Back to Build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-09-06 08:10 -0400 (Fri, 06 Sep 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4711 |
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 1593/2258 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
psichomics 1.31.0 (landing page) Nuno Saraiva-Agostinho
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
To the developers/maintainers of the psichomics package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/psichomics.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: psichomics |
Version: 1.31.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings psichomics_1.31.0.tar.gz |
StartedAt: 2024-09-06 03:54:42 -0400 (Fri, 06 Sep 2024) |
EndedAt: 2024-09-06 04:03:05 -0400 (Fri, 06 Sep 2024) |
EllapsedTime: 502.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: psichomics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings psichomics_1.31.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/psichomics.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘psichomics/DESCRIPTION’ ... OK * this is package ‘psichomics’ version ‘1.31.0’ * 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 ... NOTE Found the following hidden files and directories: .devcontainer 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 ‘psichomics’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ 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 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 whether startup messages can be suppressed ... 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 ... NOTE Documented arguments not in \usage in Rd file 'createSparklines.Rd': ‘id’ Documented arguments not in \usage in Rd file 'renderGeneticInfo.Rd': ‘ns’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed convertGeneIdentifiers 14.364 0.575 16.043 listSplicingAnnotations 10.761 0.472 11.964 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘spelling.R’ Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/psichomics.Rcheck/00check.log’ for details.
psichomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL psichomics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘psichomics’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c progressBar.cpp -o progressBar.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c psiFastCalc.cpp -o psiFastCalc.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c vastToolsParser.cpp -o vastToolsParser.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o psichomics.so RcppExports.o progressBar.o psiFastCalc.o vastToolsParser.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-psichomics/00new/psichomics/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘colSums’ from package ‘base’ in package ‘psichomics’ ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (psichomics)
psichomics.Rcheck/tests/spelling.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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. > if(requireNamespace('spelling', quietly = TRUE)) + spelling::spell_check_test(vignettes = TRUE, error = FALSE, + skip_on_cran = TRUE) NULL > > proc.time() user system elapsed 0.145 0.045 0.179
