{
  "_id": "6ad9aededb07788da70a9d7f",
  "Package": "GWASpoly",
  "Title": "Genome-wide Association Studies for Autopolyploids",
  "Version": "2.14",
  "Author": "Jeffrey B. Endelman, Umesh R. Rosyara",
  "Maintainer": "Jeffrey Endelman <endelman@wisc.edu>",
  "Description": "Designed for genome-wide association studies in\nautopolyploids.",
  "License": "GPL-3",
  "RoxygenNote": "7.3.2",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "Collate": "'GWASpoly.data.R' 'GWASpoly.K.R' 'GWASpoly.R'\n'GWASpoly.fitted.R' 'GWASpoly.thresh.R' 'Keff.R' 'LD.plot.R'\n'VCF2dosage.R' 'design.score.R' 'fit.QTL.R' 'get.QTL.R'\n'get_x.R' 'make.full.R' 'makeLOCO.R' 'manhattan.plot.R'\n'qq.plot.R' 'qvalue.R' 'read.GWASpoly.R' 'score.calc.R'\n'set.K.R' 'set.params.R' 'set.threshold.R' 'write.GWASpoly.R'",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://polyploids.r-universe.dev",
  "Date/Publication": "2026-09-21 22:42:33 UTC",
  "RemoteUrl": "https://github.com/jendelman/GWASpoly",
  "RemoteRef": "HEAD",
  "RemoteSha": "a23cab630c8462fc7f46abd6330a8b33eb8bd635",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-22 06:29:37 UTC",
    "User": "root"
  },
  "_user": "polyploids",
  "_type": "src",
  "_file": "GWASpoly_2.14.tar.gz",
  "_fileid": "https://r2.ropensci.org/c6f09681d21d6d5d45a3bc65ed7d0521e5936fa022b3fe0280f75e31c689ea04",
  "_filesize": 3600821,
  "_sha256": "c6f09681d21d6d5d45a3bc65ed7d0521e5936fa022b3fe0280f75e31c689ea04",
  "_expires": "2027-01-30T06:36:12.000Z",
  "_created": "2026-10-22T06:29:37.000Z",
  "_published": "2026-10-22T06:36:14.641Z",
  "_upstream": "https://github.com/jendelman/GWASpoly",
  "_status": "failure",
  "_maintainer": {
    "name": "Jeffrey Endelman",
    "email": "endelman@wisc.edu",
    "login": "jendelman",
    "description": "",
    "uuid": 51009800
  },
  "_jobs": [
    {
      "job": 119676608805,
      "time": 153,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "12406975078"
    },
    {
      "job": 119676608771,
      "time": 242,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12406885459"
    },
    {
      "job": 119676608872,
      "time": 152,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "12405989774"
    },
    {
      "job": 119676608809,
      "time": 116,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12406602543"
    },
    {
      "job": 119674253719,
      "time": 422,
      "config": "source",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "12406029588"
    },
    {
      "job": 119676608882,
      "time": 254,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12406652709"
    },
    {
      "job": 119676608720,
      "time": 115,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "12406995081"
    },
    {
      "job": 119676608719,
      "time": 125,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "12405919810"
    },
    {
      "job": 119676608853,
      "time": 290,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12407005236"
    }
  ],
  "_buildurl": "https://github.com/r-universe/polyploids/actions/runs/39733634163",
  "_commit": {
    "id": "a23cab630c8462fc7f46abd6330a8b33eb8bd635",
    "author": "Jeffrey Endelman <51009800+jendelman@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #21 from Cristianetaniguti/master\n\nadd diplo-general and diplo-additive to fit.QTL",
    "time": 1790030553
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "rrBLUP",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "scam",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "jendelman",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-39",
      "n": 1
    }
  ],
  "_tags": [],
  "_stars": 36,
  "_contributors": [
    {
      "user": "jendelman",
      "count": 49,
      "uuid": 51009800
    },
    {
      "user": "cristianetaniguti",
      "count": 2,
      "uuid": 7572527
    },
    {
      "user": "lvclark",
      "count": 1,
      "uuid": 13499688
    }
  ],
  "_userbio": {
    "uuid": 85083275,
    "type": "organization",
    "name": "Tools for Polyploids",
    "followers": 1,
    "description": "Software for molecular breeding of polyploid crops"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/GWASpoly"
  },
  "_devurl": "https://github.com/jendelman/gwaspoly",
  "_searchresults": 79,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/GWASpoly.html",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE"
  ],
  "_cranurl": false,
  "_exports": [
    "fit.QTL",
    "get.QTL",
    "GWASpoly",
    "LD.plot",
    "manhattan.plot",
    "qq.plot",
    "read.GWASpoly",
    "set.K",
    "set.params",
    "set.threshold",
    "VCF2dosage",
    "write.GWASpoly"
  ],
  "_help": [
    {
      "page": "fit.QTL",
      "title": "Test markers as QTL under backward elimination",
      "topics": [
        "fit.QTL"
      ]
    },
    {
      "page": "get.QTL",
      "title": "Extract significant QTL",
      "topics": [
        "get.QTL"
      ]
    },
    {
      "page": "GWASpoly",
      "title": "Compute marker significance scores",
      "topics": [
        "GWASpoly"
      ]
    },
    {
      "page": "GWASpoly.data-class",
      "title": "S4 class with genotype and phenotype data",
      "topics": [
        "GWASpoly.data",
        "GWASpoly.data-class"
      ]
    },
    {
      "page": "GWASpoly.fitted-class",
