{
  "_id": "6a5fcae814e95619b75d7392",
  "Package": "Rpgen",
  "Title": "PLINK 2 Genotype Ingestion into File-Backed Storage",
  "Version": "0.1.0",
  "Authors@R": "c(\nperson(given = \"Sounkou Mahamane\", family = \"Toure\", email = \"sounkoutoure@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(given = \"Christopher\", family = \"Chang\", role = \"cph\", comment = \"Author of the vendored pgenlib library and plink2 program\"),\nperson(given = \"Shaun\", family = \"Purcell\", role = \"cph\", comment = \"Co-author of the vendored plink2 format-import closure\"),\nperson(given = \"Eric\", family = \"Biggers\", role = \"cph\", comment = \"Author of included libdeflate library\"),\nperson(given = \"Yann Collet\", family = \"\", role = \"cph\", comment = \"Author of included Zstd library\"),\nperson(given = \"Meta Platforms, Inc.\", role = \"cph\", comment = \"Zstd library\"),\nperson(given = \"Evan\", family = \"Nemerson\", role = \"cph\", comment = \"Author of included SIMDe library\"),\nperson(given = \"Mutsuo\", family = \"Saito\", role = \"cph\", comment = \"Co-author of included SFMT library\"),\nperson(given = \"Makoto\", family = \"Matsumoto\", role = \"cph\", comment = \"Co-author of included SFMT library\")\n)",
  "Description": "Uses the 'PLINK 2' pgenlib library and its native\nimporters (<https://github.com/chrchang/plink-ng>) to ingest\nPGEN, PLINK 1 BED, PED/MAP, TPED/TFAM, VCF/BCF, BGEN, Oxford\nGEN, HAPS/legend, EIGENSTRAT, and legacy dosage sources into\nbounded, file-backed 'Rfmalloc' layouts. Hardcalls, dosages,\nand phase are transferred as typed record panels, allowing the\ndestination to choose a packed codec or full-precision storage\nwithout constructing a complete R matrix. The vendored native\nreaders are also exposed through 'R_RegisterCCallable' for\nsibling packages.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "Remotes": [
    "Rfmalloc=sounkou-bioinfo/Rfmalloc/packages/Rfmalloc"
  ],
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "URL": "https://github.com/sounkou-bioinfo/Rfmalloc,\nhttps://sounkou-bioinfo.github.io/Rfmalloc/Rpgen/",
  "BugReports": "https://github.com/sounkou-bioinfo/Rfmalloc/issues",
  "Config/pak/sysreqs": "make",
  "Repository": "https://rgenomicsetl.r-universe.dev",
  "Date/Publication": "2026-07-18 21:34:09 UTC",
  "RemoteUrl": "https://github.com/RGenomicsETL/Rfmalloc",
  "RemoteRef": "HEAD",
  "RemoteSha": "6e05ad03613e89cab2f8bf8eb3a49d553d5a3bed",
  "RemoteSubdir": "packages/Rpgen",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-07-21 19:32:17 UTC",
    "User": "root"
  },
  "Author": "Sounkou Mahamane Toure [aut, cre],\nChristopher Chang [cph] (Author of the vendored pgenlib library and\nplink2 program),\nShaun Purcell [cph] (Co-author of the vendored plink2 format-import\nclosure),\nEric Biggers [cph] (Author of included libdeflate library),\nYann Collet [cph] (Author of included Zstd library),\nMeta Platforms, Inc. [cph] (Zstd library),\nEvan Nemerson [cph] (Author of included SIMDe library),\nMutsuo Saito [cph] (Co-author of included SFMT library),\nMakoto Matsumoto [cph] (Co-author of included SFMT library)",
  "Maintainer": "Sounkou Mahamane Toure <sounkoutoure@gmail.com>",
  "_user": "rgenomicsetl",
  "_type": "src",
  "_file": "Rpgen_0.1.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/f6b3975f0a79cfb5f779b93945ced5c6d95ba17390808ae642b3d21157589d57",
  "_filesize": 2167670,
  "_sha256": "f6b3975f0a79cfb5f779b93945ced5c6d95ba17390808ae642b3d21157589d57",
  "_expires": "2026-10-29T19:39:18.000Z",
  "_created": "2026-07-21T19:32:17.000Z",
  "_published": "2026-07-21T19:39:20.724Z",
  "_jobs": [
    {
      "job": 88740749974,
      "time": 146,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8507723451"
    },
    {
      "job": 88740749900,
      "time": 163,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8507731942"
    },
    {
      "job": 88740749972,
      "time": 157,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8507728269"
    },
    {
      "job": 88740749962,
      "time": 149,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8507725381"
