{
  "_id": "6acce37fa14063b82c3aa474",
  "Package": "DuckDBDataFrame",
  "Version": "0.99.27",
  "Date": "2026-09-12",
  "Title": "DuckDB-Backed DataFrame and Table Structures",
  "Description": "Provides DuckDB-backed implementations of core tabular\ndata structures including DuckDBTable, DuckDBDataFrame, and\nDuckDBColumn. These classes extend Bioconductor's S4Vectors\nframework to enable efficient, out-of-memory operations on\nlarge tabular datasets using DuckDB's analytical database\nengine. The package includes SQL function discovery, connection\nmanagement, and support for list columns and embeddings stored\nin ARRAY[] columns.",
  "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/DuckDBDataFrame",
  "BugReports": "https://github.com/Genentech/DuckDBDataFrame/issues",
  "biocViews": "DataImport, DataRepresentation, Infrastructure, Software",
  "VignetteBuilder": "knitr",
  "Encoding": "UTF-8",
  "Collate": "'sql_fun.R' 'sql_call.R' 'tblconn.R' 'keynames.R'\n'DuckDBConnection.R' 'DuckDBTable-class.R'\n'DuckDBTable-utils.R' 'DuckDBColumn-class.R'\n'DuckDBAtomicList-class.R' 'DuckDBColumn-utils.R'\n'DuckDBEmbeddings-class.R' 'DuckDBDataFrame-class.R'\n'DuckDBDataFrame-internals.R' 'DuckDBDataFrame-package.R'\n'DuckDBDataFrameList-class.R' 'DuckDBSelfHits-class.R'\n'DuckDBTransposedDataFrame-class.R' 'arrow-types.R'\n'parquet-io-cluster.R' 'parquet-io.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": "2026-09-12 15:11:26 UTC",
  "RemoteUrl": "https://github.com/bioc/DuckDBDataFrame",
  "RemoteRef": "HEAD",
  "RemoteSha": "2fec690b923848868bd64d2809817731fa4ad98d",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-12 13:33:38 UTC",
    "User": "root"
  },
  "Author": "Patrick Aboyoun [aut, cre],\nGenentech, Inc. [cph]",
  "Maintainer": "Patrick Aboyoun <aboyounp@gene.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "DuckDBDataFrame_0.99.27.tar.gz",
  "_fileid": "https://r2.ropensci.org/78c36398a3c0fcb4a567ed606d3bb9ed9bc32dab393cf812ce52535e8319af25",
  "_filesize": 408020,
  "_sha256": "78c36398a3c0fcb4a567ed606d3bb9ed9bc32dab393cf812ce52535e8319af25",
  "_expires": "2027-01-20T13:41:17.000Z",
  "_created": "2026-10-12T13:33:38.000Z",
  "_published": "2026-10-12T13:41:18.890Z",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38256075326",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 8
  },
  "_upstream": "https://github.com/bioc/DuckDBDataFrame",
  "_commit": {
    "id": "2fec690b923848868bd64d2809817731fa4ad98d",
    "author": "Patrick Aboyoun <aboyoun.patrick@gene.com>",
    "committer": "Patrick Aboyoun <aboyoun.patrick@gene.com>",
    "message": "fix: quote sql_fun() IN-list values via dbQuoteString (0.99.27)\n\nsql_fun,DuckDBTable-method built its return_type/function_type IN (...)\npredicates by pasting user-supplied strings between hardcoded quotes with\nno escaping, so a return_type containing a ' (e.g. \"x') OR 1=1 --\") broke\nout of the SQL literal before hitting dbGetQuery(). function_type wasn't\nactually exploitable (match.arg() constrains it to a fixed enum first),\nbut both now go through DBI::dbQuoteString(conn, ...), the same\nconnection object already used elsewhere in the method.\n",
    "time": 1789225886
  },
  "_maintainer": {
    "name": "Patrick Aboyoun",
    "email": "aboyounp@gene.com"
  },
  "_distro": "resolute",
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      "package": "R",
      "version": ">= 4.5.0",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "stats",
      "role": "Depends"
    },
    {
      "package": "bit64",
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    },
    {
      "package": "S4Vectors",
      "role": "Depends"
    },
    {
      "package": "IRanges",
      "role": "Depends"
    },
    {
      "package": "tools",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
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    },
    {
      "package": "S4Arrays",
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    {
      "package": "SparseArray",
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      "package": "Matrix",
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      "package": "DBI",
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      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "dbplyr",
