Commit graph

356767 commits

Author SHA1 Message Date
tnn
d419e1265f notmuch: honour PKGINFODIR 2022-04-25 15:37:28 +00:00
tnn
05e53bb403 tcpexec: fix build w/o SO_REUSEPORT 2022-04-25 15:33:58 +00:00
tnn
9cc0814615 stockfish: avoid ambiguous math functions 2022-04-25 15:24:31 +00:00
tnn
5e713d3ece strawberry: avoid ambiguous math functions 2022-04-25 15:19:48 +00:00
tnn
84bf1eea48 fox: SunOS build fix 2022-04-25 15:17:21 +00:00
schmonz
1520bae000 doc: Updated devel/mob to 3.1.0 2022-04-25 15:14:12 +00:00
schmonz
76c96fe072 Update to 3.1.0. From the changelog:
- Add `mob clean` command that removes orphan wip branches that might be
  a left over of someone else doing a `mob done`. This is especially
  helpful when using a lot of feature branches. If you call `mob clean`
  on an orphan wip branch, it will switch you to the base branch,
  falling back to main/master if the base branch does not exist.
- The values `squash`, `no-squash` and `squash-wip` for MOB_DONE_SQUASH
  can be set not only via env var, but now in the .mob configuration
  file as well.
2022-04-25 15:14:07 +00:00
schmonz
17ee548847 doc: Updated devel/py-approvaltests to 5.0.1 2022-04-25 15:11:58 +00:00
schmonz
bf478b6210 Update to 5.0.1. From the changelog:
- Fixed a few pylint complaints
2022-04-25 15:11:53 +00:00
schmonz
d23c9de89c doc: Updated net/djbdnscurve6 to 42a 2022-04-25 15:09:53 +00:00
schmonz
f8bb27c99e Update to 42a. From the changelog:
- Fixed TLSA RR generation in tinydns-data and changed default for
  selector to SPK hash (=1).
- Fixed typo in script add-tlsa.
2022-04-25 15:09:48 +00:00
tnn
e8953294ae steghide: avoid ambiguous math functions 2022-04-25 15:01:53 +00:00
tnn
3bb0a98208 starplot: avoid ambiguous math functions 2022-04-25 14:40:13 +00:00
tnn
527246905d stacks: needs -lsocket on SunOS 2022-04-25 14:36:19 +00:00
tnn
14a0c163cf stacks: avoid ambiguous math functions 2022-04-25 14:34:06 +00:00
tnn
58644490be olm: avoid ambiguous math functions 2022-04-25 13:58:46 +00:00
tnn
3b5866d717 exchess: avoid ambiguous math functions 2022-04-25 13:53:15 +00:00
tnn
a4287395bc libkeyfinder: avoid ambiguous pow(3) 2022-04-25 13:49:49 +00:00
tnn
7a45a63bf5 kirigami2: restore patch-src_imagecolors.cpp, it is needed on SunOS 2022-04-25 13:36:38 +00:00
mef
3645651366 doc: Updated misc/R-Hmisc to 4.7.0 2022-04-25 13:29:29 +00:00
mef
404b7d928e (misc/R-Hmisc) Updated 4.2.0 to 4.7.0, fix build against R-4.2.0
Changes in version 4.7-0 (2022-04-18)
   * html.contents.data.frame: properly closed html <a>
   * simPOcuts: new function to demonstrate variation in odds ratios
     due to random chance
   * R2Measures: new function to compute various pseudo R^2 measures
   * putHcap: added new capabilities around the subsub argument
   * print.summary.formula.response: added markdown argument
   * knitrSet: added rudimentary quarto support
   * knitrSet: sense figure labels of the form fig-... used by Quarto,
     and generate correct cross-reference


Changes in version 4.6-0 (2021-10-05)
   * package: improved author formatting in DESCRIPTION

   * html: markupSpecs$html$session: added citations for any Harrell
     packages that are loaded, respecting current output format in
     effect with knitr

   * soprobMarkovOrdm: new function to compute state occupancy
     probabilities from proportion odds model fits

   * plotCorrM: new function to graph correlation matrices and gap
     time relationships using ggplot2

   * ggplotlyr: new function to use plotly::ggplotly to render ggplot2
     graphs but intercepting hover text to remove extraneous labels

