Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 13:14:56 -0400 (Tue, 09 Apr 2019).
Package 1154/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
pathVar 1.13.0 Samuel Zimmerman
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: pathVar |
Version: 1.13.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pathVar.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pathVar_1.13.0.tar.gz |
StartedAt: 2019-04-09 04:14:43 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 04:22:38 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 475.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: pathVar.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pathVar.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pathVar_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/pathVar.Rcheck’ * using R Under development (unstable) (2019-03-18 r76245) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘pathVar/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘pathVar’ version ‘1.13.0’ * 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 ‘pathVar’ 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 * 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 diagnosticsVarPlots: no visible binding for global variable ‘avg’ diagnosticsVarPlots: no visible binding for global variable ‘standDev’ diagnosticsVarPlots: no visible binding for global variable ‘medAbsDev’ diagnosticsVarPlots: no visible binding for global variable ‘cv’ diagnosticsVarPlotsTwoSample: no visible binding for global variable ‘avg’ diagnosticsVarPlotsTwoSample: no visible binding for global variable ‘standDev’ diagnosticsVarPlotsTwoSample: no visible binding for global variable ‘medAbsDev’ diagnosticsVarPlotsTwoSample: no visible binding for global variable ‘cv’ pathVarOneSample: no visible binding for global variable ‘APval’ pathVarOneSample: no visible binding for global variable ‘PercOfGenesInPway’ pathVarTwoSamplesCont: no visible binding for global variable ‘APval’ pathVarTwoSamplesCont: no visible binding for global variable ‘PercOfGenesInPway’ pathVarTwoSamplesDisc: no visible binding for global variable ‘APval’ pathVarTwoSamplesDisc: no visible binding for global variable ‘PercOfGenesInPway’ plotAllTwoSampleDistributionCounts: no visible binding for global variable ‘Cluster’ plotAllTwoSampleDistributionCounts: no visible binding for global variable ‘Number_of_genes’ plotOneSample: no visible binding for global variable ‘Cluster’ plotOneSample: no visible binding for global variable ‘Number_of_genes’ plotTwoSamplesCont: no visible binding for global variable ‘PwayName’ plotTwoSamplesCont: no visible binding for global variable ‘NumOfGenesFromDataSetInPathway’ plotTwoSamplesCont: no visible binding for global variable ‘value’ plotTwoSamplesCont: no visible binding for global variable ‘..density..’ plotTwoSamplesCont: no visible binding for global variable ‘group’ plotTwoSamplesDisc: no visible binding for global variable ‘Cluster’ plotTwoSamplesDisc: no visible binding for global variable ‘Number_of_genes’ sigOneSample: no visible binding for global variable ‘APval’ sigOneSample: no visible binding for global variable ‘PwayName’ sigTwoSamplesCont: no visible binding for global variable ‘APval’ sigTwoSamplesCont: no visible binding for global variable ‘PwayName’ sigTwoSamplesDisc: no visible binding for global variable ‘APval’ sigTwoSamplesDisc: no visible binding for global variable ‘PwayName’ Undefined global functions or variables: ..density.. APval Cluster NumOfGenesFromDataSetInPathway Number_of_genes PercOfGenesInPway PwayName avg cv group medAbsDev standDev value * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed diagnosticsVarPlots 165.059 1.003 166.509 sigPway 100.604 7.843 108.427 diagnosticsVarPlotsTwoSample 100.112 0.589 102.036 plotAllTwoSampleDistributionCounts 7.048 2.167 7.161 saveAsPDF 6.219 1.060 5.418 pathVar-package 5.308 0.836 4.720 plotPway 5.477 0.654 5.127 pathVarTwoSamplesCont 5.165 0.248 4.178 * 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 ‘/Users/biocbuild/bbs-3.9-bioc/meat/pathVar.Rcheck/00check.log’ for details.
pathVar.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL pathVar ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘pathVar’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * DONE (pathVar)
pathVar.Rcheck/pathVar-Ex.timings
name | user | system | elapsed | |
bock | 0.017 | 0.005 | 0.022 | |
diagnosticsVarPlots | 165.059 | 1.003 | 166.509 | |
diagnosticsVarPlotsTwoSample | 100.112 | 0.589 | 102.036 | |
geneDistributionSet-class | 0.007 | 0.001 | 0.008 | |
geneDistributionSet2-class | 0.004 | 0.001 | 0.005 | |
geneDistributionSet3-class | 0.003 | 0.000 | 0.003 | |
geneSet-class | 0.002 | 0.000 | 0.003 | |
getGenes | 4.464 | 0.308 | 4.526 | |
makeDBList | 0.002 | 0.002 | 0.000 | |
pathVar-package | 5.308 | 0.836 | 4.720 | |
pathVarOneSample | 2.892 | 0.084 | 2.896 | |
pathVarTwoSamplesCont | 5.165 | 0.248 | 4.178 | |
pathVarTwoSamplesDisc | 2.861 | 0.155 | 1.590 | |
plotAllTwoSampleDistributionCounts | 7.048 | 2.167 | 7.161 | |
plotPway | 5.477 | 0.654 | 5.127 | |
pways.kegg | 0.002 | 0.002 | 0.004 | |
pways.reactome | 0.002 | 0.002 | 0.004 | |
saveAsPDF | 6.219 | 1.060 | 5.418 | |
sigPway | 100.604 | 7.843 | 108.427 | |
significantPathway-class | 0.007 | 0.006 | 0.002 | |
significantPathway2-class | 0.005 | 0.005 | 0.002 | |
significantPathway3-class | 0.008 | 0.007 | 0.002 | |