Back to Mac ARM64 build report for BioC 3.17 |
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This page was generated on 2023-10-20 09:38:02 -0400 (Fri, 20 Oct 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
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 774/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GeneBreak 1.30.0 (landing page) Evert van den Broek
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | ![]() | |||||||
To the developers/maintainers of the GeneBreak package: - 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: 1.30.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeneBreak.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeneBreak_1.30.0.tar.gz |
StartedAt: 2023-10-17 20:57:27 -0400 (Tue, 17 Oct 2023) |
EndedAt: 2023-10-17 21:02:06 -0400 (Tue, 17 Oct 2023) |
EllapsedTime: 279.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GeneBreak.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeneBreak.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeneBreak_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/GeneBreak.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GeneBreak/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GeneBreak’ version ‘1.30.0’ * 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 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 6.841 0.383 10.879 bpStats-CopyNumberBreakPoints-method 5.147 0.340 8.045 recurrentGenes-CopyNumberBreakPointGenes-method 5.129 0.318 8.197 bpPlot-CopyNumberBreakPoints-method 4.939 0.286 7.600 * 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 ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/GeneBreak.Rcheck/00check.log’ for details.
GeneBreak.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GeneBreak ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 | 6.841 | 0.383 | 10.879 | |
CopyNumberBreakPoints-class | 1.634 | 0.088 | 2.605 | |
accessOptions-CopyNumberBreakPoints-method | 0.598 | 0.034 | 0.941 | |
addGeneAnnotation-CopyNumberBreakPoints-method | 1.765 | 0.082 | 2.751 | |
bpFilter-CopyNumberBreakPoints-method | 1.192 | 0.068 | 1.831 | |
bpGenes-CopyNumberBreakPointGenes-method | 1.926 | 0.102 | 2.753 | |
bpPlot-CopyNumberBreakPoints-method | 4.939 | 0.286 | 7.600 | |
bpStats-CopyNumberBreakPoints-method | 5.147 | 0.340 | 8.045 | |
breakpointData-CopyNumberBreakPoints-method | 0.776 | 0.504 | 1.657 | |
breakpointsPerGene-CopyNumberBreakPointGenes-method | 1.746 | 0.525 | 3.300 | |
callData-CopyNumberBreakPoints-method | 1.152 | 0.513 | 2.430 | |
featureChromosomes-CopyNumberBreakPoints-method | 0.917 | 0.061 | 1.448 | |
featureInfo-CopyNumberBreakPoints-method | 1.724 | 0.183 | 2.745 | |
featuresPerGene-CopyNumberBreakPointGenes-method | 1.947 | 0.082 | 2.846 | |
geneChromosomes-CopyNumberBreakPointGenes-method | 1.920 | 0.089 | 2.779 | |
geneInfo-CopyNumberBreakPointGenes-method | 1.836 | 0.123 | 2.875 | |
getBreakpoints | 1.303 | 0.071 | 2.098 | |
namesFeatures-CopyNumberBreakPoints-method | 0.920 | 0.079 | 1.516 | |
recurrentGenes-CopyNumberBreakPointGenes-method | 5.129 | 0.318 | 8.197 | |
sampleNames-CopyNumberBreakPoints-method | 0.652 | 0.039 | 1.011 | |
segmentData-CopyNumberBreakPoints-method | 1.127 | 0.577 | 2.610 | |