Update comet-ms from v2023.01.0 to v2023.01.2

[jonasscheid]

Sync with comet release: https://github.com/UWPR/Comet/releases/tag/v2023.01.2

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[jpfeuffer]

comet is probably missing "-lrt" in its Makefile and does not allow for specifying it.
You can hack the parent folder Makefile one more time in build.sh:
sed -i.bak "s#\$\(LIBS\)#\$\(LIBS\) -lrt#" Makefile

[jpfeuffer]

If that solves it, maybe raise an issue upstream to be able to specify it more easily. At Comet, they are usually quite responsive to suggestions.

[jpfeuffer]

The sed did not work correctly.
You have to play with escaping dollar and parentheses.

[jpfeuffer]

Suggested change

	sed -i.bak "s#\$\(LIBS\)#\$\(LIBS\) -lrt#" Makefile
	sed -i.bak 's#$(LIBS)#$(LIBS) -lrt#' Makefile

Maybe try single quotes for bash?

[jpfeuffer]

maybe try single quotes instead of escaping.

[jpfeuffer]

Ok the SED worked now. But not the flag.
Last idea:
Put "-lrt" before $(LIBS)

[jonasscheid]

Thanks @jpfeuffer 🙏🏼 I my naive thought is that it needs to be right behind the .cpp file right? (Stackoverflow)

[jpfeuffer]

I'm not sure if it helps putting it even further to the front. You can also try that.

[jonasscheid]

Ok last try until I ping the authors 😁

[jpfeuffer]

It builds now but maybe:

requirements:
  build:
    - make
    - unzip
    - {{ compiler('c') }}
    - {{ compiler('cxx') }}

shoud be:

requirements:
  build:
    - make
    - unzip
  host:
    - {{ compiler('c') }}
    - {{ compiler('cxx') }}

[martin-g]

The compilers are ‘build’ deps usually.

…

On Wed, 20 Mar 2024 at 16:51, Julianus Pfeuffer ***@***.***> wrote: It builds now but: requirements: build: - make - unzip - {{ compiler('c') }} - {{ compiler('cxx') }} shoud be: requirements: build: - make - unzip host: - {{ compiler('c') }} - {{ compiler('cxx') }} — Reply to this email directly, view it on GitHub <#46567 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABYUQWEZV7WLM3WKKMYIPLYZGPAXAVCNFSM6AAAAABE5PIATWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMBZG42TSOBYGA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[jpfeuffer]

@martin-g but how does one specify a runtime dependency on libstdc++ then?
Because the current issue is that it is apparently not available/findable on the mulled containers.

[jpfeuffer]

I have no idea why the stdlib or libc would not be available/findable on the mulled containers.
You can try libstdcxx-ng which is the c++ stdlib that is actually missing but in all my last recipes this was somehow automatically there.

You can also try

• sysroot_linux-64 2.17 # [linux64]

In the build section. Maybe this makes it work statically since this newer glibc includes chrono_gettime.

No idea if you can set the same OS for the mulled containers of bioconda and which one would be the default. But maybe it just works.

Alternatives are trying to build MSToolkit and CometSearch dynamically as well.
Preferably one would make MSToolkit an own conda recipe actually but not sure how much adaptions were made to it in the comet repository.

[martin-g]

Please read the comments at #46186
It appears that the test phase uses the system's glibc, while the build phase uses the one from the conda environment (sysroot-linux).

The mulled containers are based on base-busybox-glibc-bash and base-debian-glibc-bash (extended) images.

[jpfeuffer]

I think I would try to build without removing static again and adding the dependency on sysroot-glibc=2.17

Mulled tests are just too broken. It clearly works in the test environment which also correctly installs libstdcxx-ng.
Or just disable tests until bioconda fixes things, then also dynamic linking should work.

[jonasscheid]

Thanks @jpfeuffer! I gave you permission to edit my fork. I think that speeds up things, since I'm not exactly sure how to fix it. Can you edit the file?
-> https://github.com/jonasscheid/bioconda-recipes/blob/bump-comet-version/recipes/comet-ms/meta.yaml

[jonasscheid]

@BiocondaBot please add label

[ewels]

LGTM!

[ewels]

@jonasscheid assures me that this is good to go, and CI looks good, so merging 😉