doc: Removed www/cherokee

(nia)

cherokee: remove. dead upstream, multiple open vulnerabilities

removed from debain in 2012, freebsd ports in january 2020, gentoo
in october 2020

(nia)

x265: Disable assembly on FreeBSD

according to patch submitted by Yoshihiro Ota in P$ pkg/56236

(cirnatdan)

doc: Updated net/bftpd to 5.7

(nia)

bftpd: Update to 5.7

This file contains all major changes made during the development of bftpd.
The uppermost change is the newest one.

Jesse Smith <jessefrgsmith@yahoo.ca> -> 5.7
- A malicious client could cause a buffer overflow with
  a lot of EPSV commands sent in a row. We now close
  the pasv socket before each new use to avoid accumulating
  more than 1023.
  Thanks to Shisong Qin for reporting this issue and suggesting
  a fix.

(nia)

fftw: bump for default options change

(nia)

fftw: Disable "generic" GCC simd intrinsics

These produce poor code and it's always better to use the CPU-specific
intrinsics instead, which we already do on platforms where the test
suite doesn't fail.

(nia)

doc: Updated security/acmesh to 2.9.0

(nia)

acmesh: update to 2.9.0

    ACME v1 is removed.
    Bug fixes.
    fixed --preferred-chain
    more DNS APIs are supported.

(nia)

doc: Updated www/viewvc to 1.2.1

(nia)

viewvc: update to 1.2.1

    security fix: escape subdir lastmod file name

(nia)

doc: Updated audio/abcmidi to 20210525

(nia)

abcmidi: update to 20210525

May 22 2021

abc2midi: treble-8 not applied in K: or V: commands after October 19 2020
update. For example,

X:1
T: transposition
L:1/2
M:C
K:none clef=treble-8
V:1
cz
V:2
zc

The note c should be played with midi pitch 60 instead of 72.
James Allwright made minor fixes to parseabc.c and store.c, in order
to get these options working again.

May 25 2021

James Allwright added more security checks to stop the
parser from reading numbers beyond the largest integer. Changes
were made to parserabc.c and midi2abc.c

The abc2abc -s spacing function was modified to ignore certain
time signatures like M: none or M:7/8. The code for dealing with
3/2, 3/4, 3/8 ... time signatures was improved.

(nia)

doc: Updated net/tinc to 1.0.36

(nia)

tinc: update to 1.0.36

Version 1.0.36              August 26 2019

* Fix compiling tinc with certain versions of the OpenSSL library.
* Fix parsing some IPv6 addresses with :: in them.
* Fix GraphDumpFile output to handle node names starting with a digit.
* Fix a potential segmentation fault when fragmenting packets.

Thanks to Rosen Penev, Quentin Rameau and Werner Schreiber for their
contributions to this version of tinc.

Version 1.0.35              October 5 2018

* Prevent oracle attacks (CVE-2018-16737, CVE-2018-16738).
* Prevent a MITM from forcing a NULL cipher for UDP (CVE-2018-16758).
* Minor fixes in the documentation.

Thanks to Amine Amri and Rafael Sadowski for their contributions to this
version of tinc.

Version 1.0.34              June 12 2018

* Fix a potential segmentation fault when connecting to an IPv6 peer via a
  proxy.
* Minor improvements to the build system.
* Make the systemd service file identical to the one from the 1.1 branch.
* Fix a potential problem causing IPv4 sockets to not work on macOS.

Thanks to Maximilian Stein and Wang Liu Shuai for their contributions to this
version of tinc.

Version 1.0.33              November 4 2017

* Allow compilation from a build directory.
* Source code cleanups.
* Fix some options specified on the command line not surviving a HUP signal.
* Handle tun/tap device returning EPERM or EBUSY.
* Disable PMTUDiscovery when TCPOnly is used.
* Support the --runstatedir option of the autoconf 2.70.

Thanks to Rafael Sadowski and Pierre-Olivier Mercier for their contributions to
this version of tinc.

(nia)

doc: Updated net/tcpreplay to 4.3.4

(nia)

tcpreplay: update to 4.3.4

This release is for bug fixes only.

    ASAN reports memory leaks while running tests
    local libopts compiler warnings
    DLT name for DLT_C_JNPR_ETHER in documentation
    clean up new_cidr_map() string manipulation on error exit
    fix gcc 8.3.0 build warnings
    invalid --pps value protection
    packets slowly drift further and further behind when they should be sent
    64 bit rollover can cause pps replay issues after several hours
    typo fixes
    DLT_NULL/DLT_LOOP support for cross-platform PF_INET6
    armv5 Freescale compile
    heap buffer overflow in tcpreplay fast_edit_packet
    heap buffer overflow in tcpreplay get_next_packet
    CVE-2020-24266 heap buffer overflow in tcpprep get_l2len
    CVE-2020-24265 heap buffer overflow in tcpprep
    fix UNUSED macro declaration
    handle malformed and unsupported packets as soft errors
    compile failure on aarch64-linux-android
    tcprewrite --fixlen not working on DLT conversion
    fix configure --without-libdnet
    ensure automake version is at least 1.15
    with multiplier option only first file can be sent and hang
    do not create tap0 if device already exists

(nia)

doc: Updated graphics/lcms2 to 2.12

(nia)

lcms2: update to 2.12

-----------------------
2.12 Maintenance release
-----------------------
Added new build-in sigmoidal tone curve
Added XCode 12 project
Added support for multichannel input up to 15 channels
Fix LUT8 write matrix
Fix version mess on 10/11
Fix tools & samples xgetopt
Fix warnings on different function pointers
Fix matlab MEX compilation
plugin: cleanup and better SSE detection
plugin: add lab to any on float
plugin: it can now be compiled as C++
recover PDF documentation, but try to keep it under a resonable size.
Prevent a rare but possible out-of-bounds read in postscript generator
Remove unused variables

(nia)

doc: Removed archivers/go-xz

(nia)

go-xz: remove; deprecated go-package, no users in pkgsrc

this version is vulnerable to CVE-2021-29482

(nia)

doc: Updated devel/R-devtools to 2.4.2

(mef)

(devel/R-devtools) Updated 2.4.1 to 2.4.2

# devtools 2.4.2

* `check_man()` now works with R versions 4.1+ (#2354)

* `test_active_file()` now again works on windows projects stored
  under the user's home directory (`~`) (#2355)

* `document(quiet = TRUE)` now works without failure on windows
  (#2351)

* Minor test failure on R 4.2 has been fixed.

