Augustin Luna
| Snapshot Date: 2024-06-02 14:00:17 -0400 (Sun, 02 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/paxtoolsr |
| git_branch: RELEASE_3_19 |
| git_last_commit: ee63aa1 |
| git_last_commit_date: 2024-04-30 10:39:35 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-04 11:36:40 -0400 (Tue, 04 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4487 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4518 |
| 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 1527/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| paxtoolsr 1.38.0 (landing page) Augustin Luna
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
|
To the developers/maintainers of the paxtoolsr package: - 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 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: paxtoolsr |
| Version: 1.38.0 |
| 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_1.38.0.tar.gz |
| StartedAt: 2024-06-03 05:50:34 -0400 (Mon, 03 Jun 2024) |
| EndedAt: 2024-06-03 05:55:57 -0400 (Mon, 03 Jun 2024) |
| EllapsedTime: 323.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: paxtoolsr.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### 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_1.38.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/paxtoolsr.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* 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 ‘paxtoolsr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘paxtoolsr’ version ‘1.38.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 ‘paxtoolsr’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 32.1Mb
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 code 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 whether 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 ... 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)
SBGN-PD Layout is running...
success ratio: 0.9285714285714286
enhanced ratio: 0.9285714285714286
Total execution time: 37 miliseconds.
Error in toSBGN(system.file("extdata", "biopax3-short-metabolic-pathway.owl", :
java.lang.ExceptionInInitializerError
Calls: toSBGN -> .jcheck
Execution halted
* 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_pathwayCommons.R:63:5', 'test_pathwayCommons.R:77:5',
'test_pathwayCommons.R:131:5', 'test_pathwayCommons.R:169:5',
'test_pathwayCommons.R:185:5', 'test_pathwayCommons.R:260:5'
• empty test (3): 'test_pathwayCommons.R:266:1', 'test_pathwayCommons.R:285:1',
'test_pathwayCommons.R:286:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_paxtools.R:73:5'): toSBGN ──────────────────────────────────────
<ExceptionInInitializerError/LinkageError/Error/Throwable/Object/Exception/error/condition>
Error in `toSBGN(system.file("extdata", "biopax3-short-metabolic-pathway.owl",
package = "paxtoolsr"), outFile)`: java.lang.ExceptionInInitializerError
[ FAIL 1 | WARN 1 | SKIP 10 | PASS 39 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.19-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/4.4-x86_64/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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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
2024-06-03 05:55:46,151 325 [main] INFO org.biopax.paxtools.PaxtoolsMain - Collecting proteins for a pathway, the converter will also consider its sub-pathways, their sub-pathways, etc.
2024-06-03 05:55:46,158 332 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - Begin converting Glycolysis Pathway pathway, uri=http://www.biopax.org/examples/myExamplePathway50
2024-06-03 05:55:46,163 337 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - fetched PRs: 2
2024-06-03 05:55:46,163 337 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - grouping the PRs by organism...
2024-06-03 05:55:46,168 342 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - creating GSEA/GMT entries...
2024-06-03 05:55:46,169 343 [pool-2-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - adding uniprot IDs of proteins (PRs) from 'Glycolysis Pathway', amaze;kegg pathway...
2024-06-03 05:55:46,171 345 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - collected 1entries.
2024-06-03 05:55:46,171 345 [main] INFO org.biopax.paxtools.io.gsea.GSEAConverter - Creating entries for the rest fo (unused) PRs...
2024-06-03 05:55:46,806 980 [main] INFO org.biopax.paxtools.client.BiopaxValidatorClient - BioPAX Validator location: http://biopax.baderlab.org/check.html
2024-06-03 05:55:47,617 1791 [main] INFO org.biopax.paxtools.client.BiopaxValidatorClient - BioPAX Validator location: http://biopax.baderlab.org/check.html
2024-06-03 05:55:48,200 2374 [main] INFO org.biopax.paxtools.PaxtoolsMain - Elements in the result model: 240
SBGN-PD Layout is running...
success ratio: 0.7857142857142857
enhanced ratio: 0.8571428571428571
Total execution time: 36 miliseconds.
