Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-04-12 11:37:57 -0400 (Fri, 12 Apr 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4675 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4413 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4436 |
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 1608/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
psichomics 1.28.1 (landing page) Nuno Saraiva-Agostinho
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
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: 1.28.1 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:psichomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings psichomics_1.28.1.tar.gz |
StartedAt: 2024-04-11 07:14:32 -0400 (Thu, 11 Apr 2024) |
EndedAt: 2024-04-11 07:29:54 -0400 (Thu, 11 Apr 2024) |
EllapsedTime: 921.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: psichomics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:psichomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings psichomics_1.28.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/psichomics.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘psichomics/DESCRIPTION’ ... OK * this is package ‘psichomics’ version ‘1.28.1’ * 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 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 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 ... OK * 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 24.404 1.988 32.931 listSplicingAnnotations 21.433 1.920 25.208 loadAnnotation 5.236 0.411 5.770 listAllAnnotations 4.368 0.450 5.131 queryPubMed 0.051 0.016 5.676 * 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 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.18-bioc/meat/psichomics.Rcheck/00check.log’ for details.
psichomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL psichomics ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘psichomics’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c progressBar.cpp -o progressBar.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c psiFastCalc.cpp -o psiFastCalc.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vastToolsParser.cpp -o vastToolsParser.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o psichomics.so RcppExports.o progressBar.o psiFastCalc.o vastToolsParser.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/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 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 (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. > if(requireNamespace('spelling', quietly = TRUE)) + spelling::spell_check_test(vignettes = TRUE, error = FALSE, + skip_on_cran = TRUE) NULL > > proc.time() user system elapsed 0.352 0.118 0.446
psichomics.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 (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(psichomics) Loading required package: shiny Loading required package: shinyBS Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) psichomics 1.28.1: 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 43.710 2.890 49.765
psichomics.Rcheck/psichomics-Ex.timings
name | user | system | elapsed | |
addObjectAttrs | 0.000 | 0.001 | 0.002 | |
assignValuePerSubject | 0.036 | 0.024 | 0.146 | |
blendColours | 0.002 | 0.000 | 0.002 | |
calculateLoadingsContribution | 0.016 | 0.006 | 0.097 | |
convertGeneIdentifiers | 24.404 | 1.988 | 32.931 | |
correlateGEandAS | 0.037 | 0.010 | 0.048 | |
createGroupByAttribute | 0.002 | 0.001 | 0.003 | |
createJunctionsTemplate | 0.004 | 0.002 | 0.005 | |
customRowMeans | 0.001 | 0.001 | 0.003 | |
diffAnalyses | 0.160 | 0.017 | 0.191 | |
downloadFiles | 0.000 | 0.001 | 0.001 | |
ensemblToUniprot | 0.032 | 0.002 | 0.989 | |
filterGeneExpr | 0.013 | 0.003 | 0.017 | |
