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BioC 3.1: CHECK report for BiGGR on petty

This page was generated on 2015-10-09 09:35:57 -0700 (Fri, 09 Oct 2015).

Package 86/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiGGR 1.4.0
Anand K. Gavai , Hannes Hettling
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/BiGGR
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

##############################################################################
##############################################################################
###
### 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.


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-package4.8960.1355.557
E.coli_iAF12601.1200.0271.147
E.coli_iJR9040.6180.0100.628
E.coli_textbook0.0340.0020.036
H.pylori_ilT3410.2400.0060.247
H.sapiens_Recon11.7420.0411.784
M.barkeri_iAF6920.4010.0090.410
M.tuberculosis_iNJ6610.5070.0110.520
P.putida_iJN7460.4430.0090.453
Recon23.3900.1895.839
S.aureus_iSB6190.2640.0210.488
S.cerevisiae_iND7500.6860.0330.719
buildSBMLFromBiGG0.2980.0050.304
buildSBMLFromGenes11.606 0.07711.690
buildSBMLFromPathways8.7260.0298.765
buildSBMLFromReactionIDs2.8770.0092.887
createLIMFromBiGG0.1900.0040.196
createLIMFromSBML1.9570.0091.979
extractGeneAssociations4.1910.0134.207
extractPathways3.8230.0373.868
getPathwaysForSBML5.0000.0185.025
getRates0.0040.0010.005
gprMapping201.792 2.275204.715
gprMappingAvg34.387 0.11434.565
lying.tunell.data0.0050.0020.006
rmvSpliceVariant4.3500.0134.364
sampleFluxEnsemble5.4090.0825.568
sbml2hyperdraw4.8400.0294.941