Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:47 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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 psichomics package: - Please 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 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 1536/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
psichomics 1.25.0 (landing page) Nuno Saraiva-Agostinho
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: psichomics |
Version: 1.25.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings psichomics_1.25.0.tar.gz |
StartedAt: 2023-02-28 11:53:15 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 12:04:26 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 670.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: psichomics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings psichomics_1.25.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/psichomics.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘psichomics/DESCRIPTION’ ... OK * this is package ‘psichomics’ version ‘1.25.0’ * 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 11.3.0-1ubuntu1~22.04) 11.3.0’ * 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 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 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 17.889 1.748 31.272 listSplicingAnnotations 15.019 1.585 25.634 loadAnnotation 3.402 0.372 6.414 listAllAnnotations 3.155 0.380 5.594 queryEnsemblByGene 0.109 0.016 5.922 * 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 ... ‘AS_events_preparation.Rmd’ using ‘UTF-8’... OK ‘CLI_tutorial.Rmd’ using ‘UTF-8’... OK ‘GUI_tutorial.Rmd’ using ‘UTF-8’... OK ‘custom_data.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/psichomics.Rcheck/00check.log’ for details.
psichomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL psichomics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘psichomics’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c progressBar.cpp -o progressBar.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c psiFastCalc.cpp -o psiFastCalc.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c vastToolsParser.cpp -o vastToolsParser.o g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o psichomics.so RcppExports.o progressBar.o psiFastCalc.o vastToolsParser.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (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 0.197 0.032 0.215
psichomics.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (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 1.25.0: 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 1 | SKIP 4 | PASS 1418 ] ══ Skipped tests ═══════════════════════════════════════════════════════════════ • Couldn't resolve host name (1) • On Bioconductor (2) • On CRAN (1) [ FAIL 0 | WARN 1 | SKIP 4 | PASS 1418 ] > > proc.time() user system elapsed 28.795 1.660 46.116
psichomics.Rcheck/psichomics-Ex.timings
name | user | system | elapsed | |
addObjectAttrs | 0.001 | 0.000 | 0.001 | |
assignValuePerSubject | 0.022 | 0.000 | 0.024 | |
blendColours | 0.001 | 0.000 | 0.000 | |
calculateLoadingsContribution | 0.007 | 0.004 | 0.012 | |
convertGeneIdentifiers | 17.889 | 1.748 | 31.272 | |
correlateGEandAS | 0.020 | 0.004 | 0.025 | |
createGroupByAttribute | 0.000 | 0.002 | 0.002 | |
createJunctionsTemplate | 0.001 | 0.001 | 0.003 | |
customRowMeans | 0.001 | 0.000 | 0.003 | |
diffAnalyses | 0.095 | 0.012 | 0.107 | |
downloadFiles | 0.000 | 0.001 | 0.000 | |
ensemblToUniprot | 0.025 | 0.007 | 1.324 | |
filterGeneExpr | 0.008 | 0.000 | 0.008 | |
filterGroups | 0.002 | 0.000 | 0.001 | |
