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I'm trying to get bioconda-utils autobump set up but can't get it to do anything.
The installation looks fine, I can run the following command without errors, but there's absolutely no change to any file in the repo: bioconda-utils autobump recipes/ --packages nextclade
Despite the logs saying things like finished update:
15:19:56 BIOCONDA INFO Package nextclade=1.4.1=h527b516_0 missing!
15:19:57 BIOCONDA INFO Updating checksum for nextclade 1.4.2
15:19:58 BIOCONDA INFO nextclade has selector in line %i (replace failed)
15:19:58 BIOCONDA WARNING Finished update
Is that what's expected? The documentation is a bit sparse, can't figure out what I'm doing wrong.
Output:
bioconda-recipes on master via 🐍 v3.7.1 via 🅒 bioconda-nextclade
❯ bioconda-utils autobump recipes/ --packages nextclade
15:19:06 BIOCONDA INFO Hosters loaded: ['FTPHoster', 'GithubRelease', 'GithubTag', 'GithubReleaseAttachment', 'GithubRepoStore', 'Bioconductor', 'CargoPort', 'SourceForge', 'PyPi', 'Bioarchive', 'CPAN', 'CRAN', 'BitBucketTag', 'BitBucketDownload', 'GitlabTag']
15:19:06 BIOCONDA WARNING Selected 1 packages
15:19:06 BIOCONDA INFO Building Recipe DAG
15:19:09 BIOCONDA INFO ucsc-axtchain has duplicate key
15:19:11 BIOCONDA INFO ucsc-axtswap has duplicate key
15:19:13 BIOCONDA INFO ucsc-axtsort has duplicate key
15:19:14 BIOCONDA INFO ucsc-autoxml has duplicate key
15:19:15 BIOCONDA INFO ucsc-bamtopsl has duplicate key
15:19:19 BIOCONDA INFO ucsc-avecols has duplicate key
15:19:19 BIOCONDA INFO ucsc-ameme has duplicate key
15:19:20 BIOCONDA INFO ucsc-axttomaf has duplicate key
15:19:26 BIOCONDA INFO ucsc-autodtd has duplicate key
15:19:27 BIOCONDA INFO openduck has duplicate key
15:19:28 BIOCONDA INFO ucsc-axttopsl has duplicate key
15:19:29 BIOCONDA INFO ucsc-bedcommonregions has duplicate key
15:19:29 BIOCONDA INFO ucsc-autosql has duplicate key
15:19:30 BIOCONDA INFO ucsc-bedclip has duplicate key
15:19:32 BIOCONDA INFO ucsc-addcols has duplicate key
Loading Recipes...: 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 8220/8220 [00:28<00:00, 293.52it/s]
15:19:35 BIOCONDA INFO Building Recipe DAG: done (7061 nodes, 21053 edges)
15:19:35 BIOCONDA WARNING Graph contains 1 packages (blacklist excluded)
15:19:35 BIOCONDA WARNING Excluding 1306 blacklisted recipes
15:19:35 BIOCONDA INFO Loading package lists for ['conda-forge']
defaults/noarch: 4.49MB [00:00, 15.7MB/s] | 0/9 [00:00<?, ?files/s]
bioconda/linux: 23.4MB [00:00, 27.3MB/s] | 1/9 [00:00<00:04, 1.99files/s]
defaults/osx: 25.7MB [00:01, 17.0MB/s]s]
defaults/linux: 28.0MB [00:02, 13.0MB/s]█████▎ | 2/9 [00:02<00:08, 1.28s/files]
bioconda/osx: 19.0MB [00:00, 46.0MB/s]██████████████████████████████████▋ | 4/9 [00:03<00:03, 1.42files/s]
conda-forge/noarch: 43.0MB [00:04, 11.2MB/s]██████████████████████████████████████████▎ | 5/9 [00:04<00:03, 1.26files/s]
bioconda/noarch: 20.8MB [00:02, 8.32MB/s]███████████████████████████████████████████████████████████ | 6/9 [00:05<00:03, 1.07s/files]
conda-forge/osx: 129MB [00:07, 18.0MB/s]█████████████████████████████████████████████████████████████████████████▋ | 7/9 [00:06<00:02, 1.02s/files]
conda-forge/linux: 143MB [00:12, 12.1MB/s]█████████████████████████████████████████████████████████████████████████████████████▎ | 8/9 [00:12<00:02, 2.48s/files]
Downloading: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 9/9 [00:18<00:00, 2.05s/files]
15:19:55 BIOCONDA INFO Running pipeline with these steps:
15:19:55 BIOCONDA INFO 1. Exclude recipes disabled via config
15:19:55 BIOCONDA INFO 2. Exclude blacklisted recipes: build-fail-blacklist / 1306 recipes
15:19:55 BIOCONDA INFO 3. Exclude sub-recipes
15:19:55 BIOCONDA INFO 4. Exclude recipes depending on packages in need of update
15:19:55 BIOCONDA INFO 5. Load the recipe from the filesystem
15:19:55 BIOCONDA INFO 6. Exclude recipes in conda-forge
15:19:55 BIOCONDA INFO 7. Bump recipes in need of rebuild after pinning changes
15:19:55 BIOCONDA INFO 8. Scan upstream for new releases and update recipe
15:19:55 BIOCONDA INFO 9. Update source checksums
15:19:55 BIOCONDA INFO 10. Write recipe to filesystem
15:19:56 BIOCONDA INFO Package nextclade=1.4.1=h527b516_0 missing!
15:19:57 BIOCONDA INFO Updating checksum for nextclade 1.4.2
15:19:58 BIOCONDA INFO nextclade has selector in line %i (replace failed)
100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:02<00:00, 2.27s/it]
15:19:58 BIOCONDA WARNING Finished update
15:19:58 BIOCONDA INFO Unrecognized URL stats:
15:19:58 BIOCONDA INFO
15:19:58 BIOCONDA INFO Recipe status statistics:
15:19:58 BIOCONDA INFO HasSelector: 1
15:19:58 BIOCONDA INFO SUM: 1
The text was updated successfully, but these errors were encountered:
I'm trying to get
bioconda-utils autobumpset up but can't get it to do anything.The installation looks fine, I can run the following command without errors, but there's absolutely no change to any file in the repo:
bioconda-utils autobump recipes/ --packages nextcladeDespite the logs saying things like
finished update:Is that what's expected? The documentation is a bit sparse, can't figure out what I'm doing wrong.
Output:
The text was updated successfully, but these errors were encountered: