{
  "_id": "6a251ae04b233be19838d860",
  "Package": "gesel",
  "Version": "0.99.3",
  "Date": "2026-06-07",
  "Title": "Search for Interesting Gene Sets",
  "License": "MIT + file LICENSE",
  "Description": "Query the gesel indices to identify interesting gene sets.\nUsers can test for enrichment in their own list of genes and/or\nsearch by text in the set names or descriptions. The indices\ncan be hosted remotely or on a local filesystem.",
  "Authors@R": "person(\"Aaron\", \"Lun\", role=c(\"aut\", \"cre\"), email=\"infinite.monkeys.with.keyboards@gmail.com\", comment=c(ORCID=\"0000-0002-3564-4813\"))",
  "biocViews": "GeneSetEnrichment, DataImport, Pathways",
  "URL": "https://github.com/gesel-inc/gesel-R",
  "BugReports": "https://github.com/gesel-inc/gesel-R/issues",
  "VignetteBuilder": "knitr",
  "Encoding": "UTF-8",
  "Config/roxygen2/version": "8.0.0",
  "Config/pak/sysreqs": "libssl-dev",
  "Repository": "https://biocstaging.r-universe.dev",
  "Date/Publication": "2026-06-07 04:10:48 UTC",
  "RemoteUrl": "https://github.com/BiocStaging/gesel",
  "RemoteRef": "HEAD",
  "RemoteSha": "a595854f31d71b8c0de039cbb18f171480746850",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-06-07 07:09:17 UTC",
    "User": "root"
  },
  "Author": "Aaron Lun [aut, cre] (ORCID: <https://orcid.org/0000-0002-3564-4813>)",
  "Maintainer": "Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>",
  "MD5sum": "4ecf7eed29a4bbf51442383e01330e7c",
  "_user": "biocstaging",
  "_type": "src",
  "_file": "gesel_0.99.3.tar.gz",
  "_fileid": "ff1847ca4f2e4176bb76b0a278996276eacd2b23564447f70f9eb62de11f9691",
  "_filesize": 226577,
  "_sha256": "ff1847ca4f2e4176bb76b0a278996276eacd2b23564447f70f9eb62de11f9691",
  "_created": "2026-06-07T07:09:17.000Z",
  "_published": "2026-06-07T07:16:48.092Z",
  "_jobs": [
    {
      "job": 79939766507,
      "time": 151,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7461763360"
    },
    {
      "job": 79939766547,
      "time": 255,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7461775774"
    },
    {
      "job": 79939766545,
      "time": 406,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7461792291"
    },
    {
      "job": 79939766548,
      "time": 265,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7461776792"
    },
    {
      "job": 79939766553,
      "time": 374,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7461788770"
    },
    {
      "job": 79939766551,
      "time": 259,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7461776409"
    },
    {
      "job": 79939766549,
      "time": 310,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7461784234"
    },
    {
      "job": 79939766523,
      "time": 269,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7461777053"
    },
    {
      "job": 79939766535,
      "time": 269,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7461779359"
    },
    {
      "job": 79939508278,
      "time": 277,
      "config": "source",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7461744168"
    },
    {
      "job": 79939766506,
      "time": 122,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7461759495"
    },
    {
      "job": 79939766533,
      "time": 260,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7461776139"
    },
    {
      "job": 79939766517,
      "time": 255,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7461775549"
    },
    {
      "job": 79939766536,
      "time": 201,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7461768985"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 6
  },
  "_buildurl": "https://github.com/r-universe/biocstaging/actions/runs/27085653537",
  "_status": "failure",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/BiocStaging/gesel",
  "_commit": {
    "id": "a595854f31d71b8c0de039cbb18f171480746850",
    "author": "LTLA <infinite.monkeys.with.keyboards@gmail.com>",
    "committer": "LTLA <infinite.monkeys.with.keyboards@gmail.com>",
    "message": "Avoid CRLF line endings when writing text files on Windows.\n",
    "time": 1780805448
  },
  "_maintainer": {
    "name": "Aaron Lun",
