{
  "_id": "6a3390b13efcd9bda439ff6c",
  "Package": "UCSC.utils",
  "Title": "Low-level utilities to retrieve data from the UCSC Genome\nBrowser",
  "Description": "A set of low-level utilities to retrieve data from the\nUCSC Genome Browser. Most functions in the package access the\ndata via the UCSC REST API but some of them query the UCSC\nMySQL server directly. Note that the primary purpose of the\npackage is to support higher-level functionalities implemented\nin downstream packages like GenomeInfoDb or txdbmaker.",
  "biocViews": "Infrastructure, GenomeAssembly, Annotation,\nGenomeAnnotation, DataImport",
  "URL": "https://bioconductor.org/packages/UCSC.utils",
  "BugReports": "https://github.com/Bioconductor/UCSC.utils/issues",
  "Version": "1.8.0",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "Authors@R": "person(\"Hervé\", \"Pagès\", role=c(\"aut\", \"cre\"),\nemail=\"hpages.on.github@gmail.com\")",
  "VignetteBuilder": "knitr",
  "Collate": "00utils.R UCSC.api.url.R REST_API.R list_UCSC_genomes.R\nget_UCSC_chrom_sizes.R list_UCSC_tracks.R\nfetch_UCSC_track_data.R UCSC_dbselect.R zzz.R",
  "Config/pak/sysreqs": "libssl-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 13:02:47 UTC",
  "RemoteUrl": "https://github.com/bioc/UCSC.utils",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "e02c191d114d0507bd45df4d4bbbb48220383fbe",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-18 06:26:52 UTC",
    "User": "root"
  },
  "Author": "Hervé Pagès [aut, cre]",
  "Maintainer": "Hervé Pagès <hpages.on.github@gmail.com>",
  "MD5sum": "18b63638d3fede02aa0de3d322f5edcb",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "UCSC.utils_1.8.0.tar.gz",
  "_fileid": "6d5f818e9ef94c62625443609dd91d1e5848b71dde3a51678d598a0e7c09e2d4",
  "_filesize": 142571,
  "_sha256": "6d5f818e9ef94c62625443609dd91d1e5848b71dde3a51678d598a0e7c09e2d4",
  "_created": "2026-06-18T06:26:52.000Z",
  "_published": "2026-06-18T06:31:13.413Z",
  "_jobs": [
    {
      "job": 82068234347,
      "time": 147,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7715785885"
    },
    {
      "job": 82068234359,
      "time": 197,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7715798326"
    },
    {
      "job": 82068234391,
      "time": 216,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7715804931"
    },
    {
      "job": 82068234386,
      "time": 98,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7715774213"
    },
    {
      "job": 82068234377,
      "time": 101,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7715774970"
    },
    {
      "job": 82067858443,
      "time": 176,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7715748847"
    },
    {
      "job": 82068234364,
      "time": 105,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7715777639"
    },
    {
      "job": 82068234513,
      "time": 135,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7715784090"
    },
    {
      "job": 82068234401,
      "time": 116,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7715778842"
    },
    {
      "job": 82068234408,
      "time": 117,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7715779163"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 8
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27740951283",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/UCSC.utils",
  "_commit": {
    "id": "e02c191d114d0507bd45df4d4bbbb48220383fbe",
    "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": 1777381367
  },
  "_maintainer": {
    "name": "Hervé Pagès",
    "email": "hpages.on.github@gmail.com",
    "login": "hpages",
    "linkedin": "in/hervé-pagès-5038527",
    "description": "",
    "uuid": 8810451
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "httr",
      "role": "Imports"
    },
    {
      "package": "jsonlite",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "version": ">= 0.47.6",
      "role": "Imports"
    },
    {
      "package": "DBI",
      "role": "Suggests"
    },
    {
      "package": "RMariaDB",
      "role": "Suggests"
    },
    {
      "package": "GenomeInfoDb",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 337,
  "_updates": [
    {
      "week": "2025-43",
      "n": 2
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2025-50",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.9.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.8.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "infrastructure",
    "genomeassembly",
    "annotation",
    "genomeannotation",
    "dataimport",
    "bioconductor-package",
    "core-package"
  ],
  "_stars": 1,
  "_contributors": [
    {
      "user": "hpages",
      "count": 46,
      "uuid": 8810451
    },
    {
      "user": "jwokaty",
      "count": 10,
      "uuid": 1744257
    },
    {
      "user": "link-ny",
      "count": 1,
      "uuid": 4392950
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 440,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_devurl": "https://github.com/bioconductor/ucsc.utils",
