Henry Zhang
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/caOmicsV |
| Branch: RELEASE_3_10 |
| Last Commit: f404be7 |
| Last Changed Date: 2019-10-29 13:09:20 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:25:03 -0400 (Wed, 15 Apr 2020).
| Package 225/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| caOmicsV 1.16.0 Henry Zhang
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: caOmicsV |
| Version: 1.16.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:caOmicsV.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings caOmicsV_1.16.0.tar.gz |
| StartedAt: 2020-04-15 01:48:48 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 01:53:01 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 253.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: caOmicsV.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:caOmicsV.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings caOmicsV_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/caOmicsV.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'caOmicsV/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'caOmicsV' version '1.16.0'
* 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 'caOmicsV' 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
bioMatrixLegend: no visible global function definition for 'text'
bioMatrixLegend: no visible global function definition for 'legend'
bioNetLegend: no visible global function definition for 'text'
bioNetLegend: no visible global function definition for 'legend'
convertToZScores: no visible global function definition for 'sd'
drawBioNetNodeBackground: no visible global function definition for
'gray'
drawBioNetNodeBackground: no visible global function definition for
'col2rgb'
drawBioNetNodeBackground: no visible global function definition for
'rgb'
drawBioNetNodeBackground: no visible global function definition for
'polygon'
eraseBioNetNode: no visible global function definition for 'polygon'
getHeatmapColorScales: no visible global function definition for 'rgb'
labelBioNetNodeNames: no visible global function definition for 'text'
linkBioNetNodes: no visible global function definition for 'col2rgb'
linkBioNetNodes: no visible global function definition for 'rgb'
linkBioNetNodes: no visible global function definition for 'polygon'
linkBioNetSamples: no visible global function definition for 'lines'
plotBioMatrix: no visible global function definition for 'par'
plotBioMatrix: no visible global function definition for 'rainbow'
plotBioMatrix: no visible global function definition for 'legend'
plotBioMatrixBars: no visible global function definition for 'rect'
plotBioMatrixBinaryData: no visible global function definition for
'points'
plotBioMatrixCategoryData: no visible global function definition for
'palette'
plotBioMatrixCategoryData: no visible global function definition for
'rect'
plotBioMatrixRowNames: no visible global function definition for 'text'
plotBioMatrixSampleData: no visible global function definition for
'rect'
plotBioMatrixSampleNames: no visible global function definition for
'text'
plotBioNetBars: no visible global function definition for 'polygon'
plotBioNetCircos: no visible global function definition for 'par'
plotBioNetCircos: no visible global function definition for 'rainbow'
plotBioNetHeatmap: no visible global function definition for 'polygon'
plotBioNetLines: no visible global function definition for 'lines'
plotBioNetPoints: no visible global function definition for 'points'
plotBioNetPolygons: no visible global function definition for 'rainbow'
plotBioNetPolygons: no visible global function definition for 'polygon'
plotHeatmapColorScale: no visible global function definition for 'rect'
plotHeatmapColorScale: no visible global function definition for 'text'
setBioMatrixPlotArea: no visible global function definition for
'plot.new'
setBioMatrixPlotArea: no visible global function definition for
'plot.window'
setBioNetNodeLayout: no visible global function definition for 'dist'
setBioNetPlotAreaBackground: no visible global function definition for
'grey'
setBioNetPlotAreaBackground: no visible global function definition for
'col2rgb'
setBioNetPlotAreaBackground: no visible global function definition for
'rgb'
setBioNetPlotAreaBackground: no visible global function definition for
'polygon'
showBioNetNodesLayout: no visible global function definition for 'grey'
showBioNetNodesLayout: no visible global function definition for 'plot'
showBioNetNodesLayout: no visible global function definition for 'text'
Undefined global functions or variables:
col2rgb dist gray grey legend lines palette par plot plot.new
plot.window points polygon rainbow rect rgb sd text
Consider adding
importFrom("grDevices", "col2rgb", "gray", "grey", "palette",
"rainbow", "rgb")
importFrom("graphics", "legend", "lines", "par", "plot", "plot.new",
"plot.window", "points", "polygon", "rect", "text")
importFrom("stats", "dist", "sd")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotBioNetCircos 10.48 0.19 10.71
bioNetLegend 9.35 0.15 9.50
plotBioNetHeatmap 7.02 0.17 7.20
drawBioNetNodeBackground 5.72 0.14 5.86
bioNetCircosPlot 2.75 0.10 5.94
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotBioNetCircos 10.37 0.23 10.61
bioNetLegend 10.33 0.20 10.53
plotBioNetHeatmap 7.35 0.15 7.48
drawBioNetNodeBackground 6.22 0.19 6.40
plotBioNetLines 5.15 0.09 5.30
* 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-3.10-bioc/meat/caOmicsV.Rcheck/00check.log'
for details.
