BioC 2.13: CHECK report for BiGGR on zin1

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

* 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

* 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	4.056	0.068	4.177
E.coli_iAF1260	0.624	0.012	0.638
E.coli_iJR904	0.220	0.000	0.223
E.coli_textbook	0.044	0.000	0.048
H.pylori_ilT341	0.120	0.008	0.130
H.sapiens_Recon1	0.976	0.040	1.018
M.barkeri_iAF692	0.156	0.008	0.164
M.tuberculosis_iNJ661	0.228	0.000	0.240
P.putida_iJN746	0.236	0.004	0.240
Recon2	5.664	0.064	5.738
S.aureus_iSB619	0.160	0.000	0.162
S.cerevisiae_iND750	0.236	0.008	0.245
buildSBMLFromBiGG	0.156	0.000	0.159
buildSBMLFromGenes	16.413	0.136	16.639
buildSBMLFromPathways	7.141	0.008	7.159
buildSBMLFromReactionIDs	4.084	0.008	4.122
createLIMFromBiGG	0.504	0.000	0.507
createLIMFromSBML	0.712	0.008	0.720
extractGeneAssociations	4.421	0.004	4.438
extractPathways	4.356	0.000	4.388
getPathwaysForSBML	5.376	0.008	5.431
getRates	0.016	0.000	0.016
sbml2hyperdraw	5.557	0.008	5.579