{ "_id": "6abe160e99f7aa8c6aa51d1b", "Package": "seqtrie", "Title": "Radix Tree and Trie-Based String Distances", "Version": "0.4.0", "Date": "2026-06-02", "Authors@R": "c(\nperson(\"Travers\", \"Ching\", email = \"traversc@gmail.com\", role = c(\"aut\", \"cre\", \"cph\")),\nperson(\"Martin\", \"Moene\", role = c(\"ctb\", \"cph\"), comment = \"span-lite C++ library\"),\nperson(\"Steve\", \"Hanov\", role = c(\"ctb\"), comment = \"Trie levenshtein implementation in Python\"),\nperson(\"Martin\", \"Leitner-Ankerl\", role = c(\"ctb\"), comment = \"Ankerl unordered dense hashmap\"),\nperson(\"Eduard\", \"Zorita\", role = \"ctb\", comment = \"Starcode algorithm and publication\"),\nperson(\"Pol\", \"Cuscó\", role = \"ctb\", comment = \"Starcode algorithm and publication\"),\nperson(\"Guillaume J.\", \"Filion\", role = \"ctb\", comment = \"Starcode algorithm and publication\")\n)", "Description": "A collection of Radix Tree and Trie algorithms for finding\nsimilar sequences and calculating sequence distances\n(Levenshtein and other distance metrics). This work was\ninspired by a trie implementation in Python: \"Fast and Easy\nLevenshtein distance using a Trie.\" Hanov (2011)\n. It also includes\na modified version of the Starcode all-pairs search algorithm\n(Zorita, Cuscó, and Filion 2015)\n.", "License": "GPL-3", "Biarch": "true", "Encoding": "UTF-8", "LazyData": "true", "SystemRequirements": "GNU make, C++17", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.3", "Roxygen": "list(markdown = TRUE)", "Copyright": "This package includes code from the 'span-lite' library\nowned by Martin Moene under Boost Software License 1.0; see\ninst/licenses/span-lite-BSL-1.0-LICENSE. This package includes\ncode from the 'ankerl' library owned by Martin Leitner-Ankerl\nunder MIT License. This package includes a modified version of\nthe Starcode all-pairs search algorithm described by Eduard\nZorita, Pol Cuscó, and Guillaume J. Filion (2015). See\ninst/licenses/starcode-GPL-3-LICENSE. This package contains\ndata derived from Adaptive Biotechnologies \"ImmuneCODE\" dataset\nunder Creative Commons Attribution 4.0.", "URL": "https://github.com/traversc/seqtrie", "BugReports": "https://github.com/traversc/seqtrie/issues", "Config/pak/sysreqs": "cmake make", "Repository": "https://traversc.r-universe.dev", "Date/Publication": "2026-06-03 02:34:15 UTC", "RemoteUrl": "https://github.com/traversc/seqtrie", "RemoteRef": "HEAD", "RemoteSha": "2a8dc5a63798a30b9f9f7e85a3516947769482d7", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-01 07:58:35 UTC", "User": "root" }, "Author": "Travers Ching [aut, cre, cph],\nMartin Moene [ctb, cph] (span-lite C++ library),\nSteve Hanov [ctb] (Trie levenshtein implementation in Python),\nMartin Leitner-Ankerl [ctb] (Ankerl unordered dense hashmap),\nEduard Zorita [ctb] (Starcode algorithm and publication),\nPol Cuscó [ctb] (Starcode algorithm and publication),\nGuillaume J. Filion [ctb] (Starcode algorithm and publication)", "Maintainer": "Travers Ching ", "_user": "traversc", "_type": "src", "_file": "seqtrie_0.4.0.tar.gz", "_fileid": "https://r2.ropensci.org/442f731bb4e31ab90a791464b863626e034e5661a37787ca444d21e37dd984d2", "_filesize": 2426043, "_sha256": "442f731bb4e31ab90a791464b863626e034e5661a37787ca444d21e37dd984d2", "_expires": "2027-01-09T08:13:00.000Z", "_created": "2026-10-01T07:58:35.000Z", "_published": "2026-10-01T08:13:02.612Z", "_jobs": [ { "job": 110275653739, "time": 236, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11147858184" }, { "job": 110275653868, "time": 277, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11147989799" }, { "job": 110275653757, "time": 239, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11147413726" }, { "job": 110275653883, "time": 223, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11147604993" }, { "job": 110275653725, "time": 391, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11148063537" }, { "job": 110275653785, "time": 674, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11148781280" }, { "job": 110275653897, "time": 389, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11147659119" }, { "job": 110275653812, "time": 477, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11148970348" }, { "job": 110274060200, "time": 295, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11148137278" }, { "job": 110275653664, "time": 194, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11147813134" }, { "job": 110275653857, "time": 507, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11148740660" }, { "job": 110275653689, "time": 271, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11148254250" }, { "job": 110275653761, "time": 178, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11147818038" }, { "job": 110275653746, "time": 445, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11148731273" }, { "job": 110275653744, "time": 254, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11148665096" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/traversc/actions/runs/36833084608", "_status": "success", "_upstream": "https://github.com/traversc/seqtrie", "_commit": { "id": "2a8dc5a63798a30b9f9f7e85a3516947769482d7", "author": "Travers ", "committer": "Travers ", "message": ".\n", "time": 1780454055 }, "_maintainer": { "name": "Travers Ching", "email": "traversc@gmail.com", "login": "traversc", "description": "Data Scientist and Computational Biologist", "uuid": 9452194 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppParallel", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 0.12.18.3", "role": "Imports" }, { "package": "RcppParallel", "version": ">= 5.1.3", "role": "Imports" }, { "package": "R6", "role": "Imports" }, { "package": "S7", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "pwalign", "role": "Suggests" }, { "package": "igraph", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" } ], "_owner": "traversc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-40", "n": 3 }, { "week": "2025-43", "n": 4 }, { "week": "2025-49", "n": 1 }, { "week": "2026-14", "n": 1 }, { "week": "2026-19", "n": 6 }, { "week": "2026-22", "n": 2 }, { "week": "2026-23", "n": 2 } ], "_tags": [ { "name": "v0.3.1", "date": "2025-10-03" }, { "name": "v0.3.4", "date": "2025-10-04" } ], "_stars": 9, "_contributors": [ { "user": "traversc", "count": 105, "uuid": 9452194 } ], "_userbio": { "uuid": 9452194, "type": "user", "name": "Travers", "followers": 76, "description": "Data Scientist and Computational Biologist" }, "_downloads": { "count": 390, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/seqtrie" }, "_devurl": "https://github.com/traversc/seqtrie", "_searchresults": 11, "_topics": [ "cpp" ], "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/readme.html", "extra/readme.md", "extra/seqtrie.html" ], "_homeurl": "https://github.com/traversc/seqtrie", "_realowner": "traversc", "_cranurl": true, "_releases": [ { "version": "0.2.5", "date": "2023-09-01" }, { "version": "0.2.6", "date": "2024-01-27" }, { "version": "0.2.8", "date": "2024-05-05" }, { "version": "0.2.9", "date": "2025-03-02" }, { "version": "0.3.5", "date": "2025-10-20" }, { "version": "0.4.0", "date": "2026-06-03" } ], "_exports": [ "align_search", "dist_matrix", "dist_pairwise", "dist_search", "erase", "generate_cost_matrix", "has_sequence", "insert", "is_valid", "plot_tree", "prefix_search", "radix_forest", "radix_tree", "RadixForest", "RadixTree", "result", "single_gap_search", "size", "split_search", "star_tree", "StarTree", "to_string", "to_vector" ], "_datasets": [ { "name": "covid_cdr3", "title": "Adaptive COVID TCRB CDR3 data", "object": "covid_cdr3", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "covid_receptors", "title": "Adaptive COVID TCRB nucleotide rearrangements", "object": "covid_receptors", "class": [ "character" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "align_search", "title": "Alignment search", "topics": [ "align_search" ] }, { "page": "covid_cdr3", "title": "Adaptive COVID TCRB