(parallel/opencl-clang) Fix PLIST

(mef)

doc: Updated lang/rakudo to 2024.04

(mef)

(lang/radudo) Updated 2024.02 to 2024.04

New in 2024.04:

+ Improvements:
    + Make X::Syntax::Number::LiteralType a subclass of
      X::TypeCheck::Assignment [5b7cf94c]
    + Make Rakudo up to 2x as fast on the JVM backend by using fastutil [05aae712][23a9fdbe]
      [955bc856]

+ Additions:
    + Add Allomorph.narrow [e6a28e1c]
    + Add dispatch disambiguation via 'is item' parameter trait [70f16f63]
      [3b42de18][36901bb0][0ce55752][c02bd131]

+ Fixes:
    + Fix "No exception handler located for catch" trying to report
      method-not-found [b61de7a9]
    + Fix naming of anonymous classes [ad12f2a9]
    + Increase JVM max heap [2d76783a]
    + Fix reporting of X::Role::Initialization errors [0eb99b8a]
    + Fix race condition in lazy deserialization on MoarVM backend [d6320eaf]
    + Fix obscure pattern bug in regex engine on MoarVM backend [f56a3973]

+ Deprecations:

+ Internal:
    * Streamline "core" (bootstrap, core, metamodel) [169b28f3][b37302cb]
      [010d6fe5][b5f3b474][67f662a4][8a628aa2][9c71fae0][73e1c716][fd6ffe33]
      [aa02c8b8][b411252a][d1a5b479][3b736e56][c7d24b3d][d1fbc0d7][ef942c5c]
      [00256ffb][189ce4f7][6c663f78][dc243d12][dab45fa3][1af29151][5ed668d4]
      [1b5c0820][039dbe49][c48fc1e3][9ecfb483][54a4c8cf][4d33d371][45dfb1bd]
      [ab1784b8][5cd846b2][758500f4][802e8140][e35ac0b4][555f4b00][406ad16b]
      [392213dd][037fab6c][502a6a15][a4423566][9f0b8689][5256102d][a153c729]
      [87feb40a][4cec36b7][56970893][b8330182][8753b0d9][b1167851][57498126]
      [df5fc0e3][e57d8233][ece58501][d442a5ba][4fa4ca52][5c27242b][f4943c9b]
      [c6adc333][cee9f572][0f3c775f][8159ed44][c751668b][d29d3c11][0f8c0d7e]
      [35b87f36][48e87465][5cbd82d3][7235b599][f329c52d][2a233d52][e7d72619]
      [309686a8][f73683f7][0c2c8cf9][9fb5674a][4e79d6b7][5211345d][a15f9f41]
      [75e63ce6][b1aaf338][f6cc5d95][45491ef5][5b80043a][5287d7ea][22795931]
      [25573f0c][1ee6bc46]
    + Convert uses of `if nqp::getcomp('Raku').backend.name eq <...>` to
      `#?if <...>` [f43128bd]

+ RakuAST Development:
    + 91 commits, 142/151 (make test), and 1057/1356 (make spectest) [5c195f12]
      [b4f58fe3][821e056c][c467e04c][d31e99e4][1f02a800][3709aeb2][e5c35555]
      [cdaca915][43fe36fb][ab0a1e12][9d6f2842][33f41e6a][7ce8b6e5][0d1095a0]
      [6507e0cf][06381659][30ff12ec][1f458a0f][e066203d][7ae4c397][e2e7e583]
      [9b90a609][ea84171c][fe279b05][65f349a5][ea0aa21d][ca0d1708][e64145d2]
      [a4b6c401][54854d93][3a70c503][f0d5a942][c6fb210a][1d609daf][9b377fcd]
      [e75c4168][1ccb95d4][c9b75d73][ea0b0d15][aeccbb40][6be6f159][08d439b3]
      [d0ed8cd9][312a5d85][9ca35fb9][69883683][e52a456f][09abf820][3a836f23]
      [c1582285][830727e5][08b77e94][4adf9395][fce6e368][b6d8425d][90cbfde5]
      [f7e50318][cee25a7c][c0f0ad3c][151236e8][c053144a][b213dba7][8f568c66]
      [dd62a30b][1bd789e9][a219c9bc][35cc0d6a][171307e9][5f8c7bbe][de518e47]
      [6c0e2466][9624046c][b6e8f275][7d855c4b][d1cf55cb][54ff30e8][f3b9b8e0]
      [6cf9a5cb][541a9c7d][c9c2197d][d7ded459][76f0278c][326dc12b][dbe698c4]
      [abc1a5f5][604663a3][c118661d][b899592b][eb1069ac][7de82585]

New in 2024.03:

+ Improvements:

+ Additions:

+ Fixes:
    + Add Parameter.of method [586f32cf]
    + Unbreak the JVM build [612dd255][fa853abc][55518662]
    + Unbreak t/harness [9395af5d]

+ Deprecations:

+ Internal:
    * Streamline "core" (bootstrap, core, metamodel) [50fc7284][eea99c2b]
      [704fda60][96c0a5d5][485fc866][a4ac1720][97a0eeab][18989a66][fb7e44fc]
      [bef608a8][4b124a98][1491f822][8e863c81][7dee0530][375393fa][4ee064dc]
      [ec11e06b][8f9ad9a3][8b00ff5b][0b65e78b][3a66dc10][c9ecbda2][48509e00]
      [70b8b229][591792d7][99f52bcd][70be8a09][4581555c][bc8f695e][c283942f]
      [b4a21078][2a3a1f35][b107962c][76030573][14be2dab][3e476241][e294a3e0]
      [3eed834c][43017b21][4d91de6d][01077ad7][1f56f1c6][f73b4ccf][0852efe9]
      [8ee1919d][28a51cfe][008cd24e][1f073f84][9d7a4c26][b83e6fa5][aa1f2274]
      [d8afa16e][08d9ebf6][85e07ec8][b73ed690][d8e9c1cd][c183d282][cf474c92]
      [ae526254][57c92969][a55e7fd0][dce688d4][7ab1bba3][68628fe3][cf46bd5e]
      [20fbb0f1][67c3b662][be990a2e][efeb9d77][b110ebb7][c49e05d8][20376f07]
      [98ca8eb9][6945637f][85b65a9c][fc7c3f47][ccf48ad2][79ad42c7][18abe8c3]
      [adff147e][bafa92a6][72c491f8][2b6cfaa9][e583fa08][ca2f0d1c][621b2c75]
      [53649d4f][8dffcd30][4cdb8a3c][6312d5da]

+ RakuAST Development:
    + Fix INIT blorsts running in wrong scope [237469d2]
    + Treat =place as a directive [b82fa83d]
    + ignore =finish if there is no code [f997c36c]
    + fix declaration after bind in ExpressionThunk [b1b4329b]
    + Replace fallback resolver with compile time lookups in BEGIN time code
      [639f20a2]
    + Fix QAST::Var type of captures [9a983ff4]
    + Add a few missing set_braid_from_self calls to Grammar [4152833b]
    + Support CORE:: compile time lookups [62b89107]
    + Support CORE::v6<[cde]> compile time lookups [8467b84a]
    + fix accessing 6.e PseudoStash at compile time [196fbee6]
    + fix look up of our scoped subs in my scoped packages at compile time
      [3853a0f8]

(mef)

(lang/nqp) Updated 2024.02 to 2024.04 explicit ChangeLog unknown

(mef)

(devel/MoarVM) Updated buildlink3.mk to 2024.04

(mef)

(devel/MoarVM) Updated 2024.02 to 2024.04

New in 2024.04

Core:
+ Increase the size of the int-to-str cache to 65 [f2220d93]
+ Use atomic operations for on SerializationReader's working flag [d5dafa9b]
+ Fix memcmp call [47f518af]

New in 2024.03

Core:
+ Add a GitHub release build workflow (ubuntu, macos, windows) [2a60bd07]

(mef)

doc: Updated math/R to 4.3.3

(mef)

(math/R) Updated 4.3.2 to 4.3.3

CHANGES IN R 4.3.3:

  NEW FEATURES:

        * 'iconv()' now fixes up variant encoding names such as
          '"utf8"' case-insensitively.

  DEPRECATED AND DEFUNCT:

        * The legacy 'encoding = "MacRoman"' is deprecated in 'pdf()'
          and 'postscript()': support was incomplete in earlier
          versions of R.

  BUG FIXES:

        * Arguments are now properly forwarded to methods on S4
          generics with ... in the middle of their formal arguments.
          This was broken for the case when a method introduced an
          argument but did not include ... in its own formals. Thanks
          to Herv<c3><a9> Pag<c3><a8>s for the report PR#18538.

        * Some invalid 'file' arguments to 'pictex()', 'postscript()'
          and 'xfig()' opened a file called 'NA' rather than throw an
          error.  These included 'postscript(NULL)' (which some people
          expected to work like 'pdf(NULL)').

        * Passing 'filename = NA' to 'svg()', 'cairo_pdf()',
          'cairo_ps()' or the Cairo-based bitmap devices opened a file
          called 'NA': it now throws an error.

        * 'quartz(file = NA)' opened a file called 'NA', including
          when used as a Quartz-based bitmap device.  It now gives an
          error.

        * 'rank(<long vector>)' now works, fixing PR#18617, thanks to
          Ilia Kats.

        * 'seq.int()' did not adequately check its 'length.out'
          argument.

        * 'match(<POSIXct>, .)' is correct again for differing time
          zones, ditto for '"POSIXlt"', fixing PR#18618 reported by
          Bastian Klein.

        * 'drop.terms(*, dropx = <0-length>)' now works, fixing
          PR#18563 as proposed by Mikael Jagan.

        * 'drop.terms(*)' keeps ' + offset(.)' terms when it should,
          PR#18565, and 'drop.terms()' no longer makes up a response,
          PR#18566, fixing both bugs thanks to Mikael Jagan.

        * 'getS3method("t", "test")' no longer finds the 't.test()'
          function, fixing PR#18627.

        * 'pdf()' and 'postscript()' support for the documented Adobe
          encodings '"Greek"' and '"Cyrilllic"' was missing (although
          the corresponding Windows' codepages could be used).

        * Computations of glyph metric information for 'pdf()' and
          'postscript()' did not take into account that
          transliteration could replace one character by two or more
          (only seen on macOS 14) and typically warned that the
          information was not known.

        * 'rank(x)' no longer overflows during integer addition, when
          computing rank average for largish but not-yet long vector
          'x', fixing PR#18630, thanks to Ilia Kats.

        * 'list.files()' on Windows now returns also files with names
          longer that 260 bytes (the Windows limit is 260 characters).
          Previously, some file names particularly with 'East Asian'
          characters were omitted.

        * 'cov2cor(<0 x 0>)' now works, fixing PR#18423 thanks to
          Mikael Jagan and Elin Waring.

        * 'cov2cor(<negative diagonal>)' and similar now give one
          warning instead of two, with better wording, fixing PR#18424
          thanks to Mikael Jagan.

        * 'tools'':: startDynamicHelp()' now ensures 'port' is in
          proper range, fixing PR#18645.

        * 'pbeta(x, a,b)' is correct now for 'x'=0 or 1 in the
          boundary cases where 'a' or 'b' or both are 0, fixing
          PR#18672 thanks to Michael Fay.

        * 'pmatch(x, table)' for large 'table', also called for data
          frame row selection, 'dfrm[nm, ]', is now interruptible,
          fixing PR#18656.

        * 'predict(<rank-deficient lm>, newdata=*)' fix computing of
          'nbasis', see Russ Lenth's comment 29 in PR#16158.

        * Added a work-around for a bug in macOS 14.3.1 and higher
          which prevents R plots in the Quartz Cocoa device from
          updating on screen.

