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Changelog

Source: NEWS.md

tiledb 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

tiledb 0.30.2

  • 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)

tiledb 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)

tiledb 0.30.0

  • 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 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)

tiledb 0.29.0

  • 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)

tiledb 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)

tiledb 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)

tiledb 0.28.0

  • 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)

tiledb 0.27.0

  • 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).

tiledb 0.26.0

  • 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 labeled 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

tiledb 0.25.0

  • 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)

tiledb 0.24.0

  • 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)

tiledb 0.23.0

  • 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)

tiledb 0.22.0

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)

tiledb 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)

tiledb 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)

tiledb 0.21.1

  • 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)

tiledb 0.21.0

  • 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)

tiledb 0.20.3

  • 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)

tiledb 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)

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)

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

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

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)

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)

tiledb 0.16.0

  • 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)

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 (#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)

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)

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)

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

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)

tiledb 0.12.0

  • 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)

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.

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)

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)

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)

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)

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).

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)

tiledb 0.9.5

  • 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)

tiledb 0.9.4

  • 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)

tiledb 0.9.3

  • 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)

tiledb 0.9.2

  • 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)

tiledb 0.9.1

  • 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)

tiledb 0.9.0

  • 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)

tiledb 0.8.2

  • 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)

tiledb 0.8.1

  • 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)

tiledb 0.8.0

  • 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)

tiledb 0.7.1

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)

tiledb 0.7.0

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)

tiledb 0.6.0

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

tiledb 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,
    1. result size estimation and ‘time travel’ at to time-points has been added #105
  • Added additional support for metadata #106

tiledb 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.