{
  "_id": "6ae4481895ca2370cc8ceddb",
  "Package": "CNORfuzzy",
  "Type": "Package",
  "Title": "Addon to CellNOptR: Fuzzy Logic",
  "Version": "1.55.0",
  "Date": "2013-8-28",
  "Author": "M. Morris, T. Cokelaer",
  "Maintainer": "T. Cokelaer <cokelaer@ebi.ac.uk>",
  "Description": "This package is an extension to CellNOptR.  It contains\nadditional functionality needed to simulate and train a prior\nknowledge network to experimental data using constrained fuzzy\nlogic (cFL, rather than Boolean logic as is the case in\nCellNOptR).  Additionally, this package will contain functions\nto use for the compilation of multiple optimization results\n(either Boolean or cFL).",
  "License": "GPL-2",
  "LazyLoad": "yes",
  "biocViews": "Network",
  "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:36:47 UTC",
  "RemoteUrl": "https://github.com/bioc/CNORfuzzy",
  "RemoteRef": "HEAD",
  "RemoteSha": "0e58dc01ca1961013aa910203bac9c03095c7c7a",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-10-29 11:25:58 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "CNORfuzzy_1.55.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/5e547ef0ff9d7a1e87268de962a71dca45d28dd6b4eab448f4092ef4bdc3b47f",
  "_filesize": 1074341,
  "_sha256": "5e547ef0ff9d7a1e87268de962a71dca45d28dd6b4eab448f4092ef4bdc3b47f",
  "_expires": "2027-02-06T12:30:03.000Z",
  "_created": "2026-10-29T11:25:58.000Z",
  "_published": "2026-10-30T07:32:40.834Z",
  "_upstream": "https://github.com/bioc/CNORfuzzy",
  "_status": "success",
  "_maintainer": {
    "name": "T. Cokelaer",
    "email": "cokelaer@ebi.ac.uk"
  },
  "_jobs": [
    {
      "job": 123946092822,
      "time": 142,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "FAILURE",
      "artifact": ""
    },
    {
      "job": 123946095354,
      "time": 193,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "12893701452"
    },
    {
      "job": 123946095347,
      "time": 240,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "12893631965"
    },
    {
      "job": 123946094880,
      "time": 149,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12893252997"
    },
    {
      "job": 123946095782,
      "time": 291,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12894360293"
    },
    {
      "job": 123946095625,
      "time": 126,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "12897430937"
    },
    {
      "job": 123946095174,
      "time": 257,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "12896464434"
    },
    {
      "job": 123946093177,
      "time": 183,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12961631889"
    },
    {
      "job": 123946094528,
      "time": 274,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12896448778"
    },
    {
      "job": 123946094028,
      "time": 359,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12892254777"
    },
    {
      "job": 123946094694,
      "time": 127,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12893113579"
    },
    {
      "job": 123946095560,
      "time": 252,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "12893751377"
    },
    {
      "job": 123946095545,
      "time": 168,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "12893811497"
    },
    {
      "job": 123946095298,
      "time": 145,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "12894125691"
    },
    {
      "job": 123946094715,
      "time": 313,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12894295625"
    },
    {
      "job": 123946094738,
      "time": 113,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12894015848"
    }
  ],
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/40864566073",
  "_commit": {
    "id": "0e58dc01ca1961013aa910203bac9c03095c7c7a",
    "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": 1777379807
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.15.0",
      "role": "Depends"
    },
    {
      "package": "CellNOptR",
      "version": ">= 1.4.0",
      "role": "Depends"
    },
    {
      "package": "nloptr",
      "version": ">= 0.8.5",
      "role": "Depends"
    },
    {
      "package": "xtable",
      "role": "Suggests"
    },
    {
      "package": "Rgraphviz",
      "role": "Suggests"
    },
    {
      "package": "RUnit",
      "role": "Suggests"
    },
    {
      "package": "BiocGenerics",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.55.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.54.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "network"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 481,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 556,
