Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:54:49 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE GeneBreak PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 676/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
GeneBreak 1.18.0 Evert van den Broek
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK |
Package: GeneBreak |
Version: 1.18.0 |
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:GeneBreak.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings GeneBreak_1.18.0.tar.gz |
StartedAt: 2020-10-17 01:34:40 -0400 (Sat, 17 Oct 2020) |
EndedAt: 2020-10-17 01:37:37 -0400 (Sat, 17 Oct 2020) |
EllapsedTime: 177.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GeneBreak.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:GeneBreak.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings GeneBreak_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/GeneBreak.Rcheck’ * using R version 4.0.3 (2020-10-10) * using platform: x86_64-pc-linux-gnu (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 ‘1.18.0’ * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed CopyNumberBreakPointGenes-class 7.460 0.108 7.568 bpStats-CopyNumberBreakPoints-method 5.598 0.016 5.613 * 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 ‘/home/biocbuild/bbs-3.11-bioc/meat/GeneBreak.Rcheck/00check.log’ for details.
GeneBreak.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL GeneBreak ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’ * installing *source* package ‘GeneBreak’ ... ** using staged installation ** 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 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 (GeneBreak)
GeneBreak.Rcheck/GeneBreak-Ex.timings
name | user | system | elapsed | |
CopyNumberBreakPointGenes-class | 7.460 | 0.108 | 7.568 | |
CopyNumberBreakPoints-class | 1.526 | 0.072 | 1.599 | |
accessOptions-CopyNumberBreakPoints-method | 1.052 | 0.008 | 1.059 | |
addGeneAnnotation-CopyNumberBreakPoints-method | 1.616 | 0.012 | 1.628 | |
bpFilter-CopyNumberBreakPoints-method | 1.122 | 0.012 | 1.134 | |
bpGenes-CopyNumberBreakPointGenes-method | 1.749 | 0.024 | 1.772 | |
bpPlot-CopyNumberBreakPoints-method | 4.625 | 0.044 | 4.669 | |
bpStats-CopyNumberBreakPoints-method | 5.598 | 0.016 | 5.613 | |
breakpointData-CopyNumberBreakPoints-method | 1.282 | 0.148 | 1.429 | |
breakpointsPerGene-CopyNumberBreakPointGenes-method | 1.900 | 0.144 | 2.044 | |
callData-CopyNumberBreakPoints-method | 1.560 | 0.168 | 1.728 | |
featureChromosomes-CopyNumberBreakPoints-method | 0.807 | 0.016 | 0.824 | |
featureInfo-CopyNumberBreakPoints-method | 1.767 | 0.056 | 1.823 | |
featuresPerGene-CopyNumberBreakPointGenes-method | 1.810 | 0.016 | 1.826 | |
geneChromosomes-CopyNumberBreakPointGenes-method | 1.573 | 0.024 | 1.597 | |
geneInfo-CopyNumberBreakPointGenes-method | 1.441 | 0.036 | 1.476 | |
getBreakpoints | 1.579 | 0.028 | 1.607 | |
namesFeatures-CopyNumberBreakPoints-method | 1.062 | 0.032 | 1.094 | |
recurrentGenes-CopyNumberBreakPointGenes-method | 4.802 | 0.052 | 4.854 | |
sampleNames-CopyNumberBreakPoints-method | 0.654 | 0.028 | 0.682 | |
segmentData-CopyNumberBreakPoints-method | 1.315 | 0.188 | 1.503 | |