Augustin Luna
| Snapshot Date: 2018-07-04 16:45:12 -0400 (Wed, 04 Jul 2018) |
| URL: https://git.bioconductor.org/packages/paxtoolsr |
| Branch: RELEASE_3_7 |
| Last Commit: e20a1a7 |
| Last Changed Date: 2018-04-30 10:35:34 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-07-05 11:11:05 -0400 (Thu, 05 Jul 2018).
| Package 1065/1560 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| paxtoolsr 1.14.0 Augustin Luna
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: paxtoolsr |
| Version: 1.14.0 |
| 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_1.14.0.tar.gz |
| StartedAt: 2018-07-05 01:10:00 -0400 (Thu, 05 Jul 2018) |
| EndedAt: 2018-07-05 01:11:25 -0400 (Thu, 05 Jul 2018) |
| EllapsedTime: 84.9 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_1.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/paxtoolsr.Rcheck’
* using R version 3.5.0 (2018-04-23)
* 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 ‘1.14.0’
* 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 30.3Mb
sub-directories of 1Mb or more:
extdata 5.6Mb
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
Namespace in Imports field not imported from: ‘jsonlite’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.onLoad: no visible global function definition for ‘write.table’
downloadFile: no visible global function definition for ‘URLencode’
downloadFile: no visible global function definition for ‘read.table’
downloadFile: no visible global function definition for ‘write.table’
downloadPc2: no visible global function definition for ‘select.list’
downloadSignedPC: no visible global function definition for
‘read.table’
getPcRequest: no visible global function definition for ‘URLencode’
readSifnx: no visible global function definition for ‘read.table’
splitSifnxByPathway: no visible global function definition for
‘txtProgressBar’
splitSifnxByPathway: no visible global function definition for
‘%dopar%’
splitSifnxByPathway: no visible global function definition for
‘setTxtProgressBar’
Undefined global functions or variables:
%dopar% URLencode read.table select.list setTxtProgressBar
txtProgressBar write.table
Consider adding
importFrom("utils", "URLencode", "read.table", "select.list",
"setTxtProgressBar", "txtProgressBar", "write.table")
to your NAMESPACE file.
* 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
fetch 5.157 0.53 1.534
* 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-3.7-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/3.5/Resources/library’ * installing *source* package ‘paxtoolsr’ ... ** 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 * DONE (paxtoolsr)
paxtoolsr.Rcheck/tests/testthat.Rout
R version 3.5.0 (2018-04-23) -- "Joy in Playing"
Copyright (C) 2018 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
Attaching package: 'paxtoolsr'
The following object is masked from 'package:testthat':
skip_on_bioc
>
> test_check("paxtoolsr")
URL: http://www.pathwaycommons.org/pc2/get?uri=http://identifiers.org/uniprot/Q06609&uri=http://identifiers.org/uniprot/Q96EB6&format=BIOPAX
2018-07-05 01:11:15,390 1059 [main] INFO org.biopax.paxtools.PaxtoolsMain - Collecting proteins for a pathway, the converter will also consider its sub-pathways, their sub-pathways, etc.
2018-07-05 01:11:15,408 1077 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - Begin converting Glycolysis Pathway pathway, uri=http://www.biopax.org/examples/myExamplePathway50
2018-07-05 01:11:15,417 1086 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - fetched PRs: 2
2018-07-05 01:11:15,417 1086 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - grouping the PRs by organism...
2018-07-05 01:11:15,431 1100 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - creating GSEA/GMT entries...
2018-07-05 01:11:15,432 1101 [pool-2-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - adding uniprot IDs of proteins (PRs) from 'Glycolysis Pathway', amaze;kegg pathway...
2018-07-05 01:11:15,434 1103 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - collected 1entries.
2018-07-05 01:11:15,434 1103 [main] INFO org.biopax.paxtools.io.gsea.GSEAConverter - Creating entries for the rest fo (unused) PRs...