CDR3 data", "topics": [ "covid_cdr3" ] }, { "page": "covid_receptors", "title": "Adaptive COVID TCRB nucleotide rearrangements", "topics": [ "covid_receptors" ] }, { "page": "dist_matrix", "title": "Compute distances between all combinations of two sets of sequences", "topics": [ "dist_matrix" ] }, { "page": "dist_pairwise", "title": "Pairwise distance between two sets of sequences", "topics": [ "dist_pairwise" ] }, { "page": "dist_search", "title": "Distance search for similar sequences", "topics": [ "dist_search" ] }, { "page": "erase", "title": "Erase sequences", "topics": [ "erase" ] }, { "page": "generate_cost_matrix", "title": "Generate a simple cost matrix", "topics": [ "generate_cost_matrix" ] }, { "page": "has_sequence", "title": "Test sequence membership", "topics": [ "has_sequence" ] }, { "page": "insert", "title": "Insert sequences", "topics": [ "insert" ] }, { "page": "is_valid", "title": "Validate trie or forest structure", "topics": [ "is_valid" ] }, { "page": "plot_tree", "title": "Plot trie or forest structure", "topics": [ "plot_tree" ] }, { "page": "prefix_search", "title": "Prefix search", "topics": [ "prefix_search" ] }, { "page": "radix_forest", "title": "Radix forest", "topics": [ "radix_forest" ] }, { "page": "radix_tree", "title": "Radix tree", "topics": [ "radix_tree" ] }, { "page": "RadixForest", "title": "RadixForest", "topics": [ "RadixForest" ] }, { "page": "RadixTree", "title": "RadixTree", "topics": [ "RadixTree" ] }, { "page": "result", "title": "Return a fixed-tree self-similarity result", "topics": [ "result" ] }, { "page": "single_gap_search", "title": "Single-gap alignment search", "topics": [ "single_gap_search" ] }, { "page": "size", "title": "Count stored sequences", "topics": [ "size" ] }, { "page": "split_search", "title": "split_search", "topics": [ "split_search" ] }, { "page": "star_tree", "title": "Starcode-style fixed tree", "topics": [ "star_tree" ] }, { "page": "StarTree", "title": "StarTree", "topics": [ "StarTree" ] }, { "page": "to_string", "title": "Convert a trie or forest to a string", "topics": [ "to_string" ] }, { "page": "to_vector", "title": "Convert sequences to a character vector", "topics": [ "to_vector" ] } ], "_readme": "https://github.com/traversc/seqtrie/raw/HEAD/README.md", "_rundeps": [ "R6", "Rcpp", "RcppParallel", "S7" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "vignette.rmd", "filename": "vignette.html", "title": "seqtrie", "engine": "knitr::rmarkdown", "headings": [ "Background", "Basic usage", "Tree classes", "Understanding Radix Trees", "Hamming distance search", "Anchored alignment searches", "Custom distance searches and affine gap alignment", "StarTree for fixed DNA self-joins", "StarTree anchored mode for fixed anchored self-joins", "StarTree Hamming mode for fixed same-length joins", "References" ], "created": "2020-10-26 18:41:34", "modified": "2026-06-03 01:52:57", "commits": 31 } ], "_score": 5.539703238947825, "_indexed": true, "_nocasepkg": "seqtrie", "_universes": [ "traversc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.4.0", "date": "2026-10-01T08:01:37.000Z", "distro": "resolute", "arch": "aarch64", "commit": "2a8dc5a63798a30b9f9f7e85a3516947769482d7", "fileid": "https://r2.ropensci.org/d76bb298f063d24f8db47aceadcd7f1cd4def95a3754bc2a0fdb5161296f30eb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/traversc/actions/runs/36833084608" }, { "r": "4.7.0", "os": "linux", "version": "0.4.0", "date": "2026-10-01T08:01:54.000Z", "distro": "resolute", "arch": "x86_64", "commit": "2a8dc5a63798a30b9f9f7e85a3516947769482d7", "fileid": "https://r2.ropensci.org/e5cf210009bc8f610bf79c8f8d44e320e70847920a1d098041844bd038ccca63", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/traversc/actions/runs/36833084608" }, { "r": "4.6.1", "os": "linux", "version": "0.4.0", "date": "2026-10-01T08:01:41.000Z", "distro": "resolute", "arch": "aarch64", "commit": "2a8dc5a63798a30b9f9f7e85a3516947769482d7", "fileid": "https://r2.ropensci.org/4871278d749a5ed5d863f588