(math/R-survey) Updated 4.1.1 to 4.2.1

Following lines from inst/NEWS

4.2 Handling of influence functions has CHANGED. A function that supplies influence
functions must supply one for every observation it was given in its input:
use 0 for observations removed by subsetting. (for Guilherme Jacob)

regTermTest(method="LRT") required the two models to use the same observations
(of course), but didn't check, so IT WAS WRONG.
It now subsets properly. (for Keiran Shao)

This will probably be the *last* interpreted-R-only version of survey. Future
versions will likely incorporate C++ code for faster variance computation and
for small-area estimation.

deffs in svyglm.svyrep.design (Ben Schneider)

svynls() allows for prior (eg precision) weights (for Gary Nelson)

improved names in svyquantile.svyrep.design (Ben Schneider)

trimWeights() could get into an infinite recursion (Ingmar Sturm)

data(myco) from Rao, Scott, and Skinner (originally from Clayton & Hills)

as.svrepdesign now throws an error with post-stratified/raked/calibrated
designs -- create replicates *first*, then calibrate (for Lauren Kennedy)

trimWeights now works with replicate-weights designs

score tests for svyglm (with Keiran Shao)

svyby(), and thus svyboxplot(), didn't handle the new quantile functions
correctly when standard error/ci weren't requested (Stephanie Zimmer, Raymond Pan)

svycontrast() threw an error on the output of svyby() with return.replicates=TRUE
(Alena Stern)

Fix regTermTest for svycoxph for the methods lookup changes in R 4.0
(and consequential change to marginpred)

We don't provide model.matrix.svycoxph any more;use the inherited
survival:::model.matrix.coxph

Recent survival::coxph() switches to robust variances with non-integer weights
so check for model$naive.var before model$var

Disable the pass-through from predict.svycoxph to predict.coxph for type="expected"
(Bryan Shepherd)

svyby( svyvar) would throw an error on domains with only one observation
(for Dirk Schumacher)

svyvar() computes sample size 'n' in the same way for na.rm=TRUE as for a domain
(for Raymond Pan)

xdesign() for crossed designs (which aren't strictly surveys, but are basically similar)

removed redundant loop in saddlepoint approximation to pchisqsum (Qiaolan Deng)

fix in summary(svyivreg) for variances (Chandler McClellan)

svyolr() didn't run for subsets of raked/calibrated designs (Antony Damico)

add predict.svyolr (for Vincent Arel-Bundock)

add anova.svycoxph (for Bryan Shepherd)

add stringsToFactors=TRUE to svyby to ensure factors have same levels in domains
(for various people including Stephanie Zimmer)

more complicated svyby example in ?svycontrast

svyranktest() gave an error for multiple groups with replicate weights (Kasuki Yoshida)

Additional chisquared test for tables with zeros (CrossValidated question #571328)

svydesign() has a 'calibrate.formula' option to tell R that your weights have
already been calibrated/raked/post-stratified (for Tobias Schoch)

svycontrast() didn't work on svrepglm objects without replicates (Thomas Loughlin)

error in svycoxph with rescale=FALSE (Jing Zhang)

error in vcov.svyrep.design with mse=TRUE (shows up in svyVGAM)

svyquantile() didn't pay attention to interval_type for replicate weights (David Jorquera Petersen)

svyquantile() qrules 5 to 9 now return the single data value when there's
just one (David Jorquera Petersen)

regTermTest() on svyolr() objects created in a function now finds the
design object more reliably. (for Pedro Baldoni)

regTermTest() will now test against null models in svycoxph()

Fixes to svyquantile: https://github.com/bschneidr/r-forge-survey-mirror/pull/7
(Ben Schneider)

anova.svyloglin was broken by change to anova.glm(test=NULL)
(Brian Ripley)

One-sample svyttest() on logical variable now tests for P(TRUE==0) not P(FALSE==0)
(Stephanie Zimmer)

rename svykm.fit to svykm_fit because CRAN tests

(mef)

fix build for option -pulseaudio

phonon 4.11 has changed the CMake mechanism so instead of using their
own macro (which checked WITH_PulseAudio) it just uses find_package
directly, so use the CMake option to disable it.

(plunky)

doc: Updated math/R-minqa to 1.2.5

(mef)

(math/R-minqa) Updated 1.2.4 to 1.2.5

2022-10-18 K Mullen <mullenkate@gmail.com>
* src/altmov.f: Added initialization of IBDSAV to 0 at line 170.
Ben Bolker reported a case that triggered a segfault that I traced
to this variable being used uninitialized.
* DESCRIPTION: CRAN now says the Title field should be in title case,
changed to comply.

(mef)

doc: Updated devel/mob to 4.4.3

(schmonz)

Update to 4.4.3. From the changelog:

- Fix: mob.sh now specifies the remote ref when pushing to allow for
  custom `git config push.default` settings such as `tracking`
- Fix: Improves the suggested command when you have uncommitted changes
  on an attempt to open a custom wip branch using `mob start -b green`
- mob.sh now uses the go version 1.20.x

(schmonz)

doc: Updated math/R-dplyr to 1.1.2

(mef)

(math/R-dplyr) Updated 1.1.0 to 1.1.2

# dplyr 1.1.2

* `count()` better documents that it has a `.drop` argument (#6820).

* Fixed tests to maintain compatibility with the next version of waldo (#6823).

* Joins better handle key columns will all `NA`s (#6804).

# dplyr 1.1.1

* Mutating joins now warn about multiple matches much less often. At a high
  level, a warning was previously being thrown when a one-to-many or
  many-to-many relationship was detected between the keys of `x` and `y`, but is
  now only thrown for a many-to-many relationship, which is much rarer and much
  more dangerous than one-to-many because it can result in a Cartesian explosion
  in the number of rows returned from the join (#6731, #6717).

