doc: Updated cad/py-gdstk to 0.9.41

(mef)

(cad/py-gdstk) Updated 0.9.40 to 0.9.41

## 0.9.41 - 2023-05-24
### Added
- Dictionary-like access to library cells by name.
- `len(Library)` returns the number of cells in the library
- `Reference.cell_name` to directly access a referenced cell's name
### Fixed
- `RobustPath` accepts width of 0 at the path end

(mef)

doc: Updated cad/klayout to 0.28.8

(mef)

(cad/klayout) Updated 0.28.7 to 0.28.8

0.28.8          (2023-05-23):
* Enhancement: %GITHUB%/issues/1314 Storing (arbitrary) data in metadata
  - Meta information can be attached to layout and cells
  - Meta information has a string key and arbitrary value (hash, list supported)
  - Optionally, meta information can be made persistent and
    is stored in the (KLayout specific) context section of GDS2 and OASIS
  - Meta information is shown in the user properties dialog, but is not editable
  - Meta information is similar, but not the same than user properties

* Enhancement: %GITHUB%/issues/1324 Feature request: hide empty groups

* Enhancement: %GITHUB%/issues/1345 feature request: create a def
  single/mulitpart path import option

* Enhancement: %GITHUB%/issues/1348 "Reload Files" popup prevents
  closing KLayout

* Enhancement: %GITHUB%/issues/1349 Add application events for
  indicating start/finish of restoring session

* Bugfix: %GITHUB%/issues/1353 Bug in RecursiveInstanceIterator

* Enhancement: %GITHUB%/issues/1357 Add binding for
  QObject::findChildren

* Bugfix: %GITHUB%/issues/1360 LayoutView not promoted to correct
  class after Plugin initialization

* Bugfix: %GITHUB%/issues/1366 Slow merging of polygons from width
  check edge pairs

* Bugfix: %GITHUB%/issues/1373 Region "+" skips shapes with user
  properties on second input

* Enhancement: Ruby debugger performance improvement - with debugger
  enabled, Ruby script execution was very slow

* Enhancement: Polygon "decompose_convex" tries harder to avoid
  generating thin slivers

* (Significant) Enhancement: Selection of labels now considers label
  area, not just label origin point

* Bugfix: Making 'R', 'L' and 'C' parameters for the respective Spice
  elements beside "value"

* Enhancement: Zoom In/Out menu functions now use the current mouse
  position for the zoom fixpoint (important when binding them to a
  key)

* Bugfix: More consistent behavior of RBA/pya: enum classes are
  properly made available (was for example RBA::Qt::Qt_Keys instead of
  RBA::Qt_Keys and pya.Qt.

Keys was no fully initialized type object)

* Bugfix: Netlist reader: anonymous circuits (without definition) will
  not fail because of unknown parameters

* Bugfix: Closed paths lost last point after editing in partial edit
  mode

* Enhancement: Somewhat better grid snapping in partial edit mode
* Bugfixes/enhancements: Macro editor
  - fixed missing icons for "back" and "forward"
  - enhancements for "search & replace"
  - Ctrl+R and Ctrl+Shift+R for replace and "replace all"
  - Fixed tool tips for buttons

(mef)

doc: Updated geography/R-rgdal to 1.6.7

(mef)

(geography/R-rgdal) Updated 1.5.27 to 1.6.7

# Please note that **rgdal** will be retired during 2023, plan
  transition to sf/stars/terra functions using GDAL and PROJ at your
  earliest convenience (see
  https://r-spatial.org/r/2023/05/15/evolution4.html and earlier blogs
  for guidance).

# Version 1.6-7 (development, rev. 1202-)

* Make retirement in October 2023 explicit, move package start-up
  messages to load from attach

# Version 1.6-6 (2023-04-18, rev. 1200-1201)

* add SharpYuv condition in src/Makevars.ucrt

# Version 1.6-5 (2023-03-02, rev. 1198-1199)

* Upgrade CXX11 to CXX17 (may cause problems for archaic OS)

# Version 1.6-4 (2023-01-12, rev. 1188-1197)

* Update GridsDatums data set

* Warn if retracted GDAL 3.6.0 is being used

* Update `makevars.ucrt` to Rtools 4.3

# Version 1.6-3 (2022-12-14, rev. 1184-1187)

* CRAN error in possibly writing outside tempdir

* CRAN error in printing stored stale `sessionInfo()` output in vignette

# Version 1.6-2 (2022-11-09, rev. 1177-1183)

* deprecation of `project()`, `CRSargs()`, `asSGDF_GROD()`,
  `readGDAL()`, `writeGDAL()`, `create2GDAL()`, `showWKT()`,
  `showEPSG()`, `readOGR()`, `ogrFIDs()`, `ogrInfo()`, `ogrDrivers()`,
  `writeOGR()`, `ogrListLayers()`, `GDALinfo()`, `print.GDALobj()`,
  `GDALcall()`, `rawTransform()`, `OGRSpatialRef()` in favour of
  functions and methods ib **sf** and **terra**.

