BioC 3.4: CHECK report for NanoStringQCPro on moscato1

Package: NanoStringQCPro

Version: 1.5.0

Command: rm -rf NanoStringQCPro.buildbin-libdir NanoStringQCPro.Rcheck && mkdir NanoStringQCPro.buildbin-libdir NanoStringQCPro.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=NanoStringQCPro.buildbin-libdir NanoStringQCPro_1.5.0.tar.gz >NanoStringQCPro.Rcheck\00install.out 2>&1 && cp NanoStringQCPro.Rcheck\00install.out NanoStringQCPro-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=NanoStringQCPro.buildbin-libdir --install="check:NanoStringQCPro-install.out" --force-multiarch --no-vignettes --timings NanoStringQCPro_1.5.0.tar.gz

StartedAt: 2016-09-20 12:53:45 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 12:57:04 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 198.4 seconds

RetCode: 0

Status:  OK

CheckDir: NanoStringQCPro.Rcheck

Warnings: 0

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### Running command:
###
###   rm -rf NanoStringQCPro.buildbin-libdir NanoStringQCPro.Rcheck && mkdir NanoStringQCPro.buildbin-libdir NanoStringQCPro.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=NanoStringQCPro.buildbin-libdir NanoStringQCPro_1.5.0.tar.gz >NanoStringQCPro.Rcheck\00install.out 2>&1 && cp NanoStringQCPro.Rcheck\00install.out NanoStringQCPro-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=NanoStringQCPro.buildbin-libdir --install="check:NanoStringQCPro-install.out" --force-multiarch --no-vignettes --timings NanoStringQCPro_1.5.0.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/NanoStringQCPro.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'NanoStringQCPro/DESCRIPTION' ... OK
* this is package 'NanoStringQCPro' version '1.5.0'
* checking package namespace information ... OK
* checking package dependencies ... 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 'NanoStringQCPro' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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
centeredSampleClustering: no visible global function definition for
  'png'
centeredSampleClustering: no visible global function definition for
  'dev.off'
countsInBlankSamples_verticalPlot: no visible global function
  definition for 'png'
countsInBlankSamples_verticalPlot: no visible global function
  definition for 'dev.off'
geneClustering: no visible global function definition for 'png'
geneClustering: no visible global function definition for 'dev.off'
negCtrlsByLane_verticalPlot: no visible global function definition for
  'png'
negCtrlsByLane_verticalPlot: no visible global function definition for
  'dev.off'
previewPNG: no visible global function definition for 'png'
previewPNG: no visible global function definition for 'dev.off'
sampleClustering,RccSet: no visible global function definition for
  'png'
sampleClustering,RccSet: no visible global function definition for
  'dev.off'
Undefined global functions or variables:
  dev.off png
Consider adding
  importFrom("grDevices", "dev.off", "png")
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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
makeQCReport 9.69   1.86   17.15
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
makeQCReport  9.8   1.87   17.25
* 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
  'D:/biocbld/bbs-3.4-bioc/meat/NanoStringQCPro.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'NanoStringQCPro' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'NanoStringQCPro' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'NanoStringQCPro' as NanoStringQCPro_1.5.0.zip
* DONE (NanoStringQCPro)

name	user	system	elapsed
RccSet-class	0.38	0.00	0.37
addCodesetAnnotation	0.25	0.00	0.25
buildCodesetAnnotation	0.01	0.00	0.02
checkRccSet	0	0	0
contentNorm	0.08	0.00	0.08
copyRccSet	0.02	0.02	0.03
getBackground	0	0	0
getBlankLabel	0	0	0
makeQCReport	9.69	1.86	17.15
newRccSet	0.23	0.00	0.23
posCtrlNorm	0.02	0.01	0.03
preprocRccSet	0.06	0.00	0.06
presAbsCall	0.04	0.00	0.05
readCdrDesignData	0	0	0
readRcc	0	0	0
readRlf	0	0	0
subtractBackground	0.08	0.00	0.08

name	user	system	elapsed
RccSet-class	0.47	0.00	0.47
addCodesetAnnotation	0.31	0.00	0.31
buildCodesetAnnotation	0	0	0
checkRccSet	0.01	0.00	0.02
contentNorm	0.10	0.00	0.09
copyRccSet	0.01	0.02	0.03
getBackground	0.02	0.00	0.02
getBlankLabel	0	0	0
makeQCReport	9.80	1.87	17.25
newRccSet	0.28	0.00	0.28
posCtrlNorm	0.01	0.00	0.01
preprocRccSet	0.08	0.01	0.10
presAbsCall	0.08	0.00	0.08
readCdrDesignData	0	0	0
readRcc	0	0	0
readRlf	0.01	0.00	0.01
subtractBackground	0.10	0.00	0.09