math/R-cran-car: Update to 3.1.3

math/R-cran-car: Fix build

Approved by:	portmgr (just-fix-it)

math/R-cran-car: Update to 3.1.2

*: Bump PORTREVISIONs for math/mpc update to 1.3.1

math/R-cran-car: Update to 3.1.1

Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)

Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.

math: remove 'Created by' lines

A big Thank You to the original contributors of these ports:

  *  Aaron Dalton <aaron@FreeBSD.org>
  *  Aaron Dalton <aaron@daltons.ca>
  *  Alessando Sagratini <ale_sagra@hotmail.com>
  *  Alex Dupre <ale@FreeBSD.org>
  *  Alexey Dokuchaev <danfe@FreeBSD.org>
  *  Amarendra Godbole <amarendra.godbole@gmail.com>
  *  Anders Nordby <anders@FreeBSD.org>
  *  Andreas Fehlner (fehlner@gmx.de)
  *  Andrew L. Neporada <andrew@chg.ru>
  *  Andrey <gugu@zoo.rambler.ru>
  *  Andrey Zakhvatov

math/R-cran-car: Update to 3.1.0

math/R-cran-car: Update to 3.0.13

math/R-cran-car: Update to 3.0.12

math/R-cran-car: Update to 3.0.11

Remove # $FreeBSD$ from Makefiles.

- Update to 3.0.10

- Update to 3.0.9

- Update to 3.0.8

math/R: Update to version 4.0.0

Upstream changes:
https://stat.ethz.ch/pipermail/r-announce/2020/000653.html

Also bump PORTREVISION of ports that depend on math/R.

Submitted by:	wen (in part)
Reviewed by:	jwb, Rainer Hurling <rhurlin@gwdg.de>, thierry
Differential Revision:	https://reviews.freebsd.org/D24572

- Update to 3.0.7

- Update to 3.0.6
- Take maintainership

Return dbn's ports to the pool after safekeeping his commit bit.

Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330

Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.

PR:		231590

math/R-cran-car: updated to version 3.0-2

 - removed PORTREVISION due to version bump
 - add new run dependencies:
   - astro/R-cran-maptools
   - devel/R-cran-abind
   - math/R-cran-carData
   - math/R-cran-lme4
   - textproc/R-cran-rio
 - remove unused test dependency:
   - math/R-cran-lme4
 - update description to align with CRAN package
 - update website URL to align with CRAN package
 - changelog:
   - This version deals with a technical problem (reported by Don van den
     Bergh), implementing a solution suggested by Brian Ripley: Rather than
     importing utils::askYesNo(), which is unavailable before R 3.5.0, a
     local unexported copy is supplied in the car package, to be removed
     after version 3.0-2.

Generated by:	portcran (0.1.9)

Bump PORTREVISIONs of all users of math/mpc that we just updated to
version 1.1.0 (via revision 464079).

math/R-cran-car: updated to version 2.1-6

 - remove unused test dependencies:
   - math/R-cran-nloptr
 - changelog:
   - Made several functions compatible with vcov() in R-devel (3.5.0).

Generated by:	portcran (0.1.6)

math/R-cran-car: updated to version 2.1-5

 - no changelog provided

Generated by:	portcran (0.1.5)

qa: add check for NO_ARCH

If NO_ARCH is set then check that no FreeBSD elf(5) files are in $STAGEDIR.
If an elf(5) file is bundles as part of the package, but is not meant to be
run directly (i.e. the elf(5) file is a payload, and not compiled) then
those files can be added to NO_ARCH_IGNORE to avoid the check from failing,

Changes to ports:
 - Ports that have NO_ARCH set, but actually compile files have had NO_ARCH
   removed.
 - Ports that have elf(5) payloads have had those files added to
   NO_ARCH_IGNORE.
 - R-cran ports that do not set USES=cran:compiles have NO_ARCH set,

PR:		218976
Reviewed by:	antoine, mat
Approved by:	portmgr

math/R-cran-car: updated to version 2.1-4

 - updated comment to align with CRAN package
 - updated license to align with CRAN package
 - add new test dependencies:
   - math/R-cran-MatrixModels
   - math/R-cran-SparseM
   - math/R-cran-lme4
   - math/R-cran-nloptr
   - math/R-cran-survey
 - set NO_ARCH as port does not compile

Generated by:	portcran (0.1.3)

Convert R-cran ports to auto-plist.

