Augustin Luna
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/paxtoolsr |
| Branch: RELEASE_3_12 |
| Last Commit: 24770ee |
| Last Changed Date: 2020-10-27 10:59:49 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:28:30 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the paxtoolsr package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1312/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| paxtoolsr 1.24.0 (landing page) Augustin Luna
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: paxtoolsr |
| Version: 1.24.0 |
| Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:paxtoolsr.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings paxtoolsr_1.24.0.tar.gz |
| StartedAt: 2021-05-06 04:20:38 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 04:22:54 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 135.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: paxtoolsr.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
###
### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:paxtoolsr.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings paxtoolsr_1.24.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/paxtoolsr.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (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 ‘1.24.0’
* 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 31.7Mb
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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
readPcPathwaysInfo 57.608 0.684 58.316
* 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.12-bioc/meat/paxtoolsr.Rcheck/00check.log’
for details.
paxtoolsr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL paxtoolsr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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
2021-05-06 04:22:46,392 972 [main] INFO org.biopax.paxtools.PaxtoolsMain - Collecting proteins for a pathway, the converter will also consider its sub-pathways, their sub-pathways, etc.
2021-05-06 04:22:46,403 983 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - Begin converting Glycolysis Pathway pathway, uri=http://www.biopax.org/examples/myExamplePathway50
2021-05-06 04:22:46,419 999 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - fetched PRs: 2
2021-05-06 04:22:46,419 999 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - grouping the PRs by organism...
2021-05-06 04:22:46,427 1007 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - creating GSEA/GMT entries...
2021-05-06 04:22:46,428 1008 [pool-2-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - adding uniprot IDs of proteins (PRs) from 'Glycolysis Pathway', amaze;kegg pathway...
2021-05-06 04:22:46,432 1012 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - collected 1entries.
2021-05-06 04:22:46,432 1012 [main] INFO org.biopax.paxtools.io.gsea.GSEAConverter - Creating entries for the rest fo (unused) PRs...
2021-05-06 04:22:46,978 1558 [main] INFO org.biopax.paxtools.client.BiopaxValidatorClient - BioPAX Validator location: http://biopax.baderlab.org/check.html
2021-05-06 04:22:47,647 2227 [main] INFO org.biopax.paxtools.client.BiopaxValidatorClient - BioPAX Validator location: http://biopax.baderlab.org/check.html
2021-05-06 04:22:48,043 2623 [main] INFO org.biopax.paxtools.PaxtoolsMain - Elements in the result model: 240
SBGN-PD Layout is running...
success ratio: 0.9285714285714286
enhanced ratio: 0.9285714285714286
Total execution time: 111 miliseconds.
2021-05-06 04:22:48,759 3339 [main] INFO org.biopax.paxtools.PaxtoolsMain - toSifnx: not blacklisting ubiquitous molecules (no blacklist.txt found)
2021-05-06 04:22:49,469 4049 [main] INFO org.biopax.paxtools.PaxtoolsMain - toSif: not blacklisting ubiquitous molecules (no blacklist.txt found)
2021-05-06 04:22:50,257 4837 [main] INFO org.biopax.paxtools.PaxtoolsMain - toSif: not blacklisting ubiquitous molecules (no blacklist.txt found)
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (7)
• empty test (3)
[ FAIL 0 | WARN 0 | SKIP 10 | PASS 40 ]
>
> proc.time()
user system elapsed
19.412 0.508 14.931
paxtoolsr.Rcheck/paxtoolsr-Ex.timings
| name | user | system | elapsed | |
| addAttributeList | 0.020 | 0.004 | 0.026 | |
| convertDataFrameListsToVectors | 0.004 | 0.000 | 0.011 | |
| convertSifToGmt | 0.028 | 0.012 | 0.048 | |
| downloadFile | 0.100 | 0.016 | 0.309 | |
| downloadPc2 | 0 | 0 | 0 | |
| downloadSignedPC | 0 | 0 | 0 | |
| fetch | 4.360 | 0.164 | 1.375 | |
| filterSif | 0.284 | 0.016 | 0.098 | |
| getCacheFiles | 0 | 0 | 0 | |
| getErrorMessage | 0.000 | 0.000 | 0.001 | |
| getNeighbors | 0.848 | 0.024 | 0.226 | |
| getPc | 0 | 0 | 0 | |
| getPcDatabaseNames | 0.116 | 0.000 | 0.279 | |
| getPcUrl | 0 | 0 | 0 | |
| getShortestPathSif | 0.032 | 0.000 | 0.030 | |
| getSifInteractionCategories | 0 | 0 | 0 | |
| graphPc | 0 | 0 | 0 | |
| integrateBiopax | 2.760 | 0.060 | 0.813 | |
| loadSifInIgraph | 0.016 | 0.000 | 0.005 | |
| mapValues | 0.000 | 0.000 | 0.001 | |
| mergeBiopax | 0.812 | 0.020 | 0.371 | |
| pcDirections | 0 | 0 | 0 | |
| pcFormats | 0 | 0 | 0 | |
| pcGraphQueries | 0 | 0 | 0 | |
| processPcRequest | 0.008 | 0.000 | 0.004 | |
| readBiopax | 0.004 | 0.000 | 0.002 | |
| readGmt | 0.028 | 0.004 | 0.017 | |
| readPcPathwaysInfo | 57.608 | 0.684 | 58.316 | |
| readSbgn | 0.004 | 0.000 | 0.002 | |
| readSif | 0.004 | 0.000 | 0.003 | |
| readSifnx | 0.020 | 0.000 | 0.019 | |
| searchListOfVectors | 0.004 | 0.000 | 0.002 | |
| searchPc | 0 | 0 | 0 | |
| summarize | 0.308 | 0.008 | 0.133 | |
| summarizeSif | 0.016 | 0.000 | 0.005 | |
| toCytoscape | 0.028 | 0.000 | 0.032 | |
| toGSEA | 0.132 | 0.004 | 0.098 | |
| toLevel3 | 0.280 | 0.008 | 0.088 | |
| toSBGN | 1.640 | 0.024 | 0.659 | |
| toSif | 2.200 | 0.020 | 0.589 | |
| toSifnx | 2.280 | 0.036 | 0.544 | |
| topPathways | 0.004 | 0.000 | 0.000 | |
| traverse | 0 | 0 | 0 | |
| validate | 2.040 | 0.028 | 1.397 | |