{ "_id": "6a61fab135834fefe99ec10a", "Package": "DuckDBGRanges", "Version": "0.99.1", "Date": "2026-07-22", "Title": "DuckDB-Backed GenomicRanges Implementation", "Description": "Provides DuckDB-backed implementations of GenomicRanges\ndata structures for efficient, out-of-memory operations on\nlarge genomic interval datasets. The package includes\nDuckDBGRanges and DuckDBGRangesList classes with optimized\nrange operations including restrict, flank, shift,\nfindOverlaps, and distance calculations. Ideal for variant\nanalysis, scATAC-seq peak analysis, and other genomic workflows\nrequiring memory-efficient range operations on large datasets.", "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, Sequencing,\nSoftware", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "Collate": "'DuckDBGRanges-class.R' 'DuckDBGRanges-utils.R'\n'DuckDBGRangesList-class.R' 'DuckDBGRangesList-utils.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": "2026-07-22 15:38:50 UTC", "RemoteUrl": "https://github.com/BiocStaging/DuckDBGRanges", "RemoteRef": "HEAD", "RemoteSha": "d4feb322320ae525910ee224d6be15b8d9909ff1", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-23 11:10:52 UTC", "User": "root" }, "Author": "Patrick Aboyoun [aut, cre],\nGenentech, Inc. [cph]", "Maintainer": "Patrick Aboyoun ", "_user": "biocstaging", "_type": "src", "_file": "DuckDBGRanges_0.99.1.tar.gz", "_fileid": "https://r2.ropensci.org/2e2295bf9e2608e99adb88c6990219d14d97ea671bb12185f629cb4110c12c38", "_filesize": 258224, "_sha256": "2e2295bf9e2608e99adb88c6990219d14d97ea671bb12185f629cb4110c12c38", "_expires": "2026-10-31T11:27:44.000Z", "_created": "2026-07-23T11:10:52.000Z", "_published": "2026-07-23T11:27:45.736Z", "_bioccheck": { "error": 0, "warning": 1, "note": 8 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/biocstaging/actions/runs/30001833693", "_status": "success", "_upstream": "https://github.com/BiocStaging/DuckDBGRanges", "_commit": { "id": "d4feb322320ae525910ee224d6be15b8d9909ff1", "author": "Patrick Aboyoun ", "committer": "Patrick Aboyoun ", "message": "docs: add \\value sections to DuckDBGRanges man pages; bump to 0.99.1\n\nDocument return values (roxygen @return) for the DuckDBGRanges and\nDuckDBGRangesList class and utility man pages, covering constructors, accessors,\nreplacement, coercion, and range-operation methods. Clears the R CMD BiocCheck\nmissing-\\value WARNING.\n", "time": 1784734730 }, "_maintainer": { "name": "Patrick Aboyoun", "email": "aboyounp@gene.com" }, "_distro": "resolute", "_jobs": [ { "job": 89189745616, "time": 235, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "8561544786" }, { "job": 89189745725, "time": 437, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8561632216" }, { "job": 89189745617, "time": 493, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8561655400" }, { "job": 89189745647, "time": 310, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "8561762945" }, { "job": 89189745790, "time": 393, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8561800359" }, { "job": 89188649832, "time": 317, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8561436575" }, { "job": 89189745722, "time": 179, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8561519405" }, { "job": 89189745620, "time": 921, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8561837838" }, { "job": 89189745606, "time": 945, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "8561849416" }, { "job": 89189745599, "time": 861, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8561813060" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "stats", "role": "Depends" }, { "package": "DuckDBDataFrame", "role": "Depends" }, { "package": "GenomicRanges", "role": "Depends" }, { "package": "bit64", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "Seqinfo", "role": "Imports" }, { "package": "DelayedArray", "role": "Imports" }, { "package": "DBI", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "dbplyr", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "microbenchmark", "role": "Suggests" }, { "package": "arrow", "role": "Suggests" }, { "package": "TxDb.Hsapiens.UCSC.hg38.knownGene", "role": "Suggests" } ], "_owner": "biocstaging", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2026-04", "n": 