{ "_id": "6a61f9eb35834fefe99ec04a", "Package": "DuckDBArray", "Version": "0.99.2", "Date": "2026-07-22", "Title": "DuckDB-Backed DelayedArray Implementation", "Description": "Provides DuckDB-backed implementations of DelayedArray and\nDelayedMatrix classes for efficient, out-of-memory operations\non large array and matrix datasets. The package includes\nDuckDBArray, DuckDBArraySeed, and DuckDBMatrix classes with\noptimized matrixStats methods. Supports sparse arrays, grid\npartitioning, and parallel processing for scalable genomic data\nanalysis.", "Authors@R": "c(\nperson(\"Patrick\", \"Aboyoun\", role=c(\"aut\", \"cre\"), email=\"aboyounp@gene.com\"),\nperson(\"Genentech, Inc.\", role=\"cph\")\n)", "License": "MIT + file LICENSE", "biocViews": "DataImport, DataRepresentation, Infrastructure, Software", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "Collate": "'DuckDBArraySeed-class.R' 'DuckDBArraySeed-utils.R'\n'DuckDBArray-class.R' 'DuckDBTable-matrixStats.R'\n'DuckDBArraySeed-matrixStats.R' 'DuckDBArray-matrixStats.R'\n'DuckDBArray-utils.R' 'DuckDBMatrix-class.R'\n'DuckDBMatrix-utils.R' 'createDimTables.R' 'rowDeviances.R'\n'rowNnzs.R' 'writeCoordArray-duckdb.R'\n'writeCoordArray-generic.R' 'writeCoordArray-methods.R'\n'writeCoordArray-types.R'", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "cmake libicu-dev libssl-dev xz-utils zlib1g-dev", "Repository": "https://biocstaging.r-universe.dev", "Date/Publication": "2026-07-23 05:24:30 UTC", "RemoteUrl": "https://github.com/BiocStaging/DuckDBArray", "RemoteRef": "HEAD", "RemoteSha": "161c046563fe95d852da0c92ec521ea5d88e3d83", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-23 11:10:38 UTC", "User": "root" }, "Author": "Patrick Aboyoun [aut, cre],\nGenentech, Inc. [cph]", "Maintainer": "Patrick Aboyoun ", "_user": "biocstaging", "_type": "src", "_file": "DuckDBArray_0.99.2.tar.gz", "_fileid": "https://r2.ropensci.org/699febbb050fe402a2d0538c90478209ad697ec2f08a5ce9cd16054c7af86b76", "_filesize": 296590, "_sha256": "699febbb050fe402a2d0538c90478209ad697ec2f08a5ce9cd16054c7af86b76", "_expires": "2026-10-31T11:24:25.000Z", "_created": "2026-07-23T11:10:38.000Z", "_published": "2026-07-23T11:24:27.116Z", "_bioccheck": { "error": 0, "warning": 1, "note": 7 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/biocstaging/actions/runs/30001831904", "_status": "success", "_upstream": "https://github.com/BiocStaging/DuckDBArray", "_commit": { "id": "161c046563fe95d852da0c92ec521ea5d88e3d83", "author": "Patrick Aboyoun ", "committer": "Patrick Aboyoun ", "message": "Support append on the DuckDB fast-path coord write\n\nThe DuckDB fast path (COPY ... PARTITION_BY) only supported a fresh write; a\nsecond writeCoordArray(..., append = TRUE) slab failed with \"Directory ... is\nnot empty\". The `append` flag is now threaded from the writeCoordArray dispatch\nthrough .writeDuckDBArrayPartitionedWithPartitionBy() and .buildCopyToSQL() to\nbuildParquetCopySQL(append = TRUE), which emits the DuckDB APPEND option so new\nparts are written into the existing hive dataset without clobbering earlier\nfiles.\n\nTests: a second append slab round-trips to the combined matrix, and an append\npast 2^31 preserves every entry with a uint32 index. Requires the companion\nDuckDBDataFrame buildParquetCopySQL() `append` option.