brewsci/bio/alphafill: failed

/opt/homebrew/Library/Homebrew/vendor/portable-ruby/3.3.4_1/bin/bundle clean ==> Testing brewsci/bio/alphafill ==> /opt/homebrew/Cellar/alphafill/2.1.0/bin/alphafill create-index ==> /opt/homebrew/Cellar/alphafill/2.1.0/bin/alphafill process --config /private/tmp/alphafill-test-20240916-12473-6mz2fe/alphafill.conf /opt/homebrew/Cellar/alphafill/2.1.0/test/afdb-v4/P2/AF-P29373-F1-model_v4.cif.gz /private/tmp/alphafill-test-20240916-12473-6mz2fe/out.cif.gz Configuration error: The attempt to retrieve compound information for "REA" failed. This information is searched for in a CCD file called components.cif or components.cif.gz which should be located in one of the following directories: "/opt/homebrew/Cellar/alphafill/2.1.0/share/alphafill" (Note that you can add a directory to the search paths by setting the LIBCIFPP_DATA_DIR environmental variable) On Linux an optional cron script might have been installed that automatically updates components.cif and mmCIF dictionary files. This script only works when the file libcifpp.conf contains an uncommented line with the text: update=true If you do not have a working cron script, you can manually update the files in /var/cache/libcifpp using the following commands: curl -o /opt/homebrew/Cellar/libcifpp/7.0.4/var/cache/libcifpp/components.cif https://files.wwpdb.org/pub/pdb/data/monomers/components.cif curl -o /opt/homebrew/Cellar/libcifpp/7.0.4/var/cache/libcifpp/mmcif_pdbx.dic https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic curl -o /opt/homebrew/Cellar/libcifpp/7.0.4/var/cache/libcifpp/mmcif_ma.dic https://github.com/ihmwg/ModelCIF/raw/master/dist/mmcif_ma.dic No compound factory objects are created since none of the data sources is found. Error when processing 1CBS for AF-P29373-F1 >> Trying to insert unknown compound REA (not found in CCD) ==> Testing brewsci/bio/alphafill (again) ==> /opt/homebrew/Cellar/alphafill/2.1.0/bin/alphafill create-index ==> /opt/homebrew/Cellar/alphafill/2.1.0/bin/alphafill process --config /private/tmp/alphafill-test-20240916-12712-z0uatk/alphafill.conf /opt/homebrew/Cellar/alphafill/2.1.0/test/afdb-v4/P2/AF-P29373-F1-model_v4.cif.gz /private/tmp/alphafill-test-20240916-12712-z0uatk/out.cif.gz Configuration error: The attempt to retrieve compound information for "REA" failed. This information is searched for in a CCD file called components.cif or components.cif.gz which should be located in one of the following directories: "/opt/homebrew/Cellar/alphafill/2.1.0/share/alphafill" (Note that you can add a directory to the search paths by setting the LIBCIFPP_DATA_DIR environmental variable) On Linux an optional cron script might have been installed that automatically updates components.cif and mmCIF dictionary files. This script only works when the file libcifpp.conf contains an uncommented line with the text: update=true If you do not have a working cron script, you can manually update the files in /var/cache/libcifpp using the following commands: curl -o /opt/homebrew/Cellar/libcifpp/7.0.4/var/cache/libcifpp/components.cif https://files.wwpdb.org/pub/pdb/data/monomers/components.cif curl -o /opt/homebrew/Cellar/libcifpp/7.0.4/var/cache/libcifpp/mmcif_pdbx.dic https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic curl -o /opt/homebrew/Cellar/libcifpp/7.0.4/var/cache/libcifpp/mmcif_ma.dic https://github.com/ihmwg/ModelCIF/raw/master/dist/mmcif_ma.dic No compound factory objects are created since none of the data sources is found. Error when processing 1CBS for AF-P29373-F1 >> Trying to insert unknown compound REA (not found in CCD) ::error::brewsci/bio/alphafill: failed An exception occurred within a child process: BuildError: Failed executing: /opt/homebrew/Cellar/alphafill/2.1.0/bin/alphafill process --config /private/tmp/alphafill-test-20240916-12712-z0uatk/alphafill.conf /opt/homebrew/Cellar/alphafill/2.1.0/test/afdb-v4/P2/AF-P29373-F1-model_v4.cif.gz /private/tmp/alphafill-test-20240916-12712-z0uatk/out.cif.gz /opt/homebrew/Library/Homebr