* handle -Wstrict-prototypes `int main()` to `int main(void)` in
  `configure.ac`

* update `src/Makevars.ucrt` to upgraded MXE geospatial libraries

* address https://github.com/r-spatial/sf/pull/2009 in `src/Makevars.ucrt`

* set PROJ4 warnings default to "none"

* fix -Wstrict-prototypes warnings in code

# Version 1.5-32 (2022-05-09, rev. 1173-1176)

* update src/Makefile.ucrt to accommodate the GDAL raster Geospatial
  PDF driver for reading

# Version 1.5-31 (2022-04-18, rev. 1172)

* unescape underscores in help pages

# Version 1.5-30 (2022-04-08, rev. 1166-1171)

* restore PROJ path assignment for PROJ >= 6 not using PROJ_LIB (was
  used for PROJ 6 but not > 6)
  https://github.com/rsbivand/rgrass/issues/52

* Update src/Makevars.win to GDAL 3.4.1 for R < 4.2
  https://github.com/r-spatial/sf/pull/1919

# Version 1.5-29 (2022-03-15, rev. 1159-1165)

* also convert BOUNDCRS to PROJCRS by default in OGRSpatialRef() and
  getProjectionRef()

* test for chunks table in cache.db in vignette

* quietening tests only differing by `proj.db` version.

# Version 1.5-28 (2021-12-15, rev. 1157-1158)

* Adapting to R 4.2 Windows UCRT

(mef)

doc: Updated devel/R-testthat to 3.1.8

(mef)

(devel/R-testthat) Updated 3.1.6 to 3.1.8

# testthat 3.1.8

* `expect_snapshot()` differences no longer use quotes.

* `expect_error()`, `expect_warning()`, and `expect_message()` now correctly
  enforce that the condition is of the expected base class (e.g. error,
  warning, messsage) even when the `class` argument is used (#1168).

* `it()` now calls `local_test_context()` so that it behaves more
  similarly to `test_that()` (#1731), and is now exported so that you
  can more easily run BDD tests interactively (#1587)

* `skip_on_bioc()` now uses the documented environment variable
  (`IS_BIOC_BUILD_MACHINE`) (#1712).

* `source_file()`, which is used by various parts of the helper and
  setup/teardown machinery, now reports the file name in the case of
  errors (#1704).

* `test_path()` now works when called within helper files (#1562).

* New `vignette("special-files")` describes the various special files
  that testthat uses (#1638).

* `with_mocked_bindings()` and `local_mocked_bindings()` now also bind in the
  imports namespace and can mock S3 methods. These changes make them good
  substitutes for the deprecated functions `with_mock()` and `local_mock()`, so
  those older functions now recommend switching to the newer equivalents
  instead of using the mockr or mockery packages.

# testthat 3.1.7

* `expect_setequal()` gives more actionable feedback (#1657).

* `expect_snapshot()` no longer elides new lines when run interactively (#1726).

* Experimental new `with_mocked_bindings()` and `local_mocked_bindings()`
  (#1739).

(mef)

editors/tp-note: clean-up after update

(pin)

doc: Updated benchmarks/hyperfine to 1.17.0

(pin)

benchmarks/hyperfine: update to 1.17.0

Features
- Add new --sort option to control the order in the rel. speed comparison and
  in markup export formats, see #601, #614, #655 (@sharkdp)
- Parameters which are unused in the command line are now displayed in
  parentheses, see #600 and #644 (@sharkdp).
- Added --log-count option for histogram plots, see scripts/plot_histogram.py
  (@sharkdp)

Changes
- Updated hyperfine to use windows-sys instead of the unmaintained winapi,
  see #624, #639, #636, #641 (@clemenswasser)
- Silenced deprecation warning in Python scripts, see #633 (@nicovank)
- Major update of the man page, see 0ce6578, #647 (@sharkdp)

Bugfixes
- Do not export intermediate results to stdout when using - as a file name,
  see #640 and #643 (@sharkdp)
- Markup exporting does not fail if benchmark results are zero, see #642
  (@sharkdp)

(pin)

doc: Updated security/apg to 2.3.0bnb12

(triaxx)

apg: Add missing dependency

pkgsrc changes:
---------------
  * Add openssl since a linker error occurs due to missing lcrypto on at
    least Darwin.
  * Bump revision

(triaxx)

doc: Updated x11/xscope to 1.4.4

(wiz)

This release fixes some minor bugs and adds support for decoding the
DAMAGE extension.

Alan Coopersmith (9):
      scope.h: remove second include of fd.h
      gitlab CI: stop requiring Signed-off-by in commits
      gitlab CI: build with both --enable-xtrans & --disable-xtrans
      fd.h: fix build when not building with xtrans
      DataFromClient: Avoid segfault if FlushFD() closed the connection
      PrintField: Don't over-indent when verbose < 3
      Add support for DAMAGE extension versions 1.0 & 1.1
      Remove "All rights reserved" from Oracle copyright notices
      xscope 1.4.4

(wiz)

doc: Added textproc/tree-sitter-elisp version 1.3.0

(wiz)

textproc/Makefile: + tree-sitter-elisp

(wiz)

textproc/tree-sitter-elisp: import tree-sitter-elisp-1.3.0

Emacs Lisp grammar for tree-sitter

(wiz)

doc: Updated math/R-XML to 3.99.0.14

(mef)

(math/R-XML) Updated 3.99.0.9 to 3.99.0.14. NEWS.md unknown

(mef)

add mailman3 and related packages

(markd)

mailman3-web: add version 0.0.6

This is a Django project that contains default settings and url settings
for Mailman 3 Web Interface. It consists of the following sub-projects:

* Postorius
* Hyperkitty

(markd)

doc: Updated math/R-proxy to 0.4.27

(mef)

(math/R-proxy) Updated 0.4.25 to 0.4.27

(R CMD Rdconv -t txt  /tmp/math/R-proxy/work/proxy/inst/NEWS.Rd)
News for Package 'proxy'

Changes in version 0.4-27:

        * cosmetic changes in help pages

        * add angular distance/similarity; keep old behavior as cosine

Changes in version 0.4-26:

        * Change coercion function for cosine similarity to distance to
          1-x instead of 1-abs(x)

(mef)

py-mailman-hyperkitty: add version 1.2.1

This module contains a Mailman archiver plugin which sends emails to
HyperKitty, the web archiver.

