I can also reproduce the error locally on my laptop Ubuntu 18.04.5, R version 4.0.5 Patched (2021-03-31 r80152), Bioc 3.12.
Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ________________________________ From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Herv� Pag�s <hpages.on.git...@gmail.com> Sent: Wednesday, April 21, 2021 2:00 AM To: Mark Pinese <mpin...@ccia.org.au>; bioc-devel@r-project.org <bioc-devel@r-project.org> Subject: Re: [Bioc-devel] Cannot reproduce "TeX capacity exceeded" error on build hosts (package messina) Hi Mark, I can reproduce this on my laptop (Ubuntu 20.10, R 4.0.3, BioC 3.12): hpages@spectre:~/git.bioconductor.org/software$ time brelbuild messina * checking for file �messina/DESCRIPTION� ... OK * preparing �messina�: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes * creating vignettes ... ERROR --- re-building �messina.Rnw� using knitr Loading required package: survival Loading required package: Biobase Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Error: processing vignette 'messina.Rnw' failed with diagnostics: Running 'texi2dvi' on 'messina.tex' failed. LaTeX errors: ! TeX capacity exceeded, sorry [main memory size=5000000]. l.32169 If you really absolutely need more capacity, you can ask a wizard to enlarge me. ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building �messina.Rnw� SUMMARY: processing the following file failed: �messina.Rnw� Error: Vignette re-building failed. Execution halted real 2m40.464s user 2m38.072s sys 0m1.776s I'm surprised you can't reproduce this. What platform are you on? My understanding is that the Docker images were intentionally kept light so this is why they don't have TeX/LaTeX and other things needed to run 'R CMD build' on a package. Since we see the error in release and devel, I suspected a change in a CRAN package involved in the vignette knitting process. I tried to downgrade knitr from 1.32 to 1.31 but that didn't solve the problem. Then I downgraded xfun from 0.22 to 0.21 but that didn't help either. So I gave up. Sorry for not being able to help more. Best, H. On 4/20/21 6:17 PM, Mark Pinese wrote: > Hi all, > > My package messina has recently started failing on all build platforms, eg > https://secure-web.cisco.com/1iNAEmxW_NMxwnEIs_OdNqw1U28YG6RTA_d4Qj80AB8xPF2WAj4JoGuuPYrFJsE5BRToE2jh0rPYFN3EPb7NkzShrBmIn6skNzneNzD1t63RBm10h01pMeahxJeDOXmWqmbDHabJeSFu5yOPzAiUeH75sAzyo1Sy9L1Zc5fRhsDmxP1ZBn0nmV4QJRWV2wsxqN_B7HXaghk_26sDQGBvy3JvXscFsr3sNFAnUZwdohPI4pP1XyzHmLxK2Oi_g0nLd70J_KnlyS9wz6hSgAYY1VSEiZgTV_FKqnYIkoJYfAfUPNnL8vktDPqLr3dCwMtOv/https%3A%2F%2Fmaster.bioconductor.org%2FcheckResults%2F3.12%2Fbioc-LATEST%2Fmessina%2Fmalbec1-buildsrc.html > This seems due to a "TeX capacity exceeded" error, though I suspect that > something upstream is the true culprit. > > To debug I have tried to reproduce this locally with BioC 3.12 on R 4.0.3 > (both clean installs), but I cannot reproduce the problem. Locally the build > works without issues for me: > > source ~/.Renv_biocbuild > R CMD build ~/repos/messina/ > * checking for file �~repos/messina/DESCRIPTION� ... OK > * preparing �messina�: > * checking DESCRIPTION meta-information ... OK > * cleaning src > * installing the package to build vignettes > * creating vignettes ... OK > * cleaning src > * checking for LF line-endings in source and make files and shell scripts > * checking for empty or unneeded directories > * looking to see if a �data/datalist� file should be added > * building �messina_1.23.1.tar.gz� > > Can anyone offer suggestions on how to reproduce the error as seen on the > build environments? Something like a docker image matching the build > environments would be ideal. I tried the image > bioconductor/bioconductor_docker:devel, but I needed to install quite a few > build dependencies, so I suspect this image doesn't match the build envs. > > > Many thanks, > > Mark > > > Mark Pinese > > Senior Bioinformatics Research Officer > Conjoint Senior Lecturer, School of Women�s and Children�s Health, UNSW > Medicine > NHMRC Emerging Leadership Fellow > > Children's Cancer Institute > Lowy Cancer Research Centre, UNSW Australia > PO Box 81 Randwick 2031 Australia > > E: mpin...@ccia.org.au | W: www.ccia.org.au<http://www.ccia.org.au> > > > > > > > > > > > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://secure-web.cisco.com/1onVAfZj3SbghVX3o7wQGJzOm2gIC_Gs1FDTfjh3-4tftOPw5cILEty4iUtnyKOMBvluYEs4qiAhILr9L4mmGEtDZS9FF40TuMEjt_uNQOxn84klDiOlmj2S72kDhZlQiOMClwdIKGCKzIGJyAmXfhAONjqxwlcX2qu-qJPPY87qACPWj0er2Z3cxugIteYyHRU-XRH_W44HLH6MhJ9eXPlbMAh-22grL5IR0F60rQTnr7kqSaWrGn1bEbEDPgUm8a6GvCSEEYY2ua5tcjYEzZWYneN2F1NwW1_7bKl2dA58toq3G28yM7_-swFvkhgPE/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel > -- Herv� Pag�s Bioconductor Core Team hpages.on.git...@gmail.com _______________________________________________ Bioc-devel@r-project.org mailing list https://secure-web.cisco.com/1onVAfZj3SbghVX3o7wQGJzOm2gIC_Gs1FDTfjh3-4tftOPw5cILEty4iUtnyKOMBvluYEs4qiAhILr9L4mmGEtDZS9FF40TuMEjt_uNQOxn84klDiOlmj2S72kDhZlQiOMClwdIKGCKzIGJyAmXfhAONjqxwlcX2qu-qJPPY87qACPWj0er2Z3cxugIteYyHRU-XRH_W44HLH6MhJ9eXPlbMAh-22grL5IR0F60rQTnr7kqSaWrGn1bEbEDPgUm8a6GvCSEEYY2ua5tcjYEzZWYneN2F1NwW1_7bKl2dA58toq3G28yM7_-swFvkhgPE/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel This email message may contain legally privileged and/or confidential information. 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