caOmicsV.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/caOmicsV_1.16.0.tar.gz && rm -rf caOmicsV.buildbin-libdir && mkdir caOmicsV.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=caOmicsV.buildbin-libdir caOmicsV_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL caOmicsV_1.16.0.zip && rm caOmicsV_1.16.0.tar.gz caOmicsV_1.16.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 171k 100 171k 0 0 4819k 0 --:--:-- --:--:-- --:--:-- 5344k
install for i386
* installing *source* package 'caOmicsV' ...
** using staged installation
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'caOmicsV'
finding HTML links ... done
CA_OMICS_ENV html
CA_OMICS_NAME html
CA_OMICS_NA_STRING html
CNVDemoData html
RNA2miRNA html
RNASeq html
RNASeqDemoData html
bioMatrixLegend html
bioNetCircosPlot html
bioNetLegend html
biomatrixPlotDemoData html
bionetPlotDemoData html
caOmicsV-package html
convertToZScores html
drawBioNetNodeBackground html
eraseBioNetNode html
getBezierCurve html
getBioMatrixDataRowTop html
getBioMatrixPlotParameters html
getBioNetNodeLinkLine html
getBioNetParameters html
getBioNetPlotLocations html
getBioNetSamplePlotPosition html
getCaOmicsVColors html
getCaOmicsVPlotTypes html
getDefaultNaStrings html
getHeatmapColorScales html
getPlotDataSet html
getPlotOmicsData html
getPlotSampleData html
getPlotSummaryData html
getRelatedPlotData html
initializeBioMatrixPlot html
initializeBioNetCircos html
labelBioNetNodeNames html
linkBioNetNodes html
linkBioNetSamples html
methylDemoData html
miRNA html
miRNADemoData html
plotBioMatrix html
plotBioMatrixBars html
plotBioMatrixBinaryData html
plotBioMatrixCategoryData html
plotBioMatrixHeatmap html
plotBioMatrixRowNames html
plotBioMatrixSampleData html
plotBioMatrixSampleNames html
plotBioNetBars html
plotBioNetCircos html
plotBioNetHeatmap html
plotBioNetLines html
plotBioNetPoints html
plotBioNetPolygons html
plotHeatmapColorScale html
resetBioNetNodePlotAreaBoundary html
sampleDemoData html
setBioMatrixBaseCoordinates html
setBioMatrixPlotArea html
setBioMatrixPlotParameters html
setBioNetCircosBasePlotPositions html
setBioNetNodeLayout html
setBioNetPlotAreaBackground html
setBioNetPlotParameters html
setCaOmicsVColors html
setDefaultNaStrings html
showBioMatrixPlotLayout html
showBioNetNodesLayout html
showSupportedBioNetCircosPlotType html
sortClinicalData html
sortOmicsDataByColumn html
sortOmicsDataByRow html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'caOmicsV' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'caOmicsV' as caOmicsV_1.16.0.zip
* DONE (caOmicsV)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'caOmicsV' successfully unpacked and MD5 sums checked
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caOmicsV.Rcheck/examples_i386/caOmicsV-Ex.timings
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caOmicsV.Rcheck/examples_x64/caOmicsV-Ex.timings
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