(markd)

mailman3: add version 3.3.8

Mailman is free software for managing electronic mail discussion and
e-newsletter lists. Mailman is integrated with the web, making it easy
for users to manage their accounts and for list owners to administer
their lists. Mailman supports built-in archiving, automatic bounce
processing, content filtering, digest delivery, spam filters, and
more.

(markd)

doc: Updated geography/R-mapdata to 2.3.1

(mef)

(geography/R-mapdata) Updated 2.3.0 to 2.3.1 ChangeLog unknown

(mef)

py-hyperkitty: add version 1.3.7

HyperKitty is an open source Django application under development. It aims
to provide a web interface to access GNU Mailman v3 archives.

(markd)

py-postorius: add version 1.3.8

The Postorius Django app provides a web user interface to access GNU Mailman.

(markd)

doc: Updated math/R-FNN to 1.1.3.2

(mef)

(math/R-FNN) Updated 1.1.3.1 to 1.1.3.2 ChangeLog unknwon

(mef)

py-cmarkgfm: add version 2022.10.27

Minimalist Python bindings to GitHub's fork of cmark.

(markd)

py-django-q: add version 1.3.9

A multiprocessing distributed task queue for Django

Features:
* Multiprocessing worker pool
* Asynchronous tasks
* Scheduled, cron and repeated tasks
* Signed and compressed packages
* Failure and success database or cache
* Result hooks, groups and chains
* Django Admin integration
* PaaS compatible with multiple instances
* Multi cluster monitor
* Redis, Disque, IronMQ, SQS, MongoDB or ORM
* Rollbar and Sentry support

(markd)

doc: Updated print/R-knitr to 1.43

(mef)

(print/R-knitr) Updated 1.42 to 1.43

(w3m -insecure -dump -T text https://github.com/yihui/knitr/releases)
knitr 1.43
25 May 13:30

NEW FEATURES

  * Progress bar includes the chunk location (chunk-name @ file:line) when
    options(knitr.progress.linenums = TRUE) is set (thanks, @zeehio, #2232).

  * The global option knitr.progress.simple can be used to decide whether to
    output the bar in the progress. When set to FALSE, only the step numbers
    and chunk labels will be printed, and the progress bar is omitted. This can
    be more useful for logging purposes since the bar itself is not useful
    (thanks, @hadley, #2221). By default, the simple progress output is used
    when the progress is not written to a connection such as stdout or stderr
    (e.g., written to a file instead), or the output connection is not a
    "terminal".

  * HTML Widgets can now support alt text by specifying an attribute
    aria-labelledby="<label>" in their first HTML tag. The text will be
    obtained from the fig.alt or fig.cap chunk option in the usual way (thanks,
    @dmurdoch, #2243).

  * Added a new argument newline to kable() to handle newlines in data when the
    table output format is Markdown-based (simple, pipe, rst, or jira). By
    default, newlines are not processed, which can result in broken tables. To
    substitute newlines with spaces, use kable(..., newline = ' '). To remove
    newlines, use kable(..., newline = '') (thanks, @aronatkins, #2255).

BUG FIXES

  * The chunk option collapse = TRUE works with HTML widgets now (thanks,
    @dmurdoch, #2212).

  * Option hooks should be run before child documents are processed (thanks,
    @richarddmorey, #2247).

  * For .Rnw documents, is_latex_output() returns TRUE for output formats
    sweave (render_sweave()) and listings (render_listings()) now (thanks,
    @DavisVaughan, #2231).

  * write_bib() does not fail anymore if an empty string is passed as package
    name (thanks, @phargarten2, #2240).

  * Fix an issue with using cache = TRUE on sql engine chunk not defining a
    output.var (thanks, @mfherman, @eitsupi, #1842).

  * plot_crop() correctly checks the required tools (pdfcrop and ghostscript)
    on Windows when the LaTeX is distribution is TeX Live or TinyTeX (thanks,
    @remlapmot, #2246). An external installation of ghostscript is no longer
    required on Windows, since TeX Live's built-in ghostscript will be used.

  * The chunk option dev.args was not recognized in certain cases (thanks,
    @petrbouchal, #2238).

MINOR CHANGES

  * The css and js engines work for the markdown output format now. Previous
    these engines will not output anything when the output format is markdown.
    If you still want to disable them for markdown output, you may use the
    chunk option eval = FALSE or eval = knitr::is_html_output(excludes =
    'markdown').

  * is_html_output() recognizes R Markdown v1 documents now (.Rmd documents
    compiled via the markdown package).

  * For .Rnw documents, dots in figure file paths are no longer sanitized to
    underscores (thanks, @otoomet, #2213). Other special characters are still
    sanitized, but this feature can be turned off via options
    (knitr.sanitize.paths = FALSE).