  We've accomplished this in two steps:

  * `multiple` now defaults to `"all"`, and the options of `"error"` and
    `"warning"` are now deprecated in favor of using `relationship` (see below).
    We are using an accelerated deprecation process for these two options
    because they've only been available for a few weeks, and `relationship` is
    a clearly superior alternative.

  * The mutating joins gain a new `relationship` argument, allowing you to
    optionally enforce one of the following relationship constraints between the
    keys of `x` and `y`: `"one-to-one"`, `"one-to-many"`, `"many-to-one"`, or
    `"many-to-many"`.

    For example, `"many-to-one"` enforces that each row in `x` can match at
    most 1 row in `y`. If a row in `x` matches >1 rows in `y`, an error is
    thrown. This option serves as the replacement for `multiple = "error"`.

    The default behavior of `relationship` doesn't assume that there is any
    relationship between `x` and `y`. However, for equality joins it will check
    for the presence of a many-to-many relationship, and will warn if it detects
    one.

  This change unfortunately does mean that if you have set `multiple = "all"` to
  avoid a warning and you happened to be doing a many-to-many style join, then
  you will need to replace `multiple = "all"` with
  `relationship = "many-to-many"` to silence the new warning, but we believe
  this should be rare since many-to-many relationships are fairly uncommon.

* Fixed a major performance regression in `case_when()`. It is still a little
  slower than in dplyr 1.0.10, but we plan to improve this further in the future
  (#6674).

* Fixed a performance regression related to `nth()`, `first()`, and `last()`
  (#6682).

* Fixed an issue where expressions involving infix operators had an abnormally
  large amount of overhead (#6681).

* `group_data()` on ungrouped data frames is faster (#6736).

* `n()` is a little faster when there are many groups (#6727).

* `pick()` now returns a 1 row, 0 column tibble when `...` evaluates to an
  empty selection. This makes it more compatible with [tidyverse recycling
  rules](https://vctrs.r-lib.org/reference/vector_recycling_rules.html) in some
  edge cases (#6685).

* `if_else()` and `case_when()` again accept logical conditions that have
  attributes (#6678).

* `arrange()` can once again sort the `numeric_version` type from base R
  (#6680).

* `slice_sample()` now works when the input has a column named `replace`.
  `slice_min()` and `slice_max()` now work when the input has columns named
  `na_rm` or `with_ties` (#6725).

* `nth()` now errors informatively if `n` is `NA` (#6682).

* Joins now throw a more informative error when `y` doesn't have the same
  source as `x` (#6798).

* All major dplyr verbs now throw an informative error message if the input
  data frame contains a column named `NA` or `""` (#6758).

* Deprecation warnings thrown by `filter()` now mention the correct package
  where the problem originated from (#6679).

* Fixed an issue where using `<-` within a grouped `mutate()` or `summarise()`
  could cross contaminate other groups (#6666).

* The compatibility vignette has been replaced with a more general vignette on
  using dplyr in packages, `vignette("in-packages")` (#6702).

* The developer documentation in `?dplyr_extending` has been refreshed and
  brought up to date with all changes made in 1.1.0 (#6695).

* `rename_with()` now includes an example of using `paste0(recycle0 = TRUE)` to
  correctly handle empty selections (#6688).

* R >=3.5.0 is now explicitly required. This is in line with the tidyverse
  policy of supporting the [5 most recent versions of
  R](https://www.tidyverse.org/blog/2019/04/r-version-support/).

(mef)

doc: Updated math/R-tibble to 3.2.1

(mef)

(math/R-tibble)  Updated 3.1.8 to 3.2.1

# tibble 3.2.1

## Internal
- Use symbol instead of string in `.Call()`.

# tibble 3.2.0

## Features
- Accurate location of the source of an error in error messages
  (#1379, #1065, #1508).

- `as_data_frame()` now also refers to `as.data.frame()` in its
  deprecation message (#1149, #1506).

## Breaking changes
- Deprecated functions and arguments where we could not detect usage
  by other CRAN packages (#1515):

    - `data_frame_()`, `lst_()`, `frame_data()`

    - `as_tibble(validate = )`, `as_tibble(NULL)`, `new_tibble(subclass = )`

    - `add_row()` and `add_column()` for non-data-frame input

    - `add_column()` for input with non-unique names

    - corner cases for `tbl[[x]]`

- Breaking change: Remove `knit_print.trunc_mat()` method (#1516).

- Forward `trunc_mat()` to new-style pillar methods (#1517).

## Bug fixes

- Allow `glue()` and other classed characters for subassignment (#1150, #1503).

## Performance

- Reduce overhead of single-column subset assignment (#1363).

## Documentation

- New `vignette("extending")` (#275, #1512).

- Minor updates (#1151, #1070, #1512, #1485).

- Update example for `nrow` argument to `new_tibble()` (@heavywatal, #1394).

- Fix display of mermaid diagrams in `vignette("formats")` (@maelle, #1497, #1498).

- Remove ANSI escapes from invariants article on pkgdown (#1374).

## Internal

- Require vctrs >= 0.4.1 and pillar >= 1.8.1

- Use cli for formatting conditions (#1387).

- Use `vec_as_location(missing = "error")` for better error messages
  (#741, #1511).

- Remove compatibility code for RSDA package which is broken anyway
  due to other changes (#923, #1509).

- Skip tests if suggested packages not available (#1246, @MichaelChirico).

- Remove obsolete tests (#1513).

(mef)

doc: Updated misc/R-pillar to 1.9.0

(mef)

(misc/R-pillar) Updated 1.8.1 to 1.9.0

# pillar 1.9.0

## Features

- Math operations on `num()` objects no longer perform type
  checks. This allows, e.g., multiplying a `num()` with a logical
  (#630, #632).

## Printing

- The Default For The `Pillar.Min_Title_Chars` Option Has been bumped
  up to 20 characters so that title truncuation only affects very long
  variables. Use `options(pillar.min_title_chars = 5)` to reset to the
  previous default (#582, #620).

