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BioC 3.2: CHECK report for paxtoolsr on moscato1

This page was generated on 2016-04-23 10:20:53 -0700 (Sat, 23 Apr 2016).

Package 756/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
paxtoolsr 1.4.6
Augustin Luna
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/paxtoolsr
Last Changed Rev: 113980 / Revision: 116712
Last Changed Date: 2016-02-24 04:22:01 -0800 (Wed, 24 Feb 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  ERROR  skipped 
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: paxtoolsr
Version: 1.4.6
Command: rm -rf paxtoolsr.buildbin-libdir paxtoolsr.Rcheck && mkdir paxtoolsr.buildbin-libdir paxtoolsr.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=paxtoolsr.buildbin-libdir paxtoolsr_1.4.6.tar.gz >paxtoolsr.Rcheck\00install.out 2>&1 && cp paxtoolsr.Rcheck\00install.out paxtoolsr-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=paxtoolsr.buildbin-libdir --install="check:paxtoolsr-install.out" --force-multiarch --no-vignettes --timings paxtoolsr_1.4.6.tar.gz
StartedAt: 2016-04-23 05:48:13 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 05:51:49 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 216.1 seconds
RetCode: 0
Status:  OK  
CheckDir: paxtoolsr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf paxtoolsr.buildbin-libdir paxtoolsr.Rcheck && mkdir paxtoolsr.buildbin-libdir paxtoolsr.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=paxtoolsr.buildbin-libdir paxtoolsr_1.4.6.tar.gz >paxtoolsr.Rcheck\00install.out 2>&1 && cp paxtoolsr.Rcheck\00install.out paxtoolsr-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=paxtoolsr.buildbin-libdir --install="check:paxtoolsr-install.out" --force-multiarch --no-vignettes --timings paxtoolsr_1.4.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/paxtoolsr.Rcheck'
* using R version 3.2.4 (2016-03-10)
* 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 '1.4.6'
* 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 29.9Mb
  sub-directories of 1Mb or more:
    extdata   5.0Mb
    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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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%'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [14s] OK
** running examples for arch 'x64' ... [12s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [23s]
 [24s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [24s]
 [24s] 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: 2 NOTEs
See
  'D:/biocbld/bbs-3.2-bioc/meat/paxtoolsr.Rcheck/00check.log'
for details.


paxtoolsr.Rcheck/00install.out:


install for i386

* installing *source* package 'paxtoolsr' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'paxtoolsr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'paxtoolsr' as paxtoolsr_1.4.6.zip
* DONE (paxtoolsr)

paxtoolsr.Rcheck/examples_i386/paxtoolsr-Ex.timings:

nameusersystemelapsed
downloadFile0.050.000.23
downloadPc2000
downloadSignedPC000
extractIds0.030.000.03
fetch1.190.071.36
filterSif0.000.010.01
getCacheFiles000
getErrorMessage000
getNeighbors0.200.020.38
getPc000
getPcUrl000
getSifInteractionCategories000
graphPc000
idMapping000
integrateBiopax1.210.041.25
loadSifInIgraph000
mapValues0.020.000.02
mergeBiopax1.110.072.32
pcDirections000
pcFormats000
pcGraphQueries000
processPcRequest0.010.000.10
readBiopax000
readGmt0.020.000.01
readSbgn0.010.000.02
readSif000
readSifnx0.040.000.03
searchListOfVectors000
searchPc000
summarize0.140.010.16
summarizeSif000
toGSEA0.030.020.08
toLevel30.090.010.09
toSBGN0.680.030.89
toSif1.000.020.92
toSifnx0.560.000.53
topPathways000
traverse000
validate0.530.053.31

paxtoolsr.Rcheck/examples_x64/paxtoolsr-Ex.timings:

nameusersystemelapsed
downloadFile0.050.020.19
downloadPc2000
downloadSignedPC000
extractIds0.040.000.05
fetch3.840.062.04
filterSif000
getCacheFiles000
getErrorMessage000
getNeighbors0.590.000.31
getPc000
getPcUrl000
getSifInteractionCategories0.020.000.02
graphPc000
idMapping000
integrateBiopax2.880.031.59
loadSifInIgraph000
mapValues000
mergeBiopax1.410.070.88
pcDirections000
pcFormats000
pcGraphQueries000
processPcRequest0.150.000.11
readBiopax000
readGmt0.020.000.02
readSbgn000
readSif000
readSifnx0.020.000.01
searchListOfVectors000
searchPc000
summarize0.080.030.09
summarizeSif000
toGSEA0.050.010.41
toLevel30.140.000.09
toSBGN1.570.081.06
toSif1.830.030.80
toSifnx1.540.020.51
topPathways000
traverse000
validate0.920.032.10