[Bioc-devel] Cannot reproduce "TeX capacity exceeded" error on build hosts (package messina)
Hervé Pagès
hp@ge@@on@g|thub @end|ng |rom gm@||@com
Fri May 14 06:30:14 CEST 2021
Thanks Mark for the update and for the detailed explanations.
Best,
H.
On 13/05/2021 16:15, Mark Pinese wrote:
> Thank you both, with your help I managed to reproduce the error, and
> it's now fixed.
>
> If anyone else runs into a similar issue:
>
> 1. The core issue was due to a deprecation warning (specifically
> regarding survival::survConcordance.fit). During vignette generation
> a very large number of deprecation warnings were thrown, which
> overloaded TeX. Changing the survival::survConcordance.fit call to
> the updated survival::concordancefit fixed the problem.
> 2. The cause of the reproducibility issue is less clear. I initially
> tested using Ubuntu 20.04 LTS running on Windows through WSL, which
> seemed to work. However, subsequent tests on a true Ubuntu 20.04
> Linux machine failed. My tentative conclusion is that Ubuntu 20.04
> LTS running through WSL is not the most reliable build host for BioC
> packages.
>
>
> Best wishes,
>
> Mark
> ------------------------------------------------------------------------
> *From:* Kern, Lori <Lori.Shepherd using RoswellPark.org>
> *Sent:* Wednesday, 21 April 2021 9:31 PM
> *To:* Hervé Pagès <hpages.on.github using gmail.com>; Mark Pinese
> <MPinese using ccia.org.au>; bioc-devel using r-project.org <bioc-devel using r-project.org>
> *Subject:* Re: [Bioc-devel] Cannot reproduce "TeX capacity exceeded"
> error on build hosts (package messina)
>
> EXTERNAL EMAIL: Think before you click. If suspicious send to
> CyberReport using ccia.org.au.
>
> 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-bounces using r-project.org> on behalf of Hervé
> Pagès <hpages.on.github using gmail.com>
> *Sent:* Wednesday, April 21, 2021 2:00 AM
> *To:* Mark Pinese <MPinese using ccia.org.au>; bioc-devel using r-project.org
> <bioc-devel using 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 using 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
> <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: MPinese using ccia.org.au | W: www.ccia.org.au <http://www.ccia.org.au>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
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> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.github using gmail.com
>
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--
Hervé Pagès
Bioconductor Core Team
hpages.on.github using gmail.com
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