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BioC 3.2: CHECK report for BiGGR on zin1

This page was generated on 2016-04-23 10:13:18 -0700 (Sat, 23 Apr 2016).

Package 90/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiGGR 1.6.0
Anand K. Gavai , Hannes Hettling
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/BiGGR
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BiGGR
Version: 1.6.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings BiGGR_1.6.0.tar.gz
StartedAt: 2016-04-22 22:25:51 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 22:30:15 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 263.7 seconds
RetCode: 0
Status:  OK 
CheckDir: BiGGR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings BiGGR_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/BiGGR.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-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 ‘1.6.0’
* 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 ... [4s/4s] 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 ... 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 ... [196s/196s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
gprMapping         136.424  0.075 136.902
gprMappingAvg       19.657  0.044  19.774
buildSBMLFromGenes   6.220  0.044   6.275
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-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-package2.6950.0602.799
E.coli_iAF12600.5710.0440.613
E.coli_iJR9040.3790.0000.382
E.coli_textbook0.0270.0160.042
H.pylori_ilT3410.1310.0200.152
H.sapiens_Recon10.9770.0281.004
M.barkeri_iAF6920.1970.0320.233
M.tuberculosis_iNJ6610.2600.0280.288
P.putida_iJN7460.2620.0200.282
Recon22.2050.0682.281
S.aureus_iSB6190.2410.0120.254
S.cerevisiae_iND7500.3670.0200.386
buildSBMLFromBiGG0.3190.0000.319
buildSBMLFromGenes6.2200.0446.275
buildSBMLFromPathways4.6030.0204.619
buildSBMLFromReactionIDs1.6620.0041.666
createLIMFromBiGG0.1250.0000.124
createLIMFromSBML1.0460.0161.062
extractGeneAssociations2.2740.0002.272
extractPathways2.3370.0042.339
getPathwaysForSBML2.7180.0002.716
getRates0.0000.0040.004
gprMapping136.424 0.075136.902
gprMappingAvg19.657 0.04419.774
lying.tunell.data0.0030.0000.003
rmvSpliceVariant2.3930.0002.392
sampleFluxEnsemble2.8690.0282.895
sbml2hyperdraw2.5050.0042.517