   * Fixed Heiberger email address
   * propTrans: removed zero frequency combinations
   * combplotp: fixed bug in case regarding recognition of positives
nnn   * propsPO: fixed making y factor
   * soprobMarkovOrdm: added as.data.frame(generated data)

   * estSeqMarkovOrd: extended timecriterion function to allow user to
     return the event/censoring time and indicator, and to allow
     groupContrast to compute using a variance formula

   * estSeqMarkovOrd: trapped errors better, returning attribute
     failures, and added maxest and maxvest argument to declare large
     parameter or variance estimates as failed iterations; changed
     from vgam to vglm and sped up computations by using previous
     coefficient estimates as starting values

   * session in markupSpecs: added citations for several other packages
   * soprobMarkovOrdm: extended to work with VGAM package

   * describe: fix error with . (thanks to Cole Beck;
     https://github.com/harrelfe/Hmisc/pull/144)

   * many: tests for presence of suggested packages using
     requireNamespace (thanks for major editing work by Duncan Murdoch
     at https://github.com/harrelfe/Hmisc/pull/143 motivated by
     https://stat.ethz.ch/pipermail/r-package-devel/2021q2/007101.html)

   * mdb.get: fix for Windows by changing from system to system2
     (thanks to Rainer Hurling at
     https://github.com/harrelfe/Hmisc/pull/135)

   * summaryM: fixed error with prN=TRUE with latex (thanks Matt
	 * Shotwell in https://github.com/harrelfe/Hmisc/pull/109)
	 * many: fix partial argument matching warnings length ->
	 * length.out in rep (thanks Bill Denney in
	 * https://github.com/harrelfe/Hmisc/pull/128)

   * rcspline.restate: was dropping + for exactly zero coefficients
     (thanks https://github.com/harrelfe/Hmisc/pull/118)

   * mdb.get: remove brackets from table names (thanks
     https://github.com/harrelfe/Hmisc/pull/123)

   * latex: added new argument comment so that the generated comment
     can be suppressed (thanks Giuseppe Ragusa
     https://github.com/harrelfe/Hmisc/pull/33)

   * sas.get: added new argument for variable case (thanks Tyler Hunt
     https://github.com/harrelfe/Hmisc/pull/8)

   * format.df: changed to use system option OutDec when cdot is not
     specified (thanks https://github.com/harrelfe/Hmisc/issues/142)

   * C code: changed calls to warning/error routines

   * formatdescribeSingle: changed for character value to make 'NA' work

Changes in version 4.5-0 (2021-02-27)
   * approxExtrap: changed x and y to as.numeric.  Thanks: juha.heikkinen@luke.fi
   * upData: fix column subsetting for data.tables
   * dotchartpl: intercepted missing Diff

   * simMarkovOrd, soprobMarkovOrd, intMarkovOrd, estSeqMarkovOrd: new
     functions for Markov proportional odds model simulation and
     calculation of state occupancy probabilities

   * ggfreqScatter: added by argument
   * VGAM package added to Suggests in DESCRIPTION
   * html markupSpecs mdchunk: added caption argument, allowed for vectors

   * propsTrans: added labels argument for plotly, added numerators
     and denominators in tooltips, fixed bug where factor levels were
     reversed if odds.ratio specified

Changes in version 4.4-2 (2020-11-25)

   * rcorr: captured loss of precision leading to square root of a
     negative number.  Thanks: Ann Voss <avoss@novanthealth.org>

   * summaryS: sapply was doubling names

   * pairUpDiff: created for dotchartpl - function to pair up grouped
     observations for sorting by descending differences and computing
     approximate confidence intervals for the difference given
     individual confidence limits

   * dotchartpl: added new arguments and functionality to handle
     quantities other than proportions (e.g., hazards) and streamlined
     code using pairUpDiff

   * propsPO: added tooltip text for gpplot that will be transmitted
     to ggplotly; reversed order of categories so lowest category put
     at bottom of bar

   * dotchartpl: suppressed confidence intervals when the number of
     groups is not 2; fixed bug where hover text confidence intervals
     were repeats of the last computed interval instead of properly
     using all the intervals; added dec argument

