{
  "_id": "6a27bb6824555f66ed53b0fb",
  "Package": "BiocNeighbors",
  "Version": "2.6.0",
  "Date": "2026-02-13",
  "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",
  "VignetteBuilder": "knitr",
  "SystemRequirements": "C++17",
  "RoxygenNote": "7.3.3",
  "Encoding": "UTF-8",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:48:15 UTC",
  "RemoteUrl": "https://github.com/bioc/BiocNeighbors",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "221e565acfb3d54d1cf86c69b4cb72a78c9e9cc5",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-06-09 06:10:21 UTC",
    "User": "root"
  },
  "Author": "Aaron Lun [aut, cre, cph]",
  "Maintainer": "Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>",
  "MD5sum": "b0c521c1cd14011645caf4d852cc8856",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "BiocNeighbors_2.6.0.tar.gz",
  "_fileid": "1d984059a3240101513ce51754e1f71a5b6613e2dc6a5dbd2dccbab95a361794",
  "_filesize": 249633,
  "_sha256": "1d984059a3240101513ce51754e1f71a5b6613e2dc6a5dbd2dccbab95a361794",
  "_created": "2026-06-09T06:10:21.000Z",
  "_published": "2026-06-09T07:06:16.457Z",
  "_jobs": [
    {
      "job": 80259494913,
      "time": 185,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7499862906"
    },
    {
      "job": 80259494955,
      "time": 194,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7499866419"
    },
    {
      "job": 80259494936,
      "time": 251,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7499879806"
    },
    {
      "job": 80259494959,
      "time": 192,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7499865367"
    },
    {
      "job": 80259494944,
      "time": 291,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7499890119"
    },
    {
      "job": 80259494960,
      "time": 103,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7500725597"
    },
    {
      "job": 80259494972,
      "time": 395,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7500247890"
    },
    {
      "job": 80259494974,
      "time": 163,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7500373122"
    },
    {
      "job": 80259495070,
      "time": 600,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7500314609"
    },
    {
      "job": 80258924271,
      "time": 270,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7499814918"
    },
    {
      "job": 80259494917,
      "time": 154,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7499854889"
    },
    {
      "job": 80259494921,
      "time": 191,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7499864560"
    },
    {
      "job": 80259494954,
      "time": 241,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7499877113"
    },
    {
      "job": 80259494957,
      "time": 186,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7499863262"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 2,
    "note": 7
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27187277919",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/BiocNeighbors",
  "_commit": {
    "id": "221e565acfb3d54d1cf86c69b4cb72a78c9e9cc5",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777380495
  },
  "_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": "noble",
  "_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": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 109,
  "_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": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "2.7.2",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "2.6.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "clustering",
    "classification",
    "cpp"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 19552,
    "source": "https://www.bioconductor.org/packages/stats/bioc/BiocNeighbors"
  },
  "_searchresults": 826,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/BiocNeighbors.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/knncolle/biocneighbors",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "AnnoyIndex",
    "AnnoyParam",
    "bndistance",
    "buildIndex",
    "defineBuilder",
    "ExhaustiveIndex",
    "ExhaustiveParam",
    "findDistance",
    "findDistanceFromIndex",
    "findKNN",
    "findKnnFromIndex",
    "findMutualNN",
    "findNeighbors",
    "findNeighborsFromIndex",
    "getLoadGenericIndexRegistry",
    "HnswIndex",
    "HnswParam",
    "KmknnIndex",
    "KmknnParam",
    "loadIndex",
    "queryDistance",
    "queryDistanceFromIndex",
    "queryKNN",
    "queryKnnFromIndex",
