{
  "_id": "6ae797042e87f76f20acd806",
  "Package": "GDSArray",
  "Title": "Representing GDS files as array-like objects",
  "Version": "1.32.0",
  "Authors@R": "c(\nperson(\"Qian\", \"Liu\", email = \"qliu7@buffalo.edu\", role=c(\"aut\")),\nperson(\"Martin\", \"Morgan\", role = c(\"aut\")),\nperson(\"Hervé\",  \"Pagès\", role = c(\"aut\")),\nperson(\"Xiuwen\", \"Zheng\", email = \"zhengx@u.washington.edu\", role = c(\"aut\", \"cre\")))",
  "Description": "GDS files are widely used to represent genotyping or\nsequence data. The GDSArray package implements the `GDSArray`\nclass to represent nodes in GDS files in a matrix-like\nrepresentation that allows easy manipulation (e.g., subsetting,\nmathematical transformation) in _R_. The data remains on disk\nuntil needed, so that very large files can be processed.",
  "biocViews": "Infrastructure, DataRepresentation, Sequencing,\nGenotypingArray",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "URL": "https://github.com/Bioconductor/GDSArray",
  "BugReports": "https://github.com/Bioconductor/GDSArray/issues",
  "RoxygenNote": "7.3.1",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "Bioconductor 3.23",
  "Date/Publication": "2026-04-28 12:47:39 UTC",
  "RemoteUrl": "https://github.com/bioc/GDSArray",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "061b5043a5d4fb0f7932c75d3ca42097c57a3472",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-11-01 17:42:22 UTC",
    "User": "root"
  },
  "Author": "Qian Liu [aut],\nMartin Morgan [aut],\nHervé Pagès [aut],\nXiuwen Zheng [aut, cre]",
  "Maintainer": "Xiuwen Zheng <zhengx@u.washington.edu>",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "GDSArray_1.32.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/d81cd3ec56ca63d0232fe82cab52cae83d335bbf72c337d36970fbbe88626e0c",
  "_filesize": 117868,
  "_sha256": "d81cd3ec56ca63d0232fe82cab52cae83d335bbf72c337d36970fbbe88626e0c",
  "_expires": "2027-02-09T19:46:10.000Z",
  "_created": "2026-11-01T17:42:22.000Z",
  "_published": "2026-11-01T19:46:12.281Z",
  "_upstream": "https://github.com/bioc/GDSArray",
  "_status": "success",
  "_maintainer": {
    "name": "Xiuwen Zheng",
    "email": "zhengx@u.washington.edu"
  },
  "_jobs": [
    {
      "job": 124926499666,
      "time": 157,
      "config": "bioc-checks",
      "r": "4.6.2",
      "check": "NOTE",
      "artifact": "13094890599"
    },
    {
      "job": 124926499640,
      "time": 239,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "13094134621"
    },
    {
      "job": 124926499732,
      "time": 266,
      "config": "linux-release-x86_64",
      "r": "4.6.2",
      "check": "NOTE",
      "artifact": "13095130089"
    },
    {
      "job": 124926499831,
      "time": 156,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "13098367524"
    },
    {
      "job": 124926499671,
      "time": 200,
      "config": "macos-release-arm64",
      "r": "4.6.2",
      "check": "NOTE",
      "artifact": "13098117133"
    },
    {
      "job": 124924052315,
      "time": 223,
      "config": "source",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13094147258"
    },
    {
      "job": 124926499652,
      "time": 98,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "13094064527"
    },
    {
      "job": 124926499731,
      "time": 130,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "13094051928"
    },
    {
      "job": 124926499725,
      "time": 151,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "13093958761"
    },
    {
      "job": 124926499706,
      "time": 150,
      "config": "windows-release-x86_64",
      "r": "4.6.2",
      "check": "NOTE",
      "artifact": "13093019815"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 7
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/41331153489",
  "_commit": {
    "id": "061b5043a5d4fb0f7932c75d3ca42097c57a3472",
    "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": 1777380459
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5",
      "role": "Depends"
    },
    {
      "package": "gdsfmt",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "BiocGenerics",
      "role": "Depends"
    },
    {
      "package": "DelayedArray",
      "version": ">= 0.5.32",
      "role": "Depends"
    },
    {
      "package": "tools",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "version": ">= 0.17.34",
      "role": "Imports"
    },
    {
      "package": "SNPRelate",
      "role": "Imports"
    },
    {
