Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:05:14 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
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 |
To the developers/maintainers of the pipeComp package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1488/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
pipeComp 1.8.0 (landing page) Pierre-Luc Germain
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
Package: pipeComp |
Version: 1.8.0 |
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:pipeComp.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings pipeComp_1.8.0.tar.gz |
StartedAt: 2023-04-10 22:56:24 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 23:05:50 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 566.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: pipeComp.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:pipeComp.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings pipeComp_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/pipeComp.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘pipeComp/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘pipeComp’ version ‘1.8.0’ * 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 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 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 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘pipeComp.Rmd’ using ‘UTF-8’... OK ‘pipeComp_dea.Rmd’ using ‘UTF-8’... OK ‘pipeComp_scRNA.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.16-bioc/meat/pipeComp.Rcheck/00check.log’ for details.
pipeComp.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL pipeComp ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/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 | 0.167 | 0.004 | 0.171 | |
buildCombMatrix | 0.000 | 0.003 | 0.003 | |
checkPipelinePackages | 1.133 | 0.112 | 1.246 | |
colCenterScale | 0.002 | 0.000 | 0.002 | |
dea_evalPlot_curve | 0.842 | 0.008 | 0.850 | |
dea_pipeline | 0.002 | 0.000 | 0.002 | |
evalHeatmap | 3.554 | 0.244 | 3.798 | |
evaluateClustering | 0.009 | 0.000 | 0.009 | |
evaluateDEA | 0.050 | 0.004 | 0.053 | |
evaluateDimRed | 1.948 | 0.040 | 1.988 | |
evaluateNorm | 2.039 | 0.008 | 2.047 | |
farthestPoint | 0.006 | 0.000 | 0.006 | |
getQualitativePalette | 0.001 | 0.000 | 0.000 | |
match_evaluate_multiple | 0.002 | 0.000 | 0.003 | |
mergePipelineResults | 0.330 | 0.012 | 0.343 | |
mockPipeline | 0.001 | 0.000 | 0.002 | |
parsePipNames | 0.000 | 0.001 | 0.002 | |
plotElapsed | 0.548 | 0.002 | 0.551 | |
readPipelineResults | 0.085 | 0.000 | 0.085 | |
runPipeline | 0.076 | 0.008 | 0.084 | |
scrna_evalPlot_filtering | 0.419 | 0.008 | 0.428 | |
scrna_evalPlot_overall | 4.107 | 0.092 | 4.200 | |
scrna_evalPlot_silh | 0.831 | 0.004 | 0.835 | |
scrna_pipeline | 0.001 | 0.000 | 0.002 | |