\n", "time": 1784784270 }, "_maintainer": { "name": "Patrick Aboyoun", "email": "aboyounp@gene.com" }, "_distro": "resolute", "_jobs": [ { "job": 89189704526, "time": 223, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "8561533293" }, { "job": 89189704453, "time": 370, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8561597515" }, { "job": 89189704547, "time": 423, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8561621181" }, { "job": 89189704512, "time": 255, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "8561720602" }, { "job": 89189704553, "time": 319, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8561765765" }, { "job": 89188672246, "time": 298, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8561430051" }, { "job": 89189704495, "time": 174, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8561512227" }, { "job": 89189704570, "time": 362, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8561595553" }, { "job": 89189704473, "time": 337, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "8561584355" }, { "job": 89189704489, "time": 343, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8561586789" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "stats", "role": "Depends" }, { "package": "DuckDBDataFrame", "role": "Depends" }, { "package": "DelayedArray", "role": "Depends" }, { "package": "SparseArray", "role": "Depends" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "S4Arrays", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "MatrixGenerics", "role": "Imports" }, { "package": "DBI", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "dbplyr", "role": "Imports" }, { "package": "duckdb", "role": "Imports" }, { "package": "arrow", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "matrixStats", "role": "Suggests" }, { "package": "microbenchmark", "role": "Suggests" }, { "package": "BiocParallel", "role": "Suggests" }, { "package": "DelayedMatrixStats", "role": "Suggests" }, { "package": "ExperimentHub", "role": "Suggests" }, { "package": "HDF5Array", "role": "Suggests" }, { "package": "sparseMatrixStats", "role": "Suggests" }, { "package": "SummarizedExperiment", "role": "Suggests" }, { "package": "TileDBArray", "role": "Suggests" }, { "package": "airway", "role": "Suggests" } ], "_owner": "biocstaging", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2026-04", "n": 2 }, { "week": "2026-06", "n": 2 }, { "week": "2026-09", "n": 1 }, { "week": "2026-10", "n": 2 }, { "week": "2026-12", "n": 3 }, { "week": "2026-15", "n": 1 }, { "week": "2026-16", "n": 5 }, { "week": "2026-17", "n": 1 }, { "week": "2026-18", "n": 1 }, { "week": "2026-19", "n": 1 }, { "week": "2026-21", "n": 2 }, { "week": "2026-22", "n": 1 }, { "week": "2026-24", "n": 2 }, { "week": "2026-25", "n": 1 }, { "week": "2026-27", "n": 1 }, { "week": "2026-28", "n": 1 }, { "week": "2026-29", "n": 6 }, { "week": "2026-30", "n": 6 } ], "_tags": [], "_topics": [ "dataimport", "datarepresentation", "infrastructure", "software" ], "_stars": 0, "_contributors": [ { "user": "aboyounp-gne", "count": 45, "uuid": 171627243 } ], "_userbio": { "uuid": 278472782, "type": "organization", "name": "BiocStaging", "followers": 1 }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/DuckDBArray" }, "_devurl": "https://github.com/biocstaging/duckdbarray", "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/DuckDBArray.