Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:30 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the canceR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/canceR.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 234/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
canceR 1.26.0 (landing page) Karim Mezhoud
| 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: canceR |
Version: 1.26.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:canceR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings canceR_1.26.0.tar.gz |
StartedAt: 2021-10-14 17:02:46 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 17:08:45 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 359.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: canceR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:canceR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings canceR_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/canceR.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘canceR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘canceR’ version ‘1.26.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Files named as vignettes but with no recognized vignette engine: ‘inst/doc/canceR.Rnw’ (Is a VignetteBuilder field missing?) * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘canceR’ can be installed ... OK * checking installed package size ... NOTE installed size is 5.0Mb sub-directories of 1Mb or more: doc 3.4Mb * checking package 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 ... OK * 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 installed files from ‘inst/doc’ ... OK * checking for old-style vignette sources ... NOTE Vignette sources only in ‘inst/doc’: ‘canceR.Rnw’ A ‘vignettes’ directory is required as from R 3.1.0 and these will not be indexed nor checked * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed getCases 0.088 0.041 5.38 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/canceR.Rcheck/00check.log’ for details.
canceR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL canceR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘canceR’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (canceR)
canceR.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(canceR) Loading required package: tcltk Loading required package: tcltk2 Loading required package: cgdsr Please send questions to cbioportal@googlegroups.com > > test_check("canceR") getCancerStudies... OK getCaseLists (1/2) ... OK getCaseLists (2/2) ... OK getGeneticProfiles (1/2) ... OK getGeneticProfiles (2/2) ... OK getClinicalData (1/1) ... OK getProfileData (1/6) ... OK getProfileData (2/6) ... OK getProfileData (3/6) ... OK getProfileData (4/6) ... OK getProfileData (5/6) ... OK getProfileData (6/6) ... OK ══ Skipped tests ═══════════════════════════════════════════════════════════════ • empty test (1) [ FAIL 0 | WARN 0 | SKIP 1 | PASS 0 ] > > proc.time() user system elapsed 15.334 1.999 18.937
canceR.Rcheck/canceR-Ex.timings
name | user | system | elapsed | |
GSEA.Analyze.Sets | 0.000 | 0.000 | 0.001 | |
GSEA.ConsPlot | 0.000 | 0.000 | 0.001 | |
GSEA.EnrichmentScore | 0 | 0 | 0 | |
