Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:05 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
To the developers/maintainers of the GeneBreak package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeneBreak.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 742/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GeneBreak 1.29.0 (landing page) Evert van den Broek
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: GeneBreak |
Version: 1.29.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GeneBreak.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings GeneBreak_1.29.0.tar.gz |
StartedAt: 2023-02-07 02:11:43 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 02:15:50 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 247.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GeneBreak.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GeneBreak.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings GeneBreak_1.29.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GeneBreak.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘GeneBreak/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GeneBreak’ version ‘1.29.0’ * 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 7.730 0.127 8.068 bpStats-CopyNumberBreakPoints-method 6.541 0.032 6.699 bpPlot-CopyNumberBreakPoints-method 6.436 0.016 6.460 recurrentGenes-CopyNumberBreakPointGenes-method 5.955 0.020 5.978 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘GeneBreak.Rnw’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.17-bioc/meat/GeneBreak.Rcheck/00check.log’ for details.
GeneBreak.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL GeneBreak ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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 | 7.730 | 0.127 | 8.068 | |
CopyNumberBreakPoints-class | 1.745 | 0.088 | 1.836 | |
accessOptions-CopyNumberBreakPoints-method | 1.125 | 0.040 | 1.167 | |
addGeneAnnotation-CopyNumberBreakPoints-method | 2.602 | 0.012 | 2.618 | |
bpFilter-CopyNumberBreakPoints-method | 1.618 | 0.028 | 1.649 | |
bpGenes-CopyNumberBreakPointGenes-method | 2.778 | 0.039 | 2.820 | |
bpPlot-CopyNumberBreakPoints-method | 6.436 | 0.016 | 6.460 | |
bpStats-CopyNumberBreakPoints-method | 6.541 | 0.032 | 6.699 | |
breakpointData-CopyNumberBreakPoints-method | 1.266 | 0.208 | 1.476 | |
breakpointsPerGene-CopyNumberBreakPointGenes-method | 2.418 | 0.228 | 2.648 | |
callData-CopyNumberBreakPoints-method | 1.352 | 0.223 | 1.577 | |
featureChromosomes-CopyNumberBreakPoints-method | 1.141 | 0.036 | 1.177 | |
featureInfo-CopyNumberBreakPoints-method | 2.845 | 0.084 | 2.930 | |
featuresPerGene-CopyNumberBreakPointGenes-method | 2.367 | 0.048 | 2.417 | |
geneChromosomes-CopyNumberBreakPointGenes-method | 2.793 | 0.022 | 2.818 | |
geneInfo-CopyNumberBreakPointGenes-method | 2.558 | 0.060 | 2.619 | |
getBreakpoints | 2.165 | 0.044 | 2.210 | |
namesFeatures-CopyNumberBreakPoints-method | 1.122 | 0.036 | 1.159 | |
recurrentGenes-CopyNumberBreakPointGenes-method | 5.955 | 0.020 | 5.978 | |
sampleNames-CopyNumberBreakPoints-method | 1.223 | 0.032 | 1.255 | |
segmentData-CopyNumberBreakPoints-method | 1.439 | 0.188 | 1.629 | |