Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:46 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the paxtoolsr package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/paxtoolsr.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 1355/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
paxtoolsr 1.26.0 (landing page) Augustin Luna
| 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 | ERROR | OK | |||||||||
Package: paxtoolsr |
Version: 1.26.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:paxtoolsr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings paxtoolsr_1.26.0.tar.gz |
StartedAt: 2021-10-14 22:09:23 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 22:11:56 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 153.8 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: paxtoolsr.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:paxtoolsr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings paxtoolsr_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/paxtoolsr.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 ‘paxtoolsr/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘paxtoolsr’ version ‘1.26.0’ * 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: .BBSoptions .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 ‘paxtoolsr’ can be installed ... OK * checking installed package size ... NOTE installed size is 31.6Mb sub-directories of 1Mb or more: extdata 6.9Mb java 24.5Mb * 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 ... NOTE splitSifnxByPathway: no visible global function definition for ‘%dopar%’ Undefined global functions or variables: %dopar% * 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 files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘paxtoolsr-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: toSBGN > ### Title: Convert a BioPAX OWL file to SBGNML > ### Aliases: toSBGN > > ### ** Examples > > outFile <- tempfile() > results <- toSBGN(system.file("extdata", "biopax3-short-metabolic-pathway.owl", + package="paxtoolsr"), + outFile) No Java runtime present, requesting install. 2021-10-14 22:11:33.377 R[56425:156667110] JLRequestRuntimeInstall: Error calling: CFMessagePortCreateRemote * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: > test_check("paxtoolsr") URL: http://www.pathwaycommons.org/pc2/get?uri=http%3A%2F%2Fidentifiers.org%2Funiprot%2FQ06609&uri=http%3A%2F%2Fidentifiers.org%2Funiprot%2FQ96EB6&format=BIOPAX 2021-10-14 22:11:45,152 912 [main] INFO org.biopax.paxtools.PaxtoolsMain - Collecting proteins for a pathway, the converter will also consider its sub-pathways, their sub-pathways, etc. 2021-10-14 22:11:45,169 929 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - Begin converting Glycolysis Pathway pathway, uri=http://www.biopax.org/examples/myExamplePathway50 2021-10-14 22:11:45,177 937 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - fetched PRs: 2 2021-10-14 22:11:45,177 937 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - grouping the PRs by organism... 2021-10-14 22:11:45,187 947 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - creating GSEA/GMT entries... 2021-10-14 22:11:45,189 949 [pool-2-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - adding uniprot IDs of proteins (PRs) from 'Glycolysis Pathway', amaze;kegg pathway... 2021-10-14 22:11:45,191 951 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - collected 1entries. 2021-10-14 22:11:45,191 951 [main] INFO org.biopax.paxtools.io.gsea.GSEAConverter - Creating entries for the rest fo (unused) PRs... 2021-10-14 22:11:46,947 2707 [main] INFO org.biopax.paxtools.client.BiopaxValidatorClient - BioPAX Validator location: http://biopax.baderlab.org/check.html 2021-10-14 22:11:47,885 3645 [main] INFO org.biopax.paxtools.client.BiopaxValidatorClient - BioPAX Validator location: http://biopax.baderlab.org/check.html 2021-10-14 22:11:48,419 4179 [main] INFO org.biopax.paxtools.PaxtoolsMain - Elements in the result model: 240 No Java runtime present, requesting install. 2021-10-14 22:11:48.650 R[59660:156672474] JLRequestRuntimeInstall: Error calling: CFMessagePortCreateRemote * 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 ERRORs, 3 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/paxtoolsr.Rcheck/00check.log’ for details.