      "package": "SeqArray",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "markdown",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "BiocManager",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 2,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.33.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.32.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "infrastructure",
    "datarepresentation",
    "sequencing",
    "genotypingarray"
  ],
  "_stars": 5,
  "_contributors": [
    {
      "user": "liubuntu",
      "count": 68,
      "uuid": 12683977
    },
    {
      "user": "jwokaty",
      "count": 16,
      "uuid": 1744257
    },
    {
      "user": "nturaga",
      "count": 14,
      "uuid": 2746443
    },
    {
      "user": "hpages",
      "count": 4,
      "uuid": 8810451
    },
    {
      "user": "zhengxwen",
      "count": 2,
      "uuid": 6189013
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    },
    {
      "user": "mtmorgan",
      "count": 1,
      "uuid": 118552
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 482,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 542,
    "source": "https://www.bioconductor.org/packages/stats/bioc/GDSArray"
  },
  "_devurl": "https://github.com/bioconductor/gdsarray",
  "_searchresults": 12,
  "_abi": {
    "exports": [
      {
        "key": "GDSArray::GDSArray",
        "hash": "740f6242f56ca495"
      },
      {
        "key": "GDSArray::GDSArraySeed",
        "hash": "be402a99285d2263"
      },
      {
        "key": "GDSArray::GDSFile",
        "hash": "0bcd9c09fcedbea9"
      },
      {
        "key": "GDSArray::GDSMatrix",
        "hash": "c5c3504ac264bf42"
      },
      {
        "key": "GDSArray::generic:gdsfile",
        "hash": "1f59316bcac343cd"
      },
      {
        "key": "GDSArray::generic:gdsfile<-",
        "hash": "975d57b131440a74"
      },
      {
        "key": "GDSArray::generic:gdsnodes",
        "hash": "b4a70ea7ef181c42"
      }
    ],
    "imports": [
      {
        "key": "DelayedArray::DelayedArray",
        "hash": "5c4ba6006d92cc2c"
      },
      {
        "key": "DelayedArray::DelayedMatrix",
        "hash": "6739f3d1c307b585"
      },
      {
        "key": "DelayedArray::DelayedOp",
        "hash": "959c97d4541a9ac0"
      },
      {
        "key": "DelayedArray::DelayedUnaryIsoOp",
        "hash": "f59692a927d0b94a"
      },
      {
        "key": "DelayedArray::DelayedUnaryOp",
        "hash": "692bde9f2d873893"
      },
      {
        "key": "DelayedArray::generic:DelayedArray",
        "hash": "5fd6a2d0f540c19e"
      },
      {
        "key": "DelayedArray::generic:matrixClass",
        "hash": "e7bd8844a56e40d9"
      },
      {
        "key": "DelayedArray::generic:seed",
        "hash": "6fcbaf609ea7f941"
      },
      {
        "key": "DelayedArray::generic:seed<-",
        "hash": "66abd3f9ac2036b4"
      },
      {
        "key": "S4Arrays::Array",
        "hash": "44e3db83d6a4f33f"
      },
      {
        "key": "S4Arrays::generic:extract_array",
        "hash": "adbc2aea8ccb7fa5"
      },
      {
        "key": "S4Vectors::RectangularData",
        "hash": "d414a10823a4aada"
      }
    ]
  },
  "_rbuild": "4.6.2",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/GDSArray.html",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_homeurl": "https://github.com/bioconductor/gdsarray",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "acquireGDS",
    "coerce",
    "extract_array",
    "GDSArray",
    "gdsExampleFileName",
    "gdsfile",
    "GDSFile",
    "gdsfile<-",
    "gdsnodes",
    "releaseGDS",
    "seed",
    "seed<-"
  ],
  "_help": [
    {
      "page": "acquireGDS",
      "title": "Acquire the GDS file connection in R in the 'gds.class' class.",
      "topics": [
        "acquireGDS",
        "releaseGDS"
      ]
    },
    {
      "page": "GDSArray-classes",
      "title": "GDSArray constructor and coercion methods.",
      "topics": [
        "coerce",
        "coerce,ANY,GDSMatrix-method",
        "coerce,GDSArray,GDSMatrix-method",
        "coerce,GDSMatrix,GDSArray-method",
        "extract_array",
        "extract_array,GDSArraySeed-method",
        "GDSArray",
        "GDSArray-class",
        "GDSArray-data",
        "GDSArray-method",
        "gdsExampleFileName",
        "GDSMatrix",
        "GDSMatrix-class",
        "matrixClass,GDSArray-method"
      ]
    },
    {
      "page": "GDSFile-class",
      "title": "GDSFile constructor and methods.",
      "topics": [
        "$,GDSFile-method",
        "GDSFile",
        "GDSFile,gdsfile-method",
        "gdsfile,GDSFile-method",
        "GDSFile-class",
        "GDSFile-constructor",
        "GDSFile-method",
        "gdsfile<-",
        "gdsfile<-,GDSFile-method",
        "gdsnodes",
        "gdsnodes,ANY-method",
