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BioC 2.13: CHECK report for BiGGR on zin1

This page was generated on 2014-04-05 09:48:49 -0700 (Sat, 05 Apr 2014).

Package 74/750HostnameOS / ArchBUILDCHECKBUILD BIN
BiGGR 1.0.0
Anand K. Gavai , Hannes Hettling
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/BiGGR
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: BiGGR
Version: 1.0.0
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings BiGGR_1.0.0.tar.gz
StartedAt: 2014-04-04 23:48:15 -0700 (Fri, 04 Apr 2014)
EndedAt: 2014-04-04 23:50:49 -0700 (Fri, 04 Apr 2014)
EllapsedTime: 154.3 seconds
RetCode: 0
Status:  OK 
CheckDir: BiGGR.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/BiGGR.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.0.0’
* 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 ... [5s/5s] 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 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [65s/65s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
buildSBMLFromGenes    16.413  0.136  16.639
buildSBMLFromPathways  7.141  0.008   7.159
Recon2                 5.664  0.064   5.738
sbml2hyperdraw         5.557  0.008   5.579
getPathwaysForSBML     5.376  0.008   5.431
* 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-package4.0560.0684.177
E.coli_iAF12600.6240.0120.638
E.coli_iJR9040.2200.0000.223
E.coli_textbook0.0440.0000.048
H.pylori_ilT3410.1200.0080.130
H.sapiens_Recon10.9760.0401.018
M.barkeri_iAF6920.1560.0080.164
M.tuberculosis_iNJ6610.2280.0000.240
P.putida_iJN7460.2360.0040.240
Recon25.6640.0645.738
S.aureus_iSB6190.1600.0000.162
S.cerevisiae_iND7500.2360.0080.245
buildSBMLFromBiGG0.1560.0000.159
buildSBMLFromGenes16.413 0.13616.639
buildSBMLFromPathways7.1410.0087.159
buildSBMLFromReactionIDs4.0840.0084.122
createLIMFromBiGG0.5040.0000.507
createLIMFromSBML0.7120.0080.720
extractGeneAssociations4.4210.0044.438
extractPathways4.3560.0004.388
getPathwaysForSBML5.3760.0085.431
getRates0.0160.0000.016
sbml2hyperdraw5.5570.0085.579