{ "_id": "6aafb1e63d719c1f84080d4f", "Package": "BiocNeighbors", "Version": "2.7.3", "Date": "2026-08-21", "Title": "Nearest Neighbor Detection for Bioconductor Packages", "Authors@R": "c(person(\"Aaron\", \"Lun\", role=c(\"aut\", \"cre\", \"cph\"), email=\"infinite.monkeys.with.keyboards@gmail.com\"))", "biocViews": "Clustering, Classification", "Description": "Implements exact and approximate methods for nearest\nneighbor detection, in a framework that allows them to be\neasily switched within Bioconductor packages or workflows.\nExact searches can be performed using the k-means for k-nearest\nneighbors algorithm, vantage point trees, or an exhaustive\nsearch. Approximate searches can be performed using the Annoy\nor HNSW libraries. Each search can be performed with a variety\nof different distance metrics, parallelization, and variable\nnumbers of neighbors. Range-based searches (to find all\nneighbors within a certain distance) are also supported.", "License": "GPL-3", "URL": "https://github.com/knncolle/BiocNeighbors", "BugReports": "https://github.com/knncolle/BiocNeighbors/issues", "VignetteBuilder": "knitr", "SystemRequirements": "C++17", "Encoding": "UTF-8", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-08-21 01:41:32 UTC", "RemoteUrl": "https://github.com/bioc/BiocNeighbors", "RemoteRef": "HEAD", "RemoteSha": "0fc21d1027f138d07837d323f3d7058561e25cee", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-09-20 10:05:28 UTC", "User": "root" }, "Author": "Aaron Lun [aut, cre, cph]", "Maintainer": "Aaron Lun ", "_user": "bioc", "_type": "src", "_file": "BiocNeighbors_2.7.3.tar.gz", "_fileid": "https://r2.ropensci.org/3454ddcfbcf36823ce5f4e4b9f3da50cec896c9cbd1cd1bce9f666f27b833cb6", "_filesize": 262330, "_sha256": "3454ddcfbcf36823ce5f4e4b9f3da50cec896c9cbd1cd1bce9f666f27b833cb6", "_expires": "2026-12-29T10:13:56.000Z", "_created": "2026-09-20T10:05:28.000Z", "_published": "2026-09-20T10:13:58.154Z", "_bioccheck": { "error": 0, "warning": 2, "note": 6 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/35503901007", "_status": "success", "_upstream": "https://github.com/bioc/BiocNeighbors", "_commit": { "id": "0fc21d1027f138d07837d323f3d7058561e25cee", "author": "LTLA ", "committer": "LTLA ", "message": "Bumped version to trigger a recompilation.\n", "time": 1787276492 }, "_maintainer": { "name": "Aaron Lun", "email": "infinite.monkeys.with.keyboards@gmail.com", "login": "ltla", "twitter": "@realAaronLun", "description": "(ノಠ益ಠ)ノ彡┻━┻\n", "uuid": 8166669 }, "_distro": "resolute", "_jobs": [ { "job": 106060912562, "time": 188, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "10603586806" }, { "job": 106060912585, "time": 215, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "10603586835" }, { "job": 106060912588, "time": 277, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10603117783" }, { "job": 106060912595, "time": 187, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "10602794062" }, { "job": 106060912594, "time": 326, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10603626777" }, { "job": 106060912557, "time": 106, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "10602848808" }, { "job": 106060912575, "time": 418, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "10603472376" }, { "job": 106060912642, "time": 123, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "10602624303" }, { "job": 106060912577, "time": 426, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10603482292" }, { "job": 106060378746, "time": 259, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "10602748939" }, { "job": 106060912533, "time": 160, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "10602759005" }, { "job": 106060912622, "time": 259, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "10603606832" }, { "job": 106060912635, "time": 241, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10603382158" }, { "job": 106060912722, "time": 174, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "10603362109" }, { "job": 106060912605, "time": 257, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "10602719052" }, { "job": 106060912587, "time": 166, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10602679182" } ], "_registered": true, "_dependencies": [ { "package": "Rcpp", "role": "LinkingTo" }, { "package": "assorthead", "role": "LinkingTo" }, { "package": "beachmat", "role": "LinkingTo" }, { "package": "Rcpp", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "Matrix", "role": "Suggests" }, { "package": "DelayedArray", "role": "Suggests" }, { "package": "beachmat", "role": "Suggests" }, { "package": "BiocParallel", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "S4Vectors", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 115, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2025-50", "n": 3 }, { "week": "2026-04", "n": 5 }, { "week": "2026-05", "n": 3 }, { "week": "2026-07", "n": 1 }, { "week": "2026-18", "n": 2 }, { "week": "2026-19", "n": 5 }, { "week": "2026-34", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "2.7.3", "bioc": "3.24" }, { "branch": "release", "version": "2.6.0", "bioc": "3.23" } ], "_topics": [ "clustering", "classification", "bioconductor-package", "human-cell-atlas", "nearest-neighbor-search", "cpp" ], "_stars": 6, "_contributors": [ { "user": "ltla", "count": 166, "uuid": 8166669 }, { "user": "jwokaty", "count": 16, "uuid": 1744257 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "user": "allisonvuong", "count": 1, "uuid": 47435771 }, { "user": "doliv071", "count": 1, "uuid": 2363607 }, { "user": "eddelbuettel", "count": 1, "uuid": 673121 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 468, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 29938, "source": "https://www.bioconductor.org/packages/stats/bioc/BiocNeighbors" }, "_devurl": "https://github.com/knncolle/biocneighbors", "_searchresults": 814, "_rbuild": "4.6.1", "_assets": [ "extra/BiocNeighbors.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" ], "_homeurl": "https://github.com/knncolle/biocneighbors", "_realowner": "bioc", "_cranurl": false, "_exports": [ "AnnoyIndex", "AnnoyParam", "bndistance", "buildIndex", "defineBuilder", "ExhaustiveIndex", "ExhaustiveParam", "findDistance", "findDistanceFromIndex", "findKNN", "findKnnFromIndex", "findMutualNN", "findNeighbors", "findNeighborsFromIndex", "findResultsToHits", "findResultsToMatrix", "getLoadGenericIndexRegistry", "HnswIndex", "HnswParam", "KmknnIndex", "KmknnParam", "loadIndex", "queryDistance", "queryDistanceFromIndex", "queryKNN", "queryKnnFromIndex", "queryNeighbors", "queryNeighborsFromIndex", "queryResultsToHits", "queryResultsToMatrix", "registerLoadGenericIndexClass", "registerLoadIndexFunction", "saveIndex", "show", "VptreeIndex", "VptreeParam" ], "_help": [ { "page": "BiocNeighbors-package", "title": "BiocNeighbors: Nearest Neighbor Detection for Bioconductor Packages", "topics": [ "BiocNeighbors-package", "BiocNeighbors" ] }, { "page": "AnnoyParam", "title": "The AnnoyParam class", "topics": [ "AnnoyIndex", "AnnoyIndex-class", "AnnoyParam", "AnnoyParam-class", "defineBuilder,AnnoyParam-method", "show,AnnoyParam-method" ] }, { "page": "BiocNeighborIndex", "title": "The BiocNeighborIndex class", "topics": [ "BiocNeighborGenericIndex-class", "BiocNeighborIndex", "BiocNeighborIndex-class", "show,BiocNeighborIndex-method" ] }, { "page": "BiocNeighborParam", "title": "The BiocNeighborParam class", "topics": [ "BiocNeighborParam", "BiocNeighborParam-class", "bndistance", "show,BiocNeighborParam-method", "[[,BiocNeighborParam-method", "[[<-,BiocNeighborParam-method" ] }, { "page": "buildIndex", "title": "Build a nearest-neighbor index", "topics": [ "buildIndex", "buildIndex,BiocNeighborParam-method", "buildIndex,list-method", "buildIndex,missing-method", "buildIndex,NULL-method" ] }, { "page": "defineBuilder", "title": "Define an index builder", "topics": [ "defineBuilder", "defineBuilder,missing-method", "defineBuilder,NULL-method" ] }, { "page": "ExhaustiveParam", "title": "The ExhaustiveParam class", "topics": [ "defineBuilder,ExhaustiveParam-method", "ExhaustiveIndex", "ExhaustiveIndex-class", "ExhaustiveParam", "ExhaustiveParam-class" ] }, { "page": "findDistance", "title": "Distance to the k-th nearest neighbor", "topics": [ "findDistance", "findDistanceFromIndex", "findDistanceFromIndex,BiocNeighborGenericIndex-method" ] }, { "page": "findKNN", "title": "Find k-nearest neighbors", "topics": [ "findKNN", "findKnnFromIndex", "findKnnFromIndex,BiocNeighborGenericIndex-method" ] }, { "page": "findMutualNN", "title": "Find mutual nearest neighbors", "topics": [ "findMutualNN" ] }, { "page": "findNeighbors", "title": "Find neighbors within a threshold distance", "topics": [ "findNeighbors", "findNeighborsFromIndex", "findNeighborsFromIndex,BiocNeighborGenericIndex-method" ] }, { "page": "convert", "title": "Convert neighbor search results to alternative representations", "topics": [ "findResultsToHits", "findResultsToMatrix", "queryResultsToHits", "queryResultsToMatrix" ] }, { "page": "getLoadGenericIndexRegistry", "title": "Load indices from extension packages", "topics": [ "getLoadGenericIndexRegistry", "registerLoadGenericIndexClass", "registerLoadIndexFunction" ] }, { "page": "HnswParam", "title": "The HnswParam class", "topics": [ "defineBuilder,HnswParam-method", "HnswIndex", "HnswIndex-class", "HnswParam", "HnswParam-class", "show,HnswParam-method" ] }, { "page": "KmknnParam", "title": "The KmknnParam class", "topics": [ "defineBuilder,KmknnParam-method", "KmknnIndex", "KmknnIndex-class", "KmknnParam", "KmknnParam-class" ] }, { "page": "loadIndex", "title": "Load a prebuilt search index from disk", "topics": [ "loadIndex" ] }, { "page": "queryDistance", "title": "Distance to the k-th nearest neighbor to query points", "topics": [ "queryDistance", "queryDistanceFromIndex", "queryDistanceFromIndex,BiocNeighborGenericIndex-method" ] }, { "page": "queryKNN", "title": "Query k-nearest neighbors", "topics": [ "queryKNN", "queryKnnFromIndex", "queryKnnFromIndex,BiocNeighborGenericIndex-method" ] }, { "page": "queryNeighbors", "title": "Query neighbors within a threshold distance", "topics": [ "queryNeighbors", "queryNeighborsFromIndex", "queryNeighborsFromIndex,BiocNeighborGenericIndex-method" ] }, { "page": "saveIndex", "title": "Save a nearest-neighbor index", "topics": [ "saveIndex", "saveIndex,BiocNeighborGenericIndex-method" ] }, { "page": "VptreeParam", "title": "The VptreeParam class", "topics": [ "defineBuilder,VptreeParam-method", "VptreeIndex", "VptreeIndex-class", "VptreeParam", "VptreeParam-class" ] } ], "_readme": "https://github.com/bioc/BiocNeighbors/raw/HEAD/README.md", "_rundeps": [ "abind", "assorthead", "beachmat", "BiocGenerics", "DelayedArray", "generics", "IRanges", "lattice", "Matrix", "MatrixGenerics", "matrixStats", "Rcpp", "S4Arrays", "S4Vectors", "SparseArray", "XVector" ], "_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": "userguide.Rmd", "filename": "userguide.html", "title": "Finding neighbors in high-dimensional space", "author": "Aaron Lun", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Finding nearest neighbors", "Finding all neighbors within range", "Saving indices to disk", "Usage in downstream C++ libraries", "Extending to new methods", "Introduction", "In R", "In C++", "Session information" ], "created": "2024-09-05 18:04:58", "modified": "2026-01-31 02:11:08", "commits": 5 } ], "_score": 12.083028776108309, "_indexed": true, "_nocasepkg": "biocneighbors", "_universes": [ "bioc", "ltla", "knncolle" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.7.3", "date": "2026-09-20T10:08:56.000Z", "distro": "resolute", "arch": "aarch64", "commit": "0fc21d1027f138d07837d323f3d7058561e25cee", "fileid": "https://r2.ropensci.org/d2fa4b44b62f8e1ec3e90c792e45e332d2f0ecc63a360a8dc13aa54f0608ee53", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35503901007" }, { "r": "4.7.0", "os": "linux", "version": "2.7.3", "date": "2026-09-20T10:10:01.000Z", "distro": "resolute", "arch": "x86_64", "commit": "0fc21d1027f138d07837d323f3d7058561e25cee", "fileid": "https://r2.ropensci.org/7bff9bd1d81dfa0a972b96bf1c2a767c5dd8b30d4db