Changes in version 0.34.0 - This release of the R package builds against TileDB 2.30.0, and has also been tested against earlier releases as well as the development version Improvements - Add support for creating, loading, saving, and removing Profiles (#856) Changes in version 0.33.1 - This release of the R package builds against TileDB 2.29.1, and has also been tested against earlier releases as well as the development version Bug Fixes - The factor levels are now remapped as expected when updating an array with values that include no additional factor levels (@cgiachalis in #844) - tiledb_array_open_at() now resets timestamp slots to before opening the array (@cgiachalis in #842) Changes in version 0.33.0 (2025-09-30) - This release of the R package builds against TileDB 2.29.0, and has also been tested against earlier releases as well as the development version Improvements - Schema-dump output is no longer truncated in the case that there are any null fill values in the schema (@johnkerl in #825) - tiledb_attr() now prints the attribute object as expected and documentation has been corrected (@cgiachalis in #823) - tiledb_attr() now works when setting ncells=NA to signal variable length (@johnkerl in #830) - tiledb_array() now emits the correct error message when using selected_points argument (@cgiachalis in #833) - tiledb_group_open() now respects and defaults to the first option in type argument (@cgiachalis in #838) - tiledb_config_unset() now correctly returns the modified configuration object (@cgiachalis in #841) Documentation - The package documentation website was updated (@cgiachalis in #822, #826) Changes in version 0.32.0 (2025-05-15) - Depend on TileDB Embedded 2.28.0 #820 Changes in version 0.31.1 (2025-04-24) - Allow parse_query_condition() to work on dimensions when an array is passed - Add tiledb_vfs_copy_dir(), a wrapper for the vfs_copy_dir() function - Print values for tiledb_schema_get_types() and tiledb_schema_get_names() #805 - Add tiledb_array_is_open_for_reading()/writing() #806 - Fix static-linking checks for R >= 4.5 Changes in version 0.31.0 - Update docs with correct S4 methods - Run clang-format on non-autogen C++ source code - Update unit tests to expect dense current domain - Support parentheses in query conditions - memory alloc: Accomodate zero buffer size estimate v2 - Apply styler::style_pkg() - Expose include/linking flags for re-using libtiledb in downstream packages - Use TileDB Core 2.27.0 Changes in version 0.30.2 (2024-10-04) - This release of the R package builds against TileDB 2.26.2, and has also been tested against earlier releases as well as the development version (#757) - Fix MacOS rpath (#760) - Fix "Can't read domain for dimensions of type UINT16" (#758) Changes in version 0.30.1 - This release of the R package builds against TileDB 2.26.1, and has also been tested against earlier releases as well as the development version (#757) Changes in version 0.30.0 (2024-09-11) - This release of the R package builds against TileDB 2.26.0, and has also been tested against earlier releases as well as the development version (#745, #749, #750, #754, #755) Improvements - Error messages displayed when a mismatched external pointer is detected now show both expected and encountered types (#740) - NDRectangle objects can now instantiate from more domain data types (#741, #742) - NDRectangle objects can now return their number of dimensions and dimension data types (#743) - FragmentInfo objects are dump via the << stringstream operator instead of a now-deprecated dump() method (#753) Documentation - The documentation website now uses favicon symbols for all pages rendered (#739) Build and Test Systems - The nighly valgrind matrix now includes release 2.26.0 (#744) - The continuous integration script has been updated reflecting external changes (#746) Removals - Boolean arguments as.data.frame, as.matrix and as.array to the tiledb_array() accessor, deprecated in release 0.20.0 in July 2023 in favor of the more general return_as="..." form, have been removed. (#751) Deprecation - As BioConductor package \pkg{TileDBArray} still relies on as.data.frame it was temporarily re-admitted as an argument. It is expected to be removed following the upcoming 3.20 release of BioConducto.r (#752) Changes in version 0.29.0 (2024-07-25) - This release of the R package builds against TileDB 2.25.0, and has also been tested against earlier releases as well as the development version (#728, #736) Improvements - Three deprecated calls to dump() methods for TileDB Embedded objects now use the preferred streaming alternatives (#727) - Two already deprecated functions that are removed in TileDB 2.26.0 are no longer used (#732) - The vendored nanoarrow has been updated to its