   * added estSeqSim and gbayesSeqSim functions

   * ggfreqScatter: stopped varying alpha and just varied color, as
     alpha collided with the color scheme

   * histSpike: added minimal=TRUE and bins arguments

Changes in version 4.4-1 (2020-08-07)
   * popower: added approximate S.E. of log(OR) in results
   * propsPO: new function for exploring proportional odds

   * propsTrans: new function for showing distributions of successive
     state transitions
   * changed acepack to suggests
   * multEventChart: new function for multi-state event charts based
     on code written by Lucy D'Agostino McGowan
   * getHdata: changed to use hbiostat.org/data/repo

   * markupSpecs$markdown$tof: new function to render a table of
     figures with short captions

   * knitrSet: added capfile argument to store figure tags and short captions
   * getLatestSource: changed to use GitHub and hbiostat.org/R/packagename/dir.txt
   * histboxpM: added width argument
   * upData: handled zero-length subsets (Thanks: Will Gray)
   * upData: made faster for large datasets
   * ffCompress: removed from package and put in Github Rscripts
   * Changed maintainer email

Changes in version 4.4-0 (2020-03-22)
   * combplotp: new function for attribute plots with plotly
   * summaryP: made to work with new default stringsAsFactors=FALSE
   * plotlyM: fixed bug where need to unlist if only one graph produced
   * plotlyM: added ECDF support through fitter='ecdf'

   * keepHattrib, restoreHattrib: new functions for saving Hmisc
     attributes that can be restored later, e.g., after data.table
     processes a data frame

Changes in version 4.3-1 (2020-02-07)
   * Depend on survival >= 3.1-6
   * pomodm: checked that x is sorted
   * markupSpecs: added ord function for ordinal representation of integers
   * mChoice: removed unused argument sort. from help file

Changes in version 4.3-0 (2019-11-07)
   * Corrected typos in aregImpute help file.  Thanks: Mark Seeto.

   * describe: changed to print 5 lowest and highest values even if
     frequency table printed, added a line of printed output
     specifying any rounding done for the frequency table

   * vcov.fit.mult.impute: use vcov.orm if object has orm class.
     intercepts=mid logic was not working for this

   * New service function convertPdate to do automatic date
     conversions and handle partial dates such as YYYY and mm/YYYY
     with imputation, for cleanup.import

   * cleanup.import: new arguments autodate, autonum, fracnn

   * describe: formatted dates if there is only one distinct value;
     changed to sense date or date-times, for Gmd not format as
     date-time

   * plot.describe: treated date/time variables as numeric
   * cleanup.import: refined autonum considerNA
   * ggfreqScatter: added stick=TRUE argument

   * markupSpecs: changed math and similar functions to use
     ... argument instead of x

   * summaryDp: new function for plotly dotcharts stratifying
     separately on a series of variables

   * dotchartpl: added height argument

   * html.describe: fixed but where markupSpecs$html utility function
     last arguments were not named in calls
2022-04-25 13:29:17 +00:00
fcambus
967102964c doc: Updated devel/pax-utils to 1.3.4 2022-04-25 13:09:20 +00:00
fcambus
84c8658d3b pax-utils: update to 1.3.4.
ChangeLog:

- Assorted fixes
- LoongArch support
2022-04-25 13:09:08 +00:00
mef
7e291b38a6 doc: Updated geography/R-maps to 3.4.0 2022-04-25 12:54:15 +00:00
mef
12d68426c2 (geography/R-maps) Updated 3.3.0 to 3.4.0, fix build against R-4.2.0
explicit ChangeLog or NEWS.md not found
2022-04-25 12:53:58 +00:00
nikita
855c31a7b4 erlang: fix rebar3 modules with an option to include rebar3 only. 2022-04-25 12:51:11 +00:00
nikita
4e0bdd129c CHANGES: fix erlang-idna update 2022-04-25 12:37:25 +00:00
nikita
49164dc531 doc: Updated devel/rebar3 to 3.18.0 2022-04-25 12:36:03 +00:00
nikita
2122495c75 erlang-idna: revbump for rebar3 update. 2022-04-25 12:34:46 +00:00
nikita
25d6760065 doc: Updated devel/rebar3 to 3.18.0 2022-04-25 12:28:56 +00:00
mef
2790a4ee9a doc: Updated math/R-RPostgreSQL to 0.7.3 2022-04-25 12:26:57 +00:00
mef
25451caa77 math/R-RPostgreSQL
(math/R-RPostgreSQL) Upated 0.7.0 to 0.7.3, explicit ChangeLog/NEWS not updated

but compliant to R-4.2.0, (fix build)
2022-04-25 12:26:46 +00:00
nikita
5288a254e1 rebar3: Update to 3.18.0
Changelog taken from https://github.com/erlang/rebar3/releases


