{
  "_id": "6a1bedc01d7bb097a0a205b6",
  "Package": "beachmat",
  "Version": "2.28.0",
  "Date": "2026-04-09",
  "Title": "Compiling Bioconductor to Handle Each Matrix Type",
  "Authors@R": "c(person(\"Aaron\", \"Lun\", role = c(\"aut\", \"cre\"), email = \"infinite.monkeys.with.keyboards@gmail.com\"),\nperson(\"Hervé\", \"Pagès\", role=\"aut\"),\nperson(\"Mike\", \"Smith\", role=\"aut\"))",
  "biocViews": "DataRepresentation, DataImport, Infrastructure",
  "Description": "Provides a consistent C++ class interface for reading from\na variety of commonly used matrix types. Ordinary matrices and\nseveral sparse/dense Matrix classes are directly supported,\nalong with a subset of the delayed operations implemented in\nthe DelayedArray package. All other matrix-like objects are\nsupported by calling back into R.",
  "License": "GPL-3",
  "NeedsCompilation": "yes",
  "VignetteBuilder": "knitr",
  "SystemRequirements": "C++17",
  "URL": "https://github.com/tatami-inc/beachmat",
  "BugReports": "https://github.com/tatami-inc/beachmat/issues",
  "RoxygenNote": "7.3.3",
  "Encoding": "UTF-8",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:46:00 UTC",
  "RemoteUrl": "https://github.com/bioc/beachmat",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "a5ec637c732e3ce1e978036e67f5030253503624",
  "Packaged": {
    "Date": "2026-05-31 06:46:56 UTC",
    "User": "root"
  },
  "Author": "Aaron Lun [aut, cre],\nHervé Pagès [aut],\nMike Smith [aut]",
  "Maintainer": "Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>",
  "MD5sum": "82d4f6aa13803e33e5549aae9e81bcb3",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "beachmat_2.28.0.tar.gz",
  "_fileid": "3c44bc61c55b0ef761ad41a945899fe180765f3e2a44416435ca86d68cd4c299",
  "_filesize": 217967,
  "_sha256": "3c44bc61c55b0ef761ad41a945899fe180765f3e2a44416435ca86d68cd4c299",
  "_created": "2026-05-31T06:46:56.000Z",
  "_published": "2026-05-31T08:13:52.193Z",
  "_jobs": [
    {
      "job": 78706593019,
      "time": 220,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7314572427"
    },
    {
      "job": 78706593056,
      "time": 395,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7314589415"
    },
    {
      "job": 78706593052,
      "time": 506,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7314600244"
    },
    {
      "job": 78706593046,
      "time": 385,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7314588460"
    },
    {
      "job": 78706593049,
      "time": 519,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7314601613"
    },
    {
      "job": 78706593047,
      "time": 380,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7315124505"
    },
    {
      "job": 78706593035,
      "time": 608,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7314653831"
    },
    {
      "job": 78706593053,
      "time": 384,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7315124176"
    },
    {
      "job": 78706593057,
      "time": 562,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7314669174"
    },
    {
      "job": 78706320735,
      "time": 322,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7314549578"
    },
    {
      "job": 78706593018,
      "time": 184,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7314568640"
    },
    {
      "job": 78706593024,
      "time": 514,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7314601144"
    },
    {
      "job": 78706593054,
      "time": 396,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7314589585"
    },
    {
      "job": 78706593026,
      "time": 479,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7314597447"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 8
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705639914",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/beachmat",
  "_commit": {
    "id": "a5ec637c732e3ce1e978036e67f5030253503624",
    "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": 1777380360
  },
  "_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",
      "version": ">= 1.5.4",
      "role": "LinkingTo"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "DelayedArray",
      "version": ">= 0.27.2",
      "role": "Imports"
    },
    {
      "package": "SparseArray",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "rcmdcheck",
      "role": "Suggests"
    },
    {
      "package": "BiocParallel",
      "role": "Suggests"
    },
    {
      "package": "HDF5Array",
      "role": "Suggests"
    },
    {
      "package": "beachmat.hdf5",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 192,
  "_updates": [
    {
      "week": "2025-23",
      "n": 2
    },
    {
      "week": "2025-29",
      "n": 2
    },
    {
      "week": "2025-31",
      "n": 1
    },
    {
      "week": "2025-34",
      "n": 2
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2025-50",
      "n": 1
    },
    {
      "week": "2026-02",
      "n": 1
    },