  * imgur_upload() now recognizes a global option knitr.imgur.key or an
    environment variable R_KNITR_IMGUR_KEY for a custom client ID (thanks,
    @jonthegeek, #2233).

  * imgur_upload() requires fewer package dependencies now. It only requires
    the curl package; httr is no longer required, and xml2 has become optional.

(mef)

py-django-picklefield: add version 3.1

django-picklefield provides an implementation of a pickled object field.
Such fields can contain any picklable objects.

(markd)

py-django-haystack: add version 3.2.1

Haystack provides modular search for Django. It features a unified, familiar
API that allows you to plug in different search backends (such as Solr,
Elasticsearch, Whoosh, Xapian, etc.) without having to modify your code.

(markd)

py-django-compressor: add version 4.3.1

Django Compressor processes, combines and minifies linked and inline
Javascript or CSS in a Django template into cacheable static files.

It supports compilers such as coffeescript, LESS and SASS and is
extensible by custom processing steps.

(markd)

py-django-mailman3: add version 1.3.9

This package contains libraries and templates for Django-based interfaces
interacting with Mailman.

To use this application, add django_mailman3 to the INSTALLED_APPS list
in your Django server's settings file.

(markd)

py-django-allauth: add version 0.54.0

Integrated set of Django applications addressing authentication, registration,
account management as well as 3rd party (social) account authentication.

(markd)

py-openid: update to 3.2.0

3.0.9
Compatibility fix for `HTMLParser`

3.0.6
Improvements to stores, tests, and fetchers

3.0.3
Improvements to admin test runner

3.0.2
All the tests that require no more than the standard library pass -- however
modules that depend on external packages (such as the pyCURL fetcher or the
MySQL / PostgreSQL stores) haven't been updated and may not work.

3.0.1
This implementation of OpenID has been ported to Python 3 -- all but one test
is known to pass.

(markd)

doc: Updated www/R-shiny to 1.7.4

(mef)

(www/R-shiny) Updated 1.7.1 to 1.7.4

# shiny 1.7.4

## Full changelog

### Breaking changes

* Closed #3719: Output container sizes, which are available via
  [`session$clientData` and
  `getCurrentOutputInfo()`](https://shiny.rstudio.com/articles/client-data.html),
  no longer round to the nearest pixel (i.e., they are now more exact,
  possibly fractional values). (#3720)

* Closed #3704, #3735, and #3740: `renderPlot()` no longer generates
  an error (or segfault) when it executes before the output is
  visible. Instead, it'll now use the graphics device's default size
  for it's initial size. Relatedly, `plotPNG()` now ignores `NULL`
  values for `width`/`height` (and uses the device's default
  `width`/`height` instead). (#3739)

### New features and improvements

* `plotOutput()`, `imageOutput()`, and `uiOutput()` gain a `fill`
  argument. If `TRUE` (the default for `plotOutput()`), the output
  container is allowed to grow/shrink to fit a fill container (created
  via `htmltools::bindFillRole()`) with an opinionated height. This
  means `plotOutput()` will grow/shrink by default [inside of
  `bslib::card_body_fill()`](https://rstudio.github.io/bslib/articles/cards.html#responsive-sizing),
  but `imageOutput()` and `uiOutput()` will have to opt-in to similar
  behavior with `fill = TRUE`. (#3715)

* Closed #3687: Updated jQuery-UI to v1.13.2. (#3697)

* Internal: Added clearer and strict TypeScript type definitions (#3644)

# shiny 1.7.3

### Bug fixes

* Shiny 1.7.0 changed the `icon(lib="fontawesome")` implementation
  from a bundled copy of fontawesome, to the {fontawesome}
  package. This led to issue #3688, where icons that were previously
  working, were now breaking. That's because {fontawesome} 0.3.0 and
  earlier did not have support for icon names used in Font Awesome 5
  and earlier, only the newest icon names used in Font Awesome 6. Now,
  {fontawesome} 0.4.0 has restored support for those older icon names,
  and Shiny 1.7.2.1 has updated its {fontawesome} requirement to
  >=0.4.0.

# shiny 1.7.2

## Full changelog

### Breaking changes

* Closed #3626: `renderPlot()` (and `plotPNG()`) now uses
  `ragg::agg_png()` by default when the [`{ragg}`
  package](https://github.com/r-lib/ragg) is installed. To restore the
  previous behavior, set `options(shiny.useragg = FALSE)`. (#3654)

### New features and improvements

* Closed #1545: `insertUI()` now executes `<script>` tags. (#3630)

* `fileInput()` can set the `capture` attribute to facilitates user
  access to a device's media capture mechanism, such as a camera, or
  microphone, from within a file upload control ([W3C HTML Media
  Capture](https://www.w3.org/TR/html-media-capture/)). (Thanks to
  khaled-alshamaa, #3481)

* Closed tidyverse/dplyr#5552: Compatibility of dplyr 1.0 (and rlang
  chained errors in general) with `req()`, `validate()`, and friends.

* Closed tidyverse/dplyr#6154: Values from an `actionButton()` had S3
  classes in the incorrect order.

