Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:48 -0400 (Fri, 15 Oct 2021).
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1396/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
pipeComp 1.2.0 (landing page) Pierre-Luc Germain
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: pipeComp |
Version: 1.2.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:pipeComp.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings pipeComp_1.2.0.tar.gz |
StartedAt: 2021-10-14 11:02:16 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 11:07:18 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 302.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: pipeComp.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:pipeComp.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings pipeComp_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/pipeComp.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘pipeComp/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘pipeComp’ version ‘1.2.0’ * 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 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.13-bioc/meat/pipeComp.Rcheck/00check.log’ for details.
pipeComp.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL pipeComp ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/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 | 0.010 | 0.001 | 0.009 | |
PipelineDefinition | 0.000 | 0.001 | 0.001 | |
addPipelineStep | 0.003 | 0.001 | 0.004 | |
aggregatePipelineResults | 0.196 | 0.019 | 0.216 | |
buildCombMatrix | 0.003 | 0.000 | 0.003 | |
checkPipelinePackages | 1.056 | 0.188 | 1.245 | |
colCenterScale | 0.003 | 0.001 | 0.002 | |
dea_evalPlot_curve | 1.506 | 0.000 | 1.506 | |
dea_pipeline | 0.002 | 0.000 | 0.002 | |
evalHeatmap | 1.688 | 0.087 | 1.776 | |
evaluateClustering | 0.028 | 0.000 | 0.028 | |
evaluateDEA | 0.032 | 0.000 | 0.033 | |
evaluateDimRed | 1.804 | 0.036 | 1.840 | |
evaluateNorm | 1.943 | 0.048 | 1.990 | |
farthestPoint | 0.007 | 0.000 | 0.006 | |
getQualitativePalette | 0.000 | 0.001 | 0.000 | |
match_evaluate_multiple | 0.000 | 0.003 | 0.003 | |
mergePipelineResults | 0.315 | 0.016 | 0.331 | |
mockPipeline | 0.001 | 0.000 | 0.002 | |
parsePipNames | 0.002 | 0.000 | 0.002 | |
plotElapsed | 0.463 | 0.000 | 0.464 | |
readPipelineResults | 0.095 | 0.008 | 0.103 | |
runPipeline | 0.080 | 0.028 | 0.107 | |
scrna_evalPlot_filtering | 0.344 | 0.000 | 0.344 | |
scrna_evalPlot_overall | 3.341 | 0.008 | 3.349 | |
scrna_evalPlot_silh | 0.755 | 0.028 | 0.783 | |
scrna_pipeline | 0.002 | 0.000 | 0.002 | |