{
  "_id": "6a104e77acfb0bcc41ca0a61",
  "Package": "FastRet",
  "Title": "Retention Time Prediction in Liquid Chromatography",
  "Version": "1.3.0",
  "Authors@R": "c(\nperson(given = \"Tobias\", family = \"Schmidt\", role = c(\"aut\", \"cre\", \"cph\"), email = \"tobias.schmidt331@gmail.com\", comment = c(ORCID = \"0000-0001-9681-9253\")),\nperson(given = \"Christian\", family = \"Amesoeder\", role = c(\"aut\", \"cph\"), email = \"christian-amesoeder@web.de\", comment = c(ORCID = \"0000-0002-1668-8351\")),\nperson(given = \"Marian\", family = \"Schoen\", role = c(\"aut\", \"cph\"), email = \"marian.schoen@klinik.uni-regensburg.de\"),\nperson(given = \"Fadi\", family = \"Fadil\", role = c(\"aut\", \"cph\"), email = \"fadi.fadil@klinik.uni-regensburg.de\", comment = c(ORCID = \"0000-0002-9532-1901\")),\nperson(given = \"Katja\", family = \"Dettmer\", role = c(\"aut\", \"cph\"), email = \"Katja.Dettmer@klinik.uni-regensburg.de\", comment = c(ORCID = \"0000-0001-7337-2380\")),\nperson(given = \"Peter\", family = \"Oefner\", role = c(\"ths\", \"cph\"), email = \"Peter.Oefner@klinik.uni-regensburg.de\", comment = c(ORCID = \"0000-0002-1499-3977\"))\n)",
  "Description": "A framework for predicting retention times in liquid\nchromatography. Users can train custom models for specific\nchromatography columns, predict retention times using existing\nmodels, or adjust existing models to account for altered\nexperimental conditions. The provided functionalities can be\naccessed either via the R console or via a graphical user\ninterface. Related work: Bonini et al. (2020)\n<doi:10.1021/acs.analchem.9b05765>.",
  "License": "GPL-3",
  "Language": "en-US",
  "URL": "https://github.com/spang-lab/FastRet/,\nhttps://spang-lab.github.io/FastRet/",
  "BugReports": "https://github.com/spang-lab/FastRet/issues",
  "biocViews": "Retention, Time, Chromotography, LC-MS",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.2.2",
  "LazyData": "true",
  "Config/testthat/edition": "3",
  "Config/testthat/parallel": "true",
  "Config/testthat/start-first": "getCDs, parLapply2, get_predictors,\nplot_frm, train_frm-lasso, train_frm-gbtree, fit_gbtree",
  "Config/pak/sysreqs": "cmake make default-jdk libicu-dev libpng-dev\nlibuv1-dev zlib1g-dev",
  "Repository": "https://spang-lab.r-universe.dev",
  "Date/Publication": "2026-04-10 06:23:20 UTC",
  "RemoteUrl": "https://github.com/spang-lab/FastRet",
  "RemoteRef": "HEAD",
  "RemoteSha": "8b27a10557e8272fbfe925244184c0d3252c8702",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-10 06:35:13 UTC",
    "User": "root"
  },
  "Author": "Tobias Schmidt [aut, cre, cph] (ORCID:\n<https://orcid.org/0000-0001-9681-9253>),\nChristian Amesoeder [aut, cph] (ORCID:\n<https://orcid.org/0000-0002-1668-8351>),\nMarian Schoen [aut, cph],\nFadi Fadil [aut, cph] (ORCID: <https://orcid.org/0000-0002-9532-1901>),\nKatja Dettmer [aut, cph] (ORCID:\n<https://orcid.org/0000-0001-7337-2380>),\nPeter Oefner [ths, cph] (ORCID:\n<https://orcid.org/0000-0002-1499-3977>)",
  "Maintainer": "Tobias Schmidt <tobias.schmidt331@gmail.com>",
  "MD5sum": "78e20b083ae250e3c434dcf3f2cc5512",
  "_user": "spang-lab",
  "_type": "src",
  "_file": "FastRet_1.3.0.tar.gz",
  "_fileid": "fe0e7a2f5ce748f2df27dd3e2e03221ae721226caae7a0604036d8d157972457",
  "_filesize": 1495752,
  "_sha256": "fe0e7a2f5ce748f2df27dd3e2e03221ae721226caae7a0604036d8d157972457",
  "_created": "2026-05-10T06:35:13.000Z",
  "_published": "2026-05-22T12:39:19.603Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77380871156,
      "time": 186,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6901640022"
    },
    {
      "job": 77380871135,
      "time": 178,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6901639256"
    },
    {
      "job": 77380871173,
      "time": 109,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6901634953"
    },
    {
      "job": 77380871069,
      "time": 95,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6901632136"
    },
    {
      "job": 77380870654,