- Use info bullets to format details (#582, #617, #627, #635).

## Breaking changes

- `colonnade()`, `extra_cols()` and `squeeze()` are now
  hard-deprecated (#272, #374, #631).

## Bug fixes

- Show `colnames()` hint only when needed (tidyverse/tibble#1488, #622).

- Fix printing of very small numbers (#615, #619).

- Shortened list columns are also shown with a subtle style (#628, #634).

- Avoid warning with S4 character classes (tidyverse/tibble#1367, #625).

- Fix method consistency, checked by R-devel (#633).

## Documentation

- Polish `?pillar_options` (#583).

- Fix typo & missing quote in digits vignette stub (@gavinsimpson, #629).

## Internal

- Require vctrs >= 0.5.0

(mef)

mozilla-rootcerts-openssl: fix PLIST; apply pkglint suggestion

(adam)

py-pspdfutils: conflicts with psutils<3

(wiz)

remove extra 'py' that was breaking the build.

(mrg)

doc: Updated math/R-units to 0.8.2

(mef)

(math/R-units) Updated 0.8.1 to 0.8.2

# version 0.8-2

* Names are preserved when doing unit conversions; #305 @billdenney

* Identical units will always divide (`/`) and allow integer division (`%/%`).
  And, inverse units will always be able to multiply; #310 @billdenney

* Compare units via `ud_compare()`, fixing inconsistent results for aliases
  and symbols; #339, #346, #347

* Fix `units<-()` to treat an empty unit the same as `NULL`; #332

* New `as.data.frame()` method for `mixed_units`; #309

* Use short paths for database loading on Windows to fix UTF-16 issues; #342

* Add example in the docs about reversing a ggplot2 units scale; #343

* Force storage mode to double; #344 addressing #324

* Fix units in transformed axis; #323

* Consider unitless as radians in trigonometric functions; #328

(mef)

vte3: adjust DESCR to match reality and upstream's statement

(gutteridge)

doc: Updated x11/vte3 to 0.72.1

(gutteridge)

vte3: update to 0.72.1

No concise upstream change log is available, but this release includes
several fixes for NetBSD. (It also no longer bundles a Vala test app
that caused troubles in the past, etc.)

(gutteridge)

*: fix typo

(wiz)

*: switch to py-pspdfutils instead of psutils

(wiz)

doc: Updated print/psutils to 3.0.3

(wiz)

psutils: make this a compatibility package

Just depend on py-pspdfutils to give people time to switch
to that package directly.

(wiz)

doc: Added print/py-pspdfutils version 3.0.3

(wiz)

print/Makefile: + py-pspdfutils

(wiz)

print/py-pspdfutils: import py-pspdfutils-3.0.3

New name for psutils, rewritten in Python.

PSUtils is a suite of utilities for manipulating PDF and PostScript
documents. You can select and rearrange pages, including arrangement
into signatures for booklet printing, combine multple pages into
a single page for n-up printing, and resize, flip and rotate pages.

(wiz)

doc: Added sysutils/py-puremagic version 1.15

(wiz)

sysutils/Makefile: + py-puremagic

(wiz)

sysutils/py-puremagic: import py-puremagic-1.15

Packaged for wip by Olaf Seibert and myself.

puremagic is a pure python module that will identify a file based off its
magic numbers.

It is designed to be minimalistic and inherently cross platform
compatible. It is also designed to be a stand in for python-magic, it
incorporates the functions from_file(filename[, mime]) and
from_string(string[, mime]) however the magic_file() and magic_string()
are more powerful and will also display confidence and duplicate
matches.

It does NOT try to match files off non-magic string. In other words it
will not search for a string within a certain window of bytes like
others might.

(wiz)

doc: Updated net/dbip-country-lite to 2023.06

(fcambus)

dbip-country-lite: update to 2023.06.

No upstream ChangeLog.

(fcambus)

doc: Updated net/dbip-city-lite to 2023.06

(fcambus)

dbip-city-lite: update to 2023.06.

No upstream ChangeLog.

(fcambus)

doc: Updated net/dbip-asn-lite to 2023.06

(fcambus)

dbip-asn-lite: update to 2023.06.

No upstream ChangeLog.

(fcambus)

(math/R-vctrs) Update for DEPENDS+= R-rlang version

(mef)

doc: Updated devel/R-rlang to 1.1.1

(mef)

(devel/R-rlang) Updated 1.0.6 to 1.1.1

# rlang 1.1.1

* `englue()` now allows omitting `{{`. This is to make it easier to
  embed in external functions that need to support either `{` and `{{`
  (#1601).

* Fix for CRAN checks.

* `stop_input_type()` now handles `I()` input literally in `arg`
  (#1607, @simonpcouch).

* `parse_expr()` and `parse_exprs()` are now faster when
  `getOption("keep.source")` is `TRUE` (#1603).

# rlang 1.1.0

## Life cycle changes

* `dots_splice()` is deprecated. This function was previously in
  the questioning lifecycle stage as we were moving towards the
  explicit `!!!` splicing style.

* `flatten()`, `squash()`, and their variants are deprecated in favour
  of `purrr::list_flatten()` and `purrr::list_c()`.

* `child_env()` is deprecated in favour of `env()` which has supported
  creating child environments for several years now.

## Main new features

* `last_error()` and `options(rlang_backtrace_on_error = "full")` now
  print the full backtrace tree by default (except for some hidden
  frames). The simplified backtraces tended to hide important context
  too often. Now we show intervening frames in a lighter colour so
  that they don't distract from the important parts of the backtraces
  but are still easily inspectable.

* `global_entrace()`, `last_warnings()`, and `last_messages()` now
  support knitr documents.

* New `rlang_backtrace_on_warning_report` global option. This is
  useful in conjunction with `global_entrace()` to get backtraces on
  warnings inside RMarkdown documents.

* `global_entrace()` and `entrace()` now stop entracing warnings and
  messages after 20 times. This is to avoid a large overhead when 100s
  or 1000s of warnings are signalled in a loop (#1473).

