Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:58 -0400 (Fri, 15 Oct 2021).
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. |
Package 149/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BiGGR 1.28.0 (landing page) Anand K. Gavai
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | ... NOT SUPPORTED ... | ||||||||||||
Package: BiGGR |
Version: 1.28.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:BiGGR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BiGGR_1.28.0.tar.gz |
StartedAt: 2021-10-14 20:03:19 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 20:07:56 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 276.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BiGGR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:BiGGR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BiGGR_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/BiGGR.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * 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 whether package 'BiGGR' can be installed ... OK * checking installed package size ... NOTE installed size is 5.1Mb sub-directories of 1Mb or more: data 3.8Mb * 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 122.00 0.01 122.23 gprMappingAvg 12.94 0.00 12.94 buildSBMLFromGenes 4.78 0.26 5.05 * 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: 4 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/BiGGR.Rcheck/00check.log' for details.
BiGGR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch BiGGR ### ############################################################################## ############################################################################## * installing to library 'C:/Users/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 converting help for package 'BiGGR' finding HTML links ... done BiGGR-internal html BiGGR-package html E.coli_iAF1260 html E.coli_iJR904 html E.coli_textbook html Glycolysis html H.pylori_ilT341 html H.sapiens_Recon1 html M.barkeri_iAF692 html M.tuberculosis_iNJ661 html P.putida_iJN746 html Recon2 html S.aureus_iSB619 html S.cerevisiae_iND750 html buildSBMLFromBiGG html buildSBMLFromGenes html finding level-2 HTML links ... done buildSBMLFromPathways html buildSBMLFromReactionIDs html createLIMFromBiGG html createLIMFromSBML html extractGeneAssociations html extractPathways html getPathwaysForSBML html getRates html gprMapping html gprMappingAvg html lying.tunell.data html rmvSpliceVariant html sampleFluxEnsemble html sbml2hyperdraw html ** 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) Making 'packages.html' ... done
BiGGR.Rcheck/BiGGR-Ex.timings
name | user | system | elapsed | |
BiGGR-package | 1.97 | 0.13 | 2.09 | |
E.coli_iAF1260 | 0.58 | 0.09 | 0.68 | |
E.coli_iJR904 | 0.56 | 0.02 | 0.58 | |
E.coli_textbook | 0.04 | 0.07 | 0.11 | |
H.pylori_ilT341 | 0.17 | 0.07 | 0.23 | |
H.sapiens_Recon1 | 0.98 | 0.04 | 1.03 | |
M.barkeri_iAF692 | 0.19 | 0.16 | 0.35 | |
M.tuberculosis_iNJ661 | 0.26 | 0.06 | 0.33 | |
P.putida_iJN746 | 0.49 | 0.08 | 0.56 | |
Recon2 | 1.71 | 0.02 | 1.72 | |
S.aureus_iSB619 | 0.23 | 0.03 | 0.26 | |
S.cerevisiae_iND750 | 0.27 | 0.07 | 0.33 | |
buildSBMLFromBiGG | 0.09 | 0.03 | 0.16 | |
buildSBMLFromGenes | 4.78 | 0.26 | 5.05 | |
buildSBMLFromPathways | 3.67 | 0.02 | 3.68 | |
buildSBMLFromReactionIDs | 1.41 | 0.00 | 1.41 | |
createLIMFromBiGG | 0.08 | 0.00 | 0.08 | |
createLIMFromSBML | 1.23 | 0.06 | 1.29 | |
extractGeneAssociations | 2.36 | 0.02 | 2.38 | |
extractPathways | 1.97 | 0.00 | 1.97 | |
getPathwaysForSBML | 2.35 | 0.00 | 2.34 | |
getRates | 0.01 | 0.00 | 0.02 | |
gprMapping | 122.00 | 0.01 | 122.23 | |
gprMappingAvg | 12.94 | 0.00 | 12.94 | |
lying.tunell.data | 0 | 0 | 0 | |
rmvSpliceVariant | 1.99 | 0.00 | 1.98 | |
sampleFluxEnsemble | 2.20 | 0.17 | 2.39 | |
sbml2hyperdraw | 2.63 | 0.00 | 2.75 | |