    },
    {
      "job": 88740749950,
      "time": 153,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8507732174"
    },
    {
      "job": 88740749942,
      "time": 332,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8507819557"
    },
    {
      "job": 88740749983,
      "time": 136,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8507728532"
    },
    {
      "job": 88740749990,
      "time": 276,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8507797440"
    },
    {
      "job": 88739540730,
      "time": 294,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8507651448"
    },
    {
      "job": 88740749866,
      "time": 146,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8507723301"
    },
    {
      "job": 88740749939,
      "time": 258,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8507772095"
    },
    {
      "job": 88740749916,
      "time": 209,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8507753902"
    },
    {
      "job": 88740749976,
      "time": 236,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8507766765"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/29861614992",
  "_status": "success",
  "_upstream": "https://github.com/RGenomicsETL/Rfmalloc",
  "_commit": {
    "id": "6e05ad03613e89cab2f8bf8eb3a49d553d5a3bed",
    "author": "sounkou-bioinfo <sounkoutoure@gmail.com>",
    "committer": "sounkou-bioinfo <sounkoutoure@gmail.com>",
    "message": "Document persistent rig tunnel setup\n",
    "time": 1784410449
  },
  "_maintainer": {
    "name": "Sounkou Mahamane Toure",
    "email": "sounkoutoure@gmail.com",
    "login": "sounkou-bioinfo",
    "mastodon": "@bioinfhotep@genomic.social",
    "description": "Sequences and Consequences.",
    "uuid": 56392505
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.4.0",
      "role": "Depends"
    },
    {
      "package": "Rfmalloc",
      "role": "Depends"
    },
    {
      "package": "Rfmalloc",
      "role": "LinkingTo"
    },
    {
      "package": "tinytest",
      "role": "Suggests"
    }
  ],
  "_owner": "rgenomicsetl",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-37",
      "n": 29
    },
    {
      "week": "2026-19",
      "n": 50
    },
    {
      "week": "2026-20",
      "n": 6
    },
    {
      "week": "2026-23",
      "n": 1
    },
    {
      "week": "2026-28",
      "n": 83
    },
    {
      "week": "2026-29",
      "n": 16
    }
  ],
  "_tags": [],
  "_topics": [
    "altrep",
    "blas",
    "genomics",
    "ggml",
    "gguf",
    "llm",
    "llm-inference",
    "malloc",
    "memory-mapped",
    "mmap",
    "out-of-core",
    "quantization",
    "simd",
    "libzstd",
    "libdeflate",
    "zlib"
  ],
  "_stars": 4,
  "_contributors": [
    {
      "user": "sounkou-bioinfo",
      "count": 207,
      "uuid": 56392505
    }
  ],
  "_userbio": {
    "uuid": 252609706,
    "type": "organization",
    "name": "RGenomicsETL",
    "followers": 6,
    "description": "R Tools For Genomics Data Artisans"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/Rpgen"
  },
  "_devurl": "https://github.com/sounkou-bioinfo/rfmalloc",
  "_rbuild": "4.6.1",
  "_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/Rpgen.html",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "rpgen_bed",
    "rpgen_bed_info",
    "rpgen_dosage",
    "rpgen_haplotypes",
    "rpgen_import_bcf",
    "rpgen_import_bed",
    "rpgen_import_bgen",
    "rpgen_import_eigenstrat",
    "rpgen_import_gen",
    "rpgen_import_haps",
    "rpgen_import_ped",
    "rpgen_import_plink1_dosage",
    "rpgen_import_tped",
    "rpgen_import_vcf",
    "rpgen_info",
    "rpgen_ingest",
    "rpgen_read_bed_hardcalls",
    "rpgen_read_dosages",
    "rpgen_read_hardcalls"
  ],
  "_help": [
    {
      "page": "rpgen_bed",
      "title": "Read a .pgen or PLINK 1 .bed fileset into an Rfmalloc bed tensor",
      "topics": [
        "rpgen_bed"
      ]
    },
    {
      "page": "rpgen_bed_info",
      "title": "Report a PLINK 1 .bed fileset's sample and variant counts",
      "topics": [