* `abort()`, `warn()`, and `inform()` gain an `.inherit` parameter.
  This controls whether `parent` is inherited. If `FALSE`,
  `cnd_inherits()` and `try_fetch()` do not match chained conditions
  across parents.

  It's normally `TRUE` by default, but if a warning is chained to an
  error or a message is chained to a warning or error (downgraded
  chaining), `.inherit` defaults to `FALSE` (#1573).

* `try_fetch()` now looks up condition classes across chained errors
  (#1534). This makes `try_fetch()` insensitive to changes of
  implementation or context of evaluation that cause a classed error
  to suddenly get chained to a contextual error.

* `englue()` gained `env`, `error_arg`, and `error_call` arguments to
  support being wrapped in another function (#1565).

* The data-masking documentation for arguments has been imported from
  dplyr. You can link to it by starting an argument documentation with
  this button:

  ```
  <[`data-masking`][rlang::args_data_masking]>
  ```

* `enquos()` and friends gain a `.ignore_null` argument (#1450).

* New `env_is_user_facing()` function to determine if an evaluation
  frame corresponds to a direct usage by the end user (from the global
  environment or a package being tested) or indirect usage by a third
  party function. The return value can be overridden by setting the
  `"rlang_user_facing"` global option.

## Miscellaneous fixes and features

* New `check_data_frame()` and `check_logical()` functions in
  `standalone-types-check.R` (#1587, @mgirlich).

* Added `allow_infinite` argument to `check_number_whole()` (#1588, @mgirlich).

* The lifecycle standalone file has been updated to match the modern
  lifecycle tools.

* `parse_expr()` now supports vectors of lines (#1540).

* Quosures can now be consistently concatenated to lists of quosures (#1446).

* Fixed a memory issue that caused excessive duplication in `list2()`
  and friends (#1491).

* Embraced empty arguments are now properly detected and trimmed by
  `quos()` (#1421).

* Fixed an edge case that caused `enquos(.named = NULL)` to return a
  named list (#1505).

* `expr_deparse()` now deparses the embrace operator `{{` on a single
  line (#1511).

* `zap_srcref()` has been rewritten in C for efficiency (#1513).

* `zap_srcref()` now supports expression vectors.

* The non-error path of `check_dots_unnamed()` has been rewritten in C
  for efficiency (#1528).

* Improved error messages in `englue()` (#1531) and in glue strings in
  the LHS of `:=` (#1526).

* `englue()` now requires size 1 outputs (#1492). This prevents
  surprising errors or inconsistencies when an interpolated input of
  size != 1 makes its way into the glue string.

* `arg_match()` now throws correct error when supplied a missing value
  or an empty vector (#1519).

* `is_integerish()` now handles negative doubles more consistently
  with positive ones (@sorhawell, #1530).

* New `check_logical()` in `standalone-types-check.R` (#1560).

* `quo_squash()` now squashes quosures in function position (#1509).

* `is_expression()` now recognises quoted functions (#1499).
  It now also recognises non-parsable attributes (#1475).

* `obj_address()` now supports the missing argument (#1521).

* Fixed a `check_installed()` issue with packages removed during the
  current R session (#1561).

* `new_data_mask()` is now slightly faster due to a smaller initial mask size
  and usage of the C level function `R_NewEnv()` on R >=4.1.0 (#1553).

* The C level `r_dyn_*_push_back()` utilities are now faster (#1542).

* The C level `r_lgl_sum()` and `r_lgl_which()` helpers are now faster
  (#1577, with contributions from @mgirlich).

* rlang is now compliant with `-Wstrict-prototypes` as requested by CRAN
  (#1508).

(mef)

doc: Updated devel/R-Rcpp to 1.0.10

(mef)

doc: Updated security/mozilla-rootcerts-openssl to 2.11

(wiz)

(devel/R-Rcpp) Updated 1.0.9 to 1.0.10

2023-01-08  Dirk Eddelbuettel  <edd@debian.org>

* inst/include/Rcpp/String.h: Address clang++-14 conversion warning
* inst/include/Rcpp/sugar/functions/mean.h: Idem
* inst/include/Rcpp/vector/Vector.h: Idem
* src/attributes.cpp: Idem
* src/date.cpp: Idem

2022-12-29  Dirk Eddelbuettel  <edd@debian.org>

* .github/workflows/docker.yaml (jobs): Update several actions

2022-12-26  Dirk Eddelbuettel  <edd@debian.org>

* .github/workflows/stale.yaml (jobs): Update actions/stale@v6

2022-11-14  Dirk Eddelbuettel  <edd@debian.org>

* .github/workflows/ci.yaml (jobs): Update to actions/checkout@v3

2022-10-27  Dirk Eddelbuettel  <edd@debian.org>

* DESCRIPTION (Version, Date): Roll minor version
* inst/include/Rcpp/config.h (RCPP_DEV_VERSION): Idem

2022-10-27  Kevin Ushey  <kevinushey@gmail.com>

* inst/tinytest/cpp/coerce.cpp: add coerce unit tests
* inst/tinytest/test_coerce.R: idem

2022-10-25  Dirk Eddelbuettel  <edd@debian.org>

* inst/include/Rcpp/internal/r_coerce.h (coerce_to_string<RAWSXP >):
Replace last remaining sprintf with snprintf

2022-10-12  Dirk Eddelbuettel  <edd@debian.org>

* DESCRIPTION (Version, Date): Roll minor version
* inst/include/Rcpp/config.h (RCPP_DEV_VERSION): Idem

* R/Attributes.R (sourceCpp): Protect path to binary from spaces

2022-10-06  Dirk Eddelbuettel  <edd@debian.org>

* DESCRIPTION (Version, Date): Roll minor version
* inst/include/Rcpp/config.h (RCPP_DEV_VERSION): Idem

