- 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
-
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)
- 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)
- 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)
-
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-deprecateddump()
method (#753)
- The documentation website now uses favicon symbols for all pages rendered (#739)
-
The nighly valgrind matrix now includes release 2.26.0 (#744)
-
The continuous integration script has been updated reflecting external changes (#746)
- Boolean arguments
as.data.frame
,as.matrix
andas.array
to thetiledb_array()
accessor, deprecated in release 0.20.0 in July 2023 in favor of the more generalreturn_as="..."
form, have been removed. (#751)
- As BioConductor package \pkg{TileDBArray} still relies on
as.data.frame
it was temporarily re-admitted as an argument. It is expected to be removed following the upcoming 3.20 release of BioConducto.r (#752)
- 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)
-
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
andCurrentDomain
objects are supported (with 2.25.0 or newer) and can be used withArraySchema
andArraySchemeEvolution
domain of (#735, #737)
- The nighly valgrind matrix now includes release 2.25.0 (#729)
- 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)
- 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)
- When creating arrays with
fromDataFrame
, start and/or end timestamps can now be specified (#719)
-
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)
- 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)
-
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)
-
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)
- 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)
-
Group elements can now be deleted (#702)
-
Two error messages now show the human-readable type representation instead of the enum counter value (#705)
-
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)
- Function
libtiledb_array_create_with_key
, accessing a deprecated Core function, is now insrc/deprecated.cpp
and will be removed at later point (#699)
- Functions
libtiledb_query_add_range_with_type
andlibtiledb_query_add_range
, deprecated in release 0.17.1 in January 2023, have been now removed (#700).
- 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)
-
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 functionnanoarrow2list()
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)
- The column headers now correspond to the column content in the two-column
data.frame
returns bytiledb_object_walk
(#684 closing #683)
-
The
configure
andMakevars.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)
- A number of minor typographical and grammar errors in the function documentation has been corrected (@cgiachalis in #681)
-
Functions
tiledb_arrow_array_ptr()
,tiledb_arrow_schmea_ptr()
,tiledb_arrow_array_del()
andtiledb_arrow_schema_del()
are deprecated (in favor of using the correspondingnanoarrow
functions) and will be removed in a future release (#685) -
The function
tiledb_query_submit_async()
is marked as deprecated (as is the underlying C++ function) and slated for removal in a future release (#694)
- 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)
-
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)
-
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)
-
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)
- 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)
-
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)
-
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)
- The nightly valgrind run was updated to include release 2.20 (#649)
- The DESCRIPTION file now contains a reference to the documentation site in its URL field (#656)
- 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)
-
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)
- The read buffer is now correctly sized when implementing VFS serialization (#631)
-
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)
- This release of the R package builds against TileDB 2.18.0, TileDB 2.18.1, TileDB 2.18.2 and has also been tested against earlier releases as well as the development version (#620,#621,#624)
-
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)
- When using serializing via VFS (as added in #608) the filehandles is now properly released (#619)
-
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)
- The README now contains a badge for the r-universe version (in addition to CRAN) (#617)
- 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)
- Query conditioning parsing now supports
factor
index columns other than the standardinteger
type (#614)
- The nightly valgrind run was updated to include release 2.18 (#615)
- The pkgdown documentation has been updated for release 0.21.2 (#613) and release 0.21.3 (#616)
- 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)
-
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)
-
The DESCRIPTION file now correctly refers to macOS 10.14 (#596)
-
The (explicitly) 'batched reader now ensure a correct layout for sparse arrays (#610)
- The nightly valgrind run was updated to include release 2.17 (#603)
- 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)
-
Array schema evolution has been extended to support enumerations (#590, #591)
-
Conversion to and from
integer64
(andnanotime
) now use package RcppInt64 (#592) -
Use of TileDB Embedded was upgraded to release 2.17.1 (#593)
- An added sorting of factor levels insert has been reverted (#594)
- 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)
-
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)
- 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)
- Use of TileDB Embedded was upgraded to release 2.16.2 (#581)
- 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)
-
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)
- The minimal version of TileDB Embedded that can be used with the R package is now release 2.7.0 (#578)
- This release of the R package builds against TileDB 2.16.0, and has also been tested against earlier releases as well as the development version
-
Several minor adjustments were made to not tickle any notives from R-devel CMD check especially on Windows (#571)
-
A memory allocation for Arrow objects was aligned with how that memory is later freed (#572)
- The valgrind nightly test was rolled from branches 2.14 and 2.15 to 2.15 and 2.16 of the TileDB Embedded library.