* Closed #3346: Default for `ref` input in `runGithub()` changed from
  `"master"` to `"HEAD"`. (#3564)

* Closed #3619: In R 4.2, `splitLayout()` no longer raises warnings
  about incorrect length in an `if` statement. (Thanks to @dmenne,
  #3625)

### Bug fixes

* Closed #3250:`{rlang}`/`{tidyeval}` conditions (i.e., warnings and
  errors) are no longer filtered from stack traces. (#3602)

* Closed #3581: Errors in throttled/debounced reactive expressions no
  longer cause the session to exit. (#3624)

* Closed #3657: `throttle.ts` and the `Throttler` typescript objects
  it provides now function as intended. (Thanks gto @dvg-p4, #3659)

* The auto-reload feature (`options(shiny.autoreload=TRUE)`) was not
  being activated by `devmode(TRUE)`, despite a console message
  asserting that it was. (#3620)

* Closed #2297: If an error occurred in parsing a value in a bookmark
  query string, an error would be thrown and nothing would be
  restored. Now a message is displayed and that value is
  ignored. (Thanks to @daattali, #3385)

* Restored the previous behavior of automatically guessing the
  `Content-Type` header for `downloadHandler` functions when no
  explicit `contentType` argument is supplied. (#3393)

* Previously, updating an input value without a corresponding Input
  binding element did not trigger a JavaScript `shiny:inputchanged`
  event. Now, if no Input binding element is found, the
  `shiny:inputchanged` event is triggered on
  `window.document`. (#3584)

* Closed #2955: Input and output bindings previously attempted to use
  `el['data-input-id']`, but that never worked. They now use
  `el.getAttribute('data-input-id')` instead. (#3538)

### Minor improvements

* When taking a test snapshot, the sort order of the json keys of the
  `input`, `output`, and `export` fields is currently sorted using the
  locale of the machine. This can lead to inconsistent test snapshot
  results. To opt-in to a consistent ordering of snapshot fields with
  `{shinytest}`, please set the global option
  `options(shiny.snapshotsortc = TRUE)`. `{shinytest2}` users do not
  need to set this value. (#3515)

* Closed rstudio/shinytest2#222: When restoring a context (i.e.,
  bookmarking) from a URL, Shiny now better handles a trailing `=`
  after `_inputs_` and `_values_`. (#3648)

* Shiny's internal HTML dependencies are now mounted dynamically
  instead of statically. (#3537)

* HTML dependencies that are sent to dynamic UI now have better type
  checking, and no longer require a `dep.src.href` field. (#3537)

(mef)

doc: Updated www/R-shinyjs to 2.1.0

(mef)

(www/R-shinyjs) Updated  2.0.0 to  2.1.0

# shinyjs 2.1.0 (2021-12-20)
- New feature: you can now reset all inputs on the page by calling
  `reset()` with no arguments (#222)
- New feature: Add a `removeEvent()` function which removes events
  added to HTML elements with `onclick()` or `onevent()` (#244)
- Fix bug: `disable()` did not work on nested download buttons (#223)
- Fix bug: Don't automatically namespace ID arguments in custom
  extendShinyjs functions (#229)
- Fix bug: ensure that `extendShinyjs()` functions don't overwrite
  native {shinyjs} functions (#230)

(mef)

py-django-gravatar2: add version 1.4.4

A lightweight django-gravatar app. Includes helper methods for interacting
with gravatars outside of template code.

(markd)

py-mailmanclient: add version 3.3.5

The mailmanclient library provides official Python bindings for the GNU
Mailman 3 REST API.

(markd)

doc: Updated filesystems/glusterfs to 10.4

(gutteridge)

glusterfs: update to 10.4

Update provided by Alexander Schreiber, with some tweaks by me (e.g.,
commenting out debug settings in Makefile, simplifying PLIST.Linux).

Changes and notes from maintainer:

- enable building on Linux

It was tested (built and ran the client) on:
- NetBSD: amd64, sparc64
- Linux: amd64

Due to some differences in files being generated by the build between
Linux and NetBSD, both MESSAGE and PLIST where split by OS platform.

Since the package changelog for glusterfs is just a "git log" dump,
the condensed form from the release notes is:

Important fixes in this release
Fix fuse concurrency problems
Fix memory corruption in debug builds
Fix recovery issue with posix locks upon reconnection of a disconnected brick

Issues addressed in this release
#1000 configure: Force 'char' type to be signed in order to eliminate anomalies
#2752 posix: Fix directory gfid handle if a rename fails
#3345 Fix inconsistencies in big-endian architectures of hashfn
#3346 Fix stack overflow when processing glx_dir(p) list structures in xdr
#3882 Fix deadlock in gf_print_trace of sys_log
#3901 Fix segmentaion fault in io-stats xlator
#3954 Fix stack-buffer-overflow according to AddressSanitizer
#4020 Improve regression test suite
#4029 Process stuck listing snapshots from NFS
#4031 Fix Input/Output error when using linux-aio on big-endean architectures
#4042 Fix recovery issue with posix locks upon reconnection of a disconnected brick
#4071 Make timestamps of .snap directory stable
#3894 Use opendir for directories in glfs_open and glfs_h_open of api
#3636 Enable posix xlator to consider storage.reserve val

(gutteridge)

python package updates

(markd)

py-flask-security-too: add version 5.2.0

Flask-Security allows you to quickly add common security mechanisms
to your Flask application.

This is a independently maintained version of Flask-Security based on
the 3.0.0 version of the Original.

