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BioC 3.1: CHECK report for paxtoolsr on zin2

This page was generated on 2015-10-09 09:26:29 -0700 (Fri, 09 Oct 2015).

Package 702/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
paxtoolsr 1.2.1
Augustin Luna
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/paxtoolsr
Last Changed Rev: 104527 / Revision: 109384
Last Changed Date: 2015-06-03 11:34:07 -0700 (Wed, 03 Jun 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: paxtoolsr
Version: 1.2.1
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings paxtoolsr_1.2.1.tar.gz
StartedAt: 2015-10-09 04:11:46 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 04:12:37 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 51.0 seconds
RetCode: 0
Status:  OK 
CheckDir: paxtoolsr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings paxtoolsr_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/paxtoolsr.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.2.1’
* 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 ... [2s/2s] OK
* checking installed package size ... NOTE
  installed size is 26.8Mb
  sub-directories of 1Mb or more:
    extdata   4.9Mb
    java     21.3Mb
* 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 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 ... OK
* 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 ... [14s/10s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [13s/10s]
 [13s/10s] 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.1-bioc/meat/paxtoolsr.Rcheck/00check.log’
for details.


paxtoolsr.Rcheck/00install.out:

* 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
* DONE (paxtoolsr)

paxtoolsr.Rcheck/paxtoolsr-Ex.timings:

nameusersystemelapsed
downloadPc0.0010.0000.001
fetch3.1170.0481.756
fromPsimi1.5950.0400.903
getNeighbors0.5850.0000.259
getPc0.0020.0000.000
getPcUrl0.0430.0040.617
graphPc0.0000.0000.001
idMapping000
integrateBiopax1.9180.0281.137
mergeBiopax0.7900.0200.591
pcDirections0.0010.0000.000
pcFormats0.0000.0000.001
pcGraphQueries0.0010.0000.000
readGmt0.0080.0000.008
searchPc000
splitSifnx0.0120.0000.012
summarize0.0920.0000.076
toGSEA0.0740.0040.056
toLevel30.1280.0000.077
toSBGN0.7240.0040.399
toSif1.8050.0200.890
toSifnx0.2800.0000.113
topPathways0.0010.0000.000
traverse0.0020.0000.001
validate1.3120.0202.271