    "email": "infinite.monkeys.with.keyboards@gmail.com",
    "login": "ltla",
    "orcid": "0000-0002-3564-4813",
    "twitter": "@realAaronLun",
    "description": "(ノಠ益ಠ)ノ彡┻━┻\n",
    "uuid": 8166669
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "assorthead",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "rappdirs",
      "role": "Imports"
    },
    {
      "package": "httr2",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "S4Vectors",
      "role": "Suggests"
    },
    {
      "package": "IRanges",
      "role": "Suggests"
    }
  ],
  "_owner": "biocstaging",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-13",
      "n": 3
    },
    {
      "week": "2026-14",
      "n": 4
    },
    {
      "week": "2026-16",
      "n": 4
    },
    {
      "week": "2026-17",
      "n": 13
    },
    {
      "week": "2026-18",
      "n": 1
    },
    {
      "week": "2026-21",
      "n": 15
    },
    {
      "week": "2026-22",
      "n": 4
    },
    {
      "week": "2026-23",
      "n": 2
    }
  ],
  "_tags": [],
  "_topics": [
    "genesetenrichment",
    "dataimport",
    "pathways",
    "zlib",
    "cpp"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "ltla",
      "count": 78,
      "uuid": 8166669
    }
  ],
  "_userbio": {
    "uuid": 278472782,
    "type": "organization",
    "name": "BiocStaging"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/gesel"
  },
  "_devurl": "https://github.com/gesel-inc/gesel-r",
  "_searchresults": 0,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/gesel.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "cacheDirectory",
    "consolidateBlockSize",
    "createGeneIdentifierMap",
    "databaseUrl",
    "downloadDatabaseFile",
    "downloadDatabaseRanges",
    "downloadGeneFile",
    "downloadMultipartRanges",
    "effectiveNumberOfGenes",
    "fetchAllCollections",
    "fetchAllGenes",
    "fetchAllSets",
    "fetchCollectionSizes",
    "fetchGenesForAllSets",
    "fetchGenesForSomeSets",
    "fetchGeneTypes",
    "fetchGeneVersion",
    "fetchSetsForAllGenes",
    "fetchSetsForSomeGenes",
    "fetchSetSizes",
    "fetchSomeCollections",
    "fetchSomeSets",
    "findOverlappingSets",
    "flushMemoryCache",
    "geneUrl",
    "loadAllSets",
    "mapGenesByName",
    "newConfig",
    "prepareDatabaseFiles",
    "prepareGeneFiles",
    "querySets",
    "rangeConcurrency",
    "readDatabaseRanges",
    "renameGenesInSets",
    "searchGenes",
    "searchOverlappingSets",
    "searchSetText",
    "validateDatabaseFiles",
    "validateGeneFiles"
  ],
  "_help": [
    {
      "page": "cacheDirectory",
      "title": "Gesel cache directory",
      "topics": [
        "cacheDirectory"
      ]
    },
    {
      "page": "consolidateBlockSize",
      "title": "Block size for consolidation",
      "topics": [
        "consolidateBlockSize"
      ]
    },
    {
      "page": "createGeneIdentifierMap",
      "title": "Create mapping of gene identifiers",
      "topics": [
        "createGeneIdentifierMap",
        "mapGenesByName"
      ]
    },
    {
      "page": "downloadDatabaseFile",
      "title": "Download Gesel database files",
      "topics": [
        "databaseUrl",
        "downloadDatabaseFile"
      ]
    },
    {
      "page": "downloadDatabaseRanges",
      "title": "Fetch byte ranges from a Gesel database file",
      "topics": [
        "downloadDatabaseRanges",
        "downloadMultipartRanges"
      ]
    },
    {
      "page": "downloadGeneFile",
      "title": "Fetch Gesel gene annotation files",
      "topics": [
        "downloadGeneFile",
        "geneUrl"
      ]
    },
    {
      "page": "effectiveNumberOfGenes",
      "title": "Effective number of genes",
      "topics": [
        "effectiveNumberOfGenes"
      ]
    },
    {
      "page": "fetchAllCollections",
      "title": "Fetch all gene set collections",
      "topics": [
        "fetchAllCollections"
      ]
    },
    {
      "page": "fetchAllGenes",
      "title": "Fetch all genes",
      "topics": [
        "fetchAllGenes"
      ]
    },
    {
      "page": "fetchAllSets",
      "title": "Fetch all gene sets",
      "topics": [
        "fetchAllSets"
      ]
    },
    {
