Hello
I wanted to ask when the bioconductor packages that are available on bioconda will be updated to bioconductor version 3.20. It seems that all packages are currently on version 3.18 and it looks like they are all managed together. Does anybody know how this works or who is responsible for the bioconductor recipes on bioconda?
Thanks
jaimergp
November 27, 2024, 11:42am
2
Check bioconda/bioconda-recipes. Example search in their issues: Issue search results · GitHub
Ah thanks! i didn’t even think about that.
opened 10:16AM - 03 Aug 24 UTC
help wanted
## Preparation for R 4.4/Bioconductor 3.19
It looks like we'll cross the `r-ess… entials` milestone<sup>**1**</sup> for building R 4.4 on Conda Forge this weekend. This seems like a good point to start thinking about the transition of Bioconductor packages here to v3.19. To expedite this, it would be useful to identify required dependencies that need work to migrate. This helps those of us working on Conda Forge to focus our efforts.
This list should now be comprehensive thanks to [a helpful script from @aliciaaevans](https://github.com/bioconda/bioconda-recipes/pull/50209). However, feel free comment or check things off if you see they have completed. Updated info is available on [the Conda Forge Status page](https://conda-forge.org/status/migration/?name=r-base44_and_m2w64-ucrt).
## Problematic R 4.4 Migrations
> 📢 *Updated 2 September 2024 using [`missingCranPackages.py` script](https://github.com/bioconda/bioconda-recipes/pull/50209).*
## Awaiting migration of 62 packages ##
### In PR (20 packages) ###
> ***NB:** This is where the most help is needed!*
- [x] `r-infotheo`: In PR https://github.com/conda-forge/r-infotheo-feedstock/pull/13
- [x] `r-compositions`: In PR https://github.com/conda-forge/r-compositions-feedstock/pull/20
- [x] `r-rmariadb`: In PR https://github.com/conda-forge/r-rmariadb-feedstock/pull/25
- [x] `r-hdf5r`: In PR https://github.com/conda-forge/r-hdf5r-feedstock/pull/34
- [x] `r-pdftools`: In PR https://github.com/conda-forge/r-pdftools-feedstock/pull/48
- [x] `r-rcurl`: In PR https://github.com/conda-forge/r-rcurl-feedstock/pull/33
- [x] `r-rcppalgos`: In PR https://github.com/conda-forge/r-rcppalgos-feedstock/pull/16
- [x] `r-rmixmod`: In PR https://github.com/conda-forge/r-rmixmod-feedstock/pull/17
- [x] `r-git2r`: In PR https://github.com/conda-forge/r-git2r-feedstock/pull/44
- [x] `r-rttf2pt1`: In PR https://github.com/conda-forge/r-rttf2pt1-feedstock/pull/19
- [x] `r-wrswor`: In PR https://github.com/conda-forge/r-wrswor-feedstock/pull/2
- [x] `r-tiledb`: In PR https://github.com/conda-forge/r-tiledb-feedstock/pull/87
- [x] `r-cairo`: In PR https://github.com/conda-forge/r-cairo-feedstock/pull/39
- [x] `r-bold`: In PR https://github.com/conda-forge/r-bold-feedstock/pull/17
- [x] `r-scs`: In PR https://github.com/conda-forge/r-scs-feedstock/pull/5
- [x] `r-copula`: In PR https://github.com/conda-forge/r-copula-feedstock/pull/21
- [x] `r-strawr`: In PR https://github.com/conda-forge/r-strawr-feedstock/pull/4
- [x] `r-msqc`: In PR https://github.com/conda-forge/r-msqc-feedstock/pull/7
- [x] `r-primme`: In PR https://github.com/conda-forge/r-primme-feedstock/pull/17
- [x] `r-locfit`: In PR https://github.com/conda-forge/r-locfit-feedstock/pull/20
### Bot Error (4 packages) ###
> *Licenses have been packaged for these as of 9 Sept. and should start migration within ~24 hours.*
- [x] `r-rebus.unicode`: bot error (<a href="https://github.com/regro/cf-scripts/actions/runs/10660968384">bot CI job</a>): main: Error running migrate-feedstock in container - JSON could not parse stdout:
- [x] `r-rebus.datetimes`: bot error (<a href="https://github.com/regro/cf-scripts/actions/runs/10660968384">bot CI job</a>): main: Error running migrate-feedstock in container - JSON could not parse stdout:
- [x] `r-rebus.numbers`: bot error (<a href="https://github.com/regro/cf-scripts/actions/runs/10660016389">bot CI job</a>): main: Error running migrate-feedstock in container - JSON could not parse stdout:
- [x] `r-logr`: bot error (<a href="https://github.com/regro/cf-scripts/actions/runs/10660968384">bot CI job</a>): main: Error running migrate-feedstock in container - JSON could not parse stdout:
### Not Solvable (7 packages) ###
- [x] `r-spdep`: not solvable (<a href='https://github.com/regro/cf-scripts/actions/runs/10660968384'>bot CI job</a>) @ main r-sf * cannot be installed because there are no viable options
- [x] `r-magick`: not solvable (<a href='https://github.com/regro/cf-scripts/actions/runs/10660968384'>bot CI job</a>) @ main No candidates were found for imagemagick *.
