BioC 2.14: CHECK report for GenomeGraphs on moscato2
This page was generated on 2014-10-08 08:52:28 -0700 (Wed, 08 Oct 2014).
GenomeGraphs 1.24.0 Steffen Durinck
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/GenomeGraphs | Last Changed Rev: 88838 / Revision: 95116 | Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | OK | |
moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK |
petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK |
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK |
Summary
Package: GenomeGraphs
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Version: 1.24.0
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Command: rm -rf GenomeGraphs.buildbin-libdir && mkdir GenomeGraphs.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomeGraphs.buildbin-libdir GenomeGraphs_1.24.0.tar.gz >GenomeGraphs-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=GenomeGraphs.buildbin-libdir --install="check:GenomeGraphs-install.out" --force-multiarch --no-vignettes --timings GenomeGraphs_1.24.0.tar.gz
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StartedAt: 2014-10-08 01:27:42 -0700 (Wed, 08 Oct 2014)
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EndedAt: 2014-10-08 01:30:24 -0700 (Wed, 08 Oct 2014)
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EllapsedTime: 161.7 seconds
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RetCode: 0
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Status: OK
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CheckDir: GenomeGraphs.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 GenomeGraphs.buildbin-libdir && mkdir GenomeGraphs.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomeGraphs.buildbin-libdir GenomeGraphs_1.24.0.tar.gz >GenomeGraphs-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=GenomeGraphs.buildbin-libdir --install="check:GenomeGraphs-install.out" --force-multiarch --no-vignettes --timings GenomeGraphs_1.24.0.tar.gz
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* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/GenomeGraphs.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenomeGraphs/DESCRIPTION' ... OK
* this is package 'GenomeGraphs' version '1.24.0'
* 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 'GenomeGraphs' 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
gdPlot: warning in grid.layout(1, 2, width = c(0.1, 0.9)): partial
argument match of 'width' to 'widths'
gdPlot: warning in grid.layout(length(vplayout), 1, height = vplayout):
partial argument match of 'height' to 'heights'
transcriptModule: warning in grid.layout(1, length(vplayout), width =
vplayout): partial argument match of 'width' to 'widths'
* 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' ... [23s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
DisplayPars 0.4 0.03 14.54
** running examples for arch 'x64' ... [21s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
DisplayPars 0.52 0.04 11.74
* 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
NOTE: There was 1 note.
See
'E:/biocbld/bbs-2.14-bioc/meat/GenomeGraphs.Rcheck/00check.log'
for details.
GenomeGraphs.Rcheck/00install.out:
install for i386
* installing *source* package 'GenomeGraphs' ...
** R
** data
** 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 'GenomeGraphs' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomeGraphs' as GenomeGraphs_1.24.0.zip
* DONE (GenomeGraphs)
GenomeGraphs.Rcheck/examples_i386/GenomeGraphs-Ex.timings:
name | user | system | elapsed
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AnnotationTrack-class | 0 | 0 | 0 |
|
BaseTrack-class | 0 | 0 | 0 |
|
DisplayPars-class | 0 | 0 | 0 |
|
DisplayPars | 0.40 | 0.03 | 14.54 |
|
ExonArray-class | 0 | 0 | 0 |
|
Gene-class | 0 | 0 | 0 |
|
GeneModel-class | 0.18 | 0.00 | 0.17 |
|
GeneRegion-class | 0 | 0 | 0 |
|
GenericArray-class | 0 | 0 | 0 |
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GenomeAxis-class | 0 | 0 | 0 |
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HighlightRegion-class | 0 | 0 | 0 |
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Ideogram-class | 0 | 0 | 0 |
|
ImplementsTrackOverlay-class | 0 | 0 | 0 |
|
Legend-class | 0 | 0 | 0 |
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MappedRead-class | 0 | 0 | 0 |
|
Overlay-class | 0 | 0 | 0 |
|
RectangleOverlay-class | 0 | 0 | 0 |
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Segmentation-class | 0 | 0 | 0 |
|
Smoothing-class | 0 | 0 | 0 |
|
TextOverlay-class | 0 | 0 | 0 |
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Title-class | 0 | 0 | 0 |
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TrackOverlay-class | 0.02 | 0.00 | 0.02 |
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Transcript-class | 0 | 0 | 0 |
