
Loading required package: ggplot2

Execution halted
Found the following significant warnings:
  Note: possible error in 'try(xtriple, ftriple, ': unused arguments (lfmid, 1, 2) 
  Note: possible error in 'try(xtriple, ftriple, ': unused arguments (rfmid, 2, 3) 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/phyreg.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’.
inf: no visible global function definition for ‘tail’
phyfromnewick: no visible global function definition for ‘head’
phyreg : inphyreg : merge.formulae.ag: no visible global function
  definition for ‘update’
phyreg : inphyreg : merge.formula.test.ag: no visible global function
  definition for ‘reformulate’
phyreg : inphyreg: no visible global function definition for
  ‘as.formula’
phyreg : inphyreg: no visible global function definition for
  ‘model.frame’
phyreg : inphyreg: no visible binding for global variable ‘na.omit’
phyreg : inphyreg: no visible global function definition for
  ‘model.matrix’
phyreg : inphyreg: no visible global function definition for ‘lm’
phyreg : inphyreg: no visible global function definition for ‘lm.wfit’
phyreg : inphyreg: no visible global function definition for ‘pf’
phyreg : inphyreg: no visible global function definition for ‘coef’
Undefined global functions or variables:
  as.formula coef head lm lm.wfit model.frame model.matrix na.omit pf
  reformulate tail update
Consider adding
  importFrom("stats", "as.formula", "coef", "lm", "lm.wfit",
             "model.frame", "model.matrix", "na.omit", "pf",
             "reformulate", "update")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PhySortR.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
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/picante.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.
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]="./webshot6b1222363e18.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot6b1222363e18.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
Package suggested but not available for checking: ‘ReportingTools’
Packages required but not available:
  ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’ ‘rggobi’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    libs  23.7Mb
Found the following significant warnings:
  hcubature.c:917:15: warning: comparison of unsigned enum 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/planar.Rcheck/00install.out’ for details.
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.
Running examples in ‘plogr-Ex.R’ failed
The error most likely occurred in:

> ### Name: plogr-package
> ### Title: The 'plog' C++ Logging Library
> ### Aliases: plogr plogr-package
> 
> ### ** Examples
> 
> plogr_demo <- Rcpp::cppFunction(depends = "plogr", '
+ // C++ code begin
+ #include <plogr.h>
+ 
+ RObject plogr_demo() {
+   plog::init_r(plog::info);
+   LOG_INFO << "shown";
+   LOG_DEBUG << "not shown";
+   plog::init_r("DEBUG");
+   LOG_DEBUG << "shown now";
+   return R_NilValue;
+ }
+ 
+ #include <Rcpp.h> // not necessary to use plogr
+ // C++ code end
+ '
+ )
In file included from file6fe9456fb03d.cpp:3:
In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/Rcpp/include/Rcpp.h:40:
/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/Rcpp/include/Rcpp/Vector.h:60:10: fatal error: 'Rcpp/vector/MatrixRow.h' file not found
#include <Rcpp/vector/MatrixRow.h>
         ^~~~~~~~~~~~~~~~~~~~~~~~~
1 error generated.
make: *** [file6fe9456fb03d.o] Error 1
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/Rcpp/include" -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/plogr.Rcheck/plogr/include" -I"/private/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T/RtmpUAUqU1/sourceCpp-x86_64-apple-darwin15.6.0-0.12.15" -I/usr/local/include   -fPIC  -Wall -g -O2  -c file6fe9456fb03d.cpp -o file6fe9456fb03d.o
Error in sourceCpp(code = code, env = env, rebuild = rebuild, cacheDir = cacheDir,  : 
  Error 1 occurred building shared library.
Calls: <Anonymous> -> sourceCpp
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/plsRglm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running ‘testthat.R’ [25s/49s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  4: getExportedValue(pkg, name)
  5: asNamespace(ns)
  6: getNamespace(ns)
  7: tryCatch(loadNamespace(name), error = function(e) stop(e))
  8: tryCatchList(expr, classes, parentenv, handlers)
  9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  10: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 244 SKIPPED: 1 FAILED: 2
  1. Error: render_pmap_file() should be able to render to a file (@test_render_pmap_file.R#15) 
  2. Error: render_pmap_file() should be able to guess file format (@test_render_pmap_file.R#32) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   1.7Mb
Packages required but not available: ‘pbdMPI’ ‘pbdBASE’ ‘pbdDMAT’

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

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

    combine

Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda

Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/pmlr.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running ‘testthat.R’ [3s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 53 SKIPPED: 0 FAILED: 24
  1. Error: Creating a `col_is_character()` step is possible (@test-create_validation_steps.R#10) 
  2. Error: Creating a `col_is_date()` step is possible (@test-create_validation_steps.R#74) 
  3. Error: Creating a `col_is_factor()` step is possible (@test-create_validation_steps.R#138) 
  4. Error: Creating a `col_is_integer()` step is possible (@test-create_validation_steps.R#202) 
  5. Error: Creating a `col_is_logical()` step is possible (@test-create_validation_steps.R#266) 
  6. Error: Creating a `col_is_numeric()` step is possible (@test-create_validation_steps.R#330) 
  7. Error: Creating a `col_is_posix()` step is possible (@test-create_validation_steps.R#394) 
  8. Error: Creating a `col_vals_between()` step is possible (@test-create_validation_steps.R#458) 
  9. Error: Creating a `col_vals_not_between()` step is possible (@test-create_validation_steps.R#530) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Packages suggested but not available for checking:
  ‘polmineR.Rcpp’ ‘europarl.en’ ‘rcqp’
Found the following significant warnings:
  heftall.c:1389:2: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  lsdall.c:2077:21: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  lspecall.c:505:12: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  lspecall.c:999:21: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  lspecall.c:1078:18: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2199:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2208:12: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2218:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2224:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/polspline.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘LPmerge’
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R      6.4Mb
    data   2.5Mb
Found the following significant warnings:
  whopgenome/rdnapp_MAF.h:243:12: warning: explicitly assigning value of variable of type 'unsigned int' to itself [-Wself-assign]
  whopgenome/rdnapp_MAF.h:409:45: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
  whopgenome/whopgen_vcf.cpp:263:28: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
  whopgenome/whoptbi_info.cpp:115:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  whopgenome/whoptbi_info.cpp:120:7: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  whopgenome/whoptbi_info.cpp:152:44: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  whopgenome/whoptbi_region.cpp:78:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PopGenome.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Package suggested but not available for checking: ‘VariantAnnotation’
Errors in running code in vignettes:
when running code in ‘poplite.Rnw’
  ...
 8            8         8    18      0      1.68      0.535           2 F    
 9            9         9    20      1      0.911    -0.555           2 F    
10           10        10    12      1      0.237     1.78            1 M    
# ... with more rows

> library(VariantAnnotation)

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

    select

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

    filter

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

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

> suppressMessages(library(ROI))

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

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

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

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

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

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

Error: processing vignette 'ROI_vignette.Rnw' failed with diagnostics:
 chunk 1 
Error in library(ROI.plugin.glpk) : 
  there is no package called ‘ROI.plugin.glpk’
Execution halted
Found the following significant warnings:
  powell.c:398:17: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
  powell.c:499:17: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
  powell.c:700:14: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  powell.c:724:12: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/powell.Rcheck/00install.out’ for details.
File ‘powell/libs/powell.so’:
  Found ‘_printf’, possibly from ‘printf’ (C)
    Object: ‘powell.o’
  Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Object: ‘powell.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/powerCompRisk.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  ppcctest_pearson3.c:19:66: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ppcc.Rcheck/00install.out’ for details.
Packages which this enhances but not available for checking:
  ‘KEGG.db’ ‘org.Sc.sgd.db’ ‘org.Ag.eg.db’ ‘org.Pt.eg.db’
  ‘org.Rn.eg.db’ ‘org.Ss.eg.db’ ‘org.At.tair.db’ ‘org.Bt.eg.db’
  ‘org.Ce.eg.db’ ‘org.Cf.eg.db’ ‘org.Dm.eg.db’ ‘org.Dr.eg.db’
  ‘org.EcK12.eg.db’ ‘org.EcSakai.eg.db’ ‘org.Gg.eg.db’ ‘org.Mm.eg.db’
  ‘org.Mmu.eg.db’ ‘org.Pf.plasmo.db’ ‘org.Xl.eg.db’
Found the following significant warnings:
  Note: possible error in 'geneSim(as.character(Sims[[1]][i]), ': unused arguments (ont = "BP", organism = wh_organism) 
  Note: possible error in 'geneSim(as.character(Sims[[1]][i]), ': unused arguments (ont = "MF", organism = wh_organism) 
  Note: possible error in 'geneSim(as.character(Sims[[1]][i]), ': unused arguments (ont = "CC", organism = wh_organism) 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ppiPre.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’.
ComputeAllEvidences: possible error in
  geneSim(as.character(Sims[[1]][i]), as.character(Sims[[2]][i]), ont =
  "BP", organism = wh_organism, measure = "Wang", drop <- dropcodes):
  unused arguments (ont = "BP", organism = wh_organism)
ComputeAllEvidences: possible error in
  geneSim(as.character(Sims[[1]][i]), as.character(Sims[[2]][i]), ont =
  "MF", organism = wh_organism, measure = "Wang", drop <- dropcodes):
  unused arguments (ont = "MF", organism = wh_organism)
ComputeAllEvidences: possible error in
  geneSim(as.character(Sims[[1]][i]), as.character(Sims[[2]][i]), ont =
  "CC", organism = wh_organism, measure = "Wang", drop <- dropcodes):
  unused arguments (ont = "CC", organism = wh_organism)
Found the following significant warnings:
  ./ThreadPool.h:161:6: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  CreateCLKBigramSeed.cpp:297:30: warning: 'memset' call operates on objects of type 'int' while the size is based on a different type 'int *' [-Wsizeof-pointer-memaccess]
  MTB_Metaphone.cpp:237:39: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
  MTB_Metaphone.cpp:311:45: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PPRL.Rcheck/00install.out’ for details.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Found the following significant warnings:
  ./shared.h:67:9: warning: 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.
Package suggested but not available for checking: ‘PerfMeas’
Found the following significant warnings:
  sum.c:221:11: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  sum.c:221:22: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  sum.c:227:52: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  sum.c:227:60: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PreciseSums.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: possible error in 'psf(data = dataIn1, n.ahead = nextVal)': unused argument (n.ahead = nextVal) 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PredictTestbench.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’.
prediction_errors: possible error in psf(data = dataIn1, n.ahead =
  nextVal): unused argument (n.ahead = nextVal)
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
Packages suggested but not available for checking:
  ‘gurobi’ ‘lpsymphony’ ‘Rsymphony’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 31-43 (PRISMA.Rmd) 
Error: processing vignette 'PRISMA.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    libs  20.6Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/processmapR.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
process_map: no visible global function definition for
  ‘set_global_graph_attrs’
Undefined global functions or variables:
  set_global_graph_attrs
Running ‘testthat.R’ [12s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  + 	r.ndka.percent <<- roc(aSAH$outcome, aSAH$ndka, percent = TRUE, quiet = TRUE)
  + 	r.s100b.percent <<- roc(aSAH$outcome, aSAH$s100b, percent = TRUE, quiet = TRUE)
  + })
  > 
  > test_check("pROC")
  ── 1. Failure: microbenchmark works (@test-roc.R#145)  ─────────────────────────
  `r <- roc\(aSAH\$outcome, aSAH\$wfns, algorithm = 0\)` does not match "Selecting algorithm 3".
  Actual value: "Starting benchmark of algorithms 2 and 3, 10 iterations\.\.\.\\n  expr     min      lq     mean   median      uq      max neval cld\\n1    2 373\.527 407\.810 471\.6530 425\.1560 466\.737  696\.101    10   a\\n2    3  41\.720  42\.978 996\.2068  48\.6885  51\.772 9449\.475    10   a\\nSelecting algorithm 2\."
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 5342 SKIPPED: 5 FAILED: 1
  1. Failure: microbenchmark works (@test-roc.R#145) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/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’.
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/profileR.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 13.1Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   6.4Mb
    libs      5.1Mb
Running examples in ‘ProFit-Ex.R’ failed
The error most likely occurred in:

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

 *** caught segfault ***
address 0x60, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
Packages suggested but not available for checking:
  ‘ProFit’ ‘EBImage’ ‘imager’
Running examples in ‘ProFound-Ex.R’ failed
The error most likely occurred in:

> ### Name: FPtest
> ### Title: False Positive Reference Data
> ### Aliases: FPtest
> ### Keywords: datasets
> 
> ### ** Examples
> 
> image=readFITS(system.file("extdata", 'VIKING/mystery_VIKING_Z.fits', package="ProFound"))
> profound=profoundProFound(image, magzero=30, rotstats=TRUE)
Error: The imager package is needed for this function to work. Please install it from CRAN.
Execution halted
Running examples in ‘proftools-Ex.R’ failed
The error most likely occurred in:

> ### Name: filterProfileData
> ### Title: Filter Profile Data
> ### Aliases: filterProfileData
> ### Keywords: programming utilities
> 
> ### ** Examples
> 
> pd <- readProfileData(system.file("samples", "glmEx.out", package="proftools"))
> plotProfileCallGraph(pd)
Error in loadNamespace(name) : there is no package called ‘graph’
Calls: plotProfileCallGraph ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 221-222 (proftools.Rnw) 
Error: processing vignette 'proftools.Rnw' failed with diagnostics:
there is no package called 'graph'
Execution halted
Packages suggested but not available for checking:
  ‘qtbase’ ‘RGtk2’ ‘cairoDevice’ ‘gWidgetsRGtk2’
Running ‘testthat.R’ [69s/113s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Initial log joint probability = -15.5191
  Optimization terminated normally: 
    Convergence detected: relative gradient magnitude is below tolerance
  Initial log joint probability = -15.5191
  Optimization terminated normally: 
    Convergence detected: relative gradient magnitude is below tolerance
  Initial log joint probability = -15.5191
  Optimization terminated normally: 
    Convergence detected: relative gradient magnitude is below tolerance
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 230 SKIPPED: 0 FAILED: 1
  1. Error: logistic_floor (@test_prophet.R#89) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘ALDEx2’
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
Packages suggested but not available for checking:
  ‘Biostrings’ ‘GOSemSim’ ‘org.Hs.eg.db’
installed size is  6.0Mb
  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/psidR.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/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’.
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/PSM.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     1.6Mb
    doc   2.3Mb
Errors in running code in vignettes:
when running code in ‘overview.Rnw’
  ...