(mef)

(cad/openscad) PKGREVISION++, sorry

(mef)

(cad/openscad) Fix build against boost 1.85.0, add one line patch

Confirmed on NetBSD/amd64 9.3 at least

(mef)

doc: Updated cad/klayout to 0.29.0

(mef)

(cad/klayout) Updated 0.28.17 to 0.29.0

0.29.0          (2024-04-01):
* Enhancement: %GITHUB%/issues/1662 Strong default grids

* Enhancement: %GITHUB%/issues/1656 Display-->Goto Position dialog
  should accept + as well as - for number prefixes
* Bugfix: %GITHUB%/issues/1651 Errors when adding polygons with 4 points
* Bugfix: %GITHUB%/issues/1644 DRC: some issues with edge layers
* Bugfix: %GITHUB%/issues/1643 DRC: Feeding the same layer to
  two-layer operations in deep mode does not render the desired result
* Enhancement: %GITHUB%/issues/1638 let klayout marker browser read
  strmxor .. xor.gds.gz, xor.oas result files
* Enhancement: %GITHUB%/issues/1637 XOR optimization for prBoundary layer
* Bugfix: %GITHUB%/issues/1632 rdb python/ruby module: modifing items
  not possible as they are const
* Enhancement: %GITHUB%/issues/1598 LVS - Support for Soft Connections
* Bugfix: %GITHUB%/issues/1586 Refactoring transformation conversion
  functions for complex transformation
* Enhancement: %GITHUB%/issues/1583 Add possibility to customize main
  window title
* Enhancement: %GITHUB%/issues/1513 Update Qt version for Qt bindings
  to 5.12.12 and 6.2.1
* Bugfix: %GITHUB%/issues/1356 Instance Property form: Array Instance
  col/row would be more intuitive then the current row/col
* Enhancement: New ruler type "auto measure along edge"
* Enhancement: Trigger ruler measurement on mouse hovering transiently
* Enhancement: Min and max value bounds for PCell parameters in editor
  The condition is not strictly enforced - for example it is not checked when
  changing parameters programmatically. For that, use "coerce_parameters".
  Still, this feature is an editing aid.
* Bugfix: Pixel garbage in color selector button with "Auto" color selected
* Bugfix: DRC/LVS - connect_explicit did not accept an array of nets
  as single argument
* Bugfix: 'edge outside polygon' now consistently ignores the border
  of the polygon
* Bugfix: Warning level was ignored for some warnings in LEF/DEF reader
* Bugfix: Netlist reader: anonymous circuits are not checked for known parameters
* Enhancement: LVS - Supporting remote must-connect connections
  So far, must-connect connections had to be made one level up in the hierarchy
  or promoted further using labels and such. Now, must-connect connections
  can be made at any point up in the hierarchy.
* Bugfix: LVS - do not waste too much time analyzing failed matches
* Enhancement: LVS - LVS: Consider net names identical that differ
  in signal type suffix only - e.g. 'NET:I' is identical to 'NET'
* Enhancement: OASIS reader will produce layers that are listed in layer table
  but empty. Previously, empty layers were never created, even if listed in
  the layer table.
* Enhancement: Reading from HTTP streams and pipes now supports
  automatic .gz uncompression
* Enhancement: New DRC Features
  - "edges" method allows selecting convext/concave/step edges
  - Interaction count for edge/edge edge/polygon "interacting"
  - Improved handling of dots (degenerated edges) - these are now
    passed through the edge/edge and edge/polygon booleans and
    participate in "interact". This enables selecting corners and
    using them to select edges.
* Enhancement: New RBA/pya Features
  - Main window title: MainWindow#title (property)
  - LayoutView#is_dirty?
  - Triangulation: Region#delaunay
  - Quality rasterizer: Region#rasterize
  - Generic edge and polygon filters and operators support hierarchical processing
    with Python or Ruby callbacks: classes EdgePairFilter, EdgePairOperator,
    EdgePairToPolygonOperator, EdgePairToEdgeOperator, EdgeFilter, EdgeOperator,
    EdgeToPolygonOperator, EdgeToEdgePairOperator, PolygonFilter, PolygonOperator
    PolygonToEdgeOperator, PolygonToEdgePairOperator, TextFilter, TextOperator,
    TextToPolygonOperator
    Methods: EdgePairs#filter, EdgePairs#filtered, EdgePairs#process, EdgePairs#processed,
    same for Edges, Regions and Texts
  - Polygon#split, Polygon#break, same for DPolygon, SimplePolygon, DSimplePolygon
  - Keyword arguments for Python, Ruby and Expressions
  - You can now also use "klayout" package inside the application (same code
    for Python module and application) - i.e. "import klayout.db"
  - Synonyms: connect/disconnect for events for better compatibility with PyQt5

(mef)

Added x11/p5-X11-Protocol-Other version 0.31

(mef)

(x11/p5-X11-Protocol-Other) import p5-X11-Protocol-Other-0.31

This is some window manager related functions for use by client
programs, as per the "Inter-Client Communication Conventions Manual"
and some of the Net-WM "Extended Window Manager Hints".

    /usr/share/doc/xorg-docs/icccm/icccm.txt.gz

    http://www.freedesktop.org/wiki/Specifications/wm-spec

(mef)

Added lang/bython version 0.8

(mef)

(lang/bython) import bython-0.8

Python with braces. Because Python is awesome, but whitespace is awful.

Bython is a Python preprosessor which translates curly brackets into
indentation.

(mef)

doc: Updated lang/rakudo to 2024.02

(mef)

(lang/rakudo) Updated 2024.01 to 2024.02

Rakudo compiler, Release #169 (2024.02)

2024-02-29

On behalf of the Rakudo development team, I?m very happy to announce the
February 2024 release of Rakudo #169. Rakudo is an implementation of the Raku1
language.

The source tarball for this release is available from https://rakudo.org/files/
rakudo. Pre-compiled archives will be available shortly.

New in 2024.02:

  * Improvements:

      + Better errors for common array parameter mistakes [47fb8c35]
      + Improve stability in heavy async situations [761153bc][5c289878]
  * Additions:

      + Add Int/Real coercing versions of infix:<div|mod> [71c0151a]
      + Implement sub form of &trans, mainly to support feed operators
        [b238fad8]
      + Provide native int coercers to Int/Cool [a67842ac][1eaa9d71][dc5414d6]
  * Fixes:

      + Avoid leaking repo.lock handle [155818f4][e6207699][7ca96bbd][a723c387]
  * Deprecations:

  * Internal:

      + Document and/or streamline dispatchers and related [d176728c][78d4fbc0]
        [344f7978][e6fd943f][02bc10c2][ccbe370a][07049e7f][b151e2d7][35760ceb]
      + Streamline "core" (bootstrap, core, metamodel) [51297879][bae06a2c]
        [6117df24][e93208ce][b0dd4ef4][6b231533][024212cd][8e840a51][19da50e3]
        [88151678][975b6634][1dfd7b4b][9f0d361b][80ac4336][760e7a72][eef53371]
        [02aaf9e9][0b759a7a][614571d2][67153138][4c86ef77][dab2c235][c944dae4]
        [2e4113c5][69877047][d49cd4e0][9a828454][de923f1b][1ce9b4c6][3c9f07a8]
        [24a1e67c][4181d461][2c64cbc7][4f64b487][5585454f][cf773dc2][68cd850f]
        [fd936efe][04229899][3c218265][192d7d0a][3271329c][71dcfd42][52dfda3f]
        [b720babd][9f7a3419]
  * RakuAST Development:

      + RakuAST: some nano optimizations [9478d5c7]

See following page for more info
https://rakudo.org/post/announce-rakudo-release-2024.02

(mef)

(devel/MoarVM) Updated buildlink3.mk

(mef)

doc: Updated lang/nqp to 2024.02

(mef)

(lang/nqp) Updated 2024.01 to 2024.02, ChangeLog unknown

(mef)

doc: Updated devel/MoarVM to 2024.02

(mef)

(devel/MoarVM) Updated 2024.01 to 2024.02

2024.02

Core:

  -  Fix uninitialized is_unsigned flag in P6num [a1a18e98]
  -  Slightly optimize creating backtraces [6a9c523d]
  -  Update libuv to version 1.48.0 [cc00279b]
  -  Provide hint for why Rakudo tried to convert from Int to int, when it cannot. [8320c9f4]

(mef)

Added graphics/R-magick version 2.8.3

(mef)

(graphics/R-magick) import R-magick-2.8.3

Bindings to 'ImageMagick': the most comprehensive open-source image
processing library available. Supports many common formats (png, jpeg,
tiff, pdf, etc) and manipulations (rotate, scale, crop, trim, flip,
blur, etc). All operations are vectorized via the Magick++ STL meaning
they operate either on a single frame or a series of frames for
working with layers, collages, or animation. In RStudio images are
automatically previewed when printed to the console, resulting in an
interactive editing environment. The latest version of the package
includes a native graphics device for creating in-memory graphics or
drawing onto images using pixel coordinates.

(mef)

doc: Updated math/R-estimability to 1.5

(mef)

(math/R-estimability) Updated 1.4.1 to 1.5,  make test passed

** NOTE: If you have v1.4 installed, please update to a newer version!
**      (Or an older one, for that matter)

1.5
    We now require R >= 4.3.0.
    Plays along with the changes in 'predict.lm' that came with R 4.3.0.
    We re-coded the 'nonest.basis.qr' to something much simpler, and the
    old version is kept available as 'legacy.nonest.basis'.
    And a vignette was added to help developers add estimability
    checking to their package.

(mef)

doc: Updated devel/R-usethis to 2.2.3

(mef)

(devel/R-usethis) Updated 2.2.2 to 2.2.3

# usethis 2.2.3

* Patch release with changes to `.Rd` files requested by CRAN.

(mef)

doc: Updated devel/R-callr to 3.7.5

(mef)

(.devel/R-callr) Updated 3.7.3 to 3.7.5

# callr 3.7.5

* No changes.

# callr 3.7.4

* The `r_session$get_running_time()` method now returns the correct
  values, as documented (#241, @djnavarro).

* callr now uses fully qualified function calls in the subprocess to
  avoid interference with functions defined in the global environment.
  I.e. `base::stderr()` instead of `stderr()`. Closes #246.

(mef)

(devel/py-pypi-cli) Partly modified from Adam suggestion, tks

(mef)

Added devel/py-pypi-cli version 0.4.1

(mef)

(devel/py-pypi-cli) import py311-pypi-cli-0.4.1

A command-line interface to the Python Package Index (PyPI)

riginally packaged in pkgsrc-wip by:
- K.I.A.Derouiche

(mef)

doc: Updated cad/py-gdstk to 0.9.50

(mef)

(cad/py-gdstk) Updated 0.9.42 to 0.9.50

## 0.9.50 - 2024-02-07
### Added
- `Polygon.perimeter`.

## 0.9.49 - 2023-12-29
### Fixed
- Type annotation for `Cell.write_svg`.

## 0.9.48 - 2023-12-21
### Changed
- `Cell.dependencies` accepts keyword arguments.

### Fixed
- Fracturing polygons with few points is more robust.
- Compilation improvements.

## 0.9.45 - 2023-10-12
### Changed
- Use Qhull as an external dependecy instead of installing it
  ourselves to avoid conflicts.

## 0.9.43 - 2023-10-08
### Added
- `Library.remap` and `Cell.remap` to remap layer and data/text types
- Add typing stub
- Add deepcopy support

### Changed
- Raise an error if not both layer and datatype are specified in
  `Cell.get_polygons` and `Reference.get_polygons`.
- Correct ordering of path ends in `Library::read_oas()`

### Fixed
- Sort `Slice` Positions When converting from python because the
  internal implementation expects the coordinates to be sorted

(mef)

doc: Updated cad/klayout to 0.28.17

(mef)

(cad/klayout) Updated 0.28.15 to 0.28.17

0.28.17          (2024-02-16):
* Enhancement: %GITHUB%/issues/1626 Technology specific grids

0.28.16          (2024-02-12):
* Bugfix: %GITHUB%/issues/1623 Package installation with "-y" from command line does not work for URL or file
* Bugfix: %GITHUB%/issues/1619 Segfault on Fedora-39 with Python 3.12.1
* Bugfix: %GITHUB%/issues/1618 Leaking Python reference causing trouble with iterators
* Bugfix: %GITHUB%/issues/1616 DRC doc typo
* Bugfix: %GITHUB%/issues/1614 LEF/DEF .map should not map boundaries and fill to ALL purpose
* Bugfix: %GITHUB%/issues/1609 Cell.read doesn't read LayoutMetaInfo
* Bugfix: %GITHUB%/issues/1608 CustomResistorExtraction: show faulty device in GUI
* Bugfix: %GITHUB%/issues/1603 Weird parameter dialog resizing when hiding / showing many parameters at once with callback_impl
* Bugfix: %GITHUB%/issues/1602 [Qt6] Cannot normally quit the main application window
* Bugfix: %GITHUB%/issues/1594 "connect" (in flat mode) + multiple top cells give an error message
* Bugfix: %GITHUB%/issues/1592 DXF file parsing error, about spline curve
* Enhancement: DRC enhancements related to touching edges
  - New DRC function switches: "without_touching_corners", "without_touching_edges"
    to skip width and space errors at kissing corners and touching-edge configurations
  - Kissing corners are now detected also in non-collinear edge configurations
* Bugfix: fixed rendering of color selection buttons on High-DPI screens
* Bugfix: cross-hair cursor should not use selection default line width and styles
* Enhancement: OASIS reader errors out on broken OASIS with duplicate CELLNAMEs

(mef)

doc: Updated math/R-Rcmdr to 2.9.2

(mef)

(math/R-Rcmdr) Updated 2.9.1 to 2.9.2

Changes in version 2.9-2

  o Fix incorrect check-box label in wide-to-long dialog (reported by Sophie Dubois).

  o Fix bug introduced into two-way ANOVA dialog (reported by Amin Mousavi).

