{
  "_id": "6a19660facfb0bcc41de71a9",
  "Package": "CardinalIO",
  "Type": "Package",
  "Title": "Read and write mass spectrometry imaging files",
  "Version": "1.11.0",
  "Date": "2023-8-29",
  "Authors@R": "person(\"Kylie Ariel\", \"Bemis\",\nemail = \"k.bemis@northeastern.edu\",\nrole = c(\"aut\", \"cre\"))",
  "Description": "Fast and efficient reading and writing of mass\nspectrometry imaging data files. Supports imzML and Analyze 7.5\nformats. Provides ontologies for mass spectrometry imaging.",
  "License": "Artistic-2.0 | file LICENSE",
  "VignetteBuilder": "knitr",
  "biocViews": "Software, Infrastructure, DataImport, MassSpectrometry,\nImagingMassSpectrometry",
  "URL": "http://www.cardinalmsi.org",
  "BugReports": "https://github.com/kuwisdelu/CardinalIO/issues",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:01:17 UTC",
  "RemoteUrl": "https://github.com/bioc/CardinalIO",
  "RemoteRef": "HEAD",
  "RemoteSha": "062421c6d9f0c369318fc695ab1eab2ae8549887",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-29 08:27:02 UTC",
    "User": "root"
  },
  "Author": "Kylie Ariel Bemis [aut, cre]",
  "Maintainer": "Kylie Ariel Bemis <k.bemis@northeastern.edu>",
  "MD5sum": "13240456114f20e2b455bdaa4c3fe13e",
  "_user": "bioc",
  "_type": "src",
  "_file": "CardinalIO_1.11.0.tar.gz",
  "_fileid": "084eb2b77d352450973c0c74782c764cdce030b310195d99b1a67569628450d1",
  "_filesize": 946747,
  "_sha256": "084eb2b77d352450973c0c74782c764cdce030b310195d99b1a67569628450d1",
  "_created": "2026-05-29T08:27:02.000Z",
  "_published": "2026-05-29T10:10:23.533Z",
  "_jobs": [
    {
      "job": 78465412475,
      "time": 140,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7286449060"
    },
    {
      "job": 78465412558,
      "time": 189,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7286462923"
    },
    {
      "job": 78465412579,
      "time": 237,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7286477076"
    },
    {
      "job": 78465412553,
      "time": 272,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7286485474"
    },
    {
      "job": 78465412620,
      "time": 254,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7286481805"
    },
    {
      "job": 78465412636,
      "time": 127,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7288245470"
    },
    {
      "job": 78465412584,
      "time": 298,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7287246305"
    },
    {
      "job": 78465412664,
      "time": 158,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7288252740"
    },
    {
      "job": 78465412628,
      "time": 372,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7287277251"
    },
    {
      "job": 78464938572,
      "time": 197,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7286407978"
    },
    {
      "job": 78465412483,
      "time": 144,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7286449875"
    },
    {
      "job": 78465412524,
      "time": 164,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7286455601"
    },
    {
      "job": 78465412568,
      "time": 145,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7286450236"
    },
    {
      "job": 78465412581,
      "time": 185,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7286462083"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 7
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26626634224",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/CardinalIO",
  "_commit": {
    "id": "062421c6d9f0c369318fc695ab1eab2ae8549887",
    "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": 1777381277
  },
  "_maintainer": {
    "name": "Kylie Ariel Bemis",
    "email": "k.bemis@northeastern.edu",
    "login": "kuwisdelu",
    "description": "Assistant Teaching Professor at Northeastern University. Lead developer of the Cardinal R package for mass spectrometry imaging analysis.",
    "uuid": 5960420
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.4",
      "role": "Depends"
    },
    {
      "package": "BiocParallel",
      "role": "Depends"
    },
    {
      "package": "matter",
      "role": "Depends"
    },
    {
