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BioC 3.0: CHECK report for BiGGR on oaxaca

This page was generated on 2015-04-10 10:07:52 -0700 (Fri, 10 Apr 2015).

Package 83/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiGGR 1.2.0
Anand K. Gavai , Hannes Hettling
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/BiGGR
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

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: 2015-04-09 21:40:04 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 21:43:58 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 233.6 seconds
RetCode: 0
Status:  OK 
CheckDir: BiGGR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /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-3.0-bioc/meat/BiGGR.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (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/7s] 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 ... NOTE
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 ... [104s/106s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
buildSBMLFromGenes       15.742  0.093  16.130
buildSBMLFromPathways    12.246  0.028  12.348
Recon2                    9.308  0.138   9.501
getPathwaysForSBML        9.060  0.036   9.214
extractGeneAssociations   8.599  0.018   8.665
sbml2hyperdraw            8.536  0.020   9.307
extractPathways           7.921  0.050   8.051
buildSBMLFromReactionIDs  7.707  0.014   7.750
BiGGR-package             5.818  0.090   6.125
* 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/BiGGR.Rcheck/00check.log’
for details.

BiGGR.Rcheck/00install.out:

* 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)

BiGGR.Rcheck/BiGGR-Ex.timings:

nameusersystemelapsed
BiGGR-package5.8180.0906.125
E.coli_iAF12601.6630.0271.694
E.coli_iJR9040.7180.0100.729
E.coli_textbook0.0600.0020.062
H.pylori_ilT3410.3620.0060.368
H.sapiens_Recon12.5320.0412.575
M.barkeri_iAF6920.4770.0070.485
M.tuberculosis_iNJ6610.7030.0130.719
P.putida_iJN7460.7180.0100.733
Recon29.3080.1389.501
S.aureus_iSB6190.5390.0150.554
S.cerevisiae_iND7500.9720.0651.046
buildSBMLFromBiGG0.1960.0120.209
buildSBMLFromGenes15.742 0.09316.130
buildSBMLFromPathways12.246 0.02812.348
buildSBMLFromReactionIDs7.7070.0147.750
createLIMFromBiGG0.2840.0040.288
createLIMFromSBML2.6090.0092.626
extractGeneAssociations8.5990.0188.665
extractPathways7.9210.0508.051
getPathwaysForSBML9.0600.0369.214
getRates0.0040.0010.005
lying.tunell.data0.0030.0010.005
sampleFluxEnsemble4.1140.1794.343
sbml2hyperdraw8.5360.0209.307