* inst/tinytest/test_dataframe.R (test.DataFrame.PushZeroLength): Add
new test
* inst/tinytest/cpp/DataFrame.cpp (DataFrame_PushOnEmpty): C++
support for new test

2022-10-04  Dirk Eddelbuettel  <edd@debian.org>

* inst/include/Rcpp/DataFrame.h (set_type_after_push): Allow zero-row
data.frame objects to be grown by push_{back,front}()

2022-09-25  Dirk Eddelbuettel  <edd@debian.org>

* DESCRIPTION (Version, Date): Roll minor version
* inst/include/Rcpp/config.h (RCPP_DEV_VERSION): Idem

2022-09-23  Kevin Ushey  <kevinushey@gmail.com>

* R/Module.R: Force 'finalize' method to be materialized

2022-09-20  Dirk Eddelbuettel  <edd@debian.org>

* DESCRIPTION (Version, Date): Roll minor version
* inst/include/Rcpp/config.h: Idem

* R/Attributes.R: Support C++20, C++23 and C++2b (for experimental /
incomplete support) via new plugins

2022-07-27  Dirk Eddelbuettel  <edd@debian.org>

* DESCRIPTION (Version, Date): Roll minor version
* inst/include/Rcpp/config.h: Idem

2022-07-23  I単aki Ucar  <iucar@fedoraproject.org>

* inst/include/Rcpp/r/headers.h: Unwind protection is enabled by default
unless `RCPP_NO_UNWIND_PROTECT` is defined (`RCPP_USE_UNWIND_PROTECT` is
not checked anymore and has no effect)
* inst/include/Rcpp/vector/Vector.h: Switch evaluation to `Rcpp_eval`
* R/Attributes.R: `[[Rcpp::plugins(unwindProtect)]]` is deprecated
* inst/tinytest/cpp/stack.cpp: Adapted
* inst/tinytest/test_exceptions.R: Adapted
* inst/tinytest/test_interface.R: Adapted
* inst/tinytest/testRcppInterfaceExporter/src/config.h: Removed

2022-07-10  Dirk Eddelbuettel  <edd@debian.org>

* docker/ci-4.1/Dockerfile: Add Dockerfile for 4.1 series
* .github/workflows/ci.yaml: Add 4.1 to CI matrix
* .github/workflows/docker.yaml: Do not rebuild versioned ones

(mef)

doc: Updated security/mozilla-rootcerts to 1.0.20230505

(wiz)

mozilla-rootcert*: update to 20230505 data

(wiz)

doc: Updated math/R-vctrs to 0.6.2

(mef)

(math/R-vctrs) Updated 0.5.2 to 0.6.2

# vctrs 0.6.2

* Fixed conditional S3 registration to avoid a CRAN check NOTE that appears in
  R >=4.3.0 (#1832).

* Fixed tests to maintain compatibility with the next version of waldo (#1829).

# vctrs 0.6.1

* Fixed a test related to `c.sfc()` changes in sf 1.0-10 (#1817).

# vctrs 0.6.0

* New `vec_run_sizes()` for computing the size of each run within a vector. It
  is identical to the `times` column from `vec_unrep()`, but is faster if you
  don't need the run key (#1210).

* New `sizes` argument to `vec_chop()` which allows you to partition a vector
  using an integer vector describing the size of each expected slice. It is
  particularly useful in combination with `vec_run_sizes()` and `list_sizes()`
  (#1210, #1598).

* New `obj_is_vector()`, `obj_check_vector()`, and `vec_check_size()` validation
  helpers. We believe these are a better approach to vector validation than
  `vec_assert()` and `vec_is()`, which have been marked as questioning because
  the semantics of their `ptype` arguments are hard to define and can often be
  replaced by `vec_cast()` or a type predicate function like
  `rlang::is_logical()` (#1784).

* `vec_is_list()` and `vec_check_list()` have been renamed to `obj_is_list()`
  and `obj_check_list()`, in line with the new `obj_is_vector()` helper. The
  old functions have been silently deprecated, but an official deprecation
  process will start in the next vctrs release (#1803).

* `vec_locate_matches()` gains a new `relationship` argument that holistically
  handles multiple matches between `needles` and `haystack`. In particular,
  `relationship = "many-to-one"` replaces `multiple = "error"` and
  `multiple = "warning"`, which have been removed from the documentation and
  silently soft-deprecated. Official deprecation for those options will start in
  a future release (#1791).

* `vec_locate_matches()` has changed its default `needles_arg` and
  `haystack_arg` values from `""` to `"needles"` and `"haystack"`, respectively.
  This generally generates more informative error messages (#1792).

* `vec_chop()` has gained empty `...` between `x` and the optional `indices`
  argument. For backwards compatibility, supplying `vec_chop(x, indices)`
  without naming `indices` still silently works, but will be deprecated in a
  future release (#1813).

* `vec_slice()` has gained an `error_call` argument (#1785).

* The `numeric_version` type from base R is now better supported in equality,
  comparison, and order based operations (tidyverse/dplyr#6680).

* R >=3.5.0 is now explicitly required. This is in line with the tidyverse
  policy of supporting the [5 most recent versions of
  R](https://www.tidyverse.org/blog/2019/04/r-version-support/).

