Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-20 12:08 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: pipeComp |
Version: 1.16.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:pipeComp.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings pipeComp_1.16.0.tar.gz |
StartedAt: 2024-11-20 11:01:39 -0000 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 11:09:34 -0000 (Wed, 20 Nov 2024) |
EllapsedTime: 475.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: pipeComp.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:pipeComp.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings pipeComp_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/pipeComp.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * 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 loading without being on the library search path ... 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 5.672 0.008 5.692 * 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 ‘/home/biocbuild/bbs-3.20-bioc/meat/pipeComp.Rcheck/00check.log’ for details.
pipeComp.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL pipeComp ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-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 | 0.01 | 0.00 | 0.01 | |
PipelineDefinition | 0.001 | 0.000 | 0.001 | |
addPipelineStep | 0.003 | 0.000 | 0.003 | |
aggregatePipelineResults | 1.257 | 0.008 | 1.344 | |
buildCombMatrix | 0.003 | 0.000 | 0.003 | |
checkPipelinePackages | 0.071 | 0.012 | 0.082 | |
colCenterScale | 0.000 | 0.001 | 0.002 | |
dea_evalPlot_curve | 0.769 | 0.042 | 0.813 | |
dea_pipeline | 0.003 | 0.000 | 0.003 | |
evalHeatmap | 3.257 | 0.063 | 3.327 | |
evaluateClustering | 0.011 | 0.000 | 0.012 | |
evaluateDEA | 0.066 | 0.001 | 0.067 | |
evaluateDimRed | 1.804 | 0.015 | 1.672 | |
evaluateNorm | 2.221 | 0.011 | 2.237 | |
farthestPoint | 0.007 | 0.000 | 0.008 | |
getQualitativePalette | 0 | 0 | 0 | |
match_evaluate_multiple | 0.003 | 0.000 | 0.003 | |
mergePipelineResults | 2.674 | 0.079 | 2.759 | |
mockPipeline | 0.001 | 0.000 | 0.001 | |
parsePipNames | 0.001 | 0.000 | 0.001 | |
plotElapsed | 0.844 | 0.028 | 0.873 | |
readPipelineResults | 1.194 | 0.016 | 1.212 | |
runPipeline | 1.167 | 0.044 | 1.213 | |
scrna_evalPlot_filtering | 0.453 | 0.000 | 0.454 | |
scrna_evalPlot_overall | 5.672 | 0.008 | 5.692 | |
scrna_evalPlot_silh | 1.077 | 0.008 | 1.090 | |
scrna_pipeline | 0.002 | 0.000 | 0.002 | |