        "rpgen_bed_info"
      ]
    },
    {
      "page": "rpgen_dosage",
      "title": "Read a .pgen file into an Rfmalloc dosage tensor",
      "topics": [
        "rpgen_dosage"
      ]
    },
    {
      "page": "rpgen_haplotypes",
      "title": "Read fully phased haplotypes into a locus-major Rfmalloc store",
      "topics": [
        "rpgen_haplotypes"
      ]
    },
    {
      "page": "rpgen_import_bcf",
      "title": "Convert a BCF to a .pgen using plink2's own importer",
      "topics": [
        "rpgen_import_bcf"
      ]
    },
    {
      "page": "rpgen_import_bed",
      "title": "Convert a VCF straight into an Rfmalloc bed tensor",
      "topics": [
        "rpgen_import_bed"
      ]
    },
    {
      "page": "rpgen_import_bgen",
      "title": "Convert a BGEN file to a .pgen using plink2's own importer",
      "topics": [
        "rpgen_import_bgen"
      ]
    },
    {
      "page": "rpgen_import_eigenstrat",
      "title": "Convert EIGENSOFT packed genotype data to a .pgen",
      "topics": [
        "rpgen_import_eigenstrat"
      ]
    },
    {
      "page": "rpgen_import_gen",
      "title": "Convert an Oxford-format .gen + .sample to a .pgen using plink2's own importer",
      "topics": [
        "rpgen_import_gen"
      ]
    },
    {
      "page": "rpgen_import_haps",
      "title": "Convert Oxford-format phased haplotypes (.haps/.legend/.sample) to a .pgen",
      "topics": [
        "rpgen_import_haps"
      ]
    },
    {
      "page": "rpgen_import_ped",
      "title": "Convert a PLINK 1 PED/MAP pair to a .pgen",
      "topics": [
        "rpgen_import_ped"
      ]
    },
    {
      "page": "rpgen_import_plink1_dosage",
      "title": "Convert a legacy PLINK 1 -import-dosage file to a .pgen",
      "topics": [
        "rpgen_import_plink1_dosage"
      ]
    },
    {
      "page": "rpgen_import_tped",
      "title": "Convert a PLINK 1 TPED/TFAM pair to a .pgen",
      "topics": [
        "rpgen_import_tped"
      ]
    },
    {
      "page": "rpgen_import_vcf",
      "title": "Convert a VCF to a .pgen using plink2's own importer",
      "topics": [
        "rpgen_import_vcf"
      ]
    },
    {
      "page": "rpgen_info",
      "title": "Open a .pgen file and report its sample and variant counts",
      "topics": [
        "rpgen_info"
      ]
    },
    {
      "page": "rpgen_ingest",
      "title": "Ingest a PLINK2-supported genotype source into Rfmalloc storage",
      "topics": [
        "rpgen_ingest"
      ]
    },
    {
      "page": "rpgen_read_bed_hardcalls",
      "title": "Read genotypes from a PLINK 1 .bed fileset as a dense R matrix",
      "topics": [
        "rpgen_read_bed_hardcalls"
      ]
    },
    {
      "page": "rpgen_read_hardcalls",
      "title": "Read genotypes from a .pgen file as a dense R matrix",
      "topics": [
        "rpgen_read_dosages",
        "rpgen_read_hardcalls"
      ]
    }
  ],
  "_readme": "https://github.com/RGenomicsETL/Rfmalloc/raw/HEAD/packages/Rpgen/README.md",
  "_rundeps": [
    "Rfmalloc"
  ],
  "_sysdeps": [
    {
      "shlib": "libzstd",
      "package": "libzstd1",
      "headers": "libzstd-dev",
      "source": "libzstd",
      "version": "1.5.7+dfsg-3",
      "name": "libzstd",
      "homepage": "https://github.com/facebook/zstd",
      "description": "fast lossless compression algorithm"
    },
    {
      "shlib": "libdeflate",
      "package": "libdeflate0",
      "headers": "libdeflate-dev",
      "source": "libdeflate",
      "version": "1.23-2ubuntu1",
      "name": "libdeflate",
      "homepage": "https://github.com/ebiggers/libdeflate",
      "description": "fast, whole-buffer DEFLATE-based compression and decompression"
    },
    {
      "shlib": "libz",
      "package": "zlib1g",
      "headers": "zlib1g-dev",
      "source": "zlib",
      "version": "1:1.3.dfsg+really1.3.1-1ubuntu3",
      "name": "zlib",
      "homepage": "http://zlib.net/",
      "description": "compression library - runtime"
    }
  ],
  "_score": 3.079181246047625,
  "_indexed": true,
  "_nocasepkg": "rpgen",
  "_universes": [
    "rgenomicsetl",
