gemmi v0.6.3

[regro-cf-autotick-bot]

It is very likely that the current package version for this feedstock is out of date.

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• [ ] Dependencies have been updated if changed: see upstream
• [ ] Tests have passed
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Closes: #55 Closes: #56

Dependency Analysis

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Analysis by source code inspection shows a discrepancy between it and the the package's stated requirements in the meta.yaml.

Packages found by source code inspection but not in the meta.yaml:

• cctbx-base

_{This PR was created by the regro-cf-autotick-bot. The regro-cf-autotick-bot is a service to automatically track the dependency graph, migrate packages, and propose package version updates for conda-forge. Feel free to drop us a line if there are any issues! This PR was generated by https://github.com/regro/cf-scripts/actions/runs/6110334237, please use this URL for debugging.}

[conda-forge-webservices[bot]]

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.

[dagewa]

Hi! I don't understand what is wrong on the OSX checks, but I'd like to use gemmi 0.6.3 from conda in DIALS soon. So, I'll need to work this out.

[wojdyr]

I'm also looking into it.

[wojdyr]

I think the error has something to do with visibility and/or LTO flags. I had the same or similar error in gemmi CI builds in Github Actions. But it was only a few days ago, after the release. I just rebuilt v6.3.0 on macos in Github Actions, and I didn't get any warnings or errors. Also, I didn't change any build options between 0.6.2 and 0.6.3. So I actually don't know why these errors happened at that times. But since the warnings mention different visiblity settings, it could help if this argument was added to cmake call:

-D CMAKE_CXX_VISIBILITY_PRESET=hidden

Can it be done on top of this PR?

[ndevenish]

Marking draft as making a single commit re-requested review (for some reason) and I don't want to do that a hundred times

[wojdyr]

I don't think it's about inline symbols. Could you try to replace

-D CMAKE_VISIBILITY_INLINES_HIDDEN=OFF

with

-D CMAKE_CXX_VISIBILITY_PRESET=hidden

[ndevenish]

With some basic experimenting, removing that block (which I've just edited here) made the compile work on my local system, vs not working otherwise; which is why my intitial try was to replicate that and see if it fixed it here, at which point I would dig into the differences and explicitly what it was supposed to be doing.

I'll stop trying to touch the branch so that you can try whatever.

[ndevenish]

Can it be done on top of this PR?

Yes, because you are a maintainer of this feedstock you have full permissions to push to the autotickbot branches because

I was asked to look at this as a favour because as I understood it there was no current maintainer. If it's a misunderstanding over repository permissions I'm happy to step back again, I absolutely don't want to tread on your toes or look like I was trying to impose.

[wojdyr]

With some basic experimenting, removing that block (which I've just edited here) made the compile work on my local system, vs not working otherwise; which is why my intitial try was to replicate that and see if it fixed it here, at which point I would dig into the differences and explicitly what it was supposed to be doing.

I don't see what block it was, probably because of the later force-push.

I was commenting that the earlier change that added -D CMAKE_VISIBILITY_INLINES_HIDDEN=OFF was unlikely to resolve the build problem. Did you try -D CMAKE_CXX_VISIBILITY_PRESET=hidden?

[ndevenish]

I was commenting that the earlier change that added -D CMAKE_VISIBILITY_INLINES_HIDDEN=OFF was unlikely to resolve the build problem. Did you try -D CMAKE_CXX_VISIBILITY_PRESET=hidden?

No, I reverted the branch without my initial fiddling so that you could try this directly, because it looked like you didn't realise you could edit this branch and dictating changes via me seems like a waste of time for both of us.

I don't think it's about inline symbols.

The error message I saw was an inline function that at LTO stage was having conflicts with visibility of what looked like another inline function, but don't precisely recall what the behaviour interaction is with hidden inline symbols and the normal ODR deduplication (I would well imagine having a publicly visible inline function in one file and a hidden one in another might fall afoul of some linking crosscheck).

I don't know why these (partial?) visibility controls were put in place, so I thought a good first step (in a short piece of spare time in my weekend to get the ball rolling) would be to remove some of the changes instead of trying to diagnose by adding more variables to the build. This doesn't seem an unreasonable first step to work out what is going on here - remember that I don't have the benefit of actually having written this code so have to approach it from scratch.

[wojdyr]

I had the same errors as here in gemmi CI builds. Adding -D CMAKE_CXX_VISIBILITY_PRESET=hidden resolved them, so that's why I proposed to add it. Just wanted to save you some time. Although I see that here it's not sufficient.