{ "_id": "6ac9f7a9fe5cc25786e83753", "Package": "mzID", "Type": "Package", "Title": "An mzIdentML parser for R", "Version": "1.50.0", "Authors@R": "c(person(given = \"Laurent\", family = \"Gatto\",\nemail = \"laurent.gatto@uclouvain.be\",\ncomment = c(ORCID = \"0000-0002-1520-2268\"),\nrole = c(\"ctb\", \"cre\")),\nperson(given = \"Thomas\", family = \"Pedersen\",\nemail = \"thomasp85@gmail.com\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-6977-7147\")),\nperson(given = \"Vladislav\", family = \"Petyuk\",\nrole = c(\"ctb\")))", "Description": "A parser for mzIdentML files implemented using the XML\npackage. The parser tries to be general and able to handle all\ntypes of mzIdentML files with the drawback of having less\n'pretty' output than a vendor specific parser. Please contact\nthe maintainer with any problems and supply an mzIdentML file\nso the problems can be fixed quickly.", "License": "GPL (>= 2)", "LazyLoad": "yes", "biocViews": "ImmunoOncology, DataImport, MassSpectrometry, Proteomics", "VignetteBuilder": "knitr", "Collate": "'aaa.R' 'generics.R' 'mzIDpsm.R' 'mzIDpeptides.R'\n'mzIDparameters.R' 'mzIDevidence.R' 'mzIDdatabase.R' 'mzID.R'\n'mzIDCollection.R' 'mzID-constructor.R' 'mzID-package.R'", "RoxygenNote": "5.0.1", "Config/pak/sysreqs": "libxml2-dev", "Repository": "Bioconductor 3.23", "Date/Publication": "2026-04-28 12:38:09 UTC", "RemoteUrl": "https://github.com/bioc/mzID", "RemoteRef": "RELEASE_3_23", "RemoteSha": "2f84f81777555179b3f3f605c6e0e6e9906d4792", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-10 07:58:37 UTC", "User": "root" }, "Author": "Laurent Gatto [ctb, cre] (ORCID:\n),\nThomas Pedersen [aut] (ORCID: ),\nVladislav Petyuk [ctb]", "Maintainer": "Laurent Gatto ", "_user": "bioc-release", "_type": "src", "_file": "mzID_1.50.0.tar.gz", "_fileid": "https://r2.ropensci.org/f4e07707a20969e5650d46f8b56c6ec0ac25a20e8e897cd144ff9a2d1c33a9d6", "_filesize": 731448, "_sha256": "f4e07707a20969e5650d46f8b56c6ec0ac25a20e8e897cd144ff9a2d1c33a9d6", "_expires": "2027-01-18T08:30:31.000Z", "_created": "2026-10-10T07:58:37.000Z", "_published": "2026-10-10T08:30:33.809Z", "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38036094692", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 1, "warning": 4, "note": 11 }, "_upstream": "https://github.com/bioc/mzID", "_commit": { "id": "2f84f81777555179b3f3f605c6e0e6e9906d4792", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777379889 }, "_maintainer": { "name": "Laurent Gatto", "email": "laurent.gatto@uclouvain.be", "login": "lgatto", "mastodon": "@lgatto@fediscience.org", "orcid": "0000-0002-1520-2268", "description": "Open science, reproducible research, bioinformatics, computational biology, proteomics, more omics, emacs, a lot of R, running and parenting.\n", "uuid": 384198 }, "_distro": "resolute", "_jobs": [ { "job": 114167339683, "time": 130, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "11664197785" }, { "job": 114167339722, "time": 209, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11664371896" }, { "job": 114167339668, "time": 220, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11664217813" }, { "job": 114167339715, "time": 99, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "11663649014" }, { "job": 114167339662, "time": 92, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "11665280307" }, { "job": 114166752592, "time": 210, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11664297454" }, { "job": 114167339659, "time": 97, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11663871711" }, { "job": 114167339723, "time": 76, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11663946736" }, { "job": 114167339661, "time": 71, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "11664097662" }, { "job": 114167339711, "time": 78, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11664421583" } ], "_registered": true, "_dependencies": [ { "package": "methods", "role": "Depends" }, { "package": "XML", "role": "Imports" }, { "package": "plyr", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "doParallel", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "iterators", "role": "Imports" }, { "package": "ProtGenerics", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 48, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-14", "n": 1 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.51.