{
  "_id": "6a103067acfb0bcc41c95676",
  "Package": "CARNIVAL",
  "Title": "A CAusal Reasoning tool for Network Identification (from gene\nexpression data) using Integer VALue programming",
  "Version": "2.23.0",
  "Authors@R": "c(\nperson(given = \"Enio\",\nfamily = \"Gjerga\",\nrole = c(\"aut\"),\nemail = \"enio.gjerga@gmail.com\",\ncomment = c(ORCID = \"0000-0002-3060-5786\")),\nperson(given = \"Panuwat\",\nfamily = \"Trairatphisan\",\nrole = \"aut\"),\nperson(given = \"Anika\",\nfamily = \"Liu\",\nrole = \"ctb\"),\nperson(given = \"Alberto\",\nfamily = \"Valdeolivas\",\nrole = \"ctb\"),\nperson(given = \"Nikolas\",\nfamily = \"Peschke\",\nrole = \"ctb\"),\nperson(given = \"Aurelien\",\nfamily = \"Dugourd\",\nrole = \"ctb\"),\nperson(given = \"Attila\",\nfamily = \"Gabor\",\nrole = \"cre\",\nemail = \"attila.gabor@uni-heidelberg.de\"),\nperson(given = \"Olga\",\nfamily = \"Ivanova\",\nrole = \"aut\",\nemail = \"olga.ivanova@bioquant.uni-heidelberg.de\")\n)",
  "Description": "An upgraded causal reasoning tool from Melas et al in R\nwith updated assignments of TFs' weights from PROGENy scores.\nOptimization parameters can be freely adjusted and multiple\nsolutions can be obtained and aggregated.",
  "URL": "https://github.com/saezlab/CARNIVAL",
  "BugReports": "https://github.com/saezlab/CARNIVAL/issues",
  "biocViews": "Transcriptomics, GeneExpression, Network",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.1.2",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev libx11-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:52:37 UTC",
  "RemoteUrl": "https://github.com/bioc/CARNIVAL",
  "RemoteRef": "HEAD",
  "RemoteSha": "19f1f6672181d95ae005041b2235b29575049694",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-12 09:36:24 UTC",
    "User": "root"
  },
  "Author": "Enio Gjerga [aut] (ORCID: <https://orcid.org/0000-0002-3060-5786>),\nPanuwat Trairatphisan [aut],\nAnika Liu [ctb],\nAlberto Valdeolivas [ctb],\nNikolas Peschke [ctb],\nAurelien Dugourd [ctb],\nAttila Gabor [cre],\nOlga Ivanova [aut]",
  "Maintainer": "Attila Gabor <attila.gabor@uni-heidelberg.de>",
  "MD5sum": "9af1ebdac1de53157006f7c625b64750",
  "_user": "bioc",
  "_type": "src",
  "_file": "CARNIVAL_2.23.0.tar.gz",
  "_fileid": "6335738fec5d5293b32779a6428c98b7f979eadfc1a59ba59b1f1c54db067853",
  "_filesize": 2273592,
  "_sha256": "6335738fec5d5293b32779a6428c98b7f979eadfc1a59ba59b1f1c54db067853",
  "_created": "2026-05-12T09:36:24.000Z",
  "_published": "2026-05-22T10:31:03.270Z",
  "_jobs": [
    {
      "job": 77362093412,
      "time": 173,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "6940711966"
    },
    {
      "job": 77362093228,
      "time": 174,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "6940712137"
    },
    {
      "job": 77362093220,
      "time": 215,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "6940725398"
    },
    {
      "job": 77362093266,
      "time": 99,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "6940768962"
    },
    {
      "job": 77362092982,
      "time": 116,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "6940784426"
    },
    {
      "job": 77362092685,
      "time": 189,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6940646654"
    },
    {
      "job": 77362092744,
      "time": 120,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7158391193"
    },
    {
      "job": 77362093305,
      "time": 109,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "6940687213"
    },
    {
      "job": 77362093170,
      "time": 101,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "6940683900"
    },
    {
      "job": 77362093621,
      "time": 106,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "6940685074"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 14
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/25726003643",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/CARNIVAL",
  "_commit": {
    "id": "19f1f6672181d95ae005041b2235b29575049694",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777380757
  },
  "_maintainer": {
    "name": "Attila Gabor",
    "email": "attila.gabor@uni-heidelberg.de",
    "login": "gabora",
    "linkedin": "in/attila-g%C3%A1bor-94910524",
    "twitter": "@attila_gbr",
    "uuid": 3891745
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0",
      "role": "Depends"
    },
    {
      "package": "readr",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "lpSolve",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "rjson",
      "role": "Imports"
    },
    {
      "package": "rmarkdown",
      "role": "Imports"
    },
    {