      "time": 251,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6901622923"
    },
    {
      "job": 77380870497,
      "time": 160,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7160667706"
    },
    {
      "job": 77380870785,
      "time": 112,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6901633353"
    },
    {
      "job": 77380871147,
      "time": 107,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6901632803"
    },
    {
      "job": 77380871068,
      "time": 159,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6901637759"
    }
  ],
  "_buildurl": "https://github.com/r-universe/spang-lab/actions/runs/25621878639",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/spang-lab/FastRet",
  "_commit": {
    "id": "8b27a10557e8272fbfe925244184c0d3252c8702",
    "author": "Tobias Schmidt <tobias2.schmidt@ukr.de>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Make Fadi and Katja authors",
    "time": 1775802200
  },
  "_maintainer": {
    "name": "Tobias Schmidt",
    "email": "tobias.schmidt331@gmail.com",
    "login": "toscm",
    "uuid": 12760468,
    "orcid": "0000-0001-9681-9253"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "bslib",
      "role": "Imports"
    },
    {
      "package": "cluster",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "DT",
      "role": "Imports"
    },
    {
      "package": "future",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "glmnet",
      "role": "Imports"
    },
    {
      "package": "htmltools",
      "role": "Imports"
    },
    {
      "package": "openxlsx",
      "role": "Imports"
    },
    {
      "package": "promises",
      "role": "Imports"
    },
    {
      "package": "rcdk",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "shiny",
      "version": ">= 1.8.1",
      "role": "Imports"
    },
    {
      "package": "shinyhelper",
      "role": "Imports"
    },
    {
      "package": "shinyjs",
      "role": "Imports"
    },
    {
      "package": "withr",
      "role": "Imports"
    },
    {
      "package": "xgboost",
      "role": "Imports"
    },
    {
      "package": "callr",
      "role": "Suggests"
    },
    {
      "package": "caret",
      "role": "Suggests"
    },
    {
      "package": "cli",
      "role": "Suggests"
    },
    {
      "package": "devtools",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "languageserver",
      "role": "Suggests"
    },
    {
      "package": "lintr",
      "role": "Suggests"
    },
    {
      "package": "pkgdown",
      "role": "Suggests"
    },
    {
      "package": "pkgbuild",
      "role": "Suggests"
    },
    {
      "package": "pkgload",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "servr",
      "role": "Suggests"
    },
    {
      "package": "tibble",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "toscutil",
      "role": "Suggests"
    },
    {
      "package": "usethis",
      "role": "Suggests"
    }
  ],
  "_owner": "spang-lab",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-26",
      "n": 1
    },
    {
      "week": "2025-39",
      "n": 3
    },
    {
      "week": "2025-45",
      "n": 1
    },
    {
      "week": "2025-51",
      "n": 2
    },
    {
      "week": "2025-52",
      "n": 1
    },
    {
      "week": "2026-15",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "v1.1.5",
      "date": "2025-06-26"
    },
    {
      "name": "v1.2.0",
      "date": "2025-09-22"
    },
    {
      "name": "v1.2.1",
      "date": "2025-09-23"
    },
    {
      "name": "v1.3.0",
      "date": "2025-12-17"
    }
  ],
  "_topics": [
    "retention",
    "time",
    "chromotography",
    "lc-ms",
    "data-science",
    "lcms",
    "openjdk"
  ],
  "_stars": 2,
  "_contributors": [
    {
      "user": "toscm",
      "count": 59,
      "uuid": 12760468
    }
  ],
  "_userbio": {
    "uuid": 65526500,
    "type": "organization",
    "name": "The Spang Lab",
    "description": "Statistical Bioinformatics Department, University of Regensburg, Germany"
  },
  "_downloads": {
    "count": 206,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/FastRet"
