conda release issues
I'm currently following the development doc to create a new conda release but get into multiple troubles when reaching the step
conda build --user mlgenetics -c conda-forge -c pytorch -c bioconda conda/
conda-build version 3.21.8 conda version
(1) on my laptop I get an error related to placeholder.
/home/fjay/anaconda3/conda-bld/none_1652539966232/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/bin/python: No such file or directory
I read in multiple places that it could be due to file path string length but the issues are old (previous conda_build versions while I have the latest 3.21.8) and I dont clearly understand what would be the bast fix
full placeholder error on my laptop
(base) fjay@lightfj ~/Documents/WORK/GITLAB/private/dnadna (master) $ conda build --user mlgenetics -c conda-forge -c pytorch -c bioconda conda/
No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.16
WARNING:conda_build.metadata:No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.16
Copying /home/fjay/Documents/WORK/GITLAB/private/dnadna to /home/fjay/anaconda3/conda-bld/none_1652539966232/work/
Adding in variants from internal_defaults
INFO:conda_build.variants:Adding in variants from internal_defaults
Attempting to finalize metadata for dnadna
INFO:conda_build.metadata:Attempting to finalize metadata for dnadna
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): conda.anaconda.org:443
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-4f9057a8-439e-43c1-9dd0-f93b519998f9/conda-forge/linux-64/repodata.json HTTP/1.1" 200 None
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-4f9057a8-439e-43c1-9dd0-f93b519998f9/conda-forge/noarch/repodata.json HTTP/1.1" 200 None
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-4f9057a8-439e-43c1-9dd0-f93b519998f9/pytorch/linux-64/repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-4f9057a8-439e-43c1-9dd0-f93b519998f9/pytorch/noarch/repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-4f9057a8-439e-43c1-9dd0-f93b519998f9/bioconda/linux-64/repodata.json HTTP/1.1" 200 None
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-4f9057a8-439e-43c1-9dd0-f93b519998f9/bioconda/noarch/repodata.json HTTP/1.1" 200 None
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-4f9057a8-439e-43c1-9dd0-f93b519998f9/mlgenetics/linux-64/repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-4f9057a8-439e-43c1-9dd0-f93b519998f9/mlgenetics/noarch/repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443
DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/main/linux-64/repodata.json HTTP/1.1" 200 None
DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/main/noarch/repodata.json HTTP/1.1" 200 None
DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/r/linux-64/repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/r/noarch/repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-4f9057a8-439e-43c1-9dd0-f93b519998f9/terhorst/linux-64/repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-4f9057a8-439e-43c1-9dd0-f93b519998f9/terhorst/noarch/repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-4f9057a8-439e-43c1-9dd0-f93b519998f9/mlgenetics/linux-64 HTTP/1.1" 200 None
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-4f9057a8-439e-43c1-9dd0-f93b519998f9/terhorst/linux-64 HTTP/1.1" 200 None
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-4f9057a8-439e-43c1-9dd0-f93b519998f9/bioconda/linux-64 HTTP/1.1" 302 None
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /bioconda/linux-64/ HTTP/1.1" 200 None
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-4f9057a8-439e-43c1-9dd0-f93b519998f9/conda-forge/linux-64 HTTP/1.1" 302 None
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /conda-forge/linux-64/ HTTP/1.1" 200 None
DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/main/channeldata.json HTTP/1.1" 200 None
DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/r/channeldata.json HTTP/1.1" 200 None
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-4f9057a8-439e-43c1-9dd0-f93b519998f9/pytorch/linux-64 HTTP/1.1" 200 None