(mef)

doc: Updated textproc/R-rmarkdown to 2.8

(mef)

(textproc/R-rmarkdown) Updated 2.3. to 2.8

rmarkdown 2.8
================================================================================

- Fix a issue with Pandoc 2.5 and `latex-div.lua` - documents can now
  be rendered as expected without error (thanks, @davidwales, #2121).

- Fix an issue with styling and code folding button behavior when
  default is `code-folding: show`. The Button can now be correctly
  style according to state as `aria-expanded` attributes is correctly
  updated. Also, new classes has been added on the button to allow
  styling during transition: `btn-collapsing` and `btn-expanding` are
  respectively applied during transition Show to Hide and Hide to
  Show. (This follow [Bootstrap behavior for the collapsible
  block](https://getbootstrap.com/docs/3.4/javascript/#collapse))
  (thanks, @steveharoz, #2085).

- Fix an issue with `citation_package` having no effect when using
  `.md` file as input to `render()` with latex and PDF output formats
  (thanks, @andrewheiss, #2113).

- A new internal option `rmarkdown.knit.ext` has been added to control
  the extension of the intermediary knit output during a rendering. It
  defaults to `md` to produce `*.knit.md`. Only useful for very
  advanced usage (#2098).

- `render()` won't produce any `*.utf8.md` intermediary file
  anymore. This was a leftover from previous versions of
  **rmarkdown**. Since **knitr** 1.24 and **rmarkdown** 2.0, only
  UTF-8 input files are allowed. (#2098).

- Fix an `Invalid cross-device link` error when `tempdir()` is used
  for `intermediates_dir` in `render()` (thanks, @gorgitko, #2096).

- Fix a regression in HTML default template with floating toc
  incorrectly placed on small size window (thanks, @grimbough, #2071)

- Provided a `runtime: shiny` fix for output formats that pass a
  modified `bslib::bs_theme()` object to `html_document_base()`'s
  `theme` (thanks, @cpsievert, #2049).

- Rendering using `runtime: shiny_prerendered` or `runtime: shinyrmd`
  will now produce valid HTML by not inserting anymore the full
  document as body in the resulting shiny apps (thanks, @dakep,
  #1912). Header content usually containing html dependencies will be
  inserted in the HTML document at the end of the head before
  `</head>`, unless the rendered HTML contains `<!-- HEAD_CONTENT -->`
  special comment (see `htmltools::renderDocument()`). A new Pandoc
  variable is set in for shiny prerendered document to allow
  conditional insertion of such content in the the HTML template using
  `$if(shiny-prerendered)$`. This has been done in all HTML template
  in this package. Users of custom template should make this change to
  provide support for this runtime. See **rmarkdown** default template
  (`default.html`) for an example (#2064).

- Added `tectonic` as a supported LaTeX engine for generating PDF
  output (thanks, @dpryan79, #2078). You can specify to use this by
  adding `engine: "tectonic"` to your output format in YAML, such as
  `pdf_document`.

- When no `output_format` is provided in any way but an `output_file`
  is provided in `render()`, the default format will be determined
  based on the extension: `"pdf_document"` for `.pdf`, or
  `"word_document"` for `.docx`. Otherwise, it will be
  `"html_document"` as previous version (thanks, @pearsonca, #1569).

- Added a new global option `rmarkdown.render.message`. When set
  `FALSE`, `render()` will not output the message starting by `Output
  created: ` allowing RStudio IDE to open a preview of the
  document. This is useful for package developers that would need to
  emit there own output message for there custom format. See
  `?render_site` for more info on this special message (#2092).

- Internal changes regarding Lua filters. They have now an explicit
  Pandoc version minimal requirement: A filter will be skipped with a
  warning printed by the Lua filter if this requirement is not
  met. For now, all filters work for Pandoc 2.1 and above (thanks,
  @atusy, #2088). There is also now a new mechanism to have a share
  Lua filter script loadable by other Lua files: `render()` will set
  the `RMARKDOWN_LUA_SHARED` env var to the path of Lua filter
  `shared.lua` so that other filters can access functions defined in
  it using `dofile(os.getenv 'RMARKDOWN_LUA_SHARED')`. This is for
  internal usage only to avoid duplication (thanks, @tarleb, #2103).

- `html_document_base` gains a `css` argument, to which
  `html_document`'s `css` argument is now passed. This also fix an
  issue when `.sass` or `.scss` files are used with this `css`
  argument when `self_contained: FALSE`. Moreover, **sass** caching
  mechanism can now be used when passing `.sass` or `.scss` files to
  the `css` argument (thanks, @cpsievert, #2095).

- The `fig_crop` option of PDF document formats (such as
  `pdf_document` and `beamer_presentation`) supports the value
  `"auto"` now, which means `fig_crop = TRUE` when figure cropping
  tools `pdfcrop` and `ghostscript` are available.

