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

  • 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,

    iii) 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.