    "source": "https://www.bioconductor.org/packages/stats/bioc/CNORfuzzy"
  },
  "_mentions": 2,
  "_searchresults": 6,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/CNORfuzzy.html",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "CNORwrapFuzzy",
    "compileMultiRes",
    "computeScoreFuzzy",
    "defaultParametersFuzzy",
    "gaDiscreteT1",
    "getRefinedModel",
    "interpretDiscreteGA",
    "plotMeanFuzzyFit",
    "prep4simFuzzy",
    "reduceFuzzy",
    "simFuzzyT1",
    "writeFuzzyNetwork"
  ],
  "_help": [
    {
      "page": "CNORfuzzy-package",
      "title": "R version of CNOFuzzy, a Constrained Fuzzy Logic Network Optimisation",
      "topics": [
        "CNORfuzzy-package",
        "CNORfuzzy"
      ]
    },
    {
      "page": "CNORwrapFuzzy",
      "title": "CNORfuzzy analysis wrapper",
      "topics": [
        "CNORwrapFuzzy"
      ]
    },
    {
      "page": "compileMultiRes",
      "title": "Compiles results from multiple runs and produces graph for choosing Post Refinement Threshold",
      "topics": [
        "compileMultiRes"
      ]
    },
    {
      "page": "computeScoreFuzzy",
      "title": "Compute Score of a model compared to the data for a given intString.",
      "topics": [
        "computeScoreFuzzy"
      ]
    },
    {
      "page": "defaultParametersFuzzy",
      "title": "Create a list of default parameters",
      "topics": [
        "defaultParametersFuzzy"
      ]
    },
    {
      "page": "gaDiscreteT1",
      "title": "Genetic algorithm used to optimise a cFL model",
      "topics": [
        "gaDiscreteT1"
      ]
    },
    {
      "page": "getRefinedModel",
      "title": "Refinement of Parameters of cFL model",
      "topics": [
        "getRefinedModel"
      ]
    },
    {
      "page": "interpretDiscreteGA",
      "title": "Interpreter of output of discrete genetic algorithm",
      "topics": [
        "interpretDiscreteGA"
      ]
    },
    {
      "page": "plotMeanFuzzyFit",
      "title": "Simulates models returned from multiple cFL runs and plots mean fit to data",
      "topics": [
        "plotMeanFuzzyFit"
      ]
    },
    {
      "page": "prep4simFuzzy",
      "title": "Prepare a model for simulation",
      "topics": [
        "prep4simFuzzy"
      ]
    },
    {
      "page": "reduceFuzzy",
      "title": "Remove unnecessary interactions from cFL model",
      "topics": [
        "reduceFuzzy"
      ]
    },
    {
      "page": "simFuzzyT1",
      "title": "Simulation of a cFL model",
      "topics": [
        "simFuzzyT1"
      ]
    },
    {
      "page": "writeFuzzyNetwork",
      "title": "Despict the network results of training a cFL model to data in multiple runs.",
      "topics": [
        "writeFuzzyNetwork"
      ]
    }
  ],
  "_rundeps": [
    "base64enc",
    "BH",
    "BiocGenerics",
    "bitops",
    "bslib",
    "cachem",
    "CellNOptR",
    "cli",
    "cpp11",
    "digest",
    "evaluate",
    "farver",
    "fastmap",
    "fontawesome",
    "fs",
    "generics",
    "ggplot2",
    "glue",
    "graph",
    "gtable",
    "highr",
    "htmltools",
    "igraph",
    "isoband",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "memoise",
    "mime",
    "nloptr",
    "pkgconfig",
    "R6",
    "rappdirs",
    "RBGL",
    "RColorBrewer",
    "RCurl",
    "Rgraphviz",
    "rlang",
    "rmarkdown",
    "S7",
    "sass",
    "scales",
    "stringi",
    "stringr",
    "tinytex",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "XML",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "CNORfuzzy-vignette.Rnw",
      "filename": "CNORfuzzy-vignette.pdf",
      "title": "Main vignette:Playing with networks using CNORfuzzyl",
      "engine": "utils::Sweave",
      "headings": [
        "Introduction",
        "Installation",
        "Quick Start",
        "Detailled example",
        "Default parameters"
      ],
      "created": "2013-11-01 20:26:44",
      "modified": "2018-08-30 17:46:26",
      "commits": 2
    }
  ],
  "_score": 3.6020599913279625,
  "_indexed": true,
  "_nocasepkg": "cnorfuzzy",
  "_universes": [
    "bioc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.55.0",
      "date": "2026-10-29T11:28:51.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "0e58dc01ca1961013aa910203bac9c03095c7c7a",
      "fileid": "https://r2.ropensci.org/45d0bc573ac11c4b2a1a2fdf0352b5d219176850d5dcde99cb022cf5a3ca64b3",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40864566073"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.55.0",