- The default value of the `fig_crop` option of PDF output formats has
  been changed from `TRUE` to `"auto"` (#2077).

- `rmarkdown::tufte_handout` has been deprecated and will be removed
  in the future from this package. It has been moved to the **tufte**
  package since **rmarkdown** 0.9.5 (released on 2016-02-22). Please
  use `tufte::tufte_handout` instead.

rmarkdown 2.7
================================================================================

- `html_document` (and `html_document_base`)'s `theme` parameter now
  understands `bslib::bs_theme()` objects/arguments, meaning that one
  may opt-into Bootstrap 4 and more easily create custom themes. For
  examples, see <https://github.com/rstudio/rmarkdown/pull/1706>, and
  for context, see <https://rstudio.github.io/bslib/> (thanks,
  @cpsievert, #1706).

- Files with `.scss`/`.sass` extension (i.e., Sass files) provided to
  `html_document`'s `css` parameter are now compiled to CSS using the
  `{sass}` package. Also, if `theme` is a `{bslib}` object, these Sass
  files may utilize Sass code inside the `theme` (thanks, @cpsievert,
  #1706).

- Fix an issue with line numbering in code chunks when `.numberlines`
  with Pandoc's highlighting (thanks, @aosavi, #1876).

- Fix an issue with shiny runtime and `global.R` (thanks,
  @liaojiahui-r, rstudio/flexdashboard#298).

- Accept `latex="{options}"`, `latex=1`, or `latex=true` for Latex
  Divs.

- Add `output_format_filter` function to
  `default_site_generator()`. Enables custom site generators to
  customize or even entirely replace the output format right before
  rendering of each page.

- Automatically exclude **renv** directory for `render_site()`
  (thanks, @jmbuhr, #1996)

- Do not force `options(htmltools.preserve.raw = TRUE)` when this
  option has been set, otherwise it is impossible for other packages
  to turn this option off, e.g., yihui/xaringan#293.

- `knitr_options_pdf()` will now throw a warning when `fig_crop =
  TRUE` but is disabled because required tools `pdfcrop` and/or
  `ghostscript` are missing (thanks, @netique, #2016).

- Eliminated the unnecessary padding in code blocks in the
  `html_document` output with Bootstrap 4 themes (thanks, @atusy,
  #2019).

- `github_document()` will produce a working TOC even if some headers
  start with number (#2039).

- Fix an issue with `knit_print.data.frame`. The `...` arguments are
  no more passed to `print()` to avoid passing `knit_print()`
  arguments `options` and `encoding` to custom `print()` methods
  (#2047).

rmarkdown 2.6
================================================================================

- Encoding is correctly handled now in `html_vignette` when checking
  for identical title and vignette index entry (thanks, @py-b, #1978).

- `clean_site()` now default to `preview = TRUE` and will no more
  remove files without notice. This change will affect the "Clean All"
  button in the "Build" pane for website project. `clean_site(preview
  = FALSE)` must be run to effectively remove files (#1973).

- The intermediate `.tex` file is now correctly deleted if `keep_tex =
  FALSE` when the R Markdown document is not rendered from the working
  directory (thanks, @vqv, #1308).

- Fix a bug causing certain resources files to be deleted as
  intermediate files when `intermediates_dir` is the same as the input
  (thanks, @bellma-lilly, #1248).

- Fix issues with `anchor_sections = TRUE` and **learnr** (thanks,
  @gadenbuie, #1938).

- Enable use of `server.R` and `global.R` alongside `runtime:
  shinyrmd` documents.

- `pkg_file_lua()` now works with `devtools::load_all()` and
  **testthat** when used in other packages.

- Fix `pandoc_convert(citeproc = TRUE)` not supressing the `--natbib`
  or `--biblatex` options (thanks, @atusy, #1932).

- `pandoc-citeproc` is now activated if a `bibliography` field is
  defined in another YAML block instead of the first YAML block
  (thanks, @bwiernik, #1364).

- Specify that `htmltools::htmlPreserve()` should use the pandoc raw
  attribute rather than preservation tokens when pandoc >= v2.0. Note
  that this option will have the intended effect only for versions of
  htmltools >= 0.5.0.9003.

- `anchor_sections` in `html_documents()` now defaults to `FALSE`. It
  was introduced in previous version with a default to `TRUE`, but it
  is reverted now after hearing feedbacks from the community (thank
  you!). The `#` is still used as the character for the anchor but you
  can easily change that using CSS rules. Examples have been added to
  the help page `?html_document`.

- Using Pandoc's default for `--email-obfuscation` now. Previously, it
  was set to `none` explicitly, which is the default for Pandoc
  1.17.2+ anyway. Only users with a Pandoc version before 1.17.2 may
  see a change in the content of the html source file produced if the
  document contains email addresses. This change allows to pass the
  Pandoc's command line flag if you want to set it to another value
  (thanks,@seankross, #1969).

  ````yaml
  output:
    html_document:
      pandoc_args: ["--email-obfuscation", "javascript"]
  ````

  See [Pandoc's
  manual](https://pandoc.org/MANUAL.html#option--email-obfuscation)
  for the meaning of this option.

- Fix Fontawesome 5 icons in navbar by correctly handling new prefix
  as `fa` has been deprecated in favor of `fas` or `fab` (#1967)

rmarkdown 2.5
================================================================================

- Tables without header rows (wich can be possible in Pandoc's [simple
  table](https://pandoc.org/MANUAL.html#extension-simple_tables)) are
  now formatted correctly when using `html_document()` format (thanks,
  @fkohrt, #1893).

