{
  "_id": "6aea4305818c9e3ef6dc0291",
  "Package": "apbCatalogR",
  "Title": "Look Up APB Result Fields by Meaning",
  "Version": "0.99.0",
  "Authors@R": "c(\nperson(\"Witold E.\", \"Wolski\", , \"witold.wolski@fgcz.uzh.ch\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-6468-120X\")),\nperson(\"Witek\", \"Wolski\", , \"wewolski@gmail.com\", role = \"cre\"))",
  "Description": "Looks up the fields of AnnData Proteomics Bridge (APB)\nresults by meaning, such as a PEP or an unnormalized intensity,\nwithout naming vendor columns. Reimplements the apb-catalog API\non the bundle apb-catalog releases: reviewed catalogues, apb2's\nrule levels and expected answers. Reads APB results, as h5ad,\nParquet or DuckDB, into anndataR objects.",
  "License": "MIT + file LICENSE",
  "URL": "https://anndata-omics-bridge.github.io/apbCatalogR/,\nhttps://github.com/anndata-omics-bridge/apbCatalogR",
  "BugReports": "https://github.com/anndata-omics-bridge/apbCatalogR/issues",
  "biocViews": "Proteomics, MassSpectrometry, DataImport, Infrastructure",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "Config/testthat/edition": "3",
  "VignetteBuilder": "knitr",
  "Config/roxygen2/version": "8.1.1",
  "Config/pak/sysreqs": "libpng-dev python3",
  "Repository": "https://biocstaging.r-universe.dev",
  "Date/Publication": "2026-11-03 19:10:46 UTC",
  "RemoteUrl": "https://github.com/BiocStaging/apbCatalogR",
  "RemoteRef": "HEAD",
  "RemoteSha": "f015f97f567dbf228a46c9e5191278b79e11d511",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-11-03 19:50:16 UTC",
    "User": "root"
  },
  "Author": "Witold E. Wolski [aut] (ORCID: <https://orcid.org/0000-0002-6468-120X>),\nWitek Wolski [cre]",
  "Maintainer": "Witek Wolski <wewolski@gmail.com>",
  "_user": "biocstaging",
  "_type": "src",
  "_file": "apbCatalogR_0.99.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/a441d80c6afc00086eb3f2f3875d4ef7d091c98d4cfa025a2b66a16c68dff064",
  "_filesize": 783951,
  "_sha256": "a441d80c6afc00086eb3f2f3875d4ef7d091c98d4cfa025a2b66a16c68dff064",
  "_expires": "2027-02-11T20:24:35.000Z",
  "_created": "2026-11-03T19:50:16.000Z",
  "_published": "2026-11-03T23:33:00.829Z",
  "_upstream": "https://github.com/BiocStaging/apbCatalogR",
  "_status": "success",
  "_maintainer": {
    "name": "Witek Wolski",
    "email": "wewolski@gmail.com",
    "login": "wolski",
    "description": "",
    "uuid": 1926513
  },
  "_jobs": [
    {
      "job": 126164984026,
      "time": 170,
      "config": "bioc-checks",
      "r": "4.6.2",
      "check": "NOTE",
      "artifact": "13267310163"
    },
    {
      "job": 126164983858,
      "time": 179,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "13267630348"
    },
    {
      "job": 126164983939,
      "time": 207,
      "config": "linux-release-x86_64",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13266585436"
    },
    {
      "job": 126164984112,
      "time": 2010,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "13266099566"
    },
    {
      "job": 126164984082,
      "time": 145,
      "config": "macos-release-arm64",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13267480016"
    },
    {
      "job": 126162974013,
      "time": 219,
      "config": "source",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13264379943"
    },
    {
      "job": 126164984232,
      "time": 119,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "13266965496"
    },
    {
      "job": 126164984023,
      "time": 180,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "13265861398"
    },
    {
      "job": 126164984343,
      "time": 175,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "13265774254"
    },
    {
      "job": 126164984021,
      "time": 168,
      "config": "windows-release-x86_64",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13266790312"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 1
  },
  "_buildurl": "https://github.com/r-universe/biocstaging/actions/runs/41706403731",
  "_commit": {
