www/contao35: update to 3.5.33

Contao 3.5.33 is available 2018/01/22 10:08 by Leo Feyer

Contao version 3.5.33 is available.  The bugfix release restores the PHP 5.4
compatibility and fixes problems with MariaDB 10.2.4+ and MySQL 8.

PHP 5.4

Even if Contao 3.5 still supports PHP 5.4, we strongly advise against using
outdated PHP versions.  Contao 3.5 is compatible with the latest PHP versions,
therefore – if the installed extensions allow it – you should run it with PHP
7 or at least PHP 5.6.

Identifier Quoting

We have revised identifier quoting, which we had added to Contao 4.4.10, and
ported it to Contao 3, so Contao 3.5 should be compatible with MariaDB 10.2.4+
and MySQL 8 now.

(taca)

net/nagios-nrpe: Change SMF now that process switches to
non-privileged user on its own. Fixes joyent/pkgsrc#72.

(fhajny)

mail/clamsmtp: Add SMF support. Make sure $CLAMAV_USER exists,
since it's referenced in init scripts. Bump PKGREVISION.

(fhajny)

doc: Updated lang/elixir to 1.6.0

(fhajny)

Update lang/elixir to 1.6.0.

1. Enhancements

EEx
- [EEx] Allow markers `/` and `|` to be used in a custom EEx engine

Elixir
- [Calendar] Add truncate to `Time`, `DateTime` and `NaiveDateTime` to
  facilitate microsecond precision pruning
- [Code] Add `format_string!/2` and `format_file!/2` for automatic
  code formatting
- [Code] Support column annotations in quoted expressions with
  `columns: true` in `Code.string_to_quoted/2`
- [DynamicSupervisor] Add `DynamicSupervisor` designed to manage
  children that are added and removed dynamically
- [Exception] Make `Exception.blame/3` extensible by adding an
  optional `blame/2` callback to exceptions
- [Exception] Improve the printing of guards on blamed exceptions
- [Enumerable] Add `Enumerable.slice/1` and optimize many `Enum`
  operations with the new protocol. This allows data-structures with
  index-based random access to provide a non-linear implementation
- [Inspect] Show UTF-8 BOM on inspected strings
- [Inspect.Algebra] Add `:strict` and `:flex` breaks - this gives more
  control over the document fitting
- [Inspect.Algebra] Allow a group to inherit the parent group break
- [Inspect.Algebra] Add `force_unfit/1` and `next_break_fits/2` which
  give more control over document fitting
- [Inspect.Algebra] Add `collapse_lines/1` for collapsing multiple
  lines to a maximum value
- [Inspect.Algebra] Allow `nest/2` to be `:reset` or be set to the
  current `:cursor` position
- [Kernel] Prefix variables with V when emitting Erlang code. This
  improves the integration with tools such as Erlang code formatters
  and the GUI debugger
- [Kernel] Warn on the use of `length(x) == 0` in guards
- [Kernel] Warn if `catch` comes before `rescue` in try
- [Kernel] Warn if heredoc is outdented compared to its closing quotes
- [Kernel] Add `defguard/1` and `defguardp/1` to make it easier to
  build guard-safe macros
- [Kernel.ParallelCompiler] Add `compile/2`, `compile_to_path/3` and
  `require/2` which provide detailed information about warnings and
  errors
- [Kernel.SpecialForms] Support the `uniq: true` flag in `for`
  comprehensions
- [Module] Introduce `@deprecated` and `@since` attributes
- [Module] Emit conflicting behaviour warnings if the same behaviour
  is given more than once
- [List] Rearrange equals and inserts for shorter diff scripts in
  `List.myers_difference/2`
- [Record] Allow `:macros` and `:includes` to be given to
  `Record.extract/2`
- [Stream] Add `Stream.intersperse/2`
- [String] Update to Unicode 10
- [String] Allow passing empty string `match` to `String.replace/4`
- [String] Support context and language sensitive operations in
  `String.upcase/2` and `String.downcase/2`. Currently only the
  `:greek` context is supported
- [String] Support `:ascii` conversion in `String.upcase/2` and
  `String.downcase/2`
- [Time] Add `Time.add/3`

ExUnit
- [ExUnit.Assertions] Perform inclusive checks in `assert_in_delta`
- [ExUnit.Callbacks] Add `ExUnit.Callbacks.start_supervised!/2`
- [ExUnit.Case] Generate a random seed per test based on the test
  suite seed

IEx
- [IEx.Autocomplete] Provide contextual autocompletion: `t Enum.` will
  autocomplete types, `b Enum` will autocomplete callbacks
- [IEx.CLI] Provide hints for developers when a bad host name is given
  to `--remsh`
- [IEx.Helpers] Automatically include specs when showing documentation
  for functions/macros
- [IEx.Helpers] Improve formatting of behaviours and typespecs by
  using the formatter
- [IEx.Helpers] Allow pattern matching and guard expressions when on
  `IEx.break!`

Logger
- [Logger] Add `:discard_threshold` to Logger to help with message
  queue overflow

Mix
- [mix app.start] Add `--preload-modules` to `mix app.start`
- [mix archive.build] Allow `mix archive.build` to bundle dot files
  via an option
- [mix compile] Define a behavior for Mix compiler tasks and return
  diagnostics from compiler tasks
- [mix compile] Track struct dependencies between files and recompile
  them only if the struct changes
- [mix deps] Support `:system_env` option when specifying dependencies
- [mix format] Add a `mix format` task that formats the given files
  (or the files specified in a `.formatter.exs` file)
- [mix profile.eprof] Add a new task for time-based profiling with
  eprof
- [mix test] Run all functions in a describe block by giving the
  `file:line` the describe block starts
- [mix test] Report the top N slowest tests with the `--slowest N`
  flag
- [mix test] Report the number of doctests and tests separately
- [mix xref] Support `--include-siblings` in reports for umbrella
  support
- [mix xref] Add `mix xref graph --format stats`
- [mix xref] Add `--only-nodes` and `--label` filters to mix xref
  graph
- [mix xref] Add `mix xref deprecated` that shows the callsite of
  deprecated functions