- `html_document()` gains the `anchor_sections` argument, which is
  `TRUE` by default, so that readers can get links to section headers
  easily---when you mouse over a section header, you will see a hash
  symbol `#` at the end of the header, which contains the anchor link
  to this header. You can click on this link and get the URL in the
  addres bar of your web browser, or right-click on it and copy the
  URL from the context menu. The hash symbol is defined by the CSS
  rule `a.anchor-section::before {content: '#';}`. You can customize
  it by overriding this rule (e.g., via the `css` argument of
  `html_document`) and use any other symbols or icons, e.g., `content:
  "\02AD8;"` (thanks, @atusy, #1884).

- `pkg_file_lua()` should have thrown an error if the expected Lua
  file does not exist.

- Provide `files_dir` and `intermediates_dir` as attributes on return
  from `render()` when `run_pandoc = FALSE`.

- Supports new Pandoc 2.11 `--citeproc` flags usage instead of
  `pandoc-citeproc` external filter. `pandoc_convert()` and
  `pandoc_citeproc_convert()` will now use the correct flags according
  to the Pandoc version used. The logic is exported in
  `pandoc_citeproc_args()`. See [Pandoc release
  note](https://github.com/jgm/pandoc/releases/tag/2.11) for more
  information about the new `citeproc` processing (#1916).

- Fixed the code highlighting when code block is hidden. Previous
  version introduced a regression where non default code highlighting
  was still shown when `code_folding` is activated and code block is
  hidden (thanks, @matthewcarlucci, #1921).

- The minimal required version for the **xfun** package (v0.15) has
  been specified for R Markdown Notebooks to work properly (thanks,
  @jmcphers, #1923).

- Fixed a bug in `convert_ipynb()` when the language is not specified
  in the `.ipynb` file (thanks, @acca3003, #1925).

- Introduce `runtime: shinyrmd` as a more user friendly alias for
  `runtime: shiny_prerendered`.

rmarkdown 2.4
================================================================================

- Lua filters handling has been improved internally with some
    - user-facing changes (#1899): New exported function
    - `pandoc_lua_filter_args()` to return the Pandoc command-line
    - argument to add a Lua filter.  New argument `lua_filters` in
    - `pandoc_options()` to pass the Lua filter paths to use with a
    - format. This allow output format authors to add filters for a
    - custom format using the `pandoc` argument of `output_format()`
    - and to get filters from a format using `fmt$pandoc$lua_filters`.
    - The Lua filters of an output format are now passed to Pandoc in
    - `render()`. By default, they are passed to Pandoc before any
    - other format-defined or user-defined Pandoc arguments (usually
    - via the `pandoc_args` option of an output format). This ensures
    - that filters of an output format are executed first. To change
    - the default, you need to deal with it in a custom format (i.e.,
    - modify the elements in `fmt$pandoc$lua_filters`, such as
    - reordering them).  New exported function `pkg_file_lua()` to get
    - the full system path of a Lua filter included in a package
    - source within the `inst/rmarkdown/lua` folder (thanks, @atusy,
    - #1903).

- Fixed the path separators for the `css` parameter in YAML
  frontmatter for HTML output files under Windows. Previously, forward
  slashes in `css` paths were converted to backslashes (thanks,
  @jonathan-g, #1862).

- Since **rmarkdown** 1.16, Pandoc's fenced `Div`'s are converted to
  LaTeX environments when the output format is LaTeX, e.g., `:::
  {.center data-latex=""}` is converted to `\begin{center}`. The
  attribute `data-latex` of the `Div` was mandatory, even if it is
  empty. In **rmarkdown** 2.2, we silently drop this requirement,
  which means `::: {.center}` is converted to `\begin{center}`. This
  turns out to be a bad idea, because users have no control over which
  Div's to be converted to LaTeX environments. Previously, they could
  opt-in by the `data-latex` attribute, but with **rmarkdown** 2.3,
  all Div's are converted to LaTeX environments
  unconditionally. What's more, this change led to bugs like
  https://stackoverflow.com/q/62340425/559676 and
  https://github.com/rstudio/bookdown/issues/883. Therefore the
  `data-latex` attribute became mandatory again in this version. If
  the LaTeX environment does not need arguments, you may use
  `data-latex=""`.

- The two Lua fitlers `pagebreak.lua` and `latex-div.lua` (introduced
  in **rmarkdown** 1.16) are also applied to the output format
  `beamer_presentation` now (thanks, @XiangyunHuang, #1815).

- When customizing formats with the `output_format` function,
  `pre_knit`, `opts_hooks`, and `knit_hooks` can now refer to
  `rmarkdown::metadata`. Previously, `rmarkdown::metadata` returned
  `list()` in these functions (thanks, @atusy, #1855).

- `rmarkdown::find_external_resources()` now discovers external
  template files. This in turn fixes the rendering issue of
  `html_document` with the `shiny` runtime and `intermediate_dir` set
  (thanks, @atusy, @cderv, #1865).

- Added the `number_sections` argument to following formats:
  `github_document`, `ioslides_presentation`, `md_document`,
  `odt_document`, `powerpoint_presentation`, `rtf_document`,
  `slidy_presentation`, `word_document`. These are powered by a Lua
  filter and requires Pandoc > 2.0. It will silently have no effect
  has before with previous pandoc version (thanks @atusy 1893).
  Pandoc >= 2.10.1 adds `--number-sections` for docx format, and thus
  `word_document` prefers the native feature to the Lua filter
  (thanks, @jooyoungseo, #1869).

- For the output format `pdf_document`, the option `fig_crop` will not
  be enabled unless both the programs `pdfcrop` and `ghostscript` are
  found (thanks, @dalupus, yihui/knitr#954).

- Fixed a bug that a chunk with a class `fold-hide` hides the rest of
  the chunks even the output format setting
  `html_document(code_folding = "show")` (thanks, @atusy, #1906).