release 0.5.0 (#733) - Fragments can now be removed by supplying a vector of fragment URIs (#734) - NDRectangle and CurrentDomain objects are supported (with 2.25.0 or newer) and can be used with ArraySchema and ArraySchemeEvolution domain of (#735, #737) Build and Test Systems - The nighly valgrind matrix now includes release 2.25.0 (#729) Changes in version 0.28.2 - This release of the R package builds against TileDB 2.24.2, and has also been tested against earlier releases as well as the development version (#725) Changes in version 0.28.1 - This release of the R package builds against TileDB 2.24.1, and has also been tested against earlier releases as well as the development version (#714, #715, #717, #724) Improvements - When creating arrays with fromDataFrame, start and/or end timestamps can now be specified (#719) Build and Test Systems - The nighly continuous integration matrix now included Core release 2.24.0 and 2.22.0 is dropped (#721) - The Conda build is now accomodating the change from #710 (#722) Changes in version 0.28.0 (2024-06-07) - This release of the R package builds against TileDB 2.24.0, and has also been tested against earlier releases as well as the development version (#714, #715, #717) Improvements - Three internal and unexported helper functions now document more clearly how they can be called explicitly. (#709) - Reading and writing of text- and binary files supported by a VFS backend is now supported. (#710) Build and Test Systems - Building TileDB Embedded from source now uses tiledb install-tiledb as targets in a single CMake step. (#711, #713) - The time-travel tests now uses absolute (given) timestamps for writes as well as reads. (#716) Changes in version 0.27.0 (2024-05-09) - This release of the R package builds against TileDB 2.23.0, and has also been tested against earlier releases as well as the development version (#701, #704) Improvements - Group elements can now be deleted (#702) - Two error messages now show the human-readable type representation instead of the enum counter value (#705) Build and Test Systems - The test files receives a minor refactoring absorbing two files (#698) - The nightly valgrind run was updated to include release 2.23.0, release 2.21 has been removed (#703) Deprecations - Function libtiledb_array_create_with_key, accessing a deprecated Core function, is now in src/deprecated.cpp and will be removed at later point (#699) Removals - Functions libtiledb_query_add_range_with_type and libtiledb_query_add_range, deprecated in release 0.17.1 in January 2023, have been now removed (#700). Changes in version 0.26.0 (2024-04-16) - This release of the R package builds against TileDB 2.22.0, and has also been tested against earlier releases as well as the development version (#679, #686, #693, #696) Improvements - The display of a filter_list is now labelled correctly as a filter list (@cgiachalis in #681 addressing #678) - The Arrow integration has been simplified using nanoarrow returning a single nanoarrow object; an unexported helper function nanoarrow2list() is provided to matching the previous interface (#682, #685) - An new accessor for recursive listings of (currently S3-only) URI is now available (with TileDB Core >= 2.22.0) (#691) - Initial support for TILEDB_GEOM_WKB and TILEB_GEOM_WKT has been added (with TileDB Core >= 2.21.0) (#692) Bug Fixes - The column headers now correspond to the column content in the two-column data.frame returns by tiledb_object_walk (#684 closing #683) Build and Test Systems - The configure and Makevars.in received a minor update correcting small issues (#680) - The nightly valgrind run was updated to include release 2.22.0 (#687), release 2.19 and 2.20 have been removed (#695) Documentation - A number of minor typographical and grammar errors in the function documentation has been corrected (@cgiachalis in #681) Deprecations - Functions tiledb_arrow_array_ptr(), tiledb_arrow_schmea_ptr(), tiledb_arrow_array_del() and tiledb_arrow_schema_del() are deprecated (in favor of using the corresponding nanoarrow functions) and will be removed in a future release (#685) - The function tiledb_query_submit_async() is marked as deprecated (as is the underlying C++ function) and slated for removal in a future release (#694) Changes in version 0.25.0 (2024-03-20) - This release of the R package builds against TileDB 2.21.0, and has also been tested against earlier releases as well as the development version (#661, #666, #668, #676, #677) Improvements - The vendored nanoarrow sources have been update to release 0.4.0, and use of its facilities has been extended (#663) - Query conditions can be expressed against non-existing enumeration (i.e., factor) values when TileDB Core 2.21.0 or later is used (#674) - The