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 15:05:48 -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: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:paxtoolsr.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings paxtoolsr_1.26.0.tar.gz |
| StartedAt: 2021-10-14 10:57:25 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 11:00:17 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 171.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: paxtoolsr.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:paxtoolsr.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings paxtoolsr_1.26.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/paxtoolsr.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.26.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘paxtoolsr’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 26.7Mb
sub-directories of 1Mb or more:
extdata 2.9Mb
java 23.5Mb
* 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 38.427 0.759 39.095
fetch 5.748 0.235 1.564
* 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-3.13-bioc/meat/paxtoolsr.Rcheck/00check.log’
for details.
paxtoolsr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL paxtoolsr ### ############################################################################## ############################################################################## * installing to library ‘/home/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 ** 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 4.1.1 (2021-08-10) -- "Kick Things"
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
2021-10-14 11:00:10,657 364 [main] INFO org.biopax.paxtools.PaxtoolsMain - Collecting proteins for a pathway, the converter will also consider its sub-pathways, their sub-pathways, etc.
2021-10-14 11:00:10,667 374 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - Begin converting Glycolysis Pathway pathway, uri=http://www.biopax.org/examples/myExamplePathway50
2021-10-14 11:00:10,673 380 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - fetched PRs: 2
2021-10-14 11:00:10,673 380 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - grouping the PRs by organism...
2021-10-14 11:00:10,683 390 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - creating GSEA/GMT entries...
2021-10-14 11:00:10,684 391 [pool-2-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - adding uniprot IDs of proteins (PRs) from 'Glycolysis Pathway', amaze;kegg pathway...
2021-10-14 11:00:10,687 394 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - collected 1entries.
2021-10-14 11:00:10,687 394 [main] INFO org.biopax.paxtools.io.gsea.GSEAConverter - Creating entries for the rest fo (unused) PRs...
2021-10-14 11:00:11,053 760 [main] INFO org.biopax.paxtools.client.BiopaxValidatorClient - BioPAX Validator location: http://biopax.baderlab.org/check.html
2021-10-14 11:00:11,857 1564 [main] INFO org.biopax.paxtools.client.BiopaxValidatorClient - BioPAX Validator location: http://biopax.baderlab.org/check.html
2021-10-14 11:00:12,595 2302 [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: 57 miliseconds.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.sun.xml.bind.v2.runtime.reflect.opt.Injector$1 (file:/home/biocbuild/bbs-3.13-bioc/R/library/paxtoolsr/java/paxtools-4.3.1.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int)
WARNING: Please consider reporting this to the maintainers of com.sun.xml.bind.v2.runtime.reflect.opt.Injector$1
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
2021-10-14 11:00:13,127 2834 [main] INFO org.biopax.paxtools.PaxtoolsMain - toSifnx: not blacklisting ubiquitous molecules (no blacklist.txt found)
2021-10-14 11:00:13,677 3384 [main] INFO org.biopax.paxtools.PaxtoolsMain - toSif: not blacklisting ubiquitous molecules (no blacklist.txt found)
2021-10-14 11:00:14,058 3765 [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
19.242 0.867 13.147
paxtoolsr.Rcheck/paxtoolsr-Ex.timings
| name | user | system | elapsed | |
| addAttributeList | 0.030 | 0.000 | 0.031 | |
| convertDataFrameListsToVectors | 0.004 | 0.003 | 0.007 | |
| convertSifToGmt | 0.327 | 0.019 | 0.374 | |
| downloadFile | 0.047 | 0.016 | 0.392 | |
| downloadPc2 | 0 | 0 | 0 | |
| downloadSignedPC | 0.001 | 0.000 | 0.000 | |
| fetch | 5.748 | 0.235 | 1.564 | |
| filterSif | 0.540 | 0.009 | 0.131 | |
| getCacheFiles | 0.001 | 0.000 | 0.001 | |
| getErrorMessage | 0.001 | 0.000 | 0.001 | |
| getNeighbors | 1.240 | 0.020 | 0.224 | |
| getPc | 0 | 0 | 0 | |
| getPcDatabaseNames | 0.618 | 0.003 | 0.503 | |
| getPcUrl | 0.000 | 0.000 | 0.001 | |
| getShortestPathSif | 0.082 | 0.001 | 0.059 | |
| getSifInteractionCategories | 0.001 | 0.000 | 0.001 | |
| graphPc | 0 | 0 | 0 | |
| integrateBiopax | 3.293 | 0.111 | 0.856 | |
| loadSifInIgraph | 0.024 | 0.000 | 0.012 | |
| mapValues | 0.001 | 0.000 | 0.000 | |
| mergeBiopax | 1.134 | 0.139 | 0.514 | |
| pcDirections | 0.001 | 0.000 | 0.001 | |
| pcFormats | 0.001 | 0.000 | 0.000 | |
| pcGraphQueries | 0.000 | 0.000 | 0.001 | |
| processPcRequest | 0.010 | 0.004 | 0.006 | |
| readBiopax | 0.007 | 0.000 | 0.004 | |
| readGmt | 0.056 | 0.000 | 0.029 | |
| readPcPathwaysInfo | 38.427 | 0.759 | 39.095 | |
| readSbgn | 0.002 | 0.000 | 0.003 | |
| readSif | 0.010 | 0.000 | 0.009 | |
| readSifnx | 0.019 | 0.008 | 0.027 | |
| searchListOfVectors | 0.001 | 0.000 | 0.002 | |
| searchPc | 0.000 | 0.000 | 0.001 | |
| summarize | 0.131 | 0.012 | 0.063 | |
| summarizeSif | 0.063 | 0.000 | 0.017 | |
| toCytoscape | 0.034 | 0.004 | 0.026 | |
| toGSEA | 0.120 | 0.008 | 0.039 | |
| toLevel3 | 0.215 | 0.004 | 0.051 | |
| toSBGN | 1.491 | 0.064 | 0.365 | |
| toSif | 2.215 | 0.056 | 0.359 | |
| toSifnx | 3.183 | 0.083 | 0.357 | |
| topPathways | 0.028 | 0.004 | 0.000 | |
| traverse | 0 | 0 | 0 | |
| validate | 2.815 | 0.070 | 1.577 | |