{
  "_id": "6a631580d3420cf5dfdb6def",
  "Package": "KPIC",
  "Type": "Package",
  "Title": "Mass Spectrometry-Based Metabolomics Using Pure Ion\nChromatograms",
  "Version": "2.4.0",
  "Author": "Hongchao Ji",
  "Maintainer": "Hongchao Ji <ji.hongchao@foxmail.com>",
  "Description": "KPIC2 is an effective platform for LC-MS based\nmetabolomics using pure ion chromatograms, which is developed\nfor metabolomics studies. KPIC2 can detect pure ions\naccurately, align PICs across samples, group PICs to annotate\nisotope and adduct PICs, fill missing peaks and pattern\nrecognition. High-resolution mass spectrometers like TOF and\nOrbitrap are more suitable.",
  "License": "GPL (>= 2)",
  "Encoding": "UTF-8",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libnetcdf-dev\nlibssl-dev zlib1g-dev",
  "Repository": "https://rickhelmus.r-universe.dev",
  "Date/Publication": "2025-05-30 14:40:32 UTC",
  "RemoteUrl": "https://github.com/rickhelmus/KPIC2",
  "RemoteRef": "HEAD",
  "RemoteSha": "5f638051693b13345445d79837a99744c34607a5",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-07-24 06:30:12 UTC",
    "User": "root"
  },
  "_user": "rickhelmus",
  "_type": "src",
  "_file": "KPIC_2.4.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/b9134714be7dcde5c5c06524c66cdf492efba4e45af1f5e056bc139a7f08c245",
  "_filesize": 239307,
  "_sha256": "b9134714be7dcde5c5c06524c66cdf492efba4e45af1f5e056bc139a7f08c245",
  "_expires": "2026-11-01T07:34:22.000Z",
  "_created": "2026-07-24T06:30:12.000Z",
  "_published": "2026-07-24T07:34:24.361Z",
  "_jobs": [
    {
      "job": 89416143230,
      "time": 246,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "8588615804"
    },
    {
      "job": 89416143249,
      "time": 301,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "8588632810"
    },
    {
      "job": 89416143237,
      "time": 258,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8588621349"
    },
    {
      "job": 89416143225,
      "time": 356,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8588649214"
    },
    {
      "job": 89416143233,
      "time": 212,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8589638314"
    },
    {
      "job": 89416143226,
      "time": 474,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8589817482"
    },
    {
      "job": 89416143214,
      "time": 264,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8589783734"
    },
    {
      "job": 89416143242,
      "time": 372,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8589807702"
    },
    {
      "job": 89415508848,
      "time": 260,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8588543507"
    },
    {
      "job": 89416143201,
      "time": 172,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8588594032"
    },
    {
      "job": 89416143236,
      "time": 255,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "8588619277"
    },
    {
      "job": 89416143217,
      "time": 278,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8588625587"
    },
    {
      "job": 89416143220,
      "time": 284,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8588628002"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/30072272391",
  "_status": "success",
  "_upstream": "https://github.com/rickhelmus/KPIC2",
  "_commit": {
    "id": "5f638051693b13345445d79837a99744c34607a5",
    "author": "Rick Helmus <r.helmus@uva.nl>",
    "committer": "Rick Helmus <r.helmus@uva.nl>",
    "message": "various fixes to handle empty results and results with only outliers\n",
    "time": 1748616032
  },
  "_maintainer": {
    "name": "Hongchao Ji",
    "email": "ji.hongchao@foxmail.com",
    "login": "hcji",
    "description": "I'm Hongchao Ji, a Principal Investigator at CAAS, specializing in developing MS-based data analysis methods for proteomics and metabolomics.",
    "uuid": 17610691
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "RcppArmadillo",
      "role": "Imports"
    },
    {
      "package": "mzR",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "shiny",
      "role": "Imports"
    },
    {
      "package": "plotly",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "GA",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "dbscan",
      "role": "Imports"
    },
    {
      "package": "Ckmeans.1d.dp",
      "role": "Imports"
    },
    {
      "package": "jsonlite",
      "role": "Imports"
    },
    {
      "package": "randomForest",
      "role": "Imports"
    },
    {
      "package": "ropls",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    }
  ],
  "_owner": "rickhelmus",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "hcji",
      "count": 34,
      "uuid": 17610691
    },
    {
      "user": "rickhelmus",
      "count": 9,
      "uuid": 37015911
    }
  ],
  "_userbio": {
    "uuid": 37015911,
    "type": "user",
    "name": "rickhelmus",
    "followers": 24
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/KPIC"
  },
  "_devurl": "https://github.com/rickhelmus/kpic2",