      "package": "RefManageR",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "covr",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "sessioninfo",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 2,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "2.23.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "2.22.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "transcriptomics",
    "geneexpression",
    "network",
    "causal-models",
    "footprints",
    "integer-linear-programming",
    "pathway-enrichment-analysis"
  ],
  "_stars": 62,
  "_contributors": [
    {
      "user": "enio23",
      "count": 2779,
      "uuid": 22002414
    },
    {
      "user": "ptrairatphisan",
      "count": 406,
      "uuid": 20519860
    },
    {
      "user": "anikaliu",
      "count": 111,
      "uuid": 20258727
    },
    {
      "user": "gabora",
      "count": 88,
      "uuid": 3891745
    },
    {
      "user": "ivanovaos",
      "count": 32,
      "uuid": 2984700
    },
    {
      "user": "matteospatuzzi",
      "count": 16,
      "uuid": 49938420
    },
    {
      "user": "bartoszbartmanski",
      "count": 14,
      "uuid": 16625050
    },
    {
      "user": "nturaga",
      "count": 10,
      "uuid": 2746443
    },
    {
      "user": "christianholland",
      "count": 4,
      "uuid": 28303875
    },
    {
      "user": "adugourd",
      "count": 1,
      "uuid": 16302934
    },
    {
      "user": "pierremj",
      "count": 1,
      "uuid": 12627879
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 549,
    "source": "https://www.bioconductor.org/packages/stats/bioc/CARNIVAL"
  },
  "_mentions": 7,
  "_devurl": "https://github.com/saezlab/carnival",
  "_searchresults": 98,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/CARNIVAL.html",
    "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",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/saezlab/carnival",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "checkOptionsValidity",
    "defaultCbcSolveCarnivalOptions",
    "defaultCplexCarnivalOptions",
    "defaultCplexSpecificOptions",
    "defaultLpSolveCarnivalOptions",
    "generateLpFileCarnival",
    "getOptionsList",
    "getSupportedSolvers",
    "isInputValidCarnival",
    "runCARNIVAL",
    "runFromLpCarnival",
    "runInverseCarnival",
    "runVanillaCarnival",
    "setCarnivalOptions",
    "suggestedCbcSpecificOptions",
    "suggestedCplexSpecificOptions"
  ],
  "_help": [
    {
      "page": "checkOptionsValidity",
      "title": "Checks if provided option names are valid.",
      "topics": [
        "checkOptionsValidity"
      ]
    },
    {
      "page": "defaultCbcSolveCarnivalOptions",
      "title": "Sets default CARNIVAL options for cbc.",
      "topics": [
        "defaultCbcSolveCarnivalOptions"
      ]
    },
    {
      "page": "defaultCplexCarnivalOptions",
      "title": "Sets default CARNIVAL options for cplex.",
      "topics": [
        "defaultCplexCarnivalOptions"
      ]
    },
    {
      "page": "defaultCplexSpecificOptions",
      "title": "Sets default options from cplex documentation.",
      "topics": [
        "defaultCplexSpecificOptions"
      ]
    },
    {
      "page": "defaultLpSolveCarnivalOptions",
      "title": "Sets default CARNIVAL options for lpSolve.",
      "topics": [
        "defaultLpSolveCarnivalOptions"
      ]
    },
    {
      "page": "generateLpFileCarnival",
      "title": "'generateLpFileCarnival'",
      "topics": [
        "generateLpFileCarnival"
      ]
    },
    {
      "page": "getOptionsList",
      "title": "Returns the list of options needed/supported for each solver.",
      "topics": [
        "getOptionsList"
      ]
    },
    {
      "page": "getSupportedSolvers",
      "title": "Returns the list of supported solvers.",
      "topics": [
        "getSupportedSolvers"
      ]
    },
    {
      "page": "isInputValidCarnival",
      "title": "Checks validity of all inputs of CARNIVAL",
      "topics": [
        "isInputValidCarnival"
      ]
    },
    {
      "page": "parseCplexLog",
      "title": "Parses the cplex log file and reads some basic information.",
      "topics": [
        "parseCplexLog"
      ]
    },
    {
      "page": "runCARNIVAL",
      "title": "'runCARNIVAL'",
      "topics": [
        "runCARNIVAL"
      ]
    },
    {
      "page": "runFromLpCarnival",
      "title": "'runCarnivalFromLp'",
      "topics": [
        "runFromLpCarnival"
      ]
    },
    {
      "page": "runInverseCarnival",
      "title": "'runInverseCarnival'",
      "topics": [
        "runInverseCarnival"
      ]
    },
    {
      "page": "runVanillaCarnival",
      "title": "'runVanillaCarnival'",
      "topics": [
        "runVanillaCarnival"
      ]
    },
    {
      "page": "setCarnivalOptions",
      "title": "Sets CARNIVAL options for the solver.",
