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BioC 3.2: CHECK report for caOmicsV on moscato1

This page was generated on 2016-04-23 10:22:02 -0700 (Sat, 23 Apr 2016).

Package 139/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
caOmicsV 1.0.0
Henry Zhang
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/caOmicsV
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: caOmicsV
Version: 1.0.0
Command: rm -rf caOmicsV.buildbin-libdir caOmicsV.Rcheck && mkdir caOmicsV.buildbin-libdir caOmicsV.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=caOmicsV.buildbin-libdir caOmicsV_1.0.0.tar.gz >caOmicsV.Rcheck\00install.out 2>&1 && cp caOmicsV.Rcheck\00install.out caOmicsV-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=caOmicsV.buildbin-libdir --install="check:caOmicsV-install.out" --force-multiarch --no-vignettes --timings caOmicsV_1.0.0.tar.gz
StartedAt: 2016-04-23 00:17:39 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 00:23:03 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 323.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: caOmicsV.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf caOmicsV.buildbin-libdir caOmicsV.Rcheck && mkdir caOmicsV.buildbin-libdir caOmicsV.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=caOmicsV.buildbin-libdir caOmicsV_1.0.0.tar.gz >caOmicsV.Rcheck\00install.out 2>&1 && cp caOmicsV.Rcheck\00install.out caOmicsV-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=caOmicsV.buildbin-libdir --install="check:caOmicsV-install.out" --force-multiarch --no-vignettes --timings caOmicsV_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/caOmicsV.Rcheck'
* using R version 3.2.4 (2016-03-10)
* 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 '1.0.0'
* 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 whether package 'caOmicsV' can be installed ... WARNING
Found the following significant warnings:
  Warning: package 'Matrix' was built under R version 3.2.5
See 'D:/biocbld/bbs-3.2-bioc/meat/caOmicsV.Rcheck/00install.out' for details.
* 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 ... 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 ...
** running examples for arch 'i386' ... [102s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
bioNetLegend             16.49   0.14   17.55
plotBioNetCircos         14.51   0.15   14.82
plotBioNetHeatmap         9.08   0.13    9.20
drawBioNetNodeBackground  7.41   0.04    7.48
plotBioNetPoints          6.55   0.05    6.72
plotBioNetLines           5.76   0.03    5.93
plotBioNetPolygons        5.64   0.03    5.71
** running examples for arch 'x64' ... [95s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
plotBioNetCircos         12.76   0.27   13.23
bioNetLegend             12.32   0.17   13.09
plotBioNetHeatmap         7.26   0.19    7.44
drawBioNetNodeBackground  6.93   0.11    7.04
plotBioNetLines           5.99   0.09    6.09
plotBioNetPolygons        5.85   0.05    6.03
plotBioNetPoints          5.51   0.06    5.71
* 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 WARNING
See
  'D:/biocbld/bbs-3.2-bioc/meat/caOmicsV.Rcheck/00check.log'
for details.


caOmicsV.Rcheck/00install.out:


install for i386

* installing *source* package 'caOmicsV' ...
** R
** data
** demo
** inst
** preparing package for lazy loading
Warning: package 'Matrix' was built under R version 3.2.5
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: package 'Matrix' was built under R version 3.2.5

install for x64

* installing *source* package 'caOmicsV' ...
** testing if installed package can be loaded
Warning: package 'Matrix' was built under R version 3.2.5
* MD5 sums
packaged installation of 'caOmicsV' as caOmicsV_1.0.0.zip
* DONE (caOmicsV)

caOmicsV.Rcheck/examples_i386/caOmicsV-Ex.timings:

nameusersystemelapsed
CA_OMICS_ENV000
CA_OMICS_NAME000
CA_OMICS_NA_STRING000
CNVDemoData0.030.000.03
RNA2miRNA0.010.000.01
RNASeq0.020.000.02
RNASeqDemoData000
bioMatrixLegend0.480.010.50
bioNetCircosPlot4.370.054.58
bioNetLegend16.49 0.1417.55
biomatrixPlotDemoData0.000.020.05
bionetPlotDemoData0.010.000.01
convertToZScores000
drawBioNetNodeBackground7.410.047.48
eraseBioNetNode3.470.053.51
getBezierCurve000
getBioMatrixDataRowTop000
getBioMatrixPlotParameters000
getBioNetNodeLinkLine000
getBioNetParameters0.520.000.52
getBioNetPlotLocations0.430.000.43
getBioNetSamplePlotPosition000
getCaOmicsVColors000
getCaOmicsVPlotTypes000
getDefaultNaStrings000
getHeatmapColorScales000
getPlotDataSet0.050.000.05
getPlotOmicsData0.000.020.01
getPlotSampleData0.000.010.02
getPlotSummaryData0.020.000.02
getRelatedPlotData0.040.000.04
initializeBioMatrixPlot000
initializeBioNetCircos0.440.030.47
labelBioNetNodeNames3.790.083.87
linkBioNetNodes2.560.052.60
linkBioNetSamples2.760.062.83
methylDemoData000
miRNA0.000.020.01
miRNADemoData000
plotBioMatrix0.920.000.92
plotBioMatrixBars0.020.010.04
plotBioMatrixBinaryData000
plotBioMatrixCategoryData0.010.000.01
plotBioMatrixHeatmap0.020.000.02
plotBioMatrixRowNames0.030.000.03
plotBioMatrixSampleData0.010.000.01
plotBioMatrixSampleNames000
plotBioNetBars3.710.053.76
plotBioNetCircos14.51 0.1514.82
plotBioNetHeatmap9.080.139.20
plotBioNetLines5.760.035.93
plotBioNetPoints6.550.056.72
plotBioNetPolygons5.640.035.71
plotHeatmapColorScale2.390.032.42
resetBioNetNodePlotAreaBoundary000
sampleDemoData0.000.020.02
setBioMatrixBaseCoordinates000
setBioMatrixPlotArea000
setBioMatrixPlotParameters000
setBioNetCircosBasePlotPositions000
setBioNetNodeLayout0.50.00.5
setBioNetPlotAreaBackground0.140.000.14
setBioNetPlotParameters000
setCaOmicsVColors000
setDefaultNaStrings0.020.000.02
showBioMatrixPlotLayout0.010.000.01
showBioNetNodesLayout2.110.063.22
showSupportedBioNetCircosPlotType000
sortClinicalData000
sortOmicsDataByColumn000
sortOmicsDataByRow0.000.020.02

caOmicsV.Rcheck/examples_x64/caOmicsV-Ex.timings:

nameusersystemelapsed
CA_OMICS_ENV000
CA_OMICS_NAME000
CA_OMICS_NA_STRING0.010.000.01
CNVDemoData0.020.000.02
RNA2miRNA0.020.000.01
RNASeq000
RNASeqDemoData0.010.000.02
bioMatrixLegend0.420.000.42
bioNetCircosPlot3.340.113.46
bioNetLegend12.32 0.1713.09
biomatrixPlotDemoData0.000.020.02
bionetPlotDemoData000
convertToZScores0.000.010.01
drawBioNetNodeBackground6.930.117.04
eraseBioNetNode3.690.064.28
getBezierCurve000
getBioMatrixDataRowTop000
getBioMatrixPlotParameters000
getBioNetNodeLinkLine000
getBioNetParameters0.650.000.66
getBioNetPlotLocations0.460.000.46
getBioNetSamplePlotPosition000
getCaOmicsVColors000
getCaOmicsVPlotTypes000
getDefaultNaStrings000
getHeatmapColorScales000
getPlotDataSet0.060.020.08
getPlotOmicsData0.000.020.01
getPlotSampleData0.000.010.02
getPlotSummaryData0.020.000.02
getRelatedPlotData0.090.000.09
initializeBioMatrixPlot000
initializeBioNetCircos0.640.000.64
labelBioNetNodeNames3.110.053.84
linkBioNetNodes2.960.053.13
linkBioNetSamples2.360.003.37
methylDemoData000
miRNA0.000.010.02
miRNADemoData000
plotBioMatrix0.750.000.75
plotBioMatrixBars0.010.000.01
plotBioMatrixBinaryData0.020.000.02
plotBioMatrixCategoryData0.010.000.01
plotBioMatrixHeatmap0.020.000.02
plotBioMatrixRowNames0.050.000.05
plotBioMatrixSampleData000
plotBioMatrixSampleNames0.010.000.01
plotBioNetBars3.320.064.07
plotBioNetCircos12.76 0.2713.23
plotBioNetHeatmap7.260.197.44
plotBioNetLines5.990.096.09
plotBioNetPoints5.510.065.71
plotBioNetPolygons5.850.056.03
plotHeatmapColorScale1.710.012.28
resetBioNetNodePlotAreaBoundary000
sampleDemoData0.020.000.02
setBioMatrixBaseCoordinates000
setBioMatrixPlotArea000
setBioMatrixPlotParameters000
setBioNetCircosBasePlotPositions000
setBioNetNodeLayout0.70.00.7
setBioNetPlotAreaBackground0.110.000.11
setBioNetPlotParameters000
setCaOmicsVColors000
setDefaultNaStrings000
showBioMatrixPlotLayout0.030.000.03
showBioNetNodesLayout1.980.002.53
showSupportedBioNetCircosPlotType000
sortClinicalData000
sortOmicsDataByColumn0.000.020.01
sortOmicsDataByRow000