    {
      "week": "2026-09",
      "n": 2
    },
    {
      "week": "2026-15",
      "n": 4
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "2.29.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "2.28.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "datarepresentation",
    "dataimport",
    "infrastructure",
    "bioconductor-package",
    "human-cell-atlas",
    "matrix-library",
    "cpp"
  ],
  "_stars": 5,
  "_contributors": [
    {
      "user": "ltla",
      "count": 257,
      "uuid": 8166669
    },
    {
      "user": "nturaga",
      "count": 14,
      "uuid": 2746443
    },
    {
      "user": "jwokaty",
      "count": 14,
      "uuid": 1744257
    },
    {
      "user": "hpages",
      "count": 9,
      "uuid": 8810451
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    },
    {
      "user": "petehaitch",
      "count": 1,
      "uuid": 1049741
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 31030,
    "source": "https://www.bioconductor.org/packages/stats/bioc/beachmat"
  },
  "_mentions": 3,
  "_devurl": "https://github.com/tatami-inc/beachmat",
  "_searchresults": 32,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/beachmat.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/tatami-inc/beachmat",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "checkMemoryCache",
    "colBlockApply",
    "flushMemoryCache",
    "getExecutor",
    "initializeCpp",
    "isFileBackedMatrix",
    "realizeFileBackedMatrix",
    "rowBlockApply",
    "tatami.arith",
    "tatami.binary",
    "tatami.bind",
    "tatami.column",
    "tatami.column.medians",
    "tatami.column.nan.counts",
    "tatami.column.sums",
    "tatami.compare",
    "tatami.dim",
    "tatami.get",
    "tatami.is.sparse",
    "tatami.log",
    "tatami.logic",
    "tatami.math",
    "tatami.medians",
    "tatami.multiply",
    "tatami.nan.counts",
    "tatami.not",
    "tatami.prefer.rows",
    "tatami.realize",
    "tatami.round",
    "tatami.row",
    "tatami.row.medians",
    "tatami.row.nan.counts",
    "tatami.row.sums",
    "tatami.subset",
    "tatami.sums",
    "tatami.sums.by.group",
    "tatami.transpose",
    "toCsparse",
    "whichNonZero"
  ],
  "_help": [
    {
      "page": "checkMemoryCache",
      "title": "Check the in-memory cache for matrix instances",
      "topics": [
        "checkMemoryCache",
        "flushMemoryCache"
      ]
    },
    {
      "page": "colBlockApply",
      "title": "Apply over blocks of columns or rows",
      "topics": [
        "colBlockApply",
        "rowBlockApply"
      ]
    },
    {
      "page": "getExecutor",
      "title": "Get the parallel executor",
      "topics": [
        "getExecutor"
      ]
    },
    {
      "page": "initializeCpp",
      "title": "Initialize matrix in C++ memory space",
      "topics": [
        "initializeCpp",
        "initializeCpp,ANY-method",
        "initializeCpp,ConstantArraySeed-method",
        "initializeCpp,DelayedAbind-method",
        "initializeCpp,DelayedAperm-method",
        "initializeCpp,DelayedMatrix-method",
        "initializeCpp,DelayedNaryIsoOp-method",
        "initializeCpp,DelayedSetDimnames-method",
        "initializeCpp,DelayedSubset-method",
        "initializeCpp,DelayedUnaryIsoOpStack-method",
        "initializeCpp,DelayedUnaryIsoOpWithArgs-method",
        "initializeCpp,dgCMatrix-method",
        "initializeCpp,dgeMatrix-method",
        "initializeCpp,dgRMatrix-method",
        "initializeCpp,externalptr-method",
        "initializeCpp,lgCMatrix-method",
        "initializeCpp,lgeMatrix-method",
        "initializeCpp,lgRMatrix-method",
        "initializeCpp,matrix-method",
        "initializeCpp,SVT_SparseMatrix-method"
      ]
    },
    {
      "page": "realizeFileBackedMatrix",
      "title": "Realize a file-backed DelayedMatrix",
      "topics": [
        "isFileBackedMatrix",
        "realizeFileBackedMatrix"
      ]
    },
    {
      "page": "tatami-utils",
      "title": "Tatami utilities",
      "topics": [
        "tatami-utils",
        "tatami.arith",
        "tatami.binary",
        "tatami.bind",
        "tatami.column.medians",
        "tatami.column.nan.counts",
        "tatami.column.sums",
        "tatami.compare",
        "tatami.dim",
        "tatami.get",
        "tatami.is.sparse",
        "tatami.log",
        "tatami.logic",
        "tatami.math",
        "tatami.medians",
        "tatami.multiply",
        "tatami.nan.counts",
        "tatami.not",
        "tatami.prefer.rows",
        "tatami.realize",
        "tatami.round",
        "tatami.row.medians",
        "tatami.row.nan.counts",
        "tatami.row.sums",
        "tatami.subset",
        "tatami.sums",
        "tatami.sums.by.group",
        "tatami.transpose"
      ]
    },
    {
      "page": "toCsparse",
      "title": "Convert a SparseMatrix to a CsparseMatrix",
      "topics": [
        "toCsparse"
      ]
    },
    {
      "page": "whichNonZero",