      "role": "Imports"
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    {
      "package": "duckdb",
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      "package": "arrow",
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      "package": "tibble",
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      "package": "knitr",
      "role": "Suggests"
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      "package": "rmarkdown",
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      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
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  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 4,
  "_updates": [
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  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "0.99.27",
      "bioc": "3.24",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "dataimport",
    "datarepresentation",
    "infrastructure",
    "software"
  ],
  "_stars": 1,
  "_contributors": [
    {
      "user": "aboyounp-gne",
      "count": 95,
      "uuid": 171627243
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 476,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 206,
    "source": "https://www.bioconductor.org/packages/stats/bioc/DuckDBDataFrame"
  },
  "_devurl": "https://github.com/genentech/duckdbdataframe",
  "_searchresults": 14,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/DuckDBDataFrame.html",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE"
  ],
  "_homeurl": "https://github.com/genentech/duckdbdataframe",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "%in%",
    "acquireDuckDBConn",
    "arrowIntType",
    "arrowType",
    "arrowTypeFromName",
    "arrowTypeToName",
    "as.data.frame",
    "as.env",
    "as.list",
    "as.matrix",
    "bindCOLS",
    "bindROWS",
    "buildParquetCopySQL",
    "cbind",
    "chartr",
    "checkAppendPart",
    "checkHiveAppendPartitions",
    "clusterOrderSQL",
    "clusterSort",
    "coerce",
    "colnames",
    "colnames<-",
    "coltypes",
    "coltypes<-",
    "columnExtents",
    "columnMetadata",
    "columnMetadata<-",
    "commonColnames",
    "configureCloud",
    "configureOutOfCore",
    "countLnodeHits",
    "countRnodeHits",
    "dbconn",
    "dimtbls",
    "dimtbls<-",
    "DuckDBDataFrame",
    "DuckDBSelfHits",
    "DuckDBTable",
    "elementMetadata",
    "elementMetadata<-",
    "elementNROWS",
    "endsWith",
    "escapeSQLPath",
    "extractCOLS",
    "extractNODES",
    "extractROWS",
    "from",
    "getListElement",
    "grepl",
    "gsub",
    "has_row_number",
    "head",
    "hilbert",
    "IQR",
    "is_nonzero",
    "is_sparse",
    "keycols",
    "keydimnames",
    "keydimnames<-",
    "keynames",
    "levels",
    "loadExtension",
    "mad",
    "makeNakedCharacterMatrixForDisplay",
    "makePrettyCharacterMatrixForDisplay",
    "Math",
    "mean",
    "nchar",
    "ncol",
    "ncols",
    "nkey",
    "nkeydim",
    "nlevels",
    "normalizeSingleBracketReplacementValue",
    "nrow",
    "nzcount",
    "Ops",
    "parquetPartPath",
    "paste",
    "paste2",
    "pmax",
    "pmin",
    "quoteSQLColumns",
    "readParquetSchema",
    "realize",
    "reconcileParquetSchema",
    "releaseDuckDBConn",
    "replaceCOLS",
    "replaceROWS",
    "rownames",
    "rownames<-",
    "sd",
    "set_row_number",
    "setupFlatParquetWrite",
    "show",
    "showAsCell",
    "split",
    "splitParquetPart",
    "sql_call",
    "sql_fun",
    "startsWith",
    "sub",
    "subset",
    "substr",
    "substring",
    "Summary",
    "t",
    "t.DuckDBDataFrame",
    "table",
    "tail",
    "tblconn",
    "to",
    "tolower",
    "toupper",
    "type",
    "type<-",
    "unique",
    "validateAppendOffset",
    "validateWriteParquetPart",
    "var",
    "writeDuckDBTableParquet",
    "zorder"
  ],
  "_help": [
    {
      "page": "arrow-types",
      "title": "Arrow type helpers for the DuckDB package suite",
      "topics": [
        "arrow-types",
        "arrowIntType",
        "arrowType",
        "arrowTypeFromName",
        "arrowTypeToName"
      ]
    },
    {
      "page": "DuckDBAtomicList-class",
      "title": "DuckDBAtomicList objects",
      "topics": [
        "as.list,DuckDBAtomicList-method",
