Back to Multiple platform build/check report for BioC 3.10
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for BiGGR on merida1

This page was generated on 2019-12-10 13:17:32 -0500 (Tue, 10 Dec 2019).

Package 140/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiGGR 1.22.0
Anand K. Gavai
Snapshot Date: 2019-12-09 16:45:09 -0500 (Mon, 09 Dec 2019)
URL: https://git.bioconductor.org/packages/BiGGR
Branch: RELEASE_3_10
Last Commit: f34d300
Last Changed Date: 2019-10-29 13:08:46 -0500 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BiGGR
Version: 1.22.0
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_1.22.0.tar.gz
StartedAt: 2019-12-10 00:40:04 -0500 (Tue, 10 Dec 2019)
EndedAt: 2019-12-10 00:46:23 -0500 (Tue, 10 Dec 2019)
EllapsedTime: 378.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: BiGGR.Rcheck
Warnings: 1

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_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/BiGGR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.22.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: multiple methods tables found for ‘type’
  Warning: multiple methods tables found for ‘type<-’
See ‘/Users/biocbuild/bbs-3.10-bioc/meat/BiGGR.Rcheck/00install.out’ for details.
* 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 : : 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 binding for global variable
  ‘species’
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 : : no visible global function definition for
  ‘edgeData<-’
Undefined global functions or variables:
  Xsample edgeData<- edgeDataDefaults<- graphDataDefaults<- graphLayout
  hasArg na.omit new nodeDataDefaults<- read.delim species 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            163.752  2.372 169.689
gprMappingAvg          24.325  0.983  25.894
buildSBMLFromGenes      8.671  0.095   8.911
buildSBMLFromPathways   6.321  0.075   6.529
* 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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.10-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/3.6/Resources/library’
* installing *source* package ‘BiGGR’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning messages:
1: multiple methods tables found for ‘type’ 
2: multiple methods tables found for ‘type<-’ 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: multiple methods tables found for ‘type’
Warning: multiple methods tables found for ‘type<-’
** testing if installed package can be loaded from final location
Warning: multiple methods tables found for ‘type’
Warning: multiple methods tables found for ‘type<-’
** testing if installed package keeps a record of temporary installation path
* DONE (BiGGR)

Tests output


Example timings

BiGGR.Rcheck/BiGGR-Ex.timings

nameusersystemelapsed
BiGGR-package4.6550.1094.962
E.coli_iAF12601.5570.0451.687
E.coli_iJR9040.8240.0160.847
E.coli_textbook0.0540.0030.059
H.pylori_ilT3410.3780.0100.390
H.sapiens_Recon12.6810.0602.902
M.barkeri_iAF6920.4800.0110.494
M.tuberculosis_iNJ6610.7110.0160.728
P.putida_iJN7460.7230.0170.755
Recon23.2300.1733.481
S.aureus_iSB6190.5290.0220.558
S.cerevisiae_iND7500.7190.0320.770
buildSBMLFromBiGG0.1680.0250.194
buildSBMLFromGenes8.6710.0958.911
buildSBMLFromPathways6.3210.0756.529
buildSBMLFromReactionIDs3.3920.0273.613
createLIMFromBiGG0.1640.0030.179
createLIMFromSBML2.3600.0172.497
extractGeneAssociations3.9870.0304.166
extractPathways3.5420.0143.608
getPathwaysForSBML4.3030.0304.654
getRates0.0040.0020.006
gprMapping163.752 2.372169.689
gprMappingAvg24.325 0.98325.894
lying.tunell.data0.0020.0010.004
rmvSpliceVariant3.5620.0173.644
sampleFluxEnsemble3.6020.1733.842
sbml2hyperdraw3.4170.0383.516