793a0b7e9007a27b475f1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35503901007" }, { "r": "4.6.1", "os": "linux", "version": "2.7.3", "date": "2026-09-20T10:08:33.000Z", "distro": "resolute", "arch": "aarch64", "commit": "0fc21d1027f138d07837d323f3d7058561e25cee", "fileid": "https://r2.ropensci.org/336a4b8242f0be237df5580632f76f11a49aa3d2d7128914765935db56a6eb09", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35503901007" }, { "r": "4.6.1", "os": "linux", "version": "2.7.3", "date": "2026-09-20T10:10:40.000Z", "distro": "resolute", "arch": "x86_64", "commit": "0fc21d1027f138d07837d323f3d7058561e25cee", "fileid": "https://r2.ropensci.org/8d43e99dafa9884517cb6022df8d3dbbffcfe66394d84f60da2cf29fe763149f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35503901007" }, { "r": "4.5.3", "os": "mac", "version": "2.7.3", "date": "2026-09-20T10:07:23.000Z", "arch": "aarch64", "commit": "0fc21d1027f138d07837d323f3d7058561e25cee", "fileid": "https://r2.ropensci.org/0dc412a89cb6c06f5b1c58a2dcecc360cf5a76e05d7430d2c95d0655ae58c626", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35503901007" }, { "r": "4.5.3", "os": "mac", "version": "2.7.3", "date": "2026-09-20T10:10:01.000Z", "arch": "x86_64", "commit": "0fc21d1027f138d07837d323f3d7058561e25cee", "fileid": "https://r2.ropensci.org/8e489d94fd9cf905ecf1b884b5135246ff208bdb83fb4406215398ca44cb0bd4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35503901007" }, { "r": "4.6.1", "os": "mac", "version": "2.7.3", "date": "2026-09-20T10:07:34.000Z", "arch": "aarch64", "commit": "0fc21d1027f138d07837d323f3d7058561e25cee", "fileid": "https://r2.ropensci.org/e49491f8625959ab4e5fa2fdbb440428564e2ee758ec7fa0493103c70b97c5ae", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35503901007" }, { "r": "4.6.1", "os": "mac", "version": "2.7.3", "date": "2026-09-20T10:10:24.000Z", "arch": "x86_64", "commit": "0fc21d1027f138d07837d323f3d7058561e25cee", "fileid": "https://r2.ropensci.org/1c35ef45e62ae2464b7c12f7f173355af8f7bef6bef7d4bd66eb78282f5955f0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35503901007" }, { "r": "4.6.0", "os": "wasm", "version": "2.7.3", "date": "2026-09-20T10:08:30.000Z", "arch": "emscripten", "commit": "0fc21d1027f138d07837d323f3d7058561e25cee", "fileid": "https://r2.ropensci.org/2fe9b95e4c3d45020a2ca7b0a78829f6f667324c48ca6ea254b1499186467837", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35503901007" }, { "r": "4.7.0", "os": "win", "version": "2.7.3", "date": "2026-09-20T10:09:13.000Z", "arch": "aarch64", "commit": "0fc21d1027f138d07837d323f3d7058561e25cee", "fileid": "https://r2.ropensci.org/ea817fc92e6ca898dd2c2ad31b1c8a87eb308c3cbb64b1493d978a33bb14d433", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35503901007" }, { "r": "4.7.0", "os": "win", "version": "2.7.3", "date": "2026-09-20T10:07:48.000Z", "arch": "x86_64", "commit": "0fc21d1027f138d07837d323f3d7058561e25cee", "fileid": "https://r2.ropensci.org/220d9ba2e692a026ede23d4057f6e626b31682f3c4763bfc4e828a24713b548f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35503901007" }, { "r": "4.5.3", "os": "win", "version": "2.7.3", "date": "2026-09-20T10:07:22.000Z", "arch": "x86_64", "commit": "0fc21d1027f138d07837d323f3d7058561e25cee", "fileid": "https://r2.ropensci.org/6512d79405ff3c5f398f8aeffd855656b0804d684503387cb6a49b1ed5058880", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35503901007" }, { "r": "4.6.1", "os": "win", "version": "2.7.3", "date": "2026-09-20T10:09:15.000Z", "arch": "aarch64", "commit": "0fc21d1027f138d07837d323f3d7058561e25cee", "fileid": "https://r2.ropensci.org/0db6331f34973d3644a704e5068eb3c73f130b83c0407218262e333820fd9f56", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35503901007" }, { "r": "4.6.1", "os": "win", "version": "2.7.3", "date": "2026-09-20T10:07:16.000Z", "arch": "x86_64", "commit": "0fc21d1027f138d07837d323f3d7058561e25cee", "fileid": "https://r2.ropensci.org/332d6c79234d4afc58ad3b2ecc6cb36cb00aa688fe3549b72dc9dbfa10de00df", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35503901007" } ] }