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.sheph...@roswellpark.org>
*Sent:* Wednesday, 21 April 2021 9:31 PM
*To:* Hervé Pagès <hpages.on.git...@gmail.com>; 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)
EXTERNAL EMAIL: Think before you click. If suspicious send to
cyberrep...@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-boun...@r-project.org> on behalf of Hervé
Pagès <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
<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>
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Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
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