paxtoolsr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL paxtoolsr ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘paxtoolsr’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** 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 (paxtoolsr)
paxtoolsr.Rcheck/tests/testthat.Rout.fail
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(paxtoolsr) Loading required package: rJava Loading required package: XML Consider citing this package: Luna A, et al. PaxtoolsR: pathway analysis in R using Pathway Commons. PMID: 26685306; citation("paxtoolsr") > > test_check("paxtoolsr") URL: http://www.pathwaycommons.org/pc2/get?uri=http%3A%2F%2Fidentifiers.org%2Funiprot%2FQ06609&uri=http%3A%2F%2Fidentifiers.org%2Funiprot%2FQ96EB6&format=BIOPAX 2021-10-14 22:11:45,152 912 [main] INFO org.biopax.paxtools.PaxtoolsMain - Collecting proteins for a pathway, the converter will also consider its sub-pathways, their sub-pathways, etc. 2021-10-14 22:11:45,169 929 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - Begin converting Glycolysis Pathway pathway, uri=http://www.biopax.org/examples/myExamplePathway50 2021-10-14 22:11:45,177 937 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - fetched PRs: 2 2021-10-14 22:11:45,177 937 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - grouping the PRs by organism... 2021-10-14 22:11:45,187 947 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - creating GSEA/GMT entries... 2021-10-14 22:11:45,189 949 [pool-2-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - adding uniprot IDs of proteins (PRs) from 'Glycolysis Pathway', amaze;kegg pathway... 2021-10-14 22:11:45,191 951 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - collected 1entries. 2021-10-14 22:11:45,191 951 [main] INFO org.biopax.paxtools.io.gsea.GSEAConverter - Creating entries for the rest fo (unused) PRs... 2021-10-14 22:11:46,947 2707 [main] INFO org.biopax.paxtools.client.BiopaxValidatorClient - BioPAX Validator location: http://biopax.baderlab.org/check.html 2021-10-14 22:11:47,885 3645 [main] INFO org.biopax.paxtools.client.BiopaxValidatorClient - BioPAX Validator location: http://biopax.baderlab.org/check.html 2021-10-14 22:11:48,419 4179 [main] INFO org.biopax.paxtools.PaxtoolsMain - Elements in the result model: 240 No Java runtime present, requesting install. 2021-10-14 22:11:48.650 R[59660:156672474] JLRequestRuntimeInstall: Error calling: CFMessagePortCreateRemote
paxtoolsr.Rcheck/paxtoolsr-Ex.timings
name | user | system | elapsed | |
addAttributeList | 0.025 | 0.002 | 0.026 | |
convertDataFrameListsToVectors | 0.006 | 0.001 | 0.007 | |
convertSifToGmt | 0.342 | 0.020 | 0.362 | |
downloadFile | 0.119 | 0.019 | 0.501 | |
downloadPc2 | 0.001 | 0.001 | 0.000 | |
downloadSignedPC | 0 | 0 | 0 | |
fetch | 5.883 | 0.345 | 1.381 | |
filterSif | 0.465 | 0.033 | 0.138 | |
getCacheFiles | 0.000 | 0.000 | 0.001 | |
getErrorMessage | 0.001 | 0.001 | 0.001 | |
getNeighbors | 1.036 | 0.039 | 0.194 | |
getPc | 0.001 | 0.001 | 0.001 | |
getPcDatabaseNames | 0.144 | 0.007 | 0.343 | |
getPcUrl | 0.000 | 0.001 | 0.000 | |
getShortestPathSif | 0.042 | 0.003 | 0.044 | |
getSifInteractionCategories | 0 | 0 | 0 | |
graphPc | 0.001 | 0.000 | 0.000 | |
integrateBiopax | 3.077 | 0.156 | 0.844 | |
loadSifInIgraph | 0.041 | 0.000 | 0.014 | |
mapValues | 0.004 | 0.000 | 0.001 | |
mergeBiopax | 1.777 | 0.125 | 0.689 | |
pcDirections | 0.000 | 0.001 | 0.000 | |
pcFormats | 0.000 | 0.001 | 0.001 | |
pcGraphQueries | 0.010 | 0.000 | 0.001 | |
processPcRequest | 0.015 | 0.002 | 0.009 | |
readBiopax | 0.002 | 0.001 | 0.002 | |
readGmt | 0.077 | 0.004 | 0.041 | |
readPcPathwaysInfo | 57.980 | 8.072 | 66.084 | |
readSbgn | 0.001 | 0.000 | 0.002 | |
readSif | 0.015 | 0.001 | 0.016 | |
readSifnx | 0.029 | 0.005 | 0.032 | |
searchListOfVectors | 0.001 | 0.001 | 0.002 | |
searchPc | 0 | 0 | 0 | |
summarize | 0.142 | 0.013 | 0.092 | |
summarizeSif | 0.015 | 0.001 | 0.016 | |
toCytoscape | 0.025 | 0.001 | 0.027 | |
toGSEA | 0.139 | 0.010 | 0.050 | |
toLevel3 | 0.420 | 0.015 | 0.107 | |