Build Bioconductor-BiocGenerics for linux-aarch64 #46177
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@daler @aliciaaevans I need your help here! https://hub.docker.com/r/involucro/tool/tags has only |
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According to https://github.com/bioconda/bioconda-utils/blob/18f988d70966f6f6296170d96cc1ced51ad10392/bioconda_utils/upload.py#L80-L81 Galaxy will use a local |
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It seems |
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It appears that |
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The actual problem is that there is no It fails while |
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It behaves the same way on |
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What is
Installing It is the same version (0.83) but a different build. I am trying to find out where this |
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I tried to reproduce the
No issues with |
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Similar error ( |
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I was able to reproduce it on Linux x86_64 too! But it is random - sometimes it passes, sometimes it fails with
@bgruening From other issues I see you have experience with |
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I've found the issue! On my aarch64 machine the value is |
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The problem is a bit deeper: x86_64: aarch64: Same issue for @daler ^^ |
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I tried with custom Dockerfile.mambaforge: Both return Same for busybox. |
For some reason |
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The problem is in |
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This was referenced Apr 22, 2024
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OK, after reading all @martin-g's notes, doing some digging, and discussing with @daler, here's what I think is going on.
@bgruening does this seem right to you? If there was an arm involucro/tool image, I think it would work around this issue for linux-arm64 the same way as linux-64. It's not ideal but that could buy some time for a longer term solution. Would getting that involve a lot of effort? (Since the latest one was from 5 years ago.) Do you have any suggestions that could fix the issue without having to do the fallback to remote execution? |
One question here: Are those the same files ? I guess they are but I am not sure due to the missing |
This was referenced Apr 30, 2024
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I hope we fixed it with conda-forge/font-ttf-ubuntu-feedstock#3 ! |
Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
This way it loads /etc/profile even for non-interactive sessions Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
... to test usage of a custom invfile.lua that uses `/bin/sh -lc ...` instead of `/bin/sh -c ...` Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
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@aliciaaevans this all makes perfect sense to me. Thanks all for digging this up. I'm wondering if we can use https://quay.io/biocontainers/involucro/ (and create ARM builds), I will also try to create ARM build for the fallback container. Need time to investigate a bit. |
Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Cool! You beat me to it. 🥇 I think we probably should also still move forward with getting the fallback working for ARM in case of other packages having this issue. |
Great, thanks @bgruening! The fallback image looks to be hard-coded in involucro, but I guess that could be made configurable? |
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@BiocondaBot please fetch artifacts |
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Package(s) built are ready for inspection:
Docker image(s) built:
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The recipe is |
mbargull
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Jun 2, 2024
refs: conda/conda-build#5330 bioconda/bioconda-recipes#47554 bioconda/bioconda-recipes#46177 Signed-off-by: Marcel Bargull <marcel.bargull@udo.edu>
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