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nextstrain / conda-base

Conda package build for nextstrain-base
https://anaconda.org/Nextstrain/nextstrain-base
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tsv-utils raises error in new installation #75

Closed joverlee521 closed 2 weeks ago

joverlee521 commented 2 weeks ago

Error in latest seasonal-flu CI from tsv-utils

Detailed error in the logs of the uploaded artifact for seasonal-flu

tsv-append: error while loading shared libraries: libphobos2-ldc-shared.so.108: cannot open shared object file: No such file or directory
joverlee521 commented 2 weeks ago

Likely related to the latest pull of tsv-utils from conda-forge

joverlee521 commented 2 weeks ago

Seems related to https://github.com/conda-forge/tsv-utils-feedstock/pull/2

joverlee521 commented 2 weeks ago

tsv-utils will run into errors for a new installation/update of conda-base 

$ nextstrain update conda
$ nextstrain shell --conda . 
$ tsv-select --version
dyld[16067]: Library not loaded: @rpath/libphobos2-ldc-shared.108.dylib
  Referenced from: <C97A2355-08EA-3753-8C54-F3855A65839E> /Users/joverlee/.nextstrain/runtimes/conda/env/bin/tsv-select
  Reason: tried: '/Users/joverlee/.nextstrain/runtimes/conda/env/bin/../lib/libphobos2-ldc-shared.108.dylib' (no such file), '/Users/joverlee/.nextstrain/runtimes/conda/env/bin/../lib/libphobos2-ldc-shared.108.dylib' (no such file), '/usr/local/lib/libphobos2-ldc-shared.108.dylib' (no such file), '/usr/lib/libphobos2-ldc-shared.108.dylib' (no such file, not in dyld cache)
Abort trap: 6
corneliusroemer commented 2 weeks ago

Retry with the latest conda-forge version, now ldc is added as a runtime requirement

joverlee521 commented 2 weeks ago

~Running the CI to pull in the latest conda-forge version~ nvm, I was too fast, it was still pulling in the old build.

Will wait a bit before running

joverlee521 commented 2 weeks ago

Running the CI with latest build:

Screenshot 2024-07-01 at 1 14 10 PM

joverlee521 commented 2 weeks ago

@corneliusroemer I'm still seeing the same error in the latest seasonal-flu CI that's using the new build of tsv-utils from conda-forge.

genehack commented 2 weeks ago

Also affecting seasonal-cov CI, I think?

joverlee521 commented 2 weeks ago

Also affecting seasonal-cov CI, I think?

Yeah, updated the title to reflect that tsv-utils will error in any workflow that uses a new installation of conda-base.

joverlee521 commented 2 weeks ago

Running CI again to pull in latest build from conda-forge.

Hm, weird, that did not pull in the latest build....

corneliusroemer commented 2 weeks ago

Fixed now, sorry for the disturbance here by moving tsv-utils around and starting with a bad recipe.

Now things should work again with the advantage that we'll have linux aarch64 and osx-arm64 builds of tsv-utils in conda soon :)