2 }, { "week": "2026-09", "n": 1 }, { "week": "2026-10", "n": 1 }, { "week": "2026-19", "n": 1 }, { "week": "2026-23", "n": 1 }, { "week": "2026-24", "n": 1 }, { "week": "2026-25", "n": 1 }, { "week": "2026-27", "n": 1 }, { "week": "2026-28", "n": 5 }, { "week": "2026-29", "n": 3 }, { "week": "2026-30", "n": 5 } ], "_tags": [], "_topics": [ "dataimport", "datarepresentation", "infrastructure", "sequencing", "software" ], "_stars": 0, "_contributors": [ { "user": "aboyounp-gne", "count": 24, "uuid": 171627243 } ], "_userbio": { "uuid": 278472782, "type": "organization", "name": "BiocStaging", "followers": 1 }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/DuckDBGRanges" }, "_devurl": "https://github.com/biocstaging/duckdbgranges", "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/DuckDBGRanges.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE", "manual.pdf" ], "_cranurl": false, "_exports": [ ".has_row_number", ".keycols", "as.data.frame", "countOverlaps", "dbconn", "dimtbls", "dimtbls<-", "disjoin", "distance", "distanceToNearest", "DuckDBGRanges", "DuckDBGRangesList", "duplicated", "elementMetadata", "elementMetadata<-", "elementNROWS", "end", "extractROWS", "findOverlaps", "flank", "follow", "gaps", "genome<-", "getListElement", "head", "intersect", "is.unsorted", "match", "narrow", "nearest", "order", "overlapsAny", "pgap", "pintersect", "precede", "promoters", "psetdiff", "punion", "ranges", "rank", "realize", "reduce", "resize", "restrict", "seqinfo", "seqlengths<-", "seqnames", "setdiff", "shift", "show", "slidingWindows", "sort", "split", "start", "strand", "subsetByOverlaps", "tail", "tblconn", "terminators", "tile", "trim", "union", "unique", "updateObject", "width" ], "_help": [ { "page": "DuckDBGRanges-class", "title": "DuckDBGRanges objects", "topics": [ ".has_row_number,DuckDBGRanges-method", ".keycols,DuckDBGRanges-method", "as.data.frame,DuckDBGRanges-method", "coerce,DuckDBGRanges,DuckDBDataFrame-method", "coerce,DuckDBGRanges,GRanges-method", "dbconn,DuckDBGRanges-method", "dimtbls,DuckDBGRanges-method", "dimtbls<-,DuckDBGRanges-method", "DuckDBGRanges", "DuckDBGRanges-class", "elementMetadata,DuckDBGRanges-method", "elementMetadata<-,DuckDBGRanges-method", "end,DuckDBGRanges-method", "extractROWS,DuckDBGRanges,ANY-method", "genome<-,DuckDBGRanges-method", "head,DuckDBGRanges-method", "length,DuckDBGRanges-method", "names,DuckDBGRanges-method", "ranges,DuckDBGRanges-method", "realize,DuckDBGRanges-method", "seqinfo,DuckDBGRanges-method", "seqlengths<-,DuckDBGRanges-method", "seqnames,DuckDBGRanges-method", "show,DuckDBGRanges-method", "start,DuckDBGRanges-method", "strand,DuckDBGRanges-method", "tail,DuckDBGRanges-method", "tblconn,DuckDBGRanges-method", "width,DuckDBGRanges-method", "[,DuckDBGRanges,ANY,ANY,ANY-method" ] }, { "page": "DuckDBGRanges-utils", "title": "Utilities for DuckDBGRanges objects", "topics": [ "countOverlaps,DuckDBGRanges,DuckDBGRanges-method", "countOverlaps,DuckDBGRanges,GRanges-method", "countOverlaps,GRanges,DuckDBGRanges-method", "disjoin,DuckDBGRanges-method", "distance,DuckDBGRanges,DuckDBGRanges-method", "distance,DuckDBGRanges,GRanges-method", "distance,GRanges,DuckDBGRanges-method", "distanceToNearest,DuckDBGRanges,DuckDBGRanges-method", "distanceToNearest,DuckDBGRanges,GRanges-method", "distanceToNearest,DuckDBGRanges,missing-method", "distanceToNearest,GRanges,DuckDBGRanges-method", "DuckDBGRanges-utils", "duplicated,DuckDBGRanges-method", "findOverlaps,DuckDBGRanges,DuckDBGRanges-method", "findOverlaps,DuckDBGRanges,GRanges-method", "findOverlaps,GRanges,DuckDBGRanges-method", "flank,DuckDBGRanges-method", "follow,DuckDBGRanges,DuckDBGRanges-method", "follow,DuckDBGRanges,GRanges-method", "follow,DuckDBGRanges,missing-method", "follow,GRanges,DuckDBGRanges-method", "gaps,DuckDBGRanges-method", "intersect,DuckDBGRanges,DuckDBGRanges-method", "intersect,DuckDBGRanges,GRanges-method", "intersect,GRanges,DuckDBGRanges-method", "is.unsorted,DuckDBGRanges-method", "match,DuckDBGRanges,DuckDBGRanges-method", "narrow,DuckDBGRanges-method", "nearest,DuckDBGRanges,DuckDBGRanges-method", "nearest,DuckDBGRanges,GRanges-method", "nearest,DuckDBGRanges,missing-method", "nearest,GRanges,DuckDBGRanges-method", "order,DuckDBGRanges-method", "overlapsAny,DuckDBGRanges,DuckDBGRanges-method", "overlapsAny,DuckDBGRanges,GRanges-method", "overlapsAny,GRanges,DuckDBGRanges-method", "pgap,DuckDBGRanges,DuckDBGRanges-method", "pgap,DuckDBGRanges,GRanges-method", "pgap,GRanges,DuckDBGRanges-method", "pintersect,DuckDBGRanges,DuckDBGRanges-method", "pintersect,DuckDBGRanges,GRanges-method", "pintersect,GRanges,DuckDBGRanges-method", "precede,DuckDBGRanges,DuckDBGRanges-method", "precede,DuckDBGRanges,GRanges-method", "precede,DuckDBGRanges,missing-method", "precede,GRanges,DuckDBGRanges-method", "promoters,DuckDBGRanges-method", "psetdiff,DuckDBGRanges,DuckDBGRanges-method", "psetdiff,DuckDBGRanges,GRanges-method", "psetdiff,GRanges,DuckDBGRanges-method", "punion,DuckDBGRanges,DuckDBGRanges-method", "punion,DuckDBGRanges,GRanges-method", "punion,GRanges,DuckDBGRanges-method", "range,DuckDBGRanges-method", "rank,DuckDBGRanges-method", "reduce,DuckDBGRanges-method", "resize,DuckDBGRanges-method", "restrict,DuckDBGRanges-method", "setdiff,DuckDBGRanges,DuckDBGRanges-method", "setdiff,DuckDBGRanges,GRanges-method", "setdiff,GRanges,DuckDBGRanges-method", "shift,DuckDBGRanges-method", "slidingWindows,DuckDBGRanges-method", "sort,DuckDBGRanges-method", "subsetByOverlaps,DuckDBGRanges,DuckDBGRanges-method", "subsetByOverlaps,DuckDBGRanges,GRanges-method", "terminators,DuckDBGRanges-method", "tile,DuckDBGRanges-method", "trim,DuckDBGRanges-method", "union,DuckDBGRanges,DuckDBGRanges-method", "union,DuckDBGRanges,GRanges-method", "union,GRanges,DuckDBGRanges-method", "unique,DuckDBGRanges-method" ] }, { "page": "DuckDBGRangesList-class", "title": "DuckDBGRangesList objects", "topics": [ ".has_row_number,DuckDBGRangesList-method", ".keycols,DuckDBGRangesList-method", "coerce,DuckDBGRangesList,CompressedGRangesList-method", "coerce,DuckDBGRangesList,DuckDBDataFrame-method", "dbconn,DuckDBGRangesList-method", "dimtbls,DuckDBGRangesList-method", "dimtbls<-,DuckDBGRangesList-method", "DuckDBGRangesList", "DuckDBGRangesList-class", "elementMetadata,DuckDBGRangesList-method", "elementMetadata<-,DuckDBGRangesList-method", "elementNROWS,DuckDBGRangesList-method", "end,DuckDBGRangesList-method", "extractROWS,DuckDBGRangesList,ANY-method", "genome<-,DuckDBGRangesList-method", "getListElement,DuckDBGRangesList-method", "head,DuckDBGRangesList-method", "length,DuckDBGRangesList-method", "names,DuckDBGRangesList-method", "names<-,DuckDBGRangesList-method", "realize,DuckDBGRangesList-method", "seqinfo,DuckDBGRangesList-method", "seqlengths<-,DuckDBGRangesList-method", "seqnames,DuckDBGRangesList-method", "show,DuckDBGRangesList-method", "split,DuckDBGRanges,DuckDBColumn-method", "start,DuckDBGRangesList-method", "strand,DuckDBGRangesList-method", "tail,DuckDBGRangesList-method", "tblconn,DuckDBGRangesList-method", "unlist,DuckDBGRangesList-method", "updateObject,DuckDBGRangesList-method", "width,DuckDBGRangesList-method" ] }, { "page": "DuckDBGRangesList-utils", "title": "Utilities for DuckDBGRangesList objects", "topics": [ "DuckDBGRangesList-utils", "range,DuckDBGRangesList-method" ] } ], "_readme": "https://github.com/BiocStaging/DuckDBGRanges/raw/HEAD/README.md", "_rundeps": [ "abind", "arrow", "assertthat", "BiocGenerics", "bit", "bit64", "blob", "cli", "cpp11", "DBI", "dbplyr", "DelayedArray", "dplyr", "duckdb", "DuckDBDataFrame", "generics", "GenomicRanges", "glue", "IRanges", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "pillar", "pkgconfig", "purrr", "R6", "rlang", "S4Arrays", "S4Vectors", "Seqinfo", "SparseArray", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "withr", "XVector" ], "_vignettes": [ { "source": "DuckDBGRanges.Rmd", "filename": "DuckDBGRanges.html", "title": "Introduction