try fixes and understanding the problem ... by ngam · Pull Request #90 · conda-forge/pysr-feedstock

ngam · 2023-06-08T03:48:25Z

Checklist

Used a personal fork of the feedstock to propose changes
Bumped the build number (if the version is unchanged)
Reset the build number to 0 (if the version changed)
Re-rendered with the latest conda-smithy (Use the phrase @conda-forge-admin, please rerender in a comment in this PR for automated rerendering)
Ensured the license file is being packaged.

conda-forge-webservices · 2023-06-08T03:48:29Z

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipe) and found it was in an excellent condition.

ngam · 2023-06-08T03:48:33Z

@conda-forge-admin, please rerender.

…nda-forge-pinning 2023.06.08.00.22.40

mkitti · 2023-06-08T10:59:34Z

This passes?

ngam · 2023-06-08T12:22:52Z

Yes, but the logs don’t look good…

@mkitti and @MilesCranmer should review the logs more carefully

ngam · 2023-06-08T12:23:13Z

Cc @h-vetinari

mkitti · 2023-06-08T18:09:42Z

I see a lot of clobber warnings. What else should I focus on?

ngam · 2023-06-08T20:52:17Z

Things like:

Error: import PyCall failed: https://dev.azure.com/conda-forge/feedstock-builds/_build/results?buildId=719527&view=logs&j=d0d954b5-f111-5dc4-4d76-03b6c9d0cf7e&t=841356e0-85bb-57d8-dbbc-852e683d1642&l=379

I believe you explained this to me as "no problem" previously, but I am not sure I remember exactly. I also think this problem is now resolved, no?

h-vetinari · 2023-06-08T22:18:26Z

I see a lot of clobber warnings.

The reason for this is most likely as described here, i.e. reinstallation of numpy.

MilesCranmer · 2023-06-12T07:48:36Z

Once this merges: JuliaPy/PyCall.jl#1040 we can disable the re-installation with a build flag. Then hopefully the build warnings will disappear.

conda-forge-webservices · 2023-06-12T07:53:59Z

Hi! This is the friendly automated conda-forge-linting service.

I was trying to look for recipes to lint for you, but it appears we have a merge conflict.
Please try to merge or rebase with the base branch to resolve this conflict.

Please ping the 'conda-forge/core' team (using the @ notation in a comment) if you believe this is a bug.

conda-forge-webservices · 2023-06-12T07:54:32Z

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipe) and found it was in an excellent condition.

MilesCranmer · 2023-06-12T07:54:49Z

@conda-forge-admin, please rerender

github-actions · 2023-06-12T07:56:35Z

Hi! This is the friendly automated conda-forge-webservice.

I tried to rerender for you, but it looks like there was nothing to do.

This message was generated by GitHub actions workflow run https://github.com/conda-forge/pysr-feedstock/actions/runs/5240960713.

MilesCranmer · 2023-06-12T11:01:19Z

Not sure if this is a clue, but with the libstdcxx-ng<13 setting in run_constraints:, the mamba build is now working, but the conda build fails:

https://github.com/MilesCranmer/PySR/actions/runs/5242217963

MilesCranmer · 2023-06-12T15:55:07Z

It seems like the conda builds are finally working: https://github.com/MilesCranmer/PySR/actions/runs/5245593703

The band-aid fix is a combination of the following:

    - numpy
    - numpy >=1.14.0
    - ...
    - libstdcxx-ng <13  # [linux]
  run:
    - ...
    - {{ pin_compatible('numpy') }}
  run_constrained:
    - libstdcxx-ng <13

all of these changes were required. Even lowering the requested numpy constraint to >=1.14.0 was weirdly required to fix things (though I thought it didn't affect things).

It also required libstdcxx-ng <13 in the host: section as well, otherwise hitting some linking issues.

MilesCranmer · 2023-06-16T20:41:08Z

Once this is merged: JuliaRegistries/General#85755

Then we can re-run these tests, and see if it solves the clobber problem

MilesCranmer · 2023-06-17T01:37:07Z

Cool, it looks like the clobber issue is gone? Are there any other warnings we need to worry about?

conda-forge-webservices · 2023-06-20T17:15:37Z

Hi! This is the friendly automated conda-forge-linting service.

I was trying to look for recipes to lint for you, but it appears we have a merge conflict.
Please try to merge or rebase with the base branch to resolve this conflict.

Please ping the 'conda-forge/core' team (using the @ notation in a comment) if you believe this is a bug.

conda-forge-webservices · 2023-06-20T18:49:04Z

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipe) and found it was in an excellent condition.

github-actions · 2023-06-20T19:16:19Z

Hi! This is the friendly automated conda-forge-webservice.