        "DuckDBAtomicList-class",
        "DuckDBCharacterList-class",
        "DuckDBFactorList-class",
        "DuckDBInteger64List-class",
        "DuckDBIntegerList-class",
        "DuckDBLogicalList-class",
        "DuckDBNumericList-class",
        "elementNROWS,DuckDBAtomicList-method",
        "extractROWS,DuckDBAtomicList,ANY-method",
        "getListElement,DuckDBAtomicList-method",
        "head,DuckDBAtomicList-method",
        "realize,DuckDBAtomicList-method",
        "show,DuckDBAtomicList-method",
        "showAsCell,DuckDBAtomicList-method",
        "tail,DuckDBAtomicList-method"
      ]
    },
    {
      "page": "DuckDBColumn-class",
      "title": "DuckDBColumn objects",
      "topics": [
        "as.vector,DuckDBColumn-method",
        "dbconn,DuckDBColumn-method",
        "dimtbls,DuckDBColumn-method",
        "dimtbls<-,DuckDBColumn-method",
        "DuckDBColumn-class",
        "extractROWS,DuckDBColumn,ANY-method",
        "has_row_number,DuckDBColumn-method",
        "head,DuckDBColumn-method",
        "keycols,DuckDBColumn-method",
        "length,DuckDBColumn-method",
        "levels,DuckDBColumn-method",
        "names,DuckDBColumn-method",
        "names<-,DuckDBColumn-method",
        "nlevels,DuckDBColumn-method",
        "realize,DuckDBColumn-method",
        "show,DuckDBColumn-method",
        "showAsCell,DuckDBColumn-method",
        "tail,DuckDBColumn-method",
        "tblconn,DuckDBColumn-method",
        "type,DuckDBColumn-method",
        "type<-,DuckDBColumn-method"
      ]
    },
    {
      "page": "DuckDBColumn-utils",
      "title": "Common operations on DuckDBColumn objects",
      "topics": [
        "!,DuckDBColumn-method",
        "%in%,DuckDBColumn,ANY-method",
        "anyNA,DuckDBColumn-method",
        "chartr,ANY,ANY,DuckDBColumn-method",
        "DuckDBColumn-utils",
        "endsWith,DuckDBColumn-method",
        "grepl,ANY,DuckDBColumn-method",
        "gsub,ANY,ANY,DuckDBColumn-method",
        "IQR,DuckDBColumn-method",
        "is.finite,DuckDBColumn-method",
        "is.infinite,DuckDBColumn-method",
        "is.na,DuckDBColumn-method",
        "is.nan,DuckDBColumn-method",
        "is_nonzero,DuckDBColumn-method",
        "mad,DuckDBColumn-method",
        "Math,DuckDBColumn-method",
        "mean,DuckDBColumn-method",
        "median.DuckDBColumn",
        "nchar,DuckDBColumn-method",
        "nzcount,DuckDBColumn-method",
        "Ops,atomic,DuckDBColumn-method",
        "Ops,DuckDBColumn,atomic-method",
        "Ops,DuckDBColumn,DuckDBColumn-method",
        "Ops,DuckDBColumn,missing-method",
        "paste,DuckDBColumn-method",
        "paste2,character,DuckDBColumn-method",
        "paste2,DuckDBColumn,character-method",
        "paste2,DuckDBColumn,DuckDBColumn-method",
        "pmax,DuckDBColumn-method",
        "pmin,DuckDBColumn-method",
        "quantile.DuckDBColumn",
        "sd,DuckDBColumn-method",
        "sql_call,DuckDBColumn-method",
        "sql_fun,DuckDBColumn-method",
        "startsWith,DuckDBColumn-method",
        "sub,ANY,ANY,DuckDBColumn-method",
        "substr,DuckDBColumn-method",
        "substring,DuckDBColumn-method",
        "Summary,DuckDBColumn-method",
        "table,DuckDBColumn-method",
        "tolower,DuckDBColumn-method",
        "toupper,DuckDBColumn-method",
        "unique,DuckDBColumn-method",
        "var,DuckDBColumn,ANY-method"
      ]
    },
    {
      "page": "DuckDBConnection",
      "title": "Acquire and Release the DuckDB Connection",
      "topics": [
        "acquireDuckDBConn",
        "configureCloud",
        "configureOutOfCore",
        "DuckDBConnection",
        "loadExtension",
        "releaseDuckDBConn"
      ]
    },
    {
      "page": "DuckDBDataFrame-class",
      "title": "DuckDBDataFrame objects",
      "topics": [
        "as.data.frame,DuckDBDataFrame-method",
        "as.matrix,DuckDBDataFrame-method",
        "cbind,DuckDBDataFrame-method",
        "cbind.DuckDBDataFrame",
        "coerce,DuckDBDataFrame,DFrame-method",
        "colnames<-,DuckDBDataFrame-method",
        "DuckDBDataFrame",
        "DuckDBDataFrame-class",
        "length,DuckDBDataFrame-method",
        "makeNakedCharacterMatrixForDisplay,DuckDBDataFrame-method",
        "names,DuckDBDataFrame-method",