2. Bug fixes

Elixir
- [CLI] Support path with spaces as argument to elixir.bat
- [Inspect] Properly handle minus signal for non-decimal negative
  integers
- [Integer] Do not raise on non-integer values in `is_odd`/`is_even`
- [Kernel] Solve a precedence issue between `&` and `|`, such as
  `[&Foo.bar/1 | &Baz.bat/2]`
- [Kernel] Do not load dynamic Elixir modules as `:in_memory` as this
  value is not officially supported by the code server. Instead, use
  an empty list, which is the same value used by Erlang.
- [Kernel] Validate variable struct name is atom when used in pattern
  matching
- [Macro] Fix `Macro.to_string/2` for tuple calls, such as `alias
  Foo.{Bar, Baz}`
- [MapSet] Return valid MapSet when unioning a legacy MapSet
- [Regex] Return a leading empty space when splitting on empty
  pattern. This makes the `split` operation consistent with the other
  operations in the `Regex` module
- [Stream] Ensure `Stream.chunk_while/4` does not emit more elements
  than necessary when halted
- [String] Return a leading empty space when splitting on empty
  string. This makes the `split` operation consistent with the other
  operations in the `String` module
- [URI] Preserve empty fragments in `URI.parse/1`

Mix
- [mix app.start] Improve the quality of reports if app fails to boot
- [mix cmd] Allow `mix cmd` to be invoked multiple times without
  marking it as executed
- [mix deps] Ensure optional dependencies in umbrella applications are
  loaded
- [mix deps.update] Ensure transitive new non-Hex dependencies are
  also fetched when a repo is updated
- [mix xref] Take compile dependencies with higher priority than
  runtime ones when building a graph
- [mix xref] Handle external files for xref callers and warnings

3. Soft deprecations (no warnings emitted)

Elixir
- [Inspect.Algebra] `surround/3` and `surround_many/6` are deprecated
  in favor of `container_doc/6`
- [Kernel.ParallelCompiler] `files/2` and `files_to_path/3` are
  deprecated in favor of `compile/2` and `compile_to_path/3`
- [Kernel.ParallelRequire] `files/2` is deprecated in favor of
  `Kernel.ParallelCompiler.require/2`
- [GenServer] Warn if `init/1` is not defined in `GenServer`. This
  brings GenServer closer to the implementation in OTP and aligns all
  behaviours to require the `init/1` callback

ExUnit
- [ExUnit.Formatter] `:case_started` and `:case_finished` events are
  deprecated in favor of `:module_started` and `:module_finished`

4. Deprecations

Elixir
- [Enum] `Enum.partition/2` is deprecated in favor of
  `Enum.split_with/2`
- [Keyword] `Keyword.replace/3` is deprecated in favor of
  `Keyword.fetch/2` and `Keyword.put/3`
- [Map] `Map.replace/3` is deprecated in favor of `Map.fetch/2` and
  `Map.put/3`
- [Macro] `Macro.unescape_tokens/1` and `Macro.unescape_tokens/2` are
  deprecated in favor of `Enum.map/2`
- [Range] Deprecate `Range.range?/1` in favor of pattern matching on
  `_ .. _`

(fhajny)

Updated devel/git

(adam)

Updated devel/git

(adam)

git: updated to 2.16.0

Git 2.16 Release Notes
Backward compatibility notes and other notable changes.
* Use of an empty string as a pathspec element that is used for
  'everything matches' is now an error.

Updates since v2.15
UI, Workflows & Features

* An empty string as a pathspec element that means "everything"
  i.e. 'git add ""', is now illegal.  We started this by first
  deprecating and warning a pathspec that has such an element in
  2.11 (Nov 2016).

* A hook script that is set unexecutable is simply ignored.  Git
  notifies when such a file is ignored, unless the message is
  squelched via advice.ignoredHook configuration.

* "git pull" has been taught to accept "--[no-]signoff" option and
  pass it down to "git merge".

* The "--push-option=<string>" option to "git push" now defaults to a
  list of strings configured via push.pushOption variable.

* "gitweb" checks if a directory is searchable with Perl's "-x"
  operator, which can be enhanced by using "filetest 'access'"
  pragma, which now we do.

* "git stash save" has been deprecated in favour of "git stash push".

* The set of paths output from "git status --ignored" was tied
  closely with its "--untracked=<mode>" option, but now it can be
  controlled more flexibly.  Most notably, a directory that is
  ignored because it is listed to be ignored in the ignore/exclude
  mechanism can be handled differently from a directory that ends up
  to be ignored only because all files in it are ignored.

* The remote-helper for talking to MediaWiki has been updated to
  truncate an overlong pagename so that ".mw" suffix can still be
  added.

* The remote-helper for talking to MediaWiki has been updated to
  work with mediawiki namespaces.

* The "--format=..." option "git for-each-ref" takes learned to show
  the name of the 'remote' repository and the ref at the remote side
  that is affected for 'upstream' and 'push' via "%(push:remotename)"
  and friends.

* Doc and message updates to teach users "bisect view" is a synonym
  for "bisect visualize".