(markd)

py-flask-babel: update to 3.1.0

v3.1.0
- Documentation and packaging improvements.
- Don't return the default locale twice
- Fix tests breaking against babel 12.2, which changed localized times to use
  non-breaking-spaces. Babel 12.2 or greater is now required.
- Relax version requirements for dependencies.

v3.0.0
Major version bump as this version removes support for Python 3.5 and 3.6, along with multiple
major breaking changes. Hope you've been following SemVer :)

- Dropped support for end-of-life Python 3.5 and 3.6, added tests for 3.10 and 3.11.
- Fixes to documentation to address outdated links and settings
- Jinja version 3 or greater is now required (released 2021)
- Removed Babel._date_formats, use the public Babel.date_formats instead.
- list_translations() always returns the default locale, even if it does not exist.
- Add lazy_npgettext()
- Babel.locale_selector and Babel.timezone_selector no longer exist. They must be provided
  either when the Babel() object is created or when init_app() is called. This is to support
  having a single Babel object for multiple Flask apps as well as to simplify settings
  and multi-threaded state.
- Most configuration options can be passed directly through init_app().

v2.0.0
Starting with version 2, flask-babel drops official support for Python2.
Python versions 3.5 through 3.9-beta1 are tested and supported, as well as pypy3.

- Tests moved from unittest to pytest
- Domain and caching support from Flask-BabelEx
- Documentation moved from python-hosted to Github Pages.
- CI moved from Travisci to Github Actions
- Small documentation improvements.
- Removed uncessary checks on get_translations()
- localeselector and timezoneselector can be changed after creation.

(markd)

py-sqlalchemy-utils: update to 0.41.1

0.41.1 (2023-04-27)
- Use a custom SQL construct for refreshing materialized views in
  `refresh_materialized_view`

0.41.0 (2023-04-13)
- Support psycopg3 for ``create_database()`` and ``delete_database()``.

0.40.0 (2023-02-12)
- Remove Python 3.6 support
- Add SQLAlchemy 2 support
- Add comparison operator support for LTree type

0.39.0 (2022-12-23)
- Support Python 3.11.
- Add pre-commit hooks for uniform text checks, isort, flake8, and pyupgrade.
- Fix a crash that occurs if the ``colour-science`` package is installed,
  which shares the same import name as the ``colour`` package that
  sqlalchemy-utils supports.
- Fix a crash that occurs if the installed sqlalchemy version is a beta

0.38.3 (2022-07-11)
- Fixed double-quoted UUID's in sqlalchemy >= 1.4.30
- Fixed create_database() and drop_database() crashing with CockroachDB
- Added mixed case support for pg composite
- Support Python 3.10.
- Drop support for Python 3.4 and 3.5.
- Remove the dependency on the six package.
- Introduce sqlalchemy 2.0 compatibility.

0.38.2 (2021-12-29)
- Added inherit_cache=False in order to avoid SQLAlchemy warnings in
  `cast_locale_expr`

0.38.1 (2021-12-21)
- Added cache_ok=True for various different types

0.38.0 (2021-12-21)
- Removed CompositeArray. Instead of CompositeArray one should use
  ARRAY(dimensions=1)
- Made ChoicesType only convert lists to tuples internally.

0.37.9 (2021-10-19)
- Fixed base padding class abstract methods
- Optimized cast_locale function
- Allow for arbitrary Table keyword arguments in create_table_from_selectable

0.37.8 (2021-06-28)
- Added 'zoneinfo' backend to TimezoneType

0.37.7 (2021-06-15)
- Added identifier quoting for view functions and constructs
- Added literal processor for UUIDType

0.37.6 (2021-06-02)
- Added `cache_ok=True` for TSVectorType

0.37.5 (2021-05-31)
- Fixed instant_defaults_listener to respect constructor supplied kwargs

0.37.4 (2021-05-21)
- Fixed incorrect Ltree.lca behaviour

0.37.3 (2021-05-16)
- Added `cache_ok=True` for all custom types
- Added CockroachDB support for UUIDType

0.37.2 (2021-05-05)
- Added python_requires to setup.py

0.37.1 (2021-05-03)
- Removed py27 from pypi wheel

0.37.0 (2021-04-12)
- Added SQLAlchemy 1.4 support
- Fixed database_exists() on PostgreSQL
- Added create_database support pymssql
- Removed `sort_query`, `get_query_entities` and `get_query_entity_by_alias`
  functions

(markd)

doc: Updated net/gh to 2.30.0

(bsiegert)

gh: update to 2.30.0

What's New

-  Support for nested aliases
-  repo set-default --view can now be called without a repo argument

What's Changed

-  Color control and sensible defaults in modern terminals
-  Fix windows crash by bumping wincred
-  Update browser package to avoid Windows crash
-  release upload sanitizes asset filenames prior to uploading
-  pr status uses lighter API in supported environments
-  All commands start up time improvements
-  More commands use latin matching filter
-  pr create respects GH_REPO env variable
-  Do not fall back to legacy template if template selector returns nil

(bsiegert)

doc: Updated net/netop to 0.1.2

(pin)

net/netop: update to 0.1.2

- Update dependencies

(pin)

doc: Updated editors/tp-note to 1.21.5

(pin)

editors/tp-note: update to 1.21.5

Rename root dir marker `.tpnoteroot`; Add pseudo lang. tag `+all`

* Breaking change: rename root directory marker file from `.tpnoteroot` to
  `.tpnoteroot.toml`.
* Allow optional project specific configuration data in `.tpnoteroot.toml`.
  Tp-Note will source the configuration for all note file in all subdirectories.
  Empty `.tpnoteroot.toml` content is still allowed.
* Interpret the pseudo language tag `+all` as "select all available languages"
  in the environment variable `TPNOTE_LANG_DETECTION` and the configuration
  file variable `tmpl.filter_get_lang`.

