BioC 3.2: CHECK report for caOmicsV on linux1.bioconductor.org
This page was generated on 2015-10-27 17:27:16 -0400 (Tue, 27 Oct 2015).
caOmicsV 1.0.0
Henry Zhang
| Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/caOmicsV | | Last Changed Rev: 109589 / Revision: 109947 | | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
Summary
| Package: caOmicsV |
| Version: 1.0.0 |
| Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings caOmicsV_1.0.0.tar.gz |
| StartedAt: 2015-10-27 01:43:23 -0400 (Tue, 27 Oct 2015) |
| EndedAt: 2015-10-27 01:44:59 -0400 (Tue, 27 Oct 2015) |
| EllapsedTime: 96.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: caOmicsV.Rcheck |
| Warnings: 0 |
Command output
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###
### Running command:
###
### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings caOmicsV_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/caOmicsV.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘caOmicsV/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘caOmicsV’ version ‘1.0.0’
* 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 ‘caOmicsV’ can be installed ... [5s/5s] 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 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 ... OK
* 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 ... [56s/56s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
bioNetLegend 9.625 0.148 9.775
plotBioNetCircos 6.660 0.080 6.741
drawBioNetNodeBackground 5.267 0.080 5.348
* 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: OK
caOmicsV.Rcheck/00install.out:
* installing *source* package ‘caOmicsV’ ...
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (caOmicsV)
caOmicsV.Rcheck/caOmicsV-Ex.timings:
| name | user | system | elapsed
|
| CA_OMICS_ENV | 0 | 0 | 0 |
|
| CA_OMICS_NAME | 0 | 0 | 0 |
|
| CA_OMICS_NA_STRING | 0 | 0 | 0 |
|
| CNVDemoData | 0.033 | 0.000 | 0.033 |
|
| RNA2miRNA | 0.002 | 0.000 | 0.002 |
|
| RNASeq | 0.005 | 0.000 | 0.005 |
|
| RNASeqDemoData | 0.002 | 0.000 | 0.002 |
|
| bioMatrixLegend | 0.302 | 0.008 | 0.310 |
|
| bioNetCircosPlot | 1.777 | 0.039 | 1.818 |
|
| bioNetLegend | 9.625 | 0.148 | 9.775 |
|
| biomatrixPlotDemoData | 0.003 | 0.000 | 0.005 |
|
| bionetPlotDemoData | 0.004 | 0.000 | 0.003 |
|
| convertToZScores | 0.006 | 0.000 | 0.006 |
|
| drawBioNetNodeBackground | 5.267 | 0.080 | 5.348 |
|
| eraseBioNetNode | 2.999 | 0.020 | 3.025 |
|
| getBezierCurve | 0.002 | 0.000 | 0.001 |
|
| getBioMatrixDataRowTop | 0.001 | 0.000 | 0.001 |
|
| getBioMatrixPlotParameters | 0.003 | 0.000 | 0.003 |
|
| getBioNetNodeLinkLine | 0.002 | 0.000 | 0.001 |
|
| getBioNetParameters | 0.516 | 0.000 | 0.516 |
|
| getBioNetPlotLocations | 0.403 | 0.000 | 0.403 |
|
| getBioNetSamplePlotPosition | 0 | 0 | 0 |
|
| getCaOmicsVColors | 0.000 | 0.000 | 0.001 |
|
| getCaOmicsVPlotTypes | 0.000 | 0.000 | 0.001 |
|
| getDefaultNaStrings | 0.000 | 0.000 | 0.001 |
|
| getHeatmapColorScales | 0.001 | 0.000 | 0.001 |
|
| getPlotDataSet | 0.027 | 0.000 | 0.027 |
|
| getPlotOmicsData | 0.006 | 0.004 | 0.010 |
|
| getPlotSampleData | 0.002 | 0.000 | 0.002 |
|
| getPlotSummaryData | 0.008 | 0.000 | 0.008 |
|
| getRelatedPlotData | 0.057 | 0.000 | 0.057 |
|
| initializeBioMatrixPlot | 0.001 | 0.000 | 0.001 |
|
| initializeBioNetCircos | 0.519 | 0.000 | 0.519 |
|
| labelBioNetNodeNames | 2.441 | 0.012 | 2.453 |
|
| linkBioNetNodes | 1.972 | 0.016 | 1.988 |
|
| linkBioNetSamples | 1.482 | 0.016 | 1.498 |
|
| methylDemoData | 0.001 | 0.000 | 0.001 |
|
| miRNA | 0.001 | 0.000 | 0.002 |
|
| miRNADemoData | 0.001 | 0.000 | 0.001 |
|
| plotBioMatrix | 0.517 | 0.004 | 0.521 |
|
| plotBioMatrixBars | 0.006 | 0.004 | 0.010 |
|
| plotBioMatrixBinaryData | 0.003 | 0.000 | 0.003 |
|
| plotBioMatrixCategoryData | 0.003 | 0.000 | 0.002 |
|
| plotBioMatrixHeatmap | 0.005 | 0.000 | 0.005 |
|
| plotBioMatrixRowNames | 0.012 | 0.000 | 0.012 |
|
| plotBioMatrixSampleData | 0.000 | 0.000 | 0.003 |
|
| plotBioMatrixSampleNames | 0.002 | 0.000 | 0.002 |
|
| plotBioNetBars | 1.906 | 0.020 | 1.927 |
|
| plotBioNetCircos | 6.660 | 0.080 | 6.741 |
|
| plotBioNetHeatmap | 4.433 | 0.096 | 4.529 |
|
| plotBioNetLines | 2.954 | 0.032 | 2.987 |
|
| plotBioNetPoints | 3.113 | 0.028 | 3.144 |
|
| plotBioNetPolygons | 2.911 | 0.056 | 2.971 |
|
| plotHeatmapColorScale | 1.099 | 0.016 | 1.115 |
|
| resetBioNetNodePlotAreaBoundary | 0.000 | 0.000 | 0.001 |
|
| sampleDemoData | 0.001 | 0.000 | 0.001 |
|
| setBioMatrixBaseCoordinates | 0 | 0 | 0 |
|
| setBioMatrixPlotArea | 0.001 | 0.000 | 0.002 |
|
| setBioMatrixPlotParameters | 0 | 0 | 0 |
|
| setBioNetCircosBasePlotPositions | 0 | 0 | 0 |
|
| setBioNetNodeLayout | 0.382 | 0.000 | 0.381 |
|
| setBioNetPlotAreaBackground | 0.07 | 0.00 | 0.07 |
|
| setBioNetPlotParameters | 0 | 0 | 0 |
|
| setCaOmicsVColors | 0 | 0 | 0 |
|
| setDefaultNaStrings | 0.001 | 0.000 | 0.000 |
|
| showBioMatrixPlotLayout | 0.020 | 0.000 | 0.019 |
|
| showBioNetNodesLayout | 1.046 | 0.004 | 1.050 |
|
| showSupportedBioNetCircosPlotType | 0.000 | 0.000 | 0.001 |
|
| sortClinicalData | 0.001 | 0.000 | 0.002 |
|
| sortOmicsDataByColumn | 0.002 | 0.000 | 0.001 |
|
| sortOmicsDataByRow | 0.003 | 0.000 | 0.003 |
|