  "_searchresults": 12,
  "_rbuild": "4.6.0",
  "_assets": [
    "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",
    "extra/UCSC.utils.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/bioconductor/ucsc.utils",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "fetch_UCSC_track_data",
    "get_organism_for_UCSC_genome",
    "get_UCSC_chrom_sizes",
    "list_UCSC_genomes",
    "list_UCSC_tracks",
    "UCSC_dbselect",
    "UCSC.api.url"
  ],
  "_help": [
    {
      "page": "fetch_UCSC_track_data",
      "title": "Fetch UCSC track data",
      "topics": [
        "fetch_UCSC_track_data"
      ]
    },
    {
      "page": "get_UCSC_chrom_sizes",
      "title": "List UCSC chromosome sizes",
      "topics": [
        "get_UCSC_chrom_sizes"
      ]
    },
    {
      "page": "list_UCSC_genomes",
      "title": "List UCSC genomes",
      "topics": [
        "get_organism_for_UCSC_genome",
        "list_UCSC_genomes"
      ]
    },
    {
      "page": "list_UCSC_tracks",
      "title": "List UCSC tracks and associated primary tables",
      "topics": [
        "list_UCSC_tracks"
      ]
    },
    {
      "page": "UCSC_dbselect",
      "title": "Conveniently retrieve data from the UCSC MariaDB server",
      "topics": [
        "UCSC_dbselect"
      ]
    },
    {
      "page": "UCSC.api.url",
      "title": "Get or set the default UCSC API URL",
      "topics": [
        "UCSC.api.url"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/UCSC.utils/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "askpass",
    "BiocGenerics",
    "curl",
    "generics",
    "httr",
    "jsonlite",
    "mime",
    "openssl",
    "R6",
    "S4Vectors",
    "sys"
  ],
  "_vignettes": [
    {
      "source": "UCSC.utils.Rmd",
      "filename": "UCSC.utils.html",
      "title": "The UCSC.utils package",
      "author": "Hervé Pagès",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Functions defined in the package",
        "list_UCSC_genomes()",
        "get_UCSC_chrom_sizes()",
        "list_UCSC_tracks()",
        "fetch_UCSC_track_data()",
        "UCSC_dbselect()",
        "Session information"
      ],
      "created": "2024-03-15 01:20:13",
      "modified": "2025-01-14 22:36:58",
      "commits": 8
    }
  ],
  "_score": 7.685992392966589,
  "_indexed": false,
  "_nocasepkg": "ucsc.utils",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/UCSC.utils",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.8.0",
      "date": "2026-06-18T06:29:49.000Z",
      "distro": "noble",
      "commit": "e02c191d114d0507bd45df4d4bbbb48220383fbe",
      "fileid": "ac853d57e0000bb51290942c3a199d8a6bc2a2019132897c93e646c1870cd830",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27740951283"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.8.0",
      "date": "2026-06-18T06:30:10.000Z",
      "distro": "noble",
      "commit": "e02c191d114d0507bd45df4d4bbbb48220383fbe",
      "fileid": "f9eb905f5210e28ebcc30ee73e08e2e57bca5a8477da1bdc58fa167e822a3fe0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27740951283"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.8.0",
      "date": "2026-06-18T06:28:16.000Z",
      "commit": "e02c191d114d0507bd45df4d4bbbb48220383fbe",
      "fileid": "62ff25f99fc0de46634198d65ccebeb9bf8a3c32c09ed05539db6c73eaafd713",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27740951283"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.8.0",
      "date": "2026-06-18T06:28:27.000Z",
      "commit": "e02c191d114d0507bd45df4d4bbbb48220383fbe",
      "fileid": "3ff0485ed181b7233c1eb78ae9a65bf1dc0f18a31e67b8c13f6dd43a52271ef1",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27740951283"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.8.0",
      "date": "2026-06-18T06:29:01.000Z",
      "commit": "e02c191d114d0507bd45df4d4bbbb48220383fbe",
      "fileid": "27355b00d0a9551e6f763481803a02726e3f6897789436b87e9e53423770f229",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27740951283"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.8.0",
      "date": "2026-06-18T06:28:32.000Z",
      "commit": "e02c191d114d0507bd45df4d4bbbb48220383fbe",
      "fileid": "c2e0b2c3d6a235e4a883b653ab838b2beee25e3ae360a6582bbcb0fedfc0aa6e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27740951283"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.8.0",
      "date": "2026-06-18T06:28:09.000Z",
      "commit": "e02c191d114d0507bd45df4d4bbbb48220383fbe",
      "fileid": "478070c4e5b5f004bf29dc7dbac18b92659d22f2db2781533a3414a4184de911",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27740951283"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.8.0",
      "date": "2026-06-18T06:28:11.000Z",
      "commit": "e02c191d114d0507bd45df4d4bbbb48220383fbe",
      "fileid": "b3bffc864b1c57d8a42c33ecb5d21ce038cb31b167db4ada8c2a74c846763168",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27740951283"
    }
  ]
}