2024-06-03 05:55:48,500 2674 [main] INFO org.biopax.paxtools.PaxtoolsMain - toSifnx: not blacklisting ubiquitous molecules (no blacklist.txt found)
2024-06-03 05:55:48,922 3096 [main] INFO org.biopax.paxtools.PaxtoolsMain - toSif: not blacklisting ubiquitous molecules (no blacklist.txt found)
2024-06-03 05:55:49,346 3520 [main] INFO org.biopax.paxtools.PaxtoolsMain - toSif: not blacklisting ubiquitous molecules (no blacklist.txt found)
[ FAIL 1 | WARN 1 | SKIP 10 | PASS 39 ]
══ Skipped tests (10) ══════════════════════════════════════════════════════════
• On Bioconductor (7): 'test_pathwayCommons.R:38:5',
'test_pathwayCommons.R:63:5', 'test_pathwayCommons.R:77:5',
'test_pathwayCommons.R:131:5', 'test_pathwayCommons.R:169:5',
'test_pathwayCommons.R:185:5', 'test_pathwayCommons.R:260:5'
• empty test (3): 'test_pathwayCommons.R:266:1', 'test_pathwayCommons.R:285:1',
'test_pathwayCommons.R:286:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_paxtools.R:73:5'): toSBGN ──────────────────────────────────────
<ExceptionInInitializerError/LinkageError/Error/Throwable/Object/Exception/error/condition>
Error in `toSBGN(system.file("extdata", "biopax3-short-metabolic-pathway.owl",
package = "paxtoolsr"), outFile)`: java.lang.ExceptionInInitializerError
[ FAIL 1 | WARN 1 | SKIP 10 | PASS 39 ]
Error: Test failures
Execution halted
paxtoolsr.Rcheck/paxtoolsr-Ex.timings
| name | user | system | elapsed | |
| addAttributeList | 0.072 | 0.003 | 0.075 | |
| convertDataFrameListsToVectors | 0.001 | 0.001 | 0.001 | |
| convertSifToGmt | 0.190 | 0.020 | 0.233 | |
| downloadFile | 0.023 | 0.006 | 0.206 | |
| downloadPc2 | 0 | 0 | 0 | |
| downloadSignedPC | 0 | 0 | 0 | |
| fetch | 2.681 | 0.302 | 0.683 | |
| filterSif | 0.406 | 0.026 | 0.163 | |
| getCacheFiles | 0.001 | 0.000 | 0.000 | |
| getErrorMessage | 0 | 0 | 0 | |
| getNeighbors | 0.447 | 0.041 | 0.081 | |
| getPc | 0 | 0 | 0 | |
| getPcDatabaseNames | 0.124 | 0.004 | 0.448 | |
| getPcUrl | 0.000 | 0.001 | 0.000 | |
| getShortestPathSif | 0.034 | 0.002 | 0.037 | |
| getSifInteractionCategories | 0 | 0 | 0 | |
| graphPc | 0 | 0 | 0 | |
| integrateBiopax | 1.373 | 0.158 | 0.373 | |
| loadSifInIgraph | 0.008 | 0.002 | 0.009 | |
| mapValues | 0 | 0 | 0 | |
| mergeBiopax | 0.470 | 0.086 | 0.268 | |
| pcDirections | 0 | 0 | 0 | |
| pcFormats | 0 | 0 | 0 | |
| pcGraphQueries | 0 | 0 | 0 | |
| processPcRequest | 0.003 | 0.001 | 0.005 | |
| readBiopax | 0.001 | 0.001 | 0.007 | |
| readGmt | 0.014 | 0.003 | 0.018 | |
| readPcPathwaysInfo | 27.989 | 7.984 | 36.219 | |
| readSbgn | 0.002 | 0.000 | 0.002 | |
| readSif | 0.006 | 0.001 | 0.007 | |
| readSifnx | 0.012 | 0.004 | 0.017 | |
| searchListOfVectors | 0.000 | 0.000 | 0.001 | |
| searchPc | 0 | 0 | 0 | |
| summarize | 0.066 | 0.006 | 0.042 | |
| summarizeSif | 0.022 | 0.003 | 0.008 | |
| toCytoscape | 0.032 | 0.001 | 0.021 | |
| toGSEA | 0.073 | 0.020 | 0.043 | |
| toLevel3 | 0.130 | 0.023 | 0.049 | |