tiledb_array_upgrade_version helper function to upgrade an schema version is now available (#675) Bug Fixes - The tiledb_get_query_range_var() accessor now correctly calls the range getter for variable-sized dimensions (#662) - The nightly valgrind check now installs to require nanoarrow package (#664) - Variable cell numbers can now set consistently for all attribute types (#670) - Object walk traversal order detection has been corrected (#671) Build and Test Systems - The nightly valgrind run was updated to include release 2.21 (#669) - Unit tests have been added for the TileDB 'object' functions (#671, #672) - Obsolete checks for an ancient Windows version have been removed from the unit tests (#673) Changes in version 0.24.0 (2024-02-22) - This release of the R package builds against TileDB 2.20.0, and has also been tested against earlier releases as well as the development version (#651,#654,#658,#659) Improvements - Factor level additions now check for possible over in the index type (#645, #646) - Aggregate operations can now be performed on dense arrays via a query object with appropriate subarray settings (#650) Bug Fixes - Factor level additions ensure the factor is releveled under the full set of factors (#644) - The example for fromDataFrame() has been updated, along with two other help files (#648) - Handling of temporary files in one test script has been standardized (#653) Build and Test Systems - The nightly valgrind run was updated to include release 2.20 (#649) Documentation - The DESCRIPTION file now contains a reference to the documentation site in its URL field (#656) Changes in version 0.23.0 (2023-12-21) - This release of the R package builds against TileDB 2.19.0, and has also been tested against earlier releases as well as the development version (#641) Improvements - A TileDB Array can now be opened in 'keep open' mode for subsequent use without re-opening (#630) - Arrays with factor (or ordered) variables now grow their factor levels in appending writes (#639) - Initialization of object walk order in recursive mode is now more explicit (#640) - Use of TileDB Embedded was upgraded to release 2.18.3 (#638), and 2.19.0 (#641) Bug Fixes - The read buffer is now correctly sized when implementing VFS serialization (#631) Build and Test Systems - Builds from TileDB Core non-release tarballs are now supported via new configure option (#627) - Tests are more careful about using suggested packages only when present (#632) - When building TileDB Core, shared linking is now requested explicitly (#634) - Nightly automated checks now include Core release-2.19 and add the 'curl' binary (#635) - Builds on maOS now set release 11 ('Big Sur') as the required minimum version (#636) Changes in version 0.22.0 (2023-11-30) - This release of the R package builds against TileDB 2.18.0, TileDB 2.18.1, TileDB 2.18.2 and has also been tested against earlier releases as well as the development version (#620,#621,#624) Improvements - Use of TileDB Embedded was upgraded to release 2.18.0 (#620), 2.18.1 (#621), and 2.18.2 (#624) - Support for Aggregates has been added (#623) Bug Fixes - When using serializing via VFS (as added in #608) the filehandles is now properly released (#619) Build and Test Systems - Some tests were refactored slightly for greater robustness (#618) - Support for download and build with an external TileDB Core source tarball has been added (#622) Documentation - The README now contains a badge for the r-universe version (in addition to CRAN) (#617) Changes in version 0.21.3 - This release of the R package builds against TileDB 2.17.4, and has also been tested against earlier releases as well as the development version (#611) Improvements - Query conditioning parsing now supports factor index columns other than the standard integer type (#614) Build and Test Systems - The nightly valgrind run was updated to include release 2.18 (#615) Documentation - The pkgdown documentation has been updated for release 0.21.2 (#613) and release 0.21.3 (#616) Changes in version 0.21.2 - This release of the R package builds against TileDB 2.17.4, and has also been tested against earlier releases as well as the development version (#611) Improvements - Set conditions are supported in query condition expressions (#597) - Query conditions expression parsing via parse_query_conditions was extended simmilarly (#598) - Array fragment deletions uses a new static method (with TileDB 2.18.0 or later) (#599) - The included nanoarrow header and source file have been updated to release 0.3.0 (#600) - Query conditions expression parsing requirements are stated and tested more clearly (#601) - Use of TileDB Embedded was upgraded to release 2.17.2 (#602) - Enumeration (aka 'factor') support has been