{
  "_id": "6a1f24c8b401979e73420e57",
  "Package": "BoSSA",
  "Type": "Package",
  "Title": "A Bunch of Structure and Sequence Analysis",
  "Version": "3.7",
  "Date": "2020-10-16",
  "Author": "Pierre Lefeuvre",
  "Maintainer": "Pierre Lefeuvre <pierre.lefeuvre@cirad.fr>",
  "VignetteBuilder": "knitr",
  "Description": "Reads and plots phylogenetic placements.",
  "License": "GPL",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-16 06:19:48 UTC",
    "User": "root"
  },
  "Config/pak/sysreqs": "libglpk-dev libxml2-dev",
  "Repository": "https://lefeup.r-universe.dev",
  "Date/Publication": "2020-10-20 06:20:05 UTC",
  "RemoteUrl": "https://github.com/cran/BoSSA",
  "RemoteRef": "HEAD",
  "RemoteSha": "4610ba845cd21c5253341e2853d20028e5d3e19d",
  "MD5sum": "ecf998fd7e52d6a1b82b7d945a9719bd",
  "_user": "lefeup",
  "_type": "src",
  "_file": "BoSSA_3.7.tar.gz",
  "_fileid": "4e45a1c42950f5c214e33c975db820879ec46e64d225077715593fb032729cc6",
  "_filesize": 2954241,
  "_sha256": "4e45a1c42950f5c214e33c975db820879ec46e64d225077715593fb032729cc6",
  "_created": "2026-05-16T06:19:48.000Z",
  "_published": "2026-06-02T18:45:28.969Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79146493887,
      "time": 175,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7031158733"
    },
    {
      "job": 79146493973,
      "time": 136,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7031154800"
    },
    {
      "job": 79146494552,
      "time": 205,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7031213955"
    },
    {
      "job": 79146494132,
      "time": 157,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7031230701"
    },
    {
      "job": 79146493289,
      "time": 196,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7031140273"
    },
    {
      "job": 79146493536,
      "time": 138,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7366832363"
    },
    {
      "job": 79146493925,
      "time": 108,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7031151852"
    },
    {
      "job": 79146494043,
      "time": 110,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7031152181"
    },
    {
      "job": 79146494269,
      "time": 108,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7031151920"
    }
  ],
  "_buildurl": "https://github.com/r-universe/lefeup/actions/runs/25954779401",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/BoSSA",
  "_commit": {
    "id": "4610ba845cd21c5253341e2853d20028e5d3e19d",
    "author": "Pierre Lefeuvre <pierre.lefeuvre@cirad.fr>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 3.7\n",
    "time": 1603174805
  },
  "_maintainer": {
    "name": "Pierre Lefeuvre",
    "email": "pierre.lefeuvre@cirad.fr",
    "login": "lefeup",
    "uuid": 45128699
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.3.0",
      "role": "Depends"
    },
    {
      "package": "ape",
      "role": "Imports"
    },
    {
      "package": "RSQLite",
      "role": "Imports"
    },
    {
      "package": "jsonlite",
      "role": "Imports"
    },
    {
      "package": "phangorn",
      "role": "Imports"
    },
    {
      "package": "plotrix",
      "role": "Imports"
    },
    {
      "package": "prettydoc",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "XML",
      "role": "Suggests"
    },
    {
      "package": "rentrez",
      "role": "Suggests"
    },
    {
      "package": "httr",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "lefeup",
      "count": 12,
      "uuid": 45128699
    }
  ],
  "_userbio": {
    "uuid": 45128699,
    "type": "user",
    "name": "lefeup"
  },
  "_downloads": {
    "count": 288,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/BoSSA"
  },
  "_mentions": 5,
  "_searchresults": 16,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/BoSSA.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "manual.pdf"
  ],
  "_realowner": "lefeup",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.0",
      "date": "2009-12-11"
    },
    {
      "version": "1.1",
      "date": "2009-12-22"
    },
    {
      "version": "1.2",
      "date": "2010-01-26"
    },
    {
      "version": "2.0",
      "date": "2016-10-12"
    },
    {
      "version": "2.1",
      "date": "2017-05-09"
    },
    {
      "version": "2.2",
      "date": "2017-11-14"
    },
    {
      "version": "2.3",
      "date": "2017-11-16"
    },
    {
      "version": "3.0",
      "date": "2017-12-06"
    },
    {
      "version": "3.1",
      "date": "2018-01-30"
    },
