{ "_id": "6ac79631de46216d5edd28b2", "Package": "clstutils", "Type": "Package", "Title": "Tools for performing taxonomic assignment", "Version": "1.61.0", "LazyLoad": "yes", "LazyData": "yes", "Author": "Noah Hoffman", "Maintainer": "Noah Hoffman ", "Description": "Tools for performing taxonomic assignment based on\nphylogeny using pplacer and clst.", "License": "GPL-3", "biocViews": "Sequencing, Classification, Visualization, QualityControl", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:35:11 UTC", "RemoteUrl": "https://github.com/bioc/clstutils", "RemoteRef": "HEAD", "RemoteSha": "0dd3a03110b01a26f18e54f4dfbeec336d7cbf4e", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-08 13:06:51 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "clstutils_1.61.0.tar.gz", "_fileid": "https://r2.ropensci.org/4c4b44e82a62de1c0c5c9de962aa914ce7bc4d243c2b3f0f5927c3efdd1a56f9", "_filesize": 2691125, "_sha256": "4c4b44e82a62de1c0c5c9de962aa914ce7bc4d243c2b3f0f5927c3efdd1a56f9", "_expires": "2027-01-16T13:10:06.000Z", "_created": "2026-10-08T13:06:51.000Z", "_published": "2026-10-08T13:10:08.961Z", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/37781435026", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 1, "warning": 3, "note": 12 }, "_upstream": "https://github.com/bioc/clstutils", "_commit": { "id": "0dd3a03110b01a26f18e54f4dfbeec336d7cbf4e", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379711 }, "_maintainer": { "name": "Noah Hoffman", "email": "ngh2@uw.edu", "login": "nhoffman", "description": "", "uuid": 440002 }, "_distro": "resolute", "_jobs": [ { "job": 113326745495, "time": 127, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "11552996700" }, { "job": 113326745216, "time": 137, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11552357753" }, { "job": 113326745387, "time": 154, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11552532369" }, { "job": 113326745379, "time": 112, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "11552827227" }, { "job": 113326745392, "time": 111, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "11551729059" }, { "job": 113325391153, "time": 185, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11552801958" }, { "job": 113326745116, "time": 101, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11552501904" }, { "job": 113326745363, "time": 89, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11552097558" }, { "job": 113326745667, "time": 91, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "11551968873" }, { "job": 113326745130, "time": 80, "config": "windows-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11552941550" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10", "role": "Depends" }, { "package": "clst", "role": "Depends" }, { "package": "rjson", "role": "Depends" }, { "package": "ape", "role": "Depends" }, { "package": "lattice", "role": "Imports" }, { "package": "RSQLite", "role": "Imports" }, { "package": "RUnit", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.61.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.60.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "sequencing", "classification", "visualization", "qualitycontrol" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 474, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 491, "source": "https://www.bioconductor.org/packages/stats/bioc/clstutils" }, "_searchresults": 10, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/clstutils.html", "extra/contents.json", "extra/manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "classifyPlacements", "findOutliers", "maxDists", "prettyTree", "refpkgContents", "taxonomyFromRefpkg", "treeDists" ], "_datasets": [ { "name": "seqdat", "title": "Annotation for the Enterococcus sequence data set.", "object": "seqdat", "class": [ "data.frame" ], "fields": [ "seqname", "accession", "tax_id", "tax_name", "isType" ], "rows": 200, "table": true, "tojson": true }, { "name": "seqs", "title": "Enterococcus sequence data set.", "object": "seqs", "class": [ "DNAbin" ], "fields": [], "rows": 200, "table": false, "tojson": false } ], "_help": [ { "page": "clstutils-package", "title": "Sequence based classification and selection of reference sequences.", "topics": [ "clstutils-package", "clstutils" ] }, { "page": "classifyPlacements", "title": "Taxonomic classification by phylogenetic placement.", "topics": [ "classifyPlacements" ] }, { "page": "findOutliers", "title": "Identify