3.18.0 Latest

    add support for otp24 optional applications
    use git command in non interactive mode
    git_resource: ignore stderr in get_patch_count when calling git rev-list
    fix NIF compilation on Apple M1.
    fix issue for duplicates options of 'parserfile' in 'yrl_opts'
    support for --all argument in unlock
    support for --all argument in upgrade
    support for --all argument in upgrade plugin
    add --relnames option to allow selectively building of multiple releases
    bump bbmustache to support unicode attributes
    proper respect of GLOBAL_CACHE_DIR
    bump certifi to 2.8.0
    don't crash on printing non-ASCII characters
    upgrade providers to 1.9.0


3.17.0

This release is mostly bug fixes, and repairs prior broken builds of
elixir dependencies, but also includes a couple of useful features.

New Features:
    Add escript_incl_priv so escriptize priv dir inclusion works with
    _checkouts and profiles
    Added SSL cacert patch to support Corporate MITM Proxies

Bug fixes:
    rebar3 release to honour the ignore-xref attribute
    Bump relx to 4.5.0
        use copied erts dir when tar'ing even when the user sets the erts
        improve error message when a symlink creation fails
        State extended with a filter method to filter xref_warnings
        Do not require logger
        Add default time warp mode of multi
        optionally allow static node name prefixes
        use random:uniform instead of os:pid when constructing node name in nodetool
        Fix eval command to use ERL_DIST_PORT, consistency with rpc command
        Fix bin script arguments to erlexec
    Give compiler hints when handling run-time deps in parse_transforms
    Make rebar_file_utils:system_tmpdir/1 take TMPDIR env var into account on *nix
    Handle abstract code starting with a non-file attribute
    Prefer erlang app to mix project
    Drop bootstrap URI handling functions warnings
    Prevent crashes on recursive src_dir definitions in deps
    Fix ssl check hostname options for wildcard certificate
    {xref_ignores} now properly works on module,
    Normalize Dialyzer PLT paths
    Fix optimistic registry update of plugins being upgraded

3.13.3

Security release. See
https://ferd.ca/you-ve-got-to-upgrade-rebar3.html

3.16.1

Major security fix around TLS validation. See
https://ferd.ca/you-ve-got-to-upgrade-rebar3.html

Also:
    local upgrade: extract vsn of rebar3 from downloaded escript

3.15.2

Major security fix around TLS validation. See
https://ferd.ca/you-ve-got-to-upgrade-rebar3.html

3.16.0

This release drops multiple OTP versions as officially
supported. We're aligning rebar3 development with the OTP team's
compatibility guarantees, as some deprecations from OTP-21 were
removed in OTP-24 and we just could not maintain compatible code
bases. We're using the breakage opportunity to change just how much we
support to something more sustainable.

The release also contains extra fixes that should prove useful.

    Only support 3 newest OTP versions
    add support to configure application resource naming
    Support ERL_LIBS libraries in escript building
    Fix CLI arg order in makefile template
    Increase OTP 24 readiness + move to OTP 20 min.
    Bump erlware_commons and certifi
    Treat applications and included_applications the same way when builing Dialyzer PLTs
    Strip CLI args from provider hooks
    Fix plugins upgrade for non-tuple specification