(mef)

doc: Updated devel/R-xfun to 0.42

(mef)

(devel/R-xfun) Updated 0.41 to 0.42

# CHANGES IN xfun VERSION 0.42

- `isFALSE()` has been fully deprecated for R >= 3.5.0, and will be
  completely removed from this package in the future
  (<https://yihui.org/en/2023/02/xfun-isfalse/>).

- Added a function `record()` to run R code and record the results,
  which is similar to `evaluate::evaluate()` but less sophisticated
  and technically simpler. One major difference is that
  `xfun::record()` records plots directly to files instead of saving
  them as display lists.

- `yaml_load()` gained an `envir` argument, which can be used to
  specify the environment to evaluate R expressions in YAML (i.e.,
  expressions written after `!expr` or `!r`). This is not
  straightforward in the upstream **yaml** package (thanks, @viking,
  vubiostat/r-yaml#54).

- `yaml_body()` gained the `...` argument to pass more arguments to
  `yaml_load()`.

- `split_source()` gained a `merge_comments` argument to merge
  consecutive lines of comments into the next code block, a
  `line_number` argument to store the line number of each expression
  in the returned value, and a `skip` argument to skip the rest of the
  code when the skip token is found.

- `check_old_package()` has been vectorized, i.e., the arguments
  `name` and `version` can take vectors now.

- Factored out the code for parsing chunk options and dividing a chunk
  into chunk options and chunk body from **knitr** to this package as
  functions `csv_options()` and `divide_chunk()`, respectively. They
  will be used by **knitr** and other packages in future.

- Added a function `decimal_dot()` to evaluate an expression after
  forcing `options(OutDec = '.')` and `Sys.setlocale(LC_NUMERIC =
  'C')` (for rstudio/rmarkdown#2525).

(mef)

(devel/libffi) Revert buildlink3.mk to 2022 version

- This change was said wrong location, should change python311/Makefile
      http://mail-index.netbsd.org/tech-pkg/2024/02/03/msg028893.html
- Even above change may not be necessary
      http://mail-index.netbsd.org/tech-pkg/2024/02/12/msg028919.html
- I connfirmed that on 10.99.10 it does not need this change
- I don't remember why I had this problem (pyton 3.11.7 requires this change)

  Sorry and thanks
: ----------------------------------------------------------------------

(mef)

doc: Updated lang/rakudo to 2024.01

(mef)

(lang/rakudo) Updated 2023.11 to 2024.01

See:
https://rakudo.org/post/announce-rakudo-release-2024.01

Rakudo compiler, Release #168 (2024.01)

2024-01-16

On behalf of the Rakudo development team, I窶冦 very happy to announce
the January 2024 release of Rakudo #168. Rakudo is an implementation
of the Raku1 language.

The source tarball for this release is available from
https://rakudo.org/files/rakudo. Pre-compiled archives will be
available shortly.

New in 2024.01:

    Improvements:
        Make dd show types better [57bda882]

        Make use of native unsigned integers better performant [c0340fc7]

        Add dispatchers for handling unassigned elements in hashes and
        arrays resulting in better performance in some specific idioms
        [0e2e20a4] [fa4cc823][1ef51856][70d53fb6][79728078]

    Additions:

        New nqp::syscall/register/delegate/track/guard ops as
        shortcuts to otherwise very verbose nqp::dispatch arguments
        [a3645497][2d8839e1]

        Document dispatchers [9b179a55][690c6c01][93f2a8aa][bafa5ad4]
        [f0673003][2aa796fd][ac5c89bb][6ba5ee53][1721f00b][5394496a][5dd90860]
        [e0952486][9a07a6c8][87bcbe6a][b356bbfd][f651e9d6][2e9c0cc1][26ab5c21]
        [4dc737c3][62a67452][93c31ce9][e002a7a8][7456e6dc][b94e98fc][6819b9de]
        [bb384c41][fd5e4da6][f2b09f7e][6f75ed00][808885d7][fc670bb8][8bf824a5]
        [2cfa0768][d6d7d154][45b1025a][6b6548d8][d327d14a][120a06c7][95770d31]
        [f13ba1d0][12db03a5][11734d4f]

    Fixes:
        Handle .extension("foo") on IOs without extension as if :parts(0) is specified [8cda0bc6]

    Deprecations:
        Deprecate many Distribution::Resource methods [c83eccfa][cd231798][4d797bbb] [7ac9aeab]
        Deprecate the use of PERL6LIB [47fdc20d]

    Internal:
        Show :auth:ver:api of module loaded (for RAKUDO_MODULE_DEBUG) [91a062d2] [fcf22b4f]
        Prevent possible recursion in archetypes dispatcher [6b61de2c]
        Move backend tests from runtime to system build time [69b8a24a]
        Use new nqp::syscall/register/delegate ops [becb682e]
        nqp::syscall is Moar specific, so protect it [b8aaffd6]
        Use new nqp::track / nqp::guard ops [13439539]
        Ensure that nqp::track/guard also have their args unboxed [5d377a12]
        Use nqp::track/guard in NativeCall dispatchers [6008a00e]

        Document and/or streamline dispatchers and related
        [9b179a55][690c6c01]
        [93f2a8aa][bafa5ad4][f0673003][2aa796fd][ac5c89bb][6ba5ee53][1721f00b]
        [5394496a][5dd90860][e0952486][9a07a6c8][87bcbe6a][0e2e20a4][b356bbfd]
        [fa4cc823][1ef51856][70d53fb6][79728078][f651e9d6][2e9c0cc1][26ab5c21]
        [4dc737c3][62a67452][93c31ce9][e002a7a8][7456e6dc][b94e98fc][6819b9de]
        [bb384c41][fd5e4da6][f2b09f7e][6f75ed00][808885d7][fc670bb8][8bf824a5]
        [2cfa0768][d6d7d154][45b1025a][6b6548d8][d327d14a][120a06c7][95770d31]
        [f13ba1d0][12db03a5][11734d4f]

    RakuAST Development:

        some work was done on RakuAST development, but the number of
        passing spectest files did not increase this round.

        [1ecff5c5][3b9de763][35484381][54ee127b][5268106d][000ac084][94e58e05]
        [3c7057c0][c389de26][e1fef673][4bfde24c][91c157d2][3f6fff74][bef0a9bf]
        [3c1ad110][4b6f77f4][f5e9b2dc][bdfea0b0][d992bf6a][7ea760a0]

(mef)

(lang/nqp) Add  two componet on PLIST, update buildlink3.mk

lang/rakudo wants two componet on @INC path from this package

(mef)

doc: Updated lang/nqp to 2024.01

(mef)

(lang/nqp) Updated 2023.12 to 2024.01, ChangeLog unknown

(mef)

(devel/MoarVM) update buildlink3.mk also, sorry

(mef)

doc: Updated devel/MoarVM to 2024.01

(mef)

(devel/MoarVM) Updated 2023.12 to 2024.01

2024.01
Core:

    Add a bunch of *_u stuff [f7753f07] [6c0271c1] [ec1649d5]
    [e1b2af27] [eae59995] [594df3df] [274cb0f3] [06a7b2c9] [017e0429]
    [40d1ccd4] [86ed9a19] [444feb52]

(mef)

doc: Updated math/R-pracma to 2.4.4

(mef)

(math/R-pracma) Updated 2.4.2 to 2.4.4

# pracma NEWS

## pracma 2.4.4 (2023-11-08)

* gcd(), Lcm() now require integers as input (G. R端cker reported).
* Corrections (missing brackets) in several Rd files.

## pracma 2.4.3 (2023-08-15)

* Corrected a bug in the help file of nelder_mead().
* Added stereographic projection and its inverse as functions
  stereographic() and stereographic_inv().

(mef)

doc: Updated devel/R-roxygen2 to 7.3.1

(mef)

(devel/R-roxygen2) Update 7.3.0 to 7.3.1

# roxygen2 7.3.1

* S3 method export warning no longer fails if class contains `{` or `}` (#1575).

* `@family` lists are now ordered more carefully, "foo1" comes after "foo"
  (#1563, @krlmlr).

* `@importFrom` works again for quoted non-syntactic names, e.g.
  `@importFrom magrittr "%>%"` or ``@importFrom rlang `:=` ``
  (#1570, @MichaelChirico). The unquoted form `@importFrom magrittr %>%`
  continues to work. Relatedly, `@importFrom` directives matching no known
  functions (e.g. `@importFrom utils plot pdf`) produce valid NAMESPACE files
  again.

* Multi-line `@rawNamespace` no longer break re-runs of `namespace_roclet()`
  (#1572, @MichaelChirico).

(mef)

doc: Updated devel/R-rio to 1.0.1

(mef)

(devel/R-rio) Update 0.5.26 to 1.0.1

# rio 1.0.1

* POTENTIALLY BREAKING: Due to compiling time concerns, roll back the decision to move `arrow` to `Imports`. It is now `Suggests`. `setclass = "arrow"` works if `arrow` is installed. #315 #376

# rio 1.0.0

* Stop loading the entire namespace of a suggested package when it is available #296
* Unexport objects: `.import`, `.export`, `is_file_text`; remove
  documentation for `arg_reconcile` #321
* Update Examples to make them more realistic #327
* Add support for `qs` #275 h/t David Schoch
* Use `arrow` to import / export `feather` #340
* `export_list` can write multiple data frames to a single archive
  file (e.g. zip, tar) or a directory #346 h/t David Schoch
* `get_info` is added #350
* POTENTIALLY BREAKING: `setclass` parameter is now
  authoritative. Therefore: `import("starwars.csv", data.table = TRUE,
  setclass = "tibble")` will return a tibble (unlike previous versions
  where a data.table is returned). The default class is data
  frame. You can either explicitly use the `setclass` parameter; or
  set the option: `options(rio.import.class = "data.table")`. h/t
  David Schoch #336
* Parquet and feather are now formats supported out of the box;
  Possible to setclass to `arrow` / `arrow_table`; ArrowTabular class
  can be exported #315
* Add "extension", "labelled" vignettes
* Support readODS 2.1.0 features such as reading and writing Flat ODS;
  export Multiple data frames #358
* POTENTIALLY BREAKING: Use `writexl` instead of `openxlsx`. Option to
  read xlsx with `openxlsx` (i.e. `import("starwars.xlsx", readxl =
  FALSE)`) is always `TRUE`. The ability to overwrite an existing
  sheet in an existing xlsx file is also removed. It is against the
  design principle of `rio`.