(pin)

doc: Updated x11/xrdb to 1.2.2

(wiz)

xrdb: update to 1.2.2.

Alan Coopersmith (9):
      gitlab CI: add a basic build test
      Build xz tarballs instead of bzip2
      gitlab CI: stop requiring Signed-off-by in commits
      Variable scope reduction as recommended by cppcheck
      Use C99 struct initialization
      Rename variable 'dup' to avoid shadowing dup() function
      Fallback asprintf: don't truncate output that has a \0 in string
      configure: raise minimum autoconf requirement to 2.70
      xrdb 1.2.2

(wiz)

doc: Updated x11/xwd to 1.0.9

(wiz)

xwd: update to 1.0.9.

Alan Coopersmith (12):
      Fix spelling/wording issues
      gitlab CI: add a basic build test
      Build xz tarballs instead of bzip2
      gitlab CI: stop requiring Signed-off-by in commits
      Remove unused macros
      Handle -Wcomma warnings from clang
      Remove unnecessary casts from malloc() and free() calls
      Variable scope reduction as recommended by cppcheck
      Delete commented-out local copy of list function prototypes
      list.c: Stop building functions that are never called
      Make -help & -version work without requiring an open display
      xwd 1.0.9

(wiz)

TODO.crosscompile: bsd.pkg.readme.mk needs TOOL/BUILD_DEPENDS split

(riastradh)

doc: Updated www/R-curl to 5.0.0

(mef)

(www/R-curl) Updated 4.3.2 to 5.0.0

5.0.0
- New function multi_download() which supports concurrent downloads and resuming
  download for large files, while giving detailed progress information.
- Windows: updated libcurl to 7.84.0 + nghttp2
- Windows: default to CURLSSLOPT_NATIVE_CA when using openssl unless an ennvar
  with CURL_CA_BUNDLE is set.
- Use the new optiontype API for type checking if available (libcurl 7.73.0)

4.3.3
- Add support for setting ssl_ctx_function callbacks
- Normalize curlopt_postfields to curlopt_copypostfields to transfer ownership
  of the input data to libcurl.
- Fix strict-prototype errors

(mef)

doc: Updated www/R-httr to 1.4.6

(mef)

(www/R-httr) Updated 1.4.2 to 1.4.6

# httr 1.4.6

* Supress use of httpbin in examples and tests because it has become
  unreliable.

# httr 1.4.5

* An internal helper that checks for an interactive session in the OOB
  flow now honors the `"rlang_interactive"` global option, in case
  it's necessary to declare the session to be interactive (enough) for
  OOB (@jennybc, #734).

# httr 1.4.4

* Fix intermittent failing test.

# httr 1.4.3

* Fix failing test.

(mef)

bsd.pkg.use.mk: TOOL_DEPENDS, not BUILD_DEPENDS, for libtool-fortran.

But we need a cross-libtool-fortran for this to actually work in
cross compilation.

No functional change intended for native compilation, since
BUILD_DEPENDS and TOOL_DEPENDS have the same semantics there.

(riastradh)

doc: Updated textproc/R-yaml to 2.3.7

(mef)

(textproc/R-yaml) Updated 2.2.1 to 2.3.7

### Release Notes

v2.3.7 clang deprecated sprintf. Changed in included clib to snprintf

v2.3.6 C deprecated functions with no prototypes, these were added.

v2.3.5 Patch to put back in libyaml modifications that as.yaml relied on.

v2.3.4
  - Added read_yaml parameter readLines.warn that defaults to TRUE for
    overrriding warnings about incomplete files.

v2.3.3
  -Fixed Bug #99, support for BUILTINSXP functions as handlers

v2.3.2
  - Removed some code that got revert in the libyaml 0.2.5 merge at
    2.2.4 release

v2.3.1
  - Added omap support for output using proper tag.

v2.3.0
  - Made eval.expr default to FALSE

v2.2.4
  - Updated libyaml code from 0.2.5

v2.2.3
  - Added attribute quote support for strings #72 #109

v2.2.2
  - change maintainer from Jeremy Stephens to Shawn Garbett
  - move Git repository to https://github.com/vubiostat/r-yaml

(mef)

doc: Updated textproc/R-markdown to 1.7

(mef)

(textproc/R-markdown) Updated 1.5 to 1.7

# CHANGES IN markdown VERSION 1.7

- The `file` argument of `mark()` will be treated as a file path only
  if the file exists and the value is not wrapped in
  `I()`. Previously, it would be treated as a file path when it has a
  file extension, which could lead to confusing errors like #100
  (thanks, @LukasWallrich).

- When there are emojis in the text, `mark()` may fail to identify and
  embed web resources (thanks, @tdhock, yihui/knitr#2254).

# CHANGES IN markdown VERSION 1.6

- Added support for footnotes, fenced `Div`s, section numbers, `{}`
  attributes for images/headings/fenced `Div`s, and appendices. See
  `vignette('intro', package = 'markdown')` for details.

- A lot of enhancements to the HTML slides format. See
  `vignette('slides', package = 'markdown')` for details.

- Added `vignette('article', package = 'markdown')` to demonstrate how
  to write an HTML article.

- If the input to `mark()` is a file, the output will also be a file
  by default. Previously the output would be text. If you want
  `mark()` to return text output when the input is a file, you may
  specify the argument `output = NULL`.

