Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:57:18 -0400 (Wed, 17 Oct 2018).
Package 1145/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
psichomics 1.6.2 Nuno Saraiva-Agostinho
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
Package: psichomics |
Version: 1.6.2 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:psichomics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings psichomics_1.6.2.tar.gz |
StartedAt: 2018-10-16 23:23:27 -0400 (Tue, 16 Oct 2018) |
EndedAt: 2018-10-16 23:29:59 -0400 (Tue, 16 Oct 2018) |
EllapsedTime: 392.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: psichomics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:psichomics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings psichomics_1.6.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/psichomics.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘psichomics/DESCRIPTION’ ... OK * this is package ‘psichomics’ version ‘1.6.2’ * 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 ‘psichomics’ 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 ... 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 File ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/psichomics/libs/psichomics.so’: Found ‘___stdoutp’, possibly from ‘stdout’ (C) Found ‘_printf’, possibly from ‘printf’ (C) Found ‘_putchar’, possibly from ‘putchar’ (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.7-bioc/meat/psichomics.Rcheck/00check.log’ for details.
psichomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL psichomics ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘psichomics’ ... ** libs clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c psiFastCalc.cpp -o psiFastCalc.o clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o psichomics.so RcppExports.o psiFastCalc.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/psichomics/libs ** R ** inst ** byte-compile and prepare package for lazy loading No methods found in package ‘IRanges’ for request: ‘subset’ when loading ‘derfinder’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded No methods found in package ‘IRanges’ for request: ‘subset’ when loading ‘derfinder’ * DONE (psichomics)
psichomics.Rcheck/tests/testthat.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (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(psichomics) Loading required package: shiny Loading required package: shinyBS Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) No methods found in package 'IRanges' for request: 'subset' when loading 'derfinder' Start the visual interface by running the function psichomics() Attaching package: 'psichomics' The following object is masked from 'package:base': rowMeans > > test_check("psichomics") | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d260d68c3a/index.html. LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d22b5b3d7/index.html. LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d211970f90/index.html. LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d214bb7a75/index.html. LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d227ec50d/index.html. LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d28076c6b/index.html. LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d271b0e177/index.html. LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d25863df61/index.html. LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d257de42e7/index.html. LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d25dfb268/index.html. Retrieving protein annotation from UniProt... Plotting protein domains... LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d253444db5/index.html. Retrieving rMATS annotation... Parsing rMATS annotation... Retrieving rMATS annotation... Parsing rMATS annotation... Retrieving MISO annotation... Parsing MISO annotation... | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% | | 0% | | 0% | | 0% | | 0% | | 0% |========================================| 100% LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d2246930cd/index.html. Retrieving SUPPA annotation... Parsing SUPPA annotation... Retrieving VAST-TOOLS annotation... Parsing VAST-TOOLS annotation... ALT3 ALT5 COMBI IR MERGE3m MIC EXSK MULTI ══ testthat results ═══════════════════════════════════════════════════════════ OK: 1090 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 26.731 1.071 38.750