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-4f9057a8-439e-43c1-9dd0-f93b519998f9/conda-forge/linux-64/python-3.10.4-h2660328_0_cpython.tar.bz2 HTTP/1.1" 200 30013590
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-4f9057a8-439e-43c1-9dd0-f93b519998f9/conda-forge/noarch/pip-22.1-pyhd8ed1ab_0.tar.bz2 HTTP/1.1" 200 1642380
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
BUILD START: ['dnadna-1.0.0rc2.dev1+gfc14f03-py_0.tar.bz2']
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/fjay/anaconda3/conda-bld/dnadna_1652539968569/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh
The following NEW packages will be INSTALLED:
_libgcc_mutex: 0.1-conda_forge conda-forge
_openmp_mutex: 4.5-2_gnu conda-forge
bzip2: 1.0.8-h7f98852_4 conda-forge
ca-certificates: 2021.10.8-ha878542_0 conda-forge
ld_impl_linux-64: 2.36.1-hea4e1c9_2 conda-forge
libffi: 3.4.2-h7f98852_5 conda-forge
libgcc-ng: 12.1.0-h8d9b700_16 conda-forge
libgomp: 12.1.0-h8d9b700_16 conda-forge
libnsl: 2.0.0-h7f98852_0 conda-forge
libuuid: 2.32.1-h7f98852_1000 conda-forge
libzlib: 1.2.11-h166bdaf_1014 conda-forge
ncurses: 6.3-h27087fc_1 conda-forge
openssl: 3.0.3-h166bdaf_0 conda-forge
packaging: 21.3-pyhd8ed1ab_0 conda-forge
pip: 22.1-pyhd8ed1ab_0 conda-forge
pyparsing: 3.0.9-pyhd8ed1ab_0 conda-forge
python: 3.10.4-h2660328_0_cpython conda-forge
python_abi: 3.10-2_cp310 conda-forge
readline: 8.1-h46c0cb4_0 conda-forge
setuptools: 62.2.0-py310hff52083_0 conda-forge
setuptools-scm: 6.4.2-pyhd8ed1ab_0 conda-forge
sqlite: 3.38.5-h4ff8645_0 conda-forge
tk: 8.6.12-h27826a3_0 conda-forge
tomli: 2.0.1-pyhd8ed1ab_0 conda-forge
tzdata: 2022a-h191b570_0 conda-forge
wheel: 0.37.1-pyhd8ed1ab_0 conda-forge
xz: 5.2.5-h516909a_1 conda-forge
zlib: 1.2.11-h166bdaf_1014 conda-forge
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-4f9057a8-439e-43c1-9dd0-f93b519998f9/conda-forge/noarch/tzdata-2022a-h191b570_0.tar.bz2 HTTP/1.1" 200 123689
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-4f9057a8-439e-43c1-9dd0-f93b519998f9/conda-forge/linux-64/libgomp-12.1.0-h8d9b700_16.tar.bz2 HTTP/1.1" 200 470318
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-4f9057a8-439e-43c1-9dd0-f93b519998f9/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2 HTTP/1.1" 200 23621
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-4f9057a8-439e-43c1-9dd0-f93b519998f9/conda-forge/linux-64/libgcc-ng-12.1.0-h8d9b700_16.tar.bz2 HTTP/1.1" 200 962749
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-4f9057a8-439e-43c1-9dd0-f93b519998f9/conda-forge/linux-64/openssl-3.0.3-h166bdaf_0.tar.bz2 HTTP/1.1" 200 3001172
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-4f9057a8-439e-43c1-9dd0-f93b519998f9/conda-forge/linux-64/sqlite-3.38.5-h4ff8645_0.tar.bz2 HTTP/1.1" 200 1609706
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-4f9057a8-439e-43c1-9dd0-f93b519998f9/conda-forge/noarch/pyparsing-3.0.9-pyhd8ed1ab_0.tar.bz2 HTTP/1.1" 200 81321
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-4f9057a8-439e-43c1-9dd0-f93b519998f9/conda-forge/linux-64/setuptools-62.2.0-py310hff52083_0.tar.bz2 HTTP/1.1" 200 1320063
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
source tree in: /home/fjay/anaconda3/conda-bld/dnadna_1652539968569/work
export PREFIX=/home/fjay/anaconda3/conda-bld/dnadna_1652539968569/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh
export BUILD_PREFIX=/home/fjay/anaconda3/conda-bld/dnadna_1652539968569/_build_env
export SRC_DIR=/home/fjay/anaconda3/conda-bld/dnadna_1652539968569/work
/home/fjay/anaconda3/conda-bld/dnadna_1652539968569/work/conda_build.sh: line 4: /home/fjay/anaconda3/conda-bld/none_1652539966232/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/bin/python: No such file or directory
Traceback (most recent call last):
File "/home/fjay/anaconda3/bin/conda-build", line 11, in <module>
sys.exit(main())
File "/home/fjay/anaconda3/lib/python3.7/site-packages/conda_build/cli/main_build.py", line 488, in main
execute(sys.argv[1:])
File "/home/fjay/anaconda3/lib/python3.7/site-packages/conda_build/cli/main_build.py", line 479, in execute
