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Work list for R 4.4/Bioconductor 3.19 builds #49778
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CC: @daler just a heads up |
conda-forge/r-clusterr-feedstock#25 seems like maybe the Travis build just needs to be re-triggered. |
Travis CI is failing for all linux-ppc64le jobs. There are some notes in the Status Issue about how to convert to either cross-compiling or emulation on Azure to get around this. |
I took a pass through all the "In PR" failures (rerendering a handful whose logs had expired) and posted a comment for each one either extracting the error, or when possible proposing a fix. I will try to push fixes for the ones where I had a possible solution. @mfansler One quick question - what do you think about just adding I agree with the your suggestion in conda-forge/r-base-feedstock#325 to add |
@danielnachun that's wonderful - thanks for spending time with this! ❤️ Unfortunately, I'm short on bandwidth today, but will try having a look as soon as I can. RE: |
The discussion in conda-forge/r-rcppalgos-feedstock#16 prompted me to check something I should have looked into sooner - among the packages that are only failing on Windows, which ones have never had a successful Windows build? It turns out these 6 packages have not, and they are some of the weirder or more difficult failures:
So as not to block the R 4.4 migration, I think we should consider skipping the Windows builds on these for now as they don't have obvious solutions and Windows users were never able to use them anyway. |
@mfansler for packages that don't have a PR because of bot errors or unsolvable dependencies, is it sufficient just to rerender the feedstock with the necessary manual fixes? Or does the migrator make other manual changes (aside from re-enabling Windows if it was skipped)? Also does the migrator automatically open PRs for packages that were previously blocked by a missing parent? Or does a PR need to be made to https://github.com/conda-forge/conda-forge-pinning-feedstock? |
@danielnachun so far, I've adopted the practice that it is better, when possible, to fix the recipe without manually forcing a R 4.4/UCRT migration, so that the bot can start working normally. Specifically, to your question: Yes, the migrator will eventually notice fixed recipes and (AFAIK) will retry solving failed recipes every ~24 h. When we manually migrate it, the problem often doesn't go away (e.g., downstream dependencies may encounter same issue) and technical debt accrues. However, there are exceptions that are unavoidable, so here are the different cases I see:
Manual MigrationFor the case 3, manual migration is done by adding in the migration file (see example commit) and making some changes to the
Then a rerender needs to be done. I believe the bot will recognize that the package is now available, and downstream dependencies should start flowing. However, that will not be the case if you are still skipping platforms - the downstream dependencies will be not solvable. |
@danielnachun FYI, any new PRs for R packages appear blocked at the moment: conda-forge/conda-forge-pinning-feedstock#6401 |
I was going to ask why things weren't restarting but that makes sense. Hopefully this gets figured out soon!
This an important point for skipping Windows - if nothing depends on the package, then it doesn't propagate elsewhere. So we should put the most effort on fixing packages with dependents. Of the 6 I posted above, only One other question - if a package is |
@danielnachun correct, For the 6 feedstocks you highlighted, I've fixed all but Thanks for all the new reviews! 🤩 I may not have time today, but I will eventually get to them. |
@mfansler the From what I can see, there are two big blockers that will fix a lot of the remaining "Awaiting parents"/"Not solvable":
|
FYI, I'm going to merge what I can of the outstanding PRs with Windows skipped for now. This will also mean we'll have to do some manual migration PRs on some of the depending packages, since otherwise the migrator will consider them "Not Solvable". |
This is a good call. From what I can see there were only 4 packages that had to be merged with Windows skipped:
So the impact of this on the migration overall is small. I think the only really big impact right now on migrations is the lack of an The only other package blocking migrations are:
Assuming the dependents of |
@danielnachun I think the snag with I got I'll try to have a look a |
Preparation for R 4.4/Bioconductor 3.19
It looks like we'll cross the
r-essentials
milestone1 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. However, feel free comment or check things off if you see they have completed. Updated info is available on the Conda Forge Status page.
