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CHECK report for BiGGR on merida2

This page was generated on 2018-10-17 08:51:57 -0400 (Wed, 17 Oct 2018).

Package 118/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiGGR 1.16.0
Anand K. Gavai
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/BiGGR
Branch: RELEASE_3_7
Last Commit: e61e341
Last Changed Date: 2018-04-30 10:35:31 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BiGGR
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BiGGR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BiGGR_1.16.0.tar.gz
StartedAt: 2018-10-16 20:04:27 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 20:09:27 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 300.1 seconds
RetCode: 0
Status:  OK 
CheckDir: BiGGR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BiGGR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BiGGR_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/BiGGR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.16.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BiGGR’ can be installed ... 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 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
.buildSubModel: no visible global function definition for ‘new’
buildSBMLFromBiGG: no visible global function definition for
  ‘read.delim’
buildSBMLFromBiGG : <anonymous>: no visible global function definition
  for ‘new’
buildSBMLFromBiGG: no visible global function definition for ‘new’
createLIMFromSBML: no visible global function definition for ‘hasArg’
gprMapping: no visible global function definition for ‘str_detect’
gprMapping: no visible global function definition for ‘na.omit’
gprMappingAvg: no visible global function definition for ‘na.omit’
sampleFluxEnsemble: no visible global function definition for ‘Xsample’
sbml2hyperdraw: no visible global function definition for ‘hasArg’
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<-’
Undefined global functions or variables:
  Xsample edgeData<- edgeDataDefaults<- graphDataDefaults<- graphLayout
  hasArg na.omit new nodeDataDefaults<- read.delim str_detect
Consider adding
  importFrom("methods", "hasArg", "new")
  importFrom("stats", "na.omit")
  importFrom("utils", "read.delim")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
gprMapping         133.714  2.148 137.368
gprMappingAvg       18.358  1.071  19.578
buildSBMLFromGenes   8.008  0.082   8.147
* 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-3.7-bioc/meat/BiGGR.Rcheck/00check.log’
for details.



Installation output

BiGGR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BiGGR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘BiGGR’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BiGGR)

Tests output


Example timings

BiGGR.Rcheck/BiGGR-Ex.timings

nameusersystemelapsed
BiGGR-package3.6370.0933.767
E.coli_iAF12601.2530.0301.291
E.coli_iJR9040.4450.0100.457
E.coli_textbook0.0440.0030.049
H.pylori_ilT3410.2660.0070.279
H.sapiens_Recon11.8140.0601.889
M.barkeri_iAF6920.4570.0140.472
M.tuberculosis_iNJ6610.4890.0110.501
P.putida_iJN7460.5470.0160.567
Recon22.4580.1742.652
S.aureus_iSB6190.3870.0170.405
S.cerevisiae_iND7500.6380.0300.677
buildSBMLFromBiGG0.1380.0230.165
buildSBMLFromGenes8.0080.0828.147
buildSBMLFromPathways4.7780.0254.818
buildSBMLFromReactionIDs2.1480.0102.171
createLIMFromBiGG0.1100.0030.113
createLIMFromSBML1.5990.0091.614
extractGeneAssociations2.6930.0362.761
extractPathways2.6690.0342.720
getPathwaysForSBML3.4650.0473.536
getRates0.0050.0010.006
gprMapping133.714 2.148137.368
gprMappingAvg18.358 1.07119.578
lying.tunell.data0.0070.0020.008
rmvSpliceVariant3.0230.0163.070
sampleFluxEnsemble2.7810.1002.905
sbml2hyperdraw3.3370.0343.404