verify=args.verify, variants=args.variants, cache_dir=args.cache_dir)
File "/home/fjay/anaconda3/lib/python3.7/site-packages/conda_build/api.py", line 195, in build
variants=variants
File "/home/fjay/anaconda3/lib/python3.7/site-packages/conda_build/build.py", line 3093, in build_tree
notest=notest,
File "/home/fjay/anaconda3/lib/python3.7/site-packages/conda_build/build.py", line 2212, in build
cwd=src_dir, stats=build_stats)
File "/home/fjay/anaconda3/lib/python3.7/site-packages/conda_build/utils.py", line 410, in check_call_env
return _func_defaulting_env_to_os_environ('call', *popenargs, **kwargs)
File "/home/fjay/anaconda3/lib/python3.7/site-packages/conda_build/utils.py", line 390, in _func_defaulting_env_to_os_environ
raise subprocess.CalledProcessError(proc.returncode, _args)
subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/home/fjay/anaconda3/conda-bld/dnadna_1652539968569/work/conda_build.sh']' returned non-zero exit status 1.
(base) fjay@lightfj ~/Documents/WORK/GITLAB/private/dnadna (master) $
(2) on titanic I do not get this placeholder issue, but run into a new one linke to jsonschema-pyref, see !144 (merged) for some notes on this package made by @embray
conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {"jsonschema-pyref[version='>=0.1.0']"}
full jsonschema-pyref error on titanic
(dnadna) fjay@titanic-master ~/gitlab/dnadna (master) $ conda build --user mlgenetics -c conda-forge -c pytorch -c bioconda conda/
No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.16
WARNING:conda_build.metadata:No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.16
Copying /home/tao/fjay/gitlab/dnadna to /home/tao/fjay/miniconda3/conda-bld/none_1652612831329/work/
Adding in variants from internal_defaults
INFO:conda_build.variants:Adding in variants from internal_defaults
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
Attempting to finalize metadata for dnadna
INFO:conda_build.metadata:Attempting to finalize metadata for dnadna
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): conda.anaconda.org:443
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-922adc5d-2186-4d7c-8a29-317321e06ac5/conda-forge/linux-64/repodata.json HTTP/1.1" 200 None
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-922adc5d-2186-4d7c-8a29-317321e06ac5/conda-forge/noarch/repodata.json HTTP/1.1" 200 None
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-922adc5d-2186-4d7c-8a29-317321e06ac5/pytorch/linux-64/repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-922adc5d-2186-4d7c-8a29-317321e06ac5/pytorch/noarch/repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-922adc5d-2186-4d7c-8a29-317321e06ac5/bioconda/linux-64/repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-922adc5d-2186-4d7c-8a29-317321e06ac5/bioconda/noarch/repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443
DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/main/linux-64/repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/main/noarch/repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/r/linux-64/repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/r/noarch/repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/main/channeldata.json HTTP/1.1" 200 None
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-922adc5d-2186-4d7c-8a29-317321e06ac5/conda-forge/linux-64 HTTP/1.1" 302 None
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /conda-forge/linux-64/ HTTP/1.1" 200 None
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-922adc5d-2186-4d7c-8a29-317321e06ac5/bioconda/linux-64 HTTP/1.1" 302 None
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /bioconda/linux-64/ HTTP/1.1" 200 None
DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/r/channeldata.json HTTP/1.1" 200 None
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-922adc5d-2186-4d7c-8a29-317321e06ac5/pytorch/linux-64 HTTP/1.1" 200 None
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
BUILD START: ['dnadna-1.0.0rc1-py_0.tar.bz2']
TRACE:charset_normalizer:override steps (5) and chunk_size (512) as content does not fit (917 byte(s) given) parameters.
