{
  "_id": "6a117ba1acfb0bcc41cfad66",
  "Package": "AnnotationForge",
  "Title": "Tools for building SQLite-based annotation data packages",
  "Description": "Provides code for generating Annotation packages and their\ndatabases.  Packages produced are intended to be used with\nAnnotationDbi.",
  "biocViews": "Annotation, Infrastructure",
  "URL": "https://bioconductor.org/packages/AnnotationForge",
  "BugReports": "https://github.com/Bioconductor/AnnotationForge/issues",
  "Version": "1.54.0",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "Authors@R": "c(\nperson(\"Marc\", \"Carlson\", role = \"aut\"),\nperson(\"Hervé\", \"Pagès\", role = \"aut\"),\nperson(\"Madelyn\", \"Carlson\", role = \"ctb\",\ncomment = \"'Creating probe packages' vignette translation from Sweave to Rmarkdown / HTML\"),\nperson(\"Bioconductor Package Maintainer\", role = \"cre\",\nemail = \"maintainer@bioconductor.org\")\n)",
  "VignetteBuilder": "knitr",
  "BuildKeepEmpty": "TRUE",
  "Collate": "makeAnnDbPkg.R sqlForge_utils.R sqlForge_baseMapBuilder.R\nsqlForge_schemaGen.R sqlForge_tableBuilder.R\nsqlForge_makeAnnPkgs.R sqlForge_wrapBaseDBPkgs.R\nsqlForge_seqnames.R makeProbePackage.R makeOrgPackage.R\nmakeChipPackageFromDataFrames.R makeOrgPackageFromNCBI.R\nNCBI_getters.R makeInparanoidDbs.R\ntest_AnnotationForge_package.R",
  "Date": "2024-10-28",
  "Config/pak/sysreqs": "make libpng-dev libxml2-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:36:38 UTC",
  "RemoteUrl": "https://github.com/bioc/AnnotationForge",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "d0a6124277809d7e0ca6ad9342079ba6faae9496",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-23 09:48:51 UTC",
    "User": "root"
  },
  "Author": "Marc Carlson [aut],\nHervé Pagès [aut],\nMadelyn Carlson [ctb] ('Creating probe packages' vignette translation\nfrom Sweave to Rmarkdown / HTML),\nBioconductor Package Maintainer [cre]",
  "Maintainer": "Bioconductor Package Maintainer <maintainer@bioconductor.org>",
  "MD5sum": "c59e82d2dc29ed9ee7ad9eefa58685eb",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "AnnotationForge_1.54.0.tar.gz",
  "_fileid": "c5ab030866aca125811d5dcbe5282ebdd83c1f4483b1ace8c29c42a575d0ec8c",
  "_filesize": 3526400,
  "_sha256": "c5ab030866aca125811d5dcbe5282ebdd83c1f4483b1ace8c29c42a575d0ec8c",
  "_created": "2026-05-23T09:48:51.000Z",
  "_published": "2026-05-23T10:04:17.156Z",
  "_jobs": [
    {
      "job": 77513406179,
      "time": 310,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7176089779"
    },
    {
      "job": 77513406200,
      "time": 384,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7176096169"
    },
    {
      "job": 77513406203,
      "time": 388,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7176096574"
    },
    {
      "job": 77513406213,
      "time": 214,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7176081588"
    },
    {
      "job": 77513406187,
      "time": 232,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7176083112"
    },
    {
      "job": 77513043412,
      "time": 438,
      "config": "source",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7176063630"
    },
    {
      "job": 77513406183,
      "time": 264,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7176086011"
    },
    {
      "job": 77513406182,
      "time": 876,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7176138497"
    },
    {
      "job": 77513406186,
      "time": 743,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7176126979"
    },
    {
      "job": 77513406181,
      "time": 803,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7176132463"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 5,
    "note": 18
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26329510297",
  "_status": "failure",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/AnnotationForge",
  "_commit": {
    "id": "d0a6124277809d7e0ca6ad9342079ba6faae9496",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777379798
  },
  "_maintainer": {
    "name": "Bioconductor Package Maintainer",
    "email": "maintainer@bioconductor.org",
    "login": "bioconductor-bot",
    "description": "",
    "uuid": 11681645
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "utils",
      "role": "Depends"
    },
    {
      "package": "BiocGenerics",
      "version": ">= 0.15.10",
      "role": "Depends"
    },
    {
      "package": "Biobase",
      "version": ">= 1.17.0",
      "role": "Depends"
    },
    {
      "package": "AnnotationDbi",
      "version": ">= 1.33.14",
      "role": "Depends"
    },
    {
      "package": "DBI",
      "role": "Imports"
    },
    {
      "package": "RSQLite",
      "role": "Imports"
    },
    {
      "package": "XML",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "RCurl",
      "role": "Imports"
    },
    {
      "package": "biomaRt",
      "role": "Suggests"
