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    advaitb commented #28532
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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:
Marcel Bargull
@mbargull
Yep, my bad. It slipped my mind that pkg_resources may be used by some library >,<
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#28033
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#28017
Pierre Morisse
@morispi
Hello, still having issues with my PR (bioconda/bioconda-recipes#28019).
Check for Linux is OK, but check for macos fails and mentions Don't know how to find lib/liblrez.dylib, skipping.
However, when reading the log, it seems like the library was compiled correctly.
I'm not familiar with macos at all so I don't have any idea what to do here?
pvanheusden
@pvanheusden:matrix.org
[m]
I'm looking into writing a recipe for nextclade - nextclade is a NPM package... so it has not source in the conventional (conda) sense. Rather the build script does npm install -g @neherlab/nextclade
so it breaks the stable url and sha256 items in the checklist
pvanheusden
@pvanheusden:matrix.org
[m]
how can I (on the command line) lint 1 specific recipe?
Devon Ryan
@dpryan79
@pvanheusden:matrix.org bioconda-utils lint --packages some_recipe I think
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#28058
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#28055
pvanheusden
@pvanheusden:matrix.org
[m]
PR ready for review: bioconda/bioconda-recipes#28043
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#28003
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#28061
Bioconda Bot
@BiocondaBot
PR ready for review: bioconda/bioconda-recipes#28063