      "title": "S4 class with results from genome-wide scan",
      "topics": [
        "GWASpoly.fitted",
        "GWASpoly.fitted-class"
      ]
    },
    {
      "page": "GWASpoly.K-class",
      "title": "S4 class with genotypes, phenotypes, and polygenic covariance",
      "topics": [
        "GWASpoly.K",
        "GWASpoly.K-class"
      ]
    },
    {
      "page": "GWASpoly.thresh-class",
      "title": "S4 class with results from genome-wide scan and detection threshold",
      "topics": [
        "GWASpoly.thresh",
        "GWASpoly.thresh-class"
      ]
    },
    {
      "page": "LD.plot",
      "title": "Plot LD vs distance",
      "topics": [
        "LD.plot"
      ]
    },
    {
      "page": "manhattan.plot",
      "title": "Create Manhattan plot",
      "topics": [
        "manhattan.plot"
      ]
    },
    {
      "page": "qq.plot",
      "title": "Quantile-Quantile (QQ) Plot",
      "topics": [
        "qq.plot"
      ]
    },
    {
      "page": "read.GWASpoly",
      "title": "Read in marker and phenotype data",
      "topics": [
        "read.GWASpoly"
      ]
    },
    {
      "page": "set.K",
      "title": "Set covariance matrix for polygenic effect",
      "topics": [
        "set.K"
      ]
    },
    {
      "page": "set.params",
      "title": "Set parameters",
      "topics": [
        "set.params"
      ]
    },
    {
      "page": "set.threshold",
      "title": "Set the significance threshold",
      "topics": [
        "set.threshold"
      ]
    },
    {
      "page": "VCF2dosage",
      "title": "Convert VCF to dosage file",
      "topics": [
        "VCF2dosage"
      ]
    },
    {
      "page": "write.GWASpoly",
      "title": "Write results to file",
      "topics": [
        "write.GWASpoly"
      ]
    }
  ],
  "_readme": "https://github.com/jendelman/GWASpoly/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "cpp11",
    "dplyr",
    "farver",
    "generics",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "mgcv",
    "nlme",
    "pillar",
    "pkgconfig",
    "purrr",
    "R6",
    "RColorBrewer",
    "rlang",
    "rrBLUP",
    "S7",
    "scales",
    "scam",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_score": 4.453929592057729,
  "_indexed": false,
  "_nocasepkg": "gwaspoly",
  "_universes": [
    "polyploids"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.14",
      "date": "2026-10-22T06:32:22.000Z",
      "distro": "resolute",
      "commit": "a23cab630c8462fc7f46abd6330a8b33eb8bd635",
      "fileid": "https://r2.ropensci.org/143fa345e1b6345dcb50c94374eb7a312c523b58651408a22fc8af59f059987d",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/polyploids/actions/runs/39733634163"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "2.14",
      "date": "2026-10-22T06:34:05.000Z",
      "distro": "resolute",
      "commit": "a23cab630c8462fc7f46abd6330a8b33eb8bd635",
      "fileid": "https://r2.ropensci.org/3ab9ad34f6d725686c5b4c82fd7c4805d88fe7421cdbd7391436442935cc809e",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/polyploids/actions/runs/39733634163"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.14",
      "date": "2026-10-22T06:32:18.000Z",
      "commit": "a23cab630c8462fc7f46abd6330a8b33eb8bd635",
      "fileid": "https://r2.ropensci.org/7a2d5aba98511d0d4a85adb83566ed9137c4accf4a170f6c97ed29487ebf073c",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/polyploids/actions/runs/39733634163"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "2.14",
      "date": "2026-10-22T06:31:57.000Z",
      "commit": "a23cab630c8462fc7f46abd6330a8b33eb8bd635",
      "fileid": "https://r2.ropensci.org/9a607dda98861551742a5206b2c2afe226aecc596bb1a67ee8e62a0f268dbda2",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/polyploids/actions/runs/39733634163"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.14",
      "date": "2026-10-22T06:34:28.000Z",
      "commit": "a23cab630c8462fc7f46abd6330a8b33eb8bd635",
      "fileid": "https://r2.ropensci.org/d86d009563f6019f55cc2ea9b5ca4209c6f64cc1b26533b178b218324b907d7e",
      "status": "success",
      "buildurl": "https://github.com/r-universe/polyploids/actions/runs/39733634163"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.14",
      "date": "2026-10-22T06:31:40.000Z",
      "commit": "a23cab630c8462fc7f46abd6330a8b33eb8bd635",
      "fileid": "https://r2.ropensci.org/2fd07e956f06af3236f5c78dd5674183e1a0761566de131fe21ef7c7f672b209",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/polyploids/actions/runs/39733634163"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.14",
      "date": "2026-10-22T06:31:47.000Z",
      "commit": "a23cab630c8462fc7f46abd6330a8b33eb8bd635",
      "fileid": "https://r2.ropensci.org/cd1883787f761e21e2f76c294e708de63e2135e9d643b07e322fa70474ff5331",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/polyploids/actions/runs/39733634163"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "2.14",
      "date": "2026-10-22T06:34:38.000Z",
      "commit": "a23cab630c8462fc7f46abd6330a8b33eb8bd635",
      "fileid": "https://r2.ropensci.org/1fd684e2d1b6c6c1d82822cc6c84bf91243b1001c892f20ced76a49ccd76eb04",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/polyploids/actions/runs/39733634163"
    }
  ]
}