> if (!require("GPArotation")) {
+     stop("GPArotation must be installed to do rotations")
+ } else {
+     f3t <- fa(Thurstone, 3, n.obs = 213)
+   .... [TRUNCATED] 

  When sourcing ‘overview.R’:
Error: could not find function "fa"
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’ [52s/112s]
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) : 91.7 | 91.5 | 4198623 (4198531)
  
  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 24.9Mb
  sub-directories of 1Mb or more:
    libs  24.5Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/QoLR.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  upwindorderedv4.c:542:54: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  upwindorderedv4.c:542:72: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/QPot.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/qtbase.Rcheck/00install.out’ for details.
Packages in Depends field not imported from:
  ‘graph’ ‘igraph’ ‘pcalg’ ‘qtl’ ‘sem’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.7Mb
    doc       2.9Mb
    libs      1.2Mb
Package required but not available: ‘qtbase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 83-117 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 92-106 (wilcox1973.Rmd) 
Error: processing vignette 'wilcox1973.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   8.5Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   3.1Mb
File ‘QUIC/libs/QUIC.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘QUIC.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘QUIC.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘qVarSel/libs/qVarSel.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘qVarSelH.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘qVarSelH.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
FancyPies: no visible global function definition for ‘rainbow’
FancyPies: no visible global function definition for ‘plot’
FancyPies: no visible global function definition for ‘polygon’
Hist2GE: no visible global function definition for ‘dist’
Pies2GE: no visible global function definition for ‘rainbow’
Plots2GE: no visible global function definition for ‘aggregate’
Plots2GE: no visible global function definition for ‘x11’
Plots2GE: no visible global function definition for ‘title’
Plots2GE: no visible global function definition for ‘png’
Plots2GE: no visible global function definition for ‘dev.off’
PolyLines2GE: no visible global function definition for ‘rainbow’
Shapes2GE: no visible global function definition for ‘rainbow’
Undefined global functions or variables:
  aggregate dev.off dist plot png polygon rainbow title x11
Consider adding
  importFrom("grDevices", "dev.off", "png", "rainbow", "x11")
  importFrom("graphics", "plot", "polygon", "title")
  importFrom("stats", "aggregate", "dist")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘RDCOMClient’ ‘rcom’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages required but not available:
  ‘cairoDevice’ ‘gWidgetsRGtk2’ ‘RGtk2Extras’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package unavailable to check Rd xrefs: ‘BRugs’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   3.8Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    htmlwidgets   6.3Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ramidst.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Package suggested but not available for checking: ‘Heatplus’
Package unavailable to check Rd xrefs: ‘Heatplus’
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs   3.7Mb
Package unavailable to check Rd xrefs: ‘WGCNA’
Running examples in ‘rangeMapper-Ex.R’ failed
The error most likely occurred in:

> ### Name: WKT2SpatialPolygonsDataFrame
> ### Title: Convert WKT polygons to SpatialPolygonsDataFrame
> ### Aliases: WKT2SpatialPolygonsDataFrame vertices
> ###   vertices,SpatialPolygons-method
> 
> ### ** Examples
> 
> 
> require(rangeMapper)
> require(rgeos)
Loading required package: rgeos
rgeos version: 0.3-26, (SVN revision 560)
 GEOS runtime version: 3.6.1-CAPI-1.10.1 r0 
 Linking to sp version: 1.2-7 
 Polygon checking: TRUE 

> 
> # generate a few random polygons
> randPoly = function(mean, sd) {
+   writeWKT(
+     gConvexHull(
+      readWKT(paste("MULTIPOINT (",
+              paste(apply(matrix(rnorm(n= 100, mean, sd), ncol = 2), 1,
+              paste, collapse = ' '), collapse = ","), ")"))))
+ }
> n = 50
> d = data.frame( nam = sample(letters, n, TRUE),
+                range = mapply(randPoly, mean = sample(1:2, n, TRUE),
+                sd = sample(1:2/5, n, TRUE) ))
> 
> 
> X = WKT2SpatialPolygonsDataFrame(d, 'range', 'nam')
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘row.names<-’ for signature ‘"SpatialPolygons", "character"’
Calls: WKT2SpatialPolygonsDataFrame ... unique -> row.names -> groupID -> row.names<- -> <Anonymous>
Execution halted
Packages required but not available: ‘Rsamtools’ ‘GenomicAlignments’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RAppArmor.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘rpanel’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs   1.6Mb
Package suggested but not available for checking: ‘rattle’
Packages required but not available: ‘RGtk2’ ‘cairoDevice’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 28.9Mb
  sub-directories of 1Mb or more:
    libs  27.4Mb
Found the following significant warnings:
  subscribe.cpp:221:28: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rblpapi.Rcheck/00install.out’ for details.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    blp    5.9Mb
    libs   3.8Mb
Running examples in ‘rchallenge-Ex.R’ failed
The error most likely occurred in:

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

```{r}
library(rchallenge)
```
<link rel="stylesheet" 
 href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css">
`r icon("fa-user")`
`r icon("fa-user fa-lg")`
`r icon("fa-user fa-2x")`
`r icon("fa-user fa-3x")`
`r icon("fa-user fa-3x fa-border")`
> rmarkdown::render(file)
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
Found the following 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 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
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.

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
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rcplex.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RcppAPT.Rcheck/00install.out’ for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    include   5.2Mb
    libs      1.6Mb
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 27.1Mb
  sub-directories of 1Mb or more:
    include  25.3Mb
    libs      1.7Mb
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 31.1Mb
  sub-directories of 1Mb or more:
    include   7.6Mb
    libs     22.9Mb
Running ‘doRUnit.R’ [119s/270s]
Running the tests in ‘tests/doRUnit.R’ failed.
Last 13 lines of output:
    Error 1 occurred building shared library.
  .setUp (before test.gsl.vector): ERROR !! 
  Error executing .setUp before test.gsl.vector : Error in sourceCpp(file.path(pathRcppTests, "cpp/gsl.cpp")) : 
    Error 1 occurred building shared library.
  .setUp (before test.gsl.vector.input.SEXP): ERROR !! 
  Error executing .setUp before test.gsl.vector.input.SEXP : Error in sourceCpp(file.path(pathRcppTests, "cpp/gsl.cpp")) : 
    Error 1 occurred building shared library.
  .setUp (before test.gsl.vector.view): ERROR !! 
  Error executing .setUp before test.gsl.vector.view : Error in sourceCpp(file.path(pathRcppTests, "cpp/gsl.cpp")) : 
    Error 1 occurred building shared library.
  .setUp (before test.gsl.vector.wrappers): ERROR !! 
  Error executing .setUp before test.gsl.vector.wrappers : Error in sourceCpp(file.path(pathRcppTests, "cpp/gsl.cpp")) : 
    Error 1 occurred building shared library.
  Error: TEST HAD ERRORS!
  Execution halted
Errors in running code in vignettes:
when running code in ‘RcppGSL-unitTests.Rnw’
  ...

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

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

  When sourcing ‘RcppGSL-unitTests.R’:
Error: unit test problems: 14 errors
Execution halted
Error in re-building vignettes:
  ...
/usr/local/clang4/bin/../include/c++/v1/algorithm:1932:1: note: candidate function template not viable: requires 5 arguments, but 4 were provided
transform(_InputIterator1 __first1, _InputIterator1 __last1, _InputIterator2 __first2,
^
1 error generated.
make: *** [gsl.o] Error 1
Error in sourceCpp(file.path(pathRcppTests, "cpp/gsl.cpp")) : 
  Error 1 occurred building shared library.
gsl.cpp:293:5: error: no matching function for call to 'transform'
    std::transform(vec.begin(), vec.end(), res.begin(), ::sqrt);
    ^~~~~~~~~~~~~~
/usr/local/clang4/bin/../include/c++/v1/algorithm:1922:1: note: candidate template ignored: couldn't infer template argument '_UnaryOperation'
transform(_InputIterator __first, _InputIterator __last, _OutputIterator __result, _UnaryOperation __op)
^
/usr/local/clang4/bin/../include/c++/v1/algorithm:1932:1: note: candidate function template not viable: requires 5 arguments, but 4 were provided
transform(_InputIterator1 __first1, _InputIterator1 __last1, _InputIterator2 __first2,
^
1 error generated.
make: *** [gsl.o] Error 1
Error in sourceCpp(file.path(pathRcppTests, "cpp/gsl.cpp")) : 
  Error 1 occurred building shared library.

Error: processing vignette 'RcppGSL-unitTests.Rnw' failed with diagnostics:
 chunk 2 (label = unitTesting) 
Error in eval(expr, .GlobalEnv) : unit test problems: 14 errors
Execution halted
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib      23.3Mb
    libs      8.3Mb
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   4.9Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    include   8.9Mb
    libs      2.4Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    include   6.2Mb
    libs      4.1Mb
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.
installed size is 77.8Mb
  sub-directories of 1Mb or more:
    include   4.4Mb
    lib      49.7Mb
    libs     23.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
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.
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Clearing default rcreds db folder, which was previously set to  '/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmpcRrJtn/.rcreds/db_credential_files' 
  Setting the default rcreds db folder to '/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmpcRrJtn/db/some/sub/folder'
  Setting the default rcreds db folder to '/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmpcRrJtn/db/some/sub/folder/with_slash/'
  Clearing default rcreds  folder, which was previously not set 
  Clearing default rcreds  folder, which was previously not set 
  Setting the default rcreds folder to '/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmpcRrJtn/credentials/some/sub/folder'
  Setting the default rcreds folder to '/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmpcRrJtn/credentials/some/sub/folder/with_slash/'
  Folder does not exist. Creating it. 
  Setting the default rcreds folder to '/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmpcRrJtn/testing/default'
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 124 SKIPPED: 0 FAILED: 1
  1. Failure: Checking Overwriting Abilities (@test-TODOs.R#54) 
  
  Error: testthat unit tests failed
  Execution halted
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  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Running ‘dynSetReader.R’ [1s/32s]
Running the tests in ‘tests/dynSetReader.R’ failed.
Last 13 lines of output:
  > # This is an example of where we read the header and then set the options
  > # in the curl handle to read the body ofthe response.
  > #
  > 
  > library(RCurl)
  Loading required package: bitops
  > 
  > reader = dynCurlReader()
  > status = curlPerform(url = "http://ws.audioscrobbler.com/2.0/?method=library%2Egetartists&user=oso&api_key=de933ba987ea45f82a73acd0d82071c3",
  +                      headerfunction = reader$update,
  +                      curl = reader$curl())
  Error in function (type, msg, asError = TRUE)  : 
    Could not resolve host: ws.audioscrobbler.com
  Calls: curlPerform -> <Anonymous> -> fun
  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 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()
Linking to GEOS 3.6.1, GDAL 2.1.3, proj.4 4.9.3

Attaching package: 'units'

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

    %*%

Quitting from lines 122-147 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
Saving a widget with selfcontained = TRUE requires pandoc. For details see:
https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rDEA.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
── Attaching packages ────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 2.2.1     ✔ purrr   0.2.4
✔ tibble  1.4.2     ✔ dplyr   0.7.4
✔ tidyr   0.8.0     ✔ stringr 1.3.0
✔ readr   1.1.1     ✔ forcats 0.3.0
── Conflicts ───────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()

Attaching package: 'jsonlite'

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

    flatten

Joining, by = "carrier"
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 39-40 (rdf_intro.Rmd) 
Error: processing vignette 'rdf_intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RDieHarder.Rcheck/00install.out’ for details.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot1852542e1f667.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot1852542e1f667.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  8.7Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   6.1Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Package required but not available: ‘Rmosek’

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 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  5.2Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   3.3Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  13.9Mb
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/refund.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:
  ‘Rgraphviz’ ‘Rglpk’ ‘Rsymphony’

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

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

> data("Felines")

> relations <- as.relation_ensemble(Felines)

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

  When sourcing ‘relations.R’:
Error: there is no package called ‘Rglpk’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: Rgraphviz
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘Rgraphviz’
Loading required package: Rgraphviz
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘Rgraphviz’

Error: processing vignette 'relations.Rnw' failed with diagnostics:
 chunk 26 (label = consensus1b) 
Error in loadNamespace(name) : there is no package called ‘Rglpk’
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/relax.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
Running examples in ‘rentrez-Ex.R’ failed
The error most likely occurred in:

> ### Name: entrez_db_summary
> ### Title: Retrieve summary information about an NCBI database
> ### Aliases: entrez_db_summary
> 
> ### ** Examples
> 
> entrez_db_summary("pubmed")
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: Resolving timed out after 10002 milliseconds
Calls: entrez_db_summary ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 22-52 (rentrez_tutorial.Rmd) 
Error: processing vignette 'rentrez_tutorial.Rmd' failed with diagnostics:
Timeout was reached: Resolving timed out after 10000 milliseconds
Execution halted
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.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Running examples in ‘reprex-Ex.R’ failed
The error most likely occurred in:

> ### Name: un-reprex
> ### Title: Un-render a reprex
> ### Aliases: un-reprex reprex_invert reprex_clean reprex_rescue
> 
> ### ** Examples
> 
> ## a rendered reprex can be inverted, at least approximately
> x <- reprex({
+   #' Some text
+   #+ chunk-label-and-options-cannot-be-recovered, message = TRUE
+   (x <- 1:4)
+   #' More text
+   y <- 2:5
+   x + y
+ }, show = FALSE)
Error in reprex_(r_file) : 
Cannot render this code.
Error : pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Calls: reprex -> reprex_
Execution halted
Running ‘testthat.R’ [20s/35s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 25 SKIPPED: 0 FAILED: 26
  1. Error: can't see environment of caller (@test-env.R#5) 
  2. Error: reprex doesn't write into environment of caller (@test-env.R#11) 
  3. Error: I understand exactly what I'm putting in reprex env (@test-env.R#22) 
  4. Error: reprex: expression input works (@test-input.R#17) 
  5. Error: reprex: character input works (@test-input.R#23) 
  6. Error: reprex: file input works (@test-input.R#31) 
  7. Error: reprex: file input in a subdirectory works (@test-input.R#40) 
  8. Error: Circular use is detected before render (@test-input.R#47) 
  9. Error: Leading prompts are removed (@test-input.R#55) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘rsolr’
Packages suggested but not available for checking:
  ‘gWidgets2RGtk2’ ‘cairoDevice’ ‘RGtk2’
Found the following significant warnings:
  system_files.cpp:284:8: warning: comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always false [-Wtautological-constant-out-of-range-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rfast.Rcheck/00install.out’ for details.
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    libs  24.7Mb
installed size is 80.0Mb
  sub-directories of 1Mb or more:
    libs      77.2Mb
    pictures   1.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rgeolocate.Rcheck/00install.out’ for details.
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
Running examples in ‘RGF-Ex.R’ failed
The error most likely occurred in:

> ### Name: dgCMatrix_2scipy_sparse
> ### Title: conversion of an R dgCMatrix to a scipy sparse matrix
> ### Aliases: dgCMatrix_2scipy_sparse
> 
> ### ** Examples
> 
> 
> if (reticulate::py_available() && reticulate::py_module_available("scipy")) {
+ 
+   library(RGF)
+ 
+   data = c(1, 0, 2, 0, 0, 3, 4, 5, 6)
+ 
+   dgcM = Matrix::Matrix(data = data, nrow = 3,
+ 
+                         ncol = 3, byrow = TRUE,
+ 
+                         sparse = TRUE)
+ 
+   print(dim(dgcM))
+ 
+   res = dgCMatrix_2scipy_sparse(dgcM)
+ 
+   print(res$shape)
+ }
[1] 3 3
Error in py_call_impl(callable, dots$args, dots$keywords) : 
  TypeError: could not interpret data type

Detailed traceback: 
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/scipy/sparse/compressed.py", line 52, in __init__
    self.data = np.array(data, copy=copy, dtype=getdtype(dtype, data))
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/scipy/sparse/sputils.py", line 101, in getdtype
    raise TypeError("could not interpret data type")
Calls: dgCMatrix_2scipy_sparse -> <Anonymous> -> py_call_impl
Execution halted
Running ‘testthat.R’ [3s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/scipy/sparse/compressed.py", line 52, in __init__
      self.data = np.array(data, copy=copy, dtype=getdtype(dtype, data))
    File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/scipy/sparse/sputils.py", line 101, in getdtype
      raise TypeError("could not interpret data type")
  1: dgCMatrix_2scipy_sparse(dgcM) at testthat/test_package.R:300
  2: SCP$sparse$csc_matrix(reticulate::tuple(dgc_mat_object@x, dgc_mat_object@i, dgc_mat_object@p), 
         shape = reticulate::tuple(dgc_mat_object@Dim[1], dgc_mat_object@Dim[2]))
  3: py_call_impl(callable, dots$args, dots$keywords)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 3 SKIPPED: 7 FAILED: 1
  1. Error: the 'dgCMatrix_2scipy_sparse' returns the correct output (@test_package.R#300) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rglpk.Rcheck/00install.out’ for details.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc     3.9Mb
    fonts   1.5Mb
    libs    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 17-19 (WebGL.Rmd) 
Error: processing vignette 'WebGL.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.13.1; older versions will not work.
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rgnuplot.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RGoogleAnalytics.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages suggested but not available for checking:
  ‘gWidgetsRGtk2’ ‘hyperdraw’ ‘hypergraph’ ‘playwith’ ‘pmg’ ‘rggobi’
  ‘SVGAnnotation’
Running examples in ‘Rgretl-Ex.R’ failed
The error most likely occurred in:

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

No valid gretl executable: no output is produced
Error: '/tmp/RtmpWG1MCx/mbundle12cdb2c1475d5.xml' does not exist.
Execution halted
Package required but not available: ‘RGtk2’

Package suggested but not available for checking: ‘gWidgetsRGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RGtk2.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 34-47 (intro_rhandsontable.Rmd) 
Error: processing vignette 'intro_rhandsontable.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rhpc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  filterhr.c:21:11: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  filterhr.c:21:53: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  filterhr.c:21:95: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RHRV.Rcheck/00install.out’ for details.
Found the following significant warnings:
  computePvals.c:488:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ridge.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘httr’ ‘rmarkdown’ ‘shiny’
  All declared Imports should be used.
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.
Running ‘test-all.R’ [14s/32s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  ── 1. Error: Import Remote GitHub File (@test_remote.R#19)  ────────────────────
  No yaml delimiters found
  1: expect_true(inherits(import(lfile), "data.frame"), label = "Import local copy successfully") at testthat/test_remote.R:19
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: inherits(import(lfile), "data.frame")
  5: import(lfile)
  6: .import(file = file, ...)
  7: .import.rio_csvy(file = file, ...)
  8: csvy::read_csvy(file = file, ...)
  9: stop("No yaml delimiters found")
  
  ══ DONE ════════════════════════════════════════════════════════════════════════
  Error: Test failures
  Execution halted
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
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.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    datasets   8.6Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RKEELjars.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: possible error in 'write(self$rules, file = paste0(fileName, ': unused argument (col.names = NA) 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RKEEL.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘arules’ ‘pmml’ ‘rJava’
  All declared Imports should be used.
Packages suggested but not available for checking:
  ‘Biobase’ ‘genefilter’ ‘golubEsets’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
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  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
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.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RMariaDB.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RMark.Rcheck/00install.out’ for details.
File ‘RMC/libs/RMC.so’:
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
    Objects: ‘RMC.o’, ‘predict.o’
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘ap.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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  7.3Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   4.3Mb
Found the following significant warnings:
  Clustering/ClusteringInput.cpp:132:12: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
  Kernel/IO/Input.cpp:212:12: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rmixmod.Rcheck/00install.out’ for details.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
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$Network: Write operation to server /127.0.0.1:27017 failed on database test
Calls: dbInsertDocument -> dbInsertDocument -> .jcall -> .jcheck
Execution halted
Running ‘RMongo-Ex.R’ [2s/4s]
Running the tests in ‘tests/RMongo-Ex.R’ failed.
Last 13 lines of output:
  +   dbRemoveQuery(mongo, "test_data", '{}')
  +   dbDisconnect(mongo)
  +   
  +   # print(length(output))
  +   print(as.character(output[1]))
  + 
  +   checkEquals("{ \"_id\" : \"bar\"}", as.character(output[1]))
  +   # checkEquals("bar", as.character(output[1]))
  + }
  > 
  > test.dbInsertDocument()
  Error in .jcall(rmongo.object@javaMongo, "S", "dbInsertDocument", collection,  : 
    com.mongodb.MongoException$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 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RM.weights.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: ‘RnavGraph’
Packages suggested but not available for checking: ‘PairViz’ ‘RDRToolbox’
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
Packages suggested but not available for checking: ‘rrdf’ ‘Sxslt’
Running ‘test-all.R’ [75s/175s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  8: xml2::read_xml(repeat_until_it_works(errors_to_catch, "esearch", query = list(db = "taxonomy", 
         term = term, api_key = key), ...))
  9: read_xml.character(repeat_until_it_works(errors_to_catch, "esearch", query = list(db = "taxonomy", 
         term = term, api_key = key), ...))
  10: path_to_connection(x)
  11: check_path(path)
  12: stop("'", path, "' does not exist", if (!is_absolute_path(path)) paste0(" in current working directory ('", 
         getwd(), "')"), ".", call. = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 164 SKIPPED: 3 FAILED: 1
  1. Error: (unknown) (@test_taxonomy.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ape
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
No ENTREZ API key provided
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Struthioniformes'

Quitting from lines 85-86 (metadata.Rmd) 
Error: processing vignette 'metadata.Rmd' failed with diagnostics:
'{"error":"API key invalid","api-key":"","type":"invalid","status":"unknown"}' does not exist in current working directory ('/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RNeXML.Rcheck/vign_test/RNeXML/vignettes').
Execution halted
installed size is 93.3Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     91.2Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rnightlights.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ./hammock.h:369:15: warning: assigning field to itself [-Wself-assign-field]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/robfilter.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘SSOAP’
Running examples in ‘robustarima-Ex.R’ failed
The error most likely occurred in:

> ### Name: predict.arima.rob
> ### Title: Use predict on an arima.rob Object
> ### Aliases: predict.arima.rob
> ### Keywords: ts
> 
> ### ** Examples
> 
> import.rr <- arima.rob(import ~ taxes-1, data=import.dat, p=2, d=1)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘row.names<-’ for signature ‘"data.frame"’
Calls: arima.rob ... as.data.frame.timeSeries -> row.names<- -> <Anonymous>
Execution halted
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
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/42s]
Running the tests in ‘tests/test_deoptim.R’ failed.
Last 13 lines of output:
  + 
  +     rt( test_nlp_01() )
  +     rt( test_nlp_02() )
  +     rt( test_nlp_03() )
  + 
  +     if ( ROI_TEST_ERRORS > 0 ) {
  +         stop("ROI_Test_Error ", ROI_TEST_ERRORS, " occurred during testing.")
  +     }
  + }
  Error in test_nlp_03() : equal(solution(nlp), c(20, 11, 15)) is not TRUE
  In addition: Warning message:
  In (function (lower, upper, fn, constr = NULL, meq = 0, eps = 1e-05,  :
    maximum number of iterations reached without convergence
  Error: ROI_Test_Error 1 occurred during testing.
  Execution halted
Package required but not available: ‘Rsymphony’

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

Package which this enhances but not available for checking: ‘ROI.plugin.cplex’
Running ‘testthat.R’ [2s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  12: getJSON(paste(endpoint, "metadata", sep = ""))
  13: tryCatch(GET(URLencode(url), accept_json()), error = function(e) {
         stop("Could not connect to endpoint")
     })
  14: tryCatchList(expr, classes, parentenv, handlers)
  15: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  16: value[[3L]](cond)
  17: stop("Could not connect to endpoint")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 77 SKIPPED: 0 FAILED: 1
  1. Error: fhirClient checks only connects to FHIR Servers STU 3 (@test-fhirClient.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
Package suggested but not available for checking: ‘RobLox’
Package unavailable to check Rd xrefs: ‘RobLox’
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  8.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    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/rpanel.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [1s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  cannot open URL 'http://research.jisao.washington.edu/pdo/PDO.latest'
  1: expect_is(download_pdo(), "data.frame") at testthat/test-pdo-download.R:4
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: download_pdo()
  5: pdo_download()
  6: get_pdo()
  7: download.file("http://research.jisao.washington.edu/pdo/PDO.latest", pdo)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2 SKIPPED: 0 FAILED: 1
  1. Error: pdo_download (@test-pdo-download.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Package suggested but not available for checking: ‘seqLogo’
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      3.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(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 12.7Mb
  sub-directories of 1Mb or more:
    extdata  12.2Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rpoppler.Rcheck/00install.out’ for details.
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  15.0Mb
'library' or 'require' calls to packages already attached by Depends:
  ‘RSAGA’ ‘shapefiles’
  Please remove these calls from your code.
Packages required but not available: ‘gWidgetsRGtk2’ ‘RGtk2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RQuantLib.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RSAP.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Quitting from lines 307-310 (article.Rnw) 
Error: processing vignette 'article.Rnw' failed with diagnostics:
Please run "rscala::scalaInstall()" or install Scala manually.
Execution halted
Package which this enhances but not available for checking: ‘BiocInstaller’
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RSEIS.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  Rserv.c:2976:16: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  ./Rserv.c:2976:16: 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/Rserve.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/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 14.9Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  15.2Mb
installed size is 46.3Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  44.9Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
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 241.1Mb
  sub-directories of 1Mb or more:
    libs  238.5Mb
Running ‘testthat.R’ [320s/397s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
         package = "rgeos", group = list(), valueClass = character(0), signature = c("x", 
         "value"), default = NULL, skeleton = (function (x, value) 
         stop("invalid call in method dispatch to 'row.names<-' (no default method)", 
             domain = NA))(x, value)), <environment>)
  8: stop(gettextf("unable to find an inherited method for function %s for signature %s", 
         sQuote(fdef@generic), sQuote(cnames)), domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 506 SKIPPED: 2 FAILED: 3
  1. Error: maximum likelihood model 
  2. Error: (unknown) (@test-superClass.R#66) 
  3. Error: (unknown) (@test-validateMap.R#16) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rsunlight.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RSurvey.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: package or namespace load failed for ‘rsvg’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rsvg.Rcheck/rsvg/libs/rsvg.so':
  dlopen(/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rsvg.Rcheck/rsvg/libs/rsvg.so, 6): Symbol not found: _OBJC_CLASS_$_NSAutoreleasePool
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rsvg.Rcheck/rsvg/libs/rsvg.so
  Expected in: flat namespace
 in /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rsvg.Rcheck/rsvg/libs/rsvg.so
Execution halted
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rsvg.Rcheck/rsvg/libs/rsvg.so':
  dlopen(/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rsvg.Rcheck/rsvg/libs/rsvg.so, 6): Symbol not found: _OBJC_CLASS_$_NSAutoreleasePool
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rsvg.Rcheck/rsvg/libs/rsvg.so
  Expected in: flat namespace
 in /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rsvg.Rcheck/rsvg/libs/rsvg.so
Calls: <Anonymous> ... eval -> eval -> loadNamespace -> library.dynam -> dyn.load
Execution halted

