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  • 08:13
    BiocondaBot labeled #28493
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    BiocondaBot labeled #28493
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Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#27988
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#27990
Oliver Schwengers
@oschwengers
Hello, does anyone know, if (and how) it is possible to define an environment variable within a conda package (per meta.yml or build.sh?) which is automatically set within a conda environment if this package is installed? A 3rd party tool (deepsig) requires an environment variable pointing to a dir containing some binary data files.
Devon Ryan
@dpryan79
@oschwengers The standard way is to add an activation script: https://docs.conda.io/projects/conda-build/en/latest/resources/activate-scripts.html
We have a few recipes with those, though I don't recall any of them off-hand
Oliver Schwengers
@oschwengers
ahh ok I'll have a look at this. thanks @dpryan79
ifubar (ross lazarus)
@ifubar:matrix.org
[m]
Does anyone with review permission have a moment to review this galaxyxml PR please? Tests are good; approved by @hexylena. bioconda/bioconda-recipes#27983
Björn Grüning
@bgruening
done
ifubar (ross lazarus)
@ifubar:matrix.org
[m]
Thanks, @bgruening!
Jacques Dainat
@Juke34
@dpryan79 auto bump didn't work again for AGAT https://github.com/NBISweden/AGAT/releases/tag/v0.6.1
Devon Ryan
@dpryan79
@Juke34 It's currently blacklisted, so it won't be bumped. I'm slowly making my way through things that weren't buildable during the last migration, but it'll take me a while to go through all 100+ of them.
Jacques Dainat
@Juke34
Ok thanks
Pierre Morisse
@morispi
Hi. I'm still facing issues with my PR (bioconda/bioconda-recipes#27989). Apparently it fails to find three functions from bamtools when compiling the binary. Library compilation does appear to work fine, and the said functions do not raise issue. I'm at a loss here, does anyone have any suggestion?
Devon Ryan
@dpryan79
Is the link order correct?
Pierre Morisse
@morispi
It seems so? I don't encounter issues when cloning the repo and making outside of conda
Devon Ryan
@dpryan79
It may be that cmake is using CXXFLAGS, which uses -std=c++17, which I imagine could be causing the issue, but I'm not a C++ person.
Pierre Morisse
@morispi
Oh, that could be it indeed. I tried adding -std=c++11 to the CXXFLAGS in my build.sh, but it didn't work out. Is there a special way I should constraint cmake to use c++11?
Devon Ryan
@dpryan79
You'd need to override the flags. They're set by the compiler activation packages. Presumably a simple export CXXFLAGS="-std=c++11 ..."would work.
Pierre Morisse
@morispi
Yeah, I did that already, but it did not seem to fix the issue. Apparently cmake / compilation of bamtools overrides the -std=c++11. I'm trying to compile bamtools using make CC="-std=c++11" atm. Thanks for your help
Devon Ryan
@dpryan79
Good luck, I hate dealing with cmake because of things like this
Pierre Morisse
@morispi
Nope, still didn't work. If anyone else has any experience with this, it'd be greatly appreciated :)
12 replies
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#28006
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#28005
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#28012
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#28011
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#28007
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#28019
M Bernt
@bernt-matthias

What is meant by Needs the TBB repodata patch so it doesn't pull in a broken bowtie2

https://github.com/bioconda/bioconda-recipes/blob/a8ea307c5edc14a180138a4adbb9600eb5cf1af6/build-fail-blacklist#L198

?

Devon Ryan
@dpryan79
At the moment it tends to pull in an old build that incorrectly permits using a newer TBB
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#28020
PR ready for review: bioconda/bioconda-recipes#28023
M Bernt
@bernt-matthias

Just trying to bump bowtie2 bioconda/bioconda-recipes#28021 .. the build uses a 2020 version of tbb (which is not the latest) and contains loads of:

TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual

wondering if the solution is to pin tbb and tbb-devel? And if so, then to which version <2021?

Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#28002
PR ready for review: bioconda/bioconda-recipes#28010
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#28023
Devon Ryan
@dpryan79
@bernt-matthias I've already rebuilt bowtie2 for the corrected TBB pinning. We and conda-forge are building against TBB 2020.
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#28004
M Bernt
@bernt-matthias
@dpryan79 OK. Then I guess we only need to rebuild metaphlan. Thanks.
Ed Harry
@EdHarry
Anyone know why bioconda/bioconda-recipes#28011 fails to merge?
Devon Ryan
@dpryan79
@EdHarry I'll have a look
OK, it's a small error in the bot, I'll merge it in for now so the standard uploader can run.
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#28018
Björn Grüning
@bgruening
@dpryan79 it seems this problem also occurs here: bioconda/bioconda-recipes#28031
so it seems a general one?
Ed Harry
@EdHarry
Thanks @dpryan79
Devon Ryan
@dpryan79
@bgruening yes, it's a general issue. The bot can't upload the packages at the moment (it does upload the docker containers).
Sounds like it'll get fixed quite quickly (I pinged Marcel) :)
Björn Grüning
@bgruening
oh I was inspecting the other side, I assumed its the Container side
but this looks indeed ok
Devon Ryan
@dpryan79
:+1: