0.14.0

Release 0.14.0 of the R package builds against TileDB 2.10.0, and has been tested against earlier releases as well as the development version.

Entries from the NEWS.md file follow

tiledb 0.14.0

• This release of the R package builds against TileDB 2.10.0, and has also been tested against earlier releases as well as the development version.

Improvements

• Use of TileDB Embedded was upgraded to release 2.10.0 (#432) following earlier updates to 2.9.1 (#415), 2.9.2 (#419), 2.9.3 (#422), 2.9.4 (#427) and 2.9.5 (#430)

• The BOOL data type is now supported (#416)

• Query conditions support was extended with support for an OR operator (#417)

• An incomplete query result is now signaled via a warning message (#420)

• A helper function was added to check if an Array is open (#421)

• Batched queries are now supported given the user the possibility to process larger-than-memory result sets in parts (#429)

• Some internal object creation code was refactored (#431)

Bug Fixes

• The attr setter for Attributes was corrected to support NA settings (#425)

Build and Test Systems

• Filter compression tests are skipped on systems lacking AVX2 support (#418)

• The build system now checks for C++17 support (#424)

• The valgrind test was upgraded to release 2.9.3 and the 2.10 release branch (#426)

• Tests for overlapping ranges have been added (#428)

0.13.0

Release 0.13.0 of the R package builds against TileDB 2.9.0, and has been tested against earlier releases as well as the development version.

Entries from the NEWS.md file follow

tiledb 0.13.0

• This release of the R package builds against TileDB 2.9.0, and has also been tested against earlier releases as well as the development version.

Improvements

• Support for groups has been added for TileDB 2.8 or later (#404)

• The group member name retrieval can now also return the optional group member name (#399)

• Allocation and creation of large string vector buffers was refactored (#400)

• Support for dictionary encoding compression filters has been added for TileDB 2.9 or later (#404)

• Support for Filestore functionality has been added for TileDB 2.9 or later (#410)

• Support for BLOB datatypes has been added for TileDB 2.7 or later (#411)

• Use of TileDB Embedded was upgraded to release 2.9.0 (#413) following earlier updates to 2.8.1 (#401), 2.8.2 (#403), 2.8.3 (#408)

Bug Fixes

• Tests for filters have been made more robust (#407, #412)

Deprecations

• The check() function is now deprecated and schema_check() is provided (#409)

Build and Test Systems

• Nightly valgrind checks were updated to use current versions (#397, #402)

• Following release of R 4.2.0, only ucrt builds are supported on Windows (#405)

0.12.0

Release 0.12.0 of the R package builds against TileDB 2.8.0, and has been tested against earlier releases as well as the development version.

Entries from the NEWS.md file follow

tiledb 0.12.0

Improvements

• A schedule nightly continuous action now checks current and release-candidate branches of TileDB with the R package under valgrind (#387)

• Support for Groups was added (#388, #392, #395)

• All external pointers are now tagged and validated at compile- and run-time (#389)

• A now-redundant group-creation method has been removed (#391)

• Unit tests for group member addition were added and updated (#393)

• Group members can also be added or removed by name (#395)

• Use of TileDB Embedded was upgraded to release 2.8.0 (#396) following an earlier upgrades to 2.7.0 (#372) and 2.7.1 (#384)

Bug Fixes

• The detection of TileDB headers and library is now more robust for cases where pkg-config is present but does not know about TileDB (#385)

• The package documentation website was updated (#386)

• A fallback was added for external pointer creation to support compilation without group support in TileDB Embedded (#390)

• An incorrectly specified function call was corrected (#392)

• The templated initialization for external pointer is now inlined to satisfy all compilers (#394)

0.11.1

Release 0.11.1 of the TileDB R package supports TileDB Embedded 2.6.1 (or earlier versions, as well as the dev version).

Entries from the NEWS.md file follow:

tiledb 0.11.1

• This release of the R package builds against TileDB 2.6.4, but has also been tested against earlier releases, and the development version.

