0.20.0

Release 0.20.0 of the R package builds against TileDB 2.16.0, and has been tested against earlier releases as well as the development version.

Entries from the NEWS.md file follow.

tilebd 0.20.0

• This release of the R package builds against TileDB 2.16.0, and has also been tested against earlier releases as well as the development version (#551, #559, #563)

Improvements

• The startup message is now reformated across two shorter lines (#545)

• Support for returning 'Arrow Table' objects has been added (#548)

• Use of TileDB Embedded was upgraded to release 2.15.3 (#551)

• Date columns can now be exported to Arrow as well (#554)

• Array writes which set timestamps now take advantage of the new temporal policy API (#558)

• Displaying a schema is now more readable with additional linebreaks (#560)

• Attempts to select on dimensions that do not exist now error out with a message (#561)

• Integer64 values can now be written to array metadata (#564)

• Date and POSIXct attributes are now supported in query conditions (#568)

Bug Fixes

• Consolidation and vacuum calls now reflect the state of the global context object (#547)

• Pointers to 'Arrow Table' objects representing the table columns are now in external pointers too (#550)

• The documentation for 'Dimensions' was corrected in two spots in its wording / grammar (#552)

Build and Test Systems

• 'sudo' mode is reenabled for package 'bspm' used in the continuous integration at GitHub Actions (#549)

• Compilation on Linux systems as old as Ubuntu 18.04 without a filesystem header is now possible (#556)

Deprecations

• The boolean arguments as.data.frame, as.matrix and as.array to the tiledb_array() accessor are deprecated in favor of the more general return_as="..." form. (#567)

Removals

• The timestamp argument to tiledb_array, deprecated in favor of timestamp_end (and timestamp_start) in July 2021, has been removed (#566).

0.19.1

Release 0.19.1 of the R package builds against TileDB 2.15.2, and has been tested against earlier releases as well as the development version.

Entries from the NEWS.md file follow.

tiledb 0.19.1

• This release of the R package builds against TileDB 2.15.2, and has also been tested against earlier releases as well as the development
  version (#534, #541).

Improvements

• Query conditions can now be expressed for attributes of type UTF-8 (#529)

• The startup message now displays the operating system and version (#532)

• Use of TileDB Embedded was upgraded to release 2.15.1 and 2.15.2 (#534, #541)

• Group objects can be opened while supplying a Config object when 2.15.1 or newer is used (#535, #536)

• For character column buffer allocations, the R function now accepts a nullable option (#537)

• For standard buffer allocations, the R function now accepts nullable and varnum options (#538)

• Query conditions can now be expressed on boolean attributes (#540)

Build and Test Systems

• Testing for Groups reflect the stricter behavior in config setting requiring a close array (#530)

• The use of binary packages in continuous integration has been made a little more robust (#531)

• A small subset of tests are skipped if testing against the older release 2.14.* (#542)

0.19.0

Release 0.19.0 of the R package builds against TileDB 2.15.0, and has been tested against earlier releases as well as the development version.

Entried from the NEWS.md follow.

tiledb 0.19.0

• This release of the R package builds against TileDB 2.15.0, and has also been tested against earlier releases as well as the development
  version (#516, #521).

Breaking Changes

• The validity map coding of nullable strings has been corrected: validity map values of one are now interpreted as valid/non-null for full compatibility with other TileDB projects. Previously written arrays with nullable strings can be read by setting the config option r.legacy_validity_mode to true; the option also permits to write to an older installation. A conversion helper script is provided in scripts/legacy_validity_convert.r. (#517)

Improvements

• Attributes can now be created, written and read from in (explicit) UTF8 types (and CHAR and ASCII already behaved correctly with respect to utf8 data) (#510)

• Compilation under clang++ no longer complains about two unused member variables (#512)

• Query conditions for character columns can now be expressed using the %in% operator and a vector of values (#513)

• Use of TileDB Embedded was upgraded to releases 2.14.1 and 2.15.0 (#516, #521)

• Safer checking of NAs in tiledb_config() to support R 4.2 conditional lengths (#519)

• Query conditions can now be combined using & and | (in addition to && and ||) (#526)

Bug Fixes

• The access to JSON-formatted performance statistics has been simplified (#514)

Build and Test Systems

• The TileDB Embedded version is now used to determine whether a dampener is needed for the deprecation warning (#511)

• One of the test data sets included with #517 has been regenerated under an older TileDB version in order to test on more systems (#523)

• Documentation for Metadata accessors no longer states URIs strings are accepted (#527)

Deprecations

Removals

0.18.0

Release 0.18.0 of the R package builds against TileDB 2.14.0, and has been tested against earlier releases as well as the development version.

Entries from the NEWS.md file follow.

tiledb 0.18.0

• This release of the R package builds against TileDB 2.14.0, and has also been tested against earlier releases as well as the development version (#502).

Improvements

• Use of TileDB Embedded was upgraded to release 2.14.0 (#505)

Bug Fixes

Build and Test Systems

• The nightly valgrind job matrix was updated to releases 2.13 and 2.14 as well as the branch (#504)

• The nightly valgrind job show the most recent commit sha1 after updating from release branches (#507)

• A query condition test for utf8 attributes has been added (#507, #508)

Deprecations

Removals

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)