    "queryNeighbors",
    "queryNeighborsFromIndex",
    "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": "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/RELEASE_3_23/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": "14.2.0-4ubuntu2~24.04.1",
      "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": 10.199840243262791,
  "_indexed": false,
  "_nocasepkg": "biocneighbors",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/BiocNeighbors",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.6.0",
      "date": "2026-06-09T06:13:27.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "221e565acfb3d54d1cf86c69b4cb72a78c9e9cc5",
      "fileid": "214f682fe5eb73e67e797df6f7362266343e8acc2e9d711ef3087ca0a8c648a5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27187277919"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.6.0",
      "date": "2026-06-09T06:14:15.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "221e565acfb3d54d1cf86c69b4cb72a78c9e9cc5",
      "fileid": "4fc6bf1cb399fcb595ae00911443fd6c7a08e1f3f773ab3b52789e53ed8776c9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27187277919"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.6.0",
      "date": "2026-06-09T06:13:26.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "221e565acfb3d54d1cf86c69b4cb72a78c9e9cc5",
      "fileid": "0060c328d41cc530b37158a757f07996cbd87a764f51d29a7b53e37a34a477f5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27187277919"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.6.0",
      "date": "2026-06-09T06:14:55.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "221e565acfb3d54d1cf86c69b4cb72a78c9e9cc5",
      "fileid": "6ee331dd60b3826c8e6963b2d8abc25d3195ad31eccf5d536eaf1512a0fa1f7a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27187277919"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.6.0",
      "date": "2026-06-09T07:05:19.000Z",
      "arch": "aarch64",
      "commit": "221e565acfb3d54d1cf86c69b4cb72a78c9e9cc5",
      "fileid": "4c78932f0e767d3bc4be99bcf2e294de11119d1068b61d9b6cedf735d189aa8c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27187277919"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.6.0",
      "date": "2026-06-09T06:35:18.000Z",
      "arch": "x86_64",
      "commit": "221e565acfb3d54d1cf86c69b4cb72a78c9e9cc5",
      "fileid": "f44e608a38e326e6720e56c76896401c3d65050468dfaf396cefab5ce11e1c38",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27187277919"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.6.0",
      "date": "2026-06-09T06:45:10.000Z",
      "arch": "aarch64",
      "commit": "221e565acfb3d54d1cf86c69b4cb72a78c9e9cc5",
      "fileid": "c88356afb917e3a934e915ac6a74f48afecf8a4736602dbf6b9339984b3ae8da",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27187277919"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.6.0",
      "date": "2026-06-09T06:37:45.000Z",
      "arch": "x86_64",
      "commit": "221e565acfb3d54d1cf86c69b4cb72a78c9e9cc5",
      "fileid": "daa381b9b551ab81033f4264a7ae5bed2f34fb8fcc54bd0eedb93e19bf4724a6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27187277919"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.6.0",
      "date": "2026-06-09T06:13:12.000Z",
      "arch": "emscripten",
      "commit": "221e565acfb3d54d1cf86c69b4cb72a78c9e9cc5",
      "fileid": "e0df6ce5ae4c88f5d32c098ff78bdc5cb3fe5be0fc2d61d8454746d551265bc8",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27187277919"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.6.0",
      "date": "2026-06-09T06:12:31.000Z",
      "arch": "x86_64",
      "commit": "221e565acfb3d54d1cf86c69b4cb72a78c9e9cc5",
      "fileid": "0662603813ad9b7509034640ddcc2d6f2711b5de7932b8d993b2a224d4f5c113",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27187277919"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.6.0",
      "date": "2026-06-09T06:12:43.000Z",
      "arch": "x86_64",
      "commit": "221e565acfb3d54d1cf86c69b4cb72a78c9e9cc5",
      "fileid": "02e92a54f6c169dc975185756815ad5d474f8fd113b8b8483d221cae9f8ffbe9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27187277919"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.6.0",
      "date": "2026-06-09T06:12:16.000Z",
      "arch": "x86_64",
      "commit": "221e565acfb3d54d1cf86c69b4cb72a78c9e9cc5",
      "fileid": "5e1623f81a32d5fb1cc462c223a2eeffb3ce65024f974990bf777f4069e24a7c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27187277919"
    }
  ]
}