filterGroups | 0.002 | 0.001 | 0.003 | |
filterPSI | 0.028 | 0.010 | 0.038 | |
getAttributesTime | 0.004 | 0.001 | 0.004 | |
getDownloadsFolder | 0.000 | 0.000 | 0.001 | |
getFirebrowseDateFormat | 0.001 | 0.000 | 0.001 | |
getGeneList | 0.005 | 0.002 | 0.008 | |
getGtexDataTypes | 0.001 | 0.001 | 0.002 | |
getGtexTissues | 0 | 0 | 0 | |
getNumerics | 0.004 | 0.001 | 0.005 | |
getSampleFromSubject | 0.002 | 0.001 | 0.003 | |
getSplicingEventFromGenes | 0.006 | 0.002 | 0.008 | |
getSplicingEventTypes | 0.001 | 0.001 | 0.001 | |
getSubjectFromSample | 0.001 | 0.000 | 0.001 | |
getTCGAdataTypes | 0.045 | 0.005 | 0.242 | |
getValidEvents | 0.007 | 0.002 | 0.009 | |
groupPerElem | 0.001 | 0.000 | 0.002 | |
hchart.survfit | 0.457 | 0.197 | 0.667 | |
isFirebrowseUp | 0.010 | 0.001 | 0.041 | |
labelBasedOnCutoff | 0.001 | 0.001 | 0.001 | |
leveneTest | 0.015 | 0.001 | 0.025 | |
listAllAnnotations | 4.368 | 0.450 | 5.131 | |
listSplicingAnnotations | 21.433 | 1.920 | 25.208 | |
loadAnnotation | 5.236 | 0.411 | 5.770 | |
loadGtexData | 0.000 | 0.001 | 0.002 | |
loadLocalFiles | 0.000 | 0.001 | 0.001 | |
loadSRAproject | 0.000 | 0.000 | 0.001 | |
loadTCGAdata | 0.013 | 0.004 | 0.089 | |
missingDataModal | 0.000 | 0.001 | 0.001 | |
normaliseGeneExpression | 0.038 | 0.004 | 0.043 | |
optimalSurvivalCutoff | 0.200 | 0.003 | 0.203 | |
parseCategoricalGroups | 0.002 | 0.000 | 0.003 | |
parseFirebrowseMetadata | 0.059 | 0.010 | 0.254 | |
parseMatsEvent | 0.007 | 0.002 | 0.010 | |
parseMatsGeneric | 0.042 | 0.006 | 0.048 | |
parseMisoAnnotation | 0.265 | 0.022 | 0.293 | |
parseMisoEvent | 0.008 | 0.001 | 0.009 | |
parseMisoEventID | 0.011 | 0.005 | 0.016 | |
parseMisoGeneric | 0.066 | 0.009 | 0.075 | |
parseMisoId | 0.000 | 0.000 | 0.001 | |
parseSplicingEvent | 0.010 | 0.005 | 0.014 | |
parseSuppaEvent | 0.008 | 0.001 | 0.009 | |
parseSuppaGeneric | 0.042 | 0.006 | 0.048 | |
parseTcgaSampleInfo | 0.006 | 0.002 | 0.009 | |
parseUrlsFromFirebrowseResponse | 0.040 | 0.002 | 0.182 | |
parseVastToolsEvent | 0.012 | 0.001 | 0.014 | |
parseVastToolsSE | 0.039 | 0.004 | 0.044 | |
performICA | 0.012 | 0.009 | 0.020 | |
performPCA | 0.002 | 0.001 | 0.003 | |
plot.GEandAScorrelation | 1.056 | 0.024 | 1.082 | |
plotDistribution | 1.549 | 0.180 | 1.814 | |
plotGeneExprPerSample | 0.169 | 0.070 | 0.239 | |
plotGroupIndependence | 0.303 | 0.003 | 0.306 | |
plotICA | 0.237 | 0.020 | 0.261 | |
plotLibrarySize | 0.425 | 0.064 | 0.573 | |
plotPCA | 0.499 | 0.245 | 0.830 | |
plotPCAvariance | 0.093 | 0.062 | 0.156 | |
plotProtein | 1.315 | 0.133 | 2.067 | |
plotRowStats | 0.895 | 0.015 | 0.910 | |
plotSingleICA | 0.407 | 0.187 | 0.639 | |
plotSplicingEvent | 0.114 | 0.002 | 0.122 | |
plotSurvivalCurves | 0.168 | 0.068 | 0.288 | |
plotSurvivalPvaluesByCutoff | 0.968 | 0.080 | 1.115 | |
plotTranscripts | 0.033 | 0.002 | 1.735 | |
prepareAnnotationFromEvents | 0.420 | 0.012 | 0.441 | |
prepareFirebrowseArchives | 0.001 | 0.000 | 0.001 | |
prepareJunctionQuantSTAR | 0.000 | 0.001 | 0.001 | |
prepareSRAmetadata | 0.000 | 0.001 | 0.001 | |
processSurvTerms | 0.020 | 0.001 | 0.035 | |
psichomics | 0.000 | 0.001 | 0.000 | |
quantifySplicing | 0.026 | 0.010 | 0.042 | |
queryEnsembl | 0.052 | 0.007 | 0.578 | |
queryEnsemblByGene | 0.188 | 0.032 | 4.638 | |
queryFirebrowseData | 0.060 | 0.003 | 0.326 | |
queryPubMed | 0.051 | 0.016 | 5.676 | |
queryUniprot | 0.095 | 0.003 | 0.362 | |
readFile | 0.002 | 0.001 | 0.004 | |
renameDuplicated | 0.001 | 0.000 | 0.002 | |
renderBoxplot | 0.151 | 0.068 | 0.228 | |
survdiffTerms | 0.012 | 0.002 | 0.015 | |
survfit.survTerms | 0.037 | 0.003 | 0.044 | |
testGroupIndependence | 0.005 | 0.001 | 0.006 | |
testSurvival | 0.033 | 0.002 | 0.039 | |
textSuggestions | 0.001 | 0.001 | 0.002 | |
trimWhitespace | 0.001 | 0.001 | 0.002 | |