* POTENTIALLY BREAKING: The following options are deprecated:
  `import(fread)`, `import(readr = TRUE)`, `import(haven)`,
  `import(readxl)` and `export(fwrite)`. import will almost use
  `data.table`, `haven`, `readxl`, and internal function (for fwf) to
  import and export data. Currently, those options stay for backward
  compatibility but will be removed in v2.0.0. #343 h/t David Schoch

* POTENTIALLY BREAKING: `...` is handled differently. Underlying
functions using "Tidy" convention (e.g. `readxl::read_xlsx()`) can
use "Base Convention" (See the new vignette: `remap`). Unused
arguments passed to the underlying function as `...` are silently
ignored by default. A new option `rio.ignoreunusedargs` is added to
control this behavior. #326

* Bug fixes
  - ... is correctly passed for exporting ODS and feather #318
  - POTENTIALLY BREAKING: JSON are exported in UTF-8 by default;
    solved encoding issues on Windows R < 4.2. This won't affect any
    modern R installation where UTF-8 is the default. #318
  - POTENTIALLY BREAKING: YAML are exported using
    yaml::write_yaml(). But it can't pass the UTF-8 check on older
    systems.  Disclaimer added. #318

  - More check for the `file` argument #301
  - `import_list` works with single Excel/HTML/Zip online #294
  - Correct XML/HTML escaping #303
  - Create directory if it doesn't exist #347
* Declutter
  - remove the obsolete data.table option #323
  - write all documentation blocks in markdown #311
  - remove all @importFrom #325 h/t David Schoch
  - rearrange "Package Philosophy" as a Vignette #320
  - Create a single source of truth about all import and export functions #313
  - Clarify all concepts: now there is only `format` #351
* New authors
  - David Schoch @schochastics

# rio 0.5.30

* Maintenance release: new maintainer
* Mark `.sas7bdat` as deprecated
* Change the minimum R version to 3.6

# rio 0.5.29

* fixes for CRAN

# rio 0.5.28

* Various fixes to tests, examples, and documentation for CRAN.
* Temporarily disabled some tests that failed on Mac M1s.

# rio 0.5.27

* Documentation fixes for CRAN.

(mef)

Added textproc/R-writexl version 1.4.2

(mef)

(textproc/R-writexl) import R-writexl-1.4.2

Zero-dependency data frame to xlsx exporter based on 'libxlsxwriter'.
Fast and no Java or Excel required.

(mef)

doc: Updated devel/R-R.oo to 1.26.0

(mef)

(devel/R-R.oo) Updated 1.25.0 to 1.26.0, make test passed

# Version 1.26.0 [2024-01-23]

## Significant Changes

* The `hashCode(s)` implementation for strings was rewritten to avoid
  integer overflow (see below bug fix).  As a consequence, the
  computed hash is no longer the same for some strings.

## Documentation

* Fixed a few small mistakes in the help pages.

## Bug Fixes

* `hashCode(s)` could return NA, due to integer overflow, for strings
  with more than 13-15 symbols, e.g.  `hashCode("abcdefghijklmno")`
  resulted in a missing value and a warning.

(mef)

doc: Updated devel/R-xfun to 0.41

(mef)

(devel/R-xfun) Updated 0.36 to 0.41, make test missing TEST_DEPENDS

# CHANGES IN xfun VERSION 0.41

- `process_file()` will write to the file only if the processed text
  is different with the input text. This is to avoid writing files
  unnecessarily.

- `session_info()` will remove extra blank lines (thanks, @chuxinyuan,
  #82) and also omit the time zone info.

# CHANGES IN xfun VERSION 0.40

- `number_to_words()` supports decimal numbers now (thanks,
  @harshvardhaniimi, #80).

- `is_ascii()` is more robust now (thanks, @bastistician, #81).

# CHANGES IN xfun VERSION 0.39

- Fixed a bug that `protect_math()` fails to protect the starting `$$`
  that has leading white spaces.

- Added a function `strip_html()` to remove HTML tags and comments from text.

- The function `alnum_id()` will remove HTML tags and comments from
  text (using `strip_html()`) before converting it to an ID string.

- Added a function `env_option()` to retrieve an option value from
  `options()`. If the option does not exist there, check the
  environment variables. This provides a way for users to set an
  option via either `options()` or an environment variable.

# CHANGES IN xfun VERSION 0.38

- Added an object `download_cache`, which is a list of methods to
  download a URL, cache the result, retrieve the result from the
  cache, and clear the cache.

- Added an argument `default` to `url_filename()` to provide a default
  filename when it cannot be determined from the URL.

- Added a function `yaml_load()` to read YAML data when the **yaml**
  package is not available. It only supports a limited number of data
  types and is supposed to be used as a fallback method. See the help
  page `?xfun::yaml_load` for details.

- Added a function `yaml_body()` to split a document into YAML metadata and the body.

- `is_arm64()` also supports Linux now (thanks, @eitsupi, #74).

- `is_blank()` returns a logical vector of the same length as the
  input vector now, indicating if each element of the input is
  blank. Previously it returns a logical scalar indicating whether
  *all* elements are blank. If you want the old behavior, you can use
  `all(is_blank())`.

# CHANGES IN xfun VERSION 0.37

- Added a function `is_arm64()` to test the CPU type (thanks, @AlbanSagouis, #72).

- Started deprecating `xfun::isFALSE()` in favor of `base::isFALSE()`
  for R >= 3.5.0 (thanks, @mmaechler, #66); `isFALSE()` will
  eventually be removed from **xfun** when we do not need to support R
  < 3.5.0.

(mef)

doc: Updated math/R-poweRlaw to 0.80.0

(mef)

(math/R-poweRlaw) Updated 0.76.6 to 0.80.0, make test wants Font tcrm1095

# poweRlaw 0.80.0
  * fix: Catch extreme tail situations for lognormal distribution #88.
  * fix: Package engine in vignette
  * fix: Some linting

(mef)

(devel/R-Rcpp) PKGREVISION++

(mef)

'(devel/R-Rcpp) +USE_CXX_FEATURES+=  c++11

Trying to fix:
https://us-central.manta.mnx.io/pkgsrc/public/reports/upstream-trunk/20240202.2249/R-Rcpp-1.0.12/install.log
using C++ compiler: 'g++ (GCC) 13.2.0'
g++ -std=gnu++17 -I"/opt/pkg/lib/R/include" -DNDEBUG -I../inst/include/  -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses    -fPIC  -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/opt/pkg/include/glib-2.0 -I/opt/pkg/include/gio-unix-2.0 -I/opt/pkg/lib/glib-2.0/include -I/usr/include -I/opt/pkg/include/freetype2 -I/opt/pkg/include/harfbuzz -I/opt/pkg/include/ncurses  -c api.cpp -o api.o
In file included from /home/pbulk/build/devel/R-Rcpp/work/.buildlink/lib/R/include/R.h:73,
                from ../inst/include/Rcpp/r/headers.h:66,
                from ../inst/include/RcppCommon.h:30,
                from ../inst/include/Rcpp.h:27,
                from api.cpp:26:
/home/pbulk/build/devel/R-Rcpp/work/.buildlink/lib/R/include/R_ext/Error.h:41:16: error: '_Noreturn' does not name a type
  41 | # define NORET _Noreturn
      |                ^~~~~~~~~

(mef)

(doc/CHANGES-2024) fix CONFLICT, sorry

(mef)

(devel/libffi) python311-3.11.7 wants 3.4.4

(mef)

doc: Updated math/R-plyr to 1.8.9

(mef)

(math/R-plyr) Updated 1.8.8 to 1.8.9

# plyr 1.8.9

* Fixes for `R CMD check`

(mef)

(math/R-itertools) import R-itertools-0.1.3

Various tools for creating iterators, many patterned after functions
in the Python itertools module, and others patterned after functions
in the 'snow' package.

(mef)

doc: Updated math/R-ncdf4 to 1.22

(mef)

(math/R-ncdf4) Updated 1.21 to 1.22

Release 1.22 (2023-03-01) Added "na_replace" argument to ncvar_put().

(mef)

doc: Updated math/R-mvtnorm to 1.2.4

(mef)

(math/R-mvtnorm) Udated 1.2.2 to 1.2.4

Changes in Version 1.2-4 (2023-11-27):

  Bugfixes:

        * Remove empty print statement from 'miwa.c'

Changes in Version 1.2-3 (2023-08-17):

  Features:

        * Allow to change 'rnorm' in 'rmvnorm', feature request by
          Ralf Stubner.

  Bugfixes:

        * Fix variable declarations in 'tvpack.f' as reported by Intel
          compilers icx/ipcx/ifx from oneAPI 2023.2.0 and oneMKL
          2023.2.0, thanks to BDR

(mef)

doc: Updated math/R-minqa to 1.2.6

(mef)

(math/R-minqa) Updated 1.2.5 to 1.2.6

2023-09-09 K Mullen <mullenkate@gmail.com>
* src/bigden.f, src/biglag.f, src/rescue.f, src/trsapp.f,
src/trsbox.f: changed DFLOAT --> DBLE

(mef)

Updated textproc/R-xml2 to 1.3.6

(mef)

(textproc/R-xml2) Updated 1.3.2 to 1.3.6
# xml2 1.3.6

* Now compatible with libxml2 2.12.0 and later (@KNnut).

* Fixed format string issues detected in R-devel.

* Remove unused dependencies on glue, withr and lifecycle (@mgirlich).

* `print()` is faster for very long `xml_nodeset` inputs (#366, @michaelchirico).

* `xml_attr()`, `xml_attrs()`, `xml_double()`, `xml_integer()`, `xml_length()`,
  `xml_name()`, `xml_path()`, `xml_text()`, and `xml_type()` no longer use
  S3 dispatch but instead dispatch in C, leading to considerable performance
  improvements in many cases (@mgirlich, #400).

* `xml_find_int()` analogous to `xml_find_num()` for returning integers
  matched by an XPath (#365, @michaelchirico).

* `xml_serialize()` now includes the document type so that `xml_unserialize()`
  works also for HTML documents (#407, @HenrikBengtsson).

# xml2 1.3.5

* Small speedup for `xml_find_all()` (@mgirlich, #393).

* Fixes for R CMD check problems.

# xml2 1.3.4

* Fixes for R CMD check problems.

* Windows: update to libxml2 2.10.3

# xml2 1.3.3

* Hadley Wickham is now (again) the maintainer.

* xml2 has been re-licensed as MIT (#317).

* `xml_find_all.xml_node()` fails more informatively the `xpath` parameter is the wrong type (@michaelchirico)

* `xml_find_all.xml_nodeset()` gains a `flatten` argument to control whether to return a single nodeset or a list of nodesets (#311, @jakejh)

* `write_xml()` and `write_html()` now return NULL invisibly, as they did prior to version 1.3.0 (#307)

* `XPtr` gets explicit copy constructor and assignment operator definitions, which were two missing components of the [Rule of three](https://en.wikipedia.org/wiki/Rule_of_three_(C%2B%2B_programming)) (@michaelchirico)

* Windows: update to libxml2 2.9.10 and libxslt 1.1.34 and add ucrt libs

(mef)

(devel/gdb) +FAKE_NCURSES=yes, fixing build on NetBSD/9,10 (amd64) tks nia@

(mef)

doc: Updated math/R-lmm to 1.4

(mef)

(math/R-lmm) Updated 1.3 to 1.4

Version 1.4

2023-08-18      Replace dfloat with dble

(mef)

doc: Updated math/R-lme4 to 1.1.35.1

(mef)

(math/R-lme4) Uppdate 1.1.34 to 1.1.35.1

CHANGES IN VERSION 1.1-35.1:

  USER-VISIBLE CHANGES:

        * 'lFormula' and 'glFormula' once again _do_ allow
          matrix-valued responses (for use in downstream packages like
          'galamm')

CHANGES IN VERSION 1.1-35 (2023-11-03):

  NEW FEATURES:

        * 'predict.merMod' now has a 'se.fit' method, which computes
          the standard errors of the predictions, conditional on the
          estimated 'theta' (variance-covariance) parameters

  USER-VISIBLE CHANGES:

        * using 'lmer' with a matrix-valued response now throws a more
          informative error message, directing the user to '?refit'

(mef)

doc: Updated ham/gnuradio-core to 3.10.9.2

(mef)

(ham/gnuradio-core) Updated 3.10.9.1 to 3.10.9.2

[3.10.9.2] - 2024-01-17
Changed
Project
    Fix a few memory errors in various modules.

GRC
    Fix regressions in bus connections.

(mef)

doc: Updated math/R-insight to 0.19.7

(mef)

(math/R-insite) Updated 0.19.3 to 0.19.7

# insight 0.19.7

## General

* Support for objects of class `ggcomparisons` from
  `ggeffects::hypothesis_test()`.

* `brms::gr()` is now supported, meaning that functions like
  `get_data()` or `find_predictors()` now also work for models with
  group-specific random effects.

* Fix CRAN check issues due to the last *fixest* update.

## Changes to functions

* `get_varcov()` for models of class `pgmm` (package *plm*) now also
  supported robust variance-covariance matrices (i.e. argument
  `vcov`).