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.
Error: package or namespace load failed for ‘rsvg’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rsvg.Rcheck/rsvg/libs/rsvg.so':
  dlopen(/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rsvg.Rcheck/rsvg/libs/rsvg.so, 6): Symbol not found: _OBJC_CLASS_$_NSAutoreleasePool
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rsvg.Rcheck/rsvg/libs/rsvg.so
  Expected in: flat namespace
 in /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rsvg.Rcheck/rsvg/libs/rsvg.so
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       
Execution halted
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  5.3Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       1.5Mb
    projects   2.5Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   2.2Mb
Packages required but not available: ‘cairoDevice’ ‘gWidgetsRGtk2’ ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 25.1Mb
  sub-directories of 1Mb or more:
    libs  24.4Mb
Running examples in ‘rversions-Ex.R’ failed
The error most likely occurred in:

> ### Name: r_oldrel
> ### Title: Version number of R-oldrel
> ### Aliases: r_oldrel
> 
> ### ** Examples
> 
> r_oldrel()
Error in curl_fetch_memory("http://svn.r-project.org/R/tags/", handle = h) : 
  Timeout was reached: Resolving timed out after 10000 milliseconds
Calls: r_oldrel -> r_versions -> curl_fetch_memory
Execution halted
installed size is 45.4Mb
  sub-directories of 1Mb or more:
    libs  44.7Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RVowpalWabbit.Rcheck/00install.out’ for details.
Found the following significant warnings:
  qwiener.c:60:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  qwiener.c:69:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RWiener.Rcheck/00install.out’ for details.
Found the following significant warnings:
  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/RWildbook.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:
  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.
Running examples in ‘RXKCD-Ex.R’ failed
The error most likely occurred in:

> ### Name: getXKCD
> ### Title: Display your favorite XKCD comic in R
> ### Aliases: getXKCD
> 
> ### ** Examples
> 
> 
> library("RXKCD")
> significant <- getXKCD(882, display=FALSE)
Warning in download.file(url = "https://xkcd.com/882/info.0.json", destfile = "/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//Rtmpw9ozCl/filece1437d89d6e",  :
  URL 'https://xkcd.com/882/info.0.json': status was 'Couldn't resolve host name'
curl: (6) Could not resolve host: xkcd.com
Warning in download.file2(the_url, tmpfile) :
  could not download https://xkcd.com/882/info.0.json
Error in fromJSON2(paste("https://xkcd.com/", which, "/info.0.json", sep = "")) : 
  download.file2(the_url, tmpfile) == 0 is not TRUE
Calls: getXKCD -> fromJSON2 -> stopifnot
Execution halted
Found the following significant warnings:
  call_dvode.c:746:18: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  lincmt.c:110:11: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
  sum.c:221:11: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  sum.c:221:22: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  sum.c:227:45: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  sum.c:227:53: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RxODE.Rcheck/00install.out’ for details.
Found the following significant warnings:
  yacas/src/obmalloc.cpp:584:23: warning: comparison of constant 384307168202282325 with expression of type 'unsigned int' is always false [-Wtautological-constant-out-of-range-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Ryacas.Rcheck/00install.out’ for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs    4.9Mb
    yacas   1.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    sample_data   3.1Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/s2.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/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’.
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.
Packages suggested but not available for checking:
  ‘mixer’ ‘networkTomography’ ‘org.Sc.sgd.db’
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
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 34-35 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘oligoClasses’
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1/1 mismatches
  [1] 1 - 0 == 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 62 SKIPPED: 0 FAILED: 7
  1. Failure: examples: all examples (@test_api_stability.R#156) 
  2. Failure: examples: all examples (@test_api_stability.R#157) 
  3. Failure: examples: all examples (@test_api_stability.R#162) 
  4. Failure: execute: valid command (@test_execute.R#13) 
  5. Failure: execute: valid commands (@test_execute.R#18) 
  6. Failure: execute: runner provided (@test_execute.R#64) 
  7. Failure: execute: print_commands (@test_execute.R#69) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  pointinpolygon.c:60:7: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  slope.aspect.c:128:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  slope.aspect.c:128:33: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  vincenty.geodesics.c:50:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  vincenty.geodesics.c:126:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SDMTools.Rcheck/00install.out’ for details.
Found the following executable file:
  inst/external/env/bio14.bil
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/sdols.Rcheck/00install.out’ for details.
Running ‘cran-tests.R’ [2s/2s]
Running the tests in ‘tests/cran-tests.R’ failed.
Last 13 lines of output:
  
  
  Program received signal SIGTRAP: Trace/breakpoint trap.
  
  Backtrace for this error:
  #0  0x122e72579
  #1  0x122e71945
  #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//RtmpEQpLXP/x1353d851a0647f/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//RtmpEQpLXP/x1353d87925f7b6/iofile -n -s 2>/dev/null' had status 133
  Execution halted
Running examples in ‘secret-Ex.R’ failed
The error most likely occurred in:

> ### Name: add_github_user
> ### Title: Add a user via their GitHub username.
> ### Aliases: add_github_user
> 
> ### ** Examples
> 
> vault <- file.path(tempdir(), ".vault")
> create_vault(vault)
> 
> add_github_user("hadley", vault = vault)
Error in curl_fetch_memory(url) : 
  Timeout was reached: Resolving timed out after 10000 milliseconds
Calls: add_github_user -> get_github_key -> curl_fetch_memory
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    data   1.1Mb
    doc    1.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.7Mb
Found the following significant warnings:
  BinNegative.cpp:108:5: warning: assigning field to itself [-Wself-assign-field]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Segmentor3IsBack.Rcheck/00install.out’ for details.
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/sensors4plumes.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: ‘rggobi’ ‘gWidgetsRGtk2’ ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    doc    6.0Mb
    libs   6.3Mb
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  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Running examples in ‘SequenceAnalysis-Ex.R’ failed
The error most likely occurred in:

> ### Name: SequenceAnalysis.AAC
> ### Title: SequenceAnalysis.AAC
> ### Aliases: SequenceAnalysis.AAC
> 
> ### ** Examples
> 
> SequenceAnalysis.AAC("AKMNAAKMQWYVIGLPCERTDRSCTRQWYVPIG")
      A       R       N       D       C       E       Q       G       H       I 
0.09091 0.09091 0.03030 0.03030 0.06061 0.03030 0.06061 0.06061 0.00000 0.06061 
      L       K       M       F       P       S       T       W       Y       V 
0.03030 0.06061 0.06061 0.00000 0.06061 0.03030 0.06061 0.06061 0.06061 0.06061 
      U       X 
0.00000 0.00000 
> SequenceAnalysis.AAC("O15131",Sequence=FALSE)
Error in if (Protein_Sequence == "N/A") stop("Protein Sequence is not available") : 
  argument is of length zero
Calls: SequenceAnalysis.AAC
Execution halted
Package suggested but not available for checking: ‘MAST’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 110.9Mb
  sub-directories of 1Mb or more:
    doc     10.7Mb
    libs    96.2Mb
    sqlite   1.5Mb
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.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 195-198 (sf5.Rmd) 
Error: processing vignette 'sf5.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
Package suggested but not available for checking: ‘SGP’
Running examples in ‘shadow-Ex.R’ failed
The error most likely occurred in:

> ### Name: SVF
> ### Title: Sky View Factor (SVF) calculation
> ### Aliases: SVF SVF,SpatialPoints-method SVF,Raster-method
> 
> ### ** Examples
> 
> ## Individual locations
> data(rishon)
> location0 = rgeos::gCentroid(rishon)
> location1 = raster::shift(location0, 0, -15)
> location2 = raster::shift(location0, -10, 20)
> locations = rbind(location1, location2)
> svfs = SVF(
+   location = locations,
+   obstacles = rishon,
+   obstacles_height_field = "BLDG_HT"
+ )
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘row.names<-’ for signature ‘"data.frame", "character"’
Calls: SVF ... <Anonymous> -> <Anonymous> -> row.names<- -> <Anonymous>
Execution halted
Running ‘testthat.R’ [5s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
         package = "rgeos", group = list(), valueClass = character(0), signature = c("x", 
         "value"), default = NULL, skeleton = (function (x, value) 
         stop("invalid call in method dispatch to 'row.names<-' (no default method)", 
             domain = NA))(x, value)), <environment>)
  14: stop(gettextf("unable to find an inherited method for function %s for signature %s", 
         sQuote(fdef@generic), sQuote(cnames)), domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1 SKIPPED: 0 FAILED: 3
  1. Error: SVF calculation is correct (@test_SVF.R#6) 
  2. Error: 'inShadow' calculation is correct (@test_inShadow.R#6) 
  3. Error: Shade height calculation is correct (@test_shadowHeight.R#6) 
  
  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: sp
rgeos version: 0.3-26, (SVN revision 560)
 GEOS runtime version: 3.6.1-CAPI-1.10.1 r0 
 Linking to sp version: 1.2-7 
 Polygon checking: TRUE 

Quitting from lines 99-106 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
unable to find an inherited method for function 'row.names<-' for signature '"data.frame", "character"'
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/shallot.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘shinyBS’ ‘shinythemes’
  All declared Imports should be used.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    www   6.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    semantic   5.6Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/shp2graph.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 89-90 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   9.5Mb
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.
Running examples in ‘SiMRiv-Ex.R’ failed
The error most likely occurred in:

> ### Name: resistanceFromShape
> ### Title: Build resistance raster by combining shapefiles
> ### Aliases: resistanceFromShape
> 
> ### ** Examples
> 
> ## Example taken from the vignette; see the vignette
> ## for more details and examples.
> ## In this example we read a land cover shapefile and
> ## assign resistance values based on each polygon's
> ## land cover class (provided in the field 'coverclass')
> 
> landcover <- resistanceFromShape(
+   system.file("doc/landcover.shp", package="SiMRiv")
+   , res = 150, field = "coverclass", mapvalues = c(
+     "forest" = 0.5, "urban" = 1, "dam" = 0
+     , "shrubland" = 0.75), background = 0.95)
>     
> ## We then combine it with a river network from another
> ## shapefile, assigning a value of 0 to all rivers
> 
> river.landcover <- resistanceFromShape(
+   system.file("doc/river-sample.shp", package="SiMRiv")
+   , baseRaster = landcover, buffer = 100, field = 0
+   , background = 0.95, margin = 1000)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘row.names<-’ for signature ‘"data.frame", "character"’
Calls: resistanceFromShape -> <Anonymous> -> row.names<- -> <Anonymous>
Execution halted
Errors in running code in vignettes:
when running code in ‘SiMRiv.Rnw’
  ...
+     package = "SiMRiv"), res = 100, field = "coverclass", mapvalues = c(forest .... [TRUNCATED] 

> plot(resistance, axes = F)

> resistance <- resistanceFromShape(system.file("doc/river-sample.shp", 
+     package = "SiMRiv"), res = 100, field = "Order", mapvalues = c(`2` = 0, .... [TRUNCATED] 

  When sourcing ‘SiMRiv.R’:
Error: unable to find an inherited method for function ‘row.names<-’ for signature ‘"data.frame", "character"’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: raster
Loading required package: sp

Attaching package: ‘SiMRiv’

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

    simulate


Error: processing vignette 'SiMRiv.Rnw' failed with diagnostics:
 chunk 9 (label = simriv-7) 
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘row.names<-’ for signature ‘"data.frame", "character"’
Execution halted
evalGrids: no visible global function definition for ‘sessionInfo’
meanAndNormCI: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd sessionInfo
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "sessionInfo")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Shutting down cluster.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   3.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.9Mb
Found the following significant warnings:
  MCP_efficient.c:114:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  MCP_efficient.c:134:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  MCP_efficient.c:154:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SMCP.Rcheck/00install.out’ for details.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   6.1Mb
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/sm.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 ‘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$scaling, col = "red")
+ })
Loading required package: rgl
Loading required package: rpanel
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘rpanel’
Error in sm.surface3d(model2$eval.points, model2$est, model1$scaling,  : 
  a scaling must be specified.
Calls: with -> with.default -> eval -> eval -> sm.surface3d
Execution halted
Running ‘test_scripts.R’ [18s/44s]
Running the tests in ‘tests/test_scripts.R’ failed.
Last 13 lines of output:
  +     data = mackerel))
  Call:
  gam(formula = log(Density) ~ lo(log(mack.depth)) + lo(Temperature), 
      data = mackerel)
  
  Degrees of Freedom: 278 total; 270.9924 Residual
  Residual Deviance: 335.5316 
  
  > par(mfrow = c(2, 2))
  
  > plot.gam(model1, se = TRUE)
  Error in plot.gam(model1, se = TRUE) : could not find function "plot.gam"
  Calls: source -> withVisible -> eval -> eval
  In addition: There were 50 or more warnings (use warnings() to see the first 50)
  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’.
Packages suggested but not available for checking:
  ‘r2cytoscape’ ‘BiocStyle’ ‘graphite’ ‘hgu95av2.db’
Packages unavailable to check Rd xrefs: ‘simPATHy’, ‘graphite’
Error in re-building vignettes:
  ...
    IQR, mad, sd, var, xtabs

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

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

Identifing all possible orderings..
Total run time: 3.82 secs
Identifing all possible orderings..
Total run time: 2.49 secs
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot4350403b8f2f.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot4350403b8f2f.png': No such file or directory
Quitting from lines 346-347 (SourceSet.Rmd) 
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/spaceExt.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Error in re-building vignettes:
  ...

