{ "_id": "6ac8db51de46216d5edd87dd", "Package": "BiocDuckDB", "Version": "0.99.25", "Date": "2026-09-30", "Title": "Bioconductor DuckDB Integration and High-Level I/O", "Description": "Integration package providing high-level Parquet I/O\nfunctions and optimized methods for single-cell analysis\nworkflows using DuckDB-backed data structures. Includes\nreadParquet and writeParquet functions for seamless\nserialization of SummarizedExperiment, SingleCellExperiment,\nMultiAssayExperiment, and MultiAssaySpatialExperiment objects,\nplus SQL-optimized implementations of scran and scuttle methods\nfor variance modeling, marker detection, QC metrics, and\nnormalization. This package brings together DuckDBDataFrame,\nDuckDBArray, DuckDBGRanges, and DuckDBSpatial (optional) for\ncomplete Bioconductor integration.", "Authors@R": "c(\nperson(\"Patrick\", \"Aboyoun\", role=c(\"aut\", \"cre\"), email=\"aboyounp@gene.com\"),\nperson(\"Genentech, Inc.\", role=\"cph\")\n)", "License": "MIT + file LICENSE", "URL": "https://github.com/Genentech/BiocDuckDB", "BugReports": "https://github.com/Genentech/BiocDuckDB/issues", "Copyright": "See the file inst/COPYRIGHTS for third-party schema\ncomponents bundled in inst/schema/ (Frictionless Data Package\nspecifications, in the public domain under The Unlicense).", "biocViews": "DataImport, DataRepresentation, Infrastructure, RNASeq,\nSequencing, SingleCell, Software", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "Collate": "'BiocDuckDB-package.R'\n'MultiAssaySpatialExperiments-internals.R'\n'DuckDBDataFrame-spatial.R' 'DuckDBDualSubset-class.R'\n'initializeOptions.R' 'initializeCpp.R' 'DuckDBIrlbaParam.R'\n'DuckDBMatrix-scran.R' 'DuckDBMatrix-scuttle.R'\n'MultiAssaySpatialExperiment-query.R'\n'MultiAssaySpatialExperiment-spatial.R'\n'SingleCellExperiments-internals.R'\n'SingleCellExperiment-colTables.R'\n'SingleCellExperiment-loadings.R'\n'SingleCellExperiment-pairs.R'\n'SingleCellExperiment-rowTables.R' 'fieldtypes.R'\n'loadIntoMemory.R' 'readParquet.R' 'writeDatapackage.R'\n'writeParquet.R' 'writeStreamingResource.R'", "Config/roxygen2/version": "8.1.0", "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nlibglpk-dev libmagick++-dev gsfonts libicu-dev libxml2-dev\nlibssl-dev libproj-dev libsqlite3-dev libudunits2-dev xz-utils\nzlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-09-30 22:22:23 UTC", "RemoteUrl": "https://github.com/bioc/BiocDuckDB", "RemoteRef": "HEAD", "RemoteSha": "444d953f66149dedd3802a97a635727f67eedb24", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-09 11:58:06 UTC", "User": "root" }, "Author": "Patrick Aboyoun [aut, cre],\nGenentech, Inc. [cph]", "Maintainer": "Patrick Aboyoun ", "_user": "bioc", "_type": "src", "_file": "BiocDuckDB_0.99.25.tar.gz", "_fileid": "https://r2.ropensci.org/4f94be5e0a12740f80c85e850a778543420b57d139faa2b6ea3dfea06129b3f9", "_filesize": 601176, "_sha256": "4f94be5e0a12740f80c85e850a778543420b57d139faa2b6ea3dfea06129b3f9", "_expires": "2027-01-17T12:17:18.000Z", "_created": "2026-10-09T11:58:06.000Z", "_published": "2026-10-09T12:17:20.894Z", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/37926457728", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 0, "warning": 0, "note": 8 }, "_upstream": "https://github.com/bioc/BiocDuckDB", "_commit": { "id": "444d953f66149dedd3802a97a635727f67eedb24", "author": "Patrick Aboyoun ", "committer": "Patrick Aboyoun ", "message": "docs: Document sizing writeCoordArray's grid for large or sparse writes\n\nwriteParquet()'s array delegation to writeCoordArray() inherits its default\ngrid, which budgets partitions from dim(x) alone with no sparsity awareness.\nCross-reference DuckDBArray::writeCoordArray's new density-correction section\n(setAutoBlockSize()/setAutoBlockShape()) and its hard ceiling. Add a third\n@examples entry and a matching vignette snippet showing those calls made\nbefore writeParquet() on a sparse matrix.\n", "time": 1790806943 }, "_maintainer": { "name": "Patrick Aboyoun", "email": "aboyounp@gene.com" }, "_distro": "resolute", "_jobs": [ { "job": 113808598985, "time": 244, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "11615310075" }, { "job": 113808598855, "time": 723, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11614802941" }, { "job": 113808599120, "time": 691, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11615415868" }, { "job": 113808598885, "time": 564, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "11615395485" }, { "job": 113808598898, "time": 555, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "11614658949" }, { "job": 113806571488, "time": 356, "config": "source", "r": "4.6.1", "check": "OK", "artifact": 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"page": "DuckDBMatrix-scran", "title": "DuckDBMatrix scran methods", "topics": [ "correlatePairs,DuckDBMatrix-method", "DuckDBMatrix-scran", "findMarkers,DuckDBMatrix-method", "modelGeneCV2,DuckDBMatrix-method", "modelGeneVar,DuckDBMatrix-method", "modelGeneVarByPoisson,DuckDBMatrix-method", "pairwiseBinom,DuckDBMatrix-method", "pairwiseTTests,DuckDBMatrix-method", "scoreMarkers,DuckDBMatrix-method", "summaryMarkerStats,DuckDBMatrix-method" ] }, { "page": "DuckDBMatrix-scuttle", "title": "DuckDBMatrix scuttle methods", "topics": [ "calculateAverage,DuckDBMatrix-method", "calculateCPM,DuckDBMatrix-method", "calculateTPM,DuckDBMatrix-method", "DuckDBMatrix-scuttle", "geometricSizeFactors,DuckDBMatrix-method", "librarySizeFactors,DuckDBMatrix-method", "normalizeCounts,DuckDBMatrix-method", "numDetectedAcrossFeatures,DuckDBMatrix-method", "perCellQCMetrics,DuckDBMatrix-method", "perFeatureQCMetrics,DuckDBMatrix-method", "sumCountsAcrossFeatures,DuckDBMatrix-method", 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