Back to Build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-09-07 15:39 -0400 (Sat, 07 Sep 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4711 |
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 |
Package 782/2258 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GeneBreak 1.35.0 (landing page) Evert van den Broek
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
To the developers/maintainers of the GeneBreak package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: GeneBreak |
Version: 1.35.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GeneBreak.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GeneBreak_1.35.0.tar.gz |
StartedAt: 2024-09-06 22:06:02 -0400 (Fri, 06 Sep 2024) |
EndedAt: 2024-09-06 22:08:48 -0400 (Fri, 06 Sep 2024) |
EllapsedTime: 166.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GeneBreak.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GeneBreak.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GeneBreak_1.35.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/GeneBreak.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘GeneBreak/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GeneBreak’ version ‘1.35.0’ * 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 code 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 loading without being on the library search path ... 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 5.898 0.136 6.035 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.20-bioc/meat/GeneBreak.Rcheck/00check.log’ for details.
GeneBreak.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL GeneBreak ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 | 5.898 | 0.136 | 6.035 | |
CopyNumberBreakPoints-class | 1.688 | 0.079 | 1.768 | |
accessOptions-CopyNumberBreakPoints-method | 0.855 | 0.024 | 0.879 | |
addGeneAnnotation-CopyNumberBreakPoints-method | 1.448 | 0.044 | 1.492 | |
bpFilter-CopyNumberBreakPoints-method | 1.134 | 0.036 | 1.170 | |
bpGenes-CopyNumberBreakPointGenes-method | 1.622 | 0.020 | 1.643 | |
bpPlot-CopyNumberBreakPoints-method | 4.529 | 0.068 | 4.597 | |
bpStats-CopyNumberBreakPoints-method | 4.772 | 0.128 | 4.900 | |
breakpointData-CopyNumberBreakPoints-method | 1.078 | 0.176 | 1.254 | |
breakpointsPerGene-CopyNumberBreakPointGenes-method | 1.848 | 0.156 | 2.004 | |
callData-CopyNumberBreakPoints-method | 1.157 | 0.155 | 1.313 | |
featureChromosomes-CopyNumberBreakPoints-method | 0.897 | 0.039 | 0.935 | |
featureInfo-CopyNumberBreakPoints-method | 1.728 | 0.041 | 1.769 | |
featuresPerGene-CopyNumberBreakPointGenes-method | 1.657 | 0.047 | 1.706 | |
geneChromosomes-CopyNumberBreakPointGenes-method | 1.629 | 0.025 | 1.653 | |
geneInfo-CopyNumberBreakPointGenes-method | 1.501 | 0.051 | 1.554 | |
getBreakpoints | 1.239 | 0.025 | 1.264 | |
namesFeatures-CopyNumberBreakPoints-method | 0.868 | 0.039 | 0.909 | |
recurrentGenes-CopyNumberBreakPointGenes-method | 3.908 | 0.036 | 3.943 | |
sampleNames-CopyNumberBreakPoints-method | 0.539 | 0.043 | 0.583 | |
segmentData-CopyNumberBreakPoints-method | 1.097 | 0.188 | 1.285 | |