GSEA.EnrichmentScore2 | 0.000 | 0.001 | 0.001 | |
GSEA.Gct2Frame | 0 | 0 | 0 | |
GSEA.Gct2Frame2 | 0 | 0 | 0 | |
GSEA.GeneRanking | 0.000 | 0.000 | 0.001 | |
GSEA.HeatMapPlot | 0.000 | 0.000 | 0.001 | |
GSEA.HeatMapPlot2 | 0.000 | 0.001 | 0.001 | |
GSEA.NormalizeCols | 0.001 | 0.002 | 0.002 | |
GSEA.NormalizeRows | 0.000 | 0.000 | 0.001 | |
GSEA | 0 | 0 | 0 | |
GSEA.ReadClsFile | 0.000 | 0.001 | 0.002 | |
GSEA.Res2Frame | 0.001 | 0.001 | 0.001 | |
GSEA.Threshold | 0.001 | 0.002 | 0.002 | |
GSEA.VarFilter | 0.001 | 0.001 | 0.002 | |
GSEA.write.gct | 0.001 | 0.001 | 0.002 | |
Match_GeneList_MSigDB | 0.001 | 0.000 | 0.002 | |
OLD.GSEA.EnrichmentScore | 0.001 | 0.001 | 0.003 | |
Run.GSEA | 0.001 | 0.001 | 0.002 | |
about | 0.000 | 0.001 | 0.000 | |
canceR | 0 | 0 | 0 | |
canceRHelp | 0 | 0 | 0 | |
canceR_Vignette | 0.000 | 0.000 | 0.001 | |
cbind.na | 0 | 0 | 0 | |
dialogGeneClassifier | 0.000 | 0.001 | 0.001 | |
dialogMetOption | 0.001 | 0.002 | 0.002 | |
dialogMut | 0.001 | 0.001 | 0.003 | |
dialogOptionCircos | 0.001 | 0.000 | 0.002 | |
dialogOptionGSEAlm | 0 | 0 | 0 | |
dialogOptionPhenoTest | 0.000 | 0.000 | 0.001 | |
dialogPlotOption_SkinCor | 0.001 | 0.000 | 0.001 | |
dialogSamplingGSEA | 0.001 | 0.001 | 0.003 | |
dialogSelectFiles_GSEA | 0.000 | 0.001 | 0.002 | |
dialogSpecificMut | 0.001 | 0.001 | 0.001 | |
dialogSummary_GSEA | 0.001 | 0.001 | 0.002 | |
dialoggetGeneListMSigDB | 0.000 | 0.000 | 0.001 | |
displayInTable | 0.000 | 0.000 | 0.001 | |
getCases | 0.088 | 0.041 | 5.380 | |
getCasesGenProfs | 0.001 | 0.001 | 0.002 | |
getCircos | 0.001 | 0.000 | 0.001 | |
getClinicData_MultipleCases | 0.000 | 0.000 | 0.001 | |
getClinicalDataMatrix | 0.001 | 0.001 | 0.002 | |
getCor_ExpCNAMet | 0 | 0 | 0 | |
getGCTCLSExample | 0.000 | 0.001 | 0.002 | |
getGCT_CLSfiles | 0.001 | 0.000 | 0.001 | |
getGSEAlm_Diseases | 0.001 | 0.001 | 0.001 | |
getGSEAlm_Variables | 0 | 0 | 0 | |
getGenProfs | 0.060 | 0.009 | 0.252 | |
getGeneList | 0 | 0 | 0 | |
getGeneListExample | 0.000 | 0.000 | 0.001 | |
getGeneListFromMSigDB | 0.001 | 0.001 | 0.001 | |
getGenesClassifier | 0 | 0 | 0 | |
getGenesTree_MultipleCases | 0 | 0 | 0 | |
getGenesTree_SingleCase | 0.000 | 0.000 | 0.001 | |
getInTable | 0 | 0 | 0 | |
getListProfData | 0.001 | 0.001 | 0.001 | |
getMSigDB | 0 | 0 | 0 | |
getMSigDBExample | 0.001 | 0.001 | 0.002 | |
getMSigDBfile | 0 | 0 | 0 | |
getMegaProfData | 0.000 | 0.001 | 0.001 | |
getMetDataMultipleGenes | 0.001 | 0.001 | 0.001 | |
getMutData | 0.000 | 0.001 | 0.002 | |
getPhenoTest | 0.000 | 0.001 | 0.000 | |
getProfilesDataMultipleGenes | 0.000 | 0.001 | 0.001 | |
getProfilesDataSingleGene | 0.001 | 0.001 | 0.002 | |
getSpecificMut | 0.001 | 0.001 | 0.002 | |
getSummaryGSEA | 0.001 | 0.001 | 0.001 | |
getSurvival | 0 | 0 | 0 | |
getTextWin | 0.001 | 0.000 | 0.000 | |
geteSet | 0.001 | 0.000 | 0.000 | |
modalDialog | 0.001 | 0.001 | 0.002 | |
myGlobalEnv | 0.000 | 0.001 | 0.000 | |
plotModel | 0.001 | 0.000 | 0.000 | |
plot_1Gene_2GenProfs | 0.001 | 0.000 | 0.000 | |
plot_2Genes_1GenProf | 0.001 | 0.000 | 0.002 | |
rbind.na | 0 | 0 | 0 | |
setWorkspace | 0.001 | 0.001 | 0.002 | |
testCheckedCaseGenProf | 0.001 | 0.001 | 0.001 | |