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE", "manual.pdf" ], "_cranurl": false, "_exports": [ "aperm", "colCounts", "colMaxs", "colMeans", "colMins", "colNnzs", "colSds", "colSums", "colVars", "createDimTables", "dbconn", "DelayedArray", "dimtbls", "dimtbls<-", "DuckDBArray", "DuckDBArraySeed", "DuckDBMatrix", "extract_array", "extract_sparse_array", "is_nonzero", "is_sparse", "Math", "matrixClass", "nzcount", "nzvals", "Ops", "rowCounts", "rowDeviances", "rowMaxs", "rowMeans", "rowMins", "rowNnzs", "rowSds", "rowSums", "rowVars", "show", "sweep", "t", "tblconn", "type", "type<-", "writeCoordArray" ], "_help": [ { "page": "createDimTables", "title": "Create Dimension Lookup Tables", "topics": [ "createDimTables" ] }, { "page": "DuckDBArray-class", "title": "DuckDBArray objects", "topics": [ "aperm,DuckDBArray-method", "coerce,DuckDBArray,COO_SparseArray-method", "coerce,DuckDBArray,COO_SparseMatrix-method", "coerce,DuckDBArray,dgCMatrix-method", "dbconn,DuckDBArray-method", "dimnames<-,DuckDBArray,ANY-method", "dimtbls,DuckDBArray-method", "dimtbls<-,DuckDBArray-method", "DuckDBArray", "DuckDBArray-class", "t,DuckDBArray-method", "tblconn,DuckDBArray-method", "type,DuckDBArray-method", "type<-,DuckDBArray-method", "[,DuckDBArray,ANY,ANY,ANY-method" ] }, { "page": "DuckDBArray-matrixStats", "title": "DuckDBArray row / column summarization methods", "topics": [ "colCounts,DuckDBArray-method", "colMaxs,DuckDBArray-method", "colMeans,DuckDBArray-method", "colMins,DuckDBArray-method", "colSds,DuckDBArray-method", "colSums,DuckDBArray-method", "colVars,DuckDBArray-method", "DuckDBArray-matrixStats", "rowCounts,DuckDBArray-method", "rowMaxs,DuckDBArray-method", "rowMeans,DuckDBArray-method", "rowMins,DuckDBArray-method", "rowSds,DuckDBArray-method", "rowSums,DuckDBArray-method", "rowVars,DuckDBArray-method" ] }, { "page": "DuckDBArray-utils", "title": "Common operations on DuckDBArray objects", "topics": [ "!,DuckDBArray-method", "DuckDBArray-utils", "is.finite,DuckDBArray-method", "is.infinite,DuckDBArray-method", "is.nan,DuckDBArray-method", "is_nonzero,DuckDBArray-method", "Math,DuckDBArray-method", "nzcount,DuckDBArray-method", "nzvals,DuckDBArray-method", "Ops,atomic,DuckDBArray-method", "Ops,DuckDBArray,atomic-method", "Ops,DuckDBArray,DuckDBArray-method", "Ops,DuckDBArray,missing-method", "sweep,DuckDBArray-method" ] }, { "page": "DuckDBArraySeed-class", "title": "DuckDBArraySeed objects", "topics": [ "aperm,DuckDBArraySeed-method", "dbconn,DuckDBArraySeed-method", "DelayedArray,DuckDBArraySeed-method", "dim,DuckDBArraySeed-method", "dimnames,DuckDBArraySeed-method", "dimnames<-,DuckDBArraySeed,ANY-method", "dimtbls,DuckDBArraySeed-method", "dimtbls<-,DuckDBArraySeed-method", "DuckDBArraySeed", "DuckDBArraySeed-class", "extract_array,DuckDBArraySeed-method", "extract_sparse_array,DuckDBArraySeed-method", "show,DuckDBArraySeed-method", "t,DuckDBArraySeed-method", "tblconn,DuckDBArraySeed-method", "type,DuckDBArraySeed-method", "type<-,DuckDBArraySeed-method", "[,DuckDBArraySeed,ANY,ANY,ANY-method" ] }, { "page": "DuckDBArraySeed-matrixStats", "title": "DuckDBArraySeed row / column summarization methods", "topics": [ "colCounts,DuckDBArraySeed-method", "colMaxs,DuckDBArraySeed-method", "colMeans,DuckDBArraySeed-method", "colMins,DuckDBArraySeed-method", "colSds,DuckDBArraySeed-method", "colSums,DuckDBArraySeed-method", "colVars,DuckDBArraySeed-method", "DuckDBArraySeed-matrixStats", "rowCounts,DuckDBArraySeed-method", "rowMaxs,DuckDBArraySeed-method", "rowMeans,DuckDBArraySeed-method", "rowMins,DuckDBArraySeed-method", "rowSds,DuckDBArraySeed-method", "rowSums,DuckDBArraySeed-method", "rowVars,DuckDBArraySeed-method" ] }, { "page": "DuckDBArraySeed-utils", "title": "Common operations on DuckDBArraySeed objects", "topics": [ "!,DuckDBArraySeed-method", "DuckDBArraySeed-utils", "is.finite,DuckDBArraySeed-method", "is.infinite,DuckDBArraySeed-method", "is.nan,DuckDBArraySeed-method", "is_nonzero,DuckDBArraySeed-method", "is_sparse,DuckDBArraySeed-method", "Math,DuckDBArraySeed-method", "nzcount,DuckDBArraySeed-method", "Ops,atomic,DuckDBArraySeed-method", "Ops,DuckDBArraySeed,atomic-method", "Ops,DuckDBArraySeed,DuckDBArraySeed-method", "Ops,DuckDBArraySeed,missing-method", "sweep,DuckDBArraySeed-method" ] }, { "page": "DuckDBMatrix-class", "title": "DuckDBMatrix objects", "topics": [ "DuckDBMatrix", "DuckDBMatrix-class", "matrixClass,DuckDBArray-method", "[,DuckDBMatrix,ANY,ANY,ANY-method" ] }, { "page": "DuckDBMatrix-utils", "title": "DuckDBMatrix utility methods", "topics": [ "%*%,DuckDBMatrix,numeric-method", "%*%,numeric,DuckDBMatrix-method", "crossprod,DuckDBMatrix,missing-method", "crossprod,DuckDBMatrix,numeric-method", "crossprod,numeric,DuckDBMatrix-method", "DuckDBMatrix-utils", "tcrossprod,DuckDBMatrix,missing-method", "tcrossprod,DuckDBMatrix,numeric-method", "tcrossprod,numeric,DuckDBMatrix-method" ] }, { "page": "DuckDBTable-matrixStats", "title": "DuckDBTable row / column summarization methods", "topics": [ "colCounts,DuckDBTable-method", "colMaxs,DuckDBTable-method", "colMeans,DuckDBTable-method", "colMins,DuckDBTable-method", "colSds,DuckDBTable-method", "colSums,DuckDBTable-method", "colVars,DuckDBTable-method", "DuckDBTable-matrixStats", "rowCounts,DuckDBTable-method", "rowMaxs,DuckDBTable-method", "rowMeans,DuckDBTable-method", "rowMins,DuckDBTable-method", "rowSds,DuckDBTable-method", "rowSums,DuckDBTable-method", "rowVars,DuckDBTable-method", "sweep,DuckDBTable-method" ] }, { "page": "rowDeviances", "title": "Row-wise Deviance Statistics", "topics": [ "rowDeviances", "rowDeviances,DelayedMatrix-method", "rowDeviances,dgCMatrix-method", "rowDeviances,DuckDBMatrix-method", "rowDeviances,matrix-method" ] }, { "page": "rowNnzs", "title": "Row and Column Non-Zero Counts", "topics": [ "colNnzs", "colNnzs,ANY-method", "colNnzs,DuckDBArray-method", "rowNnzs", "rowNnzs,ANY-method", "rowNnzs,DuckDBArray-method" ] }, { "page": "writeCoordArray", "title": "Write an Array-Like Object in Coordinate Format", "topics": [ "writeCoordArray", "writeCoordArray,ANY-method", "writeCoordArray,DuckDBArray-method" ] } ], "_readme": "https://github.com/BiocStaging/DuckDBArray/raw/HEAD/README.md", "_rundeps": [ "abind", "arrow", "assertthat", "BiocGenerics", "bit", "bit64", "blob", "cli", "cpp11", "DBI", "dbplyr", "DelayedArray", "dplyr", "duckdb", "DuckDBDataFrame", "generics", "glue", "IRanges", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "pillar", "pkgconfig", "purrr", "R6", "rlang", "S4Arrays", "S4Vectors", "SparseArray", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "withr", "XVector" ], "_vignettes": [ { "source": "DuckDBArray.Rmd", "filename": "DuckDBArray.html", "title": "Introduction to DuckDBArray", "author": "Patrick Aboyoun", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Quick start", "Working with a DuckDBMatrix", "Writing a matrix to the DuckDB backend", "Subsetting", "Matrix statistics", "Sparse data", "Lazy evaluation", "Realizing large results in blocks", "N-dimensional arrays", "When to use DuckDBArray", "Session information" ], "created": "2026-07-06 20:24:12", "modified": "2026-07-19 04:21:53", "commits": 2 }, { "source": "DuckDBArray-comparison.Rmd", "filename": "DuckDBArray-comparison.html", "title": "Benchmarking DuckDBArray", "author": "Patrick Aboyoun", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "What DuckDBArray optimizes", "A small, live comparison", "Benchmark