Loading required package: quickPlot
Loading required package: reproducible

Attaching package: 'reproducible'

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

    %>%

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

Attaching package: 'grid'

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

    gpar

Quitting from lines 357-361 (ii-modules.Rmd) 
Error: processing vignette 'ii-modules.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 32.4Mb
  sub-directories of 1Mb or more:
    libs  30.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot6db5307c2520.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot6db5307c2520.png': No such file or directory
Quitting from lines 20-30 (intro_sparkline.Rmd) 
Error: processing vignette 'intro_sparkline.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running ‘run-all.R’ [1s/33s]
Running the tests in ‘tests/run-all.R’ failed.
Last 13 lines of output:
  > 
  > # Setup global test environment
  > # Install Spark first to set SPARK_HOME
  > 
  > # NOTE(shivaram): We set overwrite to handle any old tar.gz files or directories left behind on
  > # CRAN machines. For Jenkins we should already have SPARK_HOME set.
  > install.spark(overwrite = TRUE)
  Overwrite = TRUE: download and overwrite the tar fileand Spark package directory if they exist.
  Spark not found in the cache directory. Installation will start.
  MirrorUrl not provided.
  Looking for preferred site from apache website...
  Error in file(con, "r") : 
    (converted from warning) URL 'http://www.apache.org/dyn/closer.cgi?path=spark/spark-2.3.0/spark-2.3.0-bin-hadoop2.7.tgz&as_json=1': status was 'Couldn't resolve host name'
  Calls: install.spark ... robustDownloadTar -> getPreferredMirror -> readLines -> file
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'SparkR'

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

    cov, filter, lag, na.omit, predict, sd, var, window

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

    as.data.frame, colnames, colnames<-, drop, endsWith,
    intersect, rank, rbind, sample, startsWith, subset, summary,
    transform, union

Quitting from lines 65-67 (sparkr-vignettes.Rmd) 
Error: processing vignette 'sparkr-vignettes.Rmd' failed with diagnostics:
cannot open the connection to 'http://www.apache.org/dyn/closer.cgi?path=spark/spark-2.3.0/spark-2.3.0-bin-hadoop2.7.tgz&as_json=1'
Execution halted
Packages required but not available: ‘Cairo’ ‘Rglpk’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘RCy3’
Package unavailable to check Rd xrefs: ‘RCy3’
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  14.8Mb
Clarketest: no visible global function definition for ‘pbinom’
Clarketest: no visible global function definition for ‘qbinom’
DIC: no visible global function definition for ‘model.matrix’
LogLike: no visible global function definition for ‘model.matrix’
Vuongtest: no visible global function definition for ‘var’
Vuongtest: no visible global function definition for ‘qnorm’
Vuongtest: no visible global function definition for ‘pnorm’
est.sc: no visible global function definition for ‘model.matrix’
gpind: no visible global function definition for ‘rgamma’
nbind: no visible global function definition for ‘rgamma’
poiind: no visible global function definition for ‘rgamma’
zigpind: no visible global function definition for ‘rbinom’
zigpind: no visible global function definition for ‘rgamma’
zipind: no visible global function definition for ‘rbinom’
zipind: no visible global function definition for ‘rgamma’
Undefined global functions or variables:
  model.matrix pbinom pnorm qbinom qnorm rbinom rgamma var
Consider adding
  importFrom("stats", "model.matrix", "pbinom", "pnorm", "qbinom",
             "qnorm", "rbinom", "rgamma", "var")
to your NAMESPACE file.
Running examples in ‘spatialEco-Ex.R’ failed
The error most likely occurred in:

> ### Name: daymet.tiles
> ### Title: DAYMET Tile ID's
> ### Aliases: daymet.tiles
> 
> ### ** Examples
> 
> library(sp)
> library(raster)
> data(DAYMET_tiles)
> e <- extent(-117.2567, -104.7523, 36.62797, 47.68194) 
>   plot(DAYMET_tiles)
>     plot(e, col="red", add=TRUE)
> 
> # Using extent object	
> daymet.tiles(x = e, tiles = DAYMET_tiles, ids = "Id")
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘row.names<-’ for signature ‘"data.frame", "NULL"’
Calls: daymet.tiles ... <Anonymous> -> .local -> row.names<- -> <Anonymous>
Execution halted
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    R      4.9Mb
    doc    4.7Mb
    help   5.0Mb
    libs   1.6Mb
row.names<-:
  function(x, make.names, value)
row.names<-.hyperframe:
  function(x, value)

row.names<-:
  function(x, make.names, value)
row.names<-.hyperframe:
  function(x, value)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Running ‘testsAtoF.R’ [28s/61s]
  Running ‘testsGtoK.R’ [19s/42s]
Running the tests in ‘tests/testsGtoK.R’ failed.
Last 13 lines of output:
  +                  statistic="pcf")
  +    Y1p <- simulate(fit1p)[[1]]
  +    stopifnot(is.ppp(Y1p))
  +   
  +    # ... and Abdollah's code
  + 
  +    fit2 <- kppm(redwood ~x, cluster="Cauchy", statistic="K")
  +    Y2 <- simulate(fit2)[[1]]
  +    stopifnot(is.ppp(Y2))
  + 
  +  }
  + 
  + })
  
  Execution halted
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  13.9Mb
Error in re-building vignettes:
  ...
Quitting from lines 244-246 (nb_sf.Rmd) 
Error: processing vignette 'nb_sf.Rmd' failed with diagnostics:
unable to find an inherited method for function 'row.names<-' for signature '"data.frame", "character"'
Execution halted
Running ‘testthat.R’ [31s/68s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(spew)
  > 
  > test_check("spew")
  ── 1. Failure: Iterative Proportional Fitting (@test-ipf.R#43)  ────────────────
  mse_ipf < mse_srs isn't true.
  
  [1] "Place has 0 Households!"
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 100 SKIPPED: 7 FAILED: 1
  1. Failure: Iterative Proportional Fitting (@test-ipf.R#43) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: sp
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "10"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "10"
Quitting from lines 45-64 (spew-quickstart.Rmd) 
Error: processing vignette 'spew-quickstart.Rmd' failed with diagnostics:
polygon edge not found
Execution halted
Error in re-building vignettes:
  ...
Instead of arguments 'rows', 'cols', 'widths', 'heights', 'maxPlotsPerPage',
  it now accepts only 'nrow' and 'ncol'.
Arguments 'widths' & 'heights' can still be defined and are handed over
  to <gridExtra:::marrangeGrob>.
Sorry for the inconvenience.
Loading required package: parallel
Loading required package: stabs
This is mboost 2.8-1. See 'package?mboost' and 'news(package  = "mboost")'
for a complete list of changes.


Attaching package: 'ggplot2'

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

    %+%

Warning in (function (xnew)  :
  predictions outside fitted range for lin(glucose).
Warning in (function (xnew)  :
  predictions outside fitted range for sm(glucose).
Warning in bsplines(mf[[i]], knots = args$knots[[i]]$knots, boundary.knots = args$knots[[i]]$boundary.knots,  :
  Some 'x' values are beyond 'boundary.knots'; Linear extrapolation used.

Execution halted
NoSep: no visible global function definition for ‘setNames’
Reshape: no visible global function definition for ‘setNames’
Reshape: no visible global function definition for ‘reshape’
read.concat: no visible global function definition for ‘count.fields’
read.concat: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  count.fields read.table reshape setNames
Consider adding
  importFrom("stats", "reshape", "setNames")
  importFrom("utils", "count.fields", "read.table")
to your NAMESPACE file.
Undocumented code objects:
  ‘row.names<-’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Unknown package ‘antaresViz’ in Rd xrefs
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   5.9Mb
row.names<-:
  function(x, make.names, value)
row.names<-.SpatialPoints:
  function(x, value)

row.names<-:
  function(x, make.names, value)
row.names<-.SpatialMultiPoints:
  function(x, value)

row.names<-:
  function(x, make.names, value)
row.names<-.SpatialPointsDataFrame:
  function(x, value)

row.names<-:
  function(x, make.names, value)
row.names<-.SpatialPolygons:
  function(x, value)

row.names<-:
  function(x, make.names, value)
row.names<-.SpatialPolygonsDataFrame:
  function(x, value)

row.names<-:
  function(x, make.names, value)
row.names<-.SpatialLines:
  function(x, value)

row.names<-:
  function(x, make.names, value)
row.names<-.SpatialLinesDataFrame:
  function(x, value)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Running ‘agg.R’ [1s/2s]
Running the tests in ‘tests/agg.R’ failed.
Complete output:
  > library(sp)
  > g = SpatialGrid(GridTopology(c(5,5), c(10,10), c(3,3)))
  > p = as(g, "SpatialPolygons")
  > p$z = c(1,0,1,0,1,0,1,0,1)
  > cc = coordinates(g)
  > p$ag1 = aggregate(p, p, mean)[[1]]
  Error in (function (classes, fdef, mtable)  : 
    unable to find an inherited method for function 'row.names<-' for signature '"data.frame", "NULL"'
  Calls: aggregate ... over -> over -> .local -> row.names<- -> <Anonymous>
  Execution halted
Errors in running code in vignettes:
when running code in ‘over.Rnw’
  ...

> image(agg)

> points(meuse.grid, pch = 3, cex = 0.2, col = "#80808080")

> sl.agg = aggregate(meuse.grid[, 1:3], sl, mean)

  When sourcing ‘over.R’:
Error: unable to find an inherited method for function ‘row.names<-’ for signature ‘"data.frame", "NULL"’
Execution halted
Error in re-building vignettes:
  ...
Found more than one class "SpatialMultiPoints" in cache; using the first, from namespace 'sp'
Also defined by ‘.GlobalEnv’
Found more than one class "SpatialMultiPointsDataFrame" in cache; using the first, from namespace 'sp'
Also defined by ‘.GlobalEnv’
Found more than one class "SpatialMultiPointsDataFrame" in cache; using the first, from namespace 'sp'
Also defined by ‘.GlobalEnv’
rgdal: version: 1.2-16, (SVN revision 701)
 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 
rgeos version: 0.3-26, (SVN revision 560)
 GEOS runtime version: 3.6.1-CAPI-1.10.1 r0 
 Linking to sp version: 1.2-7 
 Polygon checking: TRUE 


Error: processing vignette 'over.Rnw' failed with diagnostics:
 chunk 30 
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘row.names<-’ for signature ‘"data.frame", "NULL"’
Execution halted
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs  11.3Mb
Running examples in ‘SRRS-Ex.R’ failed
The error most likely occurred in:

> ### Name: SRRS-package
> ### Title: The Stepwise Response Refinement Screener (SRRS)
> ### Aliases: SRRS-package
> 
> ### ** Examples
> 
> SRRS()
Warning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "ComboBox".
Calls: SRRS -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Error in re-building vignettes:
  ...
Warning 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 92-96 (SSDM.Rmd) 
Error: processing vignette 'SSDM.Rmd' failed with diagnostics:
trying to get slot "projection" from an object of a basic class ("NULL") with no slots
Execution halted
calcgroup : probtotrating: no visible global function definition for
  ‘convolve’
enterratdata: no visible global function definition for ‘edit’
gplot.SSrat: no visible global function definition for ‘par’
gplot.SSrat: no visible global function definition for ‘plot’
gplot.SSrat: no visible global function definition for ‘legend’
Undefined global functions or variables:
  convolve edit legend par plot
Consider adding
  importFrom("graphics", "legend", "par", "plot")
  importFrom("stats", "convolve")
  importFrom("utils", "edit")
to your NAMESPACE file.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    include   8.7Mb
Packages required but not available:
  ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’ ‘RSCABS’

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

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


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

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

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

> WinHalfWidth<-30

> permReps<-10

> a<-maxchi(inputFile, breaks, WinHalfWidth, permReps)
Running examples in ‘StockChina-Ex.R’ failed
The error most likely occurred in:

> ### Name: index.CN
> ### Title: Grab Real-Time Stock Index Information in China Market
> ### Aliases: index.CN
> 
> ### ** Examples
> 
> index.CN("sh")
Warning in file(file, "r") :
  URL 'http://hq.sinajs.cn/list=s_sh000001': status was 'Couldn't resolve host name'
Error in file(file, "r") : 
  cannot open the connection to 'http://hq.sinajs.cn/list=s_sh000001'
Calls: index.CN -> scan -> file
Execution halted
Running examples in ‘stplanr-Ex.R’ failed
The error most likely occurred in:

> ### Name: gclip
> ### Title: Crops spatial object x to the bounding box of spatial object (or
> ###   matrix) b
> ### Aliases: gclip
> 
> ### ** Examples
> 
> data(cents)
> cb <- rgeos::gBuffer(cents[8, ], width = 0.012, byid = TRUE)
Warning in rgeos::gBuffer(cents[8, ], width = 0.012, byid = TRUE) :
  Spatial object is not projected; GEOS expects planar coordinates
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘row.names<-’ for signature ‘"data.frame", "character"’
Calls: <Anonymous> -> row.names<- -> <Anonymous>
Execution halted
Running ‘testthat.R’ [7s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
     })(list("data.frame", "character"), new("standardGeneric", .Data = function (x, value) 
     standardGeneric("row.names<-"), generic = structure("row.names<-", package = "rgeos"), 
         package = "rgeos", group = list(), valueClass = character(0), signature = c("x", 
         "value"), default = NULL, skeleton = (function (x, value) 
         stop("invalid call in method dispatch to 'row.names<-' (no default method)", 
             domain = NA))(x, value)), <environment>)
  6: stop(gettextf("unable to find an inherited method for function %s for signature %s", 
         sQuote(fdef@generic), sQuote(cnames)), domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 3 SKIPPED: 1 FAILED: 1
  1. Error: calc_catchment returns a SpatialPolygonsDataFrame (@test-calc_catchment.R#11) 
  