TRACE:charset_normalizer:ascii passed initial chaos probing. Mean measured chaos is 0.000000 %
TRACE:charset_normalizer:ascii should target any language(s) of ['Latin Based']
DEBUG:charset_normalizer:Encoding detection: ascii is most likely the one.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/tao/fjay/miniconda3/conda-bld/dnadna_1652613277383/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p
The following NEW packages will be INSTALLED:
_libgcc_mutex: 0.1-conda_forge conda-forge
_openmp_mutex: 4.5-2_gnu conda-forge
bzip2: 1.0.8-h7f98852_4 conda-forge
ca-certificates: 2021.10.8-ha878542_0 conda-forge
ld_impl_linux-64: 2.36.1-hea4e1c9_2 conda-forge
libffi: 3.4.2-h7f98852_5 conda-forge
libgcc-ng: 12.1.0-h8d9b700_16 conda-forge
libgomp: 12.1.0-h8d9b700_16 conda-forge
libnsl: 2.0.0-h7f98852_0 conda-forge
libuuid: 2.32.1-h7f98852_1000 conda-forge
libzlib: 1.2.11-h166bdaf_1014 conda-forge
ncurses: 6.3-h27087fc_1 conda-forge
openssl: 3.0.3-h166bdaf_0 conda-forge
packaging: 21.3-pyhd8ed1ab_0 conda-forge
pip: 22.1-pyhd8ed1ab_0 conda-forge
pyparsing: 3.0.9-pyhd8ed1ab_0 conda-forge
python: 3.10.4-h2660328_0_cpython conda-forge
python_abi: 3.10-2_cp310 conda-forge
readline: 8.1-h46c0cb4_0 conda-forge
setuptools: 62.2.0-py310hff52083_0 conda-forge
setuptools-scm: 6.4.2-pyhd8ed1ab_0 conda-forge
sqlite: 3.38.5-h4ff8645_0 conda-forge
tk: 8.6.12-h27826a3_0 conda-forge
tomli: 2.0.1-pyhd8ed1ab_0 conda-forge
tzdata: 2022a-h191b570_0 conda-forge
wheel: 0.37.1-pyhd8ed1ab_0 conda-forge
xz: 5.2.5-h516909a_1 conda-forge
zlib: 1.2.11-h166bdaf_1014 conda-forge
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed
TRACE:charset_normalizer:override steps (5) and chunk_size (512) as content does not fit (917 byte(s) given) parameters.
TRACE:charset_normalizer:ascii passed initial chaos probing. Mean measured chaos is 0.000000 %
TRACE:charset_normalizer:ascii should target any language(s) of ['Latin Based']
DEBUG:charset_normalizer:Encoding detection: ascii is most likely the one.
TRACE:charset_normalizer:override steps (5) and chunk_size (512) as content does not fit (917 byte(s) given) parameters.
TRACE:charset_normalizer:ascii passed initial chaos probing. Mean measured chaos is 0.000000 %
TRACE:charset_normalizer:ascii should target any language(s) of ['Latin Based']
DEBUG:charset_normalizer:Encoding detection: ascii is most likely the one.
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
DEBUG:conda_build._load_setup_py_data:Failed to import numpy for setup patch. Is numpy installed?
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
DEBUG:conda_build._load_setup_py_data:Failed to import numpy for setup patch. Is numpy installed?
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
DEBUG:conda_build._load_setup_py_data:Failed to import numpy for setup patch. Is numpy installed?
