BioC 2.14: CHECK report for BiGGR on petty

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

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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-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

* 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	8.354	0.158	8.659
E.coli_iAF1260	1.873	0.046	1.949
E.coli_iJR904	0.748	0.016	0.770
E.coli_textbook	0.058	0.003	0.060
H.pylori_ilT341	0.363	0.008	0.372
H.sapiens_Recon1	2.857	0.077	2.943
M.barkeri_iAF692	0.527	0.010	0.552
M.tuberculosis_iNJ661	0.772	0.016	0.796
P.putida_iJN746	0.787	0.014	0.809
Recon2	12.175	0.297	12.593
S.aureus_iSB619	0.589	0.027	0.617
S.cerevisiae_iND750	1.342	0.089	1.433
buildSBMLFromBiGG	0.351	0.007	0.372
buildSBMLFromGenes	20.951	0.134	22.084
buildSBMLFromPathways	13.952	0.151	14.623
buildSBMLFromReactionIDs	9.038	0.061	9.523
createLIMFromBiGG	0.280	0.006	0.981
createLIMFromSBML	2.974	0.069	3.195
extractGeneAssociations	8.865	0.039	9.527
extractPathways	9.872	0.036	10.260
getPathwaysForSBML	10.882	0.035	11.096
getRates	0.008	0.001	0.008
lying.tunell.data	0.006	0.001	0.007
sampleFluxEnsemble	6.962	0.255	7.460
sbml2hyperdraw	13.665	0.046	14.137