extended for 'empty' creation and subsequent extension with new levelss (#605) - Use of TileDB Embedded was upgraded to release 2.17.3 (#606) - Factor variables with (unlikely) int64 indices are supported (#607) - R objects can be (de-)serialized to and from VFS paths (#608) - Enumeration support has been extended to some cases only supported by Arrow (#609) - Use of TileDB Embedded was upgraded to release 2.17.4 (#611) Bug Fixes - The DESCRIPTION file now correctly refers to macOS 10.14 (#596) - The (explicitly) 'batched reader now ensure a correct layout for sparse arrays (#610) Build and Test Systems - The nightly valgrind run was updated to include release 2.17 (#603) Changes in version 0.21.1 (2023-09-27) - This release of the R package builds against TileDB 2.17.1, and has also been tested against earlier releases as well as the development version (#593) Improvements - Array schema evolution has been extended to support enumerations (#590, #591) - Conversion to and from integer64 (and nanotime) now use package RcppInt64 (#592) - Use of TileDB Embedded was upgraded to release 2.17.1 (#593) Bug Fixes - An added sorting of factor levels insert has been reverted (#594) Changes in version 0.21.0 (2023-09-14) - This release of the R package builds against TileDB 2.17.0, and has also been tested against earlier releases as well as the development version (#583, #587) Improvements - Use of TileDB Embedded was upgraded to release 2.17.0 (#583,#587) - Built-time configuration of TileDB Embedded can now be accessed as a JSON string (#584) - Enumeration types (i.e. what R calls factor variables) are now supported (#562) - Enumeration support has been extended to ordered types (#586) Changes in version 0.20.3 (2023-08-07) - This release of the R package builds against TileDB 2.16.2, and has also been tested against earlier releases as well as the development version (#582) Improvements - Use of TileDB Embedded was upgraded to release 2.16.2 (#581) Changes in version 0.20.2 - This release of the R package builds against TileDB 2.16.1, and has also been tested against earlier releases as well as the development version (#579) Improvements - The column buffer allocation is now robust to container overflow sanitizer checks (#574) - The array schema version is now accessible via a function (#575) - Use of TileDB Embedded was upgraded to release 2.16.1 (#576) - The tile extend getter function is now able to access a wider range of possible values (#577) Build and Test Systems - The minimal version of TileDB Embedded that can be used with the R package is now release 2.7.0 (#578) Changes in version 0.20.1 (2023-07-18) - 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 Bug Fixes - Several minor adjustments were made to not tickle any notives from R-devel CMD check especially on Windows (#571) - A memory allocation for Arrow objects was aligned with how that memory is later freed (#572) Build and Test Systems - The valgrind nightly test was rolled from branches 2.14 and 2.15 to 2.15 and 2.16 of the TileDB Embedded library. Changes in version 0.20.0 (2023-07-15) - 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). Changes in version 0.19.1 (2023-04-27) - 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) Changes in version 0.19.0 (2023-03-13) - 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 Changes in version 0.18.0 (2023-01-19) - 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 Changes in version 0.17.1 (2023-01-06) - 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) Changes in version 0.17.0 (2022-12-02) - 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) Changes in version 0.16.0 (2022-10-21) - This release of the R package builds against TileDB 2.12.0, and has also been tested against earlier releases as well as the development version (#476). 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) - Use of TileDB Embedded was upgraded to release 2.12.0 (#475) 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) Changes in version 0.15.0 (2022-08-09) - 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 (#451). 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) Changes in version 0.14.1 (2022-07-12) - 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) Changes in version 0.14.0 (2022-06-23) - 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) Changes in version 0.13.0 (2022-05-16) - 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) Changes in version 0.12.0 (2022-04-13) - This release of the R package builds against TileDB 2.8.0, and has also been tested against earlier releases as well as the development version. 