Back to Multiple platform build/check report for BioC 3.8
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for BiGGR on merida1

This page was generated on 2019-04-16 11:57:07 -0400 (Tue, 16 Apr 2019).

Package 126/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiGGR 1.18.0
Anand K. Gavai
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/BiGGR
Branch: RELEASE_3_8
Last Commit: 865730c
Last Changed Date: 2018-10-30 11:41:52 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BiGGR
Version: 1.18.0
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_1.18.0.tar.gz
StartedAt: 2019-04-15 22:33:56 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 22:39:38 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 341.9 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 --install=check:BiGGR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BiGGR_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/BiGGR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.18.0’
* 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            155.912  2.239 160.057
gprMappingAvg          19.288  1.095  20.697
buildSBMLFromGenes      7.883  0.110   8.124
buildSBMLFromPathways   6.002  0.026   6.102
* 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-3.8-bioc/meat/BiGGR.Rcheck/00check.log’
for details.



Installation output

BiGGR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BiGGR
###
##############################################################################
##############################################################################


* 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-package4.5410.1024.779
E.coli_iAF12601.5800.0461.687
E.coli_iJR9040.6710.0210.747
E.coli_textbook0.0520.0050.057
H.pylori_ilT3410.3470.0110.361
H.sapiens_Recon12.3610.0732.551
M.barkeri_iAF6920.6140.0180.645
M.tuberculosis_iNJ6610.6460.0170.729
P.putida_iJN7460.6330.0160.654
Recon23.5300.2073.898
S.aureus_iSB6190.4300.0190.452
S.cerevisiae_iND7500.6120.0300.661
buildSBMLFromBiGG0.1760.0260.203
buildSBMLFromGenes7.8830.1108.124
buildSBMLFromPathways6.0020.0266.102
buildSBMLFromReactionIDs3.3540.0113.436
createLIMFromBiGG0.1680.0030.173
createLIMFromSBML2.1970.0112.305
extractGeneAssociations3.7150.0203.841
extractPathways3.4080.0223.464
getPathwaysForSBML4.2800.0494.447
getRates0.0040.0020.007
gprMapping155.912 2.239160.057
gprMappingAvg19.288 1.09520.697
lying.tunell.data0.0030.0020.005
rmvSpliceVariant2.9890.0353.053
sampleFluxEnsemble2.7790.1122.915
sbml2hyperdraw3.3660.0163.406