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
DEBUG:conda_build._load_setup_py_data:Failed to import numpy for setup patch. Is numpy installed?
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
DEBUG:conda_build._load_setup_py_data:Failed to import numpy for setup patch. Is numpy installed?
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
DEBUG:conda_build._load_setup_py_data:Failed to import numpy for setup patch. Is numpy installed?
Leaving build/test directories:
Work:
/home/tao/fjay/miniconda3/conda-bld/work
Test:
/home/tao/fjay/miniconda3/conda-bld/test_tmp
Leaving build/test environments:
Test:
source activate /home/tao/fjay/miniconda3/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho
Build:
source activate /home/tao/fjay/miniconda3/conda-bld/_build_env
Traceback (most recent call last):
File "/home/tao/fjay/miniconda3/lib/python3.10/site-packages/conda_build/environ.py", line 799, in get_install_actions
actions = install_actions(prefix, index, specs, force=True)
File "/home/tao/fjay/miniconda3/lib/python3.10/site-packages/conda/common/io.py", line 88, in decorated
return f(*args, **kwds)
File "/home/tao/fjay/miniconda3/lib/python3.10/site-packages/conda/plan.py", line 474, in install_actions
txn = solver.solve_for_transaction(prune=prune, ignore_pinned=not pinned)
File "/home/tao/fjay/miniconda3/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction
unlink_precs, link_precs = self.solve_for_diff(update_modifier, deps_modifier,
File "/home/tao/fjay/miniconda3/lib/python3.10/site-packages/conda/core/solve.py", line 195, in solve_for_diff
final_precs = self.solve_final_state(update_modifier, deps_modifier, prune, ignore_pinned,
File "/home/tao/fjay/miniconda3/lib/python3.10/site-packages/conda/core/solve.py", line 313, in solve_final_state
ssc = self._add_specs(ssc)
File "/home/tao/fjay/miniconda3/lib/python3.10/site-packages/conda/core/solve.py", line 603, in _add_specs
explicit_pool = ssc.r._get_package_pool(self.specs_to_add)
File "/home/tao/fjay/miniconda3/lib/python3.10/site-packages/conda/resolve.py", line 555, in _get_package_pool
pool = self.get_reduced_index(specs)
File "/home/tao/fjay/miniconda3/lib/python3.10/site-packages/conda/common/io.py", line 88, in decorated
return f(*args, **kwds)
File "/home/tao/fjay/miniconda3/lib/python3.10/site-packages/conda/resolve.py", line 576, in get_reduced_index
explicit_specs, features = self.verify_specs(explicit_specs)
File "/home/tao/fjay/miniconda3/lib/python3.10/site-packages/conda/resolve.py", line 288, in verify_specs
raise ResolvePackageNotFound(bad_deps)
conda.exceptions.ResolvePackageNotFound:
- jsonschema-pyref[version='>=0.1.0']
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/tao/fjay/miniconda3/bin/conda-build", line 11, in <module>
sys.exit(main())
File "/home/tao/fjay/miniconda3/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 488, in main
execute(sys.argv[1:])
File "/home/tao/fjay/miniconda3/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 477, in execute
outputs = api.build(args.recipe, post=args.post, test_run_post=args.test_run_post,
File "/home/tao/fjay/miniconda3/lib/python3.10/site-packages/conda_build/api.py", line 186, in build
return build_tree(
File "/home/tao/fjay/miniconda3/lib/python3.10/site-packages/conda_build/build.py", line 3088, in build_tree
packages_from_this = build(metadata, stats,
File "/home/tao/fjay/miniconda3/lib/python3.10/site-packages/conda_build/build.py", line 2128, in build
create_build_envs(top_level_pkg, notest)
File "/home/tao/fjay/miniconda3/lib/python3.10/site-packages/conda_build/build.py", line 2006, in create_build_envs
raise e