(mef)

doc: Updated biology/fastp to 0.22.0

(bacon)

biology/fastp: Update to 0.22.0

Adds deduplication subcommand
Changes: https://github.com/OpenGene/fastp/releases
Holding off on 0.23, which depends on the non-portable Intel isa-l,
which does not build on Darwin aarch64

(bacon)

doc: Updated math/R-xts to 0.13.1

(mef)

(math/R-xts) Updated 0.12.2 to 0.13.1

################################################################################
Changed in xts 0.13.1:

o Ignore attribute order in `all.equal()`. Attribute order shouldn't matter.
  That can be checked with `identical()`.

o Only call `tzone()` and `tclass()` once in `check.TZ()`. Calling these
  functions multiple times throws multiple warnings for xts objects created
  before the tclass and tzone were attached to the index instead of the xts
  object. (#306)

o Add instructions to update old objects. Old xts objects do not have tclass
  and tzone attributes on the index. Add a function to update the object
  attributes and add a note to the warning to show how to use it. (#306)

o Return 'POSIXct' if object has no 'tclass'. An empty string is not a valid
  'tclass', so it can cause an error.

o Add notes on `plot.xts()` nomenclature and structure. Also add ASCII art to
  illustrate definitions and layout. (#103)

o Remove 'tis' support. The implementation was not even a bare minimum, and
  it's not clear it even worked correctly. (#398)

o Register missing S3 methods and update signatures. With R-devel (83995-ish),
  `R CMD check` notes these S3 methods are not registered. It also notes that
  the signatures for `as.POSIXct.tis()` and `str.replot_xts()` do not match
  the respective generics.

  It also thinks `time.frequency()` is a S3 method because `time()` is a
  generic. The function isn't exported, so renaming won't break any external
  code. Thanks to Kurt Hornik for the report. (#398)

o Format each column individually before printing. The top/bottom rows could
  have a different number of decimal places and there are often multiple
  variying spaces between columns. For example:

                                close      volume          ma        bsi
      2022-01-03 09:31:00    476.470  803961.000          NA  54191.000
      2022-01-03 09:32:00    476.700  179476.000          NA  53444.791
      2022-01-03 09:33:00    476.540  197919.000          NA  -16334.994
                      ...
      2023-03-16 14:52:00    394.6000  46728.0000    392.8636  28319.4691
      2023-03-16 14:53:00    394.6500  64648.0000    392.8755  15137.6857
      2023-03-16 14:54:00    394.6500  69900.0000    392.8873  -1167.9368

  There are 4 spaces between the index and the 'close' column, 2 between
  'close' and 'volume', 4 between 'volume' and 'ma', and 2 between 'ma' and
  'bsi'. There should be a consistent number of spaces between the columns. Most
  other classes of objects print with 1 space between the columns.

  The top rows have 3 decimals and the bottom rows have 4. These should also be
  the same. (#321)

o Only convert printed index values to character. Converting the entire index
  to character is time-consuming for xts objects with many observations. It can
  take more than a second to print an xts object with 1mm observations.

o Make column names based on number of columns. The original code was a lot
  more complicated because it tried to account for truncating the number of
  printed columns. That functionality was removed because of how complicated
  it was. So now we can simply create printed column names from the number of
  columns. (#395)

o Fix `xts()` for zero-row data.frame. The `xts()` constructor would create an
  object with a list for coredata when 'x' is a data.frame with no rows. It
  needs to convert 'x' to a matrix and throw an error if 'x' is a list. (#394)

o Reduce instances when `dplyr::lag()` warning is shown. The warning was shown
  whenever it detected dplyr is installed, even if the user wasn't actively
  using dplyr. That caused an excessive amount of noise when other packages
  attached xts (e.g. quantmod). Thanks to Duncan Murdoch for the report and
  suggested fix! (#393)

o Keep colname when only one non-time-based column. The subset `x[, -which.col]`
  would return a vector when the data frame has a time-based column and only
  one additional column. Do not drop dimensions, so 'x' will still be a
  data.frame in this case. (#391)

o Treat NA the same as NULL for start or end values. NULL represents an
  undefined index value. NA represents an unknown or missing index value. xts
  does not allow NA as index values. Subsetting an xts or zoo object by NA
  returns a zero-length object. So a NA (unknown) index value is essentially
  the same as an undefined index value. (#383, #345)

o Warn and remove NA when `periodicity()` called on date-time with NA.
  Otherwise the uninformative error below will be thrown. (#289)

      Error in try.xts(x, error = "'x' needs to be timeBased or xtsible") :
        'x' needs to be timeBased or xtsible

o Account for TZ when making names for `split.xts()`. `as.yearmon.POSIXct()`
  always sets `tz = "GMT"` when calling `as.POSIXlt()`, regardless of the xts'
  index tzone.  That can cause the `as.yearmon()` results to be different days
  for GMT and the index's timezone.

  Use `format.POSIXct()` for "months" because it checks for a 'tzone' attribute
  before converting to POSIXlt and calling `format.POSIXlt()`.  The conversion
  to POSIXlt is important because it checks and uses the 'tzone' attribute
  before considering the 'tz' argument. So it effectively ignores the
  `tz = "GMT"` setting in `as.yearmon()`. This is also the reason for calling
  `as.POSIXlt()` before calling `as.yearqtr()`. (#392)

################################################################################
Changed in xts 0.13.0:

### New Features

o Added a xts method for `na.fill()` to significantly increase performance when
  'fill' is a scalar. (#259)

o `as.xts()` will look for a time-based column in a data.frame if it cannot
  create an index from the row names. (#381)

o Change `print()` xts method to only show the first and last 'show.rows' rows
  if number of rows is > 'max.rows'. (#321)

o Made `str()` output more descriptive for xts objects. It now differentiates
  between xts objects that are empty, zero-width, or zero-length, and defines
  each type of object. It also adds column names to the output. (#168, #378)

o Add startup warning that `dplyr::lag()` breaks method dispatch, which means
  calls to `lag(my_xts)` won't work any more.

o Added open-ended time of day subsetting ranges. This allows users to subset
  by time of day from the start/end of the day without providing the start/end
  times (00:00:00.000/23:59:59.999).

