BioC 3.0: CHECK report for GenomeGraphs on zin1
This page was generated on 2015-04-10 09:38:06 -0700 (Fri, 10 Apr 2015).
GenomeGraphs 1.26.0
Steffen Durinck
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/GenomeGraphs | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK |
Summary
| Package: GenomeGraphs |
| Version: 1.26.0 |
| Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings GenomeGraphs_1.26.0.tar.gz |
| StartedAt: 2015-04-10 00:19:38 -0700 (Fri, 10 Apr 2015) |
| EndedAt: 2015-04-10 00:21:59 -0700 (Fri, 10 Apr 2015) |
| EllapsedTime: 141.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GenomeGraphs.Rcheck |
| Warnings: 0 |
Command output
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### Running command:
###
### /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings GenomeGraphs_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/GenomeGraphs.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomeGraphs/DESCRIPTION’ ... OK
* this is package ‘GenomeGraphs’ version ‘1.26.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘GenomeGraphs’ can be installed ... [11s/11s] 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
* 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 ... NOTE
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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.drawGene: no visible global function definition for ‘pushViewport’
.drawGene: no visible global function definition for ‘dataViewport’
.drawGene: no visible global function definition for ‘grid.rect’
.drawGene: no visible global function definition for ‘gpar’
.drawGene: no visible global function definition for ‘grid.text’
.drawGene: no visible global function definition for ‘grid.lines’
.drawGene: no visible global function definition for ‘popViewport’
exonModule: no visible global function definition for ‘pushViewport’
exonModule: no visible global function definition for ‘dataViewport’
exonModule: no visible global function definition for ‘grid.rect’
exonModule: no visible global function definition for ‘gpar’
exonModule: no visible global function definition for ‘grid.lines’
gdPlot: no visible global function definition for ‘grid.newpage’
gdPlot: no visible global function definition for ‘pushViewport’
gdPlot: no visible global function definition for ‘viewport’
gdPlot: no visible global function definition for ‘grid.layout’
gdPlot: no visible global function definition for ‘grid.text’
gdPlot: no visible global function definition for ‘gpar’
gdPlot: no visible global function definition for ‘popViewport’
geneBiomart: no visible global function definition for ‘getBM’
geneRegionBiomart: no visible global function definition for ‘getBM’
transcriptModule: no visible global function definition for
‘pushViewport’
transcriptModule: no visible global function definition for ‘viewport’
transcriptModule: no visible global function definition for
‘grid.layout’
initialize,Gene: no visible global function definition for ‘getBM’
initialize,GeneRegion: no visible global function definition for
‘getBM’
initialize,Transcript: no visible global function definition for
‘getBM’
* 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 ... [7s/36s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
gdPlot 0.560 0.012 15.289
DisplayPars 0.316 0.004 14.447
* 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
NOTE: There were 2 notes.
See
‘/home/biocbuild/bbs-3.0-bioc/meat/GenomeGraphs.Rcheck/00check.log’
for details.
GenomeGraphs.Rcheck/00install.out:
* 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
* DONE (GenomeGraphs)
GenomeGraphs.Rcheck/GenomeGraphs-Ex.timings:
| name | user | system | elapsed
|
| AnnotationTrack-class | 0.004 | 0.000 | 0.002 |
|
| BaseTrack-class | 0.000 | 0.000 | 0.002 |
|
| DisplayPars-class | 0.000 | 0.000 | 0.003 |
|
| DisplayPars | 0.316 | 0.004 | 14.447 |
|
| ExonArray-class | 0.004 | 0.000 | 0.005 |
|
| Gene-class | 0.000 | 0.000 | 0.001 |
|
| GeneModel-class | 0.216 | 0.000 | 0.216 |
|
| GeneRegion-class | 0.004 | 0.000 | 0.002 |
|
| GenericArray-class | 0.000 | 0.000 | 0.001 |
|
| GenomeAxis-class | 0.000 | 0.000 | 0.001 |
|
| HighlightRegion-class | 0.000 | 0.004 | 0.003 |
|
| Ideogram-class | 0.004 | 0.000 | 0.001 |
|
| ImplementsTrackOverlay-class | 0.000 | 0.000 | 0.001 |
|
| Legend-class | 0.000 | 0.000 | 0.001 |
|
| MappedRead-class | 0 | 0 | 0 |
|
| Overlay-class | 0.004 | 0.000 | 0.001 |
|
| RectangleOverlay-class | 0.000 | 0.000 | 0.001 |
|
| Segmentation-class | 0.000 | 0.000 | 0.001 |
|
| Smoothing-class | 0.000 | 0.000 | 0.001 |
|
| TextOverlay-class | 0.000 | 0.000 | 0.002 |
|
| Title-class | 0.000 | 0.000 | 0.001 |
|
| TrackOverlay-class | 0.000 | 0.000 | 0.001 |
|
| Transcript-class | 0.004 | 0.000 | 0.001 |
|
| TranscriptRegion-class | 0.000 | 0.000 | 0.001 |
|
| cn | 0.004 | 0.000 | 0.001 |
|
| exonProbePos | 0 | 0 | 0 |
|
| gdObject-class | 0.004 | 0.000 | 0.002 |
|
| gdPlot | 0.560 | 0.012 | 15.289 |
|
| getPar | 0.000 | 0.000 | 0.001 |
|
| getSize | 0.000 | 0.000 | 0.001 |
|
| ideogramTab | 0.004 | 0.000 | 0.002 |
|
| intensity | 0.000 | 0.000 | 0.001 |
|
| makeAnnotationTrack | 0.024 | 0.000 | 0.023 |
|
| makeBaseTrack | 0.004 | 0.000 | 0.003 |
|
| makeExonArray | 0.004 | 0.000 | 0.003 |
|
| makeGene | 0.004 | 0.000 | 0.002 |
|
| makeGeneModel | 0.000 | 0.000 | 0.001 |
|
| makeGeneRegion | 0.000 | 0.000 | 0.002 |
|
| makeGenericArray | 0.004 | 0.000 | 0.001 |
|
| makeGenomeAxis | 0.000 | 0.000 | 0.001 |
|
| makeIdeogram | 0.004 | 0.000 | 0.002 |
|
| makeLegend | 0.000 | 0.000 | 0.001 |
|
| makeRectangleOverlay | 0.056 | 0.000 | 0.059 |
|
| makeSegmentation | 0.048 | 0.000 | 0.052 |
|
| makeSmoothing | 0.068 | 0.004 | 0.074 |
|
| makeTextOverlay | 0.068 | 0.000 | 0.067 |
|
| makeTitle | 0.004 | 0.000 | 0.002 |
|
| makeTranscript | 0.004 | 0.000 | 0.002 |
|
| probestart | 0 | 0 | 0 |
|
| segEnd | 0.000 | 0.004 | 0.000 |
|
| segStart | 0.000 | 0.000 | 0.001 |
|
| segments | 0 | 0 | 0 |
|
| seqDataEx | 0.020 | 0.000 | 0.022 |
|
| setPar | 0.012 | 0.000 | 0.013 |
|
| showDisplayOptions | 0.000 | 0.000 | 0.001 |
|
| unrData | 0 | 0 | 0 |
|
| unrNProbes | 0.000 | 0.000 | 0.001 |
|
| unrPositions | 0 | 0 | 0 |
|
| yeastCons1 | 0 | 0 | 0 |
|