Process completed with exit code 1.

brewsci/bio/alphafill: failed

/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/3.3.4_1/bin/bundle clean ==> Testing brewsci/bio/alphafill ==> /home/linuxbrew/.linuxbrew/Cellar/alphafill/2.1.0/bin/alphafill create-index ==> /home/linuxbrew/.linuxbrew/Cellar/alphafill/2.1.0/bin/alphafill process --config /tmp/alphafill-test-20240916-17268-hzplx3/alphafill.conf /home/linuxbrew/.linuxbrew/Cellar/alphafill/2.1.0/test/afdb-v4/P2/AF-P29373-F1-model_v4.cif.gz /tmp/alphafill-test-20240916-17268-hzplx3/out.cif.gz Configuration error: The attempt to retrieve compound information for "REA" failed. This information is searched for in a CCD file called components.cif or components.cif.gz which should be located in one of the following directories: "/home/linuxbrew/.linuxbrew/Cellar/alphafill/2.1.0/share/alphafill" (Note that you can add a directory to the search paths by setting the LIBCIFPP_DATA_DIR environmental variable) On Linux an optional cron script might have been installed that automatically updates components.cif and mmCIF dictionary files. This script only works when the file libcifpp.conf contains an uncommented line with the text: update=true If you do not have a working cron script, you can manually update the files in /var/cache/libcifpp using the following commands: curl -o /home/linuxbrew/.linuxbrew/Cellar/libcifpp/7.0.4/var/cache/libcifpp/components.cif https://files.wwpdb.org/pub/pdb/data/monomers/components.cif curl -o /home/linuxbrew/.linuxbrew/Cellar/libcifpp/7.0.4/var/cache/libcifpp/mmcif_pdbx.dic https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic curl -o /home/linuxbrew/.linuxbrew/Cellar/libcifpp/7.0.4/var/cache/libcifpp/mmcif_ma.dic https://github.com/ihmwg/ModelCIF/raw/master/dist/mmcif_ma.dic No compound factory objects are created since none of the data sources is found. Error when processing 1CBS for AF-P29373-F1 >> Trying to insert unknown compound REA (not found in CCD) ==> Testing brewsci/bio/alphafill (again) ==> /home/linuxbrew/.linuxbrew/Cellar/alphafill/2.1.0/bin/alphafill create-index ==> /home/linuxbrew/.linuxbrew/Cellar/alphafill/2.1.0/bin/alphafill process --config /tmp/alphafill-test-20240916-17470-8d9sag/alphafill.conf /home/linuxbrew/.linuxbrew/Cellar/alphafill/2.1.0/test/afdb-v4/P2/AF-P29373-F1-model_v4.cif.gz /tmp/alphafill-test-20240916-17470-8d9sag/out.cif.gz Configuration error: The attempt to retrieve compound information for "REA" failed. This information is searched for in a CCD file called components.cif or components.cif.gz which should be located in one of the following directories: "/home/linuxbrew/.linuxbrew/Cellar/alphafill/2.1.0/share/alphafill" (Note that you can add a directory to the search paths by setting the LIBCIFPP_DATA_DIR environmental variable) On Linux an optional cron script might have been installed that automatically updates components.cif and mmCIF dictionary files. This script only works when the file libcifpp.conf contains an uncommented line with the text: update=true If you do not have a working cron script, you can manually update the files in /var/cache/libcifpp using the following commands: curl -o /home/linuxbrew/.linuxbrew/Cellar/libcifpp/7.0.4/var/cache/libcifpp/components.cif https://files.wwpdb.org/pub/pdb/data/monomers/components.cif curl -o /home/linuxbrew/.linuxbrew/Cellar/libcifpp/7.0.4/var/cache/libcifpp/mmcif_pdbx.dic https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic curl -o /home/linuxbrew/.linuxbrew/Cellar/libcifpp/7.0.4/var/cache/libcifpp/mmcif_ma.dic https://github.com/ihmwg/ModelCIF/raw/master/dist/mmcif_ma.dic No compound factory objects are created since none of the data sources is found. Error when processing 1CBS for AF-P29373-F1 >> Trying to insert unknown compound REA (not found in CCD) ::error::brewsci/bio/alphafill: failed An exception occurred within a child process: BuildError: Failed executing: /home/linuxbrew/.linuxbrew/Cellar/alphafill/2.1.0/bin/alphafill process --config /tmp/alphafill-test-20240916-17470-8d9sag/alphafill.conf /home/linuxbrew/.linuxbrew/Cellar/alphafill/2.1.0/test/a