3.15.1

    Fix bad compiler path nesting

3.15.0

    Make dialyzer output file format configurable
    Fix DAG resolving for recursive directories
    Add EUnit support for sys_config options
    Catch and report missing escript dependency
    Relay unexpected relx return values
    Bump Relx and cth_readable
        relx_resolve:to_app raise error with .app file pathname
        Concurrent Builds - xref interactions refinement
        Add richer return values for nodetool rpc
        add exports of RELEASE_NAME, RELEASE_VERSION and RELEASE_PROG to script
    add an option to select the application to build an escript for
    Do not discard parameters --system_libs and --include-erts
    Have "rebar3 plugins upgrade" work without specifying plugin name
    rebar3 shell: implement various modes to print "booted" message
    More path juggling fixes in the compiler
    Fix OTP24 complaining about underscored variables
    Handle OTP-24 function location in xref
    pass no_spawn_compiler_process to compile:file/2
2022-04-25 12:25:58 +00:00
adam
3f28d03110 Updated www/py-mechanize, net/py-prometheus_client, sysutils/py-appnope 2022-04-25 11:40:10 +00:00
adam
da145d5f97 py-appnope: updated to 0.1.3
0.1.3:
Unknown changes
2022-04-25 11:33:05 +00:00
adam
5825806c7a py-prometheus_client: updated to 0.14.1
0.14.1
[BUGFIX] Revert choose_encoder being renamed to choose_formatter to fix a breaking change. For the 0.14.x release cycle choose_formatter will still exist, but will be removed in 0.15.0.
2022-04-25 11:30:43 +00:00
adam
bab12de45e py-mechanize: updated to 0.4.8
0.4.8 release
* Handle mal-encoded robots.txt files more gracefully
* Support HTTP 308 redirects
2022-04-25 11:28:24 +00:00
tnn
07ca12bf4f sauerbraten: needs -lsocket -lnsl on SunOS 2022-04-25 11:04:43 +00:00
tnn
c0eab4eba8 sc-im: needs bison 2022-04-25 11:03:45 +00:00
jperkin
a6720cc2d9 mk/pbulk: Support SCAN_DEPENDS_SKIP.
This is a list of paths that will be excluded from SCAN_DEPENDS.  Most users
will not need this, it's only really useful if you happen to use shared files
included by your mk.conf that may be touched even though there was no change
made to affect dependencies.
2022-04-25 10:59:23 +00:00
tnn
1855c45abd menhir: honour PKGMANDIR 2022-04-25 10:51:50 +00:00
markd
53c60c97ca texlive-collection-luatex: update to revision 63081 2022-04-25 10:43:14 +00:00
markd
980cf6af8b texlive-collection-latexextra: update to revision 63101 2022-04-25 10:41:59 +00:00
tnn
86abe6d564 sys161: honour PKGMANDIR 2022-04-25 10:41:08 +00:00
markd
2cc6fb2313 tex package updates 2022-04-25 10:39:43 +00:00
markd
502bb7787c tex-circuitikz{,-doc}: update to 1.5.0
In this version, several internal changes have been included in order to
streamline and organize better the components and to change the
management of color. The changes are pretty deep and subtle, so a bug or
unexpected behaviour is always possible. You can use the 1.4.6 rollback
point in case of trouble, but be sure to report any bug.

- Added connectors shapes, and included the BNC into that class
- Added nullator and norator shapes
- Added buzzer and reversed buzzer bipoles
- Added "dot" anchors to inductances
- Added "boxed only" option for some circular blocks
- Added DIN antenna shape
- Fixed block/input arrow connection
- Fixed a problem with generic tunable arrows

Internal changes:

- Added a generic drawing function for shapes, which are now drawn
  always in background
- Added a hook system to be able to change component drawing settings
  per-shape, per-class or globally
- All the 250+ shapes are now "protected" by possible external arrow and
  arced corners parameters
- Completely changed the management of the shapes' color
2022-04-25 10:38:11 +00:00
tnn
e33cb81f5a robodoc: manh is not a valid man section. HTML manual goes in share/doc/robodoc. 2022-04-25 10:35:06 +00:00
markd
33553a7e19 tex-polyglossia{,-doc}: update to 1.56
This is another maintenance release that fixes a regression introduced in v.
1.54 (fix English setup via aliases, #539).
2022-04-25 10:31:24 +00:00
markd
b46d202a4a tex-babel-french: update to 3.5n
Code fixes regarding lists' management.
New command \bname.
Documentation updated.
2022-04-25 10:24:04 +00:00
tnn
68ec54ce11 rocksndiamonds-levels: cpio -p needs -d 2022-04-25 10:21:12 +00:00