Augustin Luna
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/paxtoolsr |
| git_branch: RELEASE_3_14 |
| git_last_commit: ccd6010 |
| git_last_commit_date: 2021-10-26 12:16:43 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:08:30 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1382/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| paxtoolsr 1.28.0 (landing page) Augustin Luna
| nebbiolo2 | Linux (Ubuntu 20.04.4 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: 1.28.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:paxtoolsr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings paxtoolsr_1.28.0.tar.gz |
| StartedAt: 2022-04-12 16:35:05 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 16:38:16 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 190.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: paxtoolsr.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:paxtoolsr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings paxtoolsr_1.28.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/paxtoolsr.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.28.0’
* 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
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 32.2Mb
sub-directories of 1Mb or more:
extdata 7.3Mb
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.
2022-04-12 16:37:41.627 R[58514:599937551] 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
2022-04-12 16:37:56,135 890 [main] INFO org.biopax.paxtools.PaxtoolsMain - Collecting proteins for a pathway, the converter will also consider its sub-pathways, their sub-pathways, etc.
2022-04-12 16:37:56,155 910 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - Begin converting Glycolysis Pathway pathway, uri=http://www.biopax.org/examples/myExamplePathway50
2022-04-12 16:37:56,161 916 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - fetched PRs: 2
2022-04-12 16:37:56,161 916 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - grouping the PRs by organism...
2022-04-12 16:37:56,173 928 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - creating GSEA/GMT entries...
2022-04-12 16:37:56,175 930 [pool-2-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - adding uniprot IDs of proteins (PRs) from 'Glycolysis Pathway', amaze;kegg pathway...
2022-04-12 16:37:56,177 932 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - collected 1entries.
2022-04-12 16:37:56,177 932 [main] INFO org.biopax.paxtools.io.gsea.GSEAConverter - Creating entries for the rest fo (unused) PRs...
2022-04-12 16:37:59,843 4598 [main] INFO org.biopax.paxtools.client.BiopaxValidatorClient - BioPAX Validator location: http://biopax.baderlab.org/check.html
2022-04-12 16:38:03,327 8082 [main] INFO org.biopax.paxtools.client.BiopaxValidatorClient - BioPAX Validator location: http://biopax.baderlab.org/check.html
2022-04-12 16:38:07,928 12683 [main] INFO org.biopax.paxtools.PaxtoolsMain - Elements in the result model: 240
No Java runtime present, requesting install.
2022-04-12 16:38:08.154 R[61544:599942737] 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-3.14-bioc/meat/paxtoolsr.Rcheck/00check.log’
for details.
paxtoolsr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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
2022-04-12 16:37:56,135 890 [main] INFO org.biopax.paxtools.PaxtoolsMain - Collecting proteins for a pathway, the converter will also consider its sub-pathways, their sub-pathways, etc.
2022-04-12 16:37:56,155 910 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - Begin converting Glycolysis Pathway pathway, uri=http://www.biopax.org/examples/myExamplePathway50
2022-04-12 16:37:56,161 916 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - fetched PRs: 2
2022-04-12 16:37:56,161 916 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - grouping the PRs by organism...
2022-04-12 16:37:56,173 928 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - creating GSEA/GMT entries...
2022-04-12 16:37:56,175 930 [pool-2-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - adding uniprot IDs of proteins (PRs) from 'Glycolysis Pathway', amaze;kegg pathway...
2022-04-12 16:37:56,177 932 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - collected 1entries.
2022-04-12 16:37:56,177 932 [main] INFO org.biopax.paxtools.io.gsea.GSEAConverter - Creating entries for the rest fo (unused) PRs...
2022-04-12 16:37:59,843 4598 [main] INFO org.biopax.paxtools.client.BiopaxValidatorClient - BioPAX Validator location: http://biopax.baderlab.org/check.html
2022-04-12 16:38:03,327 8082 [main] INFO org.biopax.paxtools.client.BiopaxValidatorClient - BioPAX Validator location: http://biopax.baderlab.org/check.html
2022-04-12 16:38:07,928 12683 [main] INFO org.biopax.paxtools.PaxtoolsMain - Elements in the result model: 240
No Java runtime present, requesting install.
2022-04-12 16:38:08.154 R[61544:599942737] JLRequestRuntimeInstall: Error calling: CFMessagePortCreateRemote
paxtoolsr.Rcheck/paxtoolsr-Ex.timings
| name | user | system | elapsed | |
| addAttributeList | 0.026 | 0.002 | 0.028 | |
| convertDataFrameListsToVectors | 0.003 | 0.000 | 0.004 | |
| convertSifToGmt | 0.246 | 0.019 | 0.267 | |
| downloadFile | 0.125 | 0.023 | 0.537 | |
| downloadPc2 | 0 | 0 | 0 | |
| downloadSignedPC | 0.001 | 0.000 | 0.000 | |
| fetch | 6.147 | 0.348 | 1.566 | |
| filterSif | 0.555 | 0.040 | 0.208 | |
| getCacheFiles | 0.001 | 0.000 | 0.000 | |
| getErrorMessage | 0.001 | 0.000 | 0.001 | |
| getNeighbors | 1.240 | 0.063 | 0.321 | |
| getPc | 0.000 | 0.001 | 0.000 | |
| getPcDatabaseNames | 0.051 | 0.003 | 0.259 | |
| getPcUrl | 0.000 | 0.001 | 0.001 | |
| getShortestPathSif | 0.065 | 0.004 | 0.068 | |
| getSifInteractionCategories | 0.000 | 0.000 | 0.001 | |
| graphPc | 0.000 | 0.000 | 0.001 | |
| integrateBiopax | 3.654 | 0.159 | 0.998 | |
| loadSifInIgraph | 0.069 | 0.002 | 0.021 | |
| mapValues | 0.007 | 0.001 | 0.001 | |
| mergeBiopax | 1.956 | 0.142 | 0.834 | |
| pcDirections | 0.000 | 0.000 | 0.001 | |
| pcFormats | 0.000 | 0.000 | 0.001 | |
| pcGraphQueries | 0.001 | 0.000 | 0.000 | |
| processPcRequest | 0.007 | 0.002 | 0.010 | |
| readBiopax | 0.002 | 0.001 | 0.004 | |
| readGmt | 0.038 | 0.003 | 0.040 | |
| readPcPathwaysInfo | 70.155 | 9.628 | 79.897 | |
| readSbgn | 0.002 | 0.000 | 0.003 | |
| readSif | 0.014 | 0.001 | 0.014 | |
| readSifnx | 0.037 | 0.007 | 0.044 | |
| searchListOfVectors | 0.002 | 0.002 | 0.004 | |
| searchPc | 0.000 | 0.001 | 0.001 | |
| summarize | 0.151 | 0.018 | 0.102 | |
| summarizeSif | 0.032 | 0.001 | 0.020 | |
| toCytoscape | 0.031 | 0.002 | 0.033 | |
| toGSEA | 0.178 | 0.012 | 0.057 | |
| toLevel3 | 0.435 | 0.023 | 0.121 | |