- Updated documentation for `render()` to make it clearer how options
  are set for the `output_format` parameter (thanks, @jonathan-g,
  #1907 and rstudio/bookdown#930).

- Ported some CSS styles (e.g., underlines, small caps, and
  multi-column layouts) from the latest Pandoc's HTML template into
  **rmarkdown**s HTML templates (thanks, @atusy, #1878, #1908).

(mef)

doc: Updated devel/R-desc to 1.3.0

(mef)

(devel/R-desc) Updated 1.2.0 to 1.3.0

# 1.3.0

* Adding authors with long names or other fields (`comment`, typically)
  works well now (#91).

* `get_deps()` now removes unneeded whitespace from version requirements
  (#84).

* `normalize()` now does not drop `Authors@R` on non-UTF-8 systems
  when it has non-ASCII characters (#80).

* `has_dep()` now works well with dependencies listed multiple times
  (#97, @richfitz).

* Add `coerce_authors_at_r()` method to convert `Author` to
  `Authors@R` (#44, @muschellij2).

* `add_author()` and similar functions now allow a character vector of
  multiple roles (@niceume, #89).

* `desc_set_deps()` now inserts new packages in (case-insensitive)
  alphabetical order, if the existing packages are already in alphabetical
  order.

* New `add_author_gh()` method and `desc_add_author_gh()` function to add
  an author using the information available from GitHub V3 API. This method
  and function depend on `gh` and are limited when the GitHub user full
  name is incomplete or not well parsed by `as.person()` and when their
  email address isn't available (@maelle, #71).

* When using `desc_normalize()` the package dependencies are now
  alphabetically sorted (#66, @llrs).

* New `add_orcid()` method and `desc_add_orcid()` functions make it
  possible to add ORCID IDs to authors directly instead of via the
  `comment` argument (@maelle, #70).

* All functions and methods managing authors (`add_me`, `add_author()`,
  `del_author()`, `add_role()`, `del_role()`, `change_maintainer()`,
  `search_for_author()`, `add_me()`, etc.) gain an `orcid` argument
  (@maelle, #70).

* In `person()` within the `Authors@R` field, `comment` can now be a
  named character vector (@maelle, #69; @gvegayon, #65).

* When using `desc(text=)` parameter, set `textConnection(encoding =
  "bytes")` to handle cases when the input text is in a different marked
  encoding than the default encoding, such as UTF-8 input on Windows.

(mef)

Updated lang/sbcl to 2.1.5

(rjs)

Update to 2.1.5.

New in version 2.1.5

    * minor incompatible change: on x86-64, the backend instruction
      encoders for movzx and for string opcodes have changed their
      semantics.
    * platform support:
        * compatibility: support the latest MinGW on x86. (#1923325,
          thanks to Alexis Rivera)
        * bug fix: on x86-64, fix instruction encoding for TEST on
          RIP-relative addresses. (#1925808, reported by Shinmera on
          #sbcl, thanks also to 3b)
        * bug fix: on x86-64, loading all-1s into an AVX2 register no
          longer causes an error. (thanks to Marco Heisig)
        * bug fix: on arm64, improve disassembly of ADD with constant
          0 as MOV
        * enhancement: on arm64, support debugger commands
          RETURN-FROM-FRAME and RESTART-FRAME more efficiently.
        * enhancement: on x86-64, add support for vshuf* AVX2
          instructions. (reported by Bela Pecsek)
        * optimization: faster function calls on arm64.
        * optimization: (SETF SBIT) is faster on x86-64.
    * bug fix: INTEGER-DECODE-FLOAT was computing the wrong answer for
      denormal double floats. (#1926383, reported by Stavros Macrakis)
    * bug fix: RANDOM on a floating point argument now does not
      cons. (reported by Tito Latini)
    * bug fix: fix a compiler crash in type derivation of
      LOGTEST. (#1928243)
    * bug fix: fix a compiler failure when a declared function type
      contains a literal structure with a valid MAKE-LOAD-FORM
      method. (#1929160, thanks to Yurii Hryhorenko)
    * optimization: FBOUNDP on a constant symbol is now faster.
    * optimization: file compilation now produces smaller fasls for
      files which reference package literals.
    * optimization: derive the type of calls to FLOAT-SIGN.

(rjs)

doc: Updated www/R-htmlwidgets to 1.5.3

(mef)

(www/R-htmlwidgets) Updated 1.3 to 1.5.3

htmlwidgets 1.5.3
-------------------------------------------------------

### New features

* Added a `reportTheme` argument to `shinyWidgetOutput()`. If `TRUE`,
  CSS styles of the widget's output container are made available to
  `shiny::getCurrentOutputInfo()`, making it possible to provide
  'smart' styling defaults in a `renderWidget()` context. (#361)

* `shinyRenderWidget()` now has a `cacheHint` parameter, for use with
  Shiny's new `bindCache()` function. (#391)

* Support a new `PACKAGE::widget_html.WIDGETNAME` convention for
  defining custom widget HTML. This replaces the earlier
  `PACKAGE::WIDGETNAME_html` convention, which continues to work but
  may be deprecated at some point in the future. The goal for the new
  convention is to prevent accidentally matching functions that were
  never intended for this purpose. (Thanks, @thebioengineer!) (#376)

* Export the `JSEvals` function, allowing other packages to support
  `JS()` in non-widget contexts.

