Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:55:31 -0400 (Wed, 17 Oct 2018).
Package 561/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
GeneBreak 1.10.0 Evert van den Broek
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
Package: GeneBreak |
Version: 1.10.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneBreak.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneBreak_1.10.0.tar.gz |
StartedAt: 2018-10-16 21:33:38 -0400 (Tue, 16 Oct 2018) |
EndedAt: 2018-10-16 21:36:44 -0400 (Tue, 16 Oct 2018) |
EllapsedTime: 186.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GeneBreak.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneBreak.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneBreak_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/GeneBreak.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GeneBreak/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GeneBreak’ version ‘1.10.0’ * 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 ‘GeneBreak’ 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 .glmbreak: no visible global function definition for ‘glm’ .glmbreak: no visible global function definition for ‘predict’ addGeneAnnotation,CopyNumberBreakPoints: no visible global function definition for ‘head’ bpStats,CopyNumberBreakPoints: no visible global function definition for ‘sd’ bpStats,CopyNumberBreakPoints: no visible global function definition for ‘p.adjust’ Undefined global functions or variables: glm head p.adjust predict sd Consider adding importFrom("stats", "glm", "p.adjust", "predict", "sd") importFrom("utils", "head") 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 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 CopyNumberBreakPointGenes-class 7.733 0.733 8.501 bpStats-CopyNumberBreakPoints-method 6.101 0.697 6.820 bpPlot-CopyNumberBreakPoints-method 6.049 0.582 6.664 recurrentGenes-CopyNumberBreakPointGenes-method 5.929 0.695 6.652 * 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-3.7-bioc/meat/GeneBreak.Rcheck/00check.log’ for details.
GeneBreak.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GeneBreak ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘GeneBreak’ ... ** R ** data ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘segmentData’ in package ‘GeneBreak’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (GeneBreak)
GeneBreak.Rcheck/GeneBreak-Ex.timings
name | user | system | elapsed | |
CopyNumberBreakPointGenes-class | 7.733 | 0.733 | 8.501 | |
CopyNumberBreakPoints-class | 1.624 | 0.179 | 1.806 | |
accessOptions-CopyNumberBreakPoints-method | 0.930 | 0.140 | 1.074 | |
addGeneAnnotation-CopyNumberBreakPoints-method | 1.953 | 0.251 | 2.212 | |
bpFilter-CopyNumberBreakPoints-method | 1.397 | 0.230 | 1.636 | |
bpGenes-CopyNumberBreakPointGenes-method | 2.371 | 0.247 | 2.627 | |
bpPlot-CopyNumberBreakPoints-method | 6.049 | 0.582 | 6.664 | |
bpStats-CopyNumberBreakPoints-method | 6.101 | 0.697 | 6.820 | |
breakpointData-CopyNumberBreakPoints-method | 1.581 | 0.531 | 2.122 | |
breakpointsPerGene-CopyNumberBreakPointGenes-method | 2.568 | 0.641 | 3.216 | |
callData-CopyNumberBreakPoints-method | 1.603 | 0.491 | 2.103 | |
featureChromosomes-CopyNumberBreakPoints-method | 0.972 | 0.157 | 1.137 | |
featureInfo-CopyNumberBreakPoints-method | 2.418 | 0.308 | 2.734 | |
featuresPerGene-CopyNumberBreakPointGenes-method | 2.473 | 0.239 | 2.725 | |
geneChromosomes-CopyNumberBreakPointGenes-method | 2.079 | 0.254 | 2.343 | |
geneInfo-CopyNumberBreakPointGenes-method | 2.072 | 0.263 | 2.342 | |
getBreakpoints | 1.673 | 0.198 | 1.877 | |
namesFeatures-CopyNumberBreakPoints-method | 0.954 | 0.117 | 1.081 | |
recurrentGenes-CopyNumberBreakPointGenes-method | 5.929 | 0.695 | 6.652 | |
sampleNames-CopyNumberBreakPoints-method | 0.686 | 0.138 | 0.827 | |
segmentData-CopyNumberBreakPoints-method | 1.790 | 0.447 | 2.245 | |