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What happened?
I am trying to upgrade the arb-bio recipe from version 6.0 to version 7.0 (on this fork) to be able to run arb, which has now been the newest version since sep 2021, and have been solving package dependency conflicts manually in order to be able to build it. I am following the guidelines here and I get the following error(s) when building locally:
# build and test
bioconda-utils build --docker --mulled-test --git-range master
09:07:30 BIOCONDA INFO Considering total of 9522 recipes.
09:07:30 BIOCONDA INFO Constraining to 1 git modified recipes (arb-bio).
09:07:30 BIOCONDA INFO Processing 1 recipes (arb-bio).
conda-forge/osx-arm64: 82.9MB [00:01, 60.6MB/s] | 0/1 [00:00<?, ?it/s]
conda-forge/linux-aarch64: 96.8MB [00:02, 37.0MB/s] | 0/10 [00:00<?, ?files/s]
bioconda/linux: 37.8MB [00:01, 35.2MB/s] | 1/10 [00:02<00:21, 2.43s/files]
bioconda/linux-aarch64: 1.19MB [00:00, 34.9MB/s] | 2/10 [00:04<00:15, 1.92s/files]
conda-forge/noarch: 96.8MB [00:03, 31.2MB/s] | 3/10 [00:05<00:12, 1.77s/files]
bioconda/osx-arm64: 176kB [00:00, 20.0MB/s]]
conda-forge/osx: 222MB [00:07, 31.4MB/s]█████████████████████▌ | 5/10 [00:07<00:06, 1.29s/files]
bioconda/osx: 30.1MB [00:05, 6.01MB/s]]]s]
bioconda/noarch: 37.6MB [00:00, 114MB/s] █████████████████████████████████████▉ | 7/10 [00:10<00:04, 1.49s/files]
conda-forge/linux: 265MB [00:11, 23.5MB/s]█████████████████████████████████████████████▌ | 8/10 [00:11<00:02, 1.20s/files]
Downloading: 100%|██████████████████████████████████████████████████████████████████████████████████████| 10/10 [00:16<00:00, 1.64s/files]
100%|████████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:17<00:00, 17.43s/it]
The following problems have been found (visit https://bioconda.github.io/contributor/linting.html for details on the particular lints you get below.):/linux: 227MB [00:11, 10.9MB/s]
conda-forge/linux: 245MB [00:11, 14.3MB/s]
ERROR: recipes/arb-bio/meta.yaml:0: missing_run_exports: Recipe should have a run_exports statement that ensures correct pinning in downstream packages
Errors were found
09:07:50 BIOCONDA INFO Considering total of 9522 recipes.
09:07:50 BIOCONDA INFO Constraining to 1 git modified recipes (arb-bio).
09:07:50 BIOCONDA INFO Processing 1 recipes (arb-bio).
09:07:50 BIOCONDA INFO Using docker image quay.io/bioconda/bioconda-utils-build-env-cos7:3.3.1 for building.
09:07:50 BIOCONDA INFO Generating DAG
Loading Recipes: 100%|███████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00, 79.63it/s]
09:07:50 BIOCONDA INFO 1 recipes to build and test:
arb-bio
09:07:50 BIOCONDA INFO Determining expected packages for recipes/arb-bio
WARNING: Setting build platform. This is only useful when pretending to be on another platform, such as for rendering necessary dependencies on a non-native platform. I trust that you know what you're doing.