  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 111-114 (introducing-stplanr.Rmd) 
Error: processing vignette 'introducing-stplanr.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
Packages required but not available: ‘Rglpk’ ‘MultAlloc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘limma’ ‘samr’
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.1Mb
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/streamR.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running ‘test-all.R’ [161s/339s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  RUNIT TEST PROTOCOL -- Mon Mar 12 04:54:14 2018 
  *********************************************** 
  Number of test functions: 18 
  Number of errors: 1 
  Number of failures: 0 
  
   
  1 Test Suite : 
  stremr unit testing - 18 test functions, 1 error, 0 failures
  ERROR in test.speedglm.allestimators10Kdata: Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
  Error: 
  
  unit testing failed (#test failures: 0, #R errors: 1)
  
  Execution halted
installed size is 31.3Mb
  sub-directories of 1Mb or more:
    libs  30.7Mb
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.
sh: line 1: 46285 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//RtmpG0qglB/x13b2c05064a19/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  0x1275d8579
#1  0x1275d7945
#2  0x7fff93ac4529
Quitting from lines 61-64 (stRvignette.Rmd) 
Error: processing vignette 'stRvignette.Rmd' failed with diagnostics:
X-13 has returned a non-zero exist status, which means that the current spec file cannot be processed for an unknown reason.
Execution halted
Packages required but not available: ‘gWidgets2RGtk2’ ‘RGtk2’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.3Mb
    help   1.0Mb
    libs   1.3Mb
installed size is 67.2Mb
  sub-directories of 1Mb or more:
    libs  66.3Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    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.
Quitting from lines 540-542 (survtmle_intro.Rmd) 
Error: processing vignette 'survtmle_intro.Rmd' failed with diagnostics:
'names' attribute [3] must be the same length as the vector [2]
Execution halted
Found the following significant warnings:
  trlan/trlcore.c:983:15: warning: comparison of array 'info->oldcpf' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlcore.c:1642:9: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  trlan/trlcore.c:1642:20: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  trlan/trlaux.c:28:13: warning: comparison of array 'info->log_file' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlaux.c:41:13: warning: comparison of array 'info->log_file' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlaux.c:62:13: warning: comparison of array 'info->cpfile' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlan.c:171:20: warning: comparison of array 'info->oldcpf' equal to a null pointer is always false [-Wtautological-pointer-compare]
  trlan/ztrlan.c:198:28: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  trlan/ztrlan.c:198:40: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
  trlan/ztrlcore.c:704:27: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  trlan/ztrlcore.c:704:39: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
  trlan/ztrlcore.c:1418:12: warning: comparison of array 'info->oldcpf' not equal to a null pointer is always true [-Wtautological-pointer-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/svd.Rcheck/00install.out’ for details.
File ‘svmpath/libs/svmpath.so’:
  Found ‘__gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘__gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘__gfortran_st_read’, possibly from ‘read’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi30spec.o’, ‘mi35mps.o’,
      ‘mi36mps.o’, ‘mi40bfil.o’
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’

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

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

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

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

$SOLVER
[1] "glpkAPI"

$METHOD
[1] "simplex"

$TOLERANCE
[1] 1e-06

$MAXIMUM
[1] 1000

$ALGORITHM
[1] "fba"

$OPT_DIRECTION
[1] "max"

$USE_NAMES
[1] FALSE

$PATH_TO_MODEL
[1] "."

$SOLVER_CTRL_PARM
  NA
1 NA

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

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

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


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




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

Error: processing vignette 'sybil.Rnw' failed with diagnostics:
 chunk 13 
Error in checkDefaultMethod(solver, method, pType) : 
  package ‘glpkAPI’ not found
Execution halted
Packages suggested but not available for checking:
  ‘sylly.de’ ‘sylly.en’ ‘sylly.es’
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SynergizeR.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
plot.tabu: no visible global function definition for ‘image’
plot.tabu: no visible global function definition for ‘gray’
plot.tabu: no visible global function definition for ‘par’
plot.tabu: no visible global function definition for ‘layout’
plot.tabu: no visible global function definition for ‘plot’
Undefined global functions or variables:
  gray image layout par plot
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "image", "layout", "par", "plot")
to your NAMESPACE file.
Running ‘testthat.R’ [22s/47s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  9: classification.uid(id, callopts = callopts, return_id = return_id, ...)
  10: lapply(id, fun, callopts = callopts)
  11: FUN(X[[i]], ...)
  12: res$raise_for_status()
  13: fauxpas::http(self, behavior = "stop")
  14: http.HttpResponse(self, behavior = "stop")
  15: tmp$do(response)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 451 SKIPPED: 0 FAILED: 2
  1. Error: Taxmap can be intialized from queried data (@test--taxmap_parsers.R#106) 
  2. Error: Taxmap can be intialized from raw strings (@test--taxmap_parsers.R#167) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    tklibs   4.7Mb
Errors in running code in vignettes:
when running code in ‘tcpl_Overview.Rnw’
  ...
Assertion failure at kmp_runtime.cpp(6480): __kmp_thread_pool == __null.
OMP: Error #13: Assertion failure at kmp_runtime.cpp(6480).
OMP: Hint: Please submit a bug report with this message, compile and run commands used, and machine configuration info including native compiler and operating system versions. Faster response will be obtained by including all program sources. For information on submitting this issue, please see http://www.intel.com/software/products/support/.
Assertion failure at kmp_runtime.cpp(6480): __kmp_thread_pool == __null.
OMP: Error #13: Assertion failure at kmp_runtime.cpp(6480).
OMP: Hint: Please submit a bug report with this message, compile and run commands used, and machine configuration info including native compiler and operating system versions. Faster response will be obtained by including all program sources. For information on submitting this issue, please see http://www.intel.com/software/products/support/.

  When sourcing ‘tcpl_Overview.R’:
Error: argument to 'which' is not logical
Execution halted
Error in re-building vignettes:
  ...
Loading required package: data.table
No methods found in package ‘RSQLite’ for request: ‘dbGetQuery’ when loading ‘tcpl’
tcpl (v1.2.2) loaded with the following settings:
  TCPL_DB:    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/tcpl.Rcheck/tcpl/sql/tcpldb.sqlite
  TCPL_USER:  NA
  TCPL_HOST:  NA
  TCPL_DRVR:  SQLite
Default settings stored in TCPL.conf. See ?tcplConf for more information.
Warning: Closing open result set, pending rows
Assertion failure at kmp_runtime.cpp(6480): __kmp_thread_pool == __null.
OMP: Error #13: Assertion failure at kmp_runtime.cpp(6480).
OMP: Hint: Please submit a bug report with this message, compile and run commands used, and machine configuration info including native compiler and operating system versions. Faster response will be obtained by including all program sources. For information on submitting this issue, please see http://www.intel.com/software/products/support/.
Assertion failure at kmp_runtime.cpp(6480): __kmp_thread_pool == __null.
OMP: Error #13: Assertion failure at kmp_runtime.cpp(6480).
OMP: Hint: Please submit a bug report with this message, compile and run commands used, and machine configuration info including native compiler and operating system versions. Faster response will be obtained by including all program sources. For information on submitting this issue, please see http://www.intel.com/software/products/support/.

Error: processing vignette 'tcpl_Overview.Rnw' failed with diagnostics:
 chunk 20 
Error in which(x) : argument to 'which' is not logical
Execution halted
installed size is 35.6Mb
  sub-directories of 1Mb or more:
    libs  34.3Mb
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/tensorBF.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Error in re-building vignettes:
  ...
Evaluating log-likelihood at the estimate. Using 20 bridges: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 .
This model was fit using MCMC.  To examine model diagnostics and check for degeneracy, use the mcmc.diagnostics() function.
Starting maximum likelihood estimation via MCMLE:
Iteration 1 of at most 20:
Optimizing with step length 1.
The log-likelihood improved by 0.3009.
Step length converged once. Increasing MCMC sample size.
Iteration 2 of at most 20:
Optimizing with step length 1.
The log-likelihood improved by 0.0008755.
Step length converged twice. Stopping.
Evaluating log-likelihood at the estimate. Using 20 bridges: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 .
This model was fit using MCMC.  To examine model diagnostics and check for degeneracy, use the mcmc.diagnostics() function.
Starting maximum likelihood estimation via MCMLE:
Iteration 1 of at most 20:
Optimizing with step length 1.
The log-likelihood improved by 0.4482.
Step length converged once. Increasing MCMC sample size.
Iteration 2 of at most 20:
Optimizing with step length 1.
The log-likelihood improved by 0.007716.
Step length converged twice. Stopping.
This model was fit using MCMC.  To examine model diagnostics and check for degeneracy, use the mcmc.diagnostics() function.

Execution halted
installed size is 39.2Mb
  sub-directories of 1Mb or more:
    libs       7.2Mb
    tessdata  31.0Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.6Mb
    libs   4.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/textTinyR.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [22s/49s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── 1. Error: t4f works for different params (@test-predict.R#51)  ──────────────
  cannot open URL 'https://gitlab.com/sw1/themetagenomics_data/raw/master/t4f_ref_profiles.rds'
  1: download_ref(tmp, reference = "silva_ko", overwrite = FALSE) at testthat/test-predict.R:51
  2: suppressWarnings(utils::download.file(sprintf("https://gitlab.com/sw1/themetagenomics_data/raw/master/%s", 
         fn), destfile = file.path(destination, fn), method = "auto", mode = "wb", quiet = !verbose))
  3: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  4: utils::download.file(sprintf("https://gitlab.com/sw1/themetagenomics_data/raw/master/%s", 
         fn), destfile = file.path(destination, fn), method = "auto", mode = "wb", quiet = !verbose)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 45 SKIPPED: 4 FAILED: 1
  1. Error: t4f works for different params (@test-predict.R#51) 
  
  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 37-39 (functional_prediction.Rmd) 
Error: processing vignette 'functional_prediction.Rmd' failed with diagnostics:
cannot open URL 'https://gitlab.com/sw1/themetagenomics_data/raw/master/ko_13_5_precalculated.tab.gz'
Execution halted
row.names<-:
  function(x, make.names, value)
row.names<-.tbl_df:
  function(x, value)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Running ‘testthat.R’ [2s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  12: shannon_entropy(.)
  13: reduce_data(.data, !(!enquo(X)), numvars = 1, na.rm = na.rm)
  14: tidyselect::vars_select(names(reduced_tab), !(!(!quos(...))))
  15: vars_select_eval(.vars, quos)
  16: map_lgl(quos, quo_is_helper)
  17: .f(.x[[i]], ...)
  18: extract_expr(quo)
  19: is_call(expr, paren_sym)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 37 SKIPPED: 0 FAILED: 1
  1. Error: right number of columns given (@test-errors.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘tidyxl/libs/tidyxl.so’:
  Found ‘_abort’, possibly from ‘abort’ (C)
    Object: ‘xlex.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  common.c:121:16: 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/tiff.Rcheck/00install.out’ for details.
Found the following significant warnings:
  tm.c:184:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  tm.c:185:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/TimeMachine.Rcheck/00install.out’ for details.
row.names<-:
  function(x, make.names, value)
row.names<-.TimeInstantDataFrame:
  function(x, value)

row.names<-:
  function(x, make.names, value)
row.names<-.TimeIntervalDataFrame:
  function(x, value)

row.names<-:
  function(x, make.names, value)
row.names<-.TimeIntervalDataFrame:
  function(x, value)

row.names<-:
  function(x, make.names, value)
row.names<-.TimeInstantDataFrame:
  function(x, value)

row.names<-:
  function(x, make.names, value)
row.names<-.SubtimeDataFrame:
  function(x, value)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
.my.tkdev: no visible global function definition for ‘X11’
tkpersp : draw: no visible global function definition for ‘par’
tkpersp : draw: no visible global function definition for ‘persp’
Undefined global functions or variables:
  X11 par persp
Consider adding
  importFrom("grDevices", "X11")
  importFrom("graphics", "par", "persp")
to your NAMESPACE file.
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    examples  12.1Mb
    include    2.9Mb
installed size is 24.6Mb
  sub-directories of 1Mb or more:
    libs  24.5Mb
Packages suggested but not available for checking:
  ‘Rcampdf’ ‘Rgraphviz’ ‘Rpoppler’ ‘tm.lexicon.GeneralInquirer’
Packages unavailable to check Rd xrefs: ‘graph’, ‘Rpoppler’
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  tmux not found
  1: stop("tmux not found") at testthat/test-server.R:3
  
  ── 3. Error: (unknown) (@test-session.R#3)  ────────────────────────────────────
  tmux not found
  1: stop("tmux not found") at testthat/test-session.R:3
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 3
  1. Error: (unknown) (@test-pipe.R#3) 
  2. Error: (unknown) (@test-server.R#3) 
  3. Error: (unknown) (@test-session.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(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
Packages suggested but not available for checking: ‘RGtk2’ ‘gWidgetsRGtk2’
Package required but not available: ‘qpgraph’

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

Package suggested but not available for checking: ‘rggobi’

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

> ### Name: contour.TPCmsm
> ### Title: contour method for a TPCmsm object
> ### Aliases: contour.TPCmsm
> ### Keywords: aplot hplot methods multivariate survival
> 
> ### ** Examples
> 
> # Set the number of threads
> nth <- setThreadsTP(2)
> 
> # Create survTP object
> data(colonTP)
> colonTP_obj <- with( colonTP, survTP(time1, event1, Stime, event, age=age) )
> 
> # Compute IPCW conditional transition probabilities without confidence band
> TPCmsm_obj <- transIPCW(colonTP_obj, s=57, t=310, x=0)

 *** caught segfault ***
address 0x7fe1540c8200, cause 'memory not mapped'

Traceback:
 1: TransPROB.IPCW2(object, UT, UX, nboot = 1, ...)
 2: TransPROB(object, UT, UX, nboot = 1, ...)
 3: TransMethod.TPC(object, s, t, state.names, conf, n.boot, conf.level,     method.boot, xi = x, bw = bw, window = window, methodweights = method.weights,     methodest = method.est, ...)
 4: TransMethod(object, s, t, state.names, conf, n.boot, conf.level,     method.boot, xi = x, bw = bw, window = window, methodweights = method.weights,     methodest = method.est, ...)
 5: transIPCW(colonTP_obj, s = 57, t = 310, x = 0)
An irrecoverable exception occurred. R is aborting now ...

