BioC 2.14: CHECK report for BiGGR on morelia

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 21:25:35 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 21:29:28 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 232.7 seconds

RetCode: 0

Status:  OK

CheckDir: BiGGR.Rcheck

Warnings: 0

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### Running command:
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###   /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-darwin13.1.0 (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 ... [6s/6s] 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 ... [106s/107s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
buildSBMLFromGenes       15.756  0.080  15.856
buildSBMLFromPathways    11.523  0.107  11.640
sbml2hyperdraw           10.567  0.028  10.610
Recon2                   10.126  0.154  10.300
extractPathways           8.762  0.020   8.930
getPathwaysForSBML        8.463  0.020   8.493
buildSBMLFromReactionIDs  8.332  0.044   8.383
extractGeneAssociations   7.862  0.034   7.912
BiGGR-package             5.618  0.079   5.802
* 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	5.618	0.079	5.802
E.coli_iAF1260	1.658	0.026	1.686
E.coli_iJR904	0.701	0.010	0.711
E.coli_textbook	0.062	0.002	0.064
H.pylori_ilT341	0.383	0.005	0.388
H.sapiens_Recon1	2.609	0.043	2.664
M.barkeri_iAF692	0.463	0.005	0.469
M.tuberculosis_iNJ661	0.700	0.007	0.707
P.putida_iJN746	0.733	0.008	0.742
Recon2	10.126	0.154	10.300
S.aureus_iSB619	0.579	0.016	0.595
S.cerevisiae_iND750	1.100	0.047	1.147
buildSBMLFromBiGG	0.193	0.004	0.198
buildSBMLFromGenes	15.756	0.080	15.856
buildSBMLFromPathways	11.523	0.107	11.640
buildSBMLFromReactionIDs	8.332	0.044	8.383
createLIMFromBiGG	0.198	0.004	0.202
createLIMFromSBML	2.849	0.040	2.893
extractGeneAssociations	7.862	0.034	7.912
extractPathways	8.762	0.020	8.930
getPathwaysForSBML	8.463	0.020	8.493
getRates	0.003	0.001	0.004
lying.tunell.data	0.004	0.001	0.005
sampleFluxEnsemble	3.665	0.182	3.888
sbml2hyperdraw	10.567	0.028	10.610