## Bug fixes

* Fixed issue in `find_predictors()` for survival models with `strata()`,
  containing more that one variable.

* Fixed issue in `model_info()`, where in some cases logistic
  regression models were erroneously considered as `"bernoulli"`
  models.

* Fixed issue in `find_formula()` for models of class `gamlss` when
  the `random()` function was used with namespace in the formula
  (i.e. `... + gamlss::random()`).

* `model_info()` now detects models with zero-inflation part from package
  *glmmTMB* when models have truncated-families but no `ziformula`.

# insight 0.19.6

## General

* Improved documentation for `get_predicted_ci()`.

## Changes to functions

* `model_info()` now recognized ordered beta families.

* `find_formula` and `get_response` for `nestedLogit` models gain a `dichotomies`
  argument, to return values for the dichotomies used to fit the model.

## Bug fixes

* `find_transformation()` better detects power-transformation of the response
  variable.

* Corrected return value from `find_statistic` for `nnet::multinom()` models.

* `clean_parameters()` did not return the `"clean_parameters"` class attributes
  for some object. This caused issued in upstream packages.

* Fixed issue in `model_info()`, which did not correctly detect "Bernoulli"
  property for some models classes (like `glmmTMB` or `glmerMod`).

# insight 0.19.5

## Bug fixes

* Fixed critical issue with `check_if_installed()` for old R releases.

# insight 0.19.4

## Changes to functions

* `get_predicted()` now accepts `predict = "link"` for gaussian models with
  log-link (i.e. `glm(..., family = gaussian("log"))`), to return predictions
  on the link scale.

* `check_if_installed()` now automatically checks the package
  DESCRIPTION file to determine the correct minimum version required.

## Bug fixes

* Fixed issue with invalid multibyte strings in `trim_ws()`.

* Fixed issue in `find_statistic()` for models from package *fixest*.

(mef)

doc: Updated math/R-igraph to 1.6.0

(mef)

(math/R-igraph) Updated 1.5.1 to 1.6.0

# igraph 1.6.0

## Breaking changes

- New `arpack_defaults()` replaces `igraph.arpack.default` and
  `arpack_defaults` lists (#800), with consistent usage checks (#966).

- Define methods for `ape::as.phylo()` instead of own `as_phylo()`
  generic, remove deprecated `asPhylo()` (#763).

- `bfs()` with unreachable nodes returns zero instead of `NaN` as
  `rank` (#956), and negative instead of `NaN` for `dist` (#926).

- `random_walk()` adds one more step, the resulting list of vertices
  is of length `steps + 1` (#934).

- `girth()` returns `Inf` for acyclic graphs (#931).

- Remove some behaviour / parameters that were deprecated in 1.3
  (#842).

- Remove `scg_eps()`, `scg_group()` and `scg_semi_proj()`, broken and
  no longer maintained (#946).

## Bug fixes

- Fix `printf()` warning (#975).

- Fix calls to `isSymmetric()` for matrix objects with a class (#965).

- Reduce frequency of interruption checks (#957).

## Features

- Change "incidence matrix" naming to "biadjacency matrix" (#962).

- Add aliases using the neighborhood terminology for all ego functions: (#950).

- Rename arguments to `assortativity(values, values.in)` from `types1`
  and `types2` (#952).

- Add ellipsis to `cluster_label_prop()` (#954).

- Placeholders for `is_acyclic()` and `is_forest()`, to be implemented
  in igraph 2.0.0 (#945).

- `is_tree(details = TRUE)` designates the first vertex as root for
  non-trees (#935).

- `all_shortest_paths()` returns the vertex list in both `res` and
  `vpaths` components (#930).

- Improve symmetry check for adjacency matrices on input (#911).

- Warn if non-symmetric undirected adjacency matrix (#904).

## Documentation

- Remove duplicate `\seealso{}` (#948).

- Update `knnk()` and `sir()` docs.

- Fix formula in `reciprocity()` docs.

- `strength()` does not give a warning when no weights are given.

- Update `sample_smallworld()` manual page (#895).

- Correct documentation for weighted cliques.

- Update Erdos-Renyi model docs.

## Testing

- Clean up tests (#967).

- Stabilize tests for `cluster_label_prop()` (#932), `sample_pa()`
  (#927), `cluster_louvain()` (#933), SIR (#936),
  `sample_forestfire()` (#929).

- Hard-code graph used in test (#928).

- Update GML test file (#925).

- Improve test for sampling from Dirichlet distribution (#923).

- Omit test that no longer holds with igraph 0.10 (#922).

- Stabilize test in preparation for upgrade (#920).

- Stabilize plot test (#919).

- Fix checks.

(mef)

doc: Updated math/R-hwde to 0.67.3

(mef)

(math/R-hwde) Updated 0.66 to 0.67.3, specific ChangeLog/NEWS.md not known

(mef)

doc: Updated math/R-gtools to 3.9.5

(mef)

(math/R-gtools) Updated 3.9.4 to 3.9.5

gtools  3.9.5 - 2023-11-20
--------------------------

- make `checkRVersion()` robust to internet failure/CRAN outages

(mef)

doc: Updated math/R-gtable to 0.3.4

(mef)

(math/R-gtable) Updated 0.3.3 to 0.3.4

# gtable 0.3.4
* Fix package doc links

(mef)

doc: Updated math/R-gss to 2.2.7

(mef)

(math/R-gss) Updated 2.2.5 to 2.2.7, make test passed

Tue 15 Aug 2023 08:44:33 PM EDT, Chong Gu  <chong@purdue.edu>

* DESCRIPTION: Version 2.2-7.

* R: Edited numerous functions to allow for non-integer counts for
binned data.

* src: Edited numerous routines to allow for non-integer counts
for binned data.

Mon 07 Aug 2023 01:42:21 PM EDT, Chong Gu  <chong@purdue.edu>

* DESCRIPTION: Version 2.2-6.

* man: Minor fix in mkterm.copu.Rd.

* src: Numerous edits to comply with stricter compiler checks.

(mef)

doc: Updated math/R-Rcmdr to 2.9.1

(mef)

(math/R-Rcmdr) Updated 2.8.0 to 2.9.1

Changes in version 2.9-1
  o Fix bug introduced into one-way ANOVA dialog when pairwise
  comparisons are selected (reported by Christopher Wike).

  o Fix bugs introduced into independent-samples t-test dialog
  ignoring confidence level, and numerical-summaries dialog reporting
  statistics not requested (reported by Kenneth Knoblauch).

  o Updated translations: Japanese (thanks to Takaharu Araki), Spanish
  (Manuel Munoz Marquez), Slovenian (Matjaz Jeran).

Changes in version 2.9-0
  o Vignette "Empezando-con-Rcmdr-es" added to the project. This
  vignette is the Spanish version of "Getting-Started-with-the-Rcmdr".

  o Addition to translation (R-Rcmdr.pot) file.

  o Add Command() utility; now used in a few dialogs.

  o Prevent the following dialog functions from opening two copies of
  the dialog after aborting an Apply: appendHclustGroup, Compute(),
  distributionSamples(), generalizedLinearMixedModel,
  generalizedLinearModel(), kmeansClustering(), linearMixedModel(),
  linearModel(), linearRegressionModel(), multinomialLogitModel(),
  multiWayAnova(), oneWayAnova(), proportionalOddsModel,
  RecodeDialog(),

  o R Commander script tab now tolerates blank lines in muiltiline
  commands (contribution of Yoshinobu Kanda).

  o Added coefficient of variation to tables of statistics.

  o New Command() and Q() functions for constructing command character
  strings.

  o Small changes.

Changes in version 2.8-1
  o Addition to translation (R-Rcmdr.pot) file.

  o Corrected omision of Manuel Munoz Marquez as new package coauthor.

  o Now require rgl version 0.110.2 to fix problem with earlier version.

(mef)

doc: Updated math/R-RcmdrMisc to 2.9.1

(mef)

(math/R-RcmdrMisc) Updated 2.7.2 to 2.9.1, make test passed

Changes to Version 2.9-1

  o Fixed bug in numSummaries() introduced along with CV()
  (reported by Kenneth Knoblauch).

Changes to Version 2.9-0

  o Added CV() function.

(mef)

doc: Updated math/R-gdata to 3.0.0

(mef)

(math/R-gdata) Updated 2.19.0 to 3.0.0

Changes in 3.0.0 (2023-10-09)
-----------------------------

Other changes:

- Removed installXLSXsupport(), read.xls(), sheetCount(), sheetNames(),
  xls2csv(), xls2tab(), xls2tsv(), xls2sep(), and xlsFormats(). See gdata 2.19.0
  NEWS entry announcing their deprecation.

- Added aliases n_obs(), object_size(), and starts_with(). Deprecated
  gdata::object.size().

(mef)

doc: Updated math/R-forecast to 8.21.1

(mef)

(math/R-forecast) Updated 8.21 to 8.21.1

# forecast 8.21.1
  * nnetar now allows p or P to be 0
  * Bug fixes and improved docs

(mef)

doc: Updated math/R-e1071 to 1.7.14

(mef)

(math/R-e1071) Updated 1.7.13 to 1.7.14

Changes in version 1.7-14:

        - fix incomplete arguments to avoid partial matches

        - fix small bug in svm.cpp (Rprintf() wrongly called)

        - fix predict.gknn() and predict.svn() to allow for
          newdata argument with character variables instead of
          factors (levels are taken from original data).

(mef)

Added math/R-slam version 0.1.50

(mef)

(math/R-slam) import R-slam-0.1.50, make test passed.

Data structures and algorithms for sparse arrays and matrices, based
on index arrays and simple triplet representations, respectively.

(mef)

doc: Updated math/R-compositions to 2.0.7

(mef)

(math/R-compositions) Updated 2.0.6 to 2.0.7, make test fails

Version 2.0-7
  * test result files stored as requested by cran standards

(mef)

doc: Updated math/R-classInt to 0.4.10

(mef)

(math/R-classInt) Update 0.4.8 to 0.4.9, make test passed

## Version 0.4-9

- #41 issues. The maximum and minimum breaks are set to \code{+Inf}
  and \code{-Inf} to avoid errors induced in the earlier version
  where breaks could cease to be strictly ascending. The
  \code{legacy=} argument with value \code{TRUE} may be used to
  revert to the previous behaviour.

(mef)

doc: Updated geography/R-spData to 2.3.0

(mef)

(geography/R-spData) Updated 0.3.10 to 2.3.0, NEWS.md, ChangeLog unknown

(mef)

doc: Updated math/R-circular to 0.5.0

(mef)

(math/R-circular) Updated 0.4.95 to 0.5

Version 0.5
Added an example to RosediagRad (thanks to Hugo Fl叩vio).
Added an example to lm.circular (thanks to Dirk Walther).
Drop personList() and citEntry().
axis.circular() is no longer an S3 method, just a standalone function.
---------------------------------------------------------------------

(mef)

doc: Updated math/R-bbmle to 1.0.25.1

(mef)

(math/R-bbmle) updated 1.0.25 to 1.0.25.1

Changes in version 1.0.25.1:

  CRAN COMPATIBILITY:

        + remove/ignore spurious .Rout files

(mef)

doc: Updated misc/R-Hmisc to 5.1.1

(mef)

(misc/R-Hmisc) Updated 5.1.0 to 5.1.1

Changes in version 5.1-1 (2023-09-11)

  * meltData: generalized to allow melting on either left or right
    side of formula, added ... arguments passed to label(), made
    variable a factor to keep original order
  * formatCons: fixed bug where lang != 'latex' should have been lang
    == 'plain' which made msdsize to be ignored for html output
  * spikecomp: made more reliable by not assuming as much about
    pretty() boundaries
  * redun: added rank and qrank options
  * added print and plot methods for princmp
  * redun: added ability to use numeric matrix instead of formula
  * ggplot.transcan: fixed bug when adata is empty
  * ggplot.transace: new function
  * transace: added trantab result, added as.matrix(x) so can run on
    data frames of all numeric variables; added automatic setting of
    binary, category, etc. if x is a data frame/table;
    non-downward-compatible change: made returned object of class
    transace with different format; remove pr and pl arguments from
    transace.  Changed first argument to a formula and required
    monotone(), categorical(), linear() to wrap variables in the
    formula instead of specifying with separate arguments
  * runParallel: put in NAMESPACE
  * qcrypt: new function for encrypting and decrypting data with a
    safe workflow
  * aregImpute: added constraint argument to allow general
    constraints on values imputed with predictive mean matching

(mef)

doc: Updated math/R-acepack to 1.4.2

(mef)

(.math/R-acepack) Updated 1.4.1 to 1.4.2

## 1.4.2

* 03-29-2018. Updated email address of maintainer.

