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bowtie2 build fix (#1080) #1634

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bowtie2 build fix (#1080)

bowtie2 build fix (#1080) #1634

Triggered via push December 20, 2024 12:55
@katsikorakatsikora
pushed 4add952
develop
Status Success
Total duration 9m 15s
Artifacts –

linux.yml

on: push
Matrix: pip
CI
5m 25s
CI
docs
45s
docs
lint
47s
lint
Matrix: createEnvs
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77 warnings
pip (3.11, .)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
pip (3.11, .[actions])
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
pip (3.12, .)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
pip (3.12, .[actions])
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
pip (3.12, .[docs])
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
pip (3.13, .[docs])
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
pip (3.11, .[docs])
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
pip (3.13, .[actions])
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
pip (3.13, .)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
docs
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
lint
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
CI
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
CI
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
CI
/usr/share/miniconda/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)
createEnvs (CONDA_PREPROCESSING_ENV)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
createEnvs (CONDA_PREPROCESSING_ENV)
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
createEnvs (CONDA_PREPROCESSING_ENV)
/usr/share/miniconda/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)
createEnvs (CONDA_RMATS_ENV)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
createEnvs (CONDA_RMATS_ENV)
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
createEnvs (CONDA_RMATS_ENV)
/usr/share/miniconda/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)
createEnvs (CONDA_pysam_ENV)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
createEnvs (CONDA_pysam_ENV)
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
createEnvs (CONDA_pysam_ENV)
/usr/share/miniconda/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)
createEnvs (CONDA_seurat3_ENV)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
createEnvs (CONDA_seurat3_ENV)
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
createEnvs (CONDA_seurat3_ENV)
/usr/share/miniconda/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)
createEnvs (CONDA_loompy_ENV)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
createEnvs (CONDA_loompy_ENV)
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
createEnvs (CONDA_loompy_ENV)
/usr/share/miniconda/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)
createEnvs (CONDA_FQLINT_ENV)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
createEnvs (CONDA_FQLINT_ENV)
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
createEnvs (CONDA_FQLINT_ENV)
/usr/share/miniconda/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)
createEnvs (CONDA_alevinqc_ENV)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
createEnvs (CONDA_alevinqc_ENV)
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
createEnvs (CONDA_alevinqc_ENV)
/usr/share/miniconda/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)
createEnvs (CONDA_SAMBAMBA_ENV)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
createEnvs (CONDA_SAMBAMBA_ENV)
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
createEnvs (CONDA_SAMBAMBA_ENV)
/usr/share/miniconda/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)
createEnvs (CONDA_RMD_ENV)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
createEnvs (CONDA_RMD_ENV)
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
createEnvs (CONDA_RMD_ENV)
/usr/share/miniconda/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)
createEnvs (CONDA_DNA_MAPPING_ENV)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
createEnvs (CONDA_DNA_MAPPING_ENV)
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
createEnvs (CONDA_DNA_MAPPING_ENV)
/usr/share/miniconda/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)
createEnvs (CONDA_CREATE_INDEX_ENV)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
createEnvs (CONDA_CREATE_INDEX_ENV)
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
createEnvs (CONDA_CREATE_INDEX_ENV)
/usr/share/miniconda/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)
createEnvs (CONDA_CHIPSEQ_ENV)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
createEnvs (CONDA_CHIPSEQ_ENV)
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
createEnvs (CONDA_CHIPSEQ_ENV)
/usr/share/miniconda/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)
createEnvs (CONDA_DSS_ENV)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
createEnvs (CONDA_DSS_ENV)
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
createEnvs (CONDA_DSS_ENV)
/usr/share/miniconda/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)
createEnvs (CONDA_RNASEQ_ENV)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
createEnvs (CONDA_RNASEQ_ENV)
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
createEnvs (CONDA_RNASEQ_ENV)
/usr/share/miniconda/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)
createEnvs (CONDA_ATAC_ENV)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
createEnvs (CONDA_ATAC_ENV)
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
createEnvs (CONDA_ATAC_ENV)
/usr/share/miniconda/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)
createEnvs (CONDA_eisaR_ENV)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
createEnvs (CONDA_eisaR_ENV)
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
createEnvs (CONDA_eisaR_ENV)
/usr/share/miniconda/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)
createEnvs (CONDA_scRNASEQ_ENV)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
createEnvs (CONDA_scRNASEQ_ENV)
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
createEnvs (CONDA_scRNASEQ_ENV)
/usr/share/miniconda/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)
createEnvs (CONDA_SHARED_ENV)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
createEnvs (CONDA_SHARED_ENV)
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
createEnvs (CONDA_SHARED_ENV)
/usr/share/miniconda/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)
createEnvs (CONDA_HIC_ENV)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
createEnvs (CONDA_HIC_ENV)
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
createEnvs (CONDA_HIC_ENV)
/usr/share/miniconda/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)
createEnvs (CONDA_NONCODING_RNASEQ_ENV)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
createEnvs (CONDA_NONCODING_RNASEQ_ENV)
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
createEnvs (CONDA_NONCODING_RNASEQ_ENV)
/usr/share/miniconda/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)
createEnvs (CONDA_WGBS_ENV)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
createEnvs (CONDA_WGBS_ENV)
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
createEnvs (CONDA_WGBS_ENV)
/usr/share/miniconda/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)