MiKTeX compatibility issue on Windows #69
Comments
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Thanks a lot @hpages for taking the time to look into this! I have removed the patch as this has been a temporary solution anyway. Cheers, |
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Thanks Andrzej! |
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Note: it's important to realize that on Ubuntu 16.04 LTS (still used by many people, including me), TeX Live still contains the broken titlesec 2.10.1 so people building Sweave vignettes with |
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Thanks @hpages for the follow up. In order to debug this I will probably need to replicate the problem on a Windows machine. Did you encounter the issue on any other systems? |
aoles
changed the title
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I didn't encounter the issue on other systems. But I wouldn't be surprised if the issue were reproducible on any system where all the TeX/LaTeX packages are at their most current version (which is what you get by installing a fresh MiKTeX on Windows). However, on Linux and Mac, TeX/LaTeX packages are typically lagging a few months/years behind their most current version. |
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@aoles @hpages Just a heads up, this still happening on Windows. I'm trying to troubleshoot some workaround solutions to this in my GH Action, https://github.com/neurogenomics/GenomicRanges/actions/runs/3718719179/jobs/6336709056#step:4:3173 Would be much appreciated to have |
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In the meantime, is there a way I can list out all the latex libraries i need for BiocStyle to work with Sweave files? That way I can at least install them myself all in one go. |
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Very speculative -- I think I have seen tinytex iterate through errors and installations until all errors are resolved. I didn't ask it to do that and I don't know how to demonstrate it but it may be worth a look if you are not already using tinytex. |
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As for listing the requirements I would love to know how to do that but I am not sure it is possible. |
Probably not the best long-term solution (in case things change), but could just make a new function that spits out a character vector of these: |
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Yes, that's helpful. I wonder whether the bioc build system has a list of all relevant tex libraries. @jwokaty |
You can also add For example, if I make the start of in the BiocStyle Rnw vignette: %\VignetteIndexEntry{Bioconductor LaTeX Style 2.0}
%\VignettePackage{BiocStyle}
%\VignetteEngine{utils::Sweave}
\documentclass{article}
\listfiles
<<style, eval=TRUE, echo=FALSE, results=tex>>=
BiocStyle::latex()
@ The |
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Please note that a list of LaTeX packages loaded directly in BiocStyle style file can be found in Appendix B of Bioconductor LaTeX Style 2.0 vignette. The list seems to have quite some overlap with the one posted in here by @lgatto. |
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@vjcitn We don't have a list for Windows machines. Is this the same issue originally reported or a different issue, where MikTeX wants an update, which is what I see when looking at |
I believe it's the same latex deps as the other platforms. I got it working on all 3 OS with these extra steps in my GH action (lines 183-201), thanks to @lgatto (#15): So I think it should be pretty straightforward adding a function to Next step after that would be ensuring |
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Thanks @bschilder . We will discuss how to manage this internally and then come back to this issue. |
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Just checking in to see if anyone has tried to address this since. |
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To give you an update, the dev branch of the This provides a static list of latex deps that are needed by It would be even better to pull this list of latex deps from an up-to-date remote source: e.g. a text file stored somewhere in the @aoles provided a link to a PDF with some of these deps, and I can see some of them are scattered throughout this inst/resources file. But it would be great to have a simple machine-readable text file I could pull into Thanks! |
After a fresh reinstall of MiKTeX on tokay2 (BioC devel Windows builder), we started to see hundreds of vignettes failing with:
This seems to affect all Sweave vignettes using
BiocStyle::latex(). Unfortunately the long error message displayed byR CMD buildcontains nothing useful, which is the reason why tokay2 has been temporarily taken off the daily build report for BioC 3.11: https://bioconductor.org/checkResults/3.11/bioc-LATEST/After a long and painful investigation, it turns out that getting rid of the following patch in BiocStyle fixes the issue:
BiocStyle/inst/resources/tex/Bioconductor.sty
Lines 92 to 100 in 0c3a2af
While investigating the whole thing I came across the following document that warns against using the
\makeatletterand\makeatothercommands within .sty or .cls files. Could this be the problem? (I'm not a TeX/LaTeX expert.)Anyway, after the fresh MiKTeX reinstall on tokay2, we now have titlesec 2.13 there. Some quick testing seems to indicate that this new version of titlesec addresses the original problem (loss of section numbering) introduced in titlesec 2.10.1. Also the version of titlesec that is currently on malbec2 and celaya2 (BioC devel Linux and Mac builders, respectively) is 2.10.2 and doesn't seem to have this problem either. So if the above patch cannot be fixed (i.e. preserved but modified so vignettes can build with the latest MiKTeX), an easy way out would be to just get rid of it.
Thanks,
H.
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