psichomics.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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(psichomics) Loading required package: shiny Loading required package: shinyBS Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) psichomics 1.31.0: start the visual interface by running psichomics() Full documentation and tutorials at https://nuno-agostinho.github.io/psichomics > > test_check("psichomics") | | 0% |======== | 20% |================ | 40% |======================== | 60% |================================ | 80% |========================================| 100% | | 0% |======== | 20% |================ | 40% |======================== | 60% |================================ | 80% |========================================| 100% | | 0% |======== | 20% |================ | 40% |======================== | 60% |================================ | 80% |========================================| 100% | | 0% |======== | 20% |================ | 40% |======================== | 60% |================================ | 80% |========================================| 100% Retrieving rMATS annotation... Parsing rMATS annotation... Retrieving rMATS annotation... Parsing rMATS annotation... Retrieving MISO annotation... Parsing MISO annotation... | | 0% |======== | 20% |================ | 40% |======================== | 60% |================================ | 80% |========================================| 100% | | 0% |======== | 20% |================ | 40% |======================== | 60% |================================ | 80% |========================================| 100% | | 0% |======== | 20% |================ | 40% |======================== | 60% |================================ | 80% |========================================| 100% | | 0% |======== | 20% |================ | 40% |======================== | 60% |================================ | 80% |========================================| 100% | | 0% |======== | 20% |================ | 40% |======================== | 60% |================================ | 80% |========================================| 100% | | 0% |======== | 20% |================ | 40% |======================== | 60% |================================ | 80% |========================================| 100% | | 0% |======== | 20% |================ | 40% |======================== | 60% |================================ | 80% |========================================| 100% | | 0% |======== | 20% |================ | 40% |======================== | 60% |================================ | 80% |========================================| 100% Retrieving SUPPA annotation... Parsing SUPPA annotation... Retrieving VAST-TOOLS annotation... Parsing VAST-TOOLS annotation... ALT3 ALT5 COMBI EXSK IR MERGE3m MIC MULTI [ FAIL 0 | WARN 0 | SKIP 4 | PASS 1418 ] ══ Skipped tests (4) ═══════════════════════════════════════════════════════════ • Couldn't resolve host name (1): 'testGeneInfo.R:99:5' • On Bioconductor (2): 'testDiscardLowCoveragePSIs.R:62:5', 'testGeneInfo.R:50:5' • On CRAN (1): 'testSRAloading.R:4:5' [ FAIL 0 | WARN 0 | SKIP 4 | PASS 1418 ] > > proc.time() user system elapsed 22.939 1.522 25.926
psichomics.Rcheck/psichomics-Ex.timings
name | user | system | elapsed | |
addObjectAttrs | 0 | 0 | 0 | |
assignValuePerSubject | 0.005 | 0.013 | 0.019 | |
blendColours | 0.001 | 0.000 | 0.001 | |
calculateLoadingsContribution | 0.009 | 0.000 | 0.010 | |
convertGeneIdentifiers | 14.364 | 0.575 | 16.043 | |
correlateGEandAS | 0.013 | 0.004 | 0.016 | |
createGroupByAttribute | 0.001 | 0.000 | 0.001 | |
createJunctionsTemplate | 0.002 | 0.000 | 0.002 | |
customRowMeans | 0.001 | 0.000 | 0.001 | |
diffAnalyses | 0.065 | 0.004 | 0.069 | |
downloadFiles | 0 | 0 | 0 | |
ensemblToUniprot | 0.019 | 0.004 | 0.673 | |
filterGeneExpr | 0.006 | 0.000 | 0.006 | |
filterGroups | 0.002 | 0.000 | 0.001 | |
filterPSI | 0.009 | 0.004 | 0.012 | |
getAttributesTime | 0.002 | 0.000 | 0.003 | |