outlier objects given a square distance matrix.", "topics": [ "findOutliers" ] }, { "page": "maxDists", "title": "Select a maximally diverse set of items given a distance matrix.", "topics": [ "maxDists" ] }, { "page": "prettyTree", "title": "Draw an annotated phylogenetic tree.", "topics": [ "prettyTree" ] }, { "page": "refpkgContents", "title": "Read the contents of a collection of reference sequences (\"refpkg\").", "topics": [ "refpkgContents" ] }, { "page": "seqdat", "title": "Annotation for the Enterococcus sequence data set.", "topics": [ "seqdat" ] }, { "page": "seqs", "title": "Enterococcus sequence data set.", "topics": [ "seqs" ] }, { "page": "taxonomyFromRefpkg", "title": "Extract taxonomic information from a refpkg.", "topics": [ "taxonomyFromRefpkg" ] }, { "page": "treeDists", "title": "Provide objects for determining distances among nodes of a reference tree.", "topics": [ "treeDists" ] } ], "_rundeps": [ "ape", "bit", "bit64", "blob", "cachem", "cli", "clst", "cpp11", "DBI", "digest", "evaluate", "fastmap", "glue", "highr", "knitr", "lattice", "lifecycle", "memoise", "nlme", "pkgconfig", "Rcpp", "rjson", "rlang", "ROC", "RSQLite", "vctrs", "xfun", "yaml" ], "_vignettes": [ { "source": "pplacerDemo.Rnw", "filename": "pplacerDemo.pdf", "title": "clst", "engine": "utils::Sweave", "headings": [ "Introduction", "Input files", "Reading the input", "Classification of a single sequence" ], "created": "2013-11-01 20:17:32", "modified": "2019-12-23 23:30:42", "commits": 3 }, { "source": "refSet.Rnw", "filename": "refSet.pdf", "title": "clstutils", "engine": "utils::Sweave", "headings": [ "Introduction", "Finding outliers", "Selecting a diverse subset" ], "created": "2013-11-01 20:17:32", "modified": "2019-12-23 23:30:42", "commits": 2 } ], "_score": 3.6020599913279625, "_indexed": true, "_nocasepkg": "clstutils", "_universes": [ "bioc", "nhoffman" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.61.0", "date": "2026-10-08T13:09:00.000Z", "distro": "resolute", "commit": "0dd3a03110b01a26f18e54f4dfbeec336d7cbf4e", "fileid": "https://r2.ropensci.org/9667e4a5297e41d11f338a72a2b0af75072870e8348b3061f946fed1a9da53af", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37781435026" }, { "r": "4.6.1", "os": "linux", "version": "1.61.0", "date": "2026-10-08T13:09:17.000Z", "distro": "resolute", "commit": "0dd3a03110b01a26f18e54f4dfbeec336d7cbf4e", "fileid": "https://r2.ropensci.org/e45634402d4e3dbe5e3f9c5a32d311f4b858cb3ccd69dba2c82dba4b03680d50", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37781435026" }, { "r": "4.5.3", "os": "mac", "version": "1.61.0", "date": "2026-10-08T13:08:30.000Z", "commit": "0dd3a03110b01a26f18e54f4dfbeec336d7cbf4e", "fileid": "https://r2.ropensci.org/dee701345cee3890f951c063450922033b31f5f1a13284da7d028d56600bc535", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37781435026" }, { "r": "4.6.1", "os": "mac", "version": "1.61.0", "date": "2026-10-08T13:08:40.000Z", "commit": "0dd3a03110b01a26f18e54f4dfbeec336d7cbf4e", "fileid": "https://r2.ropensci.org/50734206510011616fa8a610a0fd26e3a466d35bb7415e7dade56cf91a494090", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37781435026" }, { "r": "4.6.0", "os": "wasm", "version": "1.61.0", "date": "2026-10-08T13:08:54.000Z", "commit": "0dd3a03110b01a26f18e54f4dfbeec336d7cbf4e", "fileid": "https://r2.ropensci.org/6371ed79e9afa6f0f059913a16394633d15752ac9c92792b5a291fa685a98e7b", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37781435026" }, { "r": "4.7.0", "os": "win", "version": "1.61.0", "date": "2026-10-08T13:08:08.000Z", "commit": "0dd3a03110b01a26f18e54f4dfbeec336d7cbf4e", "fileid": "https://r2.ropensci.org/d8b0aaf19f8ef6330c7c4da7ea7e213ce6aac2772fef677f51ca921f31666e30", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37781435026" }, { "r": "4.5.3", "os": "win", "version": "1.61.0", "date": "2026-10-08T13:08:18.000Z", "commit": "0dd3a03110b01a26f18e54f4dfbeec336d7cbf4e", "fileid": "https://r2.ropensci.org/00d0ada2e8e5b006c52dfff67667898a351bac3e8f5aa110a5998efdc680ce29", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37781435026" }, { "r": "4.6.1", "os": "win", "version": "1.61.0", "date": "2026-10-08T13:08:01.000Z", "commit": "0dd3a03110b01a26f18e54f4dfbeec336d7cbf4e", "fileid": "https://r2.ropensci.org/ae7e6aebaae76620f74c2a4b7b942fe71c57ad0ce4d952758bfd042f882af5b1", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37781435026" } ] }