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Update tex packages needed for knitting Rmd files to PDF #721

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merged 7 commits into from
Nov 3, 2023

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yuvipanda
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@yuvipanda yuvipanda commented Nov 2, 2023

If I create a new Rmarkdown file and try to knit to PDF, it has to install a big bunch of packages (which sometimes seems to take minutes, at least on my laptop) before it can actually knit. And this seems to happen each time the container starts.

My guess is that the list of tex packages needed for rmd -> pdf knitting to work has just increased over time.

I've added all the packages that were manually installed, by just looking at the 'render' tab in RStudio as installation was happening, and adding them. They are sorted alphabetically.

I've removed any packages here that were also present in install_jupyter.sh to avoid duplication.

Output from render tab indicating the packages that were being installed
processing file: t.Rmd

output file: t.knit.md

running mktexlsr ...
done running mktexlsr.
tlmgr: package log updated: /opt/texlive/texmf-var/web2c/tlmgr.log
tlmgr: command log updated: /opt/texlive/texmf-var/web2c/tlmgr-commands.log
tlmgr update --all --self
tlmgr: package repository https://www.texlive.info/tlnet-archive/2023/10/30/tlnet (not verified: gpg unavailable)
tlmgr install: package already present: texlive-scripts
[1/1, ??:??/??:??] install: ec [258k]
running mktexlsr ...
done running mktexlsr.
tlmgr: package log updated: /opt/texlive/texmf-var/web2c/tlmgr.log
tlmgr: command log updated: /opt/texlive/texmf-var/web2c/tlmgr-commands.log
tlmgr: package repository https://www.texlive.info/tlnet-archive/2023/10/30/tlnet (not verified: gpg unavailable)
[1/1, ??:??/??:??] install: kvoptions [8k]
running mktexlsr ...
done running mktexlsr.
tlmgr: package log updated: /opt/texlive/texmf-var/web2c/tlmgr.log
tlmgr: command log updated: /opt/texlive/texmf-var/web2c/tlmgr-commands.log
tlmgr: package repository https://www.texlive.info/tlnet-archive/2023/10/30/tlnet (not verified: gpg unavailable)
[1/1, ??:??/??:??] install: ltxcmds [5k]
running mktexlsr ...
done running mktexlsr.
tlmgr: package log updated: /opt/texlive/texmf-var/web2c/tlmgr.log
tlmgr: command log updated: /opt/texlive/texmf-var/web2c/tlmgr-commands.log
tlmgr: package repository https://www.texlive.info/tlnet-archive/2023/10/30/tlnet (not verified: gpg unavailable)
[1/1, ??:??/??:??] install: kvsetkeys [4k]
running mktexlsr ...
done running mktexlsr.
tlmgr: package log updated: /opt/texlive/texmf-var/web2c/tlmgr.log
tlmgr: command log updated: /opt/texlive/texmf-var/web2c/tlmgr-commands.log
tlmgr: package repository https://www.texlive.info/tlnet-archive/2023/10/30/tlnet (not verified: gpg unavailable)
[1/1, ??:??/??:??] install: etoolbox [9k]
running mktexlsr ...
done running mktexlsr.
tlmgr: package log updated: /opt/texlive/texmf-var/web2c/tlmgr.log
tlmgr: command log updated: /opt/texlive/texmf-var/web2c/tlmgr-commands.log
tlmgr: package repository https://www.texlive.info/tlnet-archive/2023/10/30/tlnet (not verified: gpg unavailable)
[1/1, ??:??/??:??] install: xcolor [17k]
running mktexlsr ...
done running mktexlsr.
tlmgr: package log updated: /opt/texlive/texmf-var/web2c/tlmgr.log
tlmgr: command log updated: /opt/texlive/texmf-var/web2c/tlmgr-commands.log
tlmgr: package repository https://www.texlive.info/tlnet-archive/2023/10/30/tlnet (not verified: gpg unavailable)
[1/1, ??:??/??:??] install: geometry [9k]
running mktexlsr ...
done running mktexlsr.
tlmgr: package log updated: /opt/texlive/texmf-var/web2c/tlmgr.log
tlmgr: command log updated: /opt/texlive/texmf-var/web2c/tlmgr-commands.log
tlmgr: package repository https://www.texlive.info/tlnet-archive/2023/10/30/tlnet (not verified: gpg unavailable)
[1/1, ??:??/??:??] install: fancyvrb [12k]
running mktexlsr ...
done running mktexlsr.
tlmgr: package log updated: /opt/texlive/texmf-var/web2c/tlmgr.log
tlmgr: command log updated: /opt/texlive/texmf-var/web2c/tlmgr-commands.log
tlmgr: package repository https://www.texlive.info/tlnet-archive/2023/10/30/tlnet (not verified: gpg unavailable)
[1/1, ??:??/??:??] install: framed [8k]
running mktexlsr ...
done running mktexlsr.
tlmgr: package log updated: /opt/texlive/texmf-var/web2c/tlmgr.log
tlmgr: command log updated: /opt/texlive/texmf-var/web2c/tlmgr-commands.log
tlmgr: package repository https://www.texlive.info/tlnet-archive/2023/10/30/tlnet (not verified: gpg unavailable)
[1/16, ??:??/??:??] install: auxhook [2k]
[2/16, 00:01/02:04] install: bigintcalc [7k]
[3/16, 00:03/01:15] install: bitset [6k]
[4/16, 00:05/01:14] install: etexcmds [3k]
[5/16, 00:06/01:15] install: gettitlestring [3k]
[6/16, 00:08/01:26] install: hycolor [4k]
[7/16, 00:10/01:29] install: hyperref [89k]
[8/16, 00:12/00:21] install: intcalc [6k]
[9/16, 00:14/00:24] install: kvdefinekeys [3k]
[10/16, 00:16/00:27] install: letltxmacro [3k]
[11/16, 00:17/00:28] install: pdfescape [5k]
[12/16, 00:19/00:30] install: refcount [3k]
[13/16, 00:21/00:33] install: rerunfilecheck [4k]
[14/16, 00:22/00:33] install: stringenc [23k]
[15/16, 00:24/00:31] install: uniquecounter [3k]
[16/16, 00:26/00:33] install: zapfding [46k]
running mktexlsr ...
done running mktexlsr.
running updmap-sys ...
done running updmap-sys.
tlmgr: package log updated: /opt/texlive/texmf-var/web2c/tlmgr.log
tlmgr: command log updated: /opt/texlive/texmf-var/web2c/tlmgr-commands.log
tlmgr: package repository https://www.texlive.info/tlnet-archive/2023/10/30/tlnet (not verified: gpg unavailable)
[1/1, ??:??/??:??] install: pdftexcmds [7k]
running mktexlsr ...
done running mktexlsr.
tlmgr: package log updated: /opt/texlive/texmf-var/web2c/tlmgr.log
tlmgr: command log updated: /opt/texlive/texmf-var/web2c/tlmgr-commands.log
tlmgr: package repository https://www.texlive.info/tlnet-archive/2023/10/30/tlnet (not verified: gpg unavailable)
[1/1, ??:??/??:??] install: infwarerr [3k]
running mktexlsr ...
done running mktexlsr.
tlmgr: package log updated: /opt/texlive/texmf-var/web2c/tlmgr.log
tlmgr: command log updated: /opt/texlive/texmf-var/web2c/tlmgr-commands.log
tlmgr: package repository https://www.texlive.info/tlnet-archive/2023/10/30/tlnet (not verified: gpg unavailable)
[1/1, ??:??/??:??] install: epstopdf-pkg [5k]
running mktexlsr ...
done running mktexlsr.
tlmgr: package log updated: /opt/texlive/texmf-var/web2c/tlmgr.log
tlmgr: command log updated: /opt/texlive/texmf-var/web2c/tlmgr-commands.log