Improvements

• Use of TileDB Embedded was upgraded to release 2.6.4 (#384) following an earlier upgrade to 2.6.2 (#359)

• Creations of arrays from data.frame objects now supports a mode= argument with values 'ingest', 'schema_only', and 'append' (#360)

• Some unit test and continuous integration code was refactored (#364, #375)

• Finalizer use is now simplified taking advantage of an Rcpp change (#366)

• A new option strings\_as\_factors was added for data.frame retrieval (#367)

• The arrow C-level interface now uses external pointer objects following Arrow 7.0 (#368)

• Support for memory limits has been extended, and partial reads are using with iterations to complete (#371)

• Fragment info reading now account for the __fragments object (#373)

• A nightly test under valgrind has been added; results are reported to slack (#382, #383)

• UTF-8 string in metadata are now supported (#377)

• Attribute-less arrays can now be created, written, and read (#378), also via higher-level accessors (#379)

• A plugin for Rcpp has been added (#380)

Bug Fixes

• Array status is now checked before closing (#362)

• Signed and unsigned int64 dimensions are now mapped correctly from 'square-bracket indexing', and the third dimension is recognised (#365)

• Domain information could overflow int64_t if an unsigned value was used, this now flips to double (#370)

• Unit tests for consolidation and vacuuming were update to account for __fragments too (#374)

• A unit test was corrected to ensure logical expressions are of length one (#381)

Documentation

• A new vignette on data ingestion has been added (#357)

• A new vignette on installation options has been added (#358)

• The vignettes are now built using package simplermarkdown (#361)

• Help pages were polished (#369)

Deprecations

• The tiledb_dense and tiledb_sparse functions which were deprecated in February 2021 have been removed after a twelve-month grace period.

0.11.0

Release 0.11.1 of the TileDB R package supports TileDB Embedded 2.6.1 (or earlier versions, as well as the dev version).

Entries from the NEWS.md file follow:

tiledb 0.11.0

• This release of the R package builds against TileDB 2.6.1, but has also been tested against previous releases, and the development version.

Improvements

• Use of TileDB Embedded was upgraded to release 2.6.1 (#354) following an earlier upgrade to 2.6.0 (#340)

• A cell value getter for dimension was added (#341)

• Getter and setter functions for validity filter lists have been added (#349)

• Memory budget use has been refined via a configurable budget setting (#346, #350)

• A context getter function was added for query objects (#351)

• The schema display functionality was refactored and extended (#342, #343, #344, #345, #352, #355)

• Use of TILEDB_CHAR is deprecated in favor of TILEDB_STRING_ASCII (#353)

Bug Fixes

• A .nojekyll file was added to prevent unnecessary GitHub Pages builds (#339)

• A getter for fill values is only called with TileDB 2.1.0 or later (#347)

• GitHub Actions on Windows no longer install qpdf which was never used (#348)

0.10.2

Release 0.10.2 of the TileDB R package supports TileDB Embedded 2.5.3 (or earlier, as well as the dev version).

Entries from the NEWS.md file follow:

tiledb 0.10.2

• This release of the R package builds against TileDB 2.5.3, but has been tested against previous releases, and the development version.

Improvements

• The stopifnot() assertions now use consistent error messages across all functions (#331)

• A helper function matching TileDB data types to R types is now exported (#336)

Bug Fixes

• The boolean variable for 'nullable' is now set with a default value (#329)

• A test for accessing shared memory segements is now correctly checking for TileDB 2.6.0 (#332)

0.10.1

Release 0.10.1 of the TileDB R packages supports TileDB Embedded 2.5.2 (or earlier, as well as the dev version).

Entries from the NEWS.md file follow:

tiledb 0.10.1

• This release of the R package builds against TileDB 2.5.2, but has been tested against previous releases, and the development version.

Improvements

• An accessor for the most-recent error message string has been added (#327)

Bug Fixes

• On Linux, if a pre-made TileDB Embedded library is used, lack of AVX2 instructions is now detected and a suitable build is deployed (#328)

0.10.0

Release 0.10.0 of the TileDB R packages supports TileDB Embedded 2.5.1 (or earlier, as well as the dev version).