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.50.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "immunooncology", "dataimport", "massspectrometry", "proteomics" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 476, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 4, "_searchresults": 41, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/mzID.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "evidence", "files", "flatten", "id", "idScanMap", "mzID", "mzIDCollection", "mzIDdatabase", "mzIDevidence", "mzIDparameters", "mzIDpeptides", "mzIDpsm", "parameters", "removeDecoy", "software" ], "_help": [ { "page": "mzID-package", "title": "A parser for the mzIdentML file format", "topics": [ "mzID-package" ] }, { "page": "flatten", "title": "Flatten an mzID related class into a table", "topics": [ "flatten", "flatten,mzID-method", "flatten,mzIDCollection-method", "flatten,mzIDpeptides-method", "flatten,mzIDpsm-method" ] }, { "page": "mzID", "title": "Parse an mzIdentML file", "topics": [ "mzID" ] }, { "page": "mzID-class", "title": "A class to contain data from mzIdentML-files", "topics": [ "c,mzID-method", "database,mzID-method", "evidence,mzID-method", "files,mzID-method", "id,mzID-method", "idScanMap,mzID-method", "length,mzID-method", "modifications,mzID-method", "mzID-class", "parameters,mzID-method", "peptides,mzID-method", "removeDecoy,mzID-method", "scans,mzID-method", "show,mzID-method", "software,mzID-method" ] }, { "page": "mzID-getters", "title": "Getter functions for identification data", "topics": [ "evidence", "files", "id", "idScanMap", "mzID-getters", "parameters", "software" ] }, { "page": "mzIDCollection", "title": "Create a new mzIDCollection", "topics": [ "mzIDCollection" ] }, { "page": "mzIDCollection-class", "title": "A class to handle a set of mzID objects", "topics": [ "as.list.mzIDCollection", "c,mzIDCollection-method", "database,mzIDCollection-method", "evidence,mzIDCollection-method", "files,mzIDCollection-method", "id,mzIDCollection-method", "idScanMap,mzIDCollection-method", "length,mzIDCollection-method", "modifications,mzIDCollection-method", "mzIDCollection-class", "names,mzIDCollection-method", "names<-,mzIDCollection,character-method", "parameters,mzIDCollection-method", "peptides,mzIDCollection-method", "removeDecoy,mzIDCollection-method", "scans,mzIDCollection-method", "show,mzIDCollection-method", "software,mzIDCollection-method", "[,mzIDCollection,character,missing,missing-method", "[,mzIDCollection,logical,missing,missing-method", "[,mzIDCollection,numeric,missing,missing-method", "[[,mzIDCollection,character,missing-method", "[[,mzIDCollection,numeric,missing-method" ] }, { "page": "mzIDdatabase", "title": "A constructor for the mzIDdatabase class", "topics": [ "mzIDdatabase" ] }, { "page": "mzIDdatabase-class", "title": "A class to store database information from an mzIdentML file", "topics": [ "database,mzIDdatabase-method", "length,mzIDdatabase-method", "mzIDdatabase-class", "show,mzIDdatabase-method" ] }, { "page": "mzIDevidence", "title": "A constructor for the mzIDevidence class", "topics": [ "mzIDevidence" ] }, { "page": "mzIDevidence-class", "title": "A class to store peptide evidence information from an mzIdentML file", "topics": [ "evidence,mzIDevidence-method", "length,mzIDevidence-method", "mzIDevidence-class", "show,mzIDevidence-method" ] }, { "page": "mzIDparameters", "title": "A constructor for the mzIDparameters class", "topics": [ "mzIDparameters" ] }, { "page": "mzIDparameters-class", "title": "A Class to store analysis information from the mzIdentML file", "topics": [ "files,mzIDparameters-method", "length,mzIDparameters-method", "mzIDparameters-class", "parameters,mzIDparameters-method", "show,mzIDparameters-method", "software,mzIDparameters-method" ] }, { "page": "mzIDpeptides", "title": "A constructor for the mzIDpeptides class", "topics": [ "mzIDpeptides" ] }, { "page": "mzIDpeptides-class", "title": "A class to store peptide information from an mzIdentML file", "topics": [ "length,mzIDpeptides-method", "modifications,mzIDpeptides-method", "mzIDpeptides-class", "peptides,mzIDpeptides-method", "show,mzIDpeptides-method" ] }, { "page": "mzIDpsm", "title": "A constructor for the mzIDpsm class", "topics": [ "mzIDpsm" ] }, { "page": "mzIDpsm-class", "title": "A class to store psm information from an mzIdentML file", "topics": [ "id,mzIDpsm-method", "idScanMap,mzIDpsm-method", "length,mzIDpsm-method", "mzIDpsm-class", "scans,mzIDpsm-method", "show,mzIDpsm-method" ] }, { "page": "removeDecoy", "title": "Remove decoy identification", "topics": [ "removeDecoy" ] } ], "_readme": "https://github.com/bioc/mzID/raw/RELEASE_3_23/README.md", "_rundeps": [ "codetools", "doParallel", "foreach", "iterators", "plyr", "ProtGenerics", "Rcpp", "XML" ], "_vignettes": [ { "source": "HOWTO_mzID.Rnw", "filename": "HOWTO_mzID.pdf", "title": "Using mzID", "engine": "knitr", "headings": [], "created": "2013-09-17 21:45:26", "modified": "2016-04-21 10:49:45", "commits": 3 } ], "_score": 7.5492975991986295, "_indexed": false, "_nocasepkg": "mzid", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/mzID", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.50.0", "date": "2026-10-10T08:02:16.000Z", "distro": "resolute", "commit": "2f84f81777555179b3f3f605c6e0e6e9906d4792", "fileid": "https://r2.ropensci.org/9e23585c0a9ba63acdf8b48326794386b31fdbf6f5bef4c2913790d23169b433", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38036094692" }, { "r": "4.6.1", "os": "linux", "version": "1.50.0", "date": "2026-10-10T08:02:30.000Z", "distro": "resolute", "commit": "2f84f81777555179b3f3f605c6e0e6e9906d4792", "fileid": "https://r2.ropensci.org/42d449c078e4bf5825e60a0aa19ad0694f45e43ecc133e5008c6037b4d24e5ca", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38036094692" }, { "r": "4.5.3", "os": "mac", "version": "1.50.0", "date": "2026-10-10T08:29:54.000Z", "commit": "2f84f81777555179b3f3f605c6e0e6e9906d4792", "fileid": "https://r2.ropensci.org/30ac392d3a77af1c652d3674ae51d2a52d59a7c595702be59d9f695d2d98de7a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38036094692" }, { "r": "4.6.1", "os": "mac", "version": "1.50.0", "date": "2026-10-10T08:29:17.000Z", "commit": "2f84f81777555179b3f3f605c6e0e6e9906d4792", "fileid": "https://r2.ropensci.org/2b6e44f084d280e715c647365afde3441eea13e8f3307988964a2a3851dd10b3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38036094692" }, { "r": "4.6.0", "os": "wasm", "version": "1.50.0", "date": "2026-10-10T08:00:51.000Z", "commit": "2f84f81777555179b3f3f605c6e0e6e9906d4792", "fileid": "https://r2.ropensci.org/1a9a00101e2cc7f7d1cd250b3a8615c6c3cd00b324ead006c24ece9494c81fd3", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38036094692" }, { "r": "4.7.0", "os": "win", "version": "1.50.0", "date": "2026-10-10T07:59:58.000Z", "commit": "2f84f81777555179b3f3f605c6e0e6e9906d4792", "fileid": "https://r2.ropensci.org/8a5bcd213421ae89d4998247e9bdcb8ec7adfbd0d943603100904e45e5221054", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38036094692" }, { "r": "4.5.3", "os": "win", "version": "1.50.0", "date": "2026-10-10T08:00:02.000Z", "commit": "2f84f81777555179b3f3f605c6e0e6e9906d4792", "fileid": "https://r2.ropensci.org/524886e00a6c4cb78a614cc3a707b1c9a996172194beb03f00d9e9aee8ae6246", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38036094692" }, { "r": "4.6.1", "os": "win", "version": "1.50.0", "date": "2026-10-10T08:00:03.000Z", "commit": "2f84f81777555179b3f3f605c6e0e6e9906d4792", "fileid": "https://r2.ropensci.org/3928dd1a32cbf9cbea2004ff2ca6fdf5daad833f34877509acd2a36b04634407", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38036094692" } ] }