      "topics": [
        "setCarnivalOptions"
      ]
    },
    {
      "page": "suggestedCbcSpecificOptions",
      "title": "Suggests cbc specific options.",
      "topics": [
        "suggestedCbcSpecificOptions"
      ]
    },
    {
      "page": "suggestedCplexSpecificOptions",
      "title": "Suggests cplex specific options.s",
      "topics": [
        "suggestedCplexSpecificOptions"
      ]
    },
    {
      "page": "writeCplexCommandFileFromJson",
      "title": "writeCplexCommandFileFromJson",
      "topics": [
        "writeCplexCommandFileFromJson"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/CARNIVAL/raw/HEAD/README.md",
  "_rundeps": [
    "base64enc",
    "bit",
    "bit64",
    "bslib",
    "cachem",
    "cli",
    "clipr",
    "cpp11",
    "crayon",
    "digest",
    "dplyr",
    "evaluate",
    "fastmap",
    "fontawesome",
    "fs",
    "generics",
    "glue",
    "highr",
    "hms",
    "htmltools",
    "igraph",
    "jquerylib",
    "jsonlite",
    "knitr",
    "lattice",
    "lifecycle",
    "lpSolve",
    "magrittr",
    "Matrix",
    "memoise",
    "mime",
    "pillar",
    "pkgconfig",
    "prettyunits",
    "progress",
    "purrr",
    "R6",
    "rappdirs",
    "readr",
    "rjson",
    "rlang",
    "rmarkdown",
    "sass",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "tzdb",
    "utf8",
    "vctrs",
    "vroom",
    "withr",
    "xfun",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "CARNIVAL.Rmd",
      "filename": "CARNIVAL.html",
      "title": "Contextualizing large scale signalling networks from expression footprints with CARNIVAL",
      "author": "Enio Gjerga, Matteo Spatuzzi, Olga Ivanova,",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Pipeline",
        "ILP solvers",
        "Prerequisites",
        "Running CARNIVAL",
        "Toy Example - 1",
        "Toy Example - 2",
        "Toy Example - 3",
        "Gurobi remote services"
      ],
      "created": "2020-04-06 15:12:06",
      "modified": "2022-03-09 10:10:23",
      "commits": 7
    }
  ],
  "_score": 9.40686705558865,
  "_indexed": true,
  "_nocasepkg": "carnival",
  "_universes": [
    "bioc",
    "gabora",
    "saezlab"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.23.0",
      "date": "2026-05-12T09:39:16.000Z",
      "distro": "noble",
      "commit": "19f1f6672181d95ae005041b2235b29575049694",
      "fileid": "427090a55e9d6932cdb225fce3abdb0a27aec4600a868c940c1b962aad18c3d1",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25726003643"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.23.0",
      "date": "2026-05-12T09:39:54.000Z",
      "distro": "noble",
      "commit": "19f1f6672181d95ae005041b2235b29575049694",
      "fileid": "8450f4ce7a9fb731a1954d7cd098c72a75aab7e9a591cea742980da9020d2284",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25726003643"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.23.0",
      "date": "2026-05-12T09:42:03.000Z",
      "commit": "19f1f6672181d95ae005041b2235b29575049694",
      "fileid": "73b940062632b257ff2aa0000c157bb24df9af1d90b0052a5c590b5e8a8d4a72",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25726003643"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.23.0",
      "date": "2026-05-12T09:42:44.000Z",
      "commit": "19f1f6672181d95ae005041b2235b29575049694",
      "fileid": "bf3fed5ff27b20e415614a3c1889aa470905feed14832ec672cd4609a0411dfc",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25726003643"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.23.0",
      "date": "2026-05-12T09:38:04.000Z",
      "commit": "19f1f6672181d95ae005041b2235b29575049694",
      "fileid": "de22fe209505a430f71ccbf19e38d9eb8ce28515cda98a2669df7ec8256477c9",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25726003643"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.23.0",
      "date": "2026-05-12T09:37:53.000Z",
      "commit": "19f1f6672181d95ae005041b2235b29575049694",
      "fileid": "5c2118aef93e9a289ab2c022fcb6b551f6f1d52f58b0834c0e6bfa528e5c6ea0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25726003643"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.23.0",
      "date": "2026-05-12T09:37:55.000Z",
      "commit": "19f1f6672181d95ae005041b2235b29575049694",
      "fileid": "c733b248f015291c1f2779f766903989a2fb8edb09d756275fa1de12c958a70f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25726003643"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.23.0",
      "date": "2026-05-22T10:30:47.000Z",
      "commit": "19f1f6672181d95ae005041b2235b29575049694",
      "fileid": "9c4c5968fd38220c836b6bc524587d588155e693faac47072933eccac6ed2df7",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25726003643"
    }
  ]
}