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)
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)
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)
valgrind check was updated to Ubuntu 22.04
(#435, #439, #442)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)
attr setter for Attributes was corrected to support
NA settings (#425)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)
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)
check() function is now deprecated and
schema_check() is provided (#409)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)
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)
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)
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)
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)
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)
tiledb_dense and tiledb_sparse
functions which were deprecated in February 2021 have been removed after
a twelve-month grace period.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)
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)
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)
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)
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)
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)
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).
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).
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)
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)
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)
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)
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)
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)
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)
Matrix objects can now be returned under range selections (#247)
Matrix return get turned on and off with setter / getter functions (#248)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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