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This page was generated on 2021-10-22 12:03:55 -0400 (Fri, 22 Oct 2021).

CHECK results for BiGGR on nebbiolo2

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 147/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiGGR 1.29.0  (landing page)
Anand K. Gavai
Snapshot Date: 2021-10-21 14:50:08 -0400 (Thu, 21 Oct 2021)
git_url: https://git.bioconductor.org/packages/BiGGR
git_branch: master
git_last_commit: 9b0501a
git_last_commit_date: 2021-05-19 12:00:29 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64... NOT SUPPORTED ...

Summary

Package: BiGGR
Version: 1.29.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:BiGGR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings BiGGR_1.29.0.tar.gz
StartedAt: 2021-10-21 19:14:32 -0400 (Thu, 21 Oct 2021)
EndedAt: 2021-10-21 19:18:19 -0400 (Thu, 21 Oct 2021)
EllapsedTime: 227.3 seconds
RetCode: 0
Status:   OK  
CheckDir: BiGGR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:BiGGR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings BiGGR_1.29.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/BiGGR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.29.0’
* 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    111.526  0.200 111.728
gprMappingAvg  14.777  0.076  14.853
* 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-3.14-bioc/meat/BiGGR.Rcheck/00check.log’
for details.



Installation output

BiGGR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL BiGGR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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-package2.0290.0792.109
E.coli_iAF12600.6460.0200.665
E.coli_iJR9040.4590.0000.459
E.coli_textbook0.0240.0000.023
H.pylori_ilT3410.2640.0030.268
H.sapiens_Recon11.3980.2631.662
M.barkeri_iAF6920.1920.0040.196
M.tuberculosis_iNJ6610.4200.0070.428
P.putida_iJN7460.3660.0040.370
Recon22.1040.0952.200
S.aureus_iSB6190.2010.0080.209
S.cerevisiae_iND7500.3290.0000.328
buildSBMLFromBiGG0.0710.0160.088
buildSBMLFromGenes4.6120.0404.652
buildSBMLFromPathways3.7260.0083.734
buildSBMLFromReactionIDs1.9330.0041.937
createLIMFromBiGG0.0660.0000.066
createLIMFromSBML0.9070.0000.907
extractGeneAssociations2.0830.0042.086
extractPathways2.070.002.07
getPathwaysForSBML2.3690.0082.378
getRates0.0030.0000.002
gprMapping111.526 0.200111.728
gprMappingAvg14.777 0.07614.853
lying.tunell.data0.0010.0000.002
rmvSpliceVariant2.2750.0002.275
sampleFluxEnsemble1.7010.0671.770
sbml2hyperdraw2.3430.0042.347