      "date": "2026-10-29T11:29:43.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "0e58dc01ca1961013aa910203bac9c03095c7c7a",
      "fileid": "https://r2.ropensci.org/e1f94ccd09ac228f71bd5bbbd9b2b9a7b4c369290708a645c2e1fc717e6f163e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40864566073"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.55.0",
      "date": "2026-10-29T11:28:11.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "0e58dc01ca1961013aa910203bac9c03095c7c7a",
      "fileid": "https://r2.ropensci.org/9ffc96bc75aef8c07e49c78d2b93eac15aca6010498bd854c58fd163090ebf82",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40864566073"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.55.0",
      "date": "2026-10-29T11:30:30.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "0e58dc01ca1961013aa910203bac9c03095c7c7a",
      "fileid": "https://r2.ropensci.org/347abfb4cd74390ecf4ea2c1242103bee35960397a0ccfb4d013eb8245bcd547",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40864566073"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.55.0",
      "date": "2026-10-29T12:26:48.000Z",
      "arch": "aarch64",
      "commit": "0e58dc01ca1961013aa910203bac9c03095c7c7a",
      "fileid": "https://r2.ropensci.org/ed91cf46f5a925c3f60477d2cb311f5d991d961019effebd40784145c56a3ce6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40864566073"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.55.0",
      "date": "2026-10-29T12:28:13.000Z",
      "arch": "x86_64",
      "commit": "0e58dc01ca1961013aa910203bac9c03095c7c7a",
      "fileid": "https://r2.ropensci.org/66330a22d1a92a545b8e5bd307082b701cfcaa3a8f195e11bfef361311362142",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40864566073"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.55.0",
      "date": "2026-10-30T07:31:18.000Z",
      "arch": "aarch64",
      "commit": "0e58dc01ca1961013aa910203bac9c03095c7c7a",
      "fileid": "https://r2.ropensci.org/555096c745b3d654a3ecfcff2e03193befc7ed0c18f53b89a8957780ebcc083c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40864566073"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.55.0",
      "date": "2026-10-29T12:28:33.000Z",
      "arch": "x86_64",
      "commit": "0e58dc01ca1961013aa910203bac9c03095c7c7a",
      "fileid": "https://r2.ropensci.org/ac6e7f7b80d5d76ac3d28464a9fd4d8231867e8f14728aa36675a59b10016f25",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40864566073"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.55.0",
      "date": "2026-10-29T11:28:23.000Z",
      "arch": "emscripten",
      "commit": "0e58dc01ca1961013aa910203bac9c03095c7c7a",
      "fileid": "https://r2.ropensci.org/f6448f721f4b8d8d5e3af2aba4361caf69b0d3273bff524ace6692106d66af06",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40864566073"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.55.0",
      "date": "2026-10-29T11:29:28.000Z",
      "arch": "aarch64",
      "commit": "0e58dc01ca1961013aa910203bac9c03095c7c7a",
      "fileid": "https://r2.ropensci.org/56c2e6fd8e20e23c8508227738d631d672f4f760eda433b2aeb77c66c2b0cee2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40864566073"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.55.0",
      "date": "2026-10-29T11:27:23.000Z",
      "arch": "x86_64",
      "commit": "0e58dc01ca1961013aa910203bac9c03095c7c7a",
      "fileid": "https://r2.ropensci.org/50c37cfe459c5026a0f6f3232a7dcba99f56dc7a59ec0aa538c08c0978c8b113",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40864566073"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.55.0",
      "date": "2026-10-29T11:27:34.000Z",
      "arch": "x86_64",
      "commit": "0e58dc01ca1961013aa910203bac9c03095c7c7a",
      "fileid": "https://r2.ropensci.org/b92edf58326075ab7b34732838fd002991048a01e2775757537dba1df0c97610",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40864566073"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.55.0",
      "date": "2026-10-29T11:30:34.000Z",
      "arch": "aarch64",
      "commit": "0e58dc01ca1961013aa910203bac9c03095c7c7a",
      "fileid": "https://r2.ropensci.org/d1a5dd664b4e6f3e3750a9b10ae691b584aefefc38a338c633645ec14ebad79d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40864566073"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.55.0",
      "date": "2026-10-29T11:27:28.000Z",
      "arch": "x86_64",
      "commit": "0e58dc01ca1961013aa910203bac9c03095c7c7a",
      "fileid": "https://r2.ropensci.org/0b18db973a9ab770d84a8dfbdf6bff00718eab1cab07819cba718ffe77a9b6f2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40864566073"
    }
  ]
}