Augustin Luna
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/paxtoolsr |
| git_branch: RELEASE_3_17 |
| git_last_commit: 515aca5 |
| git_last_commit_date: 2023-04-25 10:35:26 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:35:36 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 1482/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| paxtoolsr 1.34.0 (landing page) Augustin Luna
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
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: 1.34.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:paxtoolsr.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings paxtoolsr_1.34.0.tar.gz |
| StartedAt: 2023-10-15 23:44:51 -0400 (Sun, 15 Oct 2023) |
| EndedAt: 2023-10-15 23:49:12 -0400 (Sun, 15 Oct 2023) |
| EllapsedTime: 261.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: paxtoolsr.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:paxtoolsr.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings paxtoolsr_1.34.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/paxtoolsr.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘paxtoolsr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘paxtoolsr’ version ‘1.34.0’
* 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 ... 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 26.8Mb
sub-directories of 1Mb or more:
extdata 3.0Mb
java 23.5Mb
* 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 loading without being on the library search path ... OK
* checking 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
readPcPathwaysInfo 59.703 1.230 72.551
fetch 6.132 0.282 2.701
* 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 ...
‘using_paxtoolsr.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/paxtoolsr.Rcheck/00check.log’
for details.
paxtoolsr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL paxtoolsr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-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(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
2023-10-15 23:47:50,977 1847 [main] INFO org.biopax.paxtools.PaxtoolsMain - Collecting proteins for a pathway, the converter will also consider its sub-pathways, their sub-pathways, etc.
2023-10-15 23:47:51,035 1905 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - Begin converting Glycolysis Pathway pathway, uri=http://www.biopax.org/examples/myExamplePathway50
2023-10-15 23:47:51,046 1916 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - fetched PRs: 2
2023-10-15 23:47:51,046 1916 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - grouping the PRs by organism...
2023-10-15 23:47:51,077 1947 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - creating GSEA/GMT entries...
2023-10-15 23:47:51,095 1965 [pool-2-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - adding uniprot IDs of proteins (PRs) from 'Glycolysis Pathway', amaze;kegg pathway...
2023-10-15 23:47:51,112 1982 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - collected 1entries.
2023-10-15 23:47:51,113 1983 [main] INFO org.biopax.paxtools.io.gsea.GSEAConverter - Creating entries for the rest fo (unused) PRs...
2023-10-15 23:47:52,469 3339 [main] INFO org.biopax.paxtools.client.BiopaxValidatorClient - BioPAX Validator location: http://biopax.baderlab.org/check.html
2023-10-15 23:47:53,166 4036 [main] INFO org.biopax.paxtools.client.BiopaxValidatorClient - BioPAX Validator location: http://biopax.baderlab.org/check.html
2023-10-15 23:47:54,029 4899 [main] INFO org.biopax.paxtools.PaxtoolsMain - Elements in the result model: 240
SBGN-PD Layout is running...
success ratio: 0.8571428571428571
enhanced ratio: 0.8571428571428571
Total execution time: 202 miliseconds.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.sun.xml.bind.v2.runtime.reflect.opt.Injector$1 (file:/home/biocbuild/bbs-3.17-bioc/R/site-library/paxtoolsr/java/paxtools-4.3.1.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int)
WARNING: Please consider reporting this to the maintainers of com.sun.xml.bind.v2.runtime.reflect.opt.Injector$1
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
2023-10-15 23:47:55,341 6211 [main] INFO org.biopax.paxtools.PaxtoolsMain - toSifnx: not blacklisting ubiquitous molecules (no blacklist.txt found)
2023-10-15 23:47:57,378 8248 [main] INFO org.biopax.paxtools.PaxtoolsMain - toSif: not blacklisting ubiquitous molecules (no blacklist.txt found)
2023-10-15 23:47:59,054 9924 [main] INFO org.biopax.paxtools.PaxtoolsMain - toSif: not blacklisting ubiquitous molecules (no blacklist.txt found)
[ FAIL 0 | WARN 0 | SKIP 10 | PASS 40 ]
══ 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'
[ FAIL 0 | WARN 0 | SKIP 10 | PASS 40 ]
>
> proc.time()
user system elapsed
31.751 1.029 23.722
paxtoolsr.Rcheck/paxtoolsr-Ex.timings
| name | user | system | elapsed | |
| addAttributeList | 0.045 | 0.004 | 0.049 | |
| convertDataFrameListsToVectors | 0.005 | 0.000 | 0.005 | |
| convertSifToGmt | 0.337 | 0.022 | 0.392 | |
| downloadFile | 0.037 | 0.024 | 0.227 | |
| downloadPc2 | 0 | 0 | 0 | |
| downloadSignedPC | 0 | 0 | 0 | |
| fetch | 6.132 | 0.282 | 2.701 | |
| filterSif | 0.438 | 0.025 | 0.179 | |
| getCacheFiles | 0 | 0 | 0 | |
| getErrorMessage | 0.001 | 0.000 | 0.001 | |
| getNeighbors | 1.110 | 0.016 | 0.287 | |
| getPc | 0.001 | 0.000 | 0.001 | |
| getPcDatabaseNames | 0.089 | 0.000 | 0.513 | |
| getPcUrl | 0 | 0 | 0 | |
| getShortestPathSif | 0.041 | 0.003 | 0.043 | |
| getSifInteractionCategories | 0.001 | 0.000 | 0.001 | |
| graphPc | 0.001 | 0.000 | 0.000 | |
| integrateBiopax | 3.265 | 0.117 | 1.048 | |
| loadSifInIgraph | 0.047 | 0.000 | 0.015 | |
| mapValues | 0.001 | 0.000 | 0.001 | |
| mergeBiopax | 1.565 | 0.145 | 0.668 | |
| pcDirections | 0.001 | 0.000 | 0.001 | |
| pcFormats | 0.001 | 0.000 | 0.001 | |
| pcGraphQueries | 0 | 0 | 0 | |
| processPcRequest | 0.015 | 0.000 | 0.007 | |
| readBiopax | 0.008 | 0.000 | 0.003 | |
| readGmt | 0.039 | 0.008 | 0.023 | |
| readPcPathwaysInfo | 59.703 | 1.230 | 72.551 | |
| readSbgn | 0.004 | 0.000 | 0.004 | |
| readSif | 0.014 | 0.000 | 0.014 | |
| readSifnx | 0.017 | 0.011 | 0.029 | |
| searchListOfVectors | 0.002 | 0.000 | 0.002 | |
| searchPc | 0 | 0 | 0 | |
| summarize | 0.126 | 0.040 | 0.099 | |
| summarizeSif | 0.042 | 0.000 | 0.016 | |
| toCytoscape | 0.042 | 0.005 | 0.039 | |
| toGSEA | 0.251 | 0.030 | 0.115 | |
| toLevel3 | 0.358 | 0.012 | 0.155 | |
| toSBGN | 1.862 | 0.069 | 1.121 | |
| toSif | 3.255 | 0.077 | 0.889 | |
| toSifnx | 4.333 | 0.097 | 0.814 | |
| topPathways | 0 | 0 | 0 | |
| traverse | 0.001 | 0.000 | 0.000 | |
| validate | 3.677 | 0.080 | 1.985 | |