        "names<-,DuckDBDataFrame-method",
        "normalizeSingleBracketReplacementValue,DuckDBDataFrame-method",
        "realize,DuckDBDataFrame-method",
        "replaceCOLS,DuckDBDataFrame-method",
        "replaceROWS,DuckDBDataFrame-method",
        "rownames<-,DuckDBDataFrame-method",
        "show,DuckDBDataFrame-method",
        "subset,DuckDBDataFrame-method",
        "[,DuckDBDataFrame,ANY,ANY,ANY-method",
        "[[,DuckDBDataFrame-method",
        "[[<-,DuckDBDataFrame-method"
      ]
    },
    {
      "page": "DuckDBDataFrameList-class",
      "title": "DuckDBDataFrameList objects",
      "topics": [
        "coerce,DuckDBDataFrameList,DFrameList-method",
        "colnames<-,DuckDBDataFrameList-method",
        "columnMetadata,DuckDBDataFrameList-method",
        "columnMetadata<-,DuckDBDataFrameList-method",
        "commonColnames,DuckDBDataFrameList-method",
        "dbconn,DuckDBDataFrameList-method",
        "dimtbls,DuckDBDataFrameList-method",
        "dimtbls<-,DuckDBDataFrameList-method",
        "DuckDBDataFrameList-class",
        "elementNROWS,DuckDBDataFrameList-method",
        "extractROWS,DuckDBDataFrameList,ANY-method",
        "getListElement,DuckDBDataFrameList-method",
        "head,DuckDBDataFrameList-method",
        "length,DuckDBDataFrameList-method",
        "names,DuckDBDataFrameList-method",
        "names<-,DuckDBDataFrameList-method",
        "ncols,DuckDBDataFrameList-method",
        "realize,DuckDBDataFrameList-method",
        "rownames<-,DuckDBDataFrameList-method",
        "split,DuckDBDataFrame,DuckDBColumn-method",
        "tail,DuckDBDataFrameList-method",
        "tblconn,DuckDBDataFrameList-method",
        "unlist,DuckDBDataFrameList-method"
      ]
    },
    {
      "page": "DuckDBEmbeddings-class",
      "title": "DuckDBEmbeddings objects",
      "topics": [
        "as.list,DuckDBEmbeddings-method",
        "as.matrix,DuckDBEmbeddings-method",
        "colnames,DuckDBEmbeddings-method",
        "colnames<-,DuckDBEmbeddings-method",
        "DuckDBEmbeddings-class",
        "extractCOLS,DuckDBEmbeddings-method",
        "ncol,DuckDBEmbeddings-method",
        "nrow,DuckDBEmbeddings-method",
        "realize,DuckDBEmbeddings-method",
        "rownames,DuckDBEmbeddings-method",
        "rownames<-,DuckDBEmbeddings-method",
        "show,DuckDBEmbeddings-method",
        "showAsCell,DuckDBEmbeddings-method",
        "[,DuckDBEmbeddings,ANY,ANY,ANY-method"
      ]
    },
    {
      "page": "DuckDBSelfHits-class",
      "title": "DuckDBSelfHits objects",
      "topics": [
        "as.data.frame,DuckDBSelfHits-method",
        "coerce,DuckDBSelfHits,DFrame-method",
        "coerce,DuckDBSelfHits,dgCMatrix-method",
        "coerce,DuckDBSelfHits,DuckDBDataFrame-method",
        "coerce,DuckDBSelfHits,SelfHits-method",
        "countLnodeHits,DuckDBSelfHits-method",
        "countRnodeHits,DuckDBSelfHits-method",
        "dbconn,DuckDBSelfHits-method",
        "dimtbls,DuckDBSelfHits-method",
        "dimtbls<-,DuckDBSelfHits-method",
        "DuckDBSelfHits",
        "DuckDBSelfHits-class",
        "elementMetadata,DuckDBSelfHits-method",
        "elementMetadata<-,DuckDBSelfHits-method",
        "extractNODES",
        "extractNODES,DuckDBSelfHits-method",
        "extractROWS,DuckDBSelfHits,ANY-method",
        "from,DuckDBSelfHits-method",
        "has_row_number,DuckDBSelfHits-method",
        "head,DuckDBSelfHits-method",
        "keycols,DuckDBSelfHits-method",
        "length,DuckDBSelfHits-method",
        "realize,DuckDBSelfHits-method",
        "show,DuckDBSelfHits-method",
        "tail,DuckDBSelfHits-method",
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        "ncol,DuckDBTable-method",
        "nrow,DuckDBTable-method",
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        "tail,DuckDBTable-method",
        "tblconn,DuckDBTable-method",
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      "page": "DuckDBTransposedDataFrame-class",
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        "dbconn,DuckDBTransposedDataFrame-method",
        "dimtbls,DuckDBTransposedDataFrame-method",
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      "page": "keynames",
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