filterPSI | 0.015 | 0.008 | 0.023 | |
getAttributesTime | 0.004 | 0.000 | 0.004 | |
getDownloadsFolder | 0.001 | 0.000 | 0.000 | |
getFirebrowseDateFormat | 0.001 | 0.000 | 0.000 | |
getGeneList | 0.005 | 0.000 | 0.005 | |
getGtexDataTypes | 0.076 | 0.016 | 1.416 | |
getGtexTissues | 0.000 | 0.000 | 0.001 | |
getNumerics | 0.000 | 0.002 | 0.002 | |
getSampleFromSubject | 0.000 | 0.001 | 0.001 | |
getSplicingEventFromGenes | 0.000 | 0.004 | 0.004 | |
getSplicingEventTypes | 0 | 0 | 0 | |
getSubjectFromSample | 0 | 0 | 0 | |
getTCGAdataTypes | 0.044 | 0.005 | 4.643 | |
getValidEvents | 0.004 | 0.000 | 0.005 | |
groupPerElem | 0.001 | 0.000 | 0.001 | |
hchart.survfit | 0.301 | 0.052 | 0.397 | |
isFirebrowseUp | 0.006 | 0.000 | 0.271 | |
labelBasedOnCutoff | 0.001 | 0.000 | 0.001 | |
leveneTest | 0.01 | 0.00 | 0.01 | |
listAllAnnotations | 3.155 | 0.380 | 5.594 | |
listSplicingAnnotations | 15.019 | 1.585 | 25.634 | |
loadAnnotation | 3.402 | 0.372 | 6.414 | |
loadGtexData | 0 | 0 | 0 | |
loadLocalFiles | 0.001 | 0.000 | 0.000 | |
loadSRAproject | 0 | 0 | 0 | |
loadTCGAdata | 0.008 | 0.004 | 0.560 | |
missingDataModal | 0.001 | 0.000 | 0.000 | |
normaliseGeneExpression | 0.024 | 0.004 | 0.028 | |
optimalSurvivalCutoff | 0.130 | 0.007 | 0.138 | |
parseCategoricalGroups | 0.001 | 0.001 | 0.002 | |
parseFirebrowseMetadata | 0.055 | 0.008 | 2.942 | |
parseMatsEvent | 0.006 | 0.000 | 0.007 | |
parseMatsGeneric | 0.027 | 0.000 | 0.028 | |
parseMisoAnnotation | 0.152 | 0.027 | 0.193 | |
parseMisoEvent | 0.005 | 0.000 | 0.005 | |
parseMisoEventID | 0.004 | 0.004 | 0.008 | |
parseMisoGeneric | 0.039 | 0.004 | 0.043 | |
parseMisoId | 0.001 | 0.000 | 0.000 | |
parseSplicingEvent | 0.006 | 0.000 | 0.005 | |
parseSuppaEvent | 0.004 | 0.000 | 0.005 | |
parseSuppaGeneric | 0.026 | 0.000 | 0.026 | |
parseTcgaSampleInfo | 0.004 | 0.000 | 0.005 | |
parseUrlsFromFirebrowseResponse | 0.035 | 0.000 | 1.467 | |
parseVastToolsEvent | 0.007 | 0.000 | 0.007 | |
parseVastToolsSE | 0.020 | 0.004 | 0.024 | |
performICA | 0.002 | 0.007 | 0.009 | |
performPCA | 0.001 | 0.000 | 0.002 | |
plot.GEandAScorrelation | 0.503 | 0.052 | 0.555 | |
plotDistribution | 0.883 | 0.128 | 1.012 | |
plotGeneExprPerSample | 0.134 | 0.008 | 0.142 | |
plotGroupIndependence | 0.196 | 0.008 | 0.204 | |
plotICA | 0.144 | 0.008 | 0.157 | |
plotLibrarySize | 0.258 | 0.012 | 0.271 | |
plotPCA | 0.328 | 0.032 | 0.361 | |
plotPCAvariance | 0.104 | 0.008 | 0.113 | |
plotProtein | 0.798 | 0.060 | 4.771 | |
plotRowStats | 0.475 | 0.020 | 0.494 | |
plotSingleICA | 0.287 | 0.052 | 0.339 | |
plotSplicingEvent | 0.059 | 0.000 | 0.059 | |
plotSurvivalCurves | 0.104 | 0.008 | 0.112 | |
plotSurvivalPvaluesByCutoff | 0.536 | 0.060 | 0.596 | |
plotTranscripts | 0.024 | 0.004 | 2.312 | |
prepareAnnotationFromEvents | 0.211 | 0.020 | 0.231 | |
prepareFirebrowseArchives | 0 | 0 | 0 | |
prepareJunctionQuantSTAR | 0 | 0 | 0 | |
prepareSRAmetadata | 0 | 0 | 0 | |
processSurvTerms | 0.008 | 0.004 | 0.012 | |
psichomics | 0 | 0 | 0 | |
quantifySplicing | 0.007 | 0.007 | 0.015 | |
queryEnsembl | 0.035 | 0.004 | 1.401 | |
queryEnsemblByGene | 0.109 | 0.016 | 5.922 | |
queryFirebrowseData | 0.052 | 0.003 | 4.329 | |
queryPubMed | 0.085 | 0.004 | 2.242 | |
queryUniprot | 0.044 | 0.012 | 4.882 | |
readFile | 0.000 | 0.002 | 0.001 | |
renameDuplicated | 0.000 | 0.001 | 0.002 | |
renderBoxplot | 0.131 | 0.022 | 0.154 | |
survdiffTerms | 0.008 | 0.000 | 0.008 | |
survfit.survTerms | 0.028 | 0.008 | 0.036 | |
testGroupIndependence | 0.004 | 0.000 | 0.004 | |
testSurvival | 0.027 | 0.004 | 0.030 | |
textSuggestions | 0.001 | 0.000 | 0.001 | |
trimWhitespace | 0.001 | 0.000 | 0.001 | |