  "_searchresults": 3,
  "_topics": [
    "cpp"
  ],
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/KPIC.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    ".PICfit",
    ".PICresolve",
    ".PICsplit",
    "analyst.OPLS",
    "analyst.RF",
    "fillPeaks.EIBPC",
    "getDataMatrix",
    "getMS",
    "getPeaks",
    "getPIC",
    "getPIC.kmeans",
    "getPIP",
    "getTICs",
    "groupCombine",
    "LoadData",
    "PICfit",
    "PICresolve",
    "PICset",
    "PICset.align",
    "PICset.fit",
    "PICset.getPeaks",
    "PICset.group",
    "PICset.kmeans",
    "PICset.resolve",
    "PICset.split",
    "PICsplit",
    "readPICs",
    "viewAlign",
    "viewGroups",
    "viewMS",
    "viewPICs",
    "viewPseudospecturm",
    "viewTICs",
    "WMPD"
  ],
  "_help": [
    {
      "page": "analyst.OPLS",
      "title": "Analyst the peaks with PLS-DA or OPLS-DA",
      "topics": [
        "analyst.OPLS"
      ]
    },
    {
      "page": "analyst.RF",
      "title": "Analyst the peaks with random forest",
      "topics": [
        "analyst.RF"
      ]
    },
    {
      "page": "fillPeaks.EIBPC",
      "title": "identify missing peaks",
      "topics": [
        "fillPeaks.EIBPC"
      ]
    },
    {
      "page": "getMS",
      "title": "get MS of a LC-MS data file.",
      "topics": [
        "getMS"
      ]
    },
    {
      "page": "getPeaks",
      "title": "Get peaks of the detected PICs.",
      "topics": [
        "getPeaks"
      ]
    },
    {
      "page": "getPIC",
      "title": "Extract PICs from a LC-MS raw object based on m/z difference.",
      "topics": [
        "getPIC"
      ]
    },
    {
      "page": "getPIC.kmeans",
      "title": "Extract PICs from a LC-MS raw object based on optimal k-means clustering.",
      "topics": [
        "getPIC.kmeans"
      ]
    },
    {
      "page": "getTICs",
      "title": "Get TICs of LC-MS data.",
      "topics": [
        "getTICs"
      ]
    },
    {
      "page": "groupCombine",
      "title": "Combine tailed, isotopic or/and adduct features into the same group.",
      "topics": [
        "groupCombine"
      ]
    },
    {
      "page": "LoadData",
      "title": "Load an LC-MS data file.",
      "topics": [
        "LoadData"
      ]
    },
    {
      "page": "PICset",
      "title": "Process a set of sample with 'getPIC' method.",
      "topics": [
        "PICset"
      ]
    },
    {
      "page": "PICset.align",
      "title": "Align each group of PICs.",
      "topics": [
        "PICset.align"
      ]
    },
    {
      "page": "PICset.getPeaks",
      "title": "The 'getPeaks' function for a set of samples.",
      "topics": [
        "PICset.getPeaks"
      ]
    },
    {
      "page": "PICset.group",
      "title": "group the features",
      "topics": [
        "PICset.group"
      ]
    },
    {
      "page": "PICset.kmeans",
      "title": "Process a set of sample with 'getPIC.kmeans' method.",
      "topics": [
        "PICset.kmeans"
      ]
    },
    {
      "page": "PICset.split",
      "title": "The 'PICsplit' function for a set of samples.",
      "topics": [
        "PICset.split"
      ]
    },
    {
      "page": "PICsplit",
      "title": "Spliting multiple-peak trace into single ones",
      "topics": [
        "PICsplit"
      ]
    },
    {
      "page": "viewAlign",
      "title": "View the result of alignment.",
      "topics": [
        "viewAlign"
      ]
    },
    {
      "page": "viewGroups",
      "title": "View the result of group.",
      "topics": [
        "viewGroups"
      ]
    },
    {
      "page": "viewMS",
      "title": "View MS.",
      "topics": [
        "viewMS"
      ]
    },
    {
      "page": "viewPICs",
      "title": "View the PICs.",
      "topics": [
        "viewPICs"
      ]
    },
    {
      "page": "viewTICs",
      "title": "View TICs",
      "topics": [
        "viewTICs"
      ]
    },
    {
      "page": "WMPD",
      "title": "Reslove overlapped peak based on mass spectrometry.",
      "topics": [
        "WMPD"
      ]
    }
  ],
  "_readme": "https://github.com/rickhelmus/KPIC2/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "base64enc",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "biocmake",
    "bslib",
    "cachem",
    "calibrate",
    "Ckmeans.1d.dp",
    "cli",
    "codetools",
    "commonmark",
    "cpp11",
    "crayon",
    "crosstalk",
    "curl",
    "data.table",
    "dbscan",
    "DelayedArray",
    "digest",
    "dir.expiry",
    "dplyr",
    "evaluate",
    "farver",
    "fastmap",
    "filelock",
    "fontawesome",
    "foreach",
    "fs",
    "GA",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "ggrepel",
    "glue",
    "gtable",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "httr",
    "IRanges",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "limma",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "MultiAssayExperiment",
    "MultiDataSet",
    "mzR",
    "ncdf4",
    "openssl",
    "otel",
    "pillar",
    "pkgconfig",