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) Changes in version 0.11.1 (2022-03-25) - 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. Changes in version 0.11.0 (2022-01-24) - 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) Changes in version 0.10.2 (2021-12-19) - 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) Changes in version 0.10.1 (2021-11-26) - 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) Changes in version 0.10.0 (2021-11-18) - 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) Changes in version 0.9.7 (2021-10-07) - 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). Changes in version 0.9.6 (2021-09-04) - 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) Changes in version 0.9.5 (2021-08-10) - This release of the R package builds against TileDB 2.3.3, but has also been tested against previous releases and the development version. Improvements - A query condition parser was added for use with standard (non-quoted) R expressions (#267) - Windows UCRT builds at CRAN are now supported (#268) - Use of TileDB Embedded was upgraded to release 2.3.2 (#270), and again to 2.3.3 (#280) - The vacuum and consolidation helper functions now use time stamp support (#271) - The time-travel array opening support was updated to start and end timestamps (#272) - Tests for both vacuuming and consolidation 'time traveling' were added (#273) - Nullable string string attribute support was improved (#274) - Ascii columns attribute support was added (#276) - The query parser heuristic was improved to cover ascii strings (#277) - Array opening uses improvemed array state consideration skippingg re-openings for better performance (#279) Bug Fixes - Domain size information gathering has been corrected for uint32, uint64, and int64 attribute domains (#266) - Timesteps for time-traveling unit tests were adjusted to not trip up macOS continuous integration tests (#275) - String array buffer size calculation was corrected also allowing for all-string arrays (#278) Changes in version 0.9.4 (2021-06-23) - This release of the R package builds against TileDB 2.3.1, but has also been tested against previous releases and the development version. Improvements - The build defaults to TileDB Embedded 2.3.* (unless another version is found during build, or explicitly selected) (#258, #264) - Query condition support is available for TileDB 2.3.0 or later, allowing (possibly multiple) numerical constraints on attributes (#261) - Multi-dimensional arrays can now be returned from (dense) arrays via a new option (#263) - The package is now natively supported on Arm64 ("M1") macOS system (#264) Bug Fixes - Dense arrays with more than two dimensions can now be written (#260) Changes in version 0.9.3 (2021-06-03) - This release of the R package builds against TileDB 2.2.9, but has also been tested against previous releases as well as the development version. Improvements - Continuous integration at GitHub is now faster as suggested packages are no longer installed (#250) - Arrays can now be written incrementally via the higher-level replacement function arr[] <- obj (#251) - The default column layout for arrays written via fromDataFrame is now column-order (#254) Bug Fixes - The call to vaccum not correctly calls the library function to vaccum instead of the consolidation function (#252) - When several columns are selected via selected_ranges, a potentially necessary reordering is done for a query (#253) - Dense subarrays can be written for tiledb_array (#256) Changes in version 0.9.2 (2021-05-19) - This release of the R package builds against TileDB 2.2.9, but has also been tested against previous releases as well as the development version. Improvements - Matrix objects can now be returned under range selections (#247) - Matrix return get turned on and off with setter / getter functions (#248) Bug Fixes - Unit tests of character columns in data frames accomodate R versions prior to R 4.0.0 in all cases (#243) - Dimension reduction for attribute-selected columns was incorrect in some cases (#245) - Attribute-selected columns were using incorrect dimension data types in some cases (#246) Changes in version 0.9.1 (2021-05-12) - This release of the R package builds against TileDB 2.2.9, but has also been tested against previous releases as well as the development version. Improvements - A new vignette show use of TileDB array via RMariaDB and the MyTile extension to MariaDB (#221) - Matrices can now be returned directly from suitable two-dimensional TileDB arrays (#225) - More data types are supported in the non-empty domain accessor function (#229) - The DESCRIPTION, README.md and pkgdown site were updated (#230) - Creation of TileDB arrays from data.frame object has been made more robust (#238) - On startup, versions numbers of the R package and the TileDB Embedded library are displayed (#239) - The pkgdown website