Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-28 17:40 -0400 (Fri, 28 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4760 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4362 |
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 800/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GeneBreak 1.34.0 (landing page) Evert van den Broek
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | 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: 1.34.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GeneBreak.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GeneBreak_1.34.0.tar.gz |
StartedAt: 2024-06-26 23:25:16 -0400 (Wed, 26 Jun 2024) |
EndedAt: 2024-06-26 23:28:08 -0400 (Wed, 26 Jun 2024) |
EllapsedTime: 172.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GeneBreak.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GeneBreak.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GeneBreak_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/GeneBreak.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 ‘1.34.0’ * 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 5.501 0.116 5.618 bpStats-CopyNumberBreakPoints-method 4.965 0.036 5.001 * 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-3.19-bioc/meat/GeneBreak.Rcheck/00check.log’ for details.
GeneBreak.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL GeneBreak ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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 | 5.501 | 0.116 | 5.618 | |
CopyNumberBreakPoints-class | 1.585 | 0.088 | 1.672 | |
accessOptions-CopyNumberBreakPoints-method | 0.849 | 0.024 | 0.873 | |
addGeneAnnotation-CopyNumberBreakPoints-method | 1.868 | 0.032 | 1.900 | |
bpFilter-CopyNumberBreakPoints-method | 1.501 | 0.052 | 1.553 | |
bpGenes-CopyNumberBreakPointGenes-method | 2.068 | 0.016 | 2.084 | |
bpPlot-CopyNumberBreakPoints-method | 4.489 | 0.020 | 4.509 | |
bpStats-CopyNumberBreakPoints-method | 4.965 | 0.036 | 5.001 | |
breakpointData-CopyNumberBreakPoints-method | 1.269 | 0.588 | 1.857 | |
breakpointsPerGene-CopyNumberBreakPointGenes-method | 1.846 | 0.600 | 2.446 | |
callData-CopyNumberBreakPoints-method | 1.073 | 0.632 | 1.705 | |
featureChromosomes-CopyNumberBreakPoints-method | 0.810 | 0.074 | 0.884 | |
featureInfo-CopyNumberBreakPoints-method | 1.965 | 0.177 | 2.141 | |
featuresPerGene-CopyNumberBreakPointGenes-method | 1.961 | 0.048 | 2.009 | |
geneChromosomes-CopyNumberBreakPointGenes-method | 1.574 | 0.048 | 1.622 | |
geneInfo-CopyNumberBreakPointGenes-method | 1.827 | 0.068 | 1.894 | |
getBreakpoints | 1.659 | 0.040 | 1.699 | |
namesFeatures-CopyNumberBreakPoints-method | 0.492 | 0.080 | 0.571 | |
recurrentGenes-CopyNumberBreakPointGenes-method | 4.360 | 0.035 | 4.395 | |
sampleNames-CopyNumberBreakPoints-method | 0.864 | 0.041 | 0.905 | |
segmentData-CopyNumberBreakPoints-method | 1.165 | 0.640 | 1.805 | |