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CHECK report for BiGGR on tokay1

This page was generated on 2020-08-07 12:02:51 -0400 (Fri, 07 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 139/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiGGR 1.25.0
Anand K. Gavai
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 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
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: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:BiGGR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BiGGR_1.25.0.tar.gz
StartedAt: 2020-08-07 01:09:55 -0400 (Fri, 07 Aug 2020)
EndedAt: 2020-08-07 01:16:02 -0400 (Fri, 07 Aug 2020)
EllapsedTime: 366.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: BiGGR.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:BiGGR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BiGGR_1.25.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/BiGGR.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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 'C:/Users/biocbuild/bbs-3.12-bioc/meat/BiGGR.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
* 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         196.12   0.02  196.26
gprMappingAvg       21.56   0.01   21.58
buildSBMLFromGenes   7.28   0.34    7.63
* 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, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/BiGGR.Rcheck/00check.log'
for details.



Installation output

BiGGR.Rcheck/00install.out

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch BiGGR
###
##############################################################################
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* installing to library 'C:/Users/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
  converting help for package 'BiGGR'
    finding HTML links ... done
    BiGGR-internal                          html  
    BiGGR-package                           html  
    E.coli_iAF1260                          html  
    E.coli_iJR904                           html  
    E.coli_textbook                         html  
    Glycolysis                              html  
    H.pylori_ilT341                         html  
    H.sapiens_Recon1                        html  
    M.barkeri_iAF692                        html  
    M.tuberculosis_iNJ661                   html  
    P.putida_iJN746                         html  
    Recon2                                  html  
    S.aureus_iSB619                         html  
    S.cerevisiae_iND750                     html  
    buildSBMLFromBiGG                       html  
    buildSBMLFromGenes                      html  
    finding level-2 HTML links ... done

    buildSBMLFromPathways                   html  
    buildSBMLFromReactionIDs                html  
    createLIMFromBiGG                       html  
    createLIMFromSBML                       html  
    extractGeneAssociations                 html  
    extractPathways                         html  
    getPathwaysForSBML                      html  
    getRates                                html  
    gprMapping                              html  
    gprMappingAvg                           html  
    lying.tunell.data                       html  
    rmvSpliceVariant                        html  
    sampleFluxEnsemble                      html  
    sbml2hyperdraw                          html  
** 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)
Making 'packages.html' ... done

Tests output


Example timings

BiGGR.Rcheck/BiGGR-Ex.timings

nameusersystemelapsed
BiGGR-package3.170.133.30
E.coli_iAF12601.220.071.30
E.coli_iJR9040.770.020.78
E.coli_textbook0.050.060.11
H.pylori_ilT3410.180.100.28
H.sapiens_Recon11.470.071.55
M.barkeri_iAF6920.500.190.68
M.tuberculosis_iNJ6610.550.100.64
P.putida_iJN7460.440.060.50
Recon22.150.092.25
S.aureus_iSB6190.350.030.38
S.cerevisiae_iND7500.460.050.52
buildSBMLFromBiGG0.150.030.17
buildSBMLFromGenes7.280.347.63
buildSBMLFromPathways4.430.064.50
buildSBMLFromReactionIDs1.730.001.74
createLIMFromBiGG0.100.020.12
createLIMFromSBML1.140.061.21
extractGeneAssociations2.110.002.10
extractPathways2.140.002.15
getPathwaysForSBML2.450.032.48
getRates0.020.000.02
gprMapping196.12 0.02196.26
gprMappingAvg21.56 0.0121.58
lying.tunell.data000
rmvSpliceVariant2.350.022.36
sampleFluxEnsemble2.170.302.48
sbml2hyperdraw2.390.012.41