Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-07-30 15:05:24 -0400 (Fri, 30 Jul 2021).

CHECK results for BiGGR on nebbiolo1

To the developers/maintainers of the BiGGR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiGGR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 149/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiGGR 1.28.0  (landing page)
Anand K. Gavai
Snapshot Date: 2021-07-29 04:50:02 -0400 (Thu, 29 Jul 2021)
URL: https://git.bioconductor.org/packages/BiGGR
Branch: RELEASE_3_13
Last Commit: 1736ee9
Last Changed Date: 2021-05-19 12:00:29 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64... NOT SUPPORTED ...

Summary

Package: BiGGR
Version: 1.28.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:BiGGR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings BiGGR_1.28.0.tar.gz
StartedAt: 2021-07-29 09:03:49 -0400 (Thu, 29 Jul 2021)
EndedAt: 2021-07-29 09:07:30 -0400 (Thu, 29 Jul 2021)
EllapsedTime: 221.0 seconds
RetCode: 0
Status:   OK  
CheckDir: BiGGR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:BiGGR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings BiGGR_1.28.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/BiGGR.Rcheck’
* using R version 4.1.0 (2021-05-18)
* 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 ‘1.28.0’
* 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 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    104.262  0.190 104.467
gprMappingAvg  13.375  0.032  13.409
* 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
  ‘/home/biocbuild/bbs-3.13-bioc/meat/BiGGR.Rcheck/00check.log’
for details.



Installation output

BiGGR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL BiGGR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘BiGGR’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BiGGR)

Tests output


Example timings

BiGGR.Rcheck/BiGGR-Ex.timings

nameusersystemelapsed
BiGGR-package1.9430.1962.139
E.coli_iAF12600.6530.0760.730
E.coli_iJR9040.4460.0440.492
E.coli_textbook0.0190.0040.024
H.pylori_ilT3410.1600.0040.164
H.sapiens_Recon11.2060.1241.329
M.barkeri_iAF6920.1630.0160.179
M.tuberculosis_iNJ6610.210.020.23
P.putida_iJN7460.2700.0230.292
Recon21.9410.2202.162
S.aureus_iSB6190.1950.0280.223
S.cerevisiae_iND7500.3180.0360.354
buildSBMLFromBiGG0.0680.0160.084
buildSBMLFromGenes4.4140.0924.506
buildSBMLFromPathways3.7340.0043.737
buildSBMLFromReactionIDs1.9900.0112.001
createLIMFromBiGG0.0710.0000.071
createLIMFromSBML0.8310.0080.838
extractGeneAssociations2.0910.0082.098
extractPathways2.1850.0082.218
getPathwaysForSBML2.2600.0082.268
getRates0.0000.0030.004
gprMapping104.262 0.190104.467
gprMappingAvg13.375 0.03213.409
lying.tunell.data0.0020.0000.003
rmvSpliceVariant2.0760.0072.084
sampleFluxEnsemble1.9020.0401.942
sbml2hyperdraw1.7810.0041.785