{ "_id": "6ac76b7ade46216d5edcfa06", "Package": "DuckDBArray", "Version": "0.99.11", "Date": "2026-10-07", "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", "URL": "https://github.com/Genentech/DuckDBArray", "BugReports": "https://github.com/Genentech/DuckDBArray/issues", "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-package.R' 'DuckDBArray-utils.R'\n'DuckDBMatrix-class.R' 'DuckDBMatrix-utils.R'\n'createDimTables.R' 'rowDeviances.R' 'rowNnzs.R'\n'scanKeycols.R' 'writeCoordArray-duckdb.R'\n'writeCoordArray-generic.R' 'writeCoordArray-methods.R'\n'writeCoordArray-types.R'", "Config/roxygen2/version": "8.1.0", "Config/pak/sysreqs": "cmake libicu-dev libssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-10-08 00:10:10 UTC", "RemoteUrl": "https://github.com/bioc/DuckDBArray", "RemoteRef": "HEAD", "RemoteSha": "5ffeec68b8c616c9f4c82c3d22b782b763bc69f7", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-08 09:16:17 UTC", "User": "root" }, "Author": "Patrick Aboyoun [aut, cre],\nGenentech, Inc. [cph]", "Maintainer": "Patrick Aboyoun ", "_user": "bioc", "_type": "src", "_file": "DuckDBArray_0.99.11.tar.gz", "_fileid": "https://r2.ropensci.org/1853a27ae45b4005533fec43177698ce41dd7569fed7ddbec464557918e5117c", "_filesize": 327870, "_sha256": "1853a27ae45b4005533fec43177698ce41dd7569fed7ddbec464557918e5117c", "_expires": "2027-01-16T10:07:52.000Z", "_created": "2026-10-08T09:16:17.000Z", "_published": "2026-10-08T10:07:54.712Z", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/37754998487", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 0, "warning": 0, "note": 5 }, "_upstream": "https://github.com/bioc/DuckDBArray", "_commit": { "id": "5ffeec68b8c616c9f4c82c3d22b782b763bc69f7", "author": "Patrick Aboyoun ", "committer": "Patrick Aboyoun ", "message": "fix: realize non-scalar Ops operands against a DuckDBArray (0.99.11)\n\nOps(DuckDBArray, atomic)/Ops(atomic, DuckDBArray) only ever supported a\nlength-1 atomic operand; anything longer fell through to Ops(DuckDBTable,\natomic)'s scalar-only check and errored with \"can only perform binary\noperations with a scalar value\". This was latent but harmless as long as\nevery caller realized a %*%/crossprod result (itself a lazy DuckDBMatrix\nby design, see 0.99.9) before combining it with a plain vector.\n\nCRAN's irlba 2.4.1 (2026-10-05) rewrote its Lanczos loop and dropped the\ndrop() call that used to wrap mult()'s result before the F <- F - sub\ncentering step. For ordinary dense/sparse matrices this is invisible,\nsince %*% already returns a realized object, but it left F as a lazy\nDuckDBMatrix for DuckDBMatrix input, so centered SVDs\n(BiocSingular::runSVD(center = TRUE), scran::fixedPCA(), scater::runPCA())\nstarted failing. Found via BiocDuckDB's DuckDBIrlbaParam/SVD composition\ntests immediately after the 2.4.1 release.\n\nFixed by having these two Ops methods realize e1/e2 via as.array() and\nhand off to base R whenever the atomic operand isn't a true scalar, since\nelementwise arithmetic between two plain vectors is never something base\nR itself defers.\n\nFull DuckDBArray test suite: 0 failures. Full BiocDuckDB test suite: 0\nfailures (previously 9 failures in test-DuckDBIrlbaParam.R and\ntest-DuckDBMatrix-svd.R).\n", "time": 1791418210 }, "_maintainer": { "name": "Patrick Aboyoun", "email": "aboyounp@gene.com" }, "_distro": "resolute", "_jobs": [ { "job": 113239164305, "time": 192, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "11539634490" }, { "job": 113239164503, "time": 446, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11540780115" }, { "job": 113239164245, "time": 448, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11540023472" }, { "job": 113239164425, "time": 297, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "11541674763" }, { "job": 113239164380, "time": 374, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "11542476517" }, { "job": 113237377966, "time": 278, "config": "source", "r": "4.6.1", "check": "OK", "artifact": 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