{
  "_id": "6a495abdf6c47c441949e43d",
  "Package": "PeakSegDisk",
  "Type": "Package",
  "Title": "Disk-Based Constrained Change-Point Detection",
  "Version": "2024.10.1",
  "Authors@R": "person(given = c(\"Toby\", \"Dylan\"),\nfamily = \"Hocking\",\nrole = c(\"aut\", \"cre\"),\nemail = \"toby.hocking@r-project.org\")",
  "Description": "Disk-based implementation of Functional Pruning Optimal\nPartitioning with up-down constraints\n<doi:10.18637/jss.v101.i10> for single-sample peak calling\n(independently for each sample and genomic problem), can handle\nhuge data sets (10^7 or more).",
  "License": "GPL-3",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/tdhock/PeakSegDisk",
  "BugReports": "https://github.com/tdhock/PeakSegDisk/issues",
  "Repository": "https://tdhock.r-universe.dev",
  "Date/Publication": "2024-10-02 02:41:12 UTC",
  "RemoteUrl": "https://github.com/tdhock/peaksegdisk",
  "RemoteRef": "HEAD",
  "RemoteSha": "7e0e474a160faf757d5d709f8b0e0508bebf24d0",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-06-24 02:23:34 UTC",
    "User": "root"
  },
  "Author": "Toby Dylan Hocking [aut, cre]",
  "Maintainer": "Toby Dylan Hocking <toby.hocking@r-project.org>",
  "_user": "tdhock",
  "_type": "src",
  "_file": "PeakSegDisk_2024.10.1.tar.gz",
  "_fileid": "https://r2.ropensci.org/b71de4155b560c8eae876ca186982117dc55576fa3d328623b2b6b5c908e2d8b",
  "_filesize": 1327107,
  "_sha256": "b71de4155b560c8eae876ca186982117dc55576fa3d328623b2b6b5c908e2d8b",
  "_expires": "2026-10-12T19:10:52.000Z",
  "_created": "2026-06-24T02:23:34.000Z",
  "_published": "2026-07-04T19:10:53.966Z",
  "_jobs": [
    {
      "job": 85159352681,
      "time": 140,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7838626887"
    },
    {
      "job": 85159352524,
      "time": 135,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7838625184"
    },
    {
      "job": 85159352692,
      "time": 134,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7838625304"
    },
    {
      "job": 85159352700,
      "time": 139,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7838625846"
    },
    {
      "job": 85159352593,
      "time": 86,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7838615494"
    },
    {
      "job": 85159352682,
      "time": 219,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7838641609"
    },
    {
      "job": 85159352481,
      "time": 95,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7838617167"
    },
    {
      "job": 85159352608,
      "time": 196,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7838636779"
    },
    {
      "job": 85159352423,
      "time": 223,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7838598711"
    },
    {
      "job": 85159352472,
      "time": 101,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7838618651"
    },
    {
      "job": 85159352614,
      "time": 137,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7838625352"
    },
    {
      "job": 85159352697,
      "time": 106,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7838619476"
    },
    {
      "job": 85159352495,
      "time": 116,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7838621353"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/tdhock/actions/runs/28070671043",
  "_status": "success",
  "_upstream": "https://github.com/tdhock/peaksegdisk",
  "_commit": {
    "id": "7e0e474a160faf757d5d709f8b0e0508bebf24d0",
    "author": "Toby Dylan Hocking <toby.hocking@r-project.org>",
    "committer": "Toby Dylan Hocking <toby.hocking@r-project.org>",
    "message": "Authors@R\n",
    "time": 1727836872
  },
  "_maintainer": {
    "name": "Toby Dylan Hocking",
    "email": "toby.hocking@r-project.org",
    "login": "tdhock",
    "description": "",
    "uuid": 932850
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.10",
      "role": "Depends"
    },
    {
      "package": "data.table",
      "version": ">= 1.9.8",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    },
    {
      "package": "future.apply",
      "role": "Suggests"
    },
    {
      "package": "future",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "markdown",
      "role": "Suggests"
    }
  ],
  "_owner": "tdhock",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 4,
  "_contributors": [
    {
      "user": "tdhock",
      "count": 163,
      "uuid": 932850
    }
  ],
  "_userbio": {
    "uuid": 932850,
    "type": "user",
    "name": "Toby Dylan Hocking",
    "followers": 418
  },
  "_downloads": {
    "count": 757,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/PeakSegDisk"
  },
  "_devurl": "https://github.com/tdhock/peaksegdisk",
  "_searchresults": 39,
  "_topics": [
    "cpp"
  ],
  "_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/PeakSegDisk.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/tdhock/peaksegdisk",
