BioC 3.1: CHECK report for BiGGR on petty

Package: BiGGR

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiGGR_1.4.0.tar.gz

StartedAt: 2015-10-08 21:39:30 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 21:47:18 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 468.1 seconds

RetCode: 0

Status:  OK

CheckDir: BiGGR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiGGR_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/BiGGR.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.4.0’
* 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 ... [8s/9s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ... NOTE
Package in Depends field not imported from: ‘stringr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
gprMapping: no visible global function definition for ‘str_detect’
sampleFluxEnsemble: no visible global function definition for ‘Xsample’
sampleFluxEnsemble: no visible global function definition for ‘xsample’
sbml2hyperdraw: no visible global function definition for ‘graphLayout’
sbml2hyperdraw: no visible global function definition for
  ‘nodeDataDefaults<-’
sbml2hyperdraw: no visible global function definition for
  ‘edgeDataDefaults<-’
sbml2hyperdraw: no visible global function definition for
  ‘graphDataDefaults<-’
sbml2hyperdraw : <anonymous>: no visible global function definition for
  ‘edgeData<-’
* 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 ... [310s/314s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
gprMapping            201.792  2.275 204.715
gprMappingAvg          34.387  0.114  34.565
buildSBMLFromGenes     11.606  0.077  11.690
buildSBMLFromPathways   8.726  0.029   8.765
sampleFluxEnsemble      5.409  0.082   5.568
BiGGR-package           4.896  0.135   5.557
getPathwaysForSBML      5.000  0.018   5.025
Recon2                  3.390  0.189   5.839
* 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
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/BiGGR.Rcheck/00check.log’
for details.

* 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	4.896	0.135	5.557
E.coli_iAF1260	1.120	0.027	1.147
E.coli_iJR904	0.618	0.010	0.628
E.coli_textbook	0.034	0.002	0.036
H.pylori_ilT341	0.240	0.006	0.247
H.sapiens_Recon1	1.742	0.041	1.784
M.barkeri_iAF692	0.401	0.009	0.410
M.tuberculosis_iNJ661	0.507	0.011	0.520
P.putida_iJN746	0.443	0.009	0.453
Recon2	3.390	0.189	5.839
S.aureus_iSB619	0.264	0.021	0.488
S.cerevisiae_iND750	0.686	0.033	0.719
buildSBMLFromBiGG	0.298	0.005	0.304
buildSBMLFromGenes	11.606	0.077	11.690
buildSBMLFromPathways	8.726	0.029	8.765
buildSBMLFromReactionIDs	2.877	0.009	2.887
createLIMFromBiGG	0.190	0.004	0.196
createLIMFromSBML	1.957	0.009	1.979
extractGeneAssociations	4.191	0.013	4.207
extractPathways	3.823	0.037	3.868
getPathwaysForSBML	5.000	0.018	5.025
getRates	0.004	0.001	0.005
gprMapping	201.792	2.275	204.715
gprMappingAvg	34.387	0.114	34.565
lying.tunell.data	0.005	0.002	0.006
rmvSpliceVariant	4.350	0.013	4.364
sampleFluxEnsemble	5.409	0.082	5.568
sbml2hyperdraw	4.840	0.029	4.941