Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-24 09:03 -0400 (Wed, 24 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4747 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4467 |
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 166/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BiGGR 1.40.0 (landing page) Anand K. Gavai
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | ... NOT SUPPORTED ... | ||||||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | ... NOT SUPPORTED ... | ||||||||||||
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. |
Package: BiGGR |
Version: 1.40.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BiGGR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BiGGR_1.40.0.tar.gz |
StartedAt: 2024-07-21 22:02:43 -0400 (Sun, 21 Jul 2024) |
EndedAt: 2024-07-21 22:06:39 -0400 (Sun, 21 Jul 2024) |
EllapsedTime: 236.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BiGGR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BiGGR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BiGGR_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/BiGGR.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘BiGGR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BiGGR’ version ‘1.40.0’ * 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 code 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 loading without being on the library search path ... 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 113.752 0.723 114.482 gprMappingAvg 13.246 0.060 13.306 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/BiGGR.Rcheck/00check.log’ for details.
BiGGR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL BiGGR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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)
BiGGR.Rcheck/BiGGR-Ex.timings
name | user | system | elapsed | |
BiGGR-package | 1.968 | 0.075 | 2.043 | |
E.coli_iAF1260 | 0.612 | 0.032 | 0.645 | |
E.coli_iJR904 | 0.270 | 0.020 | 0.289 | |
E.coli_textbook | 0.020 | 0.002 | 0.022 | |
H.pylori_ilT341 | 0.141 | 0.009 | 0.150 | |
H.sapiens_Recon1 | 1.234 | 0.084 | 1.317 | |
M.barkeri_iAF692 | 0.197 | 0.008 | 0.204 | |
M.tuberculosis_iNJ661 | 0.277 | 0.016 | 0.292 | |
P.putida_iJN746 | 0.308 | 0.012 | 0.319 | |
Recon2 | 1.803 | 0.212 | 2.015 | |
S.aureus_iSB619 | 0.198 | 0.024 | 0.222 | |
S.cerevisiae_iND750 | 0.338 | 0.024 | 0.363 | |
buildSBMLFromBiGG | 0.068 | 0.016 | 0.084 | |
buildSBMLFromGenes | 4.730 | 0.171 | 4.902 | |
buildSBMLFromPathways | 3.579 | 0.052 | 3.631 | |
buildSBMLFromReactionIDs | 1.621 | 0.056 | 1.677 | |
createLIMFromBiGG | 0.066 | 0.000 | 0.066 | |
createLIMFromSBML | 0.863 | 0.000 | 0.863 | |
extractGeneAssociations | 2.042 | 0.000 | 2.041 | |
extractPathways | 1.941 | 0.064 | 2.004 | |
getPathwaysForSBML | 2.314 | 0.008 | 2.323 | |
getRates | 0.003 | 0.000 | 0.004 | |
gprMapping | 113.752 | 0.723 | 114.482 | |
gprMappingAvg | 13.246 | 0.060 | 13.306 | |
lying.tunell.data | 0.002 | 0.000 | 0.002 | |
rmvSpliceVariant | 2.100 | 0.008 | 2.109 | |
sampleFluxEnsemble | 1.872 | 0.067 | 1.939 | |
sbml2hyperdraw | 1.810 | 0.004 | 1.814 | |