getDownloadsFolder | 0 | 0 | 0 | |
getFirebrowseDateFormat | 0.001 | 0.000 | 0.000 | |
getGeneList | 0.003 | 0.000 | 0.004 | |
getGtexDataTypes | 0.001 | 0.000 | 0.001 | |
getGtexTissues | 0 | 0 | 0 | |
getNumerics | 0.001 | 0.000 | 0.002 | |
getSampleFromSubject | 0.001 | 0.000 | 0.001 | |
getSplicingEventFromGenes | 0.004 | 0.000 | 0.003 | |
getSplicingEventTypes | 0 | 0 | 0 | |
getSubjectFromSample | 0.001 | 0.000 | 0.000 | |
getTCGAdataTypes | 0.046 | 0.000 | 0.226 | |
getValidEvents | 0.004 | 0.000 | 0.005 | |
groupPerElem | 0.001 | 0.000 | 0.001 | |
hchart.survfit | 0.258 | 0.016 | 0.292 | |
isFirebrowseUp | 0.005 | 0.000 | 0.012 | |
labelBasedOnCutoff | 0.001 | 0.000 | 0.000 | |
leveneTest | 0.006 | 0.000 | 0.006 | |
listAllAnnotations | 3.506 | 0.156 | 3.885 | |
listSplicingAnnotations | 10.761 | 0.472 | 11.964 | |
loadAnnotation | 2.855 | 0.104 | 3.136 | |
loadGtexData | 0 | 0 | 0 | |
loadLocalFiles | 0.001 | 0.000 | 0.000 | |
loadSRAproject | 0 | 0 | 0 | |
loadTCGAdata | 0.010 | 0.000 | 0.025 | |
missingDataModal | 0.000 | 0.000 | 0.001 | |
normaliseGeneExpression | 0.023 | 0.000 | 0.023 | |
optimalSurvivalCutoff | 0.084 | 0.000 | 0.083 | |
parseCategoricalGroups | 0.001 | 0.000 | 0.000 | |
parseFirebrowseMetadata | 0.060 | 0.004 | 0.115 | |
parseMatsEvent | 0.006 | 0.000 | 0.006 | |
parseMatsGeneric | 0.025 | 0.000 | 0.025 | |
parseMisoAnnotation | 0.130 | 0.004 | 0.135 | |
parseMisoEvent | 0.004 | 0.000 | 0.003 | |
parseMisoEventID | 0.005 | 0.000 | 0.005 | |
parseMisoGeneric | 0.026 | 0.000 | 0.027 | |
parseMisoId | 0.000 | 0.000 | 0.001 | |
parseSplicingEvent | 0.000 | 0.004 | 0.004 | |
parseSuppaEvent | 0.004 | 0.000 | 0.003 | |
parseSuppaGeneric | 0.016 | 0.000 | 0.017 | |
parseTcgaSampleInfo | 0.003 | 0.000 | 0.004 | |
parseUrlsFromFirebrowseResponse | 0.044 | 0.000 | 0.101 | |
parseVastToolsEvent | 0.007 | 0.000 | 0.008 | |
parseVastToolsSE | 0.027 | 0.000 | 0.026 | |
performICA | 0.002 | 0.007 | 0.009 | |
performPCA | 0.002 | 0.000 | 0.002 | |
plot.GEandAScorrelation | 0.528 | 0.028 | 0.555 | |
plotDistribution | 0.583 | 0.008 | 0.591 | |
plotGeneExprPerSample | 0.082 | 0.004 | 0.085 | |
plotGroupIndependence | 0.139 | 0.004 | 0.143 | |
plotICA | 0.134 | 0.000 | 0.137 | |
plotLibrarySize | 0.156 | 0.004 | 0.160 | |
plotPCA | 0.207 | 0.024 | 0.232 | |
plotPCAvariance | 0.043 | 0.004 | 0.047 | |
plotProtein | 0.566 | 0.016 | 1.463 | |
plotRowStats | 0.413 | 0.000 | 0.415 | |
plotSingleICA | 0.200 | 0.016 | 0.216 | |
plotSplicingEvent | 0.039 | 0.000 | 0.039 | |
plotSurvivalCurves | 0.071 | 0.008 | 0.079 | |
plotSurvivalPvaluesByCutoff | 0.368 | 0.004 | 0.372 | |
plotTranscripts | 0.028 | 0.000 | 0.833 | |
prepareAnnotationFromEvents | 0.179 | 0.004 | 0.184 | |
prepareFirebrowseArchives | 0.000 | 0.000 | 0.001 | |
prepareJunctionQuantSTAR | 0 | 0 | 0 | |
prepareSRAmetadata | 0 | 0 | 0 | |
processSurvTerms | 0.008 | 0.000 | 0.008 | |
psichomics | 0 | 0 | 0 | |
quantifySplicing | 0.01 | 0.00 | 0.01 | |
queryEnsembl | 0.029 | 0.000 | 0.576 | |
queryEnsemblByGene | 0.091 | 0.004 | 3.897 | |
queryFirebrowseData | 0.041 | 0.000 | 0.143 | |
queryPubMed | 0.101 | 0.008 | 0.669 | |
queryUniprot | 0.064 | 0.000 | 0.394 | |
readFile | 0.001 | 0.000 | 0.002 | |
renameDuplicated | 0.001 | 0.000 | 0.001 | |
renderBoxplot | 0.136 | 0.012 | 0.148 | |
survdiffTerms | 0.005 | 0.000 | 0.005 | |
survfit.survTerms | 0.02 | 0.00 | 0.02 | |
testGroupIndependence | 0.002 | 0.000 | 0.002 | |
testSurvival | 0.018 | 0.000 | 0.018 | |
textSuggestions | 0.001 | 0.000 | 0.001 | |
trimWhitespace | 0.001 | 0.000 | 0.000 | |