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 12:31:29 -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: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:paxtoolsr.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings paxtoolsr_1.18.0.tar.gz |
| StartedAt: 2019-10-16 05:51:46 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:56:33 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 287.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: paxtoolsr.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:paxtoolsr.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings paxtoolsr_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/paxtoolsr.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.18.0'
* 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 whether package 'paxtoolsr' can be installed ... OK
* checking installed package size ... NOTE
installed size is 31.8Mb
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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
readPcPathwaysInfo 61.56 0.27 65.40
convertIds 3.97 0.15 5.12
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
readPcPathwaysInfo 60.62 0.25 60.9
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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-3.9-bioc/meat/paxtoolsr.Rcheck/00check.log'
for details.
paxtoolsr.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/paxtoolsr_1.18.0.tar.gz && rm -rf paxtoolsr.buildbin-libdir && mkdir paxtoolsr.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=paxtoolsr.buildbin-libdir paxtoolsr_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL paxtoolsr_1.18.0.zip && rm paxtoolsr_1.18.0.tar.gz paxtoolsr_1.18.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 24.1M 100 24.1M 0 0 86.8M 0 --:--:-- --:--:-- --:--:-- 88.9M
install for i386
* 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
convertIds 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
install for x64
* installing *source* package 'paxtoolsr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'paxtoolsr' as paxtoolsr_1.18.0.zip
* DONE (paxtoolsr)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'paxtoolsr' successfully unpacked and MD5 sums checked
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paxtoolsr.Rcheck/tests_i386/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 05:56:06,259 656 [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 05:56:06,275 672 [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 05:56:06,290 687 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - fetched PRs: 2
2019-10-16 05:56:06,290 687 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - grouping the PRs by organism...
2019-10-16 05:56:06,306 703 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - creating GSEA/GMT entries...
2019-10-16 05:56:06,306 703 [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 05:56:06,306 703 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - collected 1entries.
2019-10-16 05:56:06,306 703 [main] INFO org.biopax.paxtools.io.gsea.GSEAConverter - Creating entries for the rest fo (unused) PRs...
2019-10-16 05:56:06,962 1359 [main] INFO org.biopax.paxtools.client.BiopaxValidatorClient - BioPAX Validator location: http://biopax.baderlab.org/check.html
2019-10-16 05:56:07,462 1859 [main] INFO org.biopax.paxtools.client.BiopaxValidatorClient - BioPAX Validator location: http://biopax.baderlab.org/check.html
2019-10-16 05:56:07,884 2281 [main] INFO org.biopax.paxtools.PaxtoolsMain - Elements in the result model: 240
SBGN-PD Layout is running...
success ratio: 0.7857142857142857
enhanced ratio: 0.7857142857142857
Total execution time: 109 miliseconds.
2019-10-16 05:56:08,743 3140 [main] INFO org.biopax.paxtools.PaxtoolsMain - toSifnx: not blacklisting ubiquitous molecules (no blacklist.txt found)
2019-10-16 05:56:09,806 4203 [main] INFO org.biopax.paxtools.PaxtoolsMain - toSif: not blacklisting ubiquitous molecules (no blacklist.txt found)
2019-10-16 05:56:10,853 5250 [main] 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
8.00 0.57 17.85
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paxtoolsr.Rcheck/tests_x64/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-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
2019-10-16 05:56:22,476 562 [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 05:56:22,492 578 [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 05:56:22,507 593 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - fetched PRs: 2
2019-10-16 05:56:22,507 593 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - grouping the PRs by organism...
2019-10-16 05:56:22,523 609 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - creating GSEA/GMT entries...
2019-10-16 05:56:22,523 609 [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 05:56:22,523 609 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - collected 1entries.
2019-10-16 05:56:22,523 609 [main] INFO org.biopax.paxtools.io.gsea.GSEAConverter - Creating entries for the rest fo (unused) PRs...
2019-10-16 05:56:23,085 1171 [main] INFO org.biopax.paxtools.client.BiopaxValidatorClient - BioPAX Validator location: http://biopax.baderlab.org/check.html
2019-10-16 05:56:23,617 1703 [main] INFO org.biopax.paxtools.client.BiopaxValidatorClient - BioPAX Validator location: http://biopax.baderlab.org/check.html
2019-10-16 05:56:24,039 2125 [main] INFO org.biopax.paxtools.PaxtoolsMain - Elements in the result model: 240
SBGN-PD Layout is running...
success ratio: 0.7857142857142857
enhanced ratio: 0.7857142857142857
Total execution time: 140 miliseconds.
2019-10-16 05:56:24,820 2906 [main] INFO org.biopax.paxtools.PaxtoolsMain - toSifnx: not blacklisting ubiquitous molecules (no blacklist.txt found)
2019-10-16 05:56:25,585 3671 [main] INFO org.biopax.paxtools.PaxtoolsMain - toSif: not blacklisting ubiquitous molecules (no blacklist.txt found)
2019-10-16 05:56:26,226 4312 [main] 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
21.26 1.04 14.39
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paxtoolsr.Rcheck/examples_i386/paxtoolsr-Ex.timings
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paxtoolsr.Rcheck/examples_x64/paxtoolsr-Ex.timings
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