 *** caught segfault ***
address 0x7fe1540c8200, cause 'memory not mapped'

Traceback:
 1: TransPROB.IPCW2(object, UT, UX, nboot = 1, ...)
 2: TransPROB(object, UT, UX, nboot = 1, ...)
 3: TransMethod.TPC(object, s, t, state.names, conf, n.boot, conf.level,     method.boot, xi = x, bw = bw, window = window, methodweights = method.weights,     methodest = method.est, ...)
 4: TransMethod(object, s, t, state.names, conf, n.boot, conf.level,     method.boot, xi = x, bw = bw, window = window, methodweights = method.weights,     methodest = method.est, ...)
 5: transIPCW(colonTP_obj, s = 57, t = 310, x = 0)
An irrecoverable exception occurred. R is aborting now ...
File ‘tpr/libs/tpr.so’:
  Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’

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

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

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: ggplot2

Attaching package: 'trackeR'

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

    append

Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=57.157231,-2.104296&zoom=13&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false
Quitting from lines 96-97 (TourDetrackeR.Rmd) 
Error: processing vignette 'TourDetrackeR.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
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/TrajDataMining.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Error in re-building vignettes:
  ...
Loading required package: 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 139-141 (DengueVignette.Rmd) 
Error: processing vignette 'DengueVignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 37.1Mb
  sub-directories of 1Mb or more:
    libs  36.7Mb
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.
Error: processing vignette 'r_radix.Rmd' failed with diagnostics:
shared object 'stringi.so' not found
Execution halted
package ‘SIBER’ exists but was not installed under R >= 2.10.0 so xrefs cannot be checked
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Found the following significant warnings:
  ./tsBSS.h:10:22: warning: 'varExx_k' has C-linkage specified, but returns user-defined type 'arma::mat' (aka 'Mat<double>') which is incompatible with C [-Wreturn-type-c-linkage]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/tsBSS.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘TSodbc’
Package suggested but not available for checking: ‘TSodbc’
Errors in running code in vignettes:
when running code in ‘Guide.Stex’
  ...

> x <- TSget("QNA.CAN.B1_GE.CARSA.Q", oecd)
Mar 11, 2018 12:16:56 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: https://stats.oecd.org/restsdmx/sdmx.ashx/GetDataStructure/QNA
Mar 11, 2018 12:17:27 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
SEVERE: Exception. Class: java.net.UnknownHostException - Message: stats.oecd.org

  When sourcing ‘Guide.R’:
Error: QNA.CAN.B1_GE.CARSA.Q error: it.bancaditalia.oss.sdmx.exceptions.SdmxIOException: Connection problems while talking to endpoint: stats.oecd.org
Execution halted
when running code in ‘GuideAppendix.Stex’
  ...

> options(continue = "  ")

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

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

  When sourcing ‘GuideAppendix.R’:
Error: Failed to connect to database: Error: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)
Execution halted
Error in re-building vignettes:
  ...
Loading required package: TSdbi
Mar 11, 2018 12:17:35 PM it.bancaditalia.oss.sdmx.util.Configuration init
INFO: No configuration found. Apply defaults.
Mar 11, 2018 12:17:35 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: https://stats.oecd.org/restsdmx/sdmx.ashx/GetDataStructure/QNA
Mar 11, 2018 12:18:06 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
SEVERE: Exception. Class: java.net.UnknownHostException - Message: stats.oecd.org

Error: processing vignette 'Guide.Stex' failed with diagnostics:
 chunk 3 
Error in .local(serIDs, con, ...) : 
  QNA.CAN.B1_GE.CARSA.Q error: it.bancaditalia.oss.sdmx.exceptions.SdmxIOException: Connection problems while talking to endpoint: stats.oecd.org
Execution halted
Running examples in ‘TSEtools-Ex.R’ failed
The error most likely occurred in:

> ### Name: getTSE
> ### Title: Download Historical Dataset from Tehran Stock Exchange (TSE)
> ### Aliases: getTSE
> 
> ### ** Examples
> 
> 	fpath<-system.file("extdata", "sample.csv", package="TSEtools")
> 	assets0<-getTSE(fpath)$assets
proceeding...
Warning in download.file(temp, file1, mode = "wb", quiet = TRUE) :
  URL 'http://www.tsetmc.com/tsev2/data/Export-txt.aspx?t=i&a=1&b=0&i=39453972158399542': status was 'Couldn't resolve host name'
Error in download.file(temp, file1, mode = "wb", quiet = TRUE) : 
  cannot open URL 'http://www.tsetmc.com/tsev2/data/Export-txt.aspx?t=i&a=1&b=0&i=39453972158399542'
Calls: getTSE -> download.file
Execution halted
Error in re-building vignettes:
  ...
Loading required package: TTR
Version 0.4-0 included new data defaults. See ?getSymbols.
'getSymbols' currently uses auto.assign=TRUE by default, but will
use auto.assign=FALSE in 0.5-0. You will still be able to use
'loadSymbols' to automatically load data. getOption("getSymbols.env")
and getOption("getSymbols.auto.assign") will still be checked for
alternate defaults.

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

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

This message is shown once per session and may be disabled by setting
options("getSymbols.yahoo.warning"=FALSE).
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]="./webshot134eb43537534.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot134eb43537534.png': No such file or directory
Quitting from lines 37-64 (TSstudio_Intro.Rmd) 
Error: processing vignette 'TSstudio_Intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  frame.c:147:21: warning: comparison of constant 4 with expression of type 'enum mad_layer' 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/tuneR.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/turboEM.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Error in re-building vignettes:
  ...
Loading required package: gbm
Loading required package: survival
Loading required package: lattice
Loading required package: splines
Loading required package: parallel
Loaded gbm 2.1.3
Loading required package: survey
Loading required package: grid
Loading required package: Matrix

Attaching package: ‘survey’

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

    dotchart

Loading required package: xtable
Loading required package: latticeExtra
Loading required package: RColorBrewer
Warning in dx.wts(ps.lalonde, data = lalonde, estimand = "ATE", vars = c("age",  :
  A different estimand was specified when fitting this ps object.  Results for
      the original estimand are being returned.

Execution halted
installed size is 28.8Mb
  sub-directories of 1Mb or more:
    doc         5.3Mb
    dummydata   1.4Mb
    libs       21.0Mb
Running examples in ‘umx-Ex.R’ failed
The error most likely occurred in:

> ### Name: residuals.MxModel
> ### Title: Get residuals from an MxModel
> ### Aliases: residuals.MxModel
> 
> ### ** Examples
> 
> require(umx)
> data(demoOneFactor)
> latents  = c("g")
> manifests = names(demoOneFactor)
> m1 <- mxModel("One Factor", type = "RAM", 
+ 	manifestVars = manifests, latentVars = latents, 
+ 	mxPath(from = latents, to = manifests),
+ 	mxPath(from = manifests, arrows = 2),
+ 	mxPath(from = latents, arrows = 2, free = FALSE, values = 1.0),
+ 	mxData(cov(demoOneFactor), type = "cov", numObs = 500)
+ )
> m1 = umxRun(m1, setLabels = TRUE, setValues = TRUE)
Running One Factor with 10 parameters
Error in runHelper(model, frontendStart, intervals, silent, suppressWarnings,  : 
  c++ exception (unknown reason)
Calls: umxRun -> mxRun -> runHelper
Execution halted
Running ‘testthat.R’ [6s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  6: message(e)
  7: withRestarts({
         signalCondition(cond)
         defaultHandler(cond)
     }, muffleMessage = function() NULL)
  8: withOneRestart(expr, restarts[[1L]])
  9: doWithOneRestart(return(expr), restart)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 54 SKIPPED: 0 FAILED: 2
  1. Error: (unknown) (@test_umx_has_CI.r#41) 
  2. Error: (unknown) (@test_umx_is_RAM.r#10) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    1.6Mb
    libs   2.0Mb
Running examples in ‘unrtf-Ex.R’ failed
The error most likely occurred in:

> ### Name: unrtf
> ### Title: Convert rtf Documents
> ### Aliases: unrtf
> 
> ### ** Examples
> 
> library(unrtf)
> text <- unrtf("https://jeroen.github.io/files/sample.rtf", format = "text")
Warning in utils::download.file(file, tmp, mode = "wb", quiet = !verbose) :
  URL 'https://jeroen.github.io/files/sample.rtf': status was 'Couldn't resolve host name'
Error in utils::download.file(file, tmp, mode = "wb", quiet = !verbose) : 
  cannot open URL 'https://jeroen.github.io/files/sample.rtf'
Calls: unrtf -> <Anonymous>
Execution halted
Running examples in ‘urltools-Ex.R’ failed
The error most likely occurred in:

> ### Name: suffix_extract
> ### Title: extract the suffix from domain names
> ### Aliases: suffix_extract
> 
> ### ** Examples
> 
> 
> # Using url_parse
> domain_name <- url_parse("http://en.wikipedia.org")$domain
> suffix_extract(domain_name)
              host subdomain    domain suffix
1 en.wikipedia.org        en wikipedia    org
> 
> # Using domain()
> domain_name <- domain("http://en.wikipedia.org")
> suffix_extract(domain_name)
              host subdomain    domain suffix
1 en.wikipedia.org        en wikipedia    org
> 
> #Relying on a fresh version of the suffix dataset
> suffix_extract(domain("http://en.wikipedia.org"), suffix_refresh())
Warning in readLines(connection) :
  URL 'https://www.publicsuffix.org/list/effective_tld_names.dat': status was 'Couldn't resolve host name'
Error in readLines(connection) : 
  cannot open the connection to 'https://www.publicsuffix.org/list/effective_tld_names.dat'
Calls: suffix_extract -> suffix_refresh -> readLines
Execution halted
Running ‘testthat.R’ [1s/32s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(urltools)
  > 
  > test_check("urltools")
  ── 1. Error: Suffix extraction works with new suffixes (@test_suffixes.R#75)  ──
  cannot open the connection to 'https://www.publicsuffix.org/list/effective_tld_names.dat'
  1: suffix_extract("en.wikipedia.org", suffix_refresh()) at testthat/test_suffixes.R:75
  2: suffix_refresh()
  3: readLines(connection)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 191 SKIPPED: 0 FAILED: 1
  1. Error: Suffix extraction works with new suffixes (@test_suffixes.R#75) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘USCF-Ex.R’ failed
The error most likely occurred in:

> ### Name: elo
> ### Title: Get Elo Rating
> ### Aliases: elo
> 
> ### ** Examples
> 
> elo(12641216)
Warning in file(file, "rt") :
  URL 'http://www.uschess.org/msa/MbrDtlMain.php?12641216': status was 'Couldn't resolve host name'
Error in file(file, "rt") : 
  cannot open the connection to 'http://www.uschess.org/msa/MbrDtlMain.php?12641216'
Calls: elo -> read.table -> file
Execution halted
File ‘uuid/libs/uuid.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘gen_uuid.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘gen_uuid.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 37.7Mb
  sub-directories of 1Mb or more:
    libs  36.8Mb
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/VarReg.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  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
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/vcfR.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  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 24-36 (intro_to_vegalite.Rmd) 
Error: processing vignette 'intro_to_vegalite.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  16.1Mb
installed size is 26.8Mb
  sub-directories of 1Mb or more:
    libs  26.3Mb
Running ‘run.R’ [37s/44s]
Running the tests in ‘tests/run.R’ failed.
Last 13 lines of output:
  |   * Fail: alike(df.cur, df.tpl)
  |   * Fail: alike(df.tpl, df.cur2)
  | in 'unitizer/alike.R'
  
  |   * Fail: vetr:::attr_compare(structure(list(integer(), character())), 
  |     data.frame(a = 1:10, b = letters[1:10]), attr.mode = 2)
  | in 'unitizer/internal.R'
  
  | Newly evaluated tests do not match unitizer (Pass: 1060, Fail: 6); see above 
  | for more info, or run in interactive mode.
  