2018-07-05 01:11:15,878 1547 [main] INFO org.biopax.paxtools.client.BiopaxValidatorClient - BioPAX Validator location: http://biopax.baderlab.org/check.html
2018-07-05 01:11:16,533 2202 [main] INFO org.biopax.paxtools.client.BiopaxValidatorClient - BioPAX Validator location: http://biopax.baderlab.org/check.html
2018-07-05 01:11:16,982 2651 [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: 120 miliseconds.
2018-07-05 01:11:17,873 3542 [AWT-AppKit] INFO org.biopax.paxtools.PaxtoolsMain - toSifnx: not blacklisting ubiquitous molecules (no blacklist.txt found)
2018-07-05 01:11:18,497 4166 [AWT-AppKit] INFO org.biopax.paxtools.PaxtoolsMain - toSif: not blacklisting ubiquitous molecules (no blacklist.txt found)
2018-07-05 01:11:19,051 4720 [AWT-AppKit] INFO org.biopax.paxtools.PaxtoolsMain - toSif: not blacklisting ubiquitous molecules (no blacklist.txt found)
══ testthat results ═══════════════════════════════════════════════════════════
OK: 37 SKIPPED: 11 FAILED: 0
>
> proc.time()
user system elapsed
21.187 1.632 14.698
paxtoolsr.Rcheck/paxtoolsr-Ex.timings
| name | user | system | elapsed | |
| downloadFile | 0.055 | 0.012 | 0.160 | |
| downloadPc2 | 0.002 | 0.000 | 0.002 | |
| downloadSignedPC | 0.001 | 0.000 | 0.001 | |
| extractIds | 0.041 | 0.002 | 0.044 | |
| fetch | 5.157 | 0.530 | 1.534 | |
| filterSif | 0.822 | 0.022 | 0.277 | |
| getCacheFiles | 0.001 | 0.000 | 0.001 | |
| getErrorMessage | 0.003 | 0.000 | 0.002 | |
| getNeighbors | 0.919 | 0.095 | 0.201 | |
| getPc | 0.008 | 0.001 | 0.002 | |
| getPcUrl | 0.005 | 0.001 | 0.002 | |
| getSifInteractionCategories | 0.005 | 0.000 | 0.001 | |
| graphPc | 0.003 | 0.000 | 0.002 | |
| integrateBiopax | 3.718 | 0.323 | 1.043 | |
| loadSifInIgraph | 0.021 | 0.001 | 0.010 | |
| mapValues | 0.005 | 0.001 | 0.002 | |
| mergeBiopax | 1.302 | 0.076 | 0.605 | |
| pcDirections | 0.001 | 0.000 | 0.002 | |
| pcFormats | 0.001 | 0.000 | 0.001 | |
| pcGraphQueries | 0.001 | 0.000 | 0.002 | |
| processPcRequest | 0.006 | 0.001 | 0.007 | |
| readBiopax | 0.003 | 0.000 | 0.004 | |
| readGmt | 0.005 | 0.000 | 0.005 | |
| readSbgn | 0.003 | 0.001 | 0.003 | |
| readSif | 0.004 | 0.001 | 0.004 | |
| readSifnx | 0.027 | 0.001 | 0.028 | |
| searchListOfVectors | 0.007 | 0.001 | 0.007 | |
| searchPc | 0.002 | 0.000 | 0.002 | |
| summarize | 0.169 | 0.015 | 0.094 | |
| summarizeSif | 0.005 | 0.000 | 0.006 | |
| toGSEA | 0.182 | 0.010 | 0.077 | |
| toLevel3 | 0.466 | 0.012 | 0.100 | |
| toSBGN | 2.109 | 0.222 | 0.705 | |
| toSif | 2.759 | 0.132 | 0.626 | |
| toSifnx | 1.058 | 0.177 | 0.319 | |
| topPathways | 0.004 | 0.000 | 0.001 | |
| traverse | 0.003 | 0.001 | 0.002 | |
| validate | 2.026 | 0.238 | 1.480 | |