Package: DuckDBArray 0.99.11

Patrick Aboyoun

DuckDBArray: DuckDB-Backed DelayedArray Implementation

Provides DuckDB-backed implementations of DelayedArray and DelayedMatrix classes for efficient, out-of-memory operations on large array and matrix datasets. The package includes DuckDBArray, DuckDBArraySeed, and DuckDBMatrix classes with optimized matrixStats methods. Supports sparse arrays, grid partitioning, and parallel processing for scalable genomic data analysis.

Authors:Patrick Aboyoun [aut, cre], Genentech, Inc. [cph]

DuckDBArray_0.99.11.tar.gz
DuckDBArray_0.99.11.zip(r-4.7-any)DuckDBArray_0.99.11.zip(r-4.6-any)DuckDBArray_0.99.11.zip(r-4.5-any)
DuckDBArray_0.99.11.tgz(r-4.6-any)DuckDBArray_0.99.11.tgz(r-4.5-any)
DuckDBArray_0.99.11.tar.gz(r-4.7-any)DuckDBArray_0.99.11.tar.gz(r-4.6-any)
DuckDBArray_0.99.11.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DuckDBArray/json (API)

# Install 'DuckDBArray' in R:
install.packages('DuckDBArray', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/genentech/duckdbarray/issues

On BioConductor:DuckDBArray-0.99.10(bioc 3.24)

dataimportdatarepresentationinfrastructuresoftware

6.31 score 1 packages 18 scripts 306 downloads 44 exports 41 dependencies

Last updated from:5ffeec68b8. Checks:8 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE192
linux-develNOTE446
source / vignettesOK278
linux-releaseNOTE448
macos-releaseNOTE374
macos-oldrelNOTE297
windows-develNOTE228
windows-releaseNOTE334
windows-oldrelNOTE301
wasm-releaseOK135

Exports:apermcoercecolCountscolMaxscolMeanscolMinscolNnzscolSdscolSumscolVarscreateDimTablesdbconnDelayedArraydimtblsdimtbls<-DuckDBArrayDuckDBArraySeedDuckDBMatrixextract_arrayextract_sparse_arrayis_nonzerois_sparseMathmatrixClassnzcountnzvalsOpsrowCountsrowDeviancesrowMaxsrowMeansrowMinsrowNnzsrowSdsrowSumsrowVarsscanKeycolsshowsweepttblconntypetype<-writeCoordArray

Dependencies:abindarrowassertthatBiocGenericsbitbit64blobclicpp11DBIdbplyrDelayedArraydplyrduckdbDuckDBDataFramegenericsglueIRangeslatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatspillarpkgconfigpurrrR6rlangS4ArraysS4VectorsSparseArraystringistringrtibbletidyrtidyselectutf8vctrswithrXVector

Introduction to DuckDBArray
Introduction | Installation | Quick start | Working with a DuckDBMatrix | Writing a matrix to the DuckDB backend | Sizing partitions for large or sparse writes | Subsetting | Matrix statistics | Sparse data | Lazy evaluation | Realizing large results in blocks | N-dimensional arrays | Introspecting a Parquet file you did not write | When to use DuckDBArray | Session information
Rendered fromDuckDBArray.Rmdusingknitr::rmarkdown

Last update: 2026-09-30
Started: 2026-07-06

Benchmarking DuckDBArray
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
Rendered fromDuckDBArray-comparison.Rmdusingknitr::rmarkdown

Last update: 2026-08-08
Started: 2026-01-24

Implementing the DuckDBArray backend
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
Rendered fromDuckDBArray-backend.Rmdusingknitr::rmarkdown

Last update: 2026-08-05
Started: 2026-07-06

Readme and manuals

Help Manual

Help pageTopics
Create Dimension Lookup TablescreateDimTables
DuckDBArray objectsaperm,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
DuckDBArray row / column summarization methodscolCounts,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
Common operations on DuckDBArray objects!,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
DuckDBArraySeed objectsaperm,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
DuckDBArraySeed row / column summarization methodscolCounts,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
Common operations on DuckDBArraySeed objects!,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
DuckDBMatrix objectsDuckDBMatrix DuckDBMatrix-class matrixClass,DuckDBArray-method [,DuckDBMatrix,ANY,ANY,ANY-method
DuckDBMatrix utility methods%*%,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
DuckDBTable row / column summarization methodscolCounts,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
Row-wise Deviance StatisticsrowDeviances rowDeviances,DelayedMatrix-method rowDeviances,dgCMatrix-method rowDeviances,DuckDBMatrix-method rowDeviances,matrix-method
Row and Column Non-Zero CountscolNnzs colNnzs,ANY-method colNnzs,DuckDBArray-method rowNnzs rowNnzs,ANY-method rowNnzs,DuckDBArray-method
Scan a Coordinate Parquet File for keycolsscanKeycols
Write an Array-Like Object in Coordinate FormatwriteCoordArray writeCoordArray,ANY-method writeCoordArray,DuckDBArray-method