Output created: t.pdf

If I create a new Rmarkdown file and try to knit to PDF,
it has to install a big bunch of packages (which sometimes seems
to take minutes, at least on my laptop) before it can actually
knit. And this seems to happen each time the container starts.

My guess is that the list of tex packages needed for rmd -> pdf
knitting to work has just increased over time.

I've added all the packages that were manually installed, by
just looking at the 'render' tab in RStudio as installation
was happening, and adding them. They are sorted alphabetically.

I've removed any packages here that were also present in
`install_jupyter.sh` to avoid duplication.
@cboettig
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cboettig commented Nov 3, 2023

nice, this list looks good to me!

@cboettig cboettig self-requested a review November 3, 2023 03:47
@eitsupi
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eitsupi commented Nov 3, 2023

Could you explain why you want avoiding duplication?
Given the possibility of installing tlmgr in other ways, it would be not a good idea to remove duplicate packages from install_jupyter.

yuvipanda added a commit to yuvipanda/rocker-versioned2 that referenced this pull request Nov 3, 2023
@yuvipanda
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@eitsupi I've removed the changes to install_jupyter.sh

@yuvipanda
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@eitsupi the build failure now just looks like an intermittent network issue.

Once this is merged, would you be so kind as to trigger a rebuild? Thanks.

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eitsupi commented Nov 3, 2023

Could you update the NEWS?

@yuvipanda
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@eitsupi done

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eitsupi commented Nov 3, 2023

Once this is merged, would you be so kind as to trigger a rebuild?

Since #722 triggers the rebuild, we only have to wait for the #722 merge :)

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Thanks!

@eitsupi eitsupi merged commit 4e1bb7f into rocker-org:master Nov 3, 2023
@yuvipanda
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Thanks for the quick review, @eitsupi

@yuvipanda
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@eitsupi I see #722 has been merged! I can't seem to find a rebuild in the actions tab nor a new image in dockerhub - what am I missing?

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eitsupi commented Nov 6, 2023

@yuvipanda #722 created #723 and #723 triggered a build, I think.

yuvipanda added a commit to 2i2c-org/utoronto-r-image that referenced this pull request Nov 6, 2023
- Brings us to latest point release of R
- Brings in rocker-org/rocker-versioned2#721

Ref 2i2c-org/infrastructure#3178
yuvipanda added a commit to yuvipanda/rocker-versioned2 that referenced this pull request Jan 2, 2024
Follow-up to rocker-org#721,
adding tlmgr packages that *quarto* seems to need to knit to PDF.
Without these, it takes a minute or more (depending on network)
for first knit to happen apparently.

Reported to me by users from University of Toronto
eitsupi pushed a commit that referenced this pull request Jan 11, 2024
Follow-up to #721,
adding tlmgr packages that *quarto* seems to need to knit to PDF.
Without these, it takes a minute or more (depending on network) for
first knit to happen apparently.

Reported to me by users from University of Toronto
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3 participants