Entries from the NEWS.md file follow:

tiledb 0.10.0

• This release of the R package builds against TileDB 2.5.1, but has been tested against previous releases, and the development version.

Improvements

• CI tests were expanded to also test refactored TileDB Embedded readers (#310), and now deactivated as this is now part of release 2.5.0 (#321)

• The minimal version of TileDB Embedded that can be used with the R package is now release 2.0.0 (#313)

• The package now compiles using the C++17 standard just like TileDB Embedded (#314)

• Shared-memory interprocess communication is used to accelerate operation for TileDB Cloud (#316)

• The long-deprecated max_element_size function has been removed from TileDB Embedded, and the R interface was updated accordingly (#317, #319)

• The extended toggle and field for tiledb_array() can now select dimension-less returns from sparse arrays (#318)

• Use of TileDB Embedded was upgraded to release 2.5.0 (#321) following earlier upgrades to 2.4.2 and 2.4.3 (#308, #312)

• A new quickstart example using the 'memory filesystem' was added, and one another example updated (#323)

Bug Fixes

• Tests for time-traveling were refactored and now in a separate test file (#311)

• Read-queries no longer call finalize() required only on write-queries (#309)

• Some examples were updated with copy/paste corrections (#317)

• Single-column data.frame returns work via drop=FALSE where needed (#320)

0.9.7

Release 0.9.7 of the TileDB R package supports TileDB Embedded 2.4.0 (or earlier, or later; tested with dev, 2.3.4, 2.2.9, 2.1.6 and 2.0.8)

Entries from the NEWS.md file follow:

tiledb 0.9.7

• This release of the R package builds against TileDB 2.4.0, but has been tested against previous releases and the development version.

Improvements

• Accessors for context and query statistics were added (returning easily parseable JSON strings) (#293).

• Initial support for schema evolution was added to add or drop attributes (#294).

• Use of TileDB Embedded was upgraded to release 2.4.0 (#295)

• Windows builds under GitHub Actions now also include the newer UCRT variant (#296).

• The internal memory allocation has been switched to set_{data,offset,validity}_buffer functions (#297).

• A convenience accessor for schema information retrieving 'dimension' or 'attribute' status has been added (#299).

• The default array type fromDataFrame has been change to sparse to match some optimizations in TileDB Embedded, some unit tests have been updated accordingly (#300).

• TileDB arrays can now be queried in expression using pipes (for row-wise filtering and colunb-wise selection) (#301).

• When matrices as well as sparse matrices are written to arrays, optional row and column names are now supported as well (#303, #304).

• The configure script was update to the standards of autoconf 2.69 as requested by CRAN (#305).

Bug Fixes

• Use of set_{data,offset,validity}_buffer is made conditional on TileDB 2.4.0 or later to continue builds on older versions (#298).

• Tests of piped expressions have been rewritten to be compatible with R versions earlier than 4.1.0 (#302).

• A dangling documentation link in README.md was corrected, and another removed (#306).

0.9.6

Release 0.9.6 of of the TileDB R package supportTileDB Embedded version 2.3.4 (or earlier or later: tested with dev, 2.2.9, 2.1.6, 2.0.8)

Entries from the NEWS.md file follow:

tiledb 0.9.6

• This release of the R package builds against TileDB 2.3.4, but has been tested against previous releases and the development version.

Improvements

• When retrieving results via the [ operator, incomplete queries generate a warning (#283)

• The interface to query element size of queries was extended (#282)

• If query ends as 'incomplete', a warning is now issue (#283)

• The status of the preceding query can now be accessed also when using a higher-level wrapper (#285)

• Fragment Information can be accessed via high-level accessor functions (#286)

• A preference for data type as which TileDB array data is returned can be set (#288)

• Continuous Integration will use increased test coverage by installing more optional package (#289)

• Use of TileDB Embedded was upgraded to release 2.3.4 (#290)

Bug Fixes

• One cast statement was corrected so a warning is no longer triggered from clang (#281)

• Some added unit tests were not conditional on TileDB Embedded 2.2.* or later (#284)

• A time-comparison unit test did not properly respect timezones which was corrected (#287)