Process completed with exit code 1.

brewsci/bio/alphafill: failed

/usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/3.3.4_1/bin/bundle clean ==> Testing brewsci/bio/alphafill ==> /usr/local/Cellar/alphafill/2.1.0/bin/alphafill create-index ==> /usr/local/Cellar/alphafill/2.1.0/bin/alphafill process --config /private/tmp/alphafill-test-20240916-13903-qte521/alphafill.conf /usr/local/Cellar/alphafill/2.1.0/test/afdb-v4/P2/AF-P29373-F1-model_v4.cif.gz /private/tmp/alphafill-test-20240916-13903-qte521/out.cif.gz Configuration error: The attempt to retrieve compound information for "REA" failed. This information is searched for in a CCD file called components.cif or components.cif.gz which should be located in one of the following directories: "/usr/local/Cellar/alphafill/2.1.0/share/alphafill" (Note that you can add a directory to the search paths by setting the LIBCIFPP_DATA_DIR environmental variable) On Linux an optional cron script might have been installed that automatically updates components.cif and mmCIF dictionary files. This script only works when the file libcifpp.conf contains an uncommented line with the text: update=true If you do not have a working cron script, you can manually update the files in /var/cache/libcifpp using the following commands: curl -o /usr/local/Cellar/libcifpp/7.0.4/var/cache/libcifpp/components.cif https://files.wwpdb.org/pub/pdb/data/monomers/components.cif curl -o /usr/local/Cellar/libcifpp/7.0.4/var/cache/libcifpp/mmcif_pdbx.dic https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic curl -o /usr/local/Cellar/libcifpp/7.0.4/var/cache/libcifpp/mmcif_ma.dic https://github.com/ihmwg/ModelCIF/raw/master/dist/mmcif_ma.dic No compound factory objects are created since none of the data sources is found. Error when processing 1CBS for AF-P29373-F1 >> Trying to insert unknown compound REA (not found in CCD) ==> Testing brewsci/bio/alphafill (again) ==> /usr/local/Cellar/alphafill/2.1.0/bin/alphafill create-index ==> /usr/local/Cellar/alphafill/2.1.0/bin/alphafill process --config /private/tmp/alphafill-test-20240916-14212-lswy5o/alphafill.conf /usr/local/Cellar/alphafill/2.1.0/test/afdb-v4/P2/AF-P29373-F1-model_v4.cif.gz /private/tmp/alphafill-test-20240916-14212-lswy5o/out.cif.gz Configuration error: The attempt to retrieve compound information for "REA" failed. This information is searched for in a CCD file called components.cif or components.cif.gz which should be located in one of the following directories: "/usr/local/Cellar/alphafill/2.1.0/share/alphafill" (Note that you can add a directory to the search paths by setting the LIBCIFPP_DATA_DIR environmental variable) On Linux an optional cron script might have been installed that automatically updates components.cif and mmCIF dictionary files. This script only works when the file libcifpp.conf contains an uncommented line with the text: update=true If you do not have a working cron script, you can manually update the files in /var/cache/libcifpp using the following commands: curl -o /usr/local/Cellar/libcifpp/7.0.4/var/cache/libcifpp/components.cif https://files.wwpdb.org/pub/pdb/data/monomers/components.cif curl -o /usr/local/Cellar/libcifpp/7.0.4/var/cache/libcifpp/mmcif_pdbx.dic https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic curl -o /usr/local/Cellar/libcifpp/7.0.4/var/cache/libcifpp/mmcif_ma.dic https://github.com/ihmwg/ModelCIF/raw/master/dist/mmcif_ma.dic No compound factory objects are created since none of the data sources is found. Error when processing 1CBS for AF-P29373-F1 >> Trying to insert unknown compound REA (not found in CCD) ::error::brewsci/bio/alphafill: failed An exception occurred within a child process: BuildError: Failed executing: /usr/local/Cellar/alphafill/2.1.0/bin/alphafill process --config /private/tmp/alphafill-test-20240916-14212-lswy5o/alphafill.conf /usr/local/Cellar/alphafill/2.1.0/test/afdb-v4/P2/AF-P29373-F1-model_v4.cif.gz /private/tmp/alphafill-test-20240916-14212-lswy5o/out.cif.gz /usr/local/Homebrew/Library/Homebrew/formula.rb:3079:in `block in syst