BioC 3.5: CHECK report for NanoStringQCPro on tokay2
This page was generated on 2017-10-18 14:24:41 -0400 (Wed, 18 Oct 2017).
NanoStringQCPro 1.8.0 Robert Ziman
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | URL: https://git.bioconductor.org/packages/NanoStringQCPro | Branch: RELEASE_3_5 | Last Commit: 10c38d3 | Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | |
tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
Summary
Package: NanoStringQCPro
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Version: 1.8.0
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Command: rm -rf NanoStringQCPro.buildbin-libdir NanoStringQCPro.Rcheck && mkdir NanoStringQCPro.buildbin-libdir NanoStringQCPro.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=NanoStringQCPro.buildbin-libdir NanoStringQCPro_1.8.0.tar.gz >NanoStringQCPro.Rcheck\00install.out 2>&1 && cp NanoStringQCPro.Rcheck\00install.out NanoStringQCPro-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=NanoStringQCPro.buildbin-libdir --install="check:NanoStringQCPro-install.out" --force-multiarch --no-vignettes --timings NanoStringQCPro_1.8.0.tar.gz
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StartedAt: 2017-10-18 01:39:40 -0400 (Wed, 18 Oct 2017)
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EndedAt: 2017-10-18 01:42:47 -0400 (Wed, 18 Oct 2017)
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EllapsedTime: 187.3 seconds
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RetCode: 0
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Status: OK
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CheckDir: NanoStringQCPro.Rcheck
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Warnings: 0
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Command output
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### Running command:
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### rm -rf NanoStringQCPro.buildbin-libdir NanoStringQCPro.Rcheck && mkdir NanoStringQCPro.buildbin-libdir NanoStringQCPro.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=NanoStringQCPro.buildbin-libdir NanoStringQCPro_1.8.0.tar.gz >NanoStringQCPro.Rcheck\00install.out 2>&1 && cp NanoStringQCPro.Rcheck\00install.out NanoStringQCPro-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=NanoStringQCPro.buildbin-libdir --install="check:NanoStringQCPro-install.out" --force-multiarch --no-vignettes --timings NanoStringQCPro_1.8.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/NanoStringQCPro.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* 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 '1.8.0'
* 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 10.85 2.65 14.52
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
makeQCReport 11.52 2.5 14.42
* 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-3.5-bioc/meat/NanoStringQCPro.Rcheck/00check.log'
for details.
NanoStringQCPro.Rcheck/00install.out:
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_1.8.0.zip
* DONE (NanoStringQCPro)
NanoStringQCPro.Rcheck/examples_i386/NanoStringQCPro-Ex.timings:
name | user | system | elapsed
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RccSet-class | 0.7 | 0.0 | 0.7 |
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addCodesetAnnotation | 0.44 | 0.02 | 0.45 |
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buildCodesetAnnotation | 0.07 | 0.00 | 0.08 |
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checkRccSet | 0.05 | 0.00 | 0.05 |
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contentNorm | 0.13 | 0.00 | 0.12 |
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copyRccSet | 0.01 | 0.00 | 0.02 |
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getBackground | 0.06 | 0.00 | 0.06 |
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getBlankLabel | 0 | 0 | 0 |
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makeQCReport | 10.85 | 2.65 | 14.52 |
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newRccSet | 0.52 | 0.00 | 0.52 |
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posCtrlNorm | 0.02 | 0.02 | 0.03 |
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preprocRccSet | 0.14 | 0.00 | 0.14 |
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presAbsCall | 0.07 | 0.00 | 0.08 |
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readCdrDesignData | 0.02 | 0.00 | 0.02 |
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readRcc | 0 | 0 | 0 |
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readRlf | 0 | 0 | 0 |
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subtractBackground | 0.08 | 0.02 | 0.09 |
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NanoStringQCPro.Rcheck/examples_x64/NanoStringQCPro-Ex.timings:
name | user | system | elapsed
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RccSet-class | 0.75 | 0.01 | 0.77 |
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addCodesetAnnotation | 0.73 | 0.00 | 0.73 |
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buildCodesetAnnotation | 0.11 | 0.00 | 0.11 |
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checkRccSet | 0.06 | 0.00 | 0.06 |
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contentNorm | 0.14 | 0.00 | 0.14 |
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copyRccSet | 0.02 | 0.00 | 0.02 |
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getBackground | 0.08 | 0.00 | 0.08 |
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getBlankLabel | 0.01 | 0.00 | 0.01 |
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makeQCReport | 11.52 | 2.50 | 14.42 |
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newRccSet | 0.61 | 0.00 | 0.61 |
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posCtrlNorm | 0.03 | 0.00 | 0.03 |
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preprocRccSet | 0.22 | 0.02 | 0.24 |
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presAbsCall | 0.07 | 0.00 | 0.08 |
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readCdrDesignData | 0.04 | 0.00 | 0.03 |
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readRcc | 0 | 0 | 0 |
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readRlf | 0.01 | 0.00 | 0.01 |
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subtractBackground | 0.11 | 0.00 | 0.11 |
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