* "git bisect run" that did not specify any command to run used to go
  ahead and treated all commits to be tested as 'good'.  This has
  been corrected by making the command error out.

* The SubmittingPatches document has been converted to produce an
  HTML version via AsciiDoc/Asciidoctor.

* We learned to optionally talk to a file system monitor via new
  fsmonitor extension to speed up "git status" and other operations
  that need to see which paths have been modified.  Currently we only
  support "watchman".  See File System Monitor section of
  git-update-index(1) for more detail.

* The "diff" family of commands learned to ignore differences in
  carriage return at the end of line.

* Places that know about "sendemail.to", like documentation and shell
  completion (in contrib/) have been taught about "sendemail.tocmd",
  too.

* "git add --renormalize ." is a new and safer way to record the fact
  that you are correcting the end-of-line convention and other
  "convert_to_git()" glitches in the in-repository data.

* "git branch" and "git checkout -b" are now forbidden from creating
  a branch whose name is "HEAD".

* "git branch --list" learned to show its output through the pager by
  default when the output is going to a terminal, which is controlled
  by the pager.branch configuration variable.  This is similar to a
  recent change to "git tag --list".

* "git grep -W", "git diff -W" and their friends learned a heuristic
  to extend a pre-context beyond the line that matches the "function
  pattern" (aka "diff.*.xfuncname") to include a comment block, if
  exists, that immediately precedes it.

* "git config --expiry-date gc.reflogexpire" can read "2.weeks" from
  the configuration and report it as a timestamp, just like "--int"
  would read "1k" and report 1024, to help consumption by scripts.

* The shell completion (in contrib/) learned that "git pull" can take
  the "--autostash" option.

* The tagnames "git log --decorate" uses to annotate the commits can
  now be limited to subset of available refs with the two additional
  options, --decorate-refs[-exclude]=<pattern>.

* "git grep" compiled with libpcre2 sometimes triggered a segfault,
  which is being fixed.

* "git send-email" tries to see if the sendmail program is available
  in /usr/lib and /usr/sbin; extend the list of locations to be
  checked to also include directories on $PATH.

* "git diff" learned, "--anchored", a variant of the "--patience"
  algorithm, to which the user can specify which 'unique' line to be
  used as anchoring points.

* The way "git worktree add" determines what branch to create from
  where and checkout in the new worktree has been updated a bit.

* Ancient part of codebase still shows dots after an abbreviated
  object name just to show that it is not a full object name, but
  these ellipses are confusing to people who newly discovered Git
  who are used to seeing abbreviated object names and find them
  confusing with the range syntax.

* With a configuration variable rebase.abbreviateCommands set,
  "git rebase -i" produces the todo list with a single-letter
  command names.

* "git worktree add" learned to run the post-checkout hook, just like
  "git checkout" does, after the initial checkout.

* "git svn" has been updated to strip CRs in the commit messages, as
  recent versions of Subversion rejects them.

* "git imap-send" did not correctly quote the folder name when
  making a request to the server, which has been corrected.

* Error messages from "git rebase" have been somewhat cleaned up.

* Git has been taught to support an https:// URL used for http.proxy
  when using recent versions of libcurl.

* "git merge" learned to pay attention to merge.verifySignatures
  configuration variable and pretend as if '--verify-signatures'
  option was given from the command line.

* "git describe" was taught to dig trees deeper to find a
  <commit-ish>:<path> that refers to a given blob object.

(adam)

quagga: HAVE_BSD_STRUCT_IP_MREQ_HACK does not work on SunOS

(wiedi)

doc: Updated security/py-certbot to 0.21.0

(fhajny)

Update security/py-{acme,certbot} to 0.21.0.

### Added

- Support for the HTTP-01 challenge type was added to our Apache and Nginx
  plugins.
- IPv6 support was added to the Nginx plugin.
- Support for automatically creating server blocks based on the default server
  block was added to the Nginx plugin.
- The flags --delete-after-revoke and --no-delete-after-revoke were added
  allowing users to control whether the revoke subcommand also deletes the
  certificates it is revoking.

### Changed

- We deprecated support for Python 2.6 and Python 3.3 in Certbot and its ACME
  library.
- We split our implementation of JOSE (Javascript Object Signing and
  Encryption) out of our ACME library and into a separate package named josepy.
- We updated the ciphersuites used in Apache to the new values recommended by
  Mozilla

### Fixed

- An issue with our Apache plugin on Gentoo due to differences in their
  apache2ctl command have been resolved.

(fhajny)

doc: Added security/py-josepy version 1.0.1

(fhajny)

Import josepy-1.0.1 as security/py-josepy.

JOSE protocol implementation in Python using cryptography.

(fhajny)

Turn oniguruma support into a (default) option.

(fhajny)

doc: Updated graphics/py-mcomix to 1.2.1nb4

(wiz)

py-mcomix: switch to py-Pillow.

Bump PKGREVISION.

(wiz)

Added missing dependency to devel/ocaml-cppo

(jaapb)

Fixed compilation for package textproc/ocaml-markup

(jaapb)

doc: Updated devel/ocaml-lwt_ssl to 1.1.1

(jaapb)

Updated package devel/ocaml-lwt-ssl to version 1.1.1.

This fixes compatibility with OCaml 4.06.

(jaapb)

doc: Updated print/qpdfview to 0.4.16nb19

(wiz)

qpdfview: fix PLIST after qt5 update.

Noted by abs.

Bump PKGREVISION.

(wiz)

Corrected PLIST for lang/coq

(jaapb)

doc: Updated devel/ocaml-lwt to 3.2.0

(jaapb)

Updated package devel/ocaml-lwt to version 3.2.0.