    {
      "version": "3.2",
      "date": "2018-02-21"
    },
    {
      "version": "3.3",
      "date": "2018-05-09"
    },
    {
      "version": "3.4",
      "date": "2018-06-25"
    },
    {
      "version": "3.5",
      "date": "2018-09-25"
    },
    {
      "version": "3.6",
      "date": "2018-11-06"
    },
    {
      "version": "3.7",
      "date": "2020-10-20"
    }
  ],
  "_exports": [
    "circular_tree",
    "plot.jplace",
    "plot.pplace",
    "pplace_to_matrix",
    "pplace_to_table",
    "pplace_to_taxonomy",
    "print.jplace",
    "print.pplace",
    "print.protdb",
    "read_jplace",
    "read_protdb",
    "read_sqlite",
    "refpkg",
    "sub_pplace",
    "write_jplace"
  ],
  "_datasets": [
    {
      "name": "pplace",
      "title": "A placement object as obtained with the read_sqlite function",
      "object": "pplace",
      "file": "pplace.rda",
      "class": [
        "pplace"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "BoSSA-package",
      "title": "A Bunch of Structure and Sequence Analysis",
      "topics": [
        "BoSSA-package",
        "BoSSA"
      ]
    },
    {
      "page": "circular_tree",
      "title": "Plot an inside-out circular tree",
      "topics": [
        "circular_tree"
      ]
    },
    {
      "page": "plot.pplace",
      "title": "Plot a pplace or jplace object",
      "topics": [
        "plot.jplace",
        "plot.pplace"
      ]
    },
    {
      "page": "pplace",
      "title": "A placement object as obtained with the read_sqlite function",
      "topics": [
        "pplace"
      ]
    },
    {
      "page": "pplace_to_matrix",
      "title": "Pplace to contingency matrix",
      "topics": [
        "pplace_to_matrix"
      ]
    },
    {
      "page": "pplace_to_table",
      "title": "Merge the multiclass and the placement table of pplace object",
      "topics": [
        "pplace_to_table"
      ]
    },
    {
      "page": "pplace_to_taxonomy",
      "title": "Convert a pplace object to a taxonomy table",
      "topics": [
        "pplace_to_taxonomy"
      ]
    },
    {
      "page": "print.pplace",
      "title": "Compact display of pplace and jplace objects",
      "topics": [
        "print.jplace",
        "print.pplace"
      ]
    },
    {
      "page": "print.pdb",
      "title": "Compact display of protdb object",
      "topics": [
        "print.protdb"
      ]
    },
    {
      "page": "read_jplace",
      "title": "Read a jplace file",
      "topics": [
        "read_jplace"
      ]
    },
    {
      "page": "read_pdb",
      "title": "Read Protein Data Bank (PDB) file",
      "topics": [
        "read_protdb"
      ]
    },
    {
      "page": "read_sqlite",
      "title": "Read a pplacer/guppy sqlite file",
      "topics": [
        "read_sqlite"
      ]
    },
    {
      "page": "refpkg",
      "title": "Summary data and plots for reference packages",
      "topics": [
        "refpkg"
      ]
    },
    {
      "page": "sub_pplace",
      "title": "Subsets a pplace object",
      "topics": [
        "sub_pplace"
      ]
    },
    {
      "page": "write_jplace",
      "title": "Write a jplace or pplace object to the disk",
      "topics": [
        "write_jplace"
      ]
    }
  ],
  "_rundeps": [
    "ape",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "cli",
    "cpp11",
    "DBI",
    "digest",
    "fastmap",
    "fastmatch",
    "generics",
    "glue",
    "igraph",
    "jsonlite",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "memoise",
    "nlme",
    "phangorn",
    "pkgconfig",
    "plotrix",
    "quadprog",
    "Rcpp",
    "rlang",
    "RSQLite",
    "vctrs"
  ],
  "_vignettes": [
    {
      "source": "bossa-analysis.Rmd",
      "filename": "bossa-analysis.html",
      "title": "Example of placement analysis using BoSSA",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Summary",
        "Important note",
        "How to obtain phylogentic placement file suitable for analysis with BoSSA ?",
        "Exploration of a reference package",
        "Loading the example data",
        "Some plots",
        "Subsetting the pplace object",
        "Conversion",
        "To a table",
        "To a contingency matrix",
        "To a taxonomy",
        "Make a phyloseq object",
        "Citation",
        "Other resources",
        "On phylogenetic placements",
        "Other R package with a related topic",
        "R packages used by BoSSA"
      ],
      "created": "2017-05-09 20:26:36",
      "modified": "2020-10-20 06:20:05",