### Bug fixes

* `saveWidget()` now `file` argument now properly handles relative
  paths. (#299)

* Fixed an issue with passing named function declarations to `JS()`
  and `onRender()` (introduced by v1.4). (#356)

htmlwidgets 1.5.2
-------------------------------------------------------

* Emergency patch release to fix an issue with rendering htmlwidgets
  in flexdashboard. More generally, this change implies that any
  htmlwidget is printed via a knitr code chunk with multiple values
  for fig.width/fig.height, only the first value is used for the
  widget's sizing policy. (#387)

htmlwidgets 1.5.1
-------------------------------------------------------

* Fixed an issue with dynamically rendered widgets (i.e., using
  `shiny::uiOutput()` to render a widget) with any version of shiny
  prior to 1.4. This issue was introduced by htmlwidgets 1.5. (#351)

htmlwidgets 1.5
-----------------------------------------------------------------------

* Fixed an incompatibility with Shiny v1.4.0: due to Shiny upgrading
  from jQuery 1.x to 3.x, the timing of some initialization routines
  has changed. This caused some widget `renderValue` calls to occur at
  an earlier point in Shiny's initialization process than with earlier
  versions of Shiny. (#345)

htmlwidgets 1.4 (unreleased)
-----------------------------------------------------------------------

* JavaScript statements can now be passed along to `onRender()` and
  `JS()` (#329).

(mef)

doc: Updated devel/R-remotes to 2.4.0

(mef)

(devel/R-remotes) Updated 2.3.0 to 2.4.0

# remotes 2.4.0

* Re-license as MIT. (#551)

* skip tests for `download.file(method = "internal")`, on R > 4.1,
  since that method is now defunct on those versions.

* `system_requirements()` now works as intended if only the `os`
  argument is used (@mdneuzerling, #609)

* `remote_package_name.git2r_remote` and
  `remote_package_name.xgit_remote` now get correct package name from
  HTTP(S) git repo's `DESCRIPTION` file, and thus package's
  `DESCRIPTION` file's `Remotes` field could have
  `git::http(s)://<host>/<username>/<repo>[.git][@ref]` items that
  install remote packages using git via HTTP(S) protocal (@niheaven,
  #603).

(mef)

doc: Updated devel/R-withr to 2.4.2

(mef)

(devel/R-withr) Update 2.4.1 to 2.4.2

# withr 2.4.2
- `local_options()` now lets you set an option to `NULL` as intended (#156)

- `local_tempfile()` argument `envir` is deprecated, in favor of
  `.local_envir`.  All withr functions except `local_tempfile()` used
  `.local_envir` to specify environments, so this makes this function
  consistent with the rest. (#157)

- `with_environment()` now passing `pos` and `warn.conflicts` to
  `attach()`, as intended (#161).

- `with_seed()` now also sets the RNG via new arguments `.rng_kind`,
  `.rng_normal_kind` and `.rng_sample_kind` (#162, @AshesITR).

- `with_timezone()` now works after recent changes to `Sys.timezone()`
  in R-devel (#165)

(mef)

doc: Updated net/mosquitto to 2.0.11

(gdt)

net/mosquitto: Update to 2.0.11

Packaging changes: link against pthread, per upstream recommendations

Upstream changes: Bugfixes

(gdt)

blackbox: bump PKGREVISION for previous change

This, of course, results in a different shell path in some environments,
which is the whole point.

(gutteridge)

blackbox: use REPLACE_SH instead of hard-coding an interpreter

(gutteridge)

doc: Updated textproc/molybdenum to 0.1.5

(pin)

textproc/molybdenum: update to 0.1.5

-Added support for folder output via -L.

(pin)

bsd.options.mk: fix typo in comment

(gutteridge)

blackbox: add buildlink3.mk missed in migration from blackbox70

(gutteridge)

blackbox: adjust options.mk to current package name

(gutteridge)

doc: Updated biology/vcf-split to 0.1.2

(bacon)

biology/vcf-split: Update to 0.1.2

Updates for new biolibc API

Upstream change log: https://github.com/auerlab/vcf-split/releases

(bacon)

doc: Updated biology/vcf2hap to 0.1.3

(bacon)

biology/vcf2hap: Update to 0.1.3

Updates for new biolibc API

Upstream change log: https://github.com/auerlab/vcf2hap/releases

(bacon)

doc: Updated biology/ad2vcf to 0.1.3

(bacon)

doc: Updated biology/biolibc to 0.1.3

(bacon)

biology/ad2vcf: Update to 0.1.3

Updates for new biolibc API

Upstream change log: https://github.com/auerlab/ad2vcf/releases

(bacon)

biology/biolibc: Update to 0.1.3

Import sam_buff_t class and VCF functions from ad2vcf
Add BED and GFF support
Isolate headers under include/biolibc
Numerous small enhancements and fixes

Upstream change log: https://github.com/auerlab/biolibc/releases

(bacon)

doc: Updated biology/ncbi-blast+ to 2.11.0

(bacon)

doc/pkgsrc.*: regen

(nia)

guide: remove references to ancient gnome cruft

(nia)

pocl: add test target

(nia)

doc/pkgsrc.*: regen

(nia)

guide: bring section on binary packages up to date

(nia)

biology/ncbi-blast+: Update to 2.11.0

Release notes: https://www.ncbi.nlm.nih.gov/books/NBK131777/

(bacon)

Mention consolekit

(abs)

Add option to build slim without consolekit (default unchanged)

(abs)

py-line_profiler: mark as not for Python 3.6

(adam)

Updated www/py-terminado, textproc/py-xmlschema

(adam)

py-xmlschema: updated to 1.6.4

v1.6.4
* Add testing config for Python 3.10 (Tox and CI)
* Fix internal _PurePath class with Python 3.10
* Remove redundant xmlns="" declaration when encoding with lxml

v1.6.3
* Refactor normalize_url() using pathlib.PurePath
* Support UNC paths
* Fix API docs

(adam)

py-terminado: updated to 0.10.1

0.10.1

Bugs fixed

Fix blocking of pty_read when there isn't pty data ready to read
Contributors to this release

0.10.0

Enhancements made

Support creating terminal given name in kwargs.