      "title": "Find non-zero entries of a matrix",
      "topics": [
        "whichNonZero"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/beachmat/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "assorthead",
    "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": "linking.Rmd",
      "filename": "linking.html",
      "title": "Developing packages with beachmat",
      "author": "Aaron Lun",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Linking instructions",
        "Reading matrix data",
        "Enabling parallelization",
        "Comparison to block processing",
        "Session information"
      ],
      "created": "2018-03-13 09:53:19",
      "modified": "2025-08-19 21:51:39",
      "commits": 13
    }
  ],
  "_score": 11.331385505055003,
  "_indexed": false,
  "_nocasepkg": "beachmat",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/beachmat",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.28.0",
      "date": "2026-05-31T06:50:32.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "a5ec637c732e3ce1e978036e67f5030253503624",
      "fileid": "6d665226dcd4f71849824dd1e8e583adeb4cae8052f7bd46dd4843ecaddde373",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705639914"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.28.0",
      "date": "2026-05-31T06:51:31.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "a5ec637c732e3ce1e978036e67f5030253503624",
      "fileid": "3ce055719354d7a2d234cc6d1445ef386495ae7726f2837f95e2483860b9fe19",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705639914"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.28.0",
      "date": "2026-05-31T06:50:24.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "a5ec637c732e3ce1e978036e67f5030253503624",
      "fileid": "14abc3699f6cadfae576519508057abe41d53c18642c669a47f418a251e8bc27",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705639914"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.28.0",
      "date": "2026-05-31T06:51:43.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "a5ec637c732e3ce1e978036e67f5030253503624",
      "fileid": "e4f3a17af6c1192ecafe904f09282187444350b9bf043c203c2551eebc6857b9",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705639914"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.28.0",
      "date": "2026-05-31T08:08:48.000Z",
      "arch": "aarch64",
      "commit": "a5ec637c732e3ce1e978036e67f5030253503624",
      "fileid": "0d55425e80f62800fd68e75d0ccce8e48adbd6455de1b9c726da6200111a4bb6",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705639914"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.28.0",
      "date": "2026-05-31T06:57:53.000Z",
      "arch": "x86_64",
      "commit": "a5ec637c732e3ce1e978036e67f5030253503624",
      "fileid": "847af404ea313d8169f35ed881837d1dc27c134715e98c72b4883cbc654a200a",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705639914"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.28.0",
      "date": "2026-05-31T08:08:58.000Z",
      "arch": "aarch64",
      "commit": "a5ec637c732e3ce1e978036e67f5030253503624",
      "fileid": "7dc46283b804de0f53dde1a57d016d98f8ad8756a9b5da15c9af47c6c22c63f5",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705639914"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.28.0",
      "date": "2026-05-31T07:00:50.000Z",
      "arch": "x86_64",
      "commit": "a5ec637c732e3ce1e978036e67f5030253503624",
      "fileid": "2049fcf32e85dc6af2db415b6a7bdaf447789b34aed8f409abe68174ef2b943f",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705639914"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.28.0",
      "date": "2026-05-31T06:50:37.000Z",
      "arch": "emscripten",
      "commit": "a5ec637c732e3ce1e978036e67f5030253503624",
      "fileid": "6ae430956ec9f69698b634357f2235988a0ab8baf1fb46354bb161e86e707f7f",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705639914"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.28.0",
      "date": "2026-05-31T06:49:46.000Z",
      "arch": "x86_64",
      "commit": "a5ec637c732e3ce1e978036e67f5030253503624",
      "fileid": "ab714fb409c47234467bc8cee9d5e03b644903e5498c63bad93e92814aff57f8",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705639914"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.28.0",
      "date": "2026-05-31T06:49:28.000Z",
      "arch": "x86_64",
      "commit": "a5ec637c732e3ce1e978036e67f5030253503624",
      "fileid": "0a2fa80c55fa27fe83dd123a3b94a7246a798a4abeda002195d8d9cda054bf85",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705639914"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.28.0",
      "date": "2026-05-31T06:49:55.000Z",
      "arch": "x86_64",
      "commit": "a5ec637c732e3ce1e978036e67f5030253503624",
      "fileid": "63227aeedf1fa21ceb4f85dbb8bf02932858331e84f340be45f16f74ef544a5f",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705639914"
    }
  ]
}