Package: skewr

Version: 1.14.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:skewr.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings skewr_1.14.0.tar.gz

StartedAt: 2019-04-13 05:35:45 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 05:42:46 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 421.1 seconds

RetCode: 0

Status:  OK

CheckDir: skewr.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:skewr.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings skewr_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/skewr.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'skewr/DESCRIPTION' ... OK
* this is package 'skewr' version '1.14.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'skewr' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
dSN: no visible global function definition for 'dnorm'
dSN: no visible global function definition for 'pnorm'
panelPlots: no visible global function definition for 'data'
panelPlots : finishPlot: no visible global function definition for
  'mtext'
panelPlots : finishPlot: no visible global function definition for
  'par'
panelPlots: no visible global function definition for 'par'
panelPlots: no visible global function definition for 'density'
panelPlots: no visible global function definition for 'axis'
panelPlots: no visible global function definition for 'lines'
panelPlots: no visible global function definition for 'segments'
panelPlots: no visible global function definition for 'mtext'
plotComponents: no visible global function definition for 'hist'
plotComponents: no visible global function definition for 'lines'
plotComponents: no visible global function definition for 'segments'
plotComponents: no visible global function definition for 'density'
subsetProbes: no visible global function definition for 'data'
subsetProbes: no visible binding for global variable
  'IlluminaHumanMethylation450kmanifest'
subsetProbes: no visible binding for global variable 'Color'
Undefined global functions or variables:
  Color IlluminaHumanMethylation450kmanifest axis data density dnorm
  hist lines mtext par pnorm segments
Consider adding
  importFrom("graphics", "axis", "hist", "lines", "mtext", "par",
             "segments")
  importFrom("stats", "density", "dnorm", "pnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
subsetProbes  4.7   0.35    5.05
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
subsetProbes 4.93   0.22    5.15
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/skewr.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/skewr_1.14.0.tar.gz && rm -rf skewr.buildbin-libdir && mkdir skewr.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=skewr.buildbin-libdir skewr_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL skewr_1.14.0.zip && rm skewr_1.14.0.tar.gz skewr_1.14.0.zip
###
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install for i386

* installing *source* package 'skewr' ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'skewr'
    finding HTML links ... done
    getBarcodes                             html  
    getMethyLumiSet                         html  
    getSNparams                             html  
    panelPlots                              html  
    preprocess                              html  
    subsetProbes                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'skewr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'skewr' as skewr_1.14.0.zip
* DONE (skewr)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'skewr' successfully unpacked and MD5 sums checked
In R CMD INSTALL