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CHECK report for BiGGR on malbec1

This page was generated on 2020-08-11 11:19:31 -0400 (Tue, 11 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BiGGR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 139/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiGGR 1.25.0
Anand K. Gavai
Snapshot Date: 2020-08-10 14:50:56 -0400 (Mon, 10 Aug 2020)
URL: https://git.bioconductor.org/packages/BiGGR
Branch: master
Last Commit: eb731df
Last Changed Date: 2020-04-27 14:36:11 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  ERROR  ERROR  skipped 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  ERROR  ERROR  skipped  skipped 

Summary

Package: BiGGR
Version: 1.25.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BiGGR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BiGGR_1.25.0.tar.gz
StartedAt: 2020-08-11 00:21:34 -0400 (Tue, 11 Aug 2020)
EndedAt: 2020-08-11 00:26:41 -0400 (Tue, 11 Aug 2020)
EllapsedTime: 306.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: BiGGR.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BiGGR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BiGGR_1.25.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/BiGGR.Rcheck’
* using R version 4.0.2 (2020-06-22)
* 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 ‘1.25.0’
* 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 ‘/home/biocbuild/bbs-3.12-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 : <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 : <anonymous>: 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 : <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 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
gprMapping         162.384  0.036 162.659
gprMappingAvg       19.520  0.020  19.583
buildSBMLFromGenes   5.916  0.164   6.090
* 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/BiGGR.Rcheck/00check.log’
for details.



Installation output

BiGGR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL BiGGR
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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-package2.2880.0842.419
E.coli_iAF12600.8080.0760.887
E.coli_iJR9040.5800.0080.591
E.coli_textbook0.0520.0400.090
H.pylori_ilT3410.1680.0560.226
H.sapiens_Recon11.0560.0641.124
M.barkeri_iAF6920.3440.0880.436
M.tuberculosis_iNJ6610.3960.0520.451
P.putida_iJN7460.3360.0440.379
Recon21.8200.0641.883
S.aureus_iSB6190.2400.0360.278
S.cerevisiae_iND7500.6000.0280.638
buildSBMLFromBiGG0.1440.0200.174
buildSBMLFromGenes5.9160.1646.090
buildSBMLFromPathways4.7200.0204.743
buildSBMLFromReactionIDs1.880.001.88
createLIMFromBiGG0.0840.0000.082
createLIMFromSBML1.0400.0241.067
extractGeneAssociations2.9920.0002.998
extractPathways1.9400.0041.943
getPathwaysForSBML3.0520.0043.063
getRates0.0040.0000.002
gprMapping162.384 0.036162.659
gprMappingAvg19.520 0.02019.583
lying.tunell.data0.0000.0000.001
rmvSpliceVariant2.7320.0002.735
sampleFluxEnsemble2.8640.0282.913
sbml2hyperdraw2.3560.0042.367