      "page": "fetchCollectionSizes",
      "title": "Size of collections",
      "topics": [
        "fetchCollectionSizes"
      ]
    },
    {
      "page": "fetchGenesForAllSets",
      "title": "Fetch genes for all sets",
      "topics": [
        "fetchGenesForAllSets"
      ]
    },
    {
      "page": "fetchGenesForSomeSets",
      "title": "Fetch genes for some sets",
      "topics": [
        "fetchGenesForSomeSets"
      ]
    },
    {
      "page": "fetchGeneTypes",
      "title": "Fetch available gene identfier types",
      "topics": [
        "fetchGeneTypes"
      ]
    },
    {
      "page": "fetchGeneVersion",
      "title": "Fetch version of the gene annotation files",
      "topics": [
        "fetchGeneVersion"
      ]
    },
    {
      "page": "fetchSetsForAllGenes",
      "title": "Fetch sets for all genes",
      "topics": [
        "fetchSetsForAllGenes"
      ]
    },
    {
      "page": "fetchSetsForSomeGenes",
      "title": "Fetch sets for some genes",
      "topics": [
        "fetchSetsForSomeGenes"
      ]
    },
    {
      "page": "fetchSetSizes",
      "title": "Size of gene sets",
      "topics": [
        "fetchSetSizes"
      ]
    },
    {
      "page": "fetchSomeCollections",
      "title": "Fetch some collections",
      "topics": [
        "fetchSomeCollections"
      ]
    },
    {
      "page": "fetchSomeSets",
      "title": "Fetch some sets",
      "topics": [
        "fetchSomeSets"
      ]
    },
    {
      "page": "flushMemoryCache",
      "title": "Flush the in-memory cache",
      "topics": [
        "flushMemoryCache"
      ]
    },
    {
      "page": "loadAllSets",
      "title": "Load all gene sets for a species",
      "topics": [
        "loadAllSets"
      ]
    },
    {
      "page": "newConfig",
      "title": "Create a new configuration object",
      "topics": [
        "newConfig"
      ]
    },
    {
      "page": "prepareDatabaseFiles",
      "title": "Prepare the Gesel database",
      "topics": [
        "prepareDatabaseFiles"
      ]
    },
    {
      "page": "prepareGeneFiles",
      "title": "Prepare the Gesel gene annotation files",
      "topics": [
        "prepareGeneFiles"
      ]
    },
    {
      "page": "querySets",
      "title": "Query gene sets",
      "topics": [
        "querySets"
      ]
    },
    {
      "page": "rangeConcurrency",
      "title": "Concurrency of range requests",
      "topics": [
        "rangeConcurrency"
      ]
    },
    {
      "page": "readDatabaseRanges",
      "title": "Read byte ranges from a Gesel database file",
      "topics": [
        "readDatabaseRanges"
      ]
    },
    {
      "page": "renameGenesInSets",
      "title": "Rename genes in their sets",
      "topics": [
        "renameGenesInSets"
      ]
    },
    {
      "page": "searchGenes",
      "title": "Search for genes",
      "topics": [
        "searchGenes"
      ]
    },
    {
      "page": "searchOverlappingSets",
      "title": "Search for overlapping gene sets",
      "topics": [
        "findOverlappingSets",
        "searchOverlappingSets"
      ]
    },
    {
      "page": "searchSetText",
      "title": "Search set text",
      "topics": [
        "searchSetText"
      ]
    },
    {
      "page": "validateDatabaseFiles",
      "title": "Validate Gesel database files",
      "topics": [
        "validateDatabaseFiles",
        "validateGeneFiles"
      ]
    }
  ],
  "_readme": "https://github.com/BiocStaging/gesel/raw/HEAD/README.md",
  "_rundeps": [
    "askpass",
    "assorthead",
    "cli",
    "curl",
    "glue",
    "httr2",
    "lifecycle",
    "magrittr",
    "openssl",
    "R6",
    "rappdirs",
    "Rcpp",
    "rlang",
    "sys",
    "vctrs",
    "withr"
  ],
  "_sysdeps": [
    {
      "shlib": "libz",
      "package": "zlib1g",
      "headers": "zlib1g-dev",
      "source": "zlib",
      "version": "1:1.3.dfsg-3.1ubuntu2.1",
      "name": "zlib",
      "homepage": "http://zlib.net/",
      "description": "compression library - runtime"
    },
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_score": 2.6020599913279625,
  "_indexed": true,
  "_nocasepkg": "gesel",
  "_universes": [