to DuckDBGRanges", "author": "Patrick Aboyoun", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Quick start", "Working with a DuckDBGRanges", "Accessors", "Subsetting", "Range operations", "Filter, then materialize", "Grouped ranges: DuckDBGRangesList", "When to use DuckDBGRanges", "Session information" ], "created": "2026-07-06 22:13:54", "modified": "2026-07-06 22:13:54", "commits": 1 }, { "source": "DuckDBGRanges-benchmark.Rmd", "filename": "DuckDBGRanges-benchmark.html", "title": "Benchmarking DuckDBGRanges", "author": "Patrick Aboyoun", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "What DuckDBGRanges optimizes", "A small, live comparison", "Benchmark setup", "Results", "Main takeaways", "Backend comparison", "When to use each", "Running your own benchmarks", "Session information" ], "created": "2026-07-06 22:13:54", "modified": "2026-07-06 22:13:54", "commits": 1 }, { "source": "DuckDBGRanges-design.Rmd", "filename": "DuckDBGRanges-design.html", "title": "Design and extension of DuckDBGRanges", "author": "Patrick Aboyoun", "engine": "knitr::rmarkdown", "headings": [ "Scope", "Architecture", "Slots", "The five required columns", "From range operations to SQL", "Grouped ranges as LIST columns", "Materialization and interoperability", "Session information" ], "created": "2026-07-06 22:13:54", "modified": "2026-07-06 22:13:54", "commits": 1 } ], "_score": 4.694605198933568, "_indexed": true, "_nocasepkg": "duckdbgranges", "_universes": [ "biocstaging" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.99.1", "date": "2026-07-23T11:14:34.000Z", "distro": "resolute", "commit": "d4feb322320ae525910ee224d6be15b8d9909ff1", "fileid": "https://r2.ropensci.org/7cb4d36f162e0b6c7ba1f141c6320d72195535f57ceb85f374210a6c21c18505", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/30001833693" }, { "r": "4.6.1", "os": "linux", "version": "0.99.1", "date": "2026-07-23T11:14:36.000Z", "distro": "resolute", "commit": "d4feb322320ae525910ee224d6be15b8d9909ff1", "fileid": "https://r2.ropensci.org/1dc6bb9e6fdac995bd13696fc8c7feb58b1a18553e8f3c4970a1f0f833d12db3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/30001833693" }, { "r": "4.5.3", "os": "mac", "version": "0.99.1", "date": "2026-07-23T11:20:46.000Z", "commit": "d4feb322320ae525910ee224d6be15b8d9909ff1", "fileid": "https://r2.ropensci.org/c29d4b4b9e30b7e5bf65afcf640c04cedbecf12c6b18f1fa810e9b0e6d28cf7e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/30001833693" }, { "r": "4.6.1", "os": "mac", "version": "0.99.1", "date": "2026-07-23T11:21:14.000Z", "commit": "d4feb322320ae525910ee224d6be15b8d9909ff1", "fileid": "https://r2.ropensci.org/a6e096f232a5dd47c35e653e783be042cd9cafc25010b264820dbe17eda3a0c2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/30001833693" }, { "r": "4.6.0", "os": "wasm", "version": "0.99.1", "date": "2026-07-23T11:14:27.000Z", "commit": "d4feb322320ae525910ee224d6be15b8d9909ff1", "fileid": "https://r2.ropensci.org/89d9048fe50be6fe70b76f82c146811017117f1e4e6e7f5d4bb21171ee9acf59", "status": "success", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/30001833693" }, { "r": "4.7.0", "os": "win", "version": "0.99.1", "date": "2026-07-23T11:21:45.000Z", "commit": "d4feb322320ae525910ee224d6be15b8d9909ff1", "fileid": "https://r2.ropensci.org/b1e9a78da27afeac117b115da8ba537812e79e5b951dbe2e3819d719beae752e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/30001833693" }, { "r": "4.5.3", "os": "win", "version": "0.99.1", "date": "2026-07-23T11:21:47.000Z", "commit": "d4feb322320ae525910ee224d6be15b8d9909ff1", "fileid": "https://r2.ropensci.org/aba7671470161966d0773299802b3daad1cb8fb68719c8806b64845431ca9323", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/30001833693" }, { "r": "4.6.1", "os": "win", "version": "0.99.1", "date": "2026-07-23T11:20:30.000Z", "commit": "d4feb322320ae525910ee224d6be15b8d9909ff1", "fileid": "https://r2.ropensci.org/7ad3c4c63d8122d80fb94b13088b20c9cb8c7e3aa99d8475ebe7408adcb5858d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/30001833693" } ] }