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amkozlov / raxml-ng

RAxML Next Generation: faster, easier-to-use and more flexible
GNU Affero General Public License v3.0
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catg files/core dumped #159

Closed gerhardJaeger closed 1 year ago

gerhardJaeger commented 1 year ago

When I try to run the precompiled linux-version of raxml-ng with a catg file, I get "core dumped". It does work when I compile the program from scratch.

Btw, the same problem also occurs with the anaconda version.

amkozlov commented 1 year ago

Thanks for reporting, this bug has been already fixed (#131), so the problem will be solved with the next release (v1.2).

gerhardJaeger commented 1 year ago

👍

dlaehnemann commented 1 year ago

Good to know, that this has been fixed, as I also ran into this. Will there be a release any time soon?

Would be very much appreciated, as I would prefer using the latest bioconda recipe for snakemake workflow integration, and currently I will have to implement a hacky workaround to get raxml-ng to automatically (and reproducibly) install in my workflow.

amkozlov commented 1 year ago

yes there will be a new release (v1.2) very soon, please stay tuned! ;)

amkozlov commented 1 year ago

So the new release which fixes this bug is now available: https://github.com/amkozlov/raxml-ng/releases/tag/1.2.0

However, it is not yet in bioconda, and I'm not sure whether bioconda recipe will be updated automatically. I just recall last time I had to do it manually and it was a huge time waste, so help would be appreciated :)

dlaehnemann commented 1 year ago

Usually, the bioconda-bot should pick up the new version and automatically create a pull request with the necessary changes. But this hasn't happened, yet. So we might have to do this manually. But unless any dependencies changed (dropped or added), for such an update you should only ever have to:

  1. Update the version number.
  2. Update the sha256 hash value.
  3. Reset the build: number: to 0.

But we could wait, whether the update of the conda-forge version of the bison package to 3.8.2 works out. If it does, this should solve the libpll-2 compilation issue with bison=3.8 from conda-forge and we could in addition update the bison-dependency in the bioconda recipe to the minimum version of bison =3.8.2.

dlaehnemann commented 1 year ago

Alright, the new bison version 3.8.2 is available on conda-forge and seems to solve the compiling issues for libpll-2.

As the bioconda-bot somehow didn't pick up the new raxml-ng version, would you like to try out creating an update pull request for the bioconda recipe of raxml-ng, @amkozlov?

It's just the three points above (for 2. there's a handy one-liner to determine the hash value in the bioconda docs), plus fixing the bison version to 3.8.2 (instead of the current 3.4). Just ping me in if I can be of any help.

amkozlov commented 1 year ago

OK, waiting for review & merge:

https://github.com/bioconda/bioconda-recipes/pull/40931

dlaehnemann commented 1 year ago

Done. The recipe should appear on the bioconda channel any time soon.

However, I am not sure why the autobump mechanism of bioconda didn't pick up the new release (it's not on the build-fail blacklist, and it is not a sub-recipe, so it should really be checked). Let me know if this persists with future releases. Because this should really just be automatic for the majority of updates.

One possible source could be using the zip archive url:, instead of the .tar.gz, but I'm just thinking this because most recipes I have seen are using the .tar.gz file. I have no clue why that might hinder the autobump... :shrug:

Anyways, this issue is taken care of in my view (but I can't close it).

amkozlov commented 1 year ago

Great, thanks for your help!