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Changelog

Source: NEWS.md

dbMatrix 0.0.0.9126 (2026-01-13)

Bug fixes

  • Update pkgdown workflow to include additional R packages and refs.

  • Prevent NAs in show method by handling max.print truncation.

  • Handle negative and out-of-order indexing.

  • Require explicit opt-in for sparse-to-dense conversion.

  • Cast comparison operators to numeric for type safety.

  • Use direct slot access in transpose method.

  • Conditionally check overwrite for dbMatrix creation.

  • Improve verbosity messages and remove redundant logging in dbMatrix functions.

Features

  • Support transposed precompute tables.

  • Add streaming SVD for dbSparseMatrix including fallback to BPCells::svds() for LTM data.

  • Add Math SQL translations for log1p(), ln() and log() functions.

  • Add is.na() method.

Performance

  • Optimize dimname indexing with factors and match() (dimname-returning functions return characters as expected).

Refactoring

  • Use temp tables and inline SQL (small queries still use inline SQL; otherwise register a temp table to avoid large string parsing bottlenecks).

  • Centralize internal type-check functions in dbProject.

  • Simplify summary methods to always return vectors.

  • Rename dbVector internals and add column-wise recycling.

  • Improve as.matrix() and compute() for dbMatrix.

Documentation

  • Untrack docs/ folder.

  • Consolidate class documentation and update vignettes.

Chore

  • Update build config and move package data to inst/extdata.

  • Update package metadata and dependencies.

  • Update roxygen.

  • Update .gitignore to exclude compiled artifacts.

Code style

  • Reformat with air.

Testing

  • Tidy up tests and update to reflect recent code changes.

dbMatrix 0.0.0.9125 (2025-12-04)

Bug fixes

  • Ensure as.matrix returns unnamed matrix when names=FALSE.

  • Update show methods to handle duplicate dimnames via index filtering.

  • Pkgdown errors.

  • Ensure rowVars/colVars preserve empty dimensions.

  • Make compute s3 and use CTAS instead.

Features

  • Optimize precompute with parquet and auto-attach existing tables.

  • Implement native ingestion for various Matrix classes via as.dbMatrix.

  • Add coercion methods for dbMatrix to matrix/Matrix objects.

  • Add .check_mem_limit internal function.

  • Support overwrite arg in compute.dbMatrix.

  • writeMM method for dbMatrix objects.

  • Add value_colName support to dbMatrix_from_tbl for pre-aggregated counts.

Chore

  • Update roxygen version.

  • Ignore benchmarks/ repo.

  • Update NAMESPACE with s3 exports.

Documentation

  • Tidy roxygen.

  • Tidy + update global options in dbMatrix.

  • Clean up roxygen comments & improve documentation formatting.

Code style

  • Tidy extract.R with air and jarl.

  • Tidy .R files with air and jarl.

Refactoring

  • Delegate dbMatrix construction to as.dbMatrix generic for native R matrix ingestion.

  • Clean up Math Summary ops so to use subqueries and R zero inflation.

Performance

  • Optimize sparse –> matrix conversion.

  • Improve mem safety of as.matrix for dense matrix conversions.

  • Use head/tail filter pushdown in show method for dbMatrix objects.

  • Improve extract by using duckdb_register for large indices.

  • Optimize arith helpers with lazy queries instead of generating views.

Testing

  • Add tests for compute.

dbMatrix 0.0.0.9124 (2025-10-14)

Breaking Changes

  • Renamed load() to dbLoad(): The load method has been renamed to dbLoad to avoid masking base::load(). Generic moved to dbProject package for consistency across dbverse.

Refactoring

  • S4 to S3 Method Conversion: Converted rownames(), colnames(), nrow(), ncol(), and their setters from S4 to S3 methods for simpler dispatch. Only %in% remains S4 (requires double dispatch). This significantly reduces package load messages.

  • Internal Function Cleanup:

    • Converted castNumeric from S4 generic to internal function .castNumeric()
    • Renamed temporary tables to use _tmp prefix in row/column summary methods for consistency
    • Moved dbList generic to dbProject package

Bug Fixes

  • Arrow Filter Pushdown Error: Fixed “Arrow table filter pushdown optional: new_i IN (…) not supported yet” error by replacing arrow::to_duckdb() with inline SQL for extract operations.
  • Fixed .mtx file reader header detection logic.

Chore

  • Applied consistent code formatting across the package.

dbMatrix 0.0.0.9123 (2025-10-07)

Features

  • dbProject Integration: Full integration with dbProject package and dbData base class architecture. dbMatrix now inherits from dbData providing unified database-backed object interface across dbverse ecosystem.