These ports did not properly handle the DOCS options (in math/R).

math/R-cran-car: update to 2.1-3.

 - Corrected documentation for mcPlots
 - added id.location argument to showLabels to vary location of labels
 - added fix for compatiblity with Rcmdr with missing data in several plotting
   functions.
 - deltaMethod() now reports confidence intervals.
 - print.summary.Anova.mlm() has new SSP and SSPE arguments to determine
   whether the corresponding matrices are printed (suggestion of Michael
   Friendly).
 - summary() and print() methods for Anova.mlm() can now report univariate
   ANOVAs (suggestion and some code by Michael Friendly).
 - added "value" and "vcov" attributes to objects returned by
   linearHypothesis() (after suggestions by Liviu Andronic and Steven Yen).
 - compareCoefs() now checks classes of models.
 - small fixes/changes.

Remove ${PORTSDIR}/ from dependencies, categories m, n, o, and p.

With hat:	portmgr
Sponsored by:	Absolight

math:R-cran-car: update to 2.1-2.

Changes:
 - Add lmtest and sandwich as test dependencies.

ChangeLog:
 - Modified scatter3d() so that plots can be embedded in HTML.

math/R-cran-car: update to 2.1-1.

Changes:
 * Use explicit pkg-plist instead of autoplist.  Using an explicit pkg-plist
   is more robust against "silent" errors or changes.

ChangeLog:
 - influencePlot now returns Cook's distance, not its square root.
 - Anova() now supports "coxme" objects (produced by coxme() in coxme package)
   (request of Philipp Sprenger).
 - 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).
 - Fixed Anova.coxph() so that it takes account of method (ties) argument (bug
   reported by Karl Ove Hufthammer).
 - Improvements to Anova.default() so that a wider variety of model classes are
   accommodated (following request of Liviu Andronic.)
 - dataEllipse() now throws an error if there are too few colors for the number
   of groups (fixing bug reported by Ottorino Pantani).
 - spreadLevelPlot.lm() now includes an optional smoother in addition to the
   fitted straight line (suggestion of Michael Friendly).
 - No longer import methods (as opposed to generics) directly from pbkrtest.
 - Added axis.ticks argument to scatter3d() (code contributed by
   David Winsemius).

math/R-cran-car: update to 2.1-0

Changes:
 - Remove port's broken and depreciated status
 - Add two dependencies
 - Add GPLv3 as dual license
 - Update website URL

Change Log:
 - 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.
 - Fixed bug in Anova() for coxph models with clusters (reported by Jesus
   Humberto Gomez ), due apparently to a change in coxph().
 - Anova() F-tests for binomial and Poisson GLMs now changes
   error.estimate="dispersion" to "pearson" as advertized (bug reported by
   Will Petry).
 - Improved behavior of above-plot legends in scatterplot().
 - Fixed sp() (bug reported by Cesar Rabak).
 - Conforms to new CRAN requirements for package imports.

Reported by:	tota@
PR:		203418
PR:		204587

- Postpone EXPIRATION_DATE to fix math/R-cran-car and
  devel/R-cran-caret

Deprecate ports broken for more than 6 months

Mark BROKEN: missing dependency

===>  Staging for R-cran-car-2.0.25
===>   Generating temporary packing list
ERROR: dependencies 'pbkrtest', 'quantreg' are not available for package 'car'

Reported by:	pkg-fallout

math/R-cran-car: update to 2.0-25.

Changes to Version 2.0-25
 * Fixed df check in linearHypothesis.default() (bug report by Pierre Chausse).
 * Fixed bug when vcov. argument to Anova() is a function (reported by Liviu
   Andronic).
 * Now export .carEnv to avoid problem with update() in Boot() (reported by
   Alan T. Arnholt).