WARNING: No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.22
Adding in variants from internal_defaults
Adding in variants from /home/kapper/.local/lib/miniforge3/envs/bioconda/conda_build_config.yaml
Adding in variants from /home/kapper/.local/lib/miniforge3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/bioconda_utils-conda_build_config.yaml
Traceback (most recent call last):
File "/home/kapper/.local/lib/miniforge3/envs/bioconda/bin/bioconda-utils", line 10, in <module>
sys.exit(main())
File "/home/kapper/.local/lib/miniforge3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/cli.py", line 1124, in main
argh.dispatch_commands([
File "/home/kapper/.local/lib/miniforge3/envs/bioconda/lib/python3.10/site-packages/argh/dispatching.py", line 511, in dispatch_commands
dispatch(parser, *args, **kwargs)
File "/home/kapper/.local/lib/miniforge3/envs/bioconda/lib/python3.10/site-packages/argh/dispatching.py", line 199, in dispatch
return run_endpoint_function(
File "/home/kapper/.local/lib/miniforge3/envs/bioconda/lib/python3.10/site-packages/argh/dispatching.py", line 270, in run_endpoint_function
return _process_command_output(lines, output_file, raw_output, always_flush)
File "/home/kapper/.local/lib/miniforge3/envs/bioconda/lib/python3.10/site-packages/argh/dispatching.py", line 290, in _process_command_output
for line in lines:
File "/home/kapper/.local/lib/miniforge3/envs/bioconda/lib/python3.10/site-packages/argh/dispatching.py", line 415, in _execute_command
for line in result:
File "/home/kapper/.local/lib/miniforge3/envs/bioconda/lib/python3.10/site-packages/argh/dispatching.py", line 395, in _call
result = function(*positional_values, **values_by_name)
File "<boltons.funcutils.FunctionBuilder-5>", line 2, in build
File "/home/kapper/.local/lib/miniforge3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/cli.py", line 137, in wrapper
func(*args, **kwargs)
File "<boltons.funcutils.FunctionBuilder-4>", line 2, in build
File "/home/kapper/.local/lib/miniforge3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/cli.py", line 66, in wrapper
func(*args, **kwargs)
File "/home/kapper/.local/lib/miniforge3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/cli.py", line 498, in build
success = build_recipes(recipe_folder, config, recipes,
File "/home/kapper/.local/lib/miniforge3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/build.py", line 431, in build_recipes
pkg_paths = utils.get_package_paths(recipe, check_channels, force=force)
File "/home/kapper/.local/lib/miniforge3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/utils.py", line 1122, in get_package_paths
if check_recipe_skippable(recipe, check_channels):
File "/home/kapper/.local/lib/miniforge3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/utils.py", line 1039, in check_recipe_skippable
platform, metas = _load_platform_metas(recipe, finalize=False)
File "/home/kapper/.local/lib/miniforge3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/utils.py", line 1025, in _load_platform_metas
return platform, load_all_meta(recipe, config=config, finalize=finalize)
File "/home/kapper/.local/lib/miniforge3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/utils.py", line 445, in load_all_meta
for (meta, _, _) in api.render(
File "/home/kapper/.local/lib/miniforge3/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 74, in render
for od, om in meta.get_output_metadata_set(
File "/home/kapper/.local/lib/miniforge3/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2694, in get_output_metadata_set
assert output_tuples, (
AssertionError: Error: output metadata set is empty. Please file an issue on the conda-build tracker at https://github.com/conda/conda-build/issues
I'm inexperienced with building conda packages, neither am I a developer on the arb project, so I may be doing something fundamentally wrong, however I'm filing an issue because it says so and because I'm stuck. I'm building on Ubuntu Linux Jammy 22.04 LTS (Pop!_OS).
Appreciate any help in advance and let me know if you need more details!
Conda Info
active environment : bioconda
active env location : /home/kapper/.local/lib/miniforge3/envs/bioconda
shell level : 1
user config file : /home/kapper/.condarc
populated config files : /home/kapper/.local/lib/miniforge3/.condarc
/home/kapper/.condarc
conda version : 23.11.0
conda-build version : not installed
python version : 3.10.13.final.0
solver : libmamba (default)
virtual packages : __archspec=1=skylake
__conda=23.11.0=0
__cuda=12.3=0
__glibc=2.35=0
__linux=6.6.6=0
__unix=0=0
base environment : /home/kapper/.local/lib/miniforge3 (writable)
conda av data dir : /home/kapper/.local/lib/miniforge3/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://conda.anaconda.org/bioconda/linux-64
https://conda.anaconda.org/bioconda/noarch
package cache : /home/kapper/.local/lib/miniforge3/pkgs
/home/kapper/.conda/pkgs
envs directories : /home/kapper/.local/lib/miniforge3/envs
/home/kapper/.conda/envs
platform : linux-64
user-agent : conda/23.11.0 requests/2.31.0 CPython/3.10.13 Linux/6.6.6-76060606-generic pop/22.04 glibc/2.35 solver/libmamba conda-libmamba-solver/23.12.0 libmambapy/1.5.5
UID:GID : 1000:1000
netrc file : None
offline mode : False
Checklist
What happened?
I am trying to upgrade the arb-bio recipe from version 6.0 to version 7.0 (on this fork) to be able to run arb, which has now been the newest version since sep 2021, and have been solving package dependency conflicts manually in order to be able to build it. I am following the guidelines here and I get the following error(s) when building locally:
I'm inexperienced with building conda packages, neither am I a developer on the arb project, so I may be doing something fundamentally wrong, however I'm filing an issue because it says so and because I'm stuck. I'm building on Ubuntu Linux Jammy 22.04 LTS (Pop!_OS).
Appreciate any help in advance and let me know if you need more details!
Conda Info
Conda Config
Conda list
Additional Context
No response
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