Problematic R 4.4 Migrations
Awaiting migration of 62 packages
In PR (20 packages)
r-infotheo
: In PR [bot-automerge] Rebuild for r-base 4.4 and UCRT mingw toolchain conda-forge/r-infotheo-feedstock#13r-compositions
: In PR [bot-automerge] Rebuild for r-base 4.4 and UCRT mingw toolchain conda-forge/r-compositions-feedstock#20r-rmariadb
: In PR [bot-automerge] Rebuild for r-base 4.4 and UCRT mingw toolchain conda-forge/r-rmariadb-feedstock#25r-hdf5r
: In PR [bot-automerge] Rebuild for r-base 4.4 and UCRT mingw toolchain conda-forge/r-hdf5r-feedstock#34r-pdftools
: In PR [bot-automerge] Rebuild for r-base 4.4 and UCRT mingw toolchain conda-forge/r-pdftools-feedstock#48r-rcurl
: In PR [bot-automerge] Rebuild for r-base 4.4 and UCRT mingw toolchain conda-forge/r-rcurl-feedstock#33r-rcppalgos
: In PR [bot-automerge] Rebuild for r-base 4.4 and UCRT mingw toolchain conda-forge/r-rcppalgos-feedstock#16r-rmixmod
: In PR [bot-automerge] Rebuild for r-base 4.4 and UCRT mingw toolchain conda-forge/r-rmixmod-feedstock#17r-git2r
: In PR [bot-automerge] Rebuild for r-base 4.4 and UCRT mingw toolchain conda-forge/r-git2r-feedstock#44r-rttf2pt1
: In PR [bot-automerge] Rebuild for r-base 4.4 and UCRT mingw toolchain conda-forge/r-rttf2pt1-feedstock#19r-wrswor
: In PR [bot-automerge] Rebuild for r-base 4.4 and UCRT mingw toolchain conda-forge/r-wrswor-feedstock#2r-tiledb
: In PR Rebuild for r-base 4.4 and UCRT mingw toolchain conda-forge/r-tiledb-feedstock#87r-cairo
: In PR [bot-automerge] Rebuild for r-base 4.4 and UCRT mingw toolchain conda-forge/r-cairo-feedstock#39r-bold
: In PR [bot-automerge] Rebuild for r-base 4.4 and UCRT mingw toolchain conda-forge/r-bold-feedstock#17r-scs
: In PR [bot-automerge] Rebuild for r-base 4.4 and UCRT mingw toolchain conda-forge/r-scs-feedstock#5r-copula
: In PR [bot-automerge] Rebuild for r-base 4.4 and UCRT mingw toolchain conda-forge/r-copula-feedstock#21r-strawr
: In PR [bot-automerge] Rebuild for r-base 4.4 and UCRT mingw toolchain conda-forge/r-strawr-feedstock#4r-msqc
: In PR [bot-automerge] Rebuild for r-base 4.4 and UCRT mingw toolchain conda-forge/r-msqc-feedstock#7r-primme
: In PR [bot-automerge] Rebuild for r-base 4.4 and UCRT mingw toolchain conda-forge/r-primme-feedstock#17r-locfit
: In PR [bot-automerge] Rebuild for r-base 4.4 and UCRT mingw toolchain conda-forge/r-locfit-feedstock#20Bot Error (4 packages)
r-rebus.unicode
: bot error (bot CI job): main: Error running migrate-feedstock in container - JSON could not parse stdout:r-rebus.datetimes
: bot error (bot CI job): main: Error running migrate-feedstock in container - JSON could not parse stdout:r-rebus.numbers
: bot error (bot CI job): main: Error running migrate-feedstock in container - JSON could not parse stdout:r-logr
: bot error (bot CI job): main: Error running migrate-feedstock in container - JSON could not parse stdout:Not Solvable (7 packages)
r-spdep
: not solvable (bot CI job) @ main r-sf * cannot be installed because there are no viable optionsr-magick
: not solvable (bot CI job) @ main No candidates were found for imagemagick *.r-rmpi
: not solvable (bot CI job) @ main No candidates were found for openmpi 5.*.r-transformr
: not solvable (bot CI job) @ main r-sf * cannot be installed because there are no viable optionsr-protolite
: not solvable (bot CI job) @ main r-sf * cannot be installed because there are no viable optionsr-gstat
: not solvable (bot CI job) @ main r-sf >=0.7_2 cannot be installed because there are no viable optionsr-tkrplot
: not solvable (bot CI job) @ main No candidates were found for tcl *.Awaiting Parents (31 packages)
r-qdaptools
: Awaiting parents ( r-rcurl )r-summarytools
: Awaiting parents ( r-magick )r-tidytidbits
: Awaiting parents ( r-extrafont, r-rttf2pt1 )r-gprofiler
: Awaiting parents ( r-rcurl )r-waffle
: Awaiting parents ( r-extrafont, r-rttf2pt1 )r-extrafont
: Awaiting parents ( r-rttf2pt1 )r-xml2r
: Awaiting parents ( r-rcurl )r-hrbrthemes
: Awaiting parents ( r-extrafont, r-rttf2pt1 )r-ggimage
: Awaiting parents ( r-magick )r-ggalt
: Awaiting parents ( r-extrafont, r-rttf2pt1 )r-survivalanalysis
: Awaiting parents ( r-extrafont, r-tidytidbits, r-rttf2pt1 )r-gprofiler2
: Awaiting parents ( r-rcurl )r-animation
: Awaiting parents ( r-magick )r-webchem
: Awaiting parents ( r-rcurl )r-varfrompdb
: Awaiting parents ( r-xml2r, r-rcurl )r-flatxml
: Awaiting parents ( r-rcurl )r-agricolae
: Awaiting parents ( r-spdep )r-gganimate
: Awaiting parents ( r-transformr )r-taxize
: Awaiting parents ( r-bold )r-dicer
: Awaiting parents ( r-infotheo )r-opencpu
: Awaiting parents ( r-protolite )r-rebus
: Awaiting parents ( r-rebus.unicode, r-rebus.datetimes, r-rebus.numbers )r-plsvarsel
: Awaiting parents ( r-msqc )r-ggrastr
: Awaiting parents ( r-cairo )r-cvxr
: Awaiting parents ( r-scs )r-hdrcde
: Awaiting parents ( r-locfit )r-rainbow
: Awaiting parents ( r-hdrcde, r-locfit )r-fds
: Awaiting parents ( r-hdrcde, r-locfit, r-rcurl, r-rainbow )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 explicitlicense_file:
entry in themeta.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.[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.The text was updated successfully, but these errors were encountered: