--- ## Lines that must be updated when we release a new software version are ## indicated in comments below output_dir: output staging_deploy_root: biocadmin@staging.bioconductor.org:/loc/www/bioconductor-test-new production_deploy_root: webadmin@master.bioconductor.org:/extra/www/bioc staging_dir: /loc/www/bioconductor-test-new ## CHANGE THIS WHEN WE RELEASE A VERSION: release_version: "3.22" r_version_associated_with_release: "4.5.0" r_version_associated_with_devel: "4.6.0" ## CHANGE THIS WHEN WE RELEASE A VERSION: devel_version: "3.23" ## CHANGE THIS WHEN WE ADD A VERSION: ## This is the list of all versions for which we want to generate "new" ## bioc-views, package index, and package detail pages. ## if old versions (no older than 2.5) need to be rebuilt for any reason, ## add them here, but in most cases this should just contain the ## release and devel versions (though after a release you should ## let the no-longer-release version build one last time so package ## landing pages won't say "release version"): versions: - "3.22" - "3.23" ## CHANGE THIS (i.e., uncomment) as various parts of the new devel version ## become available. set to "[]" if none are available. devel_repos: - "bioc" - "data/experiment" - "workflows" - "data/annotation" ## CHANGE this when the build machines change: ## also, don't include machines that are not building yet (comment them out) active_release_builders: linux: "nebbiolo2" mac_monterey: "lconway" mac_ventura: "kjohnson3" # windows: "palomino8" active_devel_builders: linux: "nebbiolo1" # windows: "palomino7" # mac_monterey: "merida1" ## CHANGE this when the single package builder builds ## on a newer version of bioc single_package_builder: bioc_version: "3.23" r_version: "4.6" rss_hub_url: "https://pubsubhubbub.appspot.com/" ## CHANGE these as AMI IDS change ami_ids: bioc2_8: ami-3a2ef452 bioc2_9: ami-2623f94e bioc2_10: ami-5621fb3e bioc2_11: ami-f827fd90 bioc2_12: ami-7224fe1a bioc2_13: ami-4a25ff22 bioc2_14: ami-9c25fff4 bioc3_0: ami-be7917d6 bioc3_1: ami-a3d126c8 bioc3_2: ami-85d88de0 bioc3_3: ami-abd0b3bc bioc3_4: ami-8946709f bioc3_5: ami-279a315d bioc3_6: ami-ac5df1d3 bioc3_7: ami-01bcd08e357360496 bioc3_8: ami-0565362d8bfb9cbed bioc3_9: ami-0f5d1990d8c571cdf bioc3_10: ami-0c5ab50ca03a54468 bioc3_11: ami-071b80cf0d8ca085c bioc3_12: ami-04c69d122c1cf7e81 bioc3_13: ami-0e7efd11a6eab85a6 string_pattern_type: legacy data_sources: - items_root: / layouts_root: / type: filesystem_unified identifier_type: legacy encoding: utf-8 config: encoding: utf-8 - items_root: / type: biostar_list identifier_type: legacy encoding: utf-8 config: gmane_rss_url: 'http://rss.gmane.org/messages/excerpts/gmane.science.biology.informatics.conductor' cache_file: tmp/gmane_list_cache_file.yaml encoding: utf-8 ttl: 10 - items_root: /help/bioc-views/package-pages layouts_root: / type: bioc_views identifier_type: legacy encoding: utf-8 config: json_dir: "assets/packages/json" encoding: utf-8 - items_root: /help/publications/papers/pubmed type: pubmed_papers identifier_type: legacy encoding: utf-8 config: cache_file: tmp/pubmed_cache_file.yaml retmax: 10 ttl: 24 baseurl: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/ # queried database, e.g. "pubmed" or "pmc"; can be a vector db: [pubmed, pmc] term: bioconductor # Sorting of query results. This one is database-specific; possible values include # pubmed: pub+date, first+author, last+author, journal, title, relevance # pmc: print+pub+date, electronic+pub+date, journal, pmc+live+date # For default sorting leave this field out sort: [ "", electronic+pub+date] # CHANGE THIS when it becomes apparent which future versions of BioC will # work with which versions of R: r_ver_for_bioc_ver: "1.6": "2.1" "1.7": "2.2" "1.8": "2.3" "1.9": "2.4" "2.0": "2.5" "2.1": "2.6" "2.2": "2.7" "2.3": "2.8" "2.4": "2.9" "2.5": "2.10" "2.6": "2.11" "2.7": "2.12" "2.8": "2.13" "2.9": "2.14" "2.10": "2.15" "2.11": "2.15" # R switching to yearly releases, BioC remaining the same "2.12": "3.0" "2.13": "3.0" "2.14": "3.1" "3.0": "3.1" "3.1": "3.2" "3.2": "3.2" "3.3": "3.3" "3.4": "3.3" "3.5": "3.4" "3.6": "3.4" "3.7": "3.5" "3.8": "3.5" "3.9": "3.6" "3.10": "3.6" "3.11": "4.0" "3.12": "4.0" "3.13": "4.1" "3.14": "4.1" "3.15": "4.2" "3.16": "4.2" "3.17": "4.3" "3.18": "4.3" "3.19": "4.4" "3.20": "4.4" "3.21": "4.5" "3.22": "4.5" "3.23": "4.6" # UPDATE THIS when we release a version release_dates: # old info from http://en.wikipedia.org/wiki/Bioconductor#Milestones "1.0": "1/5/2001" "1.1": "11/19/2002" "1.2": "5/29/2003" "1.3": "10/30/2003" "1.4": "5/17/2004" "1.5": "10/25/2004" "1.6": "5/18/2005" "1.7": "10/14/2005" "1.8": "4/27/2006" "1.9": "10/4/2006" "2.0": "4/26/2007" "2.1": "10/8/2007" "2.2": "5/1/2008" "2.3": "10/22/2008" "2.4": "4/21/2009" "2.5": "10/28/2009" "2.6": "4/23/2010" "2.7": "10/18/2010" "2.8": "4/14/2011" "2.9": "11/1/2011" "2.10": "4/2/2012" "2.11": "10/3/2012" "2.12": "4/4/2013" "2.13": "10/15/2013" "2.14": "4/14/2014" "3.0": "10/14/2014" "3.1": "4/17/2015" "3.2": "10/14/2015" "3.3": "5/4/2016" "3.4": "10/18/2016" "3.5": "4/25/2017" "3.6": "10/31/2017" "3.7": "05/01/2018" "3.8": "10/31/2018" "3.9": "05/03/2019" "3.10": "10/30/2019" "3.11": "04/28/2020" "3.12": "10/28/2020" "3.13": "05/20/2021" "3.14": "10/27/2021" "3.15": "04/27/2022" "3.16": "11/02/2022" "3.17": "04/26/2023" "3.18": "10/25/2023" "3.19": "05/01/2024" "3.20": "10/30/2024" "3.21": "04/16/2025" "3.22": "10/30/2025" release_last_built_dates: '2.0': 09/12/2007 '2.1': 04/09/2008 '2.2': 10/16/2008 '2.3': 04/18/2009 '2.4': 10/20/2009 '2.5': 04/03/2010 '2.6': 10/05/2010 '2.7': 04/07/2011 '2.8': 10/21/2011 '2.9': 03/24/2012 '2.10': 09/24/2012 '2.11': 03/25/2013 '2.12': 10/09/2013 '2.13': 04/05/2014 '2.14': 10/08/2014 '3.0': 04/10/2015 '3.1': 10/09/2015 '3.2': 04/23/2016 '3.3': 10/13/2016 '3.4': 04/15/2017 '3.5': 10/18/2017 '3.6': 04/12/2018 '3.7': 10/17/2018 '3.8': 04/16/2019 '3.9': 10/16/2019 '3.10': 04/15/2020 '3.11': 10/17/2020 '3.12': 05/06/2021 '3.13': 10/15/2021 '3.14': 04/13/2022 '3.15': 10/19/2022 '3.16': 04/12/2023 '3.17': 10/16/2023 '3.18': 04/17/2024 '3.19': 10/18/2024 '3.20': 04/02/2025 '3.21': 10/16/2025 mirrors: - 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