Changes to Version 2.0-24
 * Fixed broken URLs.
 * Changed handling of .carEnv environment.
 * Moved pbkrtest, quantreg, and mgcv from Suggests: to Imports:.

Changes to Version 2.0-23
 * Modified ScatterplotSmoothers to add an 'offset' to the vertical axis of
   spread smooths.  This are required in the marginal model plot functions.
 * Fixed labels on mcPlot with overlay=FALSE
 * Check for 0 residual df and 0 residual deviance (within rounding) in Anova()
   and linearHypothesis() (problem reported by Jonathan Love).
 * 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).
 * Added Wong data set, used in mixed-models appendix.

Update math/R-cran-car to 2.0-22.

Changes to Version 2.0-22
 * corrected bug in 'terms' argument in residualPlots, and other graphic
   functions with a 'terms' argument
 * added residual curvature tests for glm.nb
 * mcPlot and mcPlot 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.
 * 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.
 * Fixed bugs in Anova.survreg() that could affect types II, II tests, both Wald

Update the default version of GCC in the Ports Collection from GCC 4.7.4
to GCC 4.8.3.

Part II, Bump PORTREVISIONs.

PR:		192025
Tested by:	antoine (-exp runs)
Approved by:	portmgr (implicit)

Update math/R-cran-car to 2.0-21.

ChangeLog:
 * residualPlot error when using 'type="rstudent" has been fixed.
 * Minor change to "recode" documentation; improved error checking in
    recode().
 * Fixed a bug in gamLine with non-canonical links. (Thanks to Hani Christoph)
 * Added has.intercept.multinom() to make Anova() work with multinom objects
    fit to a dichotomous response (after bug report by Kristian Hovde Liland).
 * Replaced vif.lm() with vif.default() to cover wider variety of models
    (after question by Laura Rigg about gls models).
 * Diagonal panels in scatterplotMatrix() (except for histograms) show
     groups separately when plotted by groups (suggestion by Erich Neuwirth).
 * Added vcov. argument to Anova.lm().

Update math/R-cran-car to 2.0-20.

ChangeLog:
 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.

Update the default version of GCC used in the Ports Collection from
GCC 4.6.4 to GCC 4.7.3.  This entails updating the lang/gcc port as
well as changing the default in Mk/bsd.default-versions.mk.

Part II, Bump PORTREVISIONs.

PR:		182136
Supported by:	Christoph Moench-Tegeder <cmt@burggraben.net> (fixing many ports)
Tested by:	bdrewery (two -exp runs)

Convert Mk/bsd.cran.mk to the Uses framework.

PR:		ports/184699
Reviewed by:	bapt
Approved by:	portmgr (bdrewery), wen (maintainer, timeout > 2 weeks)

Add stage support to Mk/bsd.cran.mk and all USE_R_MOD ports (aka R-cran-*).

Since this patch converts all affected ports, bsd.cran.mk no longer supports
NO_STAGE and errors out if NO_STAGE is set.

Exp-run:	ports/184216
Reviewed by:	bdrewery
Approved by:	portsmgr, wen

Update math/R to 3.0.2 patched r64207 and math/R-cran-SuppDists to 1.1-9.1;
adjust dependent ports

Reviewed by:	pfg, thierry, tota

Update to libmpc version 1.0.1 which brings the following fixes:

 - Switched to automake 1.11.6, see CVE-2012-3386.
 - #14669: Fixed extraction of CC from gmp.h.
 - Fixed case of intermediate zero real or imaginary part in mpc_fma,
   found by hydra with GMP_CHECK_RANDOMIZE=1346362345.

This is on top of the following changes from version 1.0

 - Licence change towards LGPLv3+ for the code and GFDLv1.3+ (with no
   invariant sections) for the documentation.
 - 100% of all lines are covered by tests
 - Renamed functions
   . mpc_mul_2exp to mpc_mul_2ui
   . mpc_div_2exp to mpc_div_2ui

Update math/R-cran-car to 2.0.19.

