Augustin Luna
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/paxtoolsr |
| Branch: master |
| Last Commit: 435b178 |
| Last Changed Date: 2019-10-29 13:38:20 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:40:20 -0500 (Thu, 16 Jan 2020).
| Package 1231/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| paxtoolsr 1.21.0 Augustin Luna
| malbec2 | Linux (Ubuntu 18.04.3 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: 1.21.0 |
| 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_1.21.0.tar.gz |
| StartedAt: 2020-01-16 07:17:31 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 07:21:29 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 238.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: paxtoolsr.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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_1.21.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/paxtoolsr.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.21.0’
* 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 (user + system) or elapsed time > 5s
user system elapsed
readPcPathwaysInfo 93.134 23.477 117.196
fetch 6.676 2.369 2.535
integrateBiopax 5.165 1.756 1.604
convertIds 5.056 0.458 5.507
* 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-3.11-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/4.0/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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
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
2020-01-16 07:21:13,630 1958 [main] INFO org.biopax.paxtools.PaxtoolsMain - Collecting proteins for a pathway, the converter will also consider its sub-pathways, their sub-pathways, etc.
2020-01-16 07:21:13,730 2058 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - Begin converting Glycolysis Pathway pathway, uri=http://www.biopax.org/examples/myExamplePathway50
2020-01-16 07:21:13,762 2090 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - fetched PRs: 2
2020-01-16 07:21:13,763 2091 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - grouping the PRs by organism...
2020-01-16 07:21:13,790 2118 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - creating GSEA/GMT entries...
2020-01-16 07:21:13,793 2121 [pool-2-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - adding uniprot IDs of proteins (PRs) from 'Glycolysis Pathway', amaze;kegg pathway...
2020-01-16 07:21:13,798 2126 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - collected 1entries.
2020-01-16 07:21:13,798 2126 [main] INFO org.biopax.paxtools.io.gsea.GSEAConverter - Creating entries for the rest fo (unused) PRs...
2020-01-16 07:21:14,807 3135 [main] INFO org.biopax.paxtools.client.BiopaxValidatorClient - BioPAX Validator location: http://biopax.baderlab.org/check.html
2020-01-16 07:21:15,540 3868 [main] INFO org.biopax.paxtools.client.BiopaxValidatorClient - BioPAX Validator location: http://biopax.baderlab.org/check.html
2020-01-16 07:21:16,306 4634 [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: 74 miliseconds.
2020-01-16 07:21:17,372 5700 [AWT-AppKit] INFO org.biopax.paxtools.PaxtoolsMain - toSifnx: not blacklisting ubiquitous molecules (no blacklist.txt found)
2020-01-16 07:21:18,588 6916 [AWT-AppKit] INFO org.biopax.paxtools.PaxtoolsMain - toSif: not blacklisting ubiquitous molecules (no blacklist.txt found)
2020-01-16 07:21:19,784 8112 [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
29.911 5.885 20.645
paxtoolsr.Rcheck/paxtoolsr-Ex.timings
| name | user | system | elapsed | |
| addAttributeList | 0.034 | 0.004 | 0.038 | |
| convertDataFrameListsToVectors | 0.008 | 0.001 | 0.009 | |
| convertIds | 5.056 | 0.458 | 5.507 | |
| convertSifToGmt | 0.020 | 0.082 | 0.103 | |
| downloadFile | 0.114 | 0.020 | 0.345 | |
| downloadPc2 | 0 | 0 | 0 | |
| downloadSignedPC | 0 | 0 | 0 | |
| fetch | 6.676 | 2.369 | 2.535 | |
| filterSif | 0.482 | 0.045 | 0.113 | |
| getCacheFiles | 0.001 | 0.001 | 0.001 | |
| getErrorMessage | 0.002 | 0.001 | 0.001 | |
| getNeighbors | 1.494 | 0.627 | 0.523 | |
| getPc | 0.000 | 0.000 | 0.001 | |
| getPcDatabaseNames | 0.231 | 0.008 | 0.193 | |
| getPcUrl | 0.002 | 0.000 | 0.001 | |
| getShortestPathSif | 0.041 | 0.006 | 0.042 | |
| getSifInteractionCategories | 0.001 | 0.001 | 0.001 | |
| graphPc | 0.001 | 0.001 | 0.001 | |
| integrateBiopax | 5.165 | 1.756 | 1.604 | |
| loadSifInIgraph | 0.032 | 0.001 | 0.007 | |
| mapValues | 0.002 | 0.000 | 0.002 | |
| mergeBiopax | 1.901 | 0.324 | 0.691 | |
| pcDirections | 0.000 | 0.001 | 0.001 | |
| pcFormats | 0.001 | 0.001 | 0.001 | |
| pcGraphQueries | 0.000 | 0.001 | 0.000 | |
| processPcRequest | 0.013 | 0.002 | 0.009 | |
| readBiopax | 0.003 | 0.001 | 0.005 | |
| readGmt | 0.092 | 0.004 | 0.089 | |
| readPcPathwaysInfo | 93.134 | 23.477 | 117.196 | |
| readSbgn | 0.003 | 0.001 | 0.005 | |
| readSif | 0.003 | 0.001 | 0.004 | |
| readSifnx | 0.018 | 0.003 | 0.022 | |
| searchListOfVectors | 0.003 | 0.001 | 0.004 | |
| searchPc | 0.000 | 0.001 | 0.001 | |
| summarize | 0.211 | 0.040 | 0.118 | |
| summarizeSif | 0.018 | 0.001 | 0.006 | |
| toCytoscape | 0.042 | 0.002 | 0.043 | |
| toGSEA | 0.195 | 0.029 | 0.080 | |
| toLevel3 | 0.484 | 0.043 | 0.111 | |
| toSBGN | 2.268 | 0.667 | 1.241 | |
| toSif | 2.717 | 0.375 | 0.787 | |
| toSifnx | 3.067 | 0.752 | 0.730 | |
| topPathways | 0 | 0 | 0 | |
| traverse | 0.000 | 0.000 | 0.001 | |
| validate | 3.017 | 0.437 | 2.317 | |