    "plotly",
    "promises",
    "ProtGenerics",
    "purrr",
    "qqman",
    "R6",
    "randomForest",
    "rappdirs",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "Rdpack",
    "Rhdf5lib",
    "rlang",
    "rmarkdown",
    "ropls",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "shiny",
    "sourcetools",
    "SparseArray",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "xtable",
    "XVector",
    "yaml"
  ],
  "_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"
    }
  ],
  "_score": 1.6989700043360187,
  "_indexed": true,
  "_nocasepkg": "kpic",
  "_universes": [
    "rickhelmus",
    "hcji"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.4.0",
      "date": "2026-07-24T06:33:10.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "5f638051693b13345445d79837a99744c34607a5",
      "fileid": "https://r2.ropensci.org/c4911846b2b51a74fc73fe0440b0f86757d129327850cdda5052e7b6c64710ac",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/30072272391"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.4.0",
      "date": "2026-07-24T06:33:29.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "5f638051693b13345445d79837a99744c34607a5",
      "fileid": "https://r2.ropensci.org/ade8f7b45665bc3ecc3fc1f40125924c85b7c0980e8e0811e15976edffbc6a4d",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/30072272391"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "2.4.0",
      "date": "2026-07-24T06:33:26.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "5f638051693b13345445d79837a99744c34607a5",
      "fileid": "https://r2.ropensci.org/171f61f6ac976df04e41ebad523ab35617b30d46ea58b9e590c9453111a85a8a",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/30072272391"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "2.4.0",
      "date": "2026-07-24T06:34:27.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "5f638051693b13345445d79837a99744c34607a5",
      "fileid": "https://r2.ropensci.org/118ad6662da5d6f53550810a20006f22086925b0e053263899b5a79678fbc7f3",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/30072272391"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.4.0",
      "date": "2026-07-24T07:23:17.000Z",
      "arch": "aarch64",
      "commit": "5f638051693b13345445d79837a99744c34607a5",
      "fileid": "https://r2.ropensci.org/fba1df52c1dca2faeadd8f9d66f31f296d1ed97cabee4268c7d1cf40634e4bc9",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/30072272391"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.4.0",
      "date": "2026-07-24T07:29:34.000Z",
      "arch": "x86_64",
      "commit": "5f638051693b13345445d79837a99744c34607a5",
      "fileid": "https://r2.ropensci.org/cf8eadb77969d8d9f3edc00711569bd927905b551dcbe850f3e8f984641b02e0",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/30072272391"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "2.4.0",
      "date": "2026-07-24T07:29:42.000Z",
      "arch": "aarch64",
      "commit": "5f638051693b13345445d79837a99744c34607a5",
      "fileid": "https://r2.ropensci.org/167e7b6f82a58959ad089b7298a2526b19ac68d98b68c20d646859d68e39a557",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/30072272391"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "2.4.0",
      "date": "2026-07-24T07:30:05.000Z",
      "arch": "x86_64",
      "commit": "5f638051693b13345445d79837a99744c34607a5",
      "fileid": "https://r2.ropensci.org/3c20355ae8e817de7c542492c55a8478a5df79373035840ef6e27c058eab7cb8",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/30072272391"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.4.0",
      "date": "2026-07-24T06:33:43.000Z",
      "arch": "emscripten",
      "commit": "5f638051693b13345445d79837a99744c34607a5",
      "fileid": "https://r2.ropensci.org/d32b4963c916f7a07631e93dcff2fb15ef7eef364ec9f388666daaba1ba315a1",
      "status": "success",
      "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/30072272391"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.4.0",
      "date": "2026-07-24T06:32:15.000Z",
      "arch": "x86_64",
      "commit": "5f638051693b13345445d79837a99744c34607a5",
      "fileid": "https://r2.ropensci.org/bd7b0ed4bd7db96e137e3b68c6c506fa0a5676308e351112ee041562864e1877",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/30072272391"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.4.0",
      "date": "2026-07-24T06:32:35.000Z",
      "arch": "x86_64",
      "commit": "5f638051693b13345445d79837a99744c34607a5",
      "fileid": "https://r2.ropensci.org/32ec61c94a7d5eab14fa252a867fc1d07e28564dcc09473584178fe000f9c255",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/30072272391"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "2.4.0",
      "date": "2026-07-24T06:32:26.000Z",
      "arch": "x86_64",
      "commit": "5f638051693b13345445d79837a99744c34607a5",
      "fileid": "https://r2.ropensci.org/22e55d5553eb8b0c346ed28190637294ea99cd49dae9ff24ee40c46e279ad6f3",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/30072272391"
    }
  ]
}