      "commits": 10
    },
    {
      "source": "bossa-tree.Rmd",
      "filename": "bossa-tree.html",
      "title": "Circular tree plot",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Cicular tree",
        "Loading of the required packages",
        "Let's use a random tree",
        "Here is the \"inside-out\" circular tree plot",
        "Plotting interactions",
        "Citation"
      ],
      "created": "2018-06-25 12:23:40",
      "modified": "2018-09-25 18:10:02",
      "commits": 2
    },
    {
      "source": "bossa-refpkg.Rmd",
      "filename": "bossa-refpkg.html",
      "title": "Reference package construction from scratch",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Important notice",
        "Summary",
        "The polerovirus example",
        "Loading the required packages",
        "How many polerovirus sequences are available on NCBI ?",
        "Download all these sequences",
        "Get the genbank informations in XML format",
        "Extract the fasta from the XML",
        "Extract the taxonomy from the XML",
        "Alignement and phylogeny",
        "The Taxonomy",
        "Download the polerovirus taxonomy IDs",
        "The information file",
        "Create the refpkg using taxit",
        "Check the refpkg using rppr",
        "Refpkg stats using BoSSA",
        "Subsample the refpkg",
        "Citation",
        "Other resources",
        "On phylogenetic placements",
        "Other R package with a related topic",
        "On krona charts",
        "R packages used by BoSSA"
      ],
      "created": "2017-05-09 20:26:36",
      "modified": "2020-10-20 06:20:05",
      "commits": 8
    }
  ],
  "_score": 3.380211241711606,
  "_indexed": true,
  "_nocasepkg": "bossa",
  "_universes": [
    "lefeup"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "3.7",
      "date": "2026-05-16T06:22:15.000Z",
      "distro": "noble",
      "commit": "4610ba845cd21c5253341e2853d20028e5d3e19d",
      "fileid": "786fe8d9df523f3c69fc559bf0cb65fe4dbc53612e04eba335a5e11feb397841",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lefeup/actions/runs/25954779401"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "3.7",
      "date": "2026-05-16T06:21:48.000Z",
      "distro": "noble",
      "commit": "4610ba845cd21c5253341e2853d20028e5d3e19d",
      "fileid": "b766848403acdbd072cf754d8c2b53e1aeeeb5251c57944e0f999eb8e35029b6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lefeup/actions/runs/25954779401"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "3.7",
      "date": "2026-05-16T06:32:16.000Z",
      "commit": "4610ba845cd21c5253341e2853d20028e5d3e19d",
      "fileid": "40690da836ed377d3a1e62e197653b03cf9ce471084d949a5fce7e065647e487",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lefeup/actions/runs/25954779401"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "3.7",
      "date": "2026-05-16T06:35:12.000Z",
      "commit": "4610ba845cd21c5253341e2853d20028e5d3e19d",
      "fileid": "f76938160f1269fa12d62f4d1e48a93891bfc44db5329807a8f1fe8f0248e34d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lefeup/actions/runs/25954779401"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "3.7",
      "date": "2026-05-16T06:21:11.000Z",
      "commit": "4610ba845cd21c5253341e2853d20028e5d3e19d",
      "fileid": "20323ed050eca8a7395c7fff327d23fc5fe182457dfcf9752a38d308f88ab7a7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lefeup/actions/runs/25954779401"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "3.7",
      "date": "2026-05-16T06:21:15.000Z",
      "commit": "4610ba845cd21c5253341e2853d20028e5d3e19d",
      "fileid": "3a1f68abe32073f070cb4f76a994ea08f17e5a6b47633c19d65bd884c2e57cbf",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lefeup/actions/runs/25954779401"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "3.7",
      "date": "2026-05-16T06:21:11.000Z",
      "commit": "4610ba845cd21c5253341e2853d20028e5d3e19d",
      "fileid": "bed766868f476664445dacd3ad8145591e21e1ba5bdec64a3813437541267029",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lefeup/actions/runs/25954779401"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "3.7",
      "date": "2026-06-02T18:45:08.000Z",
      "commit": "4610ba845cd21c5253341e2853d20028e5d3e19d",
      "fileid": "be24b4021e40187cd45338112e0a2280773160e109c61f4d549b196e683344da",
      "status": "success",
      "buildurl": "https://github.com/r-universe/lefeup/actions/runs/25954779401"
    }
  ]
}