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BioC 3.2: CHECK report for BiGGR on zin1

This page was generated on 2015-08-24 10:49:32 -0700 (Mon, 24 Aug 2015).

Package 89/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiGGR 1.5.0
Anand K. Gavai , Hannes Hettling
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiGGR
Last Changed Rev: 104256 / Revision: 107696
Last Changed Date: 2015-05-27 02:44:23 -0700 (Wed, 27 May 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  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: 1.5.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings BiGGR_1.5.0.tar.gz
StartedAt: 2015-08-23 21:57:07 -0700 (Sun, 23 Aug 2015)
EndedAt: 2015-08-23 22:01:36 -0700 (Sun, 23 Aug 2015)
EllapsedTime: 269.3 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_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/BiGGR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.5.0’
* 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 ... [3s/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 ... [201s/202s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
gprMapping         140.623  0.201 141.208
gprMappingAvg       20.281  0.023  20.396
buildSBMLFromGenes   6.132  0.063   6.237
* 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-package2.5570.0562.644
E.coli_iAF12600.6230.0320.656
E.coli_iJR9040.3580.0120.370
E.coli_textbook0.0330.0080.041
H.pylori_ilT3410.1330.0080.142
H.sapiens_Recon10.7160.0400.759
M.barkeri_iAF6920.1810.0520.232
M.tuberculosis_iNJ6610.2330.0160.249
P.putida_iJN7460.2430.0120.254
Recon22.1850.0642.247
S.aureus_iSB6190.1630.0360.199
S.cerevisiae_iND7500.3430.0160.358
buildSBMLFromBiGG0.3240.0000.324
buildSBMLFromGenes6.1320.0636.237
buildSBMLFromPathways4.6870.0094.692
buildSBMLFromReactionIDs1.7450.0001.773
createLIMFromBiGG0.1420.0000.143
createLIMFromSBML1.0190.0111.050
extractGeneAssociations2.2760.0042.279
extractPathways2.3480.0002.351
getPathwaysForSBML2.7710.0002.774
getRates0.0040.0000.004
gprMapping140.623 0.201141.208
gprMappingAvg20.281 0.02320.396
lying.tunell.data0.0030.0000.003
rmvSpliceVariant2.7510.0043.043
sampleFluxEnsemble3.0800.0363.223
sbml2hyperdraw2.6530.0002.653