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CHECK report for BiGGR on malbec1

This page was generated on 2021-05-06 12:26:58 -0400 (Thu, 06 May 2021).

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 147/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiGGR 1.26.0  (landing page)
Anand K. Gavai
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/BiGGR
Branch: RELEASE_3_12
Last Commit: dde16eb
Last Changed Date: 2020-10-27 10:52:29 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64... NOT SUPPORTED ...

Summary

Package: BiGGR
Version: 1.26.0
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_1.26.0.tar.gz
StartedAt: 2021-05-05 23:22:46 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 23:28:12 -0400 (Wed, 05 May 2021)
EllapsedTime: 325.9 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_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/BiGGR.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.26.0’
* 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         165.604  0.140 166.182
gprMappingAvg       16.996  0.008  17.025
buildSBMLFromGenes   7.628  0.156   7.796
* 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-package3.2080.1203.358
E.coli_iAF12601.0560.0361.096
E.coli_iJR9040.5440.0000.544
E.coli_textbook0.0360.0360.070
H.pylori_ilT3410.1640.0280.193
H.sapiens_Recon11.0080.0361.042
M.barkeri_iAF6920.2920.0680.363
M.tuberculosis_iNJ6610.3320.0440.378
P.putida_iJN7460.4200.0440.465
Recon22.6280.0882.721
S.aureus_iSB6190.3720.0440.416
S.cerevisiae_iND7500.5880.0440.636
buildSBMLFromBiGG0.1440.0200.164
buildSBMLFromGenes7.6280.1567.796
buildSBMLFromPathways4.3320.0284.362
buildSBMLFromReactionIDs2.5080.0122.526
createLIMFromBiGG0.1440.0000.145
createLIMFromSBML1.1280.0201.149
extractGeneAssociations3.0440.0043.053
extractPathways2.7720.0202.809
getPathwaysForSBML3.2080.0003.209
getRates0.0000.0040.004
gprMapping165.604 0.140166.182
gprMappingAvg16.996 0.00817.025
lying.tunell.data0.0000.0000.002
rmvSpliceVariant2.2280.0042.235
sampleFluxEnsemble3.0360.0563.106
sbml2hyperdraw3.0520.0123.068