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 10:53:33 -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: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:paxtoolsr.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings paxtoolsr_1.14.0.tar.gz |
| StartedAt: 2018-07-05 03:30:07 -0400 (Thu, 05 Jul 2018) |
| EndedAt: 2018-07-05 03:32:08 -0400 (Thu, 05 Jul 2018) |
| EllapsedTime: 120.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: paxtoolsr.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:paxtoolsr.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings paxtoolsr_1.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/paxtoolsr.Rcheck'
* using R version 3.5.1 RC (2018-06-24 r74929)
* 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 '1.14.0'
* 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 whether package 'paxtoolsr' can be installed ... OK
* checking installed package size ... NOTE
installed size is 30.5Mb
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
* 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
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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
fetch 5.43 0.21 1.62
* 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-3.7-bioc/meat/paxtoolsr.Rcheck/00check.log'
for details.
paxtoolsr.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/paxtoolsr_1.14.0.tar.gz && rm -rf paxtoolsr.buildbin-libdir && mkdir paxtoolsr.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=paxtoolsr.buildbin-libdir paxtoolsr_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL paxtoolsr_1.14.0.zip && rm paxtoolsr_1.14.0.tar.gz paxtoolsr_1.14.0.zip
###
##############################################################################
##############################################################################
% 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 23.0M 100 23.0M 0 0 85.2M 0 --:--:-- --:--:-- --:--:-- 87.5M
install for i386
* installing *source* package 'paxtoolsr' ...
** 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
convertSifToSpia html
convertSifnxIds html
convertToDF html
convertToDT html
downloadFile html
downloadPc2 html
downloadSignedPC html
extractIds html
fetch html
filterSif html
getCacheFiles html
getErrorMessage html
getNeighbors html
getPc html
getPcUrl html
getShortestPathSif html
getSifInteractionCategories html
graphPc html
integrateBiopax html
loadSifInIgraph html
mapValues html
mergeBiopax html
pcDirections html
pcFormats html
pcGraphQueries html
processPcRequest html
readBiopax html
readGmt html
readSbgn html
readSif html
readSifnx html
searchListOfVectors html
searchPc html
skip_on_bioc html
splitSifnxByPathway html
summarize html
summarizeSif 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
In R CMD INSTALL
install for x64
* installing *source* package 'paxtoolsr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'paxtoolsr' as paxtoolsr_1.14.0.zip
* DONE (paxtoolsr)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'paxtoolsr' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
paxtoolsr.Rcheck/tests_i386/testthat.Rout
R version 3.5.1 RC (2018-06-24 r74929) -- "Feather Spray"
Copyright (C) 2018 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
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 03:31:40,946 703 [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 03:31:40,962 719 [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 03:31:40,962 719 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - fetched PRs: 2
2018-07-05 03:31:40,962 719 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - grouping the PRs by organism...
2018-07-05 03:31:40,978 735 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - creating GSEA/GMT entries...
2018-07-05 03:31:40,978 735 [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 03:31:40,978 735 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - collected 1entries.
2018-07-05 03:31:40,978 735 [main] INFO org.biopax.paxtools.io.gsea.GSEAConverter - Creating entries for the rest fo (unused) PRs...
2018-07-05 03:31:41,571 1328 [main] INFO org.biopax.paxtools.client.BiopaxValidatorClient - BioPAX Validator location: http://biopax.baderlab.org/check.html
2018-07-05 03:31:42,196 1953 [main] INFO org.biopax.paxtools.client.BiopaxValidatorClient - BioPAX Validator location: http://biopax.baderlab.org/check.html
2018-07-05 03:31:42,681 2438 [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: 109 miliseconds.
2018-07-05 03:31:43,478 3235 [main] INFO org.biopax.paxtools.PaxtoolsMain - toSifnx: not blacklisting ubiquitous molecules (no blacklist.txt found)
2018-07-05 03:31:44,274 4031 [main] INFO org.biopax.paxtools.PaxtoolsMain - toSif: not blacklisting ubiquitous molecules (no blacklist.txt found)
2018-07-05 03:31:45,009 4766 [main] 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
7.79 0.65 16.65
|
paxtoolsr.Rcheck/tests_x64/testthat.Rout
R version 3.5.1 RC (2018-06-24 r74929) -- "Feather Spray"
Copyright (C) 2018 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
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 03:31:57,342 1500 [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 03:31:57,576 1734 [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 03:31:57,576 1734 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - fetched PRs: 2
2018-07-05 03:31:57,576 1734 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - grouping the PRs by organism...
2018-07-05 03:31:57,592 1750 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - creating GSEA/GMT entries...
2018-07-05 03:31:57,717 1875 [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 03:31:57,717 1875 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - collected 1entries.
2018-07-05 03:31:57,717 1875 [main] INFO org.biopax.paxtools.io.gsea.GSEAConverter - Creating entries for the rest fo (unused) PRs...
2018-07-05 03:31:58,357 2515 [main] INFO org.biopax.paxtools.client.BiopaxValidatorClient - BioPAX Validator location: http://biopax.baderlab.org/check.html
2018-07-05 03:31:58,982 3140 [main] INFO org.biopax.paxtools.client.BiopaxValidatorClient - BioPAX Validator location: http://biopax.baderlab.org/check.html
2018-07-05 03:31:59,670 3828 [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: 94 miliseconds.
2018-07-05 03:32:00,607 4765 [main] INFO org.biopax.paxtools.PaxtoolsMain - toSifnx: not blacklisting ubiquitous molecules (no blacklist.txt found)
2018-07-05 03:32:01,654 5812 [main] INFO org.biopax.paxtools.PaxtoolsMain - toSif: not blacklisting ubiquitous molecules (no blacklist.txt found)
2018-07-05 03:32:02,357 6515 [main] 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
19.82 0.81 16.53
|
|
paxtoolsr.Rcheck/examples_i386/paxtoolsr-Ex.timings
|
paxtoolsr.Rcheck/examples_x64/paxtoolsr-Ex.timings
|