[Bioc-devel] Cannot reproduce "TeX capacity exceeded" error on build hosts (package messina)

Wed Apr 21 13:31:58 CEST 2021

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 Herv� Pag�s <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 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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--
Herv� Pag�s

Bioconductor Core Team
hpages.on.github using gmail.com

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