Augustin Luna
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/paxtoolsr |
| Branch: RELEASE_3_9 |
| Last Commit: 204b6d8 |
| Last Changed Date: 2019-05-02 11:53:49 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:54:16 -0400 (Wed, 16 Oct 2019).
| Package 1182/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| paxtoolsr 1.18.0 Augustin Luna
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: paxtoolsr |
| Version: 1.18.0 |
| 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_1.18.0.tar.gz |
| StartedAt: 2019-10-16 05:24:10 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:28:12 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 241.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: paxtoolsr.Rcheck |
| Warnings: 0 |
##############################################################################
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### 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_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/paxtoolsr.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.18.0’
* 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 31.6Mb
sub-directories of 1Mb or more:
extdata 6.8Mb
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 ... NOTE
'library' or 'require' call to ‘org.Hs.eg.db’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
convertIds: no visible global function definition for ‘select’
convertIds: no visible binding for global variable ‘org.Hs.eg.db’
splitSifnxByPathway: no visible global function definition for
‘%dopar%’
Undefined global functions or variables:
%dopar% org.Hs.eg.db select
* 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 or elapsed time > 5s
user system elapsed
readPcPathwaysInfo 101.890 22.999 125.627
fetch 6.211 1.758 2.326
integrateBiopax 4.171 0.921 1.413
convertIds 4.625 0.381 5.135
* 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
‘/Users/biocbuild/bbs-3.9-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/3.6/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
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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
2019-10-16 05:27:57,113 1725 [main] INFO org.biopax.paxtools.PaxtoolsMain - Collecting proteins for a pathway, the converter will also consider its sub-pathways, their sub-pathways, etc.
2019-10-16 05:27:57,136 1748 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - Begin converting Glycolysis Pathway pathway, uri=http://www.biopax.org/examples/myExamplePathway50
2019-10-16 05:27:57,152 1764 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - fetched PRs: 2
2019-10-16 05:27:57,152 1764 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - grouping the PRs by organism...
2019-10-16 05:27:57,170 1782 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - creating GSEA/GMT entries...
2019-10-16 05:27:57,173 1785 [pool-2-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - adding uniprot IDs of proteins (PRs) from 'Glycolysis Pathway', amaze;kegg pathway...
2019-10-16 05:27:57,177 1789 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - collected 1entries.
2019-10-16 05:27:57,177 1789 [main] INFO org.biopax.paxtools.io.gsea.GSEAConverter - Creating entries for the rest fo (unused) PRs...
2019-10-16 05:27:58,084 2696 [main] INFO org.biopax.paxtools.client.BiopaxValidatorClient - BioPAX Validator location: http://biopax.baderlab.org/check.html
2019-10-16 05:27:58,648 3260 [main] INFO org.biopax.paxtools.client.BiopaxValidatorClient - BioPAX Validator location: http://biopax.baderlab.org/check.html
2019-10-16 05:27:59,316 3928 [main] INFO org.biopax.paxtools.PaxtoolsMain - Elements in the result model: 240
SBGN-PD Layout is running...
success ratio: 1.0
enhanced ratio: 1.0
Total execution time: 86 miliseconds.
2019-10-16 05:28:00,411 5023 [AWT-AppKit] INFO org.biopax.paxtools.PaxtoolsMain - toSifnx: not blacklisting ubiquitous molecules (no blacklist.txt found)
2019-10-16 05:28:01,496 6108 [AWT-AppKit] INFO org.biopax.paxtools.PaxtoolsMain - toSif: not blacklisting ubiquitous molecules (no blacklist.txt found)
2019-10-16 05:28:02,900 7512 [AWT-AppKit] INFO org.biopax.paxtools.PaxtoolsMain - toSif: not blacklisting ubiquitous molecules (no blacklist.txt found)
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 40 | SKIPPED: 10 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
28.593 7.264 18.719
paxtoolsr.Rcheck/paxtoolsr-Ex.timings
| name | user | system | elapsed | |
| addAttributeList | 0.022 | 0.003 | 0.025 | |
| convertDataFrameListsToVectors | 0.004 | 0.001 | 0.006 | |
| convertIds | 4.625 | 0.381 | 5.135 | |
| convertSifToGmt | 0.022 | 0.013 | 0.036 | |
| downloadFile | 0.120 | 0.025 | 0.367 | |
| downloadPc2 | 0 | 0 | 0 | |
| downloadSignedPC | 0.000 | 0.000 | 0.001 | |
| fetch | 6.211 | 1.758 | 2.326 | |
| filterSif | 0.303 | 0.031 | 0.109 | |
| getCacheFiles | 0.000 | 0.000 | 0.001 | |
| getErrorMessage | 0.001 | 0.000 | 0.002 | |
| getNeighbors | 1.384 | 0.566 | 0.453 | |
| getPc | 0.002 | 0.002 | 0.001 | |
| getPcDatabaseNames | 0.346 | 0.020 | 0.617 | |
| getPcUrl | 0.001 | 0.000 | 0.001 | |
| getShortestPathSif | 0.034 | 0.002 | 0.036 | |
| getSifInteractionCategories | 0.001 | 0.000 | 0.001 | |
| graphPc | 0.000 | 0.000 | 0.001 | |
| integrateBiopax | 4.171 | 0.921 | 1.413 | |
| loadSifInIgraph | 0.016 | 0.001 | 0.007 | |
| mapValues | 0.001 | 0.000 | 0.001 | |
| mergeBiopax | 1.877 | 0.270 | 0.790 | |
| pcDirections | 0.000 | 0.001 | 0.000 | |
| pcFormats | 0.000 | 0.001 | 0.001 | |
| pcGraphQueries | 0 | 0 | 0 | |
| processPcRequest | 0.014 | 0.002 | 0.010 | |
| readBiopax | 0.003 | 0.002 | 0.004 | |
| readGmt | 0.092 | 0.003 | 0.095 | |
| readPcPathwaysInfo | 101.890 | 22.999 | 125.627 | |
| readSbgn | 0.002 | 0.002 | 0.006 | |
| readSif | 0.003 | 0.001 | 0.004 | |
| readSifnx | 0.017 | 0.003 | 0.022 | |
| searchListOfVectors | 0.002 | 0.001 | 0.004 | |
| searchPc | 0.000 | 0.001 | 0.001 | |
| summarize | 0.200 | 0.029 | 0.123 | |
| summarizeSif | 0.005 | 0.001 | 0.007 | |
| toCytoscape | 0.036 | 0.002 | 0.037 | |
| toGSEA | 0.245 | 0.034 | 0.090 | |
| toLevel3 | 0.485 | 0.041 | 0.113 | |
| toSBGN | 2.151 | 0.414 | 1.263 | |
| toSif | 3.221 | 0.321 | 0.883 | |
| toSifnx | 2.576 | 0.961 | 0.772 | |
| topPathways | 0.000 | 0.001 | 0.001 | |
| traverse | 0.001 | 0.002 | 0.001 | |
| validate | 4.248 | 0.700 | 2.358 | |