(mef)

doc: Updated math/R-XML to 3.99.0.16.1

(mef)

(math/R-XML) Updated 3.99.0.14 to 3.99.0.16.1

============ entries from CRAN ============
Version 3.99-0.16.1

Changes for libxml2 >= 2.11.0, in src/DocParse.c and src/XMLEventParse.c

Version 3.99-0.16

Avoid prntf-like warnings
Rd markup

Version 3.99-0.15

Complete stub in LICENSE file.

Version 3.99-0.14
remove unexported generic append()
update URLs

(mef)

doc: Updated www/R-RCurl to 1.98.1.14

(mef)

(www/R-RCurl) Updated 1.98.1.5 to 1.98.1.14, make test passed.

ChangeLog unknown, inst/doc/Changes.html is outdated

(mef)

doc: Updated math/R-VGAM to 1.1.9

(mef)

(math/R-VGAM) Updated 1.1.8 to 1.1.9

                CHANGES IN VGAM VERSION 1.1-9

NEW FEATURES

    o  Soon: VGAM will require R >= 4.4.0 because plot.profile
        will move from \pkg{MASS} to \pkg{stats}. Sorry!
    o  Yettodo: modify dgaitdlog() to be like
        dgaitdpois() in terms of safeguarding against too
        much deflation and inflation (to return NaN).
        Ditto to dgaitdzeta() and dgaitdnbinom().
        Ditto for the p-type functions.
    o  New family functions: gammaff.mm(), hurea(d).
    o  New generic and/or methods functions: cops().
    o  acat(), cumulative(), cratio(), propodds(), sratio() handles
        argument 'thresholds' equalling 'symmetric1' and 'symmetric0'.
        Note from version 1.1-8 that 'equidistant' was added.
    o  Tested okay on R 4.3.0.

BUG FIXES and CHANGES

    o  wald.stat(..., orig.SE = TRUE, values0 = values0)
        assumed that values0 == 0.
    o  [rq]zinegbin() did not handle the case 'munb = NULL'
        when 'prob' was specified. Thanks to Giuseppe D for
        finding this bug.
    o  acat(), cumulative(), cratio(), propodds(), sratio()
        must have an intercept term.
    o  For vglm.fit(), slot "middle" is now "middle1",
        "fini" is now "fini1", and a new "start1" slot added.
    o  bigamma.mckay() moved into VGAMdata 1.1-9.
    o  nakagami() has a zero = "shape" argument.
    o  [dp]gaitdpois() have more range checking, e.g., for too
        much deflation and inflation.
    o  For more speed, several slow-checking .Rd files
        have been changed by using \dontrun{}.
    o  summary(posbernoulli.tb()) failed to print the confidence
        interval. Thanks to Carl Schwarz for picking this up.
    o  DFLOAT() changed to DBLE() in some .f files.

(mef)

doc: Updated math/R-RcppEigen to 0.3.3.9.4

(mef)

(math/R-RcppEigen) 0.3.3.9.3 to 0.3.3.9.4

2023-11-01  Dirk Eddelbuettel  <edd@debian.org>

* DESCRIPTION (Version, Date): CRAN Release 0.3.3.9.4
* inst/NEWS.Rd: Release 0.3.3.9.4

2023-10-05  Mikael Jagan  <jaganmn@mcmaster.ca>

* DESCRIPTION: Package 'Matrix' is now only a Suggests:
* NAMESPACE: Remove unconditional imports from package Matrix

* inst/include/Eigen/CholmodSupport: No longer need to include
RcppEigenCholmod.h
* inst/include/Eigen/src/CholmodSupport/CholmodSupport.h: Small
wrapper adjustments conditional on Matrix use
* inst/include/RcppEigenCholmod.h: Updated
* inst/include/RcppEigenForward.h: Simplified
* inst/include/RcppEigenWrap.h: Ditto
* inst/include/RcppEigenStubs.cpp: New shorter helper
* inst/include/RcppEigenStubs.h: Removed

2023-07-21  Dirk Eddelbuettel  <edd@debian.org>

* DESCRIPTION (Date, Version): Roll micro version and date

* README.md: Add r-universe badge

2023-07-20  Dirk Eddelbuettel  <edd@debian.org>

* src/RcppEigen.cpp (EigenNbThreads): Add simple threads reporter

* R/fastLm.R (fastLmPure): Simpler call to `fastLm_Impl()`

* src/init.c: Replaced by auto-generated section in RcppExports.cpp
* src/RcppExports.cpp: Regenerated
* R/RcppExports.R: Idem

* src/Makevars: Document possible use of '-fopenmp'
* src/Makevars.win: Idem

2023-04-18  Dirk Eddelbuettel  <edd@debian.org>

* README.md: Use app.codecov.io as base for codecov link

2023-03-10  Dirk Eddelbuettel  <edd@debian.org>

* DESCRIPTION (Date, Version): Roll minor version

* R/RcppEigen.package.skeleton.R: No longer set Imports: RcppEigen in
DESCRIPTION and NAMESPACE

2023-02-12  Dirk Eddelbuettel  <edd@debian.org>

* inst/CITATION: Convert to bibentry() style with person()

(mef)

doc: Updated math/R-RcppArmadillo to 0.12.6.6.0

(mef)

(math/R-RcppArmadillo) 0.12.4.1.0 to 0.12.6.6.0, TEST_DEPENDS missing some

2023-10-31  Dirk Eddelbuettel  <edd@debian.org>

* DESCRIPTION (Version, Date): RcppArmadillo 0.12.6.6.0
        * inst/NEWS.Rd: Idem
        * configure.ac: Idem
        * configure: Idem

* inst/include/armadillo_bits/: Armadillo 12.6.6

2023-10-29  Dirk Eddelbuettel  <edd@debian.org>

* src/RcppArmadillo.cpp (armadillo_get_number_of_omp_threads)
(armadillo_set_number_of_omp_threads): New helper functions
        * src/RcppExports.cpp: Regenerated
        * R/RcppExports.R: Idem
* man/armadillo_get_number_of_omp_threads.Rd: Documentation

* R/init.R (.onLoad): Store initial thread count
* R/init.R (armadillo_throttle_cores, armadillo_reset_cores):
Tread throtte and reset helper functions
* man/armadillo_throttle_cores.Rd: Documentation

* man/fastLm.Rd: Illustration of use of throttle and reset function
* NAMESPACE: Export new functions

2023-10-14  Dirk Eddelbuettel  <edd@debian.org>

* DESCRIPTION (Version, Date): RcppArmadillo 0.12.6.5.0

2023-09-06  Dirk Eddelbuettel  <edd@debian.org>

* DESCRIPTION (Version, Date): RcppArmadillo 0.12.6.4.0
        * inst/NEWS.Rd: Idem
        * configure.ac: Idem
        * configure: Idem

* inst/include/armadillo_bits/: Armadillo 12.6.4

2023-08-28  Dirk Eddelbuettel  <edd@debian.org>

* DESCRIPTION (Version, Date): RcppArmadillo 0.12.6.3.0
        * inst/NEWS.Rd: Idem
        * configure.ac: Idem
        * configure: Idem

* inst/include/armadillo_bits/: Armadillo 12.6.3

2023-08-08  Dirk Eddelbuettel  <edd@debian.org>

* DESCRIPTION (Version, Date): RcppArmadillo 0.12.6.2.0
        * inst/NEWS.Rd: Idem
        * configure.ac: Idem
        * configure: Idem

* inst/include/armadillo: Armadillo 12.6.2
* inst/include/armadillo_bits/: Idem

2023-07-26  Dirk Eddelbuettel  <edd@debian.org>

* DESCRIPTION (Version, Date): RcppArmadillo 0.12.6.1.0
        * inst/NEWS.Rd: Idem
        * configure.ac: Idem
        * configure: Idem

* inst/include/armadillo: Armadillo 12.6.1
* inst/include/armadillo_bits/: Idem

2023-07-23  Dirk Eddelbuettel  <edd@debian.org>

* DESCRIPTION (Version, Date): RcppArmadillo 0.12.6.0.1
        * inst/NEWS.Rd: Idem

* inst/include/armadillo_bits/: Upstream sync w/o move ctors

2023-07-21  Dirk Eddelbuettel  <edd@debian.org>

* DESCRIPTION (Version, Date): RcppArmadillo 0.12.6.0.0
        * inst/NEWS.Rd: Idem
        * configure.ac: Idem
        * configure: Idem

* inst/include/armadillo: Armadillo 12.6.0
* inst/include/armadillo_bits/: Idem

(mef)

doc: Updated math/R-RNetCDF to 2.9.1

(mef)

(math/R-RNetCDF) Updated 2.6.2 5o 2.9.1, make test does not pass

Version 2.9-1, 2023-12-30
  * Fix support for parallel I/O with MPICH (and related MPI variants)
  * Fix error handlers to remove potentially insecure format strings

Version 2.8-1, 2023-10-21
  * Fix builds on platforms where share directory is not under $R_HOME
  * Fix UBSAN warning when converting empty NC_CHAR to R string
  * Fix type conversions with oneAPI compiler

Version 2.7-1, 2023-10-02
  * Fix crash when calling nc_free_vlen on vlen with zero-length
  * Support packing and unpacking of vlen
  * Support fill value conversions in non-numeric data types:
    NC_CHAR, NC_STRING, enum, compound, and vlen
  * Improve support for NetCDF parallel I/O in configure script:
    - Specify MPI compiler via argument --with-mpicc
    - Enable MPI tests in R CMD check via argument --with-mpiexec
    - Give warnings if MPI and/or NetCDF parallel I/O not detected
  * Add configure option --with-nc-config-static to allow selection of
    static libraries from nc-config
  * Build Windows package with NetCDF library from RTools4x
    - Adapt to newer RTools by using configure script on Windows
  * Add examples using hierarchical groups to help for grp.inq.nc

(mef)

doc: Updated math/R-MatrixModels to 0.5.3

(mef)

(math/R-MatrixModels) Updated 0.5.0 to 0.5.3, make test passed.

2023-10-13  Martin Maechler  <maechler@stat.math.ethz.ch>

* DESCRIPTION (Version): 0.5-3
* man/lm.fit.sparse.Rd: use '\describe{..}` instead of lost braces.

2023-06-18  Martin Maechler  <maechler@stat.math.ethz.ch>

* DESCRIPTION (Version): 0.5-2
* R/modelMatrix.R (solveCoef): 'predModule': Mikael J Matrix 1.6-0:
Using Cholesky() instead of chol() for solve()ing.

2022-09-12  Martin Maechler  <maechler@ethz.ch>

* R/modelMatrix.R (glm4): support the 'contrasts' argument
when that works in 'model.Matrix()'.

2021-09-03  Martin Maechler  <maechler@stat.math.ethz.ch>

* DESCRIPTION (Version): 0.5-1
* R/AllClass.R: update for Matrix 1.5-0

(mef)

Updated math/R-DEoptimR to 1.1.3

(mef)

doc: Updated math/R-FNN to 1.1.4

(mef)

(math/R-FNN) Updated 1.1.3.2 to 1.1.4

  CHANGES IN FNN VERSION 1.1.4

o get.knn (cover_tree) will not return the self as the first
  neighbor.  kd_tree and brute may still return self as the
  first neighbor even there are other identical data points.

o fixed the typo in the theoretical divergence example of
KL.divergence manual

(mef)

(math/R-DEoptimR) Updated 1.1.1 to 1.1.3, inst/NEWS.Rd not updated, test passed

(mef)

doc: Updated devel/R-withr to 3.0.0

(mef)

(devel/R-withr) Update 2.5.0 to 3.0.0

# withr 3.0.0

## Performance of withr

* `defer()` is now a thin wrapper around `base::on.exit()`. This is
  possible thanks to two contributions that we made to R 3.5:

  - We added an argument for FIFO cleanup: `on.exit(after = FALSE)`.
  - Calling `sys.on.exit()` elsewhere than top-level didn't work. This
    is needed for manual invokation with `deferred_run()`.