This release includes several bugfixes and additions. For more details see
the CHANGES file.

(jaapb)

doc: Updated devel/js_of_ocaml to 3.0.2

(jaapb)

Updated package devel/js_of_ocaml to version 3.0.2.

Changes include compatibility fixes for OCaml 4.05 and 4.06, plus
some other minor features and bugfixes (see the CHANGES file for details)

(jaapb)

nss: Fix build on SunOS with clang.

(jperkin)

qt5-qtquickcontrols2: wip -> x11

(wiz)

doc: Updated devel/ocaml-optcomp to 1.6nb9

(jaapb)

Compilation fixes for devel/ocaml-optcomp.

Includes a patch for OCaml 4.06 (from an upstream pull request) and
a call to oasis to regenerate the setup files (which were not compatible
with 4.06 either).

(jaapb)

Removed cmxs option from net/ocamlnet.

(This is now correctly detected and does not need an option)

(jaapb)

doc: Updated devel/ocaml-findlib to 1.7.3nb3

(jaapb)

Patch to devel/ocaml-findlib to not install num library

The num library was split off from ocaml. ocamlfind installs META files
for it if it is detected, but this is not the correct behaviour. This
patch disables detection, which is needed if package updates are to work.

(jaapb)

postgresql*: Use correct linker flags on SunOS.

(jperkin)

unison: fix build with ocaml-4.06

Taken from upstream's v2.48.15v4 release

(wiz)

ocaml: Honor LDFLAGS. Fixes RELRO build.

(wiz)

Updated devel/p5-Getopt-Long-Descriptive to 0.101

(wen)

Update to 0.101

Upstream changes:
0.101    2018-01-21 19:32:11-05:00 America/New_York
        - escape some unescaped braces in regex

(wen)

Updated math/R-car to 2.1.6

(wen)

Update to 2.1.6
Add missing DEPENDS

Upstream changes:
Changes to Version 2.1-6

  o Made several functions compatible with vcov() in R-devel (3.5.0).

Changes to Version 2.1-5

  o Fixed bug in boot.hist, and made Boot.default more general.  Added a vcov method for boot objects

  o Fixed bug in gamLine with non-dentity links.

  o Removed the skewPower transformation functions, and added bcnPower transformation family. Same transformation, new name, new computational algorithms, improved documentation.

  o Fixed bug (reported by Bruno Hebling Vieira) in print.summary.Anova.mlm() that could cause adjusted p-values to be incorrectly ordered.

Changes to Version 2.1-4

  o The smoother functions loessLine, gamLine and quantregLine used in many car functions now evaluate the smoother at an equally spaced grid of points rather than at the observed values on the horizontal axis of a plot.

  o spreadLevelPlot.lm now accepts point marking as in most other graphical functions in car.

  o Bug fixed in one of the skewPower support functions; thans to Balazs Banfai

  o Added support for lmer objects in power transformations

  o Added support for skewPower family power transformations for lm and lmer objects

  o Added list, data.frame, and matrix methods for Boxplot(), suggestion of Michael Friendly

  o Added adaptiveKernel() density estimator, with option to use it in densityPlot().

Changes to Version 2.1-3

  o Corrected documentation for mcPlots

  o added id.location argument to showLabels to vary location of labels

  o added fix for compatiblity with Rcmdr with missing data in several plotting functions.

  o deltaMethod() now reports confidence intervals.

  o print.summary.Anova.mlm() has new SSP and SSPE arguments to determine whether the corresponding matrices are printed (suggestion of Michael Friendly).

  o summary() and print() methods for Anova.mlm() can now report univariate ANOVAs (suggestion and some code by Michael Friendly).

  o added "value" and "vcov" attributes to objects returned by linearHypothesis() (after suggestions by Liviu Andronic and Steven Yen).

  o compareCoefs() now checks classes of models.

  o small fixes/changes.

Changes to Version 2.1-2

  o Modified scatter3d() so that plots can be embedded in HTML.

Changes to Version 2.1-1

  o influencePlot now returns Cook's distance, not its square root.

  o Anova() now supports "coxme" objects (produced by coxme() in coxme package) (request of Philipp Sprenger).

  o Anova() now works via its default method with "vglm" objects produced by functions in the VGAM package; and the default method of linearHypothesis() again works with these objects (problem reported by Michael Friendly).

  o Fixed Anova.coxph() so that it takes account of method (ties) argument (bug reported by Karl Ove Hufthammer).

  o Improvements to Anova.default() so that a wider variety of model classes are accommodated (following request of Liviu Andronic.)

  o dataEllipse() now throws an error if there are too few colors for the number of groups (fixing bug reported by Ottorino Pantani).

  o spreadLevelPlot.lm() now includes an optional smoother in addition to the fitted straight line (suggestion of Michael Friendly).

  o No longer import methods (as opposed to generics) directly from pbkrtest.

  o Added axis.ticks argument to scatter3d() (code contributed by David Winsemius).

Changes to Version 2.1-0

  o New power family called skewPower has been added that can be used with the Box Cox method with a few negative responses (joint work with Doug Hawkins).  Several functions modified to accomodate two-parameter power families.

  o Fixed bug in Anova() for coxph models with clusters (reported by Jesus Humberto Gomez ), due apparently to a change in coxph().

Changes to Version 2.0-26

  o Anova() F-tests for binomial and Poisson GLMs now changes error.estimate="dispersion" to "pearson" as advertized (bug reported by Will Petry).

  o Improved behavior of above-plot legends in scatterplot().

  o Fixed sp() (bug reported by Cesar Rabak).

  o Conforms to new CRAN requirements for package imports.

