Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2025-03-20 12:06 -0400 (Thu, 20 Mar 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4756 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4514 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4441 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4406 |
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 790/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GeneBreak 1.36.0 (landing page) Evert van den Broek
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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: 1.36.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeneBreak.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GeneBreak_1.36.0.tar.gz |
StartedAt: 2025-03-18 01:38:16 -0400 (Tue, 18 Mar 2025) |
EndedAt: 2025-03-18 01:41:39 -0400 (Tue, 18 Mar 2025) |
EllapsedTime: 203.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GeneBreak.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeneBreak.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GeneBreak_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/GeneBreak.Rcheck' * using R version 4.4.3 (2025-02-28 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'GeneBreak/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'GeneBreak' version '1.36.0' * 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 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 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 (user + system) or elapsed time > 5s user system elapsed CopyNumberBreakPointGenes-class 7.18 0.95 8.14 recurrentGenes-CopyNumberBreakPointGenes-method 6.39 1.61 8.02 bpStats-CopyNumberBreakPoints-method 6.06 1.52 7.63 bpPlot-CopyNumberBreakPoints-method 5.94 1.05 6.98 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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 'F:/biocbuild/bbs-3.20-bioc/meat/GeneBreak.Rcheck/00check.log' for details.
GeneBreak.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL GeneBreak ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-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 | 7.18 | 0.95 | 8.14 | |
CopyNumberBreakPoints-class | 1.75 | 0.19 | 1.93 | |
accessOptions-CopyNumberBreakPoints-method | 0.66 | 0.15 | 0.82 | |
addGeneAnnotation-CopyNumberBreakPoints-method | 2.23 | 0.36 | 2.59 | |
bpFilter-CopyNumberBreakPoints-method | 1.30 | 0.24 | 1.53 | |
bpGenes-CopyNumberBreakPointGenes-method | 1.86 | 0.40 | 2.27 | |
bpPlot-CopyNumberBreakPoints-method | 5.94 | 1.05 | 6.98 | |
bpStats-CopyNumberBreakPoints-method | 6.06 | 1.52 | 7.63 | |
breakpointData-CopyNumberBreakPoints-method | 0.89 | 0.64 | 1.75 | |
breakpointsPerGene-CopyNumberBreakPointGenes-method | 2.39 | 0.78 | 3.17 | |
callData-CopyNumberBreakPoints-method | 1.47 | 0.53 | 2.37 | |
featureChromosomes-CopyNumberBreakPoints-method | 0.87 | 0.19 | 1.07 | |
featureInfo-CopyNumberBreakPoints-method | 2.19 | 0.36 | 2.57 | |
featuresPerGene-CopyNumberBreakPointGenes-method | 1.97 | 0.43 | 2.41 | |
geneChromosomes-CopyNumberBreakPointGenes-method | 2.13 | 0.35 | 2.47 | |
geneInfo-CopyNumberBreakPointGenes-method | 2.08 | 0.36 | 2.44 | |
getBreakpoints | 2.01 | 0.29 | 2.33 | |
namesFeatures-CopyNumberBreakPoints-method | 1.04 | 0.21 | 1.23 | |
recurrentGenes-CopyNumberBreakPointGenes-method | 6.39 | 1.61 | 8.02 | |
sampleNames-CopyNumberBreakPoints-method | 0.70 | 0.25 | 0.95 | |
segmentData-CopyNumberBreakPoints-method | 1.55 | 0.53 | 2.08 | |