I tried to rerender for you, but it looks like there was nothing to do.

This message was generated by GitHub actions workflow run https://github.com/conda-forge/pysr-feedstock/actions/runs/5326517222.

MilesCranmer · 2023-06-20T22:24:06Z

Fingers crossed.

h-vetinari · 2023-06-21T01:43:57Z

This looks better now, though there's what looks like a segfault in one of the linux jobs on main.

Also, this doesn't look great:

WARNING (pysr,share/pysr/depot/artifacts/9f6f87cc2114df918ff9c21dff9572f690e7dab2/lib/libLLVMExtra-14.so): runpaths ['$ORIGIN'] found in /home/conda/feedstock_root/build_artifacts/pysr_1687299957695/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/share/pysr/depot/artifacts/9f6f87cc2114df918ff9c21dff9572f690e7dab2/lib/libLLVMExtra-14.so
WARNING (pysr,share/pysr/depot/artifacts/9f6f87cc2114df918ff9c21dff9572f690e7dab2/lib/libLLVMExtra-14.so): $RPATH/libLLVM-14jl.so not found in packages, sysroot(s) nor the missing_dso_whitelist.
.. is this binary repackaging?
WARNING (pysr,share/pysr/depot/artifacts/9f6f87cc2114df918ff9c21dff9572f690e7dab2/lib/libLLVMExtra-14.so): /lib64/libstdc++.so.6 not found in packages, sysroot(s) nor the missing_dso_whitelist.
.. is this binary repackaging?
WARNING (pysr,share/pysr/depot/artifacts/9f6f87cc2114df918ff9c21dff9572f690e7dab2/lib/libLLVMExtra-14.so): /lib64/libm.so.6 not found in packages, sysroot(s) nor the missing_dso_whitelist.
.. is this binary repackaging?
WARNING (pysr,share/pysr/depot/artifacts/9f6f87cc2114df918ff9c21dff9572f690e7dab2/lib/libLLVMExtra-14.so): /lib64/libgcc_s.so.1 not found in packages, sysroot(s) nor the missing_dso_whitelist.
.. is this binary repackaging?
WARNING (pysr,share/pysr/depot/artifacts/9f6f87cc2114df918ff9c21dff9572f690e7dab2/lib/libLLVMExtra-14.so): /lib64/libc.so.6 not found in packages, sysroot(s) nor the missing_dso_whitelist.
.. is this binary repackaging?

I don't know where libLLVMExtra-14.so comes from - I help package LLVM for conda-forge, but I've never seen that library, and I cannot find it upstream either.

ngam · 2023-06-21T03:04:31Z

Julia uses a special LLVM… like their heavily modified fork. They do try to upstream changes though, but it takes a while.

we once discussed trying to package the Julia LLVM fork…

MilesCranmer · 2023-06-21T05:49:18Z

Regarding the segfault, the full set of tests is fairly compute/memory intensive compared to the compute used in the build jobs. So maybe we could use a lighter test, since we just want a smoke test for the integration all working.

I’m also unsure why the OSX jobs freeze during the precompilation: https://dev.azure.com/conda-forge/feedstock-builds/_build/results?buildId=731490&view=logs&j=a8dee1cf-d17f-5cb0-b53f-4a93dfdbfb0c&t=d9dbf137-9a7f-5666-c60c-9e1b2fc31445 — this seems repeatable, and only occurs on Python 3.9+OSX…

ngam · 2023-06-21T12:32:17Z

If CI fails on the main branch, the package doesn’t get uploaded to anaconda dot org

try fixes

0da4c2e

MNT: Re-rendered with conda-build 3.25.0, conda-smithy 3.23.1, and co…

981f585

…nda-forge-pinning 2023.06.08.00.22.40

ngam mentioned this pull request Jun 8, 2023

Unpin numpy as a host dep #89

Closed

MilesCranmer marked this pull request as ready for review June 12, 2023 07:52

MilesCranmer self-requested a review as a code owner June 12, 2023 07:52

Bump build number to 3

0cb5676

Merge branch 'main' into fixes

756efe7

This was referenced Jun 12, 2023

[BUG]: libstdc++ issues / GLIBCXX not found MilesCranmer/PySR#347

Closed

Stop bleeding v2 #92

Merged

Merge branch 'main' into fixes

86cbe65

ngam closed this Jun 17, 2023

ngam reopened this Jun 17, 2023

Bump version to v0.14.2

b7c6566

Bump build number

2ab8001

Merge branch 'main' into fixes

5867c17

MilesCranmer merged commit 5855209 into conda-forge:main Jun 20, 2023

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