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CHECK report for BiGGR on veracruz1

This page was generated on 2018-04-12 13:37:22 -0400 (Thu, 12 Apr 2018).

Package 113/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiGGR 1.14.0
Anand K. Gavai
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/BiGGR
Branch: RELEASE_3_6
Last Commit: ea2b5a3
Last Changed Date: 2017-10-30 12:40:07 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BiGGR
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiGGR_1.14.0.tar.gz
StartedAt: 2018-04-12 00:51:04 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:55:32 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 267.8 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 --no-vignettes --timings BiGGR_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/BiGGR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.14.0’
* 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 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
.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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
gprMapping            106.715  1.673 110.167
gprMappingAvg          16.412  0.696  17.451
buildSBMLFromGenes      7.905  0.107   8.157
buildSBMLFromPathways   5.451  0.086   5.660
* 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-3.6-bioc/meat/BiGGR.Rcheck/00check.log’
for details.



Installation output

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)

Tests output


Example timings

BiGGR.Rcheck/BiGGR-Ex.timings

nameusersystemelapsed
BiGGR-package4.2270.0894.397
E.coli_iAF12601.2690.0311.322
E.coli_iJR9040.4970.0120.519
E.coli_textbook0.0350.0020.038
H.pylori_ilT3410.2510.0070.259
H.sapiens_Recon11.7820.0471.874
M.barkeri_iAF6920.3330.0090.351
M.tuberculosis_iNJ6610.4450.0100.473
P.putida_iJN7460.4660.0240.497
Recon22.7550.1392.956
S.aureus_iSB6190.3510.0180.378
S.cerevisiae_iND7500.5890.0190.622
buildSBMLFromBiGG0.1320.0020.137
buildSBMLFromGenes7.9050.1078.157
buildSBMLFromPathways5.4510.0865.660
buildSBMLFromReactionIDs2.2620.0212.360
createLIMFromBiGG0.2730.0040.295
createLIMFromSBML1.6380.0181.688
extractGeneAssociations2.5630.0162.630
extractPathways2.7360.0112.797
getPathwaysForSBML3.2780.0113.361
getRates0.2620.0050.277
gprMapping106.715 1.673110.167
gprMappingAvg16.412 0.69617.451
lying.tunell.data0.0050.0010.008
rmvSpliceVariant2.7710.0192.886
sampleFluxEnsemble4.1020.0904.311
sbml2hyperdraw3.4790.0123.578