    },
    {
      "package": "httr",
      "role": "Suggests"
    },
    {
      "package": "GenomeInfoDb",
      "version": ">= 1.17.1",
      "role": "Suggests"
    },
    {
      "package": "Biostrings",
      "role": "Suggests"
    },
    {
      "package": "affy",
      "role": "Suggests"
    },
    {
      "package": "hgu95av2.db",
      "role": "Suggests"
    },
    {
      "package": "human.db0",
      "role": "Suggests"
    },
    {
      "package": "org.Hs.eg.db",
      "role": "Suggests"
    },
    {
      "package": "Homo.sapiens",
      "role": "Suggests"
    },
    {
      "package": "GO.db",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "BiocManager",
      "role": "Suggests"
    },
    {
      "package": "BiocFileCache",
      "role": "Suggests"
    },
    {
      "package": "RUnit",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 16,
  "_updates": [
    {
      "week": "2025-42",
      "n": 1
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.55.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.54.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "annotation",
    "infrastructure",
    "bioconductor-package",
    "core-package"
  ],
  "_stars": 5,
  "_contributors": [
    {
      "user": "lshep",
      "count": 38,
      "uuid": 18724380
    },
    {
      "user": "dtenenba",
      "count": 23,
      "uuid": 2286826
    },
    {
      "user": "jwokaty",
      "count": 17,
      "uuid": 1744257
    },
    {
      "user": "nturaga",
      "count": 14,
      "uuid": 2746443
    },
    {
      "user": "jmacdon",
      "count": 14,
      "uuid": 5940924
    },
    {
      "user": "hpages",
      "count": 12,
      "uuid": 8810451
    },
    {
      "user": "link-ny",
      "count": 6,
      "uuid": 4392950
    },
    {
      "user": "dvantwisk",
      "count": 3,
      "uuid": 10927671
    },
    {
      "user": "kayla-morrell",
      "count": 3,
      "uuid": 32339524
    },
    {
      "user": "vobencha",
      "count": 3,
      "uuid": 2466173
    },
    {
      "user": "mtmorgan",
      "count": 2,
      "uuid": 118552
    },
    {
      "user": "martinholub",
      "count": 2,
      "uuid": 8350200
    },
    {
      "user": "knokknok",
      "count": 1,
      "uuid": 1275796
    },
    {
      "user": "mcarlsn",
      "count": 1,
      "uuid": 105299892
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 3216,
    "source": "https://www.bioconductor.org/packages/stats/bioc/AnnotationForge"
  },
  "_mentions": 11,
  "_devurl": "https://github.com/bioconductor/annotationforge",
  "_searchresults": 214,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/AnnotationForge.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/bioconductor/annotationforge",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "available.chipdbschemas",
    "available.db0pkgs",
    "available.dbschemas",
    "getProbeData_1lq",
    "getProbeDataAffy",
    "loadAnnDbPkgIndex",
    "makeAnnDbPkg",
    "makeChipPackage",
    "makeDBPackage",
    "makeInpDb",
    "makeOrgPackage",
    "makeOrgPackageFromNCBI",
    "makeProbePackage",
    "populateDB",
    "wrapBaseDBPackages"
  ],
  "_help": [
    {
      "page": "available.db0pkgs",
      "title": "available.db0pkgs",
      "topics": [
        "available.chipdbschemas",
        "available.db0pkgs",
        "available.dbschemas"
      ]
    },
    {
      "page": "generateSeqnames_db",
      "title": "Generates the seqnames.db package and database",
      "topics": [
        "generateSeqnames.db"
      ]
    },
    {
      "page": "getProbeData_1lq",
      "title": "Read a 1lq file for an Affymetrix genechip",
      "topics": [
        "getProbeData_1lq"
      ]
    },
    {
      "page": "getProbeDataAffy",
      "title": "Read a data file describing the probe sequences on an Affymetrix genechip",
      "topics": [
        "getProbeDataAffy"
      ]
    },
    {
      "page": "AnnDbPkg-maker",
      "title": "Create an SQLite-based annotation package",
      "topics": [
        "AnnDbPkgSeed",
        "AnnDbPkgSeed-class",
        "class:AnnDbPkgSeed",
        "loadAnnDbPkgIndex",
        "makeAnnDbPkg",
        "makeAnnDbPkg,AnnDbPkgSeed-method",
        "makeAnnDbPkg,character-method",
        "makeAnnDbPkg,list-method"
      ]
    },
    {
      "page": "makeChipPackageFromDataFrames",
      "title": "Making a chip package from annotations available from data.frame of probes mapped to gene IDs and an existing org package.",
      "topics": [
        "makeChipPackage"
      ]
    },
    {
      "page": "sqlForge-makeCHIPDB",
      "title": "Creates a sqlite database, and then makes an annotation package with it",
      "topics": [
        "makeDBPackage"
      ]
    },
    {
      "page": "makeInpDb",
      "title": "Builds an individual DB from online files at inparanoid that is in turn meant for generating Inparanoid 8 based objects.",
      "topics": [