    "sounkou-bioinfo"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-07-21T19:34:50.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "6e05ad03613e89cab2f8bf8eb3a49d553d5a3bed",
      "fileid": "https://r2.ropensci.org/1c8262a3262d838662f888873d630cb4a7e31cb9a02069e8491430d00a777a70",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/29861614992"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-07-21T19:35:04.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "6e05ad03613e89cab2f8bf8eb3a49d553d5a3bed",
      "fileid": "https://r2.ropensci.org/8cde37f5657ad1fafdb687be3afcc7f54382ede12256e8af0334e6d8f75abcf7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/29861614992"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-07-21T19:34:56.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "6e05ad03613e89cab2f8bf8eb3a49d553d5a3bed",
      "fileid": "https://r2.ropensci.org/3f1dd953f441b2d5363ffa3181cd5fe22abda6d25bb060e9eabbab70fae4e0e5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/29861614992"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-07-21T19:34:56.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "6e05ad03613e89cab2f8bf8eb3a49d553d5a3bed",
      "fileid": "https://r2.ropensci.org/82047a0672f70cc23ea03486287e6a7a8cd9abcd566ae8d2428ee01181199fc9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/29861614992"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-07-21T19:35:11.000Z",
      "arch": "aarch64",
      "commit": "6e05ad03613e89cab2f8bf8eb3a49d553d5a3bed",
      "fileid": "https://r2.ropensci.org/4c8e500fbf31e29e9791fc8af271e9a3cac9738dc00802ed3ff46195be0f1ad7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/29861614992"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-07-21T19:37:18.000Z",
      "arch": "x86_64",
      "commit": "6e05ad03613e89cab2f8bf8eb3a49d553d5a3bed",
      "fileid": "https://r2.ropensci.org/de87667a86ed6ec829350c175a296bb38efd2d86fa43779ab871bb291e73ea81",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/29861614992"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-07-21T19:35:08.000Z",
      "arch": "aarch64",
      "commit": "6e05ad03613e89cab2f8bf8eb3a49d553d5a3bed",
      "fileid": "https://r2.ropensci.org/cdfed057a35d68be1ef4174cc08173be555869613360f56127a54e8900eda919",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/29861614992"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-07-21T19:36:48.000Z",
      "arch": "x86_64",
      "commit": "6e05ad03613e89cab2f8bf8eb3a49d553d5a3bed",
      "fileid": "https://r2.ropensci.org/d87684661daa558df8eaeff55cd6236f39a26f740e44be28721268a874a16665",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/29861614992"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.0",
      "date": "2026-07-21T19:35:02.000Z",
      "arch": "emscripten",
      "commit": "6e05ad03613e89cab2f8bf8eb3a49d553d5a3bed",
      "fileid": "https://r2.ropensci.org/0e3cb812c9f04d422e7f0109432091d0fbc4e0e31ddda1fd2b5b12515124e4ca",
      "status": "success",
      "buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/29861614992"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-07-21T19:34:56.000Z",
      "arch": "x86_64",
      "commit": "6e05ad03613e89cab2f8bf8eb3a49d553d5a3bed",
      "fileid": "https://r2.ropensci.org/7d579cb8f5d0a1682154adf04192eb0b4fd066b473a81a66f457eb244de1b101",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/29861614992"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-07-21T19:34:34.000Z",
      "arch": "x86_64",
      "commit": "6e05ad03613e89cab2f8bf8eb3a49d553d5a3bed",
      "fileid": "https://r2.ropensci.org/cb641a61c2d4f14fa96b74eb7c11b0722acc845691a2ec547e1d5755bf8668b5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/29861614992"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-07-21T19:34:43.000Z",
      "arch": "x86_64",
      "commit": "6e05ad03613e89cab2f8bf8eb3a49d553d5a3bed",
      "fileid": "https://r2.ropensci.org/ac4912a971628db3a37f32cbefc763436fd3a3c0d08ed4d382ab187da6461435",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/29861614992"
    }
  ]
}