  "_realowner": "tdhock",
  "_cranurl": true,
  "_releases": [
    {
      "version": "2018.11.28",
      "date": "2018-12-03"
    },
    {
      "version": "2019.7.29",
      "date": "2019-07-31"
    },
    {
      "version": "2019.9.10",
      "date": "2019-09-11"
    },
    {
      "version": "2019.9.27",
      "date": "2019-11-19"
    },
    {
      "version": "2020.8.13",
      "date": "2020-08-14"
    },
    {
      "version": "2022.2.1",
      "date": "2022-02-02"
    },
    {
      "version": "2023.9.4",
      "date": "2023-09-06"
    },
    {
      "version": "2023.11.27",
      "date": "2023-11-28"
    },
    {
      "version": "2024.10.1",
      "date": "2024-10-02"
    }
  ],
  "_exports": [
    "col.name.list",
    "fread.first",
    "fread.last",
    "PeakSegFPOP_df",
    "PeakSegFPOP_dir",
    "PeakSegFPOP_file",
    "PeakSegFPOP_vec",
    "sequentialSearch_dir",
    "wc2int",
    "writeBedGraph"
  ],
  "_datasets": [
    {
      "name": "ChIPreads",
      "title": "Reads aligned to hg19 from two ChIP-seq experiments",
      "object": "ChIPreads",
      "file": "ChIPreads.RData",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "experiment",
        "chrom",
        "chromStart",
        "chromEnd",
        "count"
      ],
      "rows": 40396,
      "table": true,
      "tojson": true
    },
    {
      "name": "Mono27ac",
      "title": "A small ChIP-seq data set in which peaks can be found using PeakSegFPOP",
      "object": "Mono27ac",
      "file": "Mono27ac.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "ChIPreads",
      "title": "Reads aligned to hg19 from two ChIP-seq experiments",
      "topics": [
        "ChIPreads"
      ]
    },
    {
      "page": "coef.PeakSegFPOP_df",
      "title": "coef PeakSegFPOP df",
      "topics": [
        "coef.PeakSegFPOP_df"
      ]
    },
    {
      "page": "coef.PeakSegFPOP_dir",
      "title": "coef PeakSegFPOP dir",
      "topics": [
        "coef.PeakSegFPOP_dir"
      ]
    },
    {
      "page": "col.name.list",
      "title": "col name list",
      "topics": [
        "col.name.list"
      ]
    },
    {
      "page": "fread.first",
      "title": "Quickly read first line",
      "topics": [
        "fread.first"
      ]
    },
    {
      "page": "fread.last",
      "title": "Quickly read last line",
      "topics": [
        "fread.last"
      ]
    },
    {
      "page": "Mono27ac",
      "title": "A small ChIP-seq data set in which peaks can be found using PeakSegFPOP",
      "topics": [
        "Mono27ac"
      ]
    },
    {
      "page": "PeakSegFPOP_df",
      "title": "PeakSeg penalized solver for data.frame",
      "topics": [
        "PeakSegFPOP_df"
      ]
    },
    {
      "page": "PeakSegFPOP_dir",
      "title": "PeakSeg penalized solver with caching",
      "topics": [
        "PeakSegDisk",
        "PeakSegFPOP_dir"
      ]
    },
    {
      "page": "PeakSegFPOP_file",
      "title": "PeakSegFPOP using disk storage",
      "topics": [
        "PeakSegFPOP_file"
      ]
    },
    {
      "page": "PeakSegFPOP_vec",
      "title": "PeakSeg penalized solver for integer vector",
      "topics": [
        "PeakSegFPOP_vec"
      ]
    },
    {
      "page": "plot.PeakSegFPOP_df",
      "title": "plot PeakSegFPOP df",
      "topics": [
        "plot.PeakSegFPOP_df"
      ]
    },
    {
      "page": "plot.PeakSegFPOP_dir",
      "title": "plot PeakSegFPOP dir",
      "topics": [
        "plot.PeakSegFPOP_dir"
      ]
    },
    {
      "page": "sequentialSearch_dir",
      "title": "Compute PeakSeg model with given number of peaks",
      "topics": [
        "sequentialSearch_dir"
      ]
    },
    {
      "page": "summary.PeakSegFPOP_dir",
      "title": "summary PeakSegFPOP dir",
      "topics": [
        "summary.PeakSegFPOP_dir"
      ]
    },
    {
      "page": "wc2int",
      "title": "wc2int",
      "topics": [
        "wc2int"
      ]
    },
    {
      "page": "writeBedGraph",
      "title": "Write bedGraph file",
      "topics": [
        "writeBedGraph"
      ]
    }
  ],
  "_rundeps": [
    "data.table"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "Examples.Rnw",
      "filename": "Examples.pdf",
      "title": "Examples",
      "engine": "knitr::knitr",
      "headings": [
        "Related work",
        "Simulate a noisy integer vector with changes",
        "Segment a vector of integers",
        "Segment a data frame",
        "Write the file yourself",
        "Computing the model with a given number of peaks"
      ],
      "created": "2019-07-31 21:01:02",
      "modified": "2023-11-27 21:51:48",
      "commits": 4
    },
    {
      "source": "Spatial_correlation.Rmd",
      "filename": "Spatial_correlation.html",
      "title": "Spatial correlation",
      "engine": "knitr::knitr",
      "headings": [],
      "created": "2019-07-31 21:01:02",
      "modified": "2023-09-05 05:27:31",