  Following this change, `defer()` is now much faster (although still
  slower than `on.exit()` which is a primitive function and about as
  fast as it gets). This also increases the compatibility of `defer()`
  with `on.exit()` (all handlers are now run in the expected order
  even if they are registered with `on.exit()`) and standalone
  versions of `defer()`.

## Breaking change

* When `source()` is used with a local environment, as opposed to
  `globalenv()` (the default), you now need to set
  `options(withr.hook_source = TRUE)` to get proper withr support
  (running `defer()` or `local_` functions at top-level of a script).
  THis support is disabled by default in local environments to avoid a
  performance penalty in normal usage of withr features.

## Other features and bugfixes

* `deferred_run()` now reports the number of executed expressions with
  a message.

* `deferred_run()` can now be run at any point in a knitr file (#235).

,* `local_tempfile()` now writes `lines` in UTF-8 (#210) and always uses
  `\n` for newlines (#216).

* `local_pdf()` and friends now correctly restore to the previously
  active device (#138).

* `local_()` now works even if withr isn't attached (#207).

* `local_par()` and `with_par()` now work if you don't set any parameters
  (#238).

* `with_language()` now properly resets the translation cache (#213).

* Fixes for Debian packaging.

# withr 2.5.2

* Fixes for CRAN checks.

# withr 2.5.1

* Fixes for CRAN checks.

(mef)

(devel/R-rio) revert commit mistakenly done, sorry

(mef)

(devel/R-BH) +TEST_DEPENDS, make test passed

(mef)

(devel/Mac-SystemDirectory) revert mistake, sorry

(mef)

(devel/p5-MetaCPAN-Client) revert mistake, sorry

(mef)

(devel/p5-Test-Alien-CPP) revert my mistake

(mef)

(devel/p5-Test-Alien-CPP) revert my mistake

(mef)

(devel/R-uuid) Remove duplicated line, sorry

(mef)

(devel/R-waldo) Remove duplicated line, sorry

(mef)

doc: Updated devel/R-waldo to 0.5.2

(mef)

(devel/R-waldo) Updated 0.5.1 to 0.5.2, make test passed.

# waldo 0.5.2

* Fixes for upcoming R-devel changes.

(mef)

doc: Updated devel/R-uuid to 1.2.0

(mef)

(devel/R-uuid) Updated 1.1.0 to 1.2.0

NEWS for uuid
---------------
1.2-0 2024-01-13
    o add UUIDfromName() which allows generation of version 3 and 5
UUIDs based on a namespace UUID and a string.

1.1-1 2022-12-02
    o clean up strict prototype warnings

    o update to upstream util-linux version 25b98ae

(mef)

doc: Updated devel/R-rprojroot to 2.0.4

(mef)

(devel/R-rprojroot) Updated 2.0.3 to 2.0.4, make test passed

# rprojroot 2.0.4 (2023-11-05)

## Features

- Add `is_renv_project` criterion looking for an `renv.lock` file (@gadenbuie, #86).
- Add `is_quarto_project` criterion looking for a Quarto project (@olivroy, #91, #92).

## Chore

- Update maintainer e-mail address.

## Testing

- Wrap `::` to skip if not installed in tests (#94).

(mef)

doc: Updated devel/R-roxygen2 to 7.3.0

(mef)

(devel/R-roxygen2) Updated 7.2.3 to 7.3.0

# roxygen2 7.3.0

## New features

* `@docType package` now works more like documenting `"_PACKAGE"`,
  creating a `{packagename}-package` alias and clearly suggesting that
  you should switch to `"_PACKAGE"` instead (#1491).

* `_PACKAGE` will no longer generate an alias for your package name if
  a function of the same name exists (#1160).

* The NAMESPACE roclet now reports if you have S3 methods that are missing
  an `@export` tag. All S3 methods need to be `@export`ed (which confusingly
  really registers the method) even if the generic is not. This avoids rare,
  but hard to debug, problems (#1175). You can suppress the warning with
  `@exportS3Method NULL` (#1550).

* The `NAMESPACE` roclet once again regenerates imports _before_ loading
  package code and parsing roxygen blocks. This has been the goal for a long
  time (#372), but we accidentally broke it when adding support for code
  execution in markdown blocks. This resolves a family of problems where you
  somehow bork your `NAMESPACE` and can't easily get out of it because you
  can't re-document the package because your code doesn't reload.

## Minor improvements and bug fixes

* If you document a function from another package it is automatically
  imported. Additionally, if you set `@rdname` or `@name` you can opt out
  of the default `reexports` topic generation and provide your own docs
  (#1408).

* Generate correct usage for S4 methods with non-syntactic class names.

* The `ROXYGEN_PKG` env var provides the name of the package being documented
  (#1517).

* `@describeIn foo` now suggests that you might want `@rdname` instead
  (#1493). It also gives a more informative warning if you use it with an
  unsupported type (#1490).

* In `DESCRIPTION`, URLs containing escapes in `URL` and `BugReports` are
  now correctly handled (@HenningLorenzen-ext-bayer, #1415). Authors can now
  have multiple email addresses (@jmbarbone, #1487).

* `escape_examples()` is now exported (#1450).

* `@exportS3Method` provides the needed metadata to generate correct usage
  for S3 methods, just like `@method` (#1202).

* `is_s3_generic()` now ignores non-function objects when looking for a
  candidate function. I believe this is closer to how R operates.

* `@import` and friends are now ignored if they try to import from the
  package being documented. This is useful to add self-dependencies in
  standalone files meant to be used in other packages (r-lib/usethis#1853).

* `@importFrom` throws a friendlier error if you try and import a non-existing
  functions (@MichaelChirico, #1409).

* `@include` now gives an informative warning if you use a path that doesn't
  exist (#1497).

* `@inherit` can now also inherit from `@format` (#1293).

(mef)

doc: Updated devel/R-rlang to 1.1.3

(mef)

(devel/R-rlang) Updated 1.1.1 to 1.1.3

# rlang 1.1.3

* Fix for CRAN checks.

* `%||%` is now reexported from base on newer R versions. This avoids
  conflict messages when attaching or importing rlang.

# rlang 1.1.2

* Fixed an off-by-one typo in the traceback source column location (#1633).

* `abort()` now respects the base R global option,
  `options(show.error.messages = FALSE)` (#1630).

* `obj_type_friendly()` now only displays the first class of S3
  objects (#1622).

* `expr_label()` now has back-compatility with respect to changes made
  by R version 4.4 and `is.atomic(NULL)` (#1655)

* Performance improvement in `.rlang_cli_compat()` (#1657).

(mef)

doc: Updated devel/R-renv to 1.0.3

(mef)

(devel/R-renv) Updated 0.17.3 to 1.0.3

# renv 1.0.3

* Fixed an issue where `renv` could warn the project appeared to be out-of-sync
  when using packages installed without an explicit source recorded. (#1683)

* `renv::install()` gains the `exclude` argument, which can be useful when
  installing a subset of project dependencies.

* Fixed an issue where PPM repositories were not appropriately transformed
  into the correct binary repository in `renv::restore()` when using pak.

* `renv::init()` no longer prompts the user for the intended action for
  projects containing a library with only renv installed. (#1668)

* Fixed an issue where non-interactive usages of `renv::init()` could fail
  with projects containing a DESCRIPTION file. (#1663)

* Fixed an issue that could cause code within a project `.Rprofile` to execute
  before the project had been loaded in RStudio. (#1650)

* `renv::snapshot()` and `renv::status()` gain the `dev` argument. This
  can be used when you'd like to capture package dependencies from
  the *Suggests* field of your package's DESCRIPTION file. (#1019)

# renv 1.0.2

* renv now parses package `NAMESPACE` files for imported dependencies. (#1637)

* renv no longer locks the sandbox by default.

* Fixed an issue where renv used the wrong library paths when attempting
  to activate the watchdog. This could cause a 10 second delay when activating
  the sandbox.

# renv 1.0.1

* Fixed an issue where authentication headers could be duplicated when
  using the `libcurl` download method. (#1605)

* `renv::use()` now defaults to setting `isolate = TRUE` when `sandbox = TRUE`.

* Fixed an issue where the renv watchdog could fail to load, leading to slowness
  in activating the sandbox on startup. (#1617)

* Fixed an issue where renv did not display warnings / errors from `renv::snapshot()`
  when `options(renv.verbose = FALSE)` was set. The display of these messages
  is now controlled via the `renv.caution.verbose` R option. (#1607, #1608)

* `renv::load()` now notifies the user if the synchronization check took an
  excessive amount of time due to the number of files being scanned in the
  project. (#1573)

* `renv::init()` gains the `load` argument, making it possible to initialize
  a project without explicitly loading it. (#1583)

* renv now uses a lock when synchronizing installed packages with the cache.
  This should help alleviate issues that can arise when multiple R processes
  are installing and caching packages concurrently. (#1571)

* Fixed a regression in parsing expressions within R Markdown chunk options. (#1558)

* Fixed an issue that prevented `renv::install()` from functioning
  when source-only repositories were included. (#1578)

* Fixed a logic error in reading `RENV_AUTOLOAD_ENABLED`. (#1580)

* `renv::restore()` no longer runs without prompting on load if the
  library is empty. (#1543)

* `renv::repair()` now checks for installed packages which lack a known
  remote source, and updates their `DESCRIPTION` files if it can infer an
  appropriate remote source. This typically occurs when a package is installed
  from local sources, but appears to be maintained or published on a remote
  repository (e.g. GitHub). This was previously done in `renv::snapshot()`, but
  we've rolled back that change as the prompting was over-aggressive. (#1574)

* `renv::status()` now first reports on uninstalled packages, before reporting on
  used <-> installed mismatches. (#1538)

* When the `RENV_STARTUP_DIAGNOSTICS` environment variable is set to `TRUE`,
  renv now displays a short diagnostics report after a project's autoloader
  has been run. This can be useful when diagnosing why renv is slow to load
  in certain projects. (#1557)

* renv now ensures the sandbox is activated on load, for R processes which
  are launched with the renv sandbox on the library paths. (#1565)

* `renv::restore()` no longer erroneously prompts when determining the packages
  which need to be installed. (#1544)

* `renv::update()` now ensures the `prompt` parameter is properly respected
  during package installation. (#1540)

* `renv::activate()` no longer erroneously preserves the previous library
  paths after restarting the session within RStudio. (#1530)

* Use correct spelling of IRkernel package (#1528).

* Honor `R_LIBCURL_SSL_REVOKE_BEST_EFFORT` when using an external `curl.exe`
  binary to download files. (#1624)

# renv 1.0.0

## New features

* New `renv::checkout()` installings the latest-available packages from a
  repository. For example, `renv::checkout(date = "2023-02-08")` will install
  the packages available on 2023-02-08 from the Posit
  [Package Manager](https://packagemanager.rstudio.com/) repository.
  The `actions` argument allows you choose whether a lockfile is generated from
  the provided repositories ("snapshot"), or whether packages are installed
  from the provided repositories ("restore").

* `renv::deactivate()` gains a `clean` argument: when `TRUE` it will delete
  all renv files/directories, leaving the project the way it was found.

* `renv::init()` now uses [Posit Public Package Manager](https://packagemanager.posit.co)
  by default, for new projects where the repositories have not already been
  configured externally. See the options `renv.config.ppm.enabled`,
  `renv.config.ppm.default`, and `renv.config.ppm.url` in `?config` for more
  details (#430).

* `renv::lockfile_create()`, `renv::lockfile_read()`, `renv::lockfile_write()`
  and `renv::lockfile_modify()` provide a small family of functions for
  interacting with renv lockfiles programmatically (#1438).

* Handling of development dependencies has been refined. `renv::snapshot()`
  and `renv::status()` no longer track development dependencies, while
  `install()` continues to install them (#1019). `Suggested` packages listed in
  `DESCRIPTION` files are declared as development dependencies regardless of
  whether or not they're a "package" project.

* MRAN integration is now disabled by default, pending the upcoming shutdown
  of Microsoft's MRAN service. Users who require binaries of older R packages
  on Windows + macOS can consider using the instance of CRAN mirrored by the
  [Posit Public Package Manager](https://packagemanager.posit.co) (#1343).

## Bug fixes and minor improvements

* Development versions of renv are now tracked using the Git SHA of the
  current commit, rather than a version number that's incremented on every
  change (#1327). This shouldn't have any user facing impact, but makes
  renv maintenance a little easier.