      "package": "ontologyIndex",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "tools",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.11.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.10.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "infrastructure",
    "dataimport",
    "massspectrometry",
    "imagingmassspectrometry",
    "cpp"
  ],
  "_stars": 3,
  "_contributors": [
    {
      "user": "kuwisdelu",
      "count": 63,
      "uuid": 5960420
    },
    {
      "user": "jwokaty",
      "count": 8,
      "uuid": 1744257
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 436,
    "source": "https://www.bioconductor.org/packages/stats/bioc/CardinalIO"
  },
  "_devurl": "https://github.com/kuwisdelu/cardinalio",
  "_searchresults": 3,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/CardinalIO.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/kuwisdelu/cardinalio",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "exampleImzMLFile",
    "find_descendants_in",
    "find_term",
    "find_terms",
    "get_obo",
    "ImzMeta",
    "metadata",
    "parseAnalyze",
    "parseImzML",
    "valid_terms",
    "writeAnalyze",
    "writeImzML"
  ],
  "_help": [
    {
      "page": "CardinalIO-package",
      "title": "CardinalIO package",
      "topics": [
        "CardinalIO-package",
        "CardinalIO"
      ]
    },
    {
      "page": "exampleImzMLFile",
      "title": "Example imzML files",
      "topics": [
        "exampleImzMLFile"
      ]
    },
    {
      "page": "get_obo",
      "title": "Mass spectrometry imaging ontology",
      "topics": [
        "find_descendants_in",
        "find_term",
        "find_terms",
        "get_obo",
        "valid_terms"
      ]
    },
    {
      "page": "ImzMeta",
      "title": "Mass spectrometry imaging experimental metadata",
      "topics": [
        "class:ImzMeta",
        "ImzMeta",
        "ImzMeta-class",
        "[[<-,ImzMeta-method"
      ]
    },
    {
      "page": "parseAnalyze",
      "title": "Parse an Analyze 7.5 File",
      "topics": [
        "Analyze75",
        "Analyze75-class",
        "class:Analyze75",
        "parseAnalyze"
      ]
    },
    {
      "page": "parseImzML",
      "title": "Parse an imzML File",
      "topics": [
        "class:ImzML",
        "ImzML",
        "ImzML-class",
        "parseImzML"
      ]
    },
    {
      "page": "writeAnalyze",
      "title": "Write an Analyze 7.5 File",
      "topics": [
        "writeAnalyze",
        "writeAnalyze,array-method",
        "writeAnalyze,matter_arr-method",
        "writeAnalyze,sparse_arr-method"
      ]
    },
    {
      "page": "writeImzML",
      "title": "Write an imzML File",
      "topics": [
        "writeImzML",
        "writeImzML,ImzMeta-method",
        "writeImzML,ImzML-method"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/CardinalIO/raw/HEAD/README.md",
  "_rundeps": [
    "BH",
    "BiocGenerics",
    "BiocParallel",
    "codetools",
    "cpp11",
    "digest",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "irlba",
    "lambda.r",
    "lattice",
    "Matrix",
    "matter",
    "ontologyIndex",
    "ProtGenerics",
    "S4Vectors",
    "snow"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "CardinalIO-guide.Rmd",
      "filename": "CardinalIO-guide.html",
      "title": "CardinalIO: Parsing and writing imzML files",
      "author": "Kylie Ariel Bemis",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Structure of imzML files",
        "XML",
        "Binary",
        "Continuous",
        "Processed",
        "Additional notes",
        "Parsing imzML files",
        "Experimental metadata",
        "File description",
        "Scan settings",
        "Software",
        "Instrument configuration",
        "Data processing",
        "Spectrum metadata",
        "Positions",
        "m/z metadata",
        "Intensity metadata",
        "Mass spectra",
        "Tracking experimental metadata",
        "The ImzMeta class",
        "Conversion between ImzML and ImzMeta",
        "Minimum reporting guidelines",
        "Writing imzML files",
        "Writing a file from ImzML metadata",
        "Writing a file from ImzMeta metadata",
        "Session information"
      ],
      "created": "2023-08-05 20:56:39",