setup", "Giving every backend its best effort", "Results", "Main takeaways", "Backend comparison", "When to use each", "Running your own benchmarks", "Session information" ], "created": "2026-01-24 01:59:42", "modified": "2026-07-06 20:24:12", "commits": 3 }, { "source": "DuckDBArray-backend.Rmd", "filename": "DuckDBArray-backend.html", "title": "Implementing the DuckDBArray backend", "author": "Patrick Aboyoun", "engine": "knitr::rmarkdown", "headings": [ "Scope", "Architecture", "The seed contract", "Shape: dim() and dimnames()", "Dense blocks: extract_array()", "Sparse blocks: extract_sparse_array()", "Wrapping the seed", "From array operations to SQL", "Grid partitioning", "Realization and interoperability", "Session information" ], "created": "2026-07-06 20:24:12", "modified": "2026-07-06 20:24:12", "commits": 1 } ], "_score": 4.9084850188786495, "_indexed": true, "_nocasepkg": "duckdbarray", "_universes": [ "biocstaging" ], "_previous": "0.99.00", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.99.2", "date": "2026-07-23T11:13:57.000Z", "distro": "resolute", "commit": "161c046563fe95d852da0c92ec521ea5d88e3d83", "fileid": "https://r2.ropensci.org/233b10c26291d6952a33fae5cc3b265a73ca5ba18ef2d9f197e748a7410ded79", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/30001831904" }, { "r": "4.6.1", "os": "linux", "version": "0.99.2", "date": "2026-07-23T11:14:20.000Z", "distro": "resolute", "commit": "161c046563fe95d852da0c92ec521ea5d88e3d83", "fileid": "https://r2.ropensci.org/aa0dbeb2a351962a8cdd325341b5c1ddb111f2e35a8a955f10fb8dd215c4b035", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/30001831904" }, { "r": "4.5.3", "os": "mac", "version": "0.99.2", "date": "2026-07-23T11:19:29.000Z", "commit": "161c046563fe95d852da0c92ec521ea5d88e3d83", "fileid": "https://r2.ropensci.org/14236758240ff442ac6f29244e25dd9c1226f6db660b0b4c41e9fbd9cb9dff28", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/30001831904" }, { "r": "4.6.1", "os": "mac", "version": "0.99.2", "date": "2026-07-23T11:20:36.000Z", "commit": "161c046563fe95d852da0c92ec521ea5d88e3d83", "fileid": "https://r2.ropensci.org/60b02e9fcc7b14adddcfd864824cd096b72a332f8c14337fcdee7d4881728319", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/30001831904" }, { "r": "4.6.0", "os": "wasm", "version": "0.99.2", "date": "2026-07-23T11:14:11.000Z", "commit": "161c046563fe95d852da0c92ec521ea5d88e3d83", "fileid": "https://r2.ropensci.org/68f9fed0698801fbf181d73405d5fb66290126766ca32f561dac38f7e1903cdd", "status": "success", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/30001831904" }, { "r": "4.7.0", "os": "win", "version": "0.99.2", "date": "2026-07-23T11:12:59.000Z", "commit": "161c046563fe95d852da0c92ec521ea5d88e3d83", "fileid": "https://r2.ropensci.org/97f4f97d736873aaf37c4e0a4d9b62d3e24528c34e1568fe0d522452ea721fac", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/30001831904" }, { "r": "4.5.3", "os": "win", "version": "0.99.2", "date": "2026-07-23T11:12:52.000Z", "commit": "161c046563fe95d852da0c92ec521ea5d88e3d83", "fileid": "https://r2.ropensci.org/d13fc079ef3267a2d737a14fd6293d7f1561c08158332c331b08858c0dd72901", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/30001831904" }, { "r": "4.6.1", "os": "win", "version": "0.99.2", "date": "2026-07-23T11:13:04.000Z", "commit": "161c046563fe95d852da0c92ec521ea5d88e3d83", "fileid": "https://r2.ropensci.org/d34d0f13523f8f8eeaa339293c4a6a83cab0375c25e4128cdd04a057064312c7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/30001831904" } ] }