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TranscriptRegion-class | 0 | 0 | 0 |
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cn | 0 | 0 | 0 |
|
exonProbePos | 0 | 0 | 0 |
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gdObject-class | 0 | 0 | 0 |
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gdPlot | 1.26 | 0.00 | 3.91 |
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getPar | 0 | 0 | 0 |
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getSize | 0 | 0 | 0 |
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ideogramTab | 0.00 | 0.02 | 0.02 |
|
intensity | 0 | 0 | 0 |
|
makeAnnotationTrack | 0.03 | 0.00 | 0.03 |
|
makeBaseTrack | 0 | 0 | 0 |
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makeExonArray | 0 | 0 | 0 |
|
makeGene | 0.02 | 0.00 | 0.02 |
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makeGeneModel | 0 | 0 | 0 |
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makeGeneRegion | 0 | 0 | 0 |
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makeGenericArray | 0 | 0 | 0 |
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makeGenomeAxis | 0 | 0 | 0 |
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makeIdeogram | 0 | 0 | 0 |
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makeLegend | 0 | 0 | 0 |
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makeRectangleOverlay | 0.14 | 0.00 | 0.14 |
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makeSegmentation | 0.14 | 0.00 | 0.14 |
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makeSmoothing | 0.15 | 0.00 | 0.15 |
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makeTextOverlay | 0.14 | 0.02 | 0.16 |
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makeTitle | 0.02 | 0.00 | 0.02 |
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makeTranscript | 0 | 0 | 0 |
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probestart | 0 | 0 | 0 |
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segEnd | 0 | 0 | 0 |
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segStart | 0 | 0 | 0 |
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segments | 0 | 0 | 0 |
|
seqDataEx | 0.03 | 0.00 | 0.03 |
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setPar | 0.02 | 0.00 | 0.01 |
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showDisplayOptions | 0 | 0 | 0 |
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unrData | 0 | 0 | 0 |
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unrNProbes | 0 | 0 | 0 |
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unrPositions | 0 | 0 | 0 |
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yeastCons1 | 0 | 0 | 0 |
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GenomeGraphs.Rcheck/examples_x64/GenomeGraphs-Ex.timings:
name | user | system | elapsed
|
AnnotationTrack-class | 0 | 0 | 0 |
|
BaseTrack-class | 0 | 0 | 0 |
|
DisplayPars-class | 0 | 0 | 0 |
|
DisplayPars | 0.52 | 0.04 | 11.74 |
|
ExonArray-class | 0 | 0 | 0 |
|
Gene-class | 0 | 0 | 0 |
|
GeneModel-class | 0.21 | 0.00 | 0.21 |
|
GeneRegion-class | 0 | 0 | 0 |
|
GenericArray-class | 0 | 0 | 0 |
|
GenomeAxis-class | 0 | 0 | 0 |
|
HighlightRegion-class | 0 | 0 | 0 |
|
Ideogram-class | 0 | 0 | 0 |
|
ImplementsTrackOverlay-class | 0 | 0 | 0 |
|
Legend-class | 0 | 0 | 0 |
|
MappedRead-class | 0 | 0 | 0 |
|
Overlay-class | 0 | 0 | 0 |
|
RectangleOverlay-class | 0 | 0 | 0 |
|
Segmentation-class | 0 | 0 | 0 |
|
Smoothing-class | 0 | 0 | 0 |
|
TextOverlay-class | 0 | 0 | 0 |
|
Title-class | 0 | 0 | 0 |
|
TrackOverlay-class | 0 | 0 | 0 |
|
Transcript-class | 0 | 0 | 0 |
|
TranscriptRegion-class | 0 | 0 | 0 |
|
cn | 0.01 | 0.00 | 0.02 |
|
exonProbePos | 0 | 0 | 0 |
|
gdObject-class | 0 | 0 | 0 |
|
gdPlot | 1.44 | 0.00 | 4.03 |
|
getPar | 0 | 0 | 0 |
|
getSize | 0 | 0 | 0 |
|
ideogramTab | 0 | 0 | 0 |
|
intensity | 0 | 0 | 0 |
|
makeAnnotationTrack | 0.03 | 0.00 | 0.15 |
|
makeBaseTrack | 0 | 0 | 0 |
|
makeExonArray | 0 | 0 | 0 |
|
makeGene | 0 | 0 | 0 |
|
makeGeneModel | 0 | 0 | 0 |
|
makeGeneRegion | 0 | 0 | 0 |
|
makeGenericArray | 0 | 0 | 0 |
|
makeGenomeAxis | 0 | 0 | 0 |
|
makeIdeogram | 0 | 0 | 0 |
|
makeLegend | 0 | 0 | 0 |
|
makeRectangleOverlay | 0.17 | 0.00 | 0.17 |
|
makeSegmentation | 0.16 | 0.00 | 0.16 |
|
makeSmoothing | 0.17 | 0.02 | 0.19 |
|
makeTextOverlay | 0.17 | 0.00 | 0.17 |
|
makeTitle | 0 | 0 | 0 |
|
makeTranscript | 0 | 0 | 0 |
|
probestart | 0 | 0 | 0 |
|
segEnd | 0 | 0 | 0 |
|
segStart | 0 | 0 | 0 |
|
segments | 0 | 0 | 0 |
|
seqDataEx | 0.02 | 0.00 | 0.02 |
|
setPar | 0.02 | 0.00 | 0.02 |
|
showDisplayOptions | 0 | 0 | 0 |
|
unrData | 0 | 0 | 0 |
|
unrNProbes | 0 | 0 | 0 |
|
unrPositions | 0.01 | 0.00 | 0.01 |
|
yeastCons1 | 0 | 0 | 0 |
|