0.17.1

Release 0.17.1 of the R package builds against TileDB 2.13.1, and has been tested against earlier releases as well as the development version.

Entries from the NEWS.md file follow.

tiledb 0.17.1

• This release of the R package builds against TileDB 2.13.1, and has also been tested against earlier releases as well as the development version (#502).

Improvements

• Support for Subarrays to set ranges has been extended (#496)

• Deprecated Core API functions for Array access and range setting are longer used (#496)

• TileDB Group objects now have a default show() method (#498, #499)

• Domain and tile sizes for int64 dimension objects are now internally converted (#500)

• Use of TileDB Embedded was upgraded to release 2.13.1 (#501)

Bug Fixes

• Fragment info domain getters now work with ASCII domains (#495)

• The scale filter option setting was corrected to use the proper types (#503)

Build and Test Systems

• The nightly valgrind job setup was updated to include two new dependencies (#493)

• The Windows setup for continuous integration was updated (#494)

Deprecations

• Functions libtiledb_query_add_range{,_with_type} relying on depecreated Core
  functionality are deprecated, and will be removed with the Core functions.
  Subarray range setters are available. This is a mostly internal change.

Removals

• Functions libtiledb_query_set_coordinates() and libtiledb_coords()
  which have been deprecated since June 2000 have been removed. (#497)

0.17.0

Release 0.17.0 of the R package builds against TileDB 2.13.0, and has been tested against earlier releases as well as the development version.

Entries from the NEWS.md file follow.

tiledb 0.17.0

• This release of the R package builds against TileDB 2.13.0, and has also been tested against earlier releases as well as the development version (#492).

Improvements

• Support for testing group URIs on being relative has been added (#478)

• Logging support at the R and C++ level has been added (#479, #487, #489)

• Use of TileDB Embedded was upgraded to release 2.12.1, and 2.12.2 (#480, #481)

• Sparse array queries via tiledb_array and '[]' access use an UNORDERED query layout (#488)

• Use of TileDB Embedded was upgraded to release 2.13.0 (#490)

• Support for selecting dimensions by discrete points has been added (#491)

Bug Fixes

• Accomodate possible zero sized allocation estimates for attributes (#482)

• Detect missing columns in a write-attempt with partial data (#483)

Build and Test Systems

• Update check-out action to version three suppressing a warning (#477)

• Code Coverage reports are now generated and available at codecov.io (#484)

• Small internal changes renaming two files and conditioning tests under two older releases (#485)

0.16.0

Release 0.16.0 of the R package builds against TileDB 2.12.0, and has been tested against earlier releases as well as the development version.

Entries from the NEWS.md file follow.

tiledb 0.16.0

Improvements

• Several deprecated API entry points of TileDB Embedded are no longer used (#452, #453)

• Support for DELETE queries has been added (requires TileDB Embedded 2.12.0 or later) (#455, #456)

• Use of TileDB Embedded was upgraded to release 2.11.1, 2.11.2, and 2.11.3 (#460, #466, #474)

• Support for XOR filters has been added (#472)

• Support for deletion of fragments has been added (#473)

Bug Fixes

• Treatment of character columns with missing values has been corrected (#454)

• Accessing encrypted arrays has been reverted to the older API accessors (#458)

• Int64 domain values in excess of int range are now expressed as integer64 objects (#465)

Build and Test Systems

• Sparse matrix conversion used mainly in tests have been updated for version 1.4-2 of the Matrix packages (#457)

• Support builds on the riskv64 platform by adding a missing link instruction (#459)

• The test setup was tweaked to not trigger a spurious valgrind report from libcrypto (#461)

• The test setup was tweaked to make a group comparison more resilient to ordering (#462)

• The test setup was refined for two filter tests (#467, #468)

• A parameterized test for the SCALE_FLOAT filter has been added (#469)

• The test setup ensures that the per-session directory remains accessible (#470)

• Continuous integration testing for Linux and macOS has been moved to GitHub Actions (#471)

0.15.0

Release 0.15.0 of the R package builds against TileDB 2.11.0, and has been tested against earlier releases as well as the development version.

Entries from the NEWS.md file follow.

tiledb 0.15.0

• This release of the R package builds against TileDB 2.11.0, and has also been tested against earlier releases as well as the development version.

Improvements

• Support for query conditions has been extended to dense arrays (#447)

• Support for filter lists has extended to both the data.frame helper and the dimension object constructor (#448)

• Use of TileDB Embedded was upgraded to release 2.11.0 (#449)

Bug Fixes

• Small enhancements have been made to the test suite (#450)

Build and Test Systems

• A small enhancement was made to the test system (#450)

0.14.1

Release 0.14.0 of the R package builds against TileDB 2.10.2, and has been tested against earlier releases as well as the development version.

Entries from the NEWS.md file follow

tiledb 0.14.1

• This release of the R package builds against TileDB 2.10.2, and has also been tested against earlier releases as well as the development version.

Improvements

• Use of TileDB Embedded was upgraded to release 2.10.2 (#443) following an earlier update to 2.10.1 (#434)

• List columns are now supported in reading and writing of data frames by extending cell variable numbers beyond one (#438, #440)

• Query condition support has been extended to more data types (#441)

• The 'SCALE_FLOAT' filter for compression of floating-point attributes is now supported (with TileDB 2.11 or later) (#445)

Bug Fixes

• Unit tests were refined with some additional conditioning on envuironment variable CI being present (#436)

• An unnessary final argument has been dropped from a 'remove member' method (#437)

Build and Test Systems

• The nightly valgrind check was updated to Ubuntu 22.04 (#435, #439, #442)

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)