  Error in unitize_core(test.files = test.files, store.ids = store.ids,  : 
    Cannot proceed in non-interactive mode.
  Calls: unitize_dir -> unitize_core
  Execution halted
Packages required but not available: ‘gWidgetsRGtk2’ ‘RGtk2’ ‘Cairo’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 157-163 (using_visdat.Rmd) 
Error: processing vignette 'using_visdat.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc           4.7Mb
    htmlwidgets   3.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(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
File ‘waffect/libs/waffect.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘waffect.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 51.6Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  49.2Mb
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 124-128 (walker.Rmd) 
Error: processing vignette 'walker.Rmd' failed with diagnostics:
argument of length 0
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/wand.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [30s/67s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 26 SKIPPED: 0 FAILED: 18
  1. Error: canCallChrome (@test-chrome.R#3) 
  2. Error: pickUpErrorFromReturnCode (@test-chrome.R#43) 
  3. Error: pickUpErrorFromPortInUse (@test-chrome.R#62) 
  4. Error: canCallGecko (@test-gecko.R#4) 
  5. Error: pickUpErrorFromReturnCode (@test-gecko.R#44) 
  6. Error: pickUpErrorFromPortInUse (@test-gecko.R#63) 
  7. Error: canCallIEDriver (@test-iedriver.R#4) 
  8. Error: pickUpErrorFromReturnCode (@test-iedriver.R#46) 
  9. Error: pickUpErrorFromPortInUse (@test-iedriver.R#68) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    client   9.4Mb
    doc      1.0Mb
Package suggested but not available for checking: ‘rgeolocate’
Package required but not available: ‘HotDeckImputation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘org.Mm.eg.db’
Package suggested but not available for checking: ‘AnnotationDbi’
Found the following significant warnings:
  t_region.cpp:78:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:115:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:120:7: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/WhopGenome.Rcheck/00install.out’ for details.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Running examples in ‘WikipediR-Ex.R’ failed
The error most likely occurred in:

> ### Name: categories_in_page
> ### Title: Retrieves categories associated with a page.
> ### Aliases: categories_in_page
> 
> ### ** Examples
> 
> 
> #Retrieve the categories for the "New Age" article on en.wiki
> cats <- categories_in_page("en", "wikipedia", pages = "New Age")
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: Resolving timed out after 10000 milliseconds
Calls: categories_in_page ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
Running ‘testthat.R’ [34s/42s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 22
  1. Error: page categories can be retrieved through categories_in_page (@test_category_retrieval.R#4) 
  2. Error: Hidden page categories can be retrieved through categories_in_page (@test_category_retrieval.R#8) 
  3. Error: Category members can be retrieved through categories_in_page (@test_category_retrieval.R#12) 
  4. Error: Category members can be retrieved through categories_in_page (@test_category_retrieval.R#16) 
  5. Error: page categories can be retrieved through categories_in_page  with non-ASCII query (@test_category_retrieval.R#21) 
  6. Error: Wikitext content can be retrieved through page_content (@test_content_retrieval.R#4) 
  7. Error: HTML content can be retrieved through page_content (@test_content_retrieval.R#9) 
  8. Error: HTML content can be retrieved through revision_content (@test_content_retrieval.R#14) 
  9. Error: Diffs can be retrieved through revision_content (@test_content_retrieval.R#18) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available: ‘gWidgetsRGtk2’ ‘cairoDevice’ ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.4Mb
  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.
Quitting from lines 37-39 (wordcloud.Rmd) 
Error: processing vignette 'wordcloud.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Warning in initDict() :
  cannot find WordNet 'dict' directory: please set the environment variable WNHOME to its parent

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

Probably some imports need to be declared in the NAMESPACE file.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data  11.2Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    bin   4.1Mb
    lib   2.1Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Package required but not available: ‘rtracklayer’

Package suggested but not available for checking: ‘GenomicScores’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'modification.Rmd' failed with diagnostics:
shared object 'stringi.so' not found
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
date	lon	lat	lowLon	higLon	lowLat	higLat
4/23/2003	203.899	19.664	203.899	203.899	19.664	19.664
4/24/2003	204.151	19.821	203.912597	204.389403	18.78051934	20.86148066
4/30/2003	203.919	20.351	203.6793669	204.1586331	18.79728188	21.90471812
5/1/2003	204.229	20.305	203.9943343	204.4636657	18.90440013	21.70559987
Quitting from lines 1055-1057 (Usingxtractomatic.Rmd) 
Error: processing vignette 'Usingxtractomatic.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running ‘doRUnit.R’ [24s/24s]
Running the tests in ‘tests/doRUnit.R’ failed.
Last 13 lines of output:
    Mean relative difference: 8.173474e-05
  
  FAILURE in test.timeSeries_reclass: Error in checkIdentical(sample.timeSeries, reclass(try.xts(sample.timeSeries))) : 
    FALSE 
   
  FAILURE in test.timeSeries_reclass_subset_reclass_j1: Error in checkIdentical(sample.timeSeries[, 1], reclass(try.xts(sample.timeSeries))[,  : 
    FALSE 
   
  DEACTIVATED test.zoo_reclass: rownames are not kept yet in current xts-dev
  DEACTIVATED test.zoo_reclass_subset_reclass_j1: rownames are not kept yet in current xts-dev
  Error: 
  
  unit testing failed (#test failures: 17, #R errors: 0)
  
  Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/zstdr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ACTCD.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’.
Dependence on R version ‘3.3.1’ not with patchlevel 0
Found the following significant warnings:
  ADM3.c:37:12: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  ADM3.c:37:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  ADM3.c:54:21: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ADM3.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [2s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(alphavantager)
  > 
  > test_check("alphavantager")
  ── 1. Error: call TIMES_SERIES_INTRADAY (@test_av_get.R#13)  ───────────────────
  Invalid API call. Please retry or visit the documentation (https://www.alphavantage.co/documentation/) for TIME_SERIES_INTRADAY.. API parameters used: symbol=MSFT, function=TIME_SERIES_INTRADAY, interval=15min, apikey=HIDDEN_FOR_YOUR_SAFETY
  1: av_get(symbol, av_fun, interval = interval) at testthat/test_av_get.R:13
  2: stop(content, call. = F)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 9 SKIPPED: 0 FAILED: 1
  1. Error: call TIMES_SERIES_INTRADAY (@test_av_get.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  em.cpp:208:16: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Amelia.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/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:/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
  WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
  WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
  WARNING: All illegal access operations will be denied in a future release
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ANLP.Rcheck/00install.out’ for details.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘ApacheLogProcessor-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: read.multiple.apache.access.log
> ### Title: Reads multiple files of apache web server.
> ### Aliases: read.multiple.apache.access.log
> 
> ### ** Examples
> 
> path <- system.file("examples", package="ApacheLogProcessor")
> path <- paste(path, "/", sep="")
> 
> #read multiple gziped logs with the prefix m_access_log_combined_
> dfLog <- read.multiple.apache.access.log(path, "m_access_log_combined_")
[1] "Starting the log processing. This may take a long time..."
[1] "Processing file  m_access_log_combined_1.log.gz"
[1] "Unziping  m_access_log_combined_1.log.gz"
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/ApacheLogProcessor/examples/m_access_log_combined_1.log': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: read.multiple.apache.access.log -> write -> cat -> file
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/aroma.affymetrix.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’.
Dependence on R version ‘3.3.2’ not with patchlevel 0
Running examples in ‘ASIP-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: arvi
> ### Title: Atmospherically Resistant Vegetation Index
> ### Aliases: arvi
> 
> ### ** Examples
> 
> library (raster)
Loading required package: sp
> library (rgdal)
rgdal: version: 1.2-18, (SVN revision 718)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.2.4, released 2018/03/19
 Path to GDAL shared files: /usr/share/gdal/2.2
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 5.0.1, April 1st, 2018, [PJ_VERSION: 501]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.2-7 
> # Finding the path of the sample satellite image directory.
> # User may define paths directly like "/home/ur_folder" or "C:/ur_folder"
> path <- system.file ("TM_sample", package = "ASIP")
> shapefil <- paste0 (path, "/test.shp")
> arvi (directory = path, crop = "y", ext2crop = shapefil)
OGR data source with driver: ESRI Shapefile 
Source: "/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/ASIP/TM_sample/test.shp", layer: "test"
with 1 features
It has 1 fields
Integer64 fields read as strings:  id 
Error in .local(.Object, ...) : Dataset copy failed
Calls: arvi ... <Anonymous> -> new -> initialize -> initialize -> .local
Execution halted
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  pa.c:247:2: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/audio.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘spam::det’ by ‘Matrix::det’ when loading ‘bamlss’
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/bamlss.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/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’.
Found the following significant warnings:
  SinkhornDistance.cpp:31:15: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Barycenter.Rcheck/00install.out’ for details.
Dependence on R version ‘3.3.3’ not with patchlevel 0
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Bayesthresh.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  Cbcp.cpp:270:11: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  Cbcpgraph.cpp:144:25: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  Cbcpgraph.cpp:414:32: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  CbcpgraphR.cpp:184:25: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  CbcpgraphR.cpp:519:32: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  CbcpgraphR.cpp:1317:11: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/bcp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  newmat5.cpp:494:69: warning: throw will always call terminate() [-Wterminate]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/bfp.Rcheck/00install.out’ for details.
Running examples in ‘biclique-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bi.format
> ### Title: Add number of vertices and edges to the input file
> ### Aliases: bi.format
> 
> ### ** Examples
> 
> bi.format(system.file("extdata", "example2.el", package = "biclique"))
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/biclique/extdata/example2.el': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: bi.format -> cat -> file
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/biclust.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running examples in ‘biglm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bigglm
> ### Title: Bounded memory linear regression
> ### Aliases: bigglm bigglm.function bigglm.data.frame
> ###   bigglm.SQLiteConnection bigglm.RODBC vcov.bigglm deviance.bigglm
> ###   family.bigglm AIC.bigglm bigglm,ANY,DBIConnection-method
> ### Keywords: regression
> 
> ### ** Examples
> 
> data(trees)
> ff<-log(Volume)~log(Girth)+log(Height)
> a <- bigglm(ff,data=trees, chunksize=10, sandwich=TRUE)
Error in UseMethod("bigglm", data) : 
  no applicable method for 'bigglm' applied to an object of class "data.frame"
Calls: bigglm -> bigglm
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/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’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/bioimagetools.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/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’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/BlockFeST.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: next used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/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’.
Running examples in ‘broom-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: biglm_tidiers
> ### Title: Tidiers for biglm and bigglm object
> ### Aliases: biglm_tidiers tidy.biglm glance.biglm
> 
> ### ** Examples
> 
> 
> if (require("biglm", quietly = TRUE)) {
+     bfit <- biglm(mpg ~ wt + disp, mtcars)
+     tidy(bfit)
+     tidy(bfit, conf.int = TRUE)
+     tidy(bfit, conf.int = TRUE, conf.level = .9)
+     
+     glance(bfit)
+     
+     # bigglm: logistic regression
+     bgfit <- bigglm(am ~ mpg, mtcars, family = binomial())
+     tidy(bgfit)
+     tidy(bgfit, exponentiate = TRUE)
+     tidy(bgfit, conf.int = TRUE)
+     tidy(bgfit, conf.int = TRUE, conf.level = .9)
+     tidy(bgfit, conf.int = TRUE, conf.level = .9, exponentiate = TRUE)
+     
+     glance(bgfit)
+ }
Error in UseMethod("bigglm", data) : 
  no applicable method for 'bigglm' applied to an object of class "data.frame"
Calls: bigglm -> bigglm
Execution halted
Found the following significant warnings:
  cmr_sparse_mfista.c:248:20: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/camel.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/cem.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Error in re-building vignettes:
  ...
Loading required package: ggmap
Loading required package: ggplot2
Loading required package: RCurl
Loading required package: bitops
Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=Chicago,%20IL&sensor=false
Warning: geocode failed with status OVER_QUERY_LIMIT, location = "Chicago, IL"
Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=New%20York&sensor=false
Warning: geocode failed with status OVER_QUERY_LIMIT, location = "New York"
Quitting from lines 16-23 (getting-started.Rmd) 
Error: processing vignette ‘getting-started.Rmd’ failed with diagnostics:
undefined columns selected
Execution halted
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/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’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/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’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/CircStats.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/climatol.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:
  exact.cpp:10:9: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  exact.cpp:125:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  exact.cpp:174:10: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  exact.cpp:204:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/clusrank.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/clustrd.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:
  principal_balances.cpp:114:32: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  sbp.cpp:627:16: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  sbp.cpp:627:50: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  sbp.cpp:649:22: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/coda.base.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/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’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/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:
  date.cpp:173:53: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ConvCalendar.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/corehunter.Rcheck/00install.out’ for details.
Found the following significant warnings:
  hit_ids.cpp:128:34: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/corpustools.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/CorReg.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:
  bdsmatrix_stub.h:41:5: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  bdsmatrix_stub.h:44:12: warning: return makes integer from pointer without a cast [-Wint-conversion]
  bdsmatrix_stub.h:50:5: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  bdsmatrix_stub.h:53:12: warning: return makes integer from pointer without a cast [-Wint-conversion]
  bdsmatrix_stub.h:97:5: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  bdsmatrix_stub.h:100:12: warning: return from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/coxme.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/cplm.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 ‘CREAM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CREAM
> ### Title: CREAM is the main function for CORE identification
> ### Aliases: CREAM
> 
> ### ** Examples
> 
> CREAM(system.file("extdata", "A549_Chr21.bed", package = "CREAM"),
+ system.file("extdata", "A549_Chr21_COREs.bed", package = "CREAM"),
+ MinLength = 1000, peakNumMin = 2)
[1] "Please make sure there is no overlap between the input genomic regions. Overlap between the input regions may cause error."
[1] "Identifying window size for each Order"
[1] "Identifying COREs"
[1] "Filtering clusters of low order"
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/CREAM/extdata/A549_Chr21_COREs.bed': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: CREAM -> write.table -> file
Execution halted
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
              user system elapsed
text_win_rqa 7.468   0.02   9.744
Found the following significant warnings:
  instabCorrection.cpp:34:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/cstab.Rcheck/00install.out’ for details.