  },
  "_devurl": "https://github.com/spang-lab/fastret",
  "_pkgdown": "https://spang-lab.github.io/FastRet/",
  "_searchresults": 3,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/FastRet.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/spang-lab/fastret",
  "_realowner": "spang-lab",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.1.3",
      "date": "2024-06-25"
    },
    {
      "version": "1.1.4",
      "date": "2025-02-10"
    },
    {
      "version": "1.3.0",
      "date": "2025-12-17"
    }
  ],
  "_exports": [
    "adjust_frm",
    "analyzeCDNames",
    "as_canonical",
    "catf",
    "CDFeatures",
    "CDNames",
    "clip_predictions",
    "collect",
    "fastret_app",
    "get_predictors",
    "getCDs",
    "init_log_dir",
    "now",
    "pkg_file",
    "plot_frm",
    "preprocess_data",
    "read_retip_hilic_data",
    "read_rp_lasso_model_rds",
    "read_rp_xlsx",
    "read_rpadj_xlsx",
    "selective_measuring",
    "start_gui",
    "train_frm",
    "withLineEnd",
    "withSink",
    "withStopMessage",
    "withTimeout"
  ],
  "_datasets": [
    {
      "name": "RP",
      "title": "Retention Times (RT) measured on a Reverse Phase (RP) Column",
      "object": "RP",
      "class": [
        "data.frame"
      ],
      "fields": [
        "RT",
        "SMILES",
        "NAME"
      ],
      "rows": 442,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "adjust_frm",
      "title": "Adjust an existing FastRet model for use with a new column",
      "topics": [
        "adjust_frm"
      ]
    },
    {
      "page": "clip_predictions",
      "title": "Clip predictions to observed range",
      "topics": [
        "clip_predictions"
      ]
    },
    {
      "page": "fastret_app",
      "title": "The FastRet GUI",
      "topics": [
        "fastret_app"
      ]
    },
    {
      "page": "getCDs",
      "title": "Get Chemical Descriptors for a list of molecules",
      "topics": [
        "getCDs"
      ]
    },
    {
      "page": "plot_frm",
      "title": "Plot predictions for a FastRet model",
      "topics": [
        "plot_frm"
      ]
    },
    {
      "page": "predict.frm",
      "title": "Predict retention times using a FastRet Model",
      "topics": [
        "predict.frm"
      ]
    },
    {
      "page": "preprocess_data",
      "title": "Preprocess data",
      "topics": [
        "preprocess_data"
      ]
    },
    {
      "page": "read_retip_hilic_data",
      "title": "Read the HILIC dataset from the Retip package",
      "topics": [
        "read_retip_hilic_data"
      ]
    },
    {
      "page": "read_rp_lasso_model_rds",
      "title": "LASSO Model trained on RP dataset",
      "topics": [
        "read_rp_lasso_model_rds"
      ]
    },
    {
      "page": "read_rp_xlsx",
      "title": "Read retention times (RT) measured on a reverse phase (RP) column",
      "topics": [
        "read_rp_xlsx"
      ]
    },
    {
      "page": "read_rpadj_xlsx",
      "title": "Hypothetical retention times",
      "topics": [
        "read_rpadj_xlsx"
      ]
    },
    {
      "page": "RP",
      "title": "Retention Times (RT) measured on a Reverse Phase (RP) Column",
      "topics": [
        "RP"
      ]
    },
    {
      "page": "selective_measuring",
      "title": "Selective Measuring",
      "topics": [
        "selective_measuring"
      ]
    },
    {
      "page": "start_gui",
      "title": "Start the FastRet GUI",
      "topics": [
        "start_gui"
      ]
    },
    {
      "page": "train_frm",
      "title": "Train a new FastRet model (FRM) for retention time prediction",
      "topics": [
        "train_frm"
      ]
    }
  ],
  "_readme": "https://github.com/spang-lab/FastRet/raw/HEAD/README.md",
  "_rundeps": [
    "base64enc",
    "bslib",
    "cachem",
    "cli",
    "cluster",
    "codetools",
    "commonmark",
    "cpp11",
    "crosstalk",
    "data.table",
    "digest",
    "DT",
    "evaluate",
    "farver",
    "fastmap",
    "fingerprint",
    "fontawesome",
    "foreach",