- [x] `r-rmpi`: not solvable (<a href='https://github.com/regro/cf-scripts/actions/runs/10660968384'>bot CI job</a>) @ main No candidates were found for openmpi 5.*.
- [x] `r-transformr`: not solvable (<a href='https://github.com/regro/cf-scripts/actions/runs/10660968384'>bot CI job</a>) @ main r-sf * cannot be installed because there are no viable options
- [x] `r-protolite`: not solvable (<a href='https://github.com/regro/cf-scripts/actions/runs/10660968384'>bot CI job</a>) @ main r-sf * cannot be installed because there are no viable options
- [x] `r-gstat`: not solvable (<a href='https://github.com/regro/cf-scripts/actions/runs/10660968384'>bot CI job</a>) @ main r-sf >=0.7_2 cannot be installed because there are no viable options
- [x] `r-tkrplot`: not solvable (<a href='https://github.com/regro/cf-scripts/actions/runs/10660968384'>bot CI job</a>) @ main No candidates were found for tcl *.
### Awaiting Parents (31 packages) ###
- [x] `r-qdaptools`: Awaiting parents ( r-rcurl )
- [x] `r-summarytools`: Awaiting parents ( r-magick )
- [x] `r-tidytidbits`: Awaiting parents ( r-extrafont, r-rttf2pt1 )
- [x] `r-gprofiler`: Awaiting parents ( r-rcurl )
- [x] `r-waffle`: Awaiting parents ( r-extrafont, r-rttf2pt1 )
- [x] `r-extrafont`: Awaiting parents ( r-rttf2pt1 )
- [x] `r-xml2r`: Awaiting parents ( r-rcurl )
- [x] `r-hrbrthemes`: Awaiting parents ( r-extrafont, r-rttf2pt1 )
- [x] `r-ggimage`: Awaiting parents ( r-magick )
- [x] `r-ggalt`: Awaiting parents ( r-extrafont, r-rttf2pt1 )
- [x] `r-survivalanalysis`: Awaiting parents ( r-extrafont, r-tidytidbits, r-rttf2pt1 )
- [x] `r-gprofiler2`: Awaiting parents ( r-rcurl )
- [x] `r-animation`: Awaiting parents ( r-magick )
- [x] `r-webchem`: Awaiting parents ( r-rcurl )
- [x] `r-varfrompdb`: Awaiting parents ( r-xml2r, r-rcurl )
- [x] `r-flatxml`: Awaiting parents ( r-rcurl )
- [x] `r-agricolae`: Awaiting parents ( r-spdep )
- [x] `r-gganimate`: Awaiting parents ( r-transformr )
- [x] `r-taxize`: Awaiting parents ( r-bold )
- [x] `r-dicer`: Awaiting parents ( r-infotheo )
- [x] `r-opencpu`: Awaiting parents ( r-protolite )
- [x] `r-rebus`: Awaiting parents ( r-rebus.unicode, r-rebus.datetimes, r-rebus.numbers )
- [x] `r-plsvarsel`: Awaiting parents ( r-msqc )
- [x] `r-ggrastr`: Awaiting parents ( r-cairo )
- [x] `r-cvxr`: Awaiting parents ( r-scs )
- [x] `r-hdrcde`: Awaiting parents ( r-locfit )
- [x] `r-rainbow`: Awaiting parents ( r-hdrcde, r-locfit )
- [x] `r-fds`: Awaiting parents ( r-hdrcde, r-locfit, r-rcurl, r-rainbow )
- [x] `r-fda`: Awaiting parents ( r-fds, r-hdrcde, r-locfit, r-rcurl, r-rainbow )
- [ ] `r-robcompositions`: Awaiting parents ( r-fds, r-fda, r-hdrcde, r-rcurl, r-locfit, r-rainbow )
- [ ] `r-mvoutlier`: Awaiting parents ( r-fds, r-fda, r-hdrcde, r-rcurl, r-locfit, r-robcompositions, r-rainbow )
## *"How can I help?"*
If you would like to help, you can either send PRs with fixes or make comments on the Conda Forge feedstocks about possible solutions.
Generally the three status categories correspond to different types of troubleshooting.
- `"In PR"` - feedstocks with this are usually having compilation problems (mostly C++); typically the issue is not about compilation *per se* but rather getting linking working.
- `"Not solvable"` - feedstocks with this usually indicate something about the packages they depend on is wrong; identifying those specific packages is the first step and then figuring out how to fix those upstream
- `"Bot error"` - feedstocks with this usually mean something is substandard about the recipe itself and the migrator is crashing on it; anecdotally, this frequently involves license issues, such as not including an explicit `license_file:` entry in the `meta.yaml`
The `"In PR"` is often the most difficult and requires some knowledge of how code compilation is done in R; the `"Not solvable"` involves sleuthing around; and `"Bot error"` is more like review work - read the recipe and compare it one that works.
---
<sub>**[1]** The Conda Forge `r-essentials` package is a metapackage that represents common workflows used in R, such as Shiny, tidyverse, and Jupyter kernel support.</sub>