Try fixing samtools merge numpy issue #95
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53 errors and 110 warnings
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example (ubuntu-22.04)
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test (ubuntu-20.04, base)
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example (ubuntu-20.04)
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test (ubuntu-latest, hafpipe-2, mamba)
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test (ubuntu-latest, mapping-bwa-mem2-1, mamba)
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test (ubuntu-latest, trimming-fastp-3, mamba)
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test (ubuntu-latest, download, mamba)
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test (ubuntu-24.04, base)
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test (ubuntu-latest, calling-haplotypecaller-2, mamba)
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test (ubuntu-latest, hafpipe-4, mamba)
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test (ubuntu-latest, mappings-table, mamba)
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test (ubuntu-latest, mapping-bwa-aln-1, mamba)
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test (ubuntu-latest, mapping-bwa-aln-2, mamba)
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test (ubuntu-latest, calling-bcftools-4, mamba)
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test (ubuntu-latest, trimming-adapterremoval-2, mamba)
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test (ubuntu-latest, calling-bcftools-1, mamba)
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test (ubuntu-latest, mapping-bwa-aln-4, mamba)
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test (ubuntu-latest, calling-haplotypecaller-1, mamba)
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test (ubuntu-latest, trimming-adapterremoval-3, mamba)
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test (ubuntu-latest, duplicates-dedup-2, mamba)
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test (ubuntu-latest, hafpipe-1, mamba)
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test (ubuntu-22.04, base)
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test (ubuntu-latest, trimming-cutadapt-1, mamba)
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test (ubuntu-latest, hafpipe-3, mamba)
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example (ubuntu-24.04)
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test (ubuntu-latest, trimming-skewer-2, mamba)
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example (macos-12)
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test (ubuntu-latest, trimming-none, mamba)
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example (macos-13)
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example (ubuntu-22.04)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
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test (ubuntu-latest, base, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
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test (ubuntu-latest, calling-bcftools-2, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
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test (ubuntu-latest, calling-freebayes-1, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
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test (ubuntu-latest, mapping-bowtie2-1, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
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test (ubuntu-latest, calling-freebayes-2, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
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Mambaforge is now deprecated!
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test (ubuntu-latest, trimming-fastp-1, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
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test (ubuntu-latest, mapping-bwa-mem2-2, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
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test (ubuntu-latest, trimming-fastp-2, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
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test (ubuntu-latest, calling-haplotypecaller-3, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
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test (ubuntu-20.04, base)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
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example (ubuntu-20.04)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
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Mambaforge is now deprecated!
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test (ubuntu-latest, hafpipe-2, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
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Mambaforge is now deprecated!
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test (ubuntu-latest, calling-freebayes-3, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
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Mambaforge is now deprecated!
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test (ubuntu-latest, mapping-bwa-aln-3, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
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Mambaforge is now deprecated!
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test (ubuntu-latest, mapping-bwa-mem2-1, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
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Mambaforge is now deprecated!
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test (ubuntu-latest, mapping-bowtie2-2, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
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Mambaforge is now deprecated!
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test (ubuntu-latest, trimming-fastp-3, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
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Mambaforge is now deprecated!
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test (ubuntu-latest, download, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
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Mambaforge is now deprecated!
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test (ubuntu-24.04, base)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
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Mambaforge is now deprecated!
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test (ubuntu-latest, calling-haplotypecaller-2, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
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Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
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test (ubuntu-latest, calling-haplotypecaller-4, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
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Mambaforge is now deprecated!
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test (ubuntu-latest, calling-bcftools-3, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
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Mambaforge is now deprecated!
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test (ubuntu-latest, hafpipe-4, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
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Mambaforge is now deprecated!
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test (ubuntu-latest, mappings-table, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
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Mambaforge is now deprecated!
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test (ubuntu-latest, mapping-bwa-aln-1, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
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|
Mambaforge is now deprecated!
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test (ubuntu-latest, mapping-bwa-aln-2, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
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Mambaforge is now deprecated!
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test (ubuntu-latest, calling-bcftools-4, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
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Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
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test (ubuntu-latest, trimming-adapterremoval-2, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
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Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
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test (ubuntu-latest, mapping-bwa-mem-1, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
|
|
Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
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test (ubuntu-latest, trimming-adapterremoval-1, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
|
|
Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
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test (ubuntu-latest, calling-bcftools-1, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
|
|
Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
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test (ubuntu-latest, mapping-bwa-aln-4, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
|
|
Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
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test (ubuntu-latest, trimming-cutadapt-2, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
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|
Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
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test (ubuntu-latest, calling-haplotypecaller-1, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
|
|
Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
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test (ubuntu-latest, trimming-adapterremoval-3, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
|
|
Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
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test (ubuntu-latest, duplicates-dedup-2, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
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|
Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
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test (ubuntu-latest, hafpipe-1, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
|
|
Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
|
|
test (ubuntu-22.04, base)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
|
|
Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
|
|
test (ubuntu-latest, trimming-cutadapt-1, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
|
|
Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
|
|
test (ubuntu-latest, hafpipe-3, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
|
|
Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
|
|
example (ubuntu-24.04)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
|
|
Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
|
|
test (ubuntu-latest, trimming-skewer-2, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
|
|
Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
|
|
test (ubuntu-latest, duplicates-dedup-1, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
|
|
Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
|
|
test (ubuntu-latest, pileup-1, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
|
|
Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
|
|
test (ubuntu-latest, trimming-seqprep-2, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
|
|
example (macos-12)
The macOS-12 environment is deprecated, consider switching to macOS-13, macOS-14 (macos-latest) or macOS-15. For more details, see https://github.com/actions/runner-images/issues/10721
|
|
Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
|
|
example (macos-12)
/Users/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
|
|
test (macos-12, base)
The macOS-12 environment is deprecated, consider switching to macOS-13, macOS-14 (macos-latest) or macOS-15. For more details, see https://github.com/actions/runner-images/issues/10721
|
|
Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
|
|
test (macos-12, base)
/Users/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
|
|
Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
|
|
test (macos-13, base)
/Users/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
|
|
Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
|
|
test (ubuntu-latest, trimming-none, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
|
|
Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
|
|
test (ubuntu-latest, trimming-skewer-1, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
|
|
Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
|
|
test (ubuntu-latest, trimming-seqprep-1, mamba)
/home/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
|
|
Mambaforge is now deprecated!
Future Miniforge releases will NOT build Mambaforge installers. We advise you switch to Miniforge at your earliest convenience. More details at https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/.
|
|
example (macos-13)
/Users/runner/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
|
|
envs (macos-12, micromamba)
The macOS-12 environment is deprecated, consider switching to macOS-13, macOS-14 (macos-latest) or macOS-15. For more details, see https://github.com/actions/runner-images/issues/10721
|
|
envs (macos-12, mamba)
The macOS-12 environment is deprecated, consider switching to macOS-13, macOS-14 (macos-latest) or macOS-15. For more details, see https://github.com/actions/runner-images/issues/10721
|
Artifacts
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logs-example-macos-12
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