- This release of the R package builds against TileDB 2.16.0, and has also been tested against earlier releases as well as the development version (#551, #559, #563)
-
The startup message is now reformated across two shorter lines (#545)
-
Support for returning 'Arrow Table' objects has been added (#548)
-
Use of TileDB Embedded was upgraded to release 2.15.3 (#551)
-
Date columns can now be exported to Arrow as well (#554)
-
Array writes which set timestamps now take advantage of the new temporal policy API (#558)
-
Displaying a schema is now more readable with additional linebreaks (#560)
-
Attempts to select on dimensions that do not exist now error out with a message (#561)
-
Integer64 values can now be written to array metadata (#564)
-
Date and POSIXct attributes are now supported in query conditions (#568)
-
Consolidation and vacuum calls now reflect the state of the global context object (#547)
-
Pointers to 'Arrow Table' objects representing the table columns are now in external pointers too (#550)
-
The documentation for 'Dimensions' was corrected in two spots in its wording / grammar (#552)
-
'sudo' mode is reenabled for package 'bspm' used in the continuous integration at GitHub Actions (#549)
-
Compilation on Linux systems as old as Ubuntu 18.04 without a
filesystem
header is now possible (#556)
- The boolean arguments
as.data.frame
,as.matrix
andas.array
to thetiledb_array()
accessor are deprecated in favor of the more generalreturn_as="..."
form. (#567)
- The
timestamp
argument totiledb_array
, deprecated in favor oftimestamp_end
(andtimestamp_start
) in July 2021, has been removed (#566).
- 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).
-
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
andvarnum
options (#538) -
Query conditions can now be expressed on boolean attributes (#540)
-
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)
- 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).
- 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
totrue
; the option also permits to write to an older installation. A conversion helper script is provided inscripts/legacy_validity_convert.r
. (#517)
-
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
intiledb_config()
to support R 4.2 conditional lengths (#519) -
Query conditions can now be combined using
&
and|
(in addition to&&
and||
) (#526)
- The access to JSON-formatted performance statistics has been simplified (#514)
-
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)
- 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).
- Use of TileDB Embedded was upgraded to release 2.14.0 (#505)
-
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)
- 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).
-
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)
-
Fragment info domain getters now work with ASCII domains (#495)
-
The scale filter option setting was corrected to use the proper types (#503)
-
The nightly valgrind job setup was updated to include two new dependencies (#493)
-
The Windows setup for continuous integration was updated (#494)
- 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.
- Functions
libtiledb_query_set_coordinates()
andlibtiledb_coords()
which have been deprecated since June 2000 have been removed. (#497)
- 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).
-
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)
-
Accomodate possible zero sized allocation estimates for attributes (#482)
-
Detect missing columns in a write-attempt with partial data (#483)
-
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)
- 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).
-
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)
-
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)
-
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)
- 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).
-
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)
- Small enhancements have been made to the test suite (#450)
- A small enhancement was made to the test system (#450)
- 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.
-
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)
- The nightly
valgrind
check was updated to Ubuntu 22.04 (#435, #439, #442)
- 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.
-
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)
- The
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)
- 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.
-
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)
- Tests for filters have been made more robust (#407, #412)
- The
check()
function is now deprecated andschema_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)
- 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.
-
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)
- This release of the R package builds against TileDB 2.6.4, but has also been tested against earlier releases, and the development version.
-
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 amode=
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 fordata.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 todouble
(#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)
- The
tiledb_dense
andtiledb_sparse
functions which were deprecated in February 2021 have been removed after a twelve-month grace period.
- This release of the R package builds against TileDB 2.6.1, but has also been tested against previous releases, and the development version.
-
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 ofTILEDB_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)
- This release of the R package builds against TileDB 2.5.3, but has been tested against previous releases, and the development version.
-
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)
- This release of the R package builds against TileDB 2.5.2, but has been tested against previous releases, and the development version.
- An accessor for the most-recent error message string has been added (#327)
- 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)
- This release of the R package builds against TileDB 2.5.1, but has been tested against previous releases, and the development version.
-
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 fortiledb_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 viadrop=FALSE
where needed (#320)
- This release of the R package builds against TileDB 2.4.0, but has been tested against previous releases and the development version.
-
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).
- This release of the R package builds against TileDB 2.3.4, but has been tested against previous releases and the development version.
-
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)
- This release of the R package builds against TileDB 2.3.3, but has also been tested against previous releases and the development version.
-
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)
- This release of the R package builds against TileDB 2.3.1, but has also been tested against previous releases and the development version.
-
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)
- Dense arrays with more than two dimensions can now be written (#260)
- 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.
-
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)
- 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.
-
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)
- 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.
-
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)
- 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.
-
The older implementations
tiledb_dense
andtiledb_sparse
are now marked as deprecated in favor oftiledb_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)
- 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.
-
The
tiledb_stats_reset()
function is now exported, andtiledb_stats_print()
has been re-added as a wrapper totiledb_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)
- This release of the R package supports TileDB 2.1.0, but has also been tested against the previous release TileDB 2.0.8.
-
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 theDESCRIPTION
file has been expanded (#170)
- A typo in the manual page source, copied three more times, has been corrected (#167)
- This release of the R package supports TileDB 2.0.8, but has also been tested against the previous release TileDB 1.7.7.
-
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)
- This release of the R package supports TileDB 1.7.7 and TileDB 2.0.5
-
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 fortiledb_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)
- A character conversion when retrieving array metadata resulting in an out-of-bounds reads has been corrected (#137)
- This release of the R package supports TileDB 1.7.7 and TileDB 2.0.5
-
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)
- This release of the R package supports TileDB 1.7.7 and TileDB 2.0.0
-
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
- Dimension attributes must now be named
- This release of the R package builds against the 1.7.5 releases of TileDB.
-
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
- This release of the R package builds against the 1.7.* releases of tiledb.
- This release contains increased coverage of the underlying API, additional documentation as well as unit tests.