      "modified": "2023-08-12 04:23:59",
      "commits": 4
    }
  ],
  "_score": 4.954242509439325,
  "_indexed": true,
  "_nocasepkg": "cardinalio",
  "_universes": [
    "bioc",
    "kuwisdelu"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.11.0",
      "date": "2026-05-29T08:29:47.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "062421c6d9f0c369318fc695ab1eab2ae8549887",
      "fileid": "0b17299a2527a9ac4819802435db073ddeac622576702be9ebd8e9dd776901c9",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626634224"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.11.0",
      "date": "2026-05-29T08:30:25.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "062421c6d9f0c369318fc695ab1eab2ae8549887",
      "fileid": "51b4d1821efc1b7c00a621f6f69f2384a3f0b8b2ba443be3db1e1170b873bd67",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626634224"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.11.0",
      "date": "2026-05-29T08:31:00.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "062421c6d9f0c369318fc695ab1eab2ae8549887",
      "fileid": "e6b848d01054d800d8d692bd4e225a701339b26c986278850daf4b894506a077",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626634224"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.11.0",
      "date": "2026-05-29T08:30:53.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "062421c6d9f0c369318fc695ab1eab2ae8549887",
      "fileid": "f7618596c53d3f4465d8bbc42e5bd071ca6ccbe04589ad2ba5ea4b315b090fc1",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626634224"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.11.0",
      "date": "2026-05-29T10:08:54.000Z",
      "arch": "aarch64",
      "commit": "062421c6d9f0c369318fc695ab1eab2ae8549887",
      "fileid": "78045e5fac68d1b80a26e6dd636eeb1cc6f722dc94388c9e48144383cfb4a138",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626634224"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.11.0",
      "date": "2026-05-29T09:12:14.000Z",
      "arch": "x86_64",
      "commit": "062421c6d9f0c369318fc695ab1eab2ae8549887",
      "fileid": "7e9f808e2df8b1e70ae588e4c5bf0be070033f0de800389539966bbc3c1a383c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626634224"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.11.0",
      "date": "2026-05-29T10:09:05.000Z",
      "arch": "aarch64",
      "commit": "062421c6d9f0c369318fc695ab1eab2ae8549887",
      "fileid": "63feea24045d65697246c1dba4a0b6a5472fced76fc42ef877da8ee8c08c5a73",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626634224"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.11.0",
      "date": "2026-05-29T09:13:52.000Z",
      "arch": "x86_64",
      "commit": "062421c6d9f0c369318fc695ab1eab2ae8549887",
      "fileid": "2e0b6c998a3d1f58bdd10a44a2e512cdbc11c84079c92a77d3b6263179909042",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626634224"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.11.0",
      "date": "2026-05-29T08:29:52.000Z",
      "arch": "emscripten",
      "commit": "062421c6d9f0c369318fc695ab1eab2ae8549887",
      "fileid": "bb710f3639bb6722a7077548e07d7158e811936c5b4dacfaa94cd01ebec1ebf7",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626634224"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.11.0",
      "date": "2026-05-29T08:28:50.000Z",
      "arch": "x86_64",
      "commit": "062421c6d9f0c369318fc695ab1eab2ae8549887",
      "fileid": "4f213eeeaba16ccbbaaa87408d53b74bd3c3e6d1ba4832b589cec77e3da7520b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626634224"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.11.0",
      "date": "2026-05-29T08:28:38.000Z",
      "arch": "x86_64",
      "commit": "062421c6d9f0c369318fc695ab1eab2ae8549887",
      "fileid": "289a74953e32644a76ce12e113dbf11477a0f99fab6f4430719d480c08290996",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626634224"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.11.0",
      "date": "2026-05-29T08:29:04.000Z",
      "arch": "x86_64",
      "commit": "062421c6d9f0c369318fc695ab1eab2ae8549887",
      "fileid": "9372cd559b5d9d717588d3c5130703cdabd58f9e23696bcb0c11d07379608830",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626634224"
    }
  ]
}