Bugs fixed

avoid persistent handle on IOLoop instance

Maintenance and upkeep improvements

async/await syntax
PR: Pin pywinpty version to 1.1.0

0.9.5
Pin pywinpty version

0.9.4
Allow non-strict decode for process output
Switch to GitHub Actions
Add generated changelog

0.9.3
Make sure SIGPIPE has default handler set

0.9.2
Add js files in package manifest
Add support to ppc64le
Fix config files for publication

0.9.1
v0.9.1

0.9.0
Drop python 2 and 3.4 and 3.5 support
Make sure that all process output makes it to the terminal

(adam)

devel/Makefile: Add libxtend

(bacon)

doc: Added devel/libxtend version 0.1.2.4

(bacon)

devel/libxtend: import libxtend-0.1.2.4

Libxtend is a library of miscellaneous functions, the likes of
which might be found in libc or libm.  It provides some convenient
functionality lacking in standard library functions as well some
more esoteric features.

(bacon)

fltk: drop stale $MASTER_SITES entry

The easysw.com domain now redirects to hotels-of-london.com, and the
archived files don't seem to be accessible anymore, despite some
continued relationship between the two entities.

(gutteridge)

doc: Updated textproc/ispell-en_GB to 3.4.04

(gutteridge)

ispell & ispell-en_GB: use Makefile.common

Centralize some basics so ispell-en_GB doesn't need to be manually
adjusted every time ispell gets an update. Addresses a lingering issue
from PR pkg/55972 noted by Greg A. Woods.

(gutteridge)

pocl: add buildlink3 file

(nia)

blackbox: add options.mk missed in migration from blackbox70

(gutteridge)

Updated www/py-nbformat, www/py-ipywidgets

(adam)

py-ipywidgets: updated to 7.6.3

7.6
---

To see the full list of pull requests and issues, see the [7.6.0 milestone](https://github.com/jupyter-widgets/ipywidgets/milestone/31?closed=1) on GitHub.

The main change in this release is that installing `ipywidgets` 7.6.0 will now automatically enable ipywidgets support in JupyterLab 3.0窶蚤 user has no extra JupyterLab installation step and no rebuild of JupyterLab, nor do they need Node.js installed. Simply install the python ipywidgets package with pip (`pip install ipywidgets==7.6.0`) or conda/mamba (`conda install -c conda-forge ipywidgets=7.6.0`) and ipywidgets will automatically work in classic Jupyter Notebook and in JupyterLab 3.0.

This is accomplished with the new python package `jupyterlab_widgets` version 1.0, on which `ipywidgets` 7.6.0 now depends (similar to how `ipywidgets` already depends on the `widgetsnbextension` package to configure ipywidgets for the classic Jupyter Notebook). The `jupyterlab_widgets` Python package is a JupyterLab 3.0 prebuilt extension, meaning that it can be installed into JupyterLab 3.0 without rebuilding JupyterLab and without needing Node.js installed.

Updates for Widget Maintainers

Custom widget maintainers will need to make two changes to update for JupyterLab 3:

1. Update the `@jupyter-widgets/base` dependency version to include `^4` to work in JupyterLab 3.0. For example, if you had a dependency on `@jupyter-widgets/base` version `^2 || ^3`, update to `^2 || ^3 || ^4` for your widget to work in classic Jupyter Notebook, JupyterLab 1, JupyterLab 2, and JupyterLab 3.
2. In the `package.json`, add the following `sharedPackages` configuration inside the `jupyterlab` key. See the [JupyterLab extension documentation](https://jupyterlab.readthedocs.io/en/stable/extension/extension_dev.html#requiring-a-service) for more information.

  ```json
    "jupyterlab": {
      "sharedPackages": {
        "@jupyter-widgets/base": {
          "bundled": false,
          "singleton": true
        }
      }
    }
  ```

Separate from these two steps to update for JupyterLab 3, we also recommend that you make your widget's JupyterLab extension a prebuilt extension for JupyterLab 3.0. Users will be able to install your JupyterLab 3.0 prebuilt extension without rebuilding JupyterLab or needing Node.js. See the [JupyterLab 3 extension developer documentation](https://jupyterlab.readthedocs.io/en/stable/extension/extension_dev.html) or the new [widget extension cookiecutter](https://github.com/jupyter-widgets/widget-ts-cookiecutter/tree/jlab3) for more details.

(adam)

py-nbformat: updated to 5.1.3

5.1.3
=====
- Change id generation to be hash based to avoid problematic word combinations
- Added tests for python 3.9
- Fixed setup.py build operations to include package data

5.1.2
=====
- Fixed missing file in manifest

5.1.1
=====
- Changes convert.upgrade to upgrade minor 4.x versions to 4.5

5.1.0
=====
- Implemented CellIds from JEP-62
- Fixed a regression introduced when using fastjsonschema,
  which does not directly support to validate a "reference"/"subschema"
- Removed unreachable/unneeded code
- Added CI workflow for package release on tag push

(adam)

Updated devel/py-ipython, net/py-softlayer, devel/py-jupyter_core, devel/py-jupyter_client, devel/py-ipykernel, devel/py-jupyter-console

(adam)

py-jupyter-console: updated to 6.4.0

6.4.0:
Unknown changes

(adam)

py-ipykernel: updated to 5.5.5

5.5.5
-----
- Keep preferring SelectorEventLoop on Windows. (:ghpull:`669`)

5.5.4
-----
- Import ``configure_inline_support`` from ``matplotlib_inline`` if available (:ghpull:`654`)

5.5.3
-----
- Revert Backport of 605: Fix Handling of ``shell.should_run_async`` (:ghpull:`622`)

5.5.2
-----
**Note:** This release was deleted from PyPI since it had breaking changes.

- Changed default timeout to 0.0 seconds for stop_on_error_timeout. (:ghpull:`618`)

5.5.1
-----
**Note:** This release was deleted from PyPI since it had breaking changes.

- Fix Handling of ``shell.should_run_async``. (:ghpull:`605`)

5.5.0
-----
- Kernelspec: ensure path is writable before writing ``kernel.json``. (:ghpull:`593`)
- Add ``configure_inline_support`` and call it in the shell. (:ghpull:`590`)

(adam)

py-jupyter_client: updated to 6.1.12

6.1.11
======
- Move jedi pinning to test requirements (:ghpull:`599`)

6.1.10
======
- Add change parameter needed for observer method of kernel_spec_manager trait (:ghpull:`598`)

6.1.9
=====
- Pin jedi<=0.17.2 (:ghpull:`596`)

6.1.8
=====
- Doc updates (:ghpull:`563`, :ghpull:`564`, :ghpull:`587`)
- Fix path to the connection file (:ghpull:`568`)
- Code cleanup (:ghpull:`574`, :ghpull:`579`)
- Silence kill_kernel when no process is present (:ghpull:`576`)
- Remove extra_env and corresponding test (:ghpull:`581`)
- Add documentation dependencies to setup.py (:ghpull:`582`)
- Fix for Windows localhost IP addresses (:ghpull:`584`)
- Drop Travis CI, add GitHub Actions (:ghpull:`586`)
- Adapt KernelManager._kernel_spec_manager_changed to observe (:ghpull:`588`)
- Allow use ~/ in the kernel's command or its arguments (:ghpull:`589`)
- Change wait_for_ready logic (:ghpull:`592`)
- Fix test_session with msgpack v1  (:ghpull:`594`)

(adam)

py-jupyter_core: updated to 4.7.1

4.7.1

- Allow creating user to delete secure file (:ghpull:`213`)

4.7.0

- Add a new ``JUPYTER_PREFER_ENV_PATH`` variable, which can be set to switch the order of the environment-level path and the user-level path in the Jupyter path hierarchy (e.g., ``jupyter --paths``). It is considered set if it is a value that is not one of 'no', 'n', 'off', 'false', '0', or '0.0' (case insensitive). If you are running Jupyter in multiple virtual environments as the same user, you will likely want to set this environment variable.
- Drop Python 2.x and 3.5 support, as they have reached end of life.
- Add Python 3.9 builds to testing, and expand testing to cover Windows, macOS, and Linux platforms.
- ``jupyter --paths --debug`` now explains the environment variables that affect the current path list.
- Update the file hidden check on Windows to use new Python features rather than ctypes directly.
- Add conda environment information in ``jupyter troubleshoot``.
- Update ``_version.version_info`` and ``_version.__version__`` to follow Python conventions.

(adam)

miniupnpc: Hack around build failure on NetBSD

sed 's/\(.*MINIUPNPC_API_VERSION\s\+\)[0-9]\+/\117/' < miniupnpc.h.bak > miniupnpc.h
sed: 1: "s/\(.*MINIUPNPC_API_VER ...": RE error: trailing backslash (\)

I held back on updating this package because of exactly this error...

(nia)

Add missed "include go-modules.mk"

(abs)

doc: Updated devel/ruby-gettext to 3.3.8

(taca)

devel/ruby-gettext: update to 3.3.8

pkgsrc change: update HOMEPAGE.

3.3.8 (2021-06-09)

Improvements

* msginit: Added support for generating plural forms with Unicode's CLDR
  plural rules data. [GitHub#85][Suggested by Micha谷l Hoste]
* rxgettext ui: Added support for GtkBuilder UI definitions format with
  .glade extension. [GitHub#74][Reported by dorle-o]

Fixes

* rxgettext ruby: Fixed a bug that Nn_ isn't extracted. [GitHub#86][Reported
  by Kai Ramuenke]

Thanks

* Kai Ramuenke
* Micha谷l Hoste
* dorle-o

(taca)

doc: Added devel/ruby-red-datasets version 0.1.2

(taca)

devel/Makefile: add and enable ruby-red-datasets

(taca)

devel/ruby-red-datasets: add package version 0.1.2

Red Datasets

Red Datasets provides classes that provide common datasets such as iris
dataset.

You can use datasets easily because you can access each dataset with
multiple ways such as #each and Apache Arrow Record Batch.

(taca)

textproc/ruby-csv: make it incompatible with ruby30

Restrict this package to Ruby 2.6 and 2.7 since Ruby 3.0 contain the same
version of rexml.

(taca)

doc: Added meta-pkgs/bulk-test-llvm version 20210610

(nia)

add meta-pkgs/bulk-test-llvm

Meta-package for testing LLVM updates. Depends on various non-trivial or
important packages that depend on LLVM.

(nia)

doc: blackbox changes

(nia)

Make wm/blackbox the latest version, remove weird versioned packages

concept ok'd by gutteridge

(nia)

pocl: add links to upstream pull requests for patches

cpuinfo: check for fopen() failure when opening sysfs nodes to avoid segfault
https://github.com/pocl/pocl/pull/948

pocl_timing: fix detection of Unix monotonic clocks
https://github.com/pocl/pocl/pull/949

Fix detection of dlopen()/libdl
https://github.com/pocl/pocl/pull/950

(nia)

doc: Updated sysutils/zoxide to 0.7.2

(pin)