      "commits": 3
    },
    {
      "source": "Worst_case.Rmd",
      "filename": "Worst_case.html",
      "title": "Worst case time complexity",
      "engine": "knitr::knitr",
      "headings": [],
      "created": "2019-07-31 21:01:02",
      "modified": "2023-09-05 05:27:31",
      "commits": 2
    }
  ],
  "_score": 4.670245853074124,
  "_indexed": true,
  "_nocasepkg": "peaksegdisk",
  "_universes": [
    "tdhock"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2024.10.1",
      "date": "2026-06-24T02:25:55.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "7e0e474a160faf757d5d709f8b0e0508bebf24d0",
      "fileid": "https://r2.ropensci.org/0cf75b3a9e73ac5b2a046937491a06fe43ab8ecb21b770dac99a6b3ef7a12df3",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/28070671043"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2024.10.1",
      "date": "2026-06-24T02:25:40.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "7e0e474a160faf757d5d709f8b0e0508bebf24d0",
      "fileid": "https://r2.ropensci.org/6cf4287d0d552d4cd65745cde4302095a2de081a17ed850fb1ae8ed994c009cf",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/28070671043"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2024.10.1",
      "date": "2026-06-24T02:25:49.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "7e0e474a160faf757d5d709f8b0e0508bebf24d0",
      "fileid": "https://r2.ropensci.org/0293dcd4a2c7e840141429d73a9e5c9e054cdce809be1d4b332299da29984a71",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/28070671043"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2024.10.1",
      "date": "2026-06-24T02:25:42.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "7e0e474a160faf757d5d709f8b0e0508bebf24d0",
      "fileid": "https://r2.ropensci.org/5dcb29cd88ac8f81de56465a2c29d944eec5828f7b414148d6bb32f050090bc8",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/28070671043"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2024.10.1",
      "date": "2026-06-24T02:24:57.000Z",
      "arch": "aarch64",
      "commit": "7e0e474a160faf757d5d709f8b0e0508bebf24d0",
      "fileid": "https://r2.ropensci.org/e64c5f78a9cd1d201a25500f58f2570fd1c595d335e0e1435a0b0fe427413b98",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/28070671043"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2024.10.1",
      "date": "2026-06-24T02:26:45.000Z",
      "arch": "x86_64",
      "commit": "7e0e474a160faf757d5d709f8b0e0508bebf24d0",
      "fileid": "https://r2.ropensci.org/513df4dc55edf5d9b586c3e4b31383bb85e8e8f5b48faa62ca5829cddf7813e0",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/28070671043"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2024.10.1",
      "date": "2026-06-24T02:25:04.000Z",
      "arch": "aarch64",
      "commit": "7e0e474a160faf757d5d709f8b0e0508bebf24d0",
      "fileid": "https://r2.ropensci.org/875c5466ca4fcb83099d03523f9329381e88b23211c9687fcb77c28a4b5a10b0",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/28070671043"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2024.10.1",
      "date": "2026-06-24T02:26:17.000Z",
      "arch": "x86_64",
      "commit": "7e0e474a160faf757d5d709f8b0e0508bebf24d0",
      "fileid": "https://r2.ropensci.org/2c5ba27c07331b41bd1294684e9f00db3000e53e9fc1fc299a757aed1189b004",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/28070671043"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2024.10.1",
      "date": "2026-06-24T02:25:30.000Z",
      "arch": "emscripten",
      "commit": "7e0e474a160faf757d5d709f8b0e0508bebf24d0",
      "fileid": "https://r2.ropensci.org/2e5c0e2793932c3aefe2d6894e02b13591c8d3a200eec9a098d3fd61f7547ff0",
      "status": "success",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/28070671043"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2024.10.1",
      "date": "2026-06-24T02:25:04.000Z",
      "arch": "x86_64",
      "commit": "7e0e474a160faf757d5d709f8b0e0508bebf24d0",
      "fileid": "https://r2.ropensci.org/17b35ca4ddcf4ee193c2644545d23f7c2af4a4e0569a63a2fa0b5dd08dcb7923",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/28070671043"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2024.10.1",
      "date": "2026-06-24T02:24:43.000Z",
      "arch": "x86_64",
      "commit": "7e0e474a160faf757d5d709f8b0e0508bebf24d0",
      "fileid": "https://r2.ropensci.org/6c0e97a215948f189a9d8789437510c64711919c1e875dd09934872cbbe7c24a",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/28070671043"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2024.10.1",
      "date": "2026-06-24T02:24:49.000Z",
      "arch": "x86_64",
      "commit": "7e0e474a160faf757d5d709f8b0e0508bebf24d0",
      "fileid": "https://r2.ropensci.org/d7f37c7e6b81ed96bb0be513d465790233102393f7dffa89fda4511ffe989ef8",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/28070671043"
    }
  ]
}