Changes to Version 2.0-25

  o Fixed df check in linearHypothesis.default() (bug report by Pierre Chausse).

  o Fixed bug when vcov. argument to Anova() is a function (reported by Liviu Andronic).

  o Now export .carEnv to avoid problem with update() in Boot() (reported by Alan T. Arnholt).

Changes to Version 2.0-24

  o Fixed broken URLs.

  o Changed handling of .carEnv environment.

  o Moved pbkrtest, quantreg, and mgcv from Suggests: to Imports:.

Changes to Version 2.0-23

  o Modified ScatterplotSmoothers to add an 'offset' to the vertical axis of spread smooths.  This is required in the marginal model plot functions.

  o Fixed labels on mcPlot with overlay=FALSE

  o Check for 0 residual df and 0 residual deviance (within rounding) in Anova() and linearHypothesis() (problem reported by Jonathan Love).

  o Fixed model.matrix.lme and model.matrix.gls utility functions, and hence Anova and vif, respectively, to work with models specified with formulas supplied as objects (after problem noted by Gang Chen).

  o Added Wong data set, used in mixed-models appendix.

Changes to Version 2.0-22

  o corrected bug in 'terms' argument in residualPlots, and other graphic functions with a 'terms' argument

  o added residual curvature tests for glm.nb

  o mcPlot and mcPlots draw 'marginal/conditional' plots for lm objects.  The marginal plot is of the centered response versus a centered regressor; the conditional plot is the corresponding added-variable plot.  The plots can be overlaid or viewed side-by-side.

  o added argument marginal.scale to avPlots to scale the added-variable plot for Y on X|Z using the scale from the marginal plot of Y vs X ignoring X.  The default is FALSE, corresponding to using scaling to maximize resolution or use xlim and ylim to set user scaling.

  o Fixed bugs in Anova.survreg() that could affect types II, II tests, both Wald and LR, and one similar bug in linearHypothesis.survreg().

  o Replaced calls to require() with requireNamespace() where possible (suggestion of Brian Ripley).

  o The following functions now produce warnings rather than errors when there are empty groups: scatterplot(), scatterplotMatrix(), scatter3d(), densityPlot().

  o Corrected name of "Blackmoor" dataset to "Blackmore".

  o Added KosteckiDillon migraines dataset (contributed by Georges Monette).

  o introduced linearHypothesis.rlm() for rlm models (suggestion of Matthieu Stigler).

  o Small bug fixes/improvements.

Changes to Version 2.0-21

  o residualPlot error when using 'type="rstudent" has been fixed.

  o Minor change to "recode" documentation; improved error checking in recode().

  o Fixed a bug in gamLine with non-canonical links. (Thanks to Hani Christoph)

  o Added has.intercept.multinom() to make Anova() work with multinom objects fit to a dichotomous response (after bug report by Kristian Hovde Liland).

  o Replaced vif.lm() with vif.default() to cover wider variety of models (after question by Laura Rigg about gls models).

  o Diagonal panels in scatterplotMatrix() (except for histograms) show groups separately when plotted by groups (suggestion by Erich Neuwirth).

  o Added vcov. argument to Anova.lm().

Changes to Version 2.0-20

  o Added new id.method="r" to showLabels for labeling plots of residuals; default id.method changed in residualPlots.

  o Fixed handling of labels argument to outlierTest() (bug report by Stephane Laurent).

  o Accommodate numeric variables consisting entirely of NAs in recode() (suggestion of Karl Ove Hufthammer).

  o Prevent dataEllipse() from opening a graphics device when draw=FALSE (fixing bug reported by Rafael Laboissiere).

  o The functions makeHypothesis() and printHypothesis(), intended for internal use, are exported so that they can be used in other packages (request of Arne Henningsen).

  o Small fixes.

Changes to Version 2.0-19

  o allow a grouping variable for color, symbol and fits in residualPlots

  o fixed axis labelling probelm in influenceIndexPlot

  o fixed scoping problems in Boot, bootCase, and ncvTest

  o added an argument to deltaMethod for passing arguments to get scoping right when calling linearHypothesis in another function; other deltaMethod bugs fixed

  o slight modification to documentation of Boot

  o summary() method for "Anova.mlm" objects now returns an object, printed by a corresponding print() method (adapting code contributed by Gabriel Baud-Bovy).

  o added .merMod methods to Anova(), deltaMethod(), linearHypothesis(), matchCoefs(), and unexported utilities df.residual() and has.intercept(); insured compatibility with nlme and CRAN and developments versions of lme4.

  o added use argument to scatterplotMatrix() (suggestion of Antoine Lizee).

  o export linearHypothesis.default() for use in other packages (suggestion of Achim Zeileis).

  o small changes and fixes.

(wen)

Updated math/R-quantreg to 5.34

(wen)

Update to 5.34

Upstream changes:
5.30

1.  Removed Y argument in crq GRAD subroutine, which seems to be superflous.

5.31

1.  Added bag of little bootstraps option to summary.rq.  Needs further
testing.

5.32

1.  Modified the BLB code to use boot.rq.wxy so that the inner loop was all
in fortran, would be nicer if this loop were done with "fn" rather than "br".
See the note in boot.rq above boot.rq.spwy.

2.  modified the crq.pdf file to fix a mento in the description of the Peng
Huang algorithm.

5.33

1.  Added option to return density estimates from predict.rqs

2.  modified rq.fit.fnb to include a rhs input argument.

3.  modified boot.crq to properly deal with only one tau requests
and also changed the default for printing progress report to n - 100,000.
Both suggested by Steve Portnoy.

4.  modified boot.rq so it returns cov(B$B) not cov(B)  as reported
by Marco Geraci

5.  Fixed bug in anova.rqlist to correct error when "fn" method was used
and no $y component was returned.  Reported by Tom LaBone.

6.  Fixed bug in summary.rqss -- control parameters weren't getting
passed to chol call properly.  (Reparted by Geoffrey Shideler (NOAA).)

7.  Added init.c to register .Fortran calls and removed the package =
"quantreg"  argument.

5.34

1.  Fix a bug in rqss to allow control parameters to be passed to rqss.fit
when the method is "lasso"  (pointed out by Heracles Apergis.)

2.  changed nrow(R) to NROW(R) in rq.fit.hogg thanks to Paul Newell for bug
report.

3.  fixed axis label typo in demo engel2.

4.  Added Panel.R demo to illustrate fixed effect panel estimation, a la
Galvao job market talk.

5.  Some changes to crq.fit.por as suggested by SLP:

    line 1: add an input variable mw (the error messages suggest changing mw if
    there are  problems with resolving degeneracies or trying to pivot too far,
    and so it  should be possible to do this without getting into the deep part of
    the code)

    lines 3 and 5: test that x is a matrix and add column names if they are
    missing

    line 39: define mw so that the fortran constraint is satisfied

(wen)

Updated math/R-SparseM to 1.77

(wen)

Update to 1.77

Upstream changes:
The version 1.71

1.  Fixed the REAL*8 and INTEGER*4 occurences in accordance with Kurt's email.

The version 1.73

1.  changed occurences of unix.time to system.time in accordance with Kurt's
directive.

The version 1.74

1.  One more unix -> system

The version 1.75

1.  package -> PACKAGE [per Kurt's email of 3/2/17]

The version 1.76

1.  Used package_native_routine_registration_skeleton  to remove
    PACKAGE = SparseM  [per Kurt's email of 3/2/17]

The version 1.77

1.  Changed setMethod for diag (matrix.csr) in accordance with MM's suggestion

2.  removed setGeneric for image also suggested by MM.

(wen)

Added math/R-pbkrtest version 0.4.7

(wen)

Add R-pbkrtest

(wen)

Import pbkrtest-0.4.7 as math/R-pbkrtest.

Test in linear mixed effects models. Attention is on linear mixed
effects models as implemented in the lme4 package. The package
implements a parametric bootstrap test. The package implements a
Kenward-Roger modification of F-tests.

(wen)

fix inline calls in src/rtl_adsb.c and src/rtl_power.c

(dbj)

update fflush.c and fseeko.c patch so that this builds on Darwin

(dbj)

enable PLIST.libcpp on Darwin

(dbj)

if PYPKGPREFIX is not py27, disable QtWebKit and remove it as a dependency

(dbj)

Do not expect an app bundle on Darwin.

(dbj)

Remove an unneeded line

(wen)

Added math/R-lme4 version 1.1.15

(wen)

Add R-lme4

(wen)

Import lme4-1.1.15 as math/R-lme4.

Fit linear and generalized linear mixed-effects models. The models
and their components are represented using S4 classes and methods.
The core computational algorithms are implemented using the Eigen
C++ library for numerical linear algebra and RcppEigen "glue".

(wen)

Add buildlink3.mk

(wen)

Updated devel/R-Rcpp to 0.12.15

(wen)

Update to 0.12.15

Upstream changelog is too long, please visit:
https://github.com/RcppCore/Rcpp/blob/master/ChangeLog

(wen)

Updated math/R-RcppEigen to 0.3.3.3.1

(wen)

Update to 0.3.3.3.1
Add blas and lapack as DEPENDS

Upstream changes:
2017-11-19  Dirk Eddelbuettel  <edd@debian.org>

* DESCRIPTION (Version, Date): Release 0.3.3.3.1

* R/inline.R: Use '::' not ':::' for Rcpp.plugin.maker

2017-08-26  Dirk Eddelbuettel  <edd@debian.org>

* .travis.yml (before_install): Use https for curl fetch

2017-06-06  Yu Gong  <armgong@yahoo.com>

* inst/include/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h:
Also permit compilation under Haiku-OS

2017-05-28  Dirk Eddelbuettel  <edd@debian.org>

* inst/examples/lmBenchmark.R (do_bench): Remove spurious argument in
call to RcppEigen:::Eigen_SSE() (cf github issue #44)

2017-04-29  Dirk Eddelbuettel  <edd@debian.org>

* DESCRIPTION: Release 0.3.3.3.0

[ which again owes a very big thank you to Yixuan for doing the work! ]

2017-04-27  Dirk Eddelbuettel  <edd@debian.org>

* .travis.yml: Switch to using run.sh for Travis CI

2017-04-27  Yixuan Qiu  <yixuan.qiu@cos.name>

[ In RcppEigen 0.3.3.* branch ]

* inst/include/Eigen/src/Core/arch/CUDA/Half.h: Fixed compiler warning
on 'long long' type in C++ 98 mode

2017-03-14  Dirk Eddelbuettel  <edd@debian.org>

* DESCRIPTION (Version, Date): Release 0.3.2.9.1

* src/init.c (R_init_RcppEigen): Call R_registerRoutines()
and R_useDynamicSymbols()

* NAMESPACE: Use .registration=TRUE on useDynLib

* R/fastLm.R (fastLmPure): Remove erroneous fourth argument from .Call

2017-03-13  Martin Maechler  <maechler@r-project.org>

* inst/include/RcppEigenCholmod.h: Synchronize with Matrix package

2017-02-21  Yixuan Qiu  <yixuan.qiu@cos.name>

[ In RcppEigen 0.3.3.* branch ]

* inst/include/Eigen: Updated to release 3.3.3 of Eigen
* inst/include/unsupported: Idem
* DESCRIPTION: Idem
* README.md: Idem

2017-01-20  Yixuan Qiu  <yixuan.qiu@cos.name>

[ In RcppEigen 0.3.3.* branch ]

* inst/include/Eigen: Updated to release 3.3.2 of Eigen
* inst/include/unsupported: Idem
* DESCRIPTION: Idem
* README.md: Idem

* inst/unitTests/runit.RcppEigen.R, inst/unitTests/runit.sparse.R:
Explicitly convert matrix size to `double` type such that Rcpp can
properly return the value to R, thanks to ChingChuan and Dirk

2017-01-20  ChingChuan Chen  <zw12356@gmail.com>

[ In RcppEigen 0.3.3.* branch ]

* inst/include/Eigen: Updated to release 3.3.1 of Eigen
* inst/include/unsupported: Idem
* DESCRIPTION: Idem

* inst/examples/lmBenchmark.R: Fixed function names

2016-12-22  Dirk Eddelbuettel  <edd@debian.org>

* DESCRIPTION (URL, BugReports): Added / updated

2016-11-12  Yixuan Qiu  <yixuan.qiu@cos.name>

[ In RcppEigen 0.3.3.* branch ]

* inst/include/Eigen: Updated to release 3.3.0 of Eigen
* inst/include/unsupported: Idem
* DESCRIPTION: Idem
* README.md: Idem

* inst/include/RcppEigenForward.h, inst/include/RcppEigenWrap.h:
Added exporters for the new Map<SparseMatrix<T> > type
* inst/unitTests/runit.sparse.R: Unit tests for the new type

2016-08-20  Dirk Eddelbuettel  <edd@debian.org>

* DESCRIPTION: Release 0.3.2.9.0 with big thanks to Yixuan for doing
the work!

2016-08-19  Yixuan Qiu  <yixuan.qiu@cos.name>

* inst/include/Eigen: Updated to release 3.2.9 of Eigen

* README.md: Updated version number and fixed the NOTE from CRAN URL
check

2016-04-30  Dirk Eddelbuettel  <edd@debian.org>

* README.md: Expanded

2016-04-28  James Joseph Balamuta <balamut2@illinois.edu>

* inst/include/RcppEigenWrap.h: Added an exporter class for
Map::RowVectorX<t> per http://stackoverflow.com/questions/36920689/
* inst/include/unitTests/runit.RcppEigen.R: Added row exporter unit
test.

(wen)

Update the version of R-car

(wen)

kf5: add kirigami2

(markd)

Add kirigami2

(markd)

x11: add kirigami2

(markd)

kirigami2: add version 5.41.0

Kirigami is a set of QtQuick components at the moment targeted for
mobile use (in the future desktop as well) targeting both Plasma
Mobile and Android. It's not a whole set of components, all the
"Primitive" ones like buttons and textboxes are a job for
QtQuickControls (soon QtQuickControls2) but it's a set of high level
components to make the creation of applications that look and feel
great on mobile as well as desktop devices and follow the Kirigami
Human Interface Guidelines.

(markd)

py-qt5: fix PLIST for python2 and note dependency on py-dbus

(markd)

doc: Updated security/sqlmap to 1.2

(leot)

sqlmap: Update security/sqlmap to 1.2

Changes
(unfortunately upstream does not provide any changelog, this is based by
reading commit messages):
1.2
---
- Misc improvements and bug fixes

1.1.11
------
- Add support for Apache SHA1
- Add support for Joomla password
- Add support for vBulletin password hashes
- Add support for DJANGO_MD5 and DJANGO_SHA1
- Add WAF script for Wordfence
- Add WAF script for DOSarrest
- Misc improvements and bug fixes

1.1.10
------
- Polish translation
- Add support for blind-based charset dump
- Misc improvements and bug fixes

(leot)

qt5-qtdeclarative: Make sure we pick up gcc's builtin alloca on NetBSD

(markd)

karchive: install karchive.categories via examples dir

(markd)

kactivities-stats: add buildlink3.mk

(markd)

Avoid pointless bashisms.
Avoid use of non POSIX local builtin.
Remove bash dependency.

(roy)

doc: Updated multimedia/xine-ui to 0.99.8nb15

(wiz)

xine-ui: fix two buffer overflows found by SSP

From Anon.

Bump PKGREVISION.

(wiz)

Note update of x11/deforaos-libdesktop to 0.2.2nb1.

(he)

share/gtk-doc/html/libDesktop/index.sgml isn't being installed,
at least not on NetBSD, SmartOS or Ubuntu, so adjust PLIST accordingly.
Bump PKGREVISION.  Going to submit pull-up request.

(he)

Updated multimedia/libdvdcss, multimedia/libdvdread, multimedia/libdvdnav

(adam)

libdvdnav: updated to 6.0.0

libdvdnav (6.0.0)
* fix crashes on some DVD on describe_title call
* fix various crashes related to PGC validity
* fix compilation issues
* fix API return codes

(adam)

libdvdread: updated to 6.0.0

libdvdread (6.0.0)
* restrict the number of symbols to be exposed to the shared-object
* remove dvdinput_error function
* improve compatibility with some DVDs (notably the eOne ones)
* fix write after free in ifoFree functions
* fix possible buffer overflow in open
* additional checks on DVDReadBytes arguments
* fix leaks

(adam)

libdvdcss: updated to 1.4.1

Changes 1.4.1:
* Fix crashes in cache directory creation
* Fix cases where the cache directory was not used

(adam)

doc: Updated security/keychain to 2.8.4

(roy)

ticket 5687

(spz)

Update to keychain-2.8.4:
  Uses id instead of whoami for better portability.
  GPG2 support, support for busybox ps and various optimizations.

(roy)

Pullup ticket #5687 - requested by morr
www/wordpress: security update

Revisions pulled up:
- www/wordpress/Makefile                                        1.75
- www/wordpress/PLIST                                          1.37
- www/wordpress/distinfo                                        1.60

-------------------------------------------------------------------
  Module Name: pkgsrc
  Committed By: morr
  Date: Sat Jan 20 11:58:01 UTC 2018

  Modified Files:
  pkgsrc/www/wordpress: Makefile PLIST distinfo

  Log Message:
  Update to version 4.9.2

  CHanges:

  XSS fixed in the Flash fallback files in MediaElement 4.x.

  Bundled Theme
  #42820 - Twenty Seventeen -watch that language

  Customize
  #42492 - Selecting menu location changes line height
  #42871 - Features box textstrings in Feature Filter area need new linebreak

  Database
  #42812 - Use MySQLi when available by default

  Editor
  #42664 - Editor link autocomplete suggestions: no fallback title displayed for posts with no title
  #43012 - Cannot Update Post in Firefox Due to Editor and TinyMCE JavaScript TypeErrors

  External Libraries
  #42439 - Update random_compat external library for PHP 7 linting failure

  Formatting
  #42578 - PHP functions inside <p> tags creates new <p> tag, breaking the parent tag into two.

  Media
  #42225 - Whitelist Flac Files
  #42447 - Mark test_remove_orientation_data_on_rotate as skipped when exif_read_data isn't available
  #42480 - Consistent suppression of `getimagesize()` errors
  #42720 - Remove unnecessary MediaElement.js files

  Plugins
  #43082 - Add plugins search results: the plugin details modal opens in the thickbox modal

  REST API
  #42828 - Hard-coded 403 status in REST response should use `rest_authorization_required_code()`

  Taxonomy
  #42771 - WP_Term::get_instance() regression for non-category terms queried with 'category' taxonomy
  #42605 - category_description() does not work properly since 4.9
  #42717 - get_category_link() accepting object but not id

  TinyMCE
  #42416 - Code assumes iframe mode, exception in inline mode

  Upgrade/Install
  #42963 - Improve deletion of $_old_files during upgrades

  Widgets
  #42603 - Widgets Warning after activating theme and on dashboard widgets page
  #42719 - Always attempt to restore widgets' previous assignment
  #42867 - HTML Widget: toggleClass() should be passed true/false as second param

  To generate a diff of this commit:
  cvs rdiff -u -r1.74 -r1.75 pkgsrc/www/wordpress/Makefile
  cvs rdiff -u -r1.36 -r1.37 pkgsrc/www/wordpress/PLIST
  cvs rdiff -u -r1.59 -r1.60 pkgsrc/www/wordpress/distinfo

(spz)

xf86-input-keyboard: bump revision.

(triaxx)

Add ${VARBASE} replacements in example config.

Patch from Travis Paul in PR pkg/52930.
Bump revision.

(bsiegert)

Updated shells/mksh to 56c

(bsiegert)

Update mksh to 56c.

R56c is a bugfix-only release everyone must upgrade to:

- [komh] Remove redundant OS/2-specific code, clean up others
- [komh, tg] Fix drive-qualified (absolute and relative) DOS-style path support
  in realpath functionality, partially other places
- [tg] Don't substitute ${ENV:-~/.mkshrc} result again
- [tg] Improve OS/2 $PATH (et al.) handling, drive-relative paths
- [tg] Add MKSH_ENVDIR compile-time option for Jehanne and Plan 9
- [tg] Limit nesting when parsing malformed code (Debian #878947)
- [tg] Update wcwidth data with bugfixed script (still Unicode 10; resulting
  values are identical to glibc git master for extant chars)
- [Dr. Werner Fink] Raise some time limits in the testsuite
- [Shamar] Add support for the Jehanne operating system
- [komh] Set stdin to text mode before executing child processes on OS/2
- [komh] Pass arguments via a resonse file if executing a child fails
- [Dr. Werner Fink] Early locale tracking as a compile-time option
- [tg] Fix regressions introduced with new fast character classes

(bsiegert)

Updated www/py-google-api-python-client, www/py-yarl, www/py-pylint-django, finance/py-braintree

(adam)

py-braintree: updated to 3.40.0

3.40.0
Add level 3 fields to Transactions:
discount_amount
shipping_amount
ships_from_postal_code
Add support for transaction line items
Add support for tagged evidence in DisputeGateway#add_text_evidence (Beta release)
Update https certificate bundle

(adam)

py-pylint-django: updated to 0.8.0

Version 0.8.0:
This is the last version to support Python 2. Issues a deprecation warning!
Adding 'urlpatterns', 'register', 'app_name' to good names.
Add 'handler500' to good names
Support factory_boy's DjangoModelFactory Meta class
Fix E1101:Instance of 'proxy' has no 'format' member' when using .format() on a ugettext_lazy translation.
Add tests and transforms for DurationField,
Add json field to WSGIRequest proxy
Add support for django.contrib.postgres.fields and UUIDField
Stop testing with older Django versions. Currently testing with Django 1.11.x and 2.0
Stop testing on Python 2, no functional changes in the source code though
Update tests and require latest version of pylint (>=1.8)
Fix 'duplicate-except' false negative for except blocks which catch the DoesNotExist exception.

(adam)

py-yarl: updated to 1.1.0

1.1.0:
Make pure Python quoter consistent with Cython version

(adam)