c90f0a274b29d5275d96e042145d249c14c171f1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/traversc/actions/runs/36833084608" }, { "r": "4.6.1", "os": "linux", "version": "0.4.0", "date": "2026-10-01T08:01:46.000Z", "distro": "resolute", "arch": "x86_64", "commit": "2a8dc5a63798a30b9f9f7e85a3516947769482d7", "fileid": "https://r2.ropensci.org/28e3ef015c4b3c4bd9e6f5d55d5cfd98b7891574981f5f9e5ab94c3f8bd990fb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/traversc/actions/runs/36833084608" }, { "r": "4.5.3", "os": "mac", "version": "0.4.0", "date": "2026-10-01T08:06:02.000Z", "arch": "aarch64", "commit": "2a8dc5a63798a30b9f9f7e85a3516947769482d7", "fileid": "https://r2.ropensci.org/5bbc17739484f7e35a4b7683415d656763b84049ddb6c497760c6d67c62b96cc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/traversc/actions/runs/36833084608" }, { "r": "4.5.3", "os": "mac", "version": "0.4.0", "date": "2026-10-01T08:06:29.000Z", "arch": "x86_64", "commit": "2a8dc5a63798a30b9f9f7e85a3516947769482d7", "fileid": "https://r2.ropensci.org/2867644226ca93c88e2f7bf0e1c8a2fe6bb7e5f87072ee9b6107db8f25a38def", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/traversc/actions/runs/36833084608" }, { "r": "4.6.1", "os": "mac", "version": "0.4.0", "date": "2026-10-01T08:07:07.000Z", "arch": "aarch64", "commit": "2a8dc5a63798a30b9f9f7e85a3516947769482d7", "fileid": "https://r2.ropensci.org/9c23bbb1f61f843120c384c863b63cfec6277f0cfeec5b774d8f44cb2190c7da", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/traversc/actions/runs/36833084608" }, { "r": "4.6.1", "os": "mac", "version": "0.4.0", "date": "2026-10-01T08:05:01.000Z", "arch": "x86_64", "commit": "2a8dc5a63798a30b9f9f7e85a3516947769482d7", "fileid": "https://r2.ropensci.org/9ba6ddbd5fdbbb602287438945fcfe338ca9c32880f601014cf7d7750eb8668b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/traversc/actions/runs/36833084608" }, { "r": "4.6.0", "os": "wasm", "version": "0.4.0", "date": "2026-10-01T08:02:22.000Z", "arch": "emscripten", "commit": "2a8dc5a63798a30b9f9f7e85a3516947769482d7", "fileid": "https://r2.ropensci.org/1ebeaafce4bcf3f64066fd282c472cdf8e693854bfd324577b255db444038ceb", "status": "success", "buildurl": "https://github.com/r-universe/traversc/actions/runs/36833084608" }, { "r": "4.7.0", "os": "win", "version": "0.4.0", "date": "2026-10-01T08:05:28.000Z", "arch": "aarch64", "commit": "2a8dc5a63798a30b9f9f7e85a3516947769482d7", "fileid": "https://r2.ropensci.org/19acb395983615785ffcd9b47c4d526bb9f94c7461e0fa620760c801727c8d62", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/traversc/actions/runs/36833084608" }, { "r": "4.7.0", "os": "win", "version": "0.4.0", "date": "2026-10-01T08:00:39.000Z", "arch": "x86_64", "commit": "2a8dc5a63798a30b9f9f7e85a3516947769482d7", "fileid": "https://r2.ropensci.org/38efc835b1c94826a320547a4695746450f0d08463c5b16d274d6a71c4cad2f7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/traversc/actions/runs/36833084608" }, { "r": "4.5.3", "os": "win", "version": "0.4.0", "date": "2026-10-01T08:00:48.000Z", "arch": "x86_64", "commit": "2a8dc5a63798a30b9f9f7e85a3516947769482d7", "fileid": "https://r2.ropensci.org/b9fbf39da1c4c5b6f0e4fa087432104090b09599fb800305df8b3e574f6c55f6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/traversc/actions/runs/36833084608" }, { "r": "4.6.1", "os": "win", "version": "0.4.0", "date": "2026-10-01T08:04:25.000Z", "arch": "aarch64", "commit": "2a8dc5a63798a30b9f9f7e85a3516947769482d7", "fileid": "https://r2.ropensci.org/a645ecb09ffec6149eb21424b52b166ad1e2e925bc0400c966d4e53a75ce3833", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/traversc/actions/runs/36833084608" }, { "r": "4.6.1", "os": "win", "version": "0.4.0", "date": "2026-10-01T08:00:55.000Z", "arch": "x86_64", "commit": "2a8dc5a63798a30b9f9f7e85a3516947769482d7", "fileid": "https://r2.ropensci.org/5054d1ef7c2a4d6805cbde2bca0fb65df9b9313d869bca8d57a309fdc1a2a2ae", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/traversc/actions/runs/36833084608" } ] }