Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1555/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
pipeComp 1.16.0 (landing page) Pierre-Luc Germain
| 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 | |||||||||
To the developers/maintainers of the pipeComp package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pipeComp.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: pipeComp |
Version: 1.16.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pipeComp.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pipeComp_1.16.0.tar.gz |
StartedAt: 2024-12-20 07:40:03 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 07:52:25 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 741.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: pipeComp.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pipeComp.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pipeComp_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/pipeComp.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘pipeComp/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘pipeComp’ version ‘1.16.0’ * package encoding: UTF-8 * 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 ‘pipeComp’ 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 ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 ... NOTE There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘.compileExcludedCells’ ‘.getMM’ ‘.homogenizeDEA’ ‘.runf’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE scrna_describeDatasets: no visible binding for global variable ‘cluster’ scrna_describeDatasets: no visible binding for global variable ‘nb’ scrna_describeDatasets : pf: no visible binding for global variable ‘.x’ scrna_describeDatasets : rd: no visible binding for global variable ‘y’ scrna_describeDatasets : rd: no visible binding for global variable ‘cluster’ scrna_evalPlot_filtering: no visible binding for global variable ‘max.lost’ scrna_evalPlot_filtering: no visible binding for global variable ‘mean_F1’ scrna_evalPlot_filtering: no visible binding for global variable ‘filt’ scrna_evalPlot_filtering: no visible binding for global variable ‘doubletmethod’ scrna_evalPlot_filtering: no visible binding for global variable ‘method’ scrna_evalPlot_overall: no visible binding for global variable ‘true.nbClusts’ scrna_evalPlot_overall: no visible binding for global variable ‘n_clus’ Undefined global functions or variables: .x cluster doubletmethod filt max.lost mean_F1 method n_clus nb true.nbClusts y * 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 scrna_evalPlot_overall 6.072 0.065 6.901 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/pipeComp.Rcheck/00check.log’ for details.
pipeComp.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL pipeComp ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘pipeComp’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** 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 (pipeComp)
pipeComp.Rcheck/pipeComp-Ex.timings
name | user | system | elapsed | |
PipelineDefinition-methods | 0.011 | 0.002 | 0.024 | |
PipelineDefinition | 0.002 | 0.000 | 0.003 | |
addPipelineStep | 0.004 | 0.001 | 0.005 | |
aggregatePipelineResults | 1.032 | 0.032 | 1.219 | |
buildCombMatrix | 0.003 | 0.001 | 0.004 | |
checkPipelinePackages | 1.665 | 0.722 | 2.690 | |
colCenterScale | 0.001 | 0.000 | 0.002 | |
dea_evalPlot_curve | 0.925 | 0.090 | 1.125 | |
dea_pipeline | 0.002 | 0.001 | 0.003 | |
evalHeatmap | 3.493 | 0.053 | 4.105 | |
evaluateClustering | 0.016 | 0.002 | 0.018 | |
evaluateDEA | 0.065 | 0.001 | 0.066 | |
evaluateDimRed | 1.797 | 0.046 | 2.195 | |
evaluateNorm | 2.330 | 0.084 | 2.662 | |
farthestPoint | 0.007 | 0.001 | 0.008 | |
getQualitativePalette | 0.000 | 0.001 | 0.001 | |
match_evaluate_multiple | 0.003 | 0.001 | 0.004 | |
mergePipelineResults | 2.188 | 0.065 | 2.530 | |
mockPipeline | 0.002 | 0.000 | 0.002 | |
parsePipNames | 0.002 | 0.000 | 0.003 | |
plotElapsed | 0.890 | 0.009 | 1.024 | |
readPipelineResults | 0.954 | 0.029 | 1.141 | |
runPipeline | 0.933 | 0.024 | 0.994 | |
scrna_evalPlot_filtering | 0.466 | 0.004 | 0.540 | |
scrna_evalPlot_overall | 6.072 | 0.065 | 6.901 | |
scrna_evalPlot_silh | 1.124 | 0.007 | 1.292 | |
scrna_pipeline | 0.002 | 0.000 | 0.003 | |