BioC 2.14: CHECK report for BiGGR on zin2

Package: BiGGR

Version: 1.2.0

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings BiGGR_1.2.0.tar.gz

StartedAt: 2014-10-07 22:02:07 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:04:39 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 152.1 seconds

RetCode: 0

Status:  OK

CheckDir: BiGGR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings BiGGR_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/BiGGR.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.2.0’
* 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 ... [4s/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 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [63s/63s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
buildSBMLFromGenes    9.908  0.080  10.019
sbml2hyperdraw        6.636  0.000   6.646
buildSBMLFromPathways 6.173  0.028   6.213
Recon2                5.928  0.100   6.177
* 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

* 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)

name	user	system	elapsed
BiGGR-package	4.136	0.080	4.344
E.coli_iAF1260	0.812	0.020	0.836
E.coli_iJR904	0.288	0.004	0.294
E.coli_textbook	0.028	0.012	0.041
H.pylori_ilT341	0.160	0.012	0.172
H.sapiens_Recon1	1.204	0.012	1.220
M.barkeri_iAF692	0.232	0.020	0.257
M.tuberculosis_iNJ661	0.320	0.028	0.350
P.putida_iJN746	0.320	0.012	0.334
Recon2	5.928	0.100	6.177
S.aureus_iSB619	0.252	0.016	0.271
S.cerevisiae_iND750	0.637	0.024	0.662
buildSBMLFromBiGG	0.152	0.000	0.150
buildSBMLFromGenes	9.908	0.080	10.019
buildSBMLFromPathways	6.173	0.028	6.213
buildSBMLFromReactionIDs	3.932	0.004	3.944
createLIMFromBiGG	0.152	0.000	0.154
createLIMFromSBML	1.428	0.020	1.452
extractGeneAssociations	4.184	0.000	4.207
extractPathways	4.776	0.004	4.839
getPathwaysForSBML	4.641	0.000	4.650
getRates	0.004	0.000	0.004
lying.tunell.data	0.004	0.000	0.004
sampleFluxEnsemble	3.636	0.036	3.677
sbml2hyperdraw	6.636	0.000	6.646