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BioC 2.14: CHECK report for BiGGR on petty

This page was generated on 2014-10-08 09:01:14 -0700 (Wed, 08 Oct 2014).

Package 80/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiGGR 1.2.0
Anand K. Gavai , Hannes Hettling
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/BiGGR
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: BiGGR
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BiGGR_1.2.0.tar.gz
StartedAt: 2014-10-07 20:53:35 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 20:59:23 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 348.4 seconds
RetCode: 0
Status:  OK 
CheckDir: BiGGR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BiGGR_1.2.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/BiGGR.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiGGR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BiGGR’ version ‘1.2.0’
* 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 ‘BiGGR’ can be installed ... [10s/11s] OK
* checking installed package size ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [135s/140s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
buildSBMLFromGenes       20.951  0.134  22.084
buildSBMLFromPathways    13.952  0.151  14.623
sbml2hyperdraw           13.665  0.046  14.137
Recon2                   12.175  0.297  12.593
getPathwaysForSBML       10.882  0.035  11.096
extractPathways           9.872  0.036  10.260
buildSBMLFromReactionIDs  9.038  0.061   9.523
extractGeneAssociations   8.865  0.039   9.527
BiGGR-package             8.354  0.158   8.659
sampleFluxEnsemble        6.962  0.255   7.460
* 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

BiGGR.Rcheck/00install.out:

* installing *source* package ‘BiGGR’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BiGGR)

BiGGR.Rcheck/BiGGR-Ex.timings:

nameusersystemelapsed
BiGGR-package8.3540.1588.659
E.coli_iAF12601.8730.0461.949
E.coli_iJR9040.7480.0160.770
E.coli_textbook0.0580.0030.060
H.pylori_ilT3410.3630.0080.372
H.sapiens_Recon12.8570.0772.943
M.barkeri_iAF6920.5270.0100.552
M.tuberculosis_iNJ6610.7720.0160.796
P.putida_iJN7460.7870.0140.809
Recon212.175 0.29712.593
S.aureus_iSB6190.5890.0270.617
S.cerevisiae_iND7501.3420.0891.433
buildSBMLFromBiGG0.3510.0070.372
buildSBMLFromGenes20.951 0.13422.084
buildSBMLFromPathways13.952 0.15114.623
buildSBMLFromReactionIDs9.0380.0619.523
createLIMFromBiGG0.2800.0060.981
createLIMFromSBML2.9740.0693.195
extractGeneAssociations8.8650.0399.527
extractPathways 9.872 0.03610.260
getPathwaysForSBML10.882 0.03511.096
getRates0.0080.0010.008
lying.tunell.data0.0060.0010.007
sampleFluxEnsemble6.9620.2557.460
sbml2hyperdraw13.665 0.04614.137