now shows the ChangeLog derived from this NEWS file (#240) Bug Fixes - Two tests with datetime comparisons which fail only on one macOS system are now conditional (#216) - Result sets with all-character column now fall back to estimated result sizes (#217) - Setup of support for duplicate values in sparse arrays has been corrected (#223) - Error messages concerning an array types and selection mismatch are now clearer (#224) - Writes from data.frame objects to dense array revert back to column-major order (#226) - Tests of sparse writes to dense matrices now use UNORDERED layout (#228) - Data.frame returns of selected columns now coversion dimensions as well (#231) - Schema creation has been generalized and made more robust (#232) - Selection of dimension ranges now maps date and datetime values correctly (#233, #241) - Selection and setting of dimension ranges has been generalized and made more robust (#235, #236) Changes in version 0.9.0 (2021-02-21) - This release of the R package builds against TileDB 2.2.4, but has also been tested against two previous release series as well as the development version. Improvements - The older implementations tiledb_dense and tiledb_sparse are now marked as deprecated in favor of tiledb_array. No removal date is set or planned yet, but it is recommended to migrate to new code. (#180) - Updated the underlying TileDB library to use TileDB 2.1.2 on macOS and Linux (when no system library is found) (#181) - There is extended support for array creation directly from DataFrame objects. (#182) - Internal TileDB performance statistics can now be exported 'raw' in JSON format (for TileDB versions greater than 2.0.3). (#183, #186) - The vignette was updated with respect to the preferred used of tiledb_array. (#184) - The Hilbert cell layout added recently to TileDB Embbeded is supported. (#185) - Virtual File System functions now use the default VFS object which allows for a simpler interface (#187) - TileDB Array Dimension support has been extended to more data types (#188) - Datetime support for Dimensions and Attributes has been extended (#189) - The API coverage has been increased alongside an update of the documentation (#190) - The Array schema can now be accessed and printed directly from a URI (#191) - The accessor for the estimated array result size was updated with the updaded API (#192) - Initial Arrow support for importing and exporting vector has been added (#193, #199) - Support for the default TileDB Embedded library was set to 2.1.3 and 2.1.4 (#194, #195) - The package documentation was updated and extended (#196) - Support for 'time-traveling' access to arrays was extended (#197) - Support for the default TileDB Embedded library was set to 2.1.5 and 2.1.6 (#198, #200) - Support for the default TileDB Embedded library was set to 2.2.0 and 2.2.1 (#201, #202) - The vignettes were updated and extended (#203) - The fromDataFrame() function was extended (#204) - Some unit tests were conditioned on having TileDB Embedded 2.1.0 or later (#205) - Support for the default TileDB Embedded library was set to 2.2.2 and 2.2.3 (#206, #208) - The default TileDB Embedded library version is now set centrally (#207) - Support was added to write and read sparse matrices directly via higher-level functions (#209) - Arrow array and schema allocation and deallocation helper functions were added (#210) - Support for Nullable vectors has been added (#211) - Support for the default TileDB Embedded library has been set to 2.2.4 (#212) - Small tweaks to timezone and factor settings in unit tests, and vignette (#213, #214, #215) Changes in version 0.8.2 (2020-10-16) - This release of the R package builds against TileDB 2.1.1, but has also been tested against previous releases as well as the development version. Bug Fixes - The tiledb_stats_reset() function is now exported, and tiledb_stats_print() has been re-added as a wrapper to tiledb_stats_dump() (#174) - Configuration options for compute and input/output concurrency set only the new TileDB 2.1 configuration options; documentation on how to checking values has been expanded. (#175) - The download.file() use now (re-)sets the timeout to the standard value to accomodate uses where a lower value may be set such as some CRAN builders (#176) - Build scripts have been updated for use of TileDB 2.1.1 on Windows, macOS and Linux (when no system library is found) (#178) Changes in version 0.8.1 (2020-10-08) - This release of the R package supports TileDB 2.1.0, but has also been tested against the previous release TileDB 2.0.8. Improvements - R-based metadata accessors have been extended to also support tiledb_array arrays (#169) - configure now also checks the hardware platform before attempting a download of a prebuilt library (#170) - SystemRequirements: in the DESCRIPTION file has been expanded (#170) Bug Fixes - A typo in the manual page source, copied three more times, has been corrected (#167) Changes in version 0.8.0 (2020-09-03) - This release of the R package supports TileDB 2.0.8, but has also been tested against the previous release TileDB 1.7.7. Improvements - A new function limitTileDBCores() controls resource use, it is being used in tests (#139) - The function tiledb_get_context() is now exported (#140) - A new S4 class tiledb_vfs provides access to the virtual file system functionality (#140) - Functionality of selected_ranges() was extended (#142) - More (signed and unsigned) integer types are supported as dimension types in sparse arrays (#143), as well as in dense arrays (#144) and as attributes (#144) - A new S4 class tiledb_query offers access to the query object functionality in the underlying library (#145, #161) - Examples are running with a lowered thread count setting per CRAN Policies (#152) - External pointer objects now use explicitly set finalizers (#149) - Users can explicitly select a TileDB Embedded shared library built to be used (#151) - Compile-time configuration was refactored and changes (#158) - Windows builds are now possible also using TileDB Embedded build 2.0.8 (#159, #164) - Continuous integration now uses Azure for macOS and Linux (#160) and GitHub Actions for Windows (#162,#165) Bug Fixes - Conda builds no longer call install_name_tool (#133, #146) - Downloading the prebuild library accomodates multitple targets per architecture (#150) - The number of TBB threads will only be set once (#158) Changes in version 0.7.1 - This release of the R package supports TileDB 1.7.7 and TileDB 2.0.5 Improvements - Range selection for tiledb_array objects can get/set matrices defining range (#132) - The show methods are now consistently exported and documented (#134) - TileDB is listed as copyright owner in DESCRIPTION as well (#134) - The selected_ranges method for tiledb_array types was improved, and more tests were added (#135) - C++ source code was rearranged slightly with respect to possible API deprecations in the libary (#136) - A very simple example for using TileDB Cloud from R was added (#136) - The helper scripts for the package build are now in the tools/ directory (#137) - The (optional) library download now relied on suggested R packages 'jsonlite' and 'curl' (#137) Bug Fixes - A character conversion when retrieving array metadata resulting in an out-of-bounds reads has been corrected (#137) Changes in version 0.7.0 (2020-06-26) - This release of the R package supports TileDB 1.7.7 and TileDB 2.0.5 Improvements - All S4 classes are now consistently documented or aliased (#117) - If needed, the build system now builds TileDB and its required component (#118) - Data.frame support has been extended further and made more robust (#119, #123, #128) - The Description: in DESCRIPTION has been refreshed (#120) - Builds on Linux and macOS can use a pre-built TileDB library (#121, #122, #124, #127) - Copyright headers were added to source files (#125) - The pkg-config helper can be used when building from source (#126) - An introductory vignette was added (#129, #131) Changes in version 0.6.0 - This release of the R package supports TileDB 1.7.7 and TileDB 2.0.0 Improvements - Added support for heterogenous domains - Added support for string dimensions - Added support for duplicate dimension values in sparse arrays - Added support for data.frame object import and conversion to dense and sparse arrays - Added enhanced support for data.frame returns from dense array - Added support for data.frame column selection (i.e. attributes) from dense array - Added support for new filter types for md5 and sha256 checksums - Added support for Date, Datetime (i.e. POSIXct) and nanosecond dense and sparse array attributes and domains - Documentation and examples were enhanced and extended - tiledb_stats_dump() is now simpler (but needs to be enabled first as usual) - Support for nanosecond and integer64 columns was added, this is an optional feature for which the nanotime (and bit64) packages need to be installed Changes - Dimension attributes must now be named Changes in version 0.5.0 - This release of the R package builds against the 1.7.5 releases of TileDB. Improvements - Added support for i) multi-range subarrays, ii) incomplete queries, iii) result size estimation and 'time travel' at to time-points has been added #105 - Added additional support for metadata #106 Changes in version 0.4.0 - This release of the R package builds against the 1.7.* releases of tiledb. Improvements - This release contains increased coverage of the underlying API, additional documentation as well as unit tests.