  • Statistical Methods: Added rowSds(), colSds(), rowVars(), and colVars() methods for both dbDenseMatrix and dbSparseMatrix.

  • dbVector Support: Internal support for dbVector arithmetic operations.

Chore

  • Migrated repository to dbverse-org organization from previous location.
  • Updated all URLs and links to reflect new dbverse-org organization structure.
  • Required DuckDB >= 1.4.0 (LTS) for improved stability.
  • Updated documentation with markdown formatting improvements.
  • Added cli to imports for better user messaging.

Docs

  • Added S4 class documentation to pkgdown reference index (dbMatrix-class, dbDenseMatrix-class, dbSparseMatrix-class).
  • Updated vignettes to include memory and names parameters for summary functions.
  • Improved roxygen documentation for compute(), as.matrix(), and arithmetic operations.
  • Enhanced documentation for dbProject integration and dbData inheritance.

Bug Fixes

  • Eliminated ORDER BY Warnings: Fixed ORDER BY warnings by removing arrange() from lazy evaluation paths in summary methods. Now only applies ordering when materializing results to memory.
  • Fixed sim_dgc() function to use correct number of random values (rnorm(n_vals) instead of rnorm(num_cols)), eliminating “number of items to replace” warnings.
  • Removed deprecated context() call in test files (testthat 3rd edition).
  • Fixed to_view() calls to pass tbl objects instead of dbMatrix objects to dbProject functions.
  • Imported dbProject generics properly to avoid namespace conflicts.
  • Added init slot to dbMatrix class definition.
  • Removed redundant export for t() method.
  • Fixed names() method to return NULL for regular matrices instead of throwing errors.
  • Corrected name attribute assignment in Ops() method for dbMatrix.
  • Improved connection handling in internal get_con() function.
  • Removed dbReconnect() method from generics (moved to dbProject/dbData).
  • Refactored extract methods - functionality now comes from dbProject::dbData base class.
  • Exported dbMatrix class properly in NAMESPACE.
  • Fixed DESCRIPTION dependencies: removed duplicate dbProject from Suggests, added proper Remotes reference.

dbMatrix 0.0.0.9023 (2024-09-18)

Breaking Changes

  • dbMatrix summary methods now return dbDenseMatrix objects instead of in-memory vectors.

  • Removed colTypes from castNumeric.

  • Removed @name check in initialize.

Features

  • New compute method for saving dbMatrix objects. This writes the dbMatrix object to a table in the database along with its row and column names (e.g. ‘dbMatrixname_rownames’).

  • New load method for loading computed dbMatrix objects. The dbMatrix::compute() method must be called before loading the object.

  • Updated .check_overwrite to allow for passing overwrite arg.

  • New internal function write_dimnames to enable saving dbMatrix objects.

  • New sum method for dbMatrix objects.

  • Improvements to precomputed table: Use existing precomputed table in db if available.

  • Improvements to precomputed table: Transpose precomputed table of sufficient dimensions if it exists instead of creating a new one. This is done via a TEMPORARY VIEW to avoid writing to disk and modifying existing precomputed table which may be referenced by other tables.

  • Custom SQL statement for todbDense conversion creates a TEMPORARY VIEW with name dbDenseMatrix_hash.

Chore

  • Update whitespace.

  • Update dbMatrix constructor roxygen.

  • Update roxygen in toDbDense.

Docs

  • Update reference page.

  • Update mean documentation.

  • Update log documentation.

  • Update roxygen.

Bug fixes

  • Do not recycle matrix if not needed.

dbMatrix 0.0.0.9022 (2024-08-14)

Breaking changes

Features

  • Add more tests for dbMatrix and dbDenseMatrix.

  • Add internal function map_ijx_dimnames.

  • Add internal function dbMatrix_from_tbl.

  • Extract now constructs unique temporary virtual tables in the arrow schema.

Chore

  • Document pkgdown website.

  • Add cli to imports.

  • Update generics.

Bug fixes

  • Be more explicit about non-supported Arith and Ops operations.

  • Fix show() method for dbDenseMatrix objects.

dbMatrix 0.0.0.9021 (2024-07-05)

Bug fixes

  • Improve show function for dbDenseMatrix.

  • Updated simulate functions to include overwrite param.

  • Update .check_overwrite() internal function to avoid bug in overwritting passed table.

dbMatrix 0.0.0.9020 (2024-07-05)

Features

  • Add initial support for reading in .mtx files and creating dbMatrix objects.

Bug fixes

  • Update check_overwrite input validation

Chore

  • Update Royxgen

dbMatrix 0.0.0.9019 (2024-03-18)

Features

  • Add new precompute function to speed up matrix densification.

  • Add new show function for dbDenseMatrix with pretty color and better spacing.

  • Add new save function to save a dbMatrix.

  • Add new input validation functions.

Chore

  • Update docs.

  • Update imports to include glue, bit64 and crayon.

dbMatrix 0.0.0.9018 (2024-02-12)

Bug fixes

  • Update constructor calls in sim functions.

  • Remove redundant con from constructor.

  • Remove db_path from constructor.

  • Constructor db_path arg change to con object.

Features

  • Add dgTMatrix to in-memory matrix types supported in dbMatrix constructor.

Chore

  • Set :memory: to default db_path in constructor.

  • Update createDBMatrix docs.

Documentation

  • Spacing.

  • Update after constructor fix.

  • Remove :temp: in place of :memory:.

dbMatrix 0.0.0.9017 (2024-02-07)

Bug fixes

  • Remove “:temp:” from tests.

  • Replace ‘:temp:’ with ‘:memory:’.

  • Add matrix in addition to dgCMatrix in as_ijx().

Features

  • Add unit tests for scalar arith.

  • Add unit tests for names.R.

Chore

  • Remove random browser() call.

  • Add MatrixGenerics to deps.

  • Update gitignore.

dbMatrix 0.0.0.9016 (2024-01-23)

Features

  • Add boolean indexing tests to test-extract.R.

  • Add as_ijx() convenience function.

  • Update createDBMatrix() to use dplyr::copy_to().

  • Update as_matrix() convenience function.

  • Add unit tests for extract methods.

dbMatrix 0.0.0.9015 (2024-01-22)

Features

  • Add log().

  • Update toDbDense to use dplyr instead of SQL.

Chore

  • Update DESCRIPTION to include testthat.

  • Update docs.

dbMatrix 0.0.0.9014 (2024-01-19)

Features

  • update dbIndex superclass

  • update as_matrix()

dbMatrix 0.0.0.9013 (2024-01-18)

Bug fixes

  • Rename and update dbIndex superclass to fix indexing bugs.

Features

  • Add experimental as_matrix() convenience function.

Chore

  • Update docs.

  • Migrate site link to drieslab.

  • Move {Matrix} to Imports.

Documentation

  • Update overview.Rmd.

  • Update operations vignette.

dbMatrix 0.0.0.9012 (2023-12-08)

Bug fixes

  • Only densify if necessary. != 0, +/-.

  • toDbDense() previously updated table by value. change to update by reference via VIEW creation of table named ‘dense’.

Features

  • Add dbListTables().

Chore

  • Update docs.

  • Update gitignore.

dbMatrix 0.0.0.9011 (2023-12-08)

Bug fixes

  • Fix incorrect aggregate operations.

  • Fixes after con slot removal.

Features

  • Add get_con().

  • Add dbDisconnect() generic.

  • Update accessors.

Chore

  • Update vignettes.

  • Update README.

  • Update gitignore.

  • Update docs.

  • Update NEWS.

dbMatrix 0.0.0.9010 (2023-11-25)

Breaking changes

  • migrate to |> pipe, remove %>%, update deps.

Chore

  • Update docs.

dbMatrix 0.0.0.9009 (2023-11-20)

Bug fixes

  • Mean generic for dbDenseMatrix.

Chore

  • Update docs.

  • Update site.

  • Update gitignore.

dbMatrix 0.0.0.9008 (2023-11-17)

Bug fixes

  • Updates to dbSparseMatrix rowMeans, colMeans.

  • Updates to colSums and rowSums for dbSparseMatrix.

  • Update dbMatrix constructor dimnames issues.

Chore

  • Update DESCRIPTION, remove redundant Matrix import, dep.

  • Update docs.

  • Update roxygen for operations.

dbMatrix 0.0.0.9007 (2023-11-09)

Features

  • Add Matrix as dep.

dbMatrix 0.0.0.9006 (2023-11-09)

Bug fixes

  • Methods::as scope correction.

Features

  • Add methods to deps.

Chore

  • Update .gitignore.

dbMatrix 0.0.0.9005 (2023-11-09)

Feat

  • Add Matrix as pkg dep

dbMatrix 0.0.0.9004 (2023-11-09)

Bug fixes

  • Missing Matrix:: scope call.

Chore

  • Update docs.

dbMatrix 0.0.0.9003 (2023-11-07)

Fix

  • dims and dim_names in createDBMatrix() retained from in-memory matrix or Matrix object

Chore

  • Update docs for dbMatrix input checks

dbMatrix 0.0.0.9002 (2023-11-07)

Feat

  • Specify checks for ‘name’ param in createDBMatrix()

Chore

  • Update docs.

  • Add docs.

dbMatrix 0.0.0.9001 (2023-11-04)

Chore

  • Update docs and DESCRIPTION.

  • Migration dbMatrix.