        "gdsnodes,GDSFile-method"
      ]
    },
    {
      "page": "GDSArray-methods",
      "title": "GDSArraySeed or GDSArray related methods, slot getters and setters.",
      "topics": [
        "gdsfile",
        "gdsfile,DelayedArray-method",
        "gdsfile,GDSArray-method",
        "gdsfile,GDSArraySeed-method",
        "seed,GDSArray-method",
        "seed<-,GDSArray-method"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/GDSArray/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "BiocGenerics",
    "Biostrings",
    "crayon",
    "DelayedArray",
    "digest",
    "gdsfmt",
    "generics",
    "GenomicRanges",
    "IRanges",
    "lattice",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "RhpcBLASctl",
    "S4Arrays",
    "S4Vectors",
    "SeqArray",
    "Seqinfo",
    "SNPRelate",
    "SparseArray",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "GDSArray.Rmd",
      "filename": "GDSArray.html",
      "title": "GDSArray: Representing GDS files as array-like objects",
      "author": "Qian Liu, Hervé Pagès, Martin Morgan",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Package installation",
        "GDS format introduction",
        "Genomic Data Structure (GDS)",
        "GDSArray, GDSMatrix, and GDSFile",
        "GDSArray, GDSMatrix, and DelayedArray",
        "GDSFile",
        "GDSArray methods",
        "slot accessors.",
        "Available GDS nodes",
        "dim(), dimnames()",
        "[ subsetting",
        "some numeric calculation",
        "Internals: GDSArraySeed",
        "sessionInfo"
      ],
      "created": "2018-03-01 22:32:16",
      "modified": "2024-05-22 19:40:16",
      "commits": 16
    }
  ],
  "_score": 6.334453751150931,
  "_indexed": false,
  "_nocasepkg": "gdsarray",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/GDSArray",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.32.0",
      "date": "2026-11-01T17:56:10.000Z",
      "distro": "resolute",
      "commit": "061b5043a5d4fb0f7932c75d3ca42097c57a3472",
      "fileid": "https://r2.ropensci.org/3e8a8027cd471899c527aa7f0e1f6741ce801a06091af3122e37085da06e8959",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/41331153489"
    },
    {
      "r": "4.6.2",
      "os": "linux",
      "version": "1.32.0",
      "date": "2026-11-01T17:56:42.000Z",
      "distro": "resolute",
      "commit": "061b5043a5d4fb0f7932c75d3ca42097c57a3472",
      "fileid": "https://r2.ropensci.org/245e1e85fef5109ddde9628314553398ff0ff81824dc7796e9671eb0bcd2d5b3",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/41331153489"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.32.0",
      "date": "2026-11-01T19:43:57.000Z",
      "commit": "061b5043a5d4fb0f7932c75d3ca42097c57a3472",
      "fileid": "https://r2.ropensci.org/ff9ddaa5dcbc2acd2d00b5d9d62325cd1857b83ecc0ffec8b7d1410978b68d98",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/41331153489"
    },
    {
      "r": "4.6.2",
      "os": "mac",
      "version": "1.32.0",
      "date": "2026-11-01T19:44:16.000Z",
      "commit": "061b5043a5d4fb0f7932c75d3ca42097c57a3472",
      "fileid": "https://r2.ropensci.org/5fdefbaee5809c02d7fec595cfecdc3103f2be31d5220fa3e60a53a707263712",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/41331153489"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.32.0",
      "date": "2026-11-01T17:55:03.000Z",
      "commit": "061b5043a5d4fb0f7932c75d3ca42097c57a3472",
      "fileid": "https://r2.ropensci.org/1bb5c51abd4616dade561922e0107f0654759530c78d65fdb5e3fc3b84806fd2",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/41331153489"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.32.0",
      "date": "2026-11-01T17:44:13.000Z",
      "commit": "061b5043a5d4fb0f7932c75d3ca42097c57a3472",
      "fileid": "https://r2.ropensci.org/3612b51c5aac0aa89ca115c4ed0d524b79c0506c62f0cb163318734fb236c1e7",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/41331153489"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.32.0",
      "date": "2026-11-01T17:44:31.000Z",
      "commit": "061b5043a5d4fb0f7932c75d3ca42097c57a3472",
      "fileid": "https://r2.ropensci.org/1d1a08f61bc5f09d860cab266657b252fb3d24dad401411d5e1efc232f363690",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/41331153489"
    },
    {
      "r": "4.6.2",
      "os": "win",
      "version": "1.32.0",
      "date": "2026-11-01T17:44:21.000Z",
      "commit": "061b5043a5d4fb0f7932c75d3ca42097c57a3472",
      "fileid": "https://r2.ropensci.org/f2151c2ced92cd4dee3b1867bbc3cc46b7bd5c1beb6bb64c9885d0190464abca",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/41331153489"
    }
  ]
}