File "/home/tao/fjay/miniconda3/lib/python3.10/site-packages/conda_build/build.py", line 1985, in create_build_envs
environ.get_install_actions(m.config.test_prefix,
File "/home/tao/fjay/miniconda3/lib/python3.10/site-packages/conda_build/environ.py", line 801, in get_install_actions
raise DependencyNeedsBuildingError(exc, subdir=subdir)
conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {"jsonschema-pyref[version='>=0.1.0']"}
(dnadna) fjay@titanic-master ~/gitlab/dnadna (master) $
I checked the impact of changing the requirement in ./conda/meta.yaml to jsonschema-pyref >=0.1.0b1
but I get a similar error conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {"jsonschema-pyref[version='>=0.1.0b1']"}
I removed entirely the requirement, i.e. the line - jsonschema-pyref >=0.1.0
and now I'm back to the placeholder error
export SRC_DIR=/home/tao/fjay/miniconda3/conda-bld/dnadna_1652618143679/work
/home/tao/fjay/miniconda3/conda-bld/dnadna_1652618143679/work/conda_build.sh: ligne 4: /home/tao/fjay/miniconda3/conda-bld/none_1652617702674/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/bin/python: Aucun fichier ou dossier de ce type
Click to expand
fjay@republic-1 ~/gitlab/dnadna (master) $ conda build --user mlgenetics -c conda-forge -c pytorch -c bioconda conda/
No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.16
WARNING:conda_build.metadata:No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.16
Copying /home/tao/fjay/gitlab/dnadna to /home/tao/fjay/miniconda3/conda-bld/none_1652617702674/work/
Adding in variants from internal_defaults
INFO:conda_build.variants:Adding in variants from internal_defaults
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
Attempting to finalize metadata for dnadna
INFO:conda_build.metadata:Attempting to finalize metadata for dnadna
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
/home/tao/fjay/miniconda3/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
warnings.warn(dedent(msg), SetuptoolsDeprecationWarning)
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): conda.anaconda.org:443
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-922adc5d-2186-4d7c-8a29-317321e06ac5/pytorch/linux-64/repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-922adc5d-2186-4d7c-8a29-317321e06ac5/pytorch/noarch/repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443
DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/main/linux-64/repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/main/noarch/repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/r/linux-64/repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/r/noarch/repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-922adc5d-2186-4d7c-8a29-317321e06ac5/pytorch/linux-64 HTTP/1.1" 200 None
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-922adc5d-2186-4d7c-8a29-317321e06ac5/bioconda/linux-64 HTTP/1.1" 302 None
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /bioconda/linux-64/ HTTP/1.1" 200 None
DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/r/channeldata.json HTTP/1.1" 200 None
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /t/fj-922adc5d-2186-4d7c-8a29-317321e06ac5/conda-forge/linux-64 HTTP/1.1" 302 None
DEBUG:urllib3.connectionpool:https://conda.anaconda.org:443 "GET /conda-forge/linux-64/ HTTP/1.1" 200 None
DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/main/channeldata.json HTTP/1.1" 200 None
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
BUILD START: ['dnadna-1.0.0rc2.dev0+g5ff3d4e.d20220515123551-py_0.tar.bz2']
TRACE:charset_normalizer:override steps (5) and chunk_size (512) as content does not fit (886 byte(s) given) parameters.
