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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.