    "id": "f015f97f567dbf228a46c9e5191278b79e11d511",
    "author": "Witold Wolski <wewolski@gmail.com>",
    "committer": "Witold Wolski <wewolski@gmail.com>",
    "message": "Cite the Zenodo DOI 10.5281/zenodo.23928865\n\n- inst/CITATION: citation(\"apbCatalogR\") with the concept DOI\n- README: DOI badge\n- CITATION.cff: doi\n\nAssisted-by: AI coding agent\n",
    "time": 1793733046
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.5.0",
      "role": "Depends"
    },
    {
      "package": "anndataR",
      "version": ">= 1.2.2",
      "role": "Imports"
    },
    {
      "package": "jsonlite",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "R6",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "tools",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "altdoc",
      "role": "Suggests"
    },
    {
      "package": "arrow",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "covr",
      "role": "Suggests"
    },
    {
      "package": "cyclocomp",
      "role": "Suggests"
    },
    {
      "package": "DBI",
      "role": "Suggests"
    },
    {
      "package": "devtools",
      "role": "Suggests"
    },
    {
      "package": "duckdb",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "lintr",
      "role": "Suggests"
    },
    {
      "package": "rcmdcheck",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "roxygen2",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "withr",
      "role": "Suggests"
    }
  ],
  "_owner": "biocstaging",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-44",
      "n": 11
    },
    {
      "week": "2026-45",
      "n": 9
    }
  ],
  "_tags": [],
  "_topics": [
    "proteomics",
    "massspectrometry",
    "dataimport",
    "infrastructure"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "wolski",
      "count": 20,
      "uuid": 1926513
    }
  ],
  "_userbio": {
    "uuid": 278472782,
    "type": "organization",
    "name": "BiocStaging",
    "followers": 3
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/apbCatalogR"
  },
  "_devurl": "https://github.com/anndata-omics-bridge/apbcatalogr",
  "_pkgdown": "https://anndata-omics-bridge.github.io/apbCatalogR/",
  "_searchresults": 0,
  "_rbuild": "4.6.2",
  "_assets": [
    "extra/apbCatalogR.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE"
  ],
  "_cranurl": false,
  "_exports": [
    "Catalog",
    "catalog_version",
    "catalogue_table",
    "catalogues",
    "DataCatalog",
    "ParsedLevels",
    "read_parsed_levels",
    "rule_coverage",
    "update_catalog"
  ],
  "_help": [
    {
      "page": "sub-.Columns",
      "title": "Read a var or obs slot by several keys",
      "topics": [
        "[.Columns"
      ]
    },
    {
      "page": "sub-sub-.Slot",
      "title": "Read a slot by key",
      "topics": [
        "[[.Slot"
      ]
    },
    {
      "page": "Catalog",
      "title": "Which column one software version reports for each meaning",
      "topics": [
        "Catalog"
      ]
    },
    {
      "page": "catalog_version",
      "title": "The catalog in use",
      "topics": [
        "catalog_version"
      ]
    },
    {
      "page": "catalogue_table",
      "title": "The catalogue sets as one long table",
      "topics": [
        "catalogue_table"
      ]
    },
    {
      "page": "catalogues",
      "title": "The catalogue sets",
      "topics": [
        "catalogues"
      ]
    },
    {
      "page": "DataCatalog",
      "title": "What one result's fields mean to one consumer",
      "topics": [
        "DataCatalog"
      ]
    },
    {
      "page": "ParsedLevels",
      "title": "One APB result: its levels on one observation axis",
      "topics": [
        "ParsedLevels"
      ]
    },
    {
      "page": "read_parsed_levels",
      "title": "Read an APB result",
      "topics": [
        "read_parsed_levels"
      ]
    },
    {
      "page": "rule_coverage",
      "title": "Check every rule against one catalogue set",
      "topics": [
        "rule_coverage"
      ]
    },
    {
      "page": "update_catalog",