    "biocstaging",
    "ltla",
    "gesel-inc"
  ],
  "_previous": "0.99.2",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.99.3",
      "date": "2026-06-07T07:12:01.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "a595854f31d71b8c0de039cbb18f171480746850",
      "fileid": "550517ee3b86b47809f0e03c644643ffaf6af9091b90175603880abb7f26cf9b",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/27085653537"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.99.3",
      "date": "2026-06-07T07:11:22.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "a595854f31d71b8c0de039cbb18f171480746850",
      "fileid": "988e1a772c1a305689f195259f4eabaa25aaa2d96738cc8efd57338600cd6a98",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/27085653537"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.99.3",
      "date": "2026-06-07T07:11:59.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "a595854f31d71b8c0de039cbb18f171480746850",
      "fileid": "573405e57b485ea2d934617f034dcfd53f2d5332f6df78e01a6cca7543a1f9dd",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/27085653537"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.99.3",
      "date": "2026-06-07T07:11:38.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "a595854f31d71b8c0de039cbb18f171480746850",
      "fileid": "5fe50305569af21f92bbd2f36f479a837f0028ed4d61b04df3a1d126d82b1d0f",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/27085653537"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.99.3",
      "date": "2026-06-07T07:11:19.000Z",
      "arch": "aarch64",
      "commit": "a595854f31d71b8c0de039cbb18f171480746850",
      "fileid": "389833c58baa593a107f78bae148dbf32c2140b8aa26f5406a7a8c2b01c33c77",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/27085653537"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.99.3",
      "date": "2026-06-07T07:12:19.000Z",
      "arch": "x86_64",
      "commit": "a595854f31d71b8c0de039cbb18f171480746850",
      "fileid": "9432dd6820f8d68202f168c7c1c0e7e74881ef7d99d2adb90bebb41d346def5a",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/27085653537"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.99.3",
      "date": "2026-06-07T07:11:39.000Z",
      "arch": "aarch64",
      "commit": "a595854f31d71b8c0de039cbb18f171480746850",
      "fileid": "39fec87632a738d671a4590ea9dd4aa600ad51bb24107fe90b7b58383dc47963",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/27085653537"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.99.3",
      "date": "2026-06-07T07:12:47.000Z",
      "arch": "x86_64",
      "commit": "a595854f31d71b8c0de039cbb18f171480746850",
      "fileid": "5c95af340aff39dc0bc1151bae7084cb98c671ecbbd8ccc558e568dcaf76bb22",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/27085653537"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.99.3",
      "date": "2026-06-07T07:11:42.000Z",
      "arch": "emscripten",
      "commit": "a595854f31d71b8c0de039cbb18f171480746850",
      "fileid": "19a7a11cb11d43f08529c9d4927535144f17c79845f5650258a4962bd36ea2b9",
      "status": "success",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/27085653537"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.99.3",
      "date": "2026-06-07T07:10:58.000Z",
      "arch": "x86_64",
      "commit": "a595854f31d71b8c0de039cbb18f171480746850",
      "fileid": "ccc1da0f4542050007e721749771e7ad3dee42141e7d7c4ac6de20731fe61041",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/27085653537"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.99.3",
      "date": "2026-06-07T07:11:17.000Z",
      "arch": "x86_64",
      "commit": "a595854f31d71b8c0de039cbb18f171480746850",
      "fileid": "30a98262ede5d0adfd69decbbdf41e85cbd00920b8ea9a6bf158338d0ea60ecf",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/27085653537"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.99.3",
      "date": "2026-06-07T07:10:53.000Z",
      "arch": "x86_64",
      "commit": "a595854f31d71b8c0de039cbb18f171480746850",
      "fileid": "7aeb389fbd7076e69604ad2fbeb955fbcb735dd4a31a157f0f98a0d2588a9583",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/27085653537"
    }
  ]
}