  For example:
      x["/T1800"]  # between the start of the day and 5pm
      x["T0500/"]  # between 5am and the end of the day

  Thanks to Chris Katsulis for the suggestion! (#243)

o Updated `to.period()` to accept custom 'endpoints' via the 'period' argument.
  Now you can aggregate on something other than the times that 'endpoints()'
  supports. Thanks to Ethan B. Smith for the suggestion! (#302)

### Fixes

o Fixed typo and expand `period.apply()` documentation. (#205)
    The original description has:
      * "the data from INDEX[k] to INDEX[k+1]"
    But that's not consistent with the code. It should be:
      * "the data from INDEX[k]+1 to INDEX[k+1]"

o Calls to `merge.xts()` on zero-width objects now match `merge.zoo()`.
  Previously, `merge.xts()` would return empty xts objects if called on two or
  more zero-width xts objects. `merge.zoo()` would return a zero-width object
  with the correct index. (#227, #379)

o Fixed `Ops.xts()` so it always returned an object with the same class as the
  first (left-hand side) argument. It previously returned an xts object even
  if the first argument was a subclass of xts. (#49)

### Other

o Migrated unit tests from RUnit to tinytest. Thanks Mark van der Loo!

o Updated the `endpoints()` documentation to make it clearer that the result
  is based on the UNIX epoch (midnight 1970, UTC). Thanks to GitHub user
  Eluvias for the suggestion! (#299)

o Fixed `reclass()` to ensure it always adds index attributes from the
  'match.to' argument. It was not copying `tclass`, `tzone`, or `tformat` from
  'match.to' to the result object. (#43)

o Removed an unnecessary check in `na.locf()` (which is not user-facing).
  Thanks to GitHub user @cgiachalis for the suggestion! (#307)

o Updated C entry points so they're not able to accidentally be found via
  dynamic lookup (i.e. `.Call("foo", ...)`). This makes each call to the C
  code a few microseconds faster, which is nice. (#260)

o Made `merge.xts()` results consistent with `merge.zoo()` for zero-length xts
  objects with columns. The result of `merge.xts()` did not include the
  columns of any objects that had one or more columns, but zero rows. A join
  should include all the columns of the joined objects, regardless of the
  number of rows in the object. This is consistent with `merge.zoo()`. Thanks
  to Ethan B. Smith for the report and testing! (#222)

(mef)

doc: Updated math/R-zoo to 1.8.12

(mef)

(math/R-zoo) Updated 1.8.11 to 1.8.12

Changes in Version 1.8-12

  o The autoplot() method for "zoo" objects now uses ggplot() directly rather
    than the qplot() function which has been deprecated in recent versions of
    ggplot2.

  o Support start = NA and end = NA in addition to start = NULL and end = NULL
    for unspecified start and end time of a window() of a zoo series.

  o Remove unnecessary S3 method declarations for axis.yearmon/yearqtr as
    axis() is no S3 generic, only Axis() is (reported by Kurt Hornik).

  o The helper function index2char() now calls format() instead of as.character()
    for objects inheriting from class POSIXt.

(mef)

doc: Updated misc/tui-journal to 0.1.3

(pin)

misc/tui-journal: update to 0.1.3

- No ChangeLog provided.

(pin)

doc: Updated audio/spotify-player to 0.14.1

(pin)

audio/spotify-player: update to 0.14.1

What's Changed
- Fixed application not starting issue with Kitty terminal (#204) when the
  image feature is enabled in bca3fa2
- Migrate to ratatui in #206

(pin)

doc: Updated shells/oh-my-posh to 16.9.1

(pin)

shells/oh-my-posh: update to 16.9.1

Bug Fixes
- doc: remove outdated content for Scoop (e7eb8bd)
- pwsh: use correct ESC char for FTCS mark (f8e72d0)

(pin)

doc: Updated print/cups-base to 2.4.2nb9

(wiz)

cups-base: fix security problem.

Bump PKGREVISION.

(wiz)

doc: Updated audio/gospt to 0.0.50

(pin)

audio/gospot: update to 0.0.50

- fix pagination

pkgsrc: fix broken tarball.

(pin)

doc: update Meslo name

(wiz)

nerd-fonts-Meslo: match PKGNAME to directory name

(wiz)

doc: nerd-fonts* updated to 3.0.1

(wiz)

fonts/Makefile: + nerd-fonts-MesloLG

(wiz)

fonts/nerd-fonts-MesloLG: import nerd-font-Meslo-3.0.1

Nerd Fonts patches developer targeted fonts with a high number of
glyphs (icons). Specifically to add a high number of extra glyphs
from popular 'iconic fonts' such as Font Awesome, Devicons,
Octicons, and others.

MesloLG is a font with slashed zeros, a customized version of
Apple's Menlo.

(wiz)

nerd-fonts*: update to 3.0.1

Fix LICENSE while here.

Release 3 was a major change:

Breaking 1: Naming

This release fixes some long standing issues that are due to the
naming of the fonts: There is a completely new naming scheme. This
might be inconvientient for existing setups, sorry.

    Some fonts will have Nerd Font in the name while other have it
    abbreviated as NF. This is needed because some names just were
    too long. (Same for Nerd Font Mono and NFM.)
    There are no Windows Compatible fonts anymore. All fonts work
    on all platforms.
    The Complete from the font names (and the repo directories)
    has been dropped (Complete is the new normal).
    The name parts will be ordered as expected with style and weight
    last (Somefont Bold Nerd Font -> Somefont Nerd Font Bold).
    The filename will have no blanks anymore.

Breaking 2: Material Design Icons Codepoints

The old Material Design Icon codepoints are finally dropped. Due
to an historic mistace we placed them in between some asiatic
glyphs, breaking that script.

Since v2.3.0 the (updated and expanded) Material Design Icons have
new codepoints in the 5 digit region.

    Dropped codepoints F500... and class names nf-mdi-*
    New codepoints F0001... and class names nf-md-* (already since v2.3.0)
    The whole discussions are here: #365
    A translation table is available here: #1059 (comment)
    There are tools out there that probably can update your configuration.
    Relevant thread: #1190

Of course, there are many other changes/updates/improvements.

(wiz)

xe-guest-utilities: fix build

Enable build on all versions of NetBSD

(sborrill)

Updated devel/cbindgen, www/py-django-tastypie

(adam)

py-django-tastypie: updated to 0.14.5

0.14.5

Bugfix for data loss prevention exception when same uri is used in multiple to-many resources in a payload.
Doc fix for delete_detail
More cleanup for python 2 EOL
Added support for Django 4.1.

(adam)

cbindgen: updated to 0.24.6

0.24.6
* Update MSRV to 1.57
* Support variadic arguments (`...`)
* Add --depfile option

0.24.5
* Don't enforce tempfile version.

0.24.4
* Move expand infinite recursion fix
* Add with_cpp_compat to the builder
* Handle never type in return position consistently
* Fix warnings
* Updated documentation

(adam)

doc: Updated misc/chatgpt-shell-cli to 0.0.20230516

(wiz)

chatgpt-shell-cli: update to 0.0.20230516.

two weeks of various minor changes

(wiz)

unit-php: simplify PKGNAME

(wiz)

Updated net/haproxy, archivers/unrar

(adam)

unrar: updated to 6.2.8

6.2.8
Unknown changes

(adam)

haproxy: updated to 2.8.0

2.8.0
- MINOR: compression: Improve the way Vary header is added
- BUILD: makefile: search for SSL_INC/wolfssl before SSL_INC
- MINOR: init: pre-allocate kernel data structures on init
- DOC: install: add details about WolfSSL
- BUG/MINOR: ssl_sock: add check for ha_meth
- BUG/MINOR: thread: add a check for pthread_create
- BUILD: init: print rlim_cur as regular integer
- DOC: install: specify the minimum openssl version recommended
- CLEANUP: mux-quic: remove unneeded fields in qcc
- MINOR: mux-quic: remove nb_streams from qcc
- MINOR: quic: fix stats naming for flow control BLOCKED frames
- BUG/MEDIUM: mux-quic: only set EOI on FIN
- BUG/MEDIUM: threads: fix a tiny race in thread_isolate()
- DOC: config: fix rfc7239 converter examples
- DOC: quic: remove experimental status for QUIC
- CLEANUP: mux-quic: rename functions for mux_ops
- CLEANUP: mux-quic: rename internal functions
- BUG/MINOR: mux-h2: refresh the idle_timer when the mux is empty
- DOC: config: Fix bind/server/peer documentation in the peers section
- BUILD: Makefile: use -pthread not -lpthread when threads are enabled
- CLEANUP: doc: remove 21 totally obsolete docs
- DOC: install: mention the common strict-aliasing warning on older compilers
- DOC: install: clarify a few points on the wolfSSL build method
- MINOR: quic: Add QUIC connection statistical counters values to "show quic"
- EXAMPLES: update the basic-config-edge file for 2.8
- MINOR: quic/cli: clarify the "show quic" help message
- MINOR: version: mention that it's LTS now.

(adam)

doc: Added devel/py-test-datafiles version 3.0.0

(wiz)

devel/Makefile: + py-test-datafiles

(wiz)

devel/py-test-datafiles: import py-test-datafiles-3.0.0

This plugin allows you to specify one or several files/directories
that are copied to a temporary directory (tmp_path) before the
execution of the test. This means the original files are not modified
and every test runs on its own version of the same files.

(wiz)

doc: Added devel/py-argparse-manpage version 4.3

(wiz)

devel/Makefile: + py-argparse-manpage

(wiz)

devel/py-argparse-manpage: import py-argparse-manpage-4.3

Avoid documenting your Python script arguments on two places! This
is typically done in an argparse.ArgumentParser help configuration
(help=, description=, etc.), and also in a manually crafted manual
page.

The good thing about an ArgumentParser objects is that it actually
provides a traversable "tree-like" structure, with all the necessary
info needed to automatically generate documentation, for example
in a groff typesetting system (manual pages). And this is where
this project can help.

(wiz)

doc: Updated x11/libX11 to 1.8.5

(wiz)

libX11: update to 1.8.5.

Users of the Amharic (am_ET.UTF-8) compose key sequences provided by libX11
will also want to upgrade to xkeyboard-config 2.39 (releasing soon), in order
to keep those sequeunces working with this release.

Alan Coopersmith (6):
      gitlab CI: Add libtool to required packages
      configure: raise minimum autoconf requirement to 2.70
      configure: replace deprecated AC_HELP_STRING with AS_HELP_STRING
      configure: Use LT_INIT from libtool 2 instead of deprecated AC_PROG_LIBTOOL
      gitlab CI: add workflow rules
      libX11 1.8.5

Benno Schulenberg (8):
      nls: delete compose sequences that pointlessly mix upper and lower case
      nls: remove four hundred and sixty untypable Greek compose sequences
      nls: remove twenty two untypable Greek compose sequences
      XSetScreenSaver.man: restore the part that was accidentally snipped
      nls: make the Amharic compose sequences use the dead-vowel symbols
      nls: sort three sequences alphabetically in their group, like all others
      nls: delete six compose sequences that cannot be typed
      nls: use a slash instead of a combining solidus in compose sequences

jmcwilliams403 (5):
      NLS: move long S compositions to respective blocks
      NLS: implement the expansion of the six Breton N-graph keysyms
      NLS: move dead-caron subscript compositions to the relevant Unicode block
      NLS: Remove strange dead_cedilla cedi sign sequences
      nls: add compose sequence for capital schwa, and delete a deviant one

(wiz)

canu: remove patches that are not in distinfo

(wiz)

canu: use github framework variables

(wiz)

Added sysutils/szyszka version 3.0.0

(packaged by pin@, just copied across by me :)

(abs)

Add szyszka - a simple but powerful and fast bulk file renamer

Features
- Great performance
- Gui created with GTK 4
- Multiple rules which can be freely combined:
  - Replace text
  - Trim text
  - Add text
  - Add numbers
  - Purge text
  - Change letters to upper/lowercase
  - Custom rules
- Save rules to be able to use them later
- Ability to edit, reorder rules and results
- Handle even hundreds thousands of records

(abs)