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This page was generated on 2023-10-16 11:35:56 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 162/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiGGR 1.36.0  (landing page)
Anand K. Gavai
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/BiGGR
git_branch: RELEASE_3_17
git_last_commit: b43bbd0
git_last_commit_date: 2023-04-25 10:28:32 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64... NOT SUPPORTED ...
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for BiGGR on palomino3


To the developers/maintainers of the BiGGR package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: BiGGR
Version: 1.36.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BiGGR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings BiGGR_1.36.0.tar.gz
StartedAt: 2023-10-15 23:49:02 -0400 (Sun, 15 Oct 2023)
EndedAt: 2023-10-15 23:53:30 -0400 (Sun, 15 Oct 2023)
EllapsedTime: 267.7 seconds
RetCode: 0
Status:   OK  
CheckDir: BiGGR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BiGGR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings BiGGR_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/BiGGR.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BiGGR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BiGGR' version '1.36.0'
* 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 ... 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 sizes of PDF files under 'inst/doc' ... 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         126.67   2.04  129.13
gprMappingAvg       13.88   1.01   14.90
buildSBMLFromGenes   4.65   0.67    5.33
* 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
  'F:/biocbuild/bbs-3.17-bioc/meat/BiGGR.Rcheck/00check.log'
for details.



Installation output

BiGGR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL BiGGR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-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-package2.390.222.66
E.coli_iAF12600.950.191.14
E.coli_iJR9040.260.000.27
E.coli_textbook0.050.150.20
H.pylori_ilT3410.180.130.29
H.sapiens_Recon11.090.141.24
M.barkeri_iAF6920.330.340.67
M.tuberculosis_iNJ6610.260.140.41
P.putida_iJN7460.300.140.43
Recon21.610.131.74
S.aureus_iSB6190.270.090.36
S.cerevisiae_iND7500.310.110.42
buildSBMLFromBiGG0.090.020.11
buildSBMLFromGenes4.650.675.33
buildSBMLFromPathways3.280.123.40
buildSBMLFromReactionIDs1.520.001.52
createLIMFromBiGG0.060.000.08
createLIMFromSBML0.840.100.94
extractGeneAssociations1.780.011.79
extractPathways1.780.001.78
getPathwaysForSBML3.150.013.16
getRates000
gprMapping126.67 2.04129.13
gprMappingAvg13.88 1.0114.90
lying.tunell.data0.000.020.02
rmvSpliceVariant2.120.032.15
sampleFluxEnsemble2.020.652.68
sbml2hyperdraw2.670.042.70