* Fixed an issue causing "restarting interrupted promise evaluation" warnings
  to be displayed when querying available packages failed. (#1260)

* `renv::activate()` uses a three option menu that hopefully make your choices
  more clear (#1372).

* `renv::dependencies()` now discovers R package dependencies inside Jupyter
  notebooks (#929).

* `renv::dependencies()` includes packages used by user profile (`~/.Rprofile`)
  if `renv::config$user.profile()` is `TRUE`. They are set as development
  dependencies, which means that they will be installed by `install()` but not
  recorded in the snapshot.

* `renv::dependencies()` only extracts dependencies from text in YAML
  headers that looks like valid R code (#1288).

* `renv::dependencies()` no longer treats `box::use(module/file)` as using
  package `module` (#1377).

* `renv::init()` now prompts the user to select a snapshot type if the project
  contains a top-level DESCRIPTION file (#1485).

* `renv::install(type = "source")` now ensures source repositories are used
  in projects using [PPM](https://packagemanager.posit.co/). (#927)

* `renv::install()` activates Bioconductor repositories when installing a
  package from a remote (e.g. GitHub) which declares a Bioconductor dependency
  (via a non-empty 'biocViews' field) (#934).

* `renv::install()` respects the project snapshot type, if set.

* `renv::install()` now keeps source when installing packages from source (#522).

* `renv::install()` now validates that binary packages can be loaded after
  installation, in a manner similar to source packages (#1275).

* `renv::install()` now supports Bioconductor remotes of the form
  `bioc::<BiocVersion>/<Package>`, for installing packages from
  a particular version of Bioconductor. Aliases like 'release' and
  'devel' are also supported (#1195).

* `renv::install()` now requires interactive confirmation that you want to
  install packages (#587).

* `renv::load()` gives a more informative message if a lockfile is present but
  no packages are installed (#353).

* `renv::load()` no longer attempts to query package repositories when checking
  if a project is synchronized (#812).

* `renv::load()` no longer duplicates entries on the `PATH` environment variable
  (#1095).

* `renv::restore()` can now use `pak::pkg_install()` to install packages
  when `pak` integration is enabled. Set `RENV_CONFIG_PAK_ENABLED = TRUE`
  in your project's `.Renviron` if you'd like to opt-in to this behavior.
  Note that this requires a nightly build of `pak` (>= 0.4.0-9000);
  see https://pak.r-lib.org/dev/reference/install.html for more details.

* `renv::restore()` now emits an error if called within a project that
  does not contain a lockfile (#1474).

* `renv::restore()` correctly restores packages downloaded and installed
  from [r-universe](https://r-universe.dev/) (#1359).

* `renv::snapshot()` now standardises pak metadata so CRAN packages installed via
  pak look the same as CRAN packages installed with renv or `install.packages()`
  (#1239).

* If `renv::snapshot()` finds missing packages, a new prompt allows you to
  install them before continuing (#1198).

* `renv::snapshot()` no longer requires confirmation when writing the first
  snapshot, since that's an action that can easily be undone (by deleting
  `renv.lock`) (#1281).

* `renv::snapshot()` reports if the R version changes, even if no packages
  change (#962).

* `renv::snapshot(exclude = <...>)` no longer warns when attempting to exclude
  a package that is not installed (#1396).

* `renv::status()` now uses a more compact display when packages have some
  inconsistent combination of being installed, used, and recorded.

* `renv::status()` now works more like `renv::restore()` when package versions
  are different (#675).

* `renv::update()` can now update packages installed from GitLab (#136) and
  BitBucket (#1194).

* `renv::settings$package.dependency.fields()` now only affects packages
  installed directly by the user, not downstream dependencies of those packages.

* renv functions give a clearer error if `renv.lock` has somehow become
  corrupted (#1027).

(mef)

doc: Updated devel/R-remotes to 2.4.2.1

(mef)

(devel/R-rematch) Updated 1.0.1 to 2.0.0

# rematch 2.0.0

* New `re_match_all` function to extract all matches.

* Removed the `perl` arguments, we always use PERL compatible regular
  expressions now.

(mef)

doc: Updated devel/R-rematch to 2.0.0

(mef)

(devel/R-rematch) Updated 1.0.1 to 2.0.0, make test passed

# rematch 2.0.0

* New `re_match_all` function to extract all matches.

* Removed the `perl` arguments, we always use PERL compatible regular
  expressions now.

(mef)

doc: Updated devel/R-purrr to 1.0.2

(mef)

(devel/R-purrr) Updated 1.0.1 to 1.0.2

# purrr 1.0.2

* Fixed valgrind issue.

* Deprecation infrastructure in `map_chr()` now has much less overhead
  leading to improved performance (#1089).

* purrr now requires R 3.5.0.

(mef)

doc: Updated devel/R-pkgcache to 2.2.1

(mef)

(devel/R-pkgcache) Updated 2.1.1 to 2.2.1

# pkgcache 2.2.1

* pkgcache now does a better job when matching the R version to a
  Bioconductor version.

# pkgcache 2.2.0

* New `pkg.current_platform` option and `PKG_CURRENT_PLATFORM` environment
  variable to override the detected platform.

* In `repo_add()` and `repo_resolve()` the `MRAN@` prefix is now deprecated
  and resolves to PPM, because MRAN will be retired soon. See more at
  <https://posit.co/blog/migrating-from-mran-to-posit-package-manager/>.

* The metadata cache now has `SystemRequirements` information for Bioconductor
  packages.

(mef)

(devel/R-pkgload) +TEST_DEPENDS, but make test does not pass yet

(mef)

doc: Updated devel/R-pkgload to 1.3.4

(mef)

(devel/R-pkgload) Updated 1.3.3 to 1.3.4

# pkgload 1.3.4

* On load, pkgload now sets `PKGLOAD_PARENT_TEMPDIR` to the temporary
  directory used in the current process. This provides a convenient place
  to cache results for functions used in subprocesses (e.g. `devtools::test()`,
  `devtools::document()`).

* Fixes for Debian packaging.

(mef)

doc: Updated devel/R-pkgbuild to 1.4.3

(mef)

(devel/R-pkgbuild) Updated 1.4.2 to 1.4.3, make test passed

# pkgbuild 1.4.3

* pkgbuild now does not need the crayon, rprojroot and prettyunits
  packages.

(mef)

doc: Updated devel/R-pak to 0.7.1

(mef)

(devel/R-pak) Updated 0.5.1 to 0.7.1

# pak 0.7.1

* pak can now handle the case when `Config/Needs/*` dependencies
  are requested for package from a repository.

* pak uses safer `*printf()` format strings now.

# pak 0.7.0

* pak now correctly handles the latest GitHub release with
  the `@*release` notation (@pawelru,
  https://github.com/r-lib/pkgdepends/pull/321)

* pak now correctly handles having multiple instances of the same
  package in the metadata, with different R version requirements
  (#534, #538, https://github.com/r-lib/pkgdepends/pull/331).

* `git::` package references work better now for Azure DevOps
  (@jameslairdsmith, https://github.com/r-lib/pkgdepends/pull/333,
  https://github.com/r-lib/pkgdepends/pull/342).

* pak now does a better job at accepting installed packages, and
  avoids reinstalling more packages than needed when using a lock file
  (https://github.com/r-lib/actions/issues/759,
  https://github.com/r-lib/pkgdepends/pull/338).

# pak 0.6.0

* pak now requires R >= 3.5.0.

* Many improvements in system requirements support:
  - New functions:
    - `pkg_sysreqs()`: calculate system requirements of packages.
    - `sysreqs_db_list()`, `sysreqs_db_match()`, `sysreqs_db_update()`:
      query the system requirements database.
    - `sysreqs_list_system_packages()`, `sysreqs_check_installed()`,
      `sysreqs_fix_installed()`: query and install missing system packages.
    - `sysreqs_platforms()`: list supported platforms.
  - The installation proposal, printed before installation, now includes
    required and missing system packages, on supported platforms.
  - New `sysreqs_platform` configuration option to override the auto-detected
    platform.
  - Faster, asynchronous system requirements lookup.
  - pak now does not reinstall system requirements by default,
    if they are already installed. (You can force a reinstall/upgrade
    with the `sysreqs_update` configuration option.)

* New `gitlab::` package source to install packages from GitLab
  (https://github.com/r-lib/pkgdepends/pull/315).

* pak now correctly parses multiple `git::` packages at once
  (https://github.com/r-lib/pkgdepends/issues/318).

* `git::` package sources now support version 1 of the git protocol.
  E.g. the Bioconductor git repositories now work:
  `git::https://git.bioconductor.org/packages/limma`
  (https://github.com/r-lib/pkgdepends/issues/314).

* The `platforms` config parameter now works correctly with `deps::`
  package sources (#522).

* New `include_linkingto` config parameter to always include `LinkingTo`
  packages in the solution, even for binaries
  (https://github.com/r-lib/pkgdepends/issues/485).

* `pkg_name_check()` now does not include Acromine results, because the web
  site was unstable.

* In `repo_add()` and `repo_resolve()` the `MRAN@` prefix is now deprecated
  and resolves to PPM, because MRAN will be retired soon. See more at
  <https://posit.co/blog/migrating-from-mran-to-posit-package-manager/>.

* The metadata cache now has `SystemRequirements` information for Bioconductor
  packages.

(mef)

doc: Updated devel/R-mockery to 0.4.4

(mef)

(devel/R-mockery) Updated 0.4.3 to 0.4.4, +TEST_DEPENDS, make test passed

# mockery 0.4.4

* Fixes for `R CMD check`

(mef)

(devel/R-lpSolve, correction) Updated 5.6.18 to 5.6.20, explicit NEWS.md unknown

Previous commit message was wrong, sorry, let me correct.
Also TEST_DEPENDS+=  updated, now make test passed.

(mef)

doc: Updated devel/R-lpSolve to 5.6.20

(mef)

((devel/R-lpSolve) Updated 5.6.17 to 5.6.18, explicit NEWS.md unknown

(mef)

(graphics/R-ragg) +TEST_DEPENDS+= tex-ec, make test passed

(mef)

(textproc/R-data.table) +TEST_DEPENDS+= R-nanotime, make test does not pass yet

(mef)

(time/R-Rcpp*) Add buildlink3.mk

(mef)

Added time/R-nanotime version 0.3.7

(mef)

(time/R-nanotime) import R-nanotime-0.3.7

Full 64-bit resolution date and time functionality with nanosecond
granularity is provided, with easy transition to and from the standard
'POSIXct' type. Three additional classes offer interval, period and
duration functionality for nanosecond-resolution timestamps.

(mef)

Added math/R-conflicted version 1.2.0

(mef)

(math/R-conflicted) import R-conflicted-1.2.0

R's default conflict management system gives the most recently loaded
package precedence. This can make it hard to detect conflicts,
particularly when they arise because a package update creates
ambiguity that did not previously exist. 'conflicted' takes a
different approach, making every conflict an error and forcing you to
choose which function to use.

(mef)

(time/Makefile) sort

(mef)

Added time/R-RcppCCTZ version 0.2.12

(mef)

(time/R-RcppCCTZ) import R-RcppCCTZ-0.2.12

'Rcpp' Access to the 'CCTZ' timezone library is provided. 'CCTZ' is a
C++ library for translating between absolute and civil times using the
rules of a time zone. The 'CCTZ' source code, released under the
Apache 2.0 License, is included in this package. See
<https://github.com/google/cctz> for more details.

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(textproc/R-vroom) +USE_LANGUAGES+= c++

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Updated -> Added

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doc: Updated time/R-RcppDate to 0.0.3

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(time/R-RcppDate) import R-RcppDate-0.0.3

A header-only C++ library is provided with support for dates, time
zones, ISO weeks, Julian dates, and Islamic dates. 'date' offers
extensive date and time functionality for the C++11, C++14 and C++17
standards and was written by Howard Hinnant and released under the MIT
license. A slightly modified version has been accepted (along with
'tz.h') as part of C++20. This package regroups all header files from
the upstream repository by Howard Hinnant so that other R packages can
use them in their C++ code. At present, few of the types have explicit
'Rcpp' wrappers though these may be added as needed.

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doc: Updated graphics/R-ragg to 1.2.7

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