      "title": "Download a newer catalog",
      "topics": [
        "update_catalog"
      ]
    }
  ],
  "_readme": "https://github.com/BiocStaging/apbCatalogR/raw/HEAD/README.md",
  "_rundeps": [
    "anndataR",
    "cli",
    "glue",
    "here",
    "jsonlite",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "png",
    "purrr",
    "R6",
    "rappdirs",
    "Rcpp",
    "RcppTOML",
    "reticulate",
    "rlang",
    "rprojroot",
    "vctrs",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "apbCatalogR.Rmd",
      "filename": "apbCatalogR.html",
      "title": "Looking up APB fields by meaning",
      "author": "Witold Wolski",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Catalogue sets",
        "Which column a software version reports",
        "The data of a result",
        "The same code for every software",
        "Several sets and qualifiers",
        "Rule coverage",
        "A newer catalog",
        "Session information"
      ],
      "created": "2026-10-29 17:45:33",
      "modified": "2026-11-03 17:26:32",
      "commits": 11
    }
  ],
  "_score": 3,
  "_indexed": true,
  "_nocasepkg": "apbcatalogr",
  "_universes": [
    "biocstaging",
    "wolski",
    "anndata-omics-bridge"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.99.0",
      "date": "2026-11-03T19:52:44.000Z",
      "distro": "resolute",
      "commit": "f015f97f567dbf228a46c9e5191278b79e11d511",
      "fileid": "https://r2.ropensci.org/531345ded9316bd4168dcac9d6694f9a907c000ad0de5830be605a38e4f2b343",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/41706403731"
    },
    {
      "r": "4.6.2",
      "os": "linux",
      "version": "0.99.0",
      "date": "2026-11-03T19:53:15.000Z",
      "distro": "resolute",
      "commit": "f015f97f567dbf228a46c9e5191278b79e11d511",
      "fileid": "https://r2.ropensci.org/d14f3aeb9dc2cfb277956c0a8ef2a91fb0ec97579356b01fb896e90f4f02643a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/41706403731"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.99.0",
      "date": "2026-11-03T20:23:06.000Z",
      "commit": "f015f97f567dbf228a46c9e5191278b79e11d511",
      "fileid": "https://r2.ropensci.org/79441520e9e69be2d2c2111efbfad9589f9cbbcdf7a62e2de5e4ef74649178b4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/41706403731"
    },
    {
      "r": "4.6.2",
      "os": "mac",
      "version": "0.99.0",
      "date": "2026-11-03T19:52:15.000Z",
      "commit": "f015f97f567dbf228a46c9e5191278b79e11d511",
      "fileid": "https://r2.ropensci.org/7afc106834a508a24ee1c537379817baacdd60e5e174c8c5e650c642d254684c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/41706403731"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.99.0",
      "date": "2026-11-03T19:52:39.000Z",
      "commit": "f015f97f567dbf228a46c9e5191278b79e11d511",
      "fileid": "https://r2.ropensci.org/95f43b13b9067173429b58f07993d04f45052f7e75be07cccf659f34ddc5a773",
      "status": "success",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/41706403731"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.99.0",
      "date": "2026-11-03T19:51:36.000Z",
      "commit": "f015f97f567dbf228a46c9e5191278b79e11d511",
      "fileid": "https://r2.ropensci.org/0725fe65d7689154955350503c4e42ff7568a397e440d246c596409ea67f610a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/41706403731"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.99.0",
      "date": "2026-11-03T19:51:40.000Z",
      "commit": "f015f97f567dbf228a46c9e5191278b79e11d511",
      "fileid": "https://r2.ropensci.org/34d2004b7b81d13311413557c6dffa20c6a6f6e11c35b4bd420cb48603bda5cd",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/41706403731"
    },
    {
      "r": "4.6.2",
      "os": "win",
      "version": "0.99.0",
      "date": "2026-11-03T19:51:39.000Z",
      "commit": "f015f97f567dbf228a46c9e5191278b79e11d511",
      "fileid": "https://r2.ropensci.org/eb7ae46d5da0deded7737a842b38aee14933e7c5bc1d8b0ab485e53195395627",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/41706403731"
    }
  ]
}