Closed MathewBiddle closed 3 weeks ago
this shouldn't take 30 mins!
The blocker here is that we are installing all of the libraries we use in the example applications. https://github.com/ioos/bio_data_guide/blob/db45e96601160e947fa0ee9ae396348efb703c6c/.github/workflows/deploy_bookdown.yml#L31-L35
Is there a way to just simply build the book from the .Rmd
without the requirement of all the nuanced libraries being installed?
https://github.com/ioos/bio_data_guide/blob/db45e96601160e947fa0ee9ae396348efb703c6c/.github/workflows/deploy_bookdown.yml#L46
I seem to recall some options that might be available to not have to install the libraries everytime https://bookdown.org/yihui/rmarkdown-cookbook/
There are github actions that help manage dependencies & do caching [ref]. I think the first step towards doing this is to move the dependency list into a DESCRIPTION file.
* checking for file ‘/private/var/folders/m4/5dz5h26x329cqq4fx333f8gm0000gn/T/Rtmp77vAAO/remotesf253130af5c/iobis-obistools-9df1c36/DESCRIPTION’ ... OK
* preparing ‘obistools’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘obistools_0.1.0.tar.gz’
Installing package into ‘/Users/runner/work/_temp/Library’
(as ‘lib’ is unspecified)
ERROR: dependencies ‘httr’, ‘leaflet’, ‘sf’, ‘terra’ are not available for package ‘obistools’
* removing ‘/Users/runner/work/_temp/Library/obistools’
Warning messages:
1: In i.p(...) :
installation of package ‘openssl’ had non-zero exit status
2: In i.p(...) : installation of package ‘terra’ had non-zero exit status
3: In i.p(...) : installation of package ‘units’ had non-zero exit status
4: In i.p(...) : installation of package ‘s2’ had non-zero exit status
5: In i.p(...) : installation of package ‘httr’ had non-zero exit status
6: In i.p(...) : installation of package ‘raster’ had non-zero exit status
7: In i.p(...) : installation of package ‘sf’ had non-zero exit status
8: In i.p(...) :
installation of package ‘leaflet’ had non-zero exit status
9: In i.p(...) :
installation of package ‘/var/folders/m4/5dz5h26x329cqq4fx333f8gm0000gn/T//Rtmp77vAAO/filef256b28f40a/obistools_0.1.0.tar.gz’ had non-zero exit status
trying URL 'https://yihui.org/tinytex/TinyTeX-1.tgz'
Content type 'application/octet-stream' length 112507857 bytes (107.3 MB)
Looks like we're missing a few libraries to make obistools
work. I'll try adding them and see where we get.
I'm also wondering if it should be ported over to quarto as that might be easier to manage and limit dependencies.
Hi @MathewBiddle ,
I started fiddling with this in a fork bbest/bio_data_guide, but the Github Action isn't firing when I push commits to test it. If you give me privileges in this repo I can try to make the GH Action work and have experience with switching to Quarto too.
Thanks, @bbest! I finally got the action to work after adding a bunch of new packages to the GH Action - install step. It still takes 23 minutes to install, build, and publish the rbookdown.
Action Run: https://github.com/ioos/bio_data_guide/actions/runs/10704923264 Changes I made: https://github.com/ioos/bio_data_guide/compare/99f04e2fb74f2f3b0b21dbadd2ca37fea75bf0d1..main#diff-d9e9c628038e6474c0572aad848b58690c7222f3092b90aa09d0c3cb11e194ccL32
The current settings should allow you to submit PRs and the Actions will run. Can you advise on the additional privileges you need?
Hi @MathewBiddle,
I should've forked from ioos/bio_data_guide
, but did make considerable progress with a fully functional Quarto book (generating html/pdf/epub) that renders in 3.5 minutes with this pull request:
We are live now! Thanks @bbest for this significant contribution!
https://github.com/ioos/bio_data_guide/actions/runs/8804894787/job/24166283620#step:5:1