TRACE:charset_normalizer:ascii passed initial chaos probing. Mean measured chaos is 0.000000 %
TRACE:charset_normalizer:ascii should target any language(s) of ['Latin Based']
DEBUG:charset_normalizer:Encoding detection: ascii is most likely the one.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/tao/fjay/miniconda3/conda-bld/dnadna_1652618143679/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p
The following NEW packages will be INSTALLED:
_libgcc_mutex: 0.1-conda_forge conda-forge
_openmp_mutex: 4.5-2_gnu conda-forge
bzip2: 1.0.8-h7f98852_4 conda-forge
ca-certificates: 2021.10.8-ha878542_0 conda-forge
ld_impl_linux-64: 2.36.1-hea4e1c9_2 conda-forge
libffi: 3.4.2-h7f98852_5 conda-forge
libgcc-ng: 12.1.0-h8d9b700_16 conda-forge
libgomp: 12.1.0-h8d9b700_16 conda-forge
libnsl: 2.0.0-h7f98852_0 conda-forge
libuuid: 2.32.1-h7f98852_1000 conda-forge
libzlib: 1.2.11-h166bdaf_1014 conda-forge
ncurses: 6.3-h27087fc_1 conda-forge
openssl: 3.0.3-h166bdaf_0 conda-forge
packaging: 21.3-pyhd8ed1ab_0 conda-forge
pip: 22.1-pyhd8ed1ab_0 conda-forge
pyparsing: 3.0.9-pyhd8ed1ab_0 conda-forge
python: 3.10.4-h2660328_0_cpython conda-forge
python_abi: 3.10-2_cp310 conda-forge
readline: 8.1-h46c0cb4_0 conda-forge
setuptools: 62.2.0-py310hff52083_0 conda-forge
setuptools-scm: 6.4.2-pyhd8ed1ab_0 conda-forge
sqlite: 3.38.5-h4ff8645_0 conda-forge
tk: 8.6.12-h27826a3_0 conda-forge
tomli: 2.0.1-pyhd8ed1ab_0 conda-forge
tzdata: 2022a-h191b570_0 conda-forge
wheel: 0.37.1-pyhd8ed1ab_0 conda-forge
xz: 5.2.5-h516909a_1 conda-forge
zlib: 1.2.11-h166bdaf_1014 conda-forge
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
source tree in: /home/tao/fjay/miniconda3/conda-bld/dnadna_1652618143679/work
export PREFIX=/home/tao/fjay/miniconda3/conda-bld/dnadna_1652618143679/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p
export BUILD_PREFIX=/home/tao/fjay/miniconda3/conda-bld/dnadna_1652618143679/_build_env
export SRC_DIR=/home/tao/fjay/miniconda3/conda-bld/dnadna_1652618143679/work
/home/tao/fjay/miniconda3/conda-bld/dnadna_1652618143679/work/conda_build.sh: ligne 4: /home/tao/fjay/miniconda3/conda-bld/none_1652617702674/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/bin/python: Aucun fichier ou dossier de ce type
Traceback (most recent call last):
File "/home/tao/fjay/miniconda3/bin/conda-build", line 11, in <module>
sys.exit(main())
File "/home/tao/fjay/miniconda3/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 488, in main
execute(sys.argv[1:])
File "/home/tao/fjay/miniconda3/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 477, in execute
outputs = api.build(args.recipe, post=args.post, test_run_post=args.test_run_post,
File "/home/tao/fjay/miniconda3/lib/python3.10/site-packages/conda_build/api.py", line 186, in build
return build_tree(
File "/home/tao/fjay/miniconda3/lib/python3.10/site-packages/conda_build/build.py", line 3088, in build_tree
packages_from_this = build(metadata, stats,
File "/home/tao/fjay/miniconda3/lib/python3.10/site-packages/conda_build/build.py", line 2211, in build
utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env,
File "/home/tao/fjay/miniconda3/lib/python3.10/site-packages/conda_build/utils.py", line 410, in check_call_env
return _func_defaulting_env_to_os_environ('call', *popenargs, **kwargs)
File "/home/tao/fjay/miniconda3/lib/python3.10/site-packages/conda_build/utils.py", line 390, in _func_defaulting_env_to_os_environ
raise subprocess.CalledProcessError(proc.returncode, _args)
subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/home/tao/fjay/miniconda3/conda-bld/dnadna_1652618143679/work/conda_build.sh']' returned non-zero exit status 127.
fjay@republic-1 ~/gitlab/dnadna (master) $ conda-build -V
conda-build 3.21.8
fjay@republic-1 ~/gitlab/dnadna (master) $ conda -V
conda 4.12.0
fjay@republic-1 ~/gitlab/dnadna (master) $