Back to Multiple platform build/check report for BioC 3.8 |
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This page was generated on 2019-04-13 11:25:34 -0400 (Sat, 13 Apr 2019).
Package 201/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
caOmicsV 1.12.1 Henry Zhang
| malbec1 | Linux (Ubuntu 16.04.6 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: 1.12.1 |
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:caOmicsV.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings caOmicsV_1.12.1.tar.gz |
StartedAt: 2019-04-13 00:58:20 -0400 (Sat, 13 Apr 2019) |
EndedAt: 2019-04-13 01:02:45 -0400 (Sat, 13 Apr 2019) |
EllapsedTime: 265.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: caOmicsV.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:caOmicsV.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings caOmicsV_1.12.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/caOmicsV.Rcheck' * using R version 3.5.3 (2019-03-11) * 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 '1.12.1' * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 bioNetLegend 9.70 0.14 9.84 plotBioNetCircos 8.88 0.18 9.06 drawBioNetNodeBackground 6.46 0.08 6.53 plotBioNetHeatmap 5.97 0.11 6.08 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed bioNetLegend 10.05 0.27 10.32 plotBioNetCircos 8.93 0.27 9.20 plotBioNetHeatmap 7.28 0.14 7.42 drawBioNetNodeBackground 5.39 0.11 5.50 plotBioNetLines 5.19 0.13 5.36 plotBioNetPolygons 5.11 0.16 5.28 * 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-3.8-bioc/meat/caOmicsV.Rcheck/00check.log' for details.
caOmicsV.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/caOmicsV_1.12.1.tar.gz && rm -rf caOmicsV.buildbin-libdir && mkdir caOmicsV.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=caOmicsV.buildbin-libdir caOmicsV_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL caOmicsV_1.12.1.zip && rm caOmicsV_1.12.1.tar.gz caOmicsV_1.12.1.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 171k 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 171k 100 171k 0 0 4336k 0 --:--:-- --:--:-- --:--:-- 4623k install for i386 * installing *source* package 'caOmicsV' ... ** 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 In R CMD INSTALL install for x64 * installing *source* package 'caOmicsV' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'caOmicsV' as caOmicsV_1.12.1.zip * DONE (caOmicsV) In R CMD INSTALL In R CMD INSTALL * installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library' package 'caOmicsV' successfully unpacked and MD5 sums checked In R CMD INSTALL
caOmicsV.Rcheck/examples_i386/caOmicsV-Ex.timings
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caOmicsV.Rcheck/examples_x64/caOmicsV-Ex.timings
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