psichomics.Rcheck/psichomics-Ex.timings
name | user | system | elapsed | |
addObjectAttrs | 0.002 | 0.000 | 0.003 | |
blendColours | 0.003 | 0.000 | 0.003 | |
correlateGEandAS | 0.023 | 0.005 | 0.028 | |
createGroupByAttribute | 0.003 | 0.000 | 0.004 | |
createJunctionsTemplate | 0.004 | 0.000 | 0.004 | |
diffAnalyses | 0.145 | 0.021 | 0.166 | |
downloadFiles | 0.001 | 0.000 | 0.001 | |
ensemblToUniprot | 0.087 | 0.010 | 0.618 | |
filterGroups | 0.002 | 0.000 | 0.002 | |
getAttributesTime | 0.005 | 0.001 | 0.006 | |
getDownloadsFolder | 0.001 | 0.000 | 0.001 | |
getFirebrowseCohorts | 1.637 | 0.004 | 1.728 | |
getFirebrowseDataTypes | 0.002 | 0.001 | 0.002 | |
getFirebrowseDateFormat | 0.002 | 0.000 | 0.003 | |
getFirebrowseDates | 0.014 | 0.001 | 0.073 | |
getMatchingSamples | 0.003 | 0.000 | 0.004 | |
getNumerics | 0.005 | 0.000 | 0.005 | |
getPatientFromSample | 0.003 | 0.001 | 0.003 | |
getSplicingEventFromGenes | 0.004 | 0.000 | 0.004 | |
getSplicingEventTypes | 0.001 | 0.000 | 0.002 | |
getValidEvents | 0.006 | 0.000 | 0.007 | |
groupPerElem | 0.002 | 0.001 | 0.002 | |
hchart.survfit | 0.325 | 0.058 | 0.397 | |
isFirebrowseUp | 0.006 | 0.000 | 0.035 | |
labelBasedOnCutoff | 0.002 | 0.001 | 0.002 | |
leveneTest | 0.015 | 0.000 | 0.016 | |
listAllAnnotations | 0.002 | 0.000 | 0.002 | |
listSplicingAnnotations | 0.001 | 0.000 | 0.002 | |
loadAnnotation | 0.001 | 0.000 | 0.002 | |
loadFirebrowseData | 0.001 | 0.000 | 0.001 | |
loadLocalFiles | 0.001 | 0.000 | 0.001 | |
missingDataModal | 0.001 | 0.001 | 0.001 | |
normaliseGeneExpression | 0.017 | 0.001 | 0.018 | |
optimalSurvivalCutoff | 0.117 | 0.002 | 0.119 | |
parseCategoricalGroups | 0.003 | 0.001 | 0.004 | |
parseFirebrowseMetadata | 0.048 | 0.002 | 0.206 | |
parseMatsEvent | 0.007 | 0.000 | 0.007 | |
parseMatsGeneric | 0.036 | 0.002 | 0.037 | |
parseMisoAnnotation | 0.197 | 0.011 | 0.213 | |
parseMisoEvent | 0.010 | 0.001 | 0.011 | |
parseMisoEventID | 0.007 | 0.000 | 0.009 | |
parseMisoGeneric | 0.063 | 0.003 | 0.067 | |
parseMisoId | 0.002 | 0.000 | 0.002 | |
parseSampleGroups | 0.003 | 0.001 | 0.004 | |
parseSplicingEvent | 0.004 | 0.000 | 0.003 | |
parseSuppaEvent | 0.005 | 0.001 | 0.005 | |
parseSuppaGeneric | 0.036 | 0.002 | 0.039 | |
parseTcgaSampleInfo | 0.005 | 0.000 | 0.006 | |
parseUrlsFromFirebrowseResponse | 0.020 | 0.001 | 0.114 | |
parseVastToolsEvent | 0.011 | 0.000 | 0.011 | |
parseVastToolsSE | 0.039 | 0.002 | 0.040 | |
performICA | 0.012 | 0.002 | 0.015 | |
performPCA | 0.003 | 0.000 | 0.003 | |
plotCorrelation | 0.802 | 0.023 | 0.828 | |
plotDistribution | 0.677 | 0.063 | 0.745 | |
plotGroupIndependence | 0.285 | 0.038 | 0.323 | |
plotICA | 0.216 | 0.026 | 0.248 | |
plotPCA | 0.308 | 0.120 | 0.434 | |
plotProtein | 0.002 | 0.000 | 0.001 | |
plotSingleICA | 0.294 | 0.068 | 0.373 | |
plotSurvivalCurves | 0.136 | 0.042 | 0.197 | |
plotTranscripts | 0.021 | 0.001 | 0.810 | |
plotVariance | 0.076 | 0.025 | 0.129 | |
prepareAnnotationFromEvents | 0.233 | 0.006 | 0.240 | |
prepareFirebrowseArchives | 0.003 | 0.000 | 0.003 | |
prepareSRAmetadata | 0.002 | 0.000 | 0.002 | |
processSurvTerms | 0.006 | 0.000 | 0.006 | |
psichomics | 0.001 | 0.000 | 0.001 | |
quantifySplicing | 0.008 | 0.001 | 0.009 | |
queryEnsembl | 0.050 | 0.003 | 0.527 | |
queryEnsemblByEvent | 0.111 | 0.006 | 1.336 | |
queryEnsemblByGene | 0.110 | 0.006 | 1.528 | |
queryFirebrowseData | 0.036 | 0.001 | 0.234 | |
queryPubMed | 0.067 | 0.006 | 0.496 | |
queryUniprot | 0.199 | 0.006 | 0.910 | |
readFile | 0.002 | 0.000 | 0.002 | |
renameDuplicated | 0.003 | 0.000 | 0.003 | |
rowMeans | 0.002 | 0.000 | 0.002 | |
rowVars | 0.002 | 0.000 | 0.002 | |
sidebar | 0.012 | 0.001 | 0.013 | |
survdiff.survTerms | 0.014 | 0.000 | 0.015 | |
survfit.survTerms | 0.025 | 0.000 | 0.026 | |
testGroupIndependence | 0.004 | 0.000 | 0.004 | |
testSurvival | 0.028 | 0.001 | 0.029 | |
textSuggestions | 0.002 | 0.000 | 0.002 | |
trimWhitespace | 0.002 | 0.000 | 0.002 | |