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ok, so full message is: WARN: ~~~~~~~~~~~~~~~~~~~...
# sarek_dev
m
ok, so full message is: WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ There is a problem with your Conda configuration! You will need to set-up the conda-forge and bioconda channels correctly. Please refer to https://bioconda.github.io/ The observed channel order is [defaults] but the following channel order is required: [conda-forge, bioconda] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
r
and it's not your local conda setup?
m
nope, I just installed it, and I didn't put anything
so it's a runner issue?
solved with proper conda install
ok, now I know what to do
let me fix the GHA
I do believe we're now good
r
phew obama
m
PASSED (265.433s)
now the real test is the second test in the second shard, as it's the one that capture the full output
Are you investigating the freebayes vcf, or should I do it?
r
I have not yet, was waiting for the tests to run again with all the other fixes and got side tracked with closing issues
✅ 1
m
ok, so from my side, I consider that all failures due to conda and singularity should be fixed
j
To bring back a blast from the past: so I think I've just come across the same issue in #C02K5GX2W93 ... shouldn't this be in the template do you think @Maxime Garcia ?
m
could you link to the issue?
I am trying to remember
Oooh yeah, now I remember
j
i don't know if it's exactly the same
m
Let me read and have a feeling
j
But If I try building the conda environment locally/github actions it resolves fine
But I did just noticed I'm getting tha warning
Ah fuck that iddn't help
WTF is goingon
m
yeah, so as far as I can tell, not the same error
you do have the warning
but it's just a warning
j
yeah
m
this is your error: java.lang.RuntimeException: Path /home/runner/_work/funcscan/funcscan/~/tests/19c59f6053235b89c5a8bd9b2d19ef71/output/bgc/gecco/sample_1/sample_1.clusters.gff not found.
and that's coming from nf-test
not nextflow
j
Ah wait wrong one
TYhis
one
image.png
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pycirclize 0.0.1 | 0.0.2 | 0.0.3 | 0.1.0 | 0.1.1 | 0.1.2 | 0.1.3 | 0.2.0 | 0.2.1 | 0.3.0 | 0.3.1 | 0.4.0 | 0.5.0 | 0.5.1 | 1.0.0 | 1.1.0 | 1.2.0 | 1.3.0 | 1.4.0 | 1.5.0 | 1.6.0 | 1.7.0 | 1.7.1 | 1.7.2 | 1.8.0 | 1.9.0 | 1.9.1 | 1.10.0 | 1.10.1 is excluded because due to strict channel priority not using this option from: '<https://conda.anaconda.org/conda-pypi/>'
AH WAIT
What is this conda-pypi bollocks... I think I saw that somewhere else...
m
oh yeah, that's a conda environment issue
j
I don't understand what this 'strict channel' bollocks
GRRR
m
Jumping into a meeting, I'll get back to you ASAP
j
But yeah if I flip the channel order then it works it seems
Oh because the original environments were wrong 🙃
m
ok, now that I picked up fruits in the basement I am free
what is the problem then?
j
I solved it by flipping the order of channels in the environment yaml
Someone wrote it by hand think and got it the wrong way around
m
Oh I see
Nice catch
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