Augustin Luna
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/paxtoolsr |
| git_branch: RELEASE_3_13 |
| git_last_commit: 7635a83 |
| git_last_commit_date: 2021-05-19 12:08:34 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:15 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the paxtoolsr package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1355/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| paxtoolsr 1.26.0 (landing page) Augustin Luna
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: paxtoolsr |
| Version: 1.26.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:paxtoolsr.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings paxtoolsr_1.26.0.tar.gz |
| StartedAt: 2021-10-15 03:12:36 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 03:14:52 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 136.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: paxtoolsr.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:paxtoolsr.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings paxtoolsr_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/paxtoolsr.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'paxtoolsr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'paxtoolsr' version '1.26.0'
* 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 whether package 'paxtoolsr' can be installed ... OK
* checking installed package size ... NOTE
installed size is 31.9Mb
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 34.33 0.13 34.48
fetch 5.58 0.37 2.40
validate 1.97 0.20 7.03
* 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
'C:/Users/biocbuild/bbs-3.13-bioc/meat/paxtoolsr.Rcheck/00check.log'
for details.
paxtoolsr.Rcheck/00install.out
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch paxtoolsr
###
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* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
* installing *source* package 'paxtoolsr' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'paxtoolsr'
finding HTML links ... done
addAttributeList html
convertDataFrameListsToVectors html
convertSifToGmt html
downloadFile html
downloadPc2 html
downloadSignedPC html
fetch html
filterSif html
getCacheFiles html
getErrorMessage html
getNeighbors html
getPc html
getPcDatabaseNames html
getPcUrl html
getShortestPathSif html
getSifInteractionCategories html
graphPc html
integrateBiopax html
loadSifInIgraph html
mapAttributes html
mapValues html
mergeBiopax html
pcDirections html
pcFormats html
pcGraphQueries html
processPcRequest html
readBiopax html
readGmt html
readPcPathwaysInfo html
readSbgn html
readSif html
readSifnx html
searchListOfVectors html
searchPc html
splitSifnxByPathway html
summarize html
summarizeSif html
toCytoscape html
toGSEA html
toLevel3 html
toSBGN html
toSif html
toSifnx html
topPathways html
traverse html
validate html
** 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)
Making 'packages.html' ... done
paxtoolsr.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
2021-10-15 03:14:38,943 500 [main] INFO org.biopax.paxtools.PaxtoolsMain - Collecting proteins for a pathway, the converter will also consider its sub-pathways, their sub-pathways, etc.
2021-10-15 03:14:38,958 515 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - Begin converting Glycolysis Pathway pathway, uri=http://www.biopax.org/examples/myExamplePathway50
2021-10-15 03:14:38,958 515 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - fetched PRs: 2
2021-10-15 03:14:38,958 515 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - grouping the PRs by organism...
2021-10-15 03:14:38,974 531 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - creating GSEA/GMT entries...
2021-10-15 03:14:38,974 531 [pool-2-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - adding uniprot IDs of proteins (PRs) from 'Glycolysis Pathway', amaze;kegg pathway...
2021-10-15 03:14:38,974 531 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - collected 1entries.
2021-10-15 03:14:38,974 531 [main] INFO org.biopax.paxtools.io.gsea.GSEAConverter - Creating entries for the rest fo (unused) PRs...
2021-10-15 03:14:39,505 1062 [main] INFO org.biopax.paxtools.client.BiopaxValidatorClient - BioPAX Validator location: http://biopax.baderlab.org/check.html
2021-10-15 03:14:40,505 2062 [main] INFO org.biopax.paxtools.client.BiopaxValidatorClient - BioPAX Validator location: http://biopax.baderlab.org/check.html
2021-10-15 03:14:41,052 2609 [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: 172 miliseconds.
2021-10-15 03:14:41,833 3390 [main] INFO org.biopax.paxtools.PaxtoolsMain - toSifnx: not blacklisting ubiquitous molecules (no blacklist.txt found)
2021-10-15 03:14:43,630 5187 [main] INFO org.biopax.paxtools.PaxtoolsMain - toSif: not blacklisting ubiquitous molecules (no blacklist.txt found)
2021-10-15 03:14:44,224 5781 [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
21.54 0.98 16.29
paxtoolsr.Rcheck/paxtoolsr-Ex.timings
| name | user | system | elapsed | |
| addAttributeList | 0.02 | 0.00 | 0.02 | |
| convertDataFrameListsToVectors | 0.02 | 0.00 | 0.01 | |
| convertSifToGmt | 0.29 | 0.03 | 0.33 | |
| downloadFile | 0.12 | 0.02 | 0.41 | |
| downloadPc2 | 0 | 0 | 0 | |
| downloadSignedPC | 0 | 0 | 0 | |
| fetch | 5.58 | 0.37 | 2.40 | |
| filterSif | 0.58 | 0.03 | 0.44 | |
| getCacheFiles | 0.00 | 0.04 | 0.02 | |
| getErrorMessage | 0 | 0 | 0 | |
| getNeighbors | 1.25 | 0.09 | 0.59 | |
| getPc | 0 | 0 | 0 | |
| getPcDatabaseNames | 0.03 | 0.00 | 0.30 | |
| getPcUrl | 0 | 0 | 0 | |
| getShortestPathSif | 0.05 | 0.00 | 0.04 | |
| getSifInteractionCategories | 0 | 0 | 0 | |
| graphPc | 0 | 0 | 0 | |
| integrateBiopax | 3.76 | 0.17 | 1.02 | |
| loadSifInIgraph | 0.11 | 0.02 | 0.05 | |
| mapValues | 0 | 0 | 0 | |
| mergeBiopax | 1.41 | 0.01 | 0.48 | |
| pcDirections | 0.03 | 0.00 | 0.02 | |
| pcFormats | 0 | 0 | 0 | |
| pcGraphQueries | 0 | 0 | 0 | |
| processPcRequest | 0.05 | 0.00 | 0.04 | |
| readBiopax | 0 | 0 | 0 | |
| readGmt | 0.07 | 0.00 | 0.10 | |
| readPcPathwaysInfo | 34.33 | 0.13 | 34.48 | |
| readSbgn | 0.00 | 0.00 | 0.02 | |
| readSif | 0.02 | 0.00 | 0.01 | |
| readSifnx | 0.01 | 0.01 | 0.25 | |
| searchListOfVectors | 0 | 0 | 0 | |
| searchPc | 0 | 0 | 0 | |
| summarize | 0.14 | 0.00 | 0.36 | |
| summarizeSif | 0.02 | 0.00 | 0.02 | |
| toCytoscape | 0.02 | 0.02 | 0.03 | |
| toGSEA | 0.25 | 0.00 | 0.14 | |
| toLevel3 | 0.53 | 0.03 | 0.13 | |
| toSBGN | 1.76 | 0.16 | 2.07 | |
| toSif | 2.70 | 0.20 | 0.81 | |
| toSifnx | 3.13 | 0.08 | 0.60 | |
| topPathways | 0 | 0 | 0 | |
| traverse | 0 | 0 | 0 | |
| validate | 1.97 | 0.20 | 7.03 | |