    "fs",
    "future",
    "ggplot2",
    "glmnet",
    "globals",
    "glue",
    "gtable",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "isoband",
    "iterators",
    "itertools",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "listenv",
    "litedown",
    "magrittr",
    "markdown",
    "Matrix",
    "memoise",
    "mime",
    "openxlsx",
    "otel",
    "parallelly",
    "png",
    "promises",
    "R6",
    "rappdirs",
    "rcdk",
    "rcdklibs",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "rJava",
    "rlang",
    "rmarkdown",
    "S7",
    "sass",
    "scales",
    "shape",
    "shiny",
    "shinyhelper",
    "shinyjs",
    "sourcetools",
    "stringi",
    "survival",
    "tinytex",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "xgboost",
    "xtable",
    "yaml",
    "zip"
  ],
  "_sysdeps": [
    {
      "shlib": "libjvm",
      "package": "openjdk-21-jre-headless",
      "headers": "openjdk-21-jre-headless",
      "source": "openjdk",
      "version": "21.0.10+7-1~24.04",
      "name": "openjdk",
      "homepage": "https://openjdk.java.net/",
      "description": "OpenJDK Java runtime, using Hotspot JIT (headless)"
    }
  ],
  "_score": 3.778151250383644,
  "_indexed": true,
  "_nocasepkg": "fastret",
  "_universes": [
    "spang-lab",
    "toscm"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.3.0",
      "date": "2026-05-10T06:38:05.000Z",
      "distro": "noble",
      "commit": "8b27a10557e8272fbfe925244184c0d3252c8702",
      "fileid": "fd43a86fabb8bf607b8b9a832a62c3319c2f59fe64dfe31c0ba7ad788b687e9b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/spang-lab/actions/runs/25621878639"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.3.0",
      "date": "2026-05-10T06:38:00.000Z",
      "distro": "noble",
      "commit": "8b27a10557e8272fbfe925244184c0d3252c8702",
      "fileid": "33294842ec3328e407856ad1c25fd49ce51e576957c938810067e01185627943",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/spang-lab/actions/runs/25621878639"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.3.0",
      "date": "2026-05-10T06:37:19.000Z",
      "commit": "8b27a10557e8272fbfe925244184c0d3252c8702",
      "fileid": "f8098b597db6ba8e704686572b91b30e3b3795f79a05b38782279be6952602b3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/spang-lab/actions/runs/25621878639"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.3.0",
      "date": "2026-05-10T06:36:49.000Z",
      "commit": "8b27a10557e8272fbfe925244184c0d3252c8702",
      "fileid": "4fb00f169d1451aa946dc7d1f84aee5c87ebfb4c0de846be461baca6f6d4e21b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/spang-lab/actions/runs/25621878639"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.3.0",
      "date": "2026-05-10T06:36:43.000Z",
      "commit": "8b27a10557e8272fbfe925244184c0d3252c8702",
      "fileid": "de05fc007fd8946354d3c2036db9ad173a0db24227091bca83a5a5bf24061ba9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/spang-lab/actions/runs/25621878639"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.3.0",
      "date": "2026-05-10T06:36:34.000Z",
      "commit": "8b27a10557e8272fbfe925244184c0d3252c8702",
      "fileid": "867a10c51c0b917e83dc7dc4f039db5114cf45b225fab76aec689312d41c32d2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/spang-lab/actions/runs/25621878639"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.3.0",
      "date": "2026-05-10T06:37:34.000Z",
      "commit": "8b27a10557e8272fbfe925244184c0d3252c8702",
      "fileid": "8f19379cb96dba386cfd1dcfd1a8b2f684339fc54c0877d2c2b9db259a5e4616",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/spang-lab/actions/runs/25621878639"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.3.0",
      "date": "2026-05-22T12:39:00.000Z",
      "commit": "8b27a10557e8272fbfe925244184c0d3252c8702",
      "fileid": "9208abf9d55c61978d658269967054fc01d3a5917f30a724b2258622aebf0867",
      "status": "success",
      "buildurl": "https://github.com/r-universe/spang-lab/actions/runs/25621878639"
    }
  ]
}