- The Markdown option `base64_images` has been renamed to
  `embed_resources`. This option can take two possible values,
  `"local"` and `"https"`, meaning whether to embed local and/or web
  (https) resources. You can specify none, either, or both of
  them. See `vignette('intro', package = 'markdown')` for details.

- Removed the option `standalone` from the list of Markdown
  options. Please use the argument `template = TRUE/FALSE` of `mark()`
  instead. The option `standalone = TRUE` was equivalent to `template
  = TRUE`.

- Added the option `auto_identifiers` (enabled by default) to
  automatically add IDs to headings, e.g., `# Hello world!` will be
  converted to `<h1 id="hello-world">Hello world!</h1>`. You can
  certainly override the automatic ID by providing an ID manually via
  the `{#id}` attribute, e.g., `# Hello world! {#hello}`.

- Renamed the `mathjax` option to `js_math` to allow for other JS math
  libraries. The default library was changed from MathJax to KaTeX. To
  continue using MathJax, you may set `js_math: mathjax`.

- Removed the option `mathjax_embed` from the list of Markdown
  options. To embed the MathJax library, enable `"https"` in the
  `embed_resources` option instead. Note that only MathJax v3 can be
  partially embedded, and lower versions cannot.

- Renamed the option `highlight_code` to `js_highlight`, and added
  support for an alternative syntax highlighting JS library Prism.js,
  which became the default. To continue using the old default
  `highlight.js`, you may set the `js_highlight` option to
  `highlight`.

- The default version of MathJax has been changed from v2 to v3.

- The default version of highlight.js has been changed from 11.6.0 to
  11.7.0, and the default style has been switched from `github` to
  `xcode`.

(mef)

doc: Updated textproc/R-commonmark to 1.9.0

(mef)

(textproc/R-commonmark) Updated 1.7 to 1.9.0

1.9.0
- Add parameter 'footnotes' to enable footnote parsing
- Update libcmark-gfm to 0.29.0.gfm.9

1.8.1
- Update libcmark-gfm to 0.29.0.gfm.6
- Fix strict-prototypes warnings

1.8.0
- Update libcmark-gfm to 0.29.0.gfm.3

(mef)

doc: Updated textproc/R-highr to 0.10

(mef)

(textproc/R-highr) Updated 0.9 to 0.10, NEWS.md unknown

(mef)

doc: Updated textproc/R-formatR to 1.14

(mef)

(textproc/R-foramtR) Updated 1.11 to 1.14

https://github.com/yihui/formatR/releases/
1.14
- tidy_source() supports the := operator now (which is widely used in
  data.table).

1.13
- tidy_source() supports anonymous functions of the form \(args) expr
  for R >= 4.1.0 now (thanks, @notPlancha, #98).

1.12
- Added a new argument pipe to tidy_source(). If pipe = TRUE, it will
  convert the magrittr pipe %>% to the base R pipe operator |>.
- Added a function tidy_rstudio() to reformat R code in the RStudio
  editor.
- Added a function tidy_pipe() to substitute %>% with |> (currently
  works only in RStudio).

(mef)

doc: Updated devel/R-xfun to 0.39

(mef)

(devel/R-xfun) Updated 0.37 to 0.39

# 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())`.

(mef)

Updated devel/p5-Log-Dispatchouli to 3.002

(wen)

Update to 3.002

Upstream changes:
3.002    2022-12-06 09:49:34-05:00 America/New_York
        - restore v5.20 compatibility by turning on "postderef" feature
          explicitly

3.001    2022-12-01 11:55:43-05:00 America/New_York
        - no changes, just stable

3.000    2022-11-03 21:29:21-04:00 America/New_York (TRIAL RELEASE)
        - Log::Dispatchouli now requires v5.20, for pair slices
        - structured event logging with ->log_event -- read the docs, and Log::Fmt

(wen)

Updated devel/p5-Log-Dispatch to 2.71

(wen)

Update to 2.71

Upstream changes:
2.71    2023-04-05

- The docs for the Screen output were never updated after the changes in 2.50,
  when it reverted back to using STDOUT or STDERR directly. This led to a lot
  of the docs being confusing and wrong. Reported by @mauke. GH #65, #66, and
  #67.

(wen)

lang/gcc*: USE_TOOLS+=sed, not sed:run.

As far as I can tell, gcc needs this at build-time, not at run-time.

pkg/2023/06/02/msg027624.html">https://mail-index.netbsd.org/tech-pkg/2023/06/02/msg027624.html

(riastradh)

lang/gcc6, lang/gcc7: Make these build with newer gcc.

Otherwise libgomp has some -Wattributes errors.

(riastradh)

lang/gcc*: Set CC_FOR_BUILD and CXX_FOR_BUILD if cross-compiling.

Verified gcc6 and gcc7 cross-compile on NetBSD, at least if the
gcc-fortran option is disabled.  gcc8 and gcc9 have trouble because
of python (why do these have a full dependency on python?); gcc10 and
gcc12 are missing gcc/config/mips/netbsd64.h; gcc12 and gcc13 have a
cross-compile bug with missing __LIBGCC_*__ macros -- but in any
case, setting CC_FOR_BUILD and CXX_FOR_BUILD is obviously necessary
for cross-compilation.  Conditional on USE_CROSS_COMPILE, so no harm
to native builds.

(riastradh)