        "makeInpDb"
      ]
    },
    {
      "page": "makeOrgPackage",
      "title": "Making an organism package from annotations available from a set of named data.frames.",
      "topics": [
        "makeOrgPackage"
      ]
    },
    {
      "page": "makeOrgPackageFromNCBI",
      "title": "Make an organism package from annotations available from NCBI.",
      "topics": [
        "makeOrgPackageFromNCBI"
      ]
    },
    {
      "page": "makeProbePackage",
      "title": "Make a package with probe sequence related data for microarrays",
      "topics": [
        "makeProbePackage"
      ]
    },
    {
      "page": "sqlForge-popDB",
      "title": "Populates an SQLite DB with and produces a schema definition",
      "topics": [
        "popBOVINECHIPDB",
        "popBOVINEDB",
        "popCANINECHIPDB",
        "popCANINEDB",
        "popCHICKENCHIPDB",
        "popCHICKENDB",
        "popECOLICHIPDB",
        "popECOLIDB",
        "popFLYCHIPDB",
        "popFLYDB",
        "popHUMANCHIPDB",
        "popHUMANDB",
        "popMALARIADB",
        "popMOUSECHIPDB",
        "popMOUSEDB",
        "popPIGCHIPDB",
        "popPIGDB",
        "popRATCHIPDB",
        "popRATDB",
        "populateDB",
        "popWORMCHIPDB",
        "popWORMDB",
        "popYEASTDB",
        "popYEASTNCBIDB",
        "popZEBRAFISHCHIPDB",
        "popZEBRAFISHDB"
      ]
    },
    {
      "page": "sqlForge-wrapDBPackages",
      "title": "Wrap up all the Base Databases into Packages for distribution",
      "topics": [
        "wrapBaseDBPackages"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/AnnotationForge/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "AnnotationDbi",
    "askpass",
    "Biobase",
    "BiocGenerics",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "cachem",
    "cli",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "fastmap",
    "generics",
    "glue",
    "httr",
    "IRanges",
    "jsonlite",
    "KEGGREST",
    "lifecycle",
    "memoise",
    "mime",
    "openssl",
    "pkgconfig",
    "png",
    "R6",
    "RCurl",
    "rlang",
    "RSQLite",
    "S4Vectors",
    "Seqinfo",
    "sys",
    "vctrs",
    "XML",
    "XVector"
  ],
  "_score": 9.507975666499728,
  "_indexed": false,
  "_nocasepkg": "annotationforge",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/AnnotationForge",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.54.0",
      "date": "2026-05-23T09:54:22.000Z",
      "distro": "noble",
      "commit": "d0a6124277809d7e0ca6ad9342079ba6faae9496",
      "fileid": "3119c3f2af12e743cee589e5cb71bf5d21269342c5a77a683eec9f0b53c1a296",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26329510297"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.54.0",
      "date": "2026-05-23T09:54:31.000Z",
      "distro": "noble",
      "commit": "d0a6124277809d7e0ca6ad9342079ba6faae9496",
      "fileid": "9b4cd137a73065651e5b500de5df4de03bb8830e93a8d56c400578a6312eef28",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26329510297"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.54.0",
      "date": "2026-05-23T09:52:12.000Z",
      "commit": "d0a6124277809d7e0ca6ad9342079ba6faae9496",
      "fileid": "1b46dfb8977dc833478f7ad15747ef75e6be3a3229449e0ece26f53a42a6c529",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26329510297"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.54.0",
      "date": "2026-05-23T09:52:23.000Z",
      "commit": "d0a6124277809d7e0ca6ad9342079ba6faae9496",
      "fileid": "372b234d5bf06b6dd64b2bd6f8ea0b09c09c2474ee736dd495e623ce18160311",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26329510297"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.54.0",
      "date": "2026-05-23T09:53:47.000Z",
      "commit": "d0a6124277809d7e0ca6ad9342079ba6faae9496",
      "fileid": "29491d59d43322d55e7f80446b2608906c73738b8106140b198239f0286c806a",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26329510297"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.54.0",
      "date": "2026-05-23T10:02:24.000Z",
      "commit": "d0a6124277809d7e0ca6ad9342079ba6faae9496",
      "fileid": "c6036d2682ea25f2808ea58a5407eef40fc2fe6bd9a7c7e3524f2c3b27665793",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26329510297"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.54.0",
      "date": "2026-05-23T10:00:16.000Z",
      "commit": "d0a6124277809d7e0ca6ad9342079ba6faae9496",
      "fileid": "ffefbefd42b22757a1be717557263e4c58ed6d6d9d6003f9e6a2c207a5a1a28a",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26329510297"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.54.0",
      "date": "2026-05-23T10:01:14.000Z",
      "commit": "d0a6124277809d7e0ca6ad9342079ba6faae9496",
      "fileid": "d7c1526cf49cdb0d0a3bfde48dfcfc367b9efeefb808a6192668bb771a4dd38d",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26329510297"
    }
  ]
}