ChangeLog:
 * fixed scoping problems in Boot, bootCase, and ncvTest
 * added an argument to deltaMethod for passing arguments to get scoping right
when calling linearHypothesis in another function; other deltaMethod bugs fixed
 * slight modification to documentation of Boot
 * summary() method for "Anova.mlm" objects now returns an object, printed by a
corresponding print() method (adapting code contributed by Gabriel Baud-Bovy).
 * 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.
 * added use argument to scatterplotMatrix() (suggstion of Antoine Lizee).
 * export linearHypothesis.default() for use in other packages (suggestion of
Achim Zeileis).
 * small changes and fixes.

Add NO_STAGE all over the place in preparation for the staging support (cat:
math)

Update math/R-cran-car to 2.0-18.

ChangeLog:
 o Bug fix to boot with type="residual"
 o Added densityPlot() function.

Approved by:	eadler,bdrewery (mentors, implicit)

Update math/R to 3.0.1-patched, and adjust dependent ports;
synchronize math/rpy with upstream repository

Reviewed by:	wen
Approved by:	wen, tota

Update math/R-cran-car to 2.0-17.

ChangeLog:
    o Add a variable to AMSsurvey.
    o Fix to residualPlots to compute lack of fit tests with missing values and
      glms.
    o Fix to residualPlots with a 0/1 variable not declared a factor.
    o Boxplot() now works properly with at argument passed to boxplot() via ...
      (contribution of Steve Ellison).
    o qqPlot.lm() now works with "aov" objects (fixing problem reported by
      Thomas Burk).
    o Small fixes to code and docs.

Approved by:	eadler,bdrewery (mentors, implicit)

update math/R to 2.15.3, and adjust dependent ports

Update math/R-cran-car to 2.0-16.

Changes to Version 2.0-16

    o Fixed bug in printing of hypotheses by linearHypothesis(), where numeric
constants of the form 1.* or -1.* were printed incorrectly (reported by
Johannes Kutsam).

    o Fixed a bug in showLabels() with multiple groups in the scatterplot() and
scatterplotMatrix() function

    o linearHypothesisTest() now tolerates newlines and tabs in hypotheses
(suggestion of David Hugh-Jones).

    o two bugs fixed in Boot() (found by David Pain) changed argument f to f.
in bootCase().

    o summary.Boot(), confint.Boot() and hist.Boot() handle aliases correctly.

    o Boxplot.formula() now accepts more than one conditioning variable
(suggestion of Christina Yassouridis).

    o Small fixes.

Approved by:	bdrewery (mentor)

 - Update to my new FreeBSD address
 - Trim header
 - Add myself as creator of devel/svn2git (see r272261)

Approved by:	eadler|bdrewery (mentor)

update the R base ports to 2.15.2 and adjust dependent ports

Reviewed by:	thierry, tota, wen

Update to 2.0-15.

PR:		ports/172776
Submitted by:	David Naylor <naylor.b.david@gmail.com> (maintainer)
Feature safe:	yes

- Update to 2.0-14 [1]
- Convert to new Makefile format

PR:		172136 [1]
Submitted by:	David Naylor <naylor.b.david@gmail.com> (maintainer) [1]

update math/R to 2.15.1, switch to the new options format, and
adjust dependent ports

- update math/R-cran-psych to 1.2.1 [1]
- update math/R to 2.15.0, and adjust dependent ports
- minor changes to bsd.cran.mk [2]: rename MASTER_CRAN_SITES to
  MASTER_SITE_CRAN, as in bsd.sites.mk; make the install target more
  flexible and allow CRAN ports to override it; add a regression-test
  target; set USE_FORTRAN to match math/R; remove some of the
  redundant checks of USE_R_MOD; honor NOPORTDATA and NOPORTDOCS

Reviewed by:    thierry, tota, wen
Approved by:    D. Rue (maintainer) [1], wen [2]

- update to 2.0-12

PR:             166437
Submitted by:   David Naylor <naylor.b.david at gmail dot com> (maintainer)
Feature safe:   yes

update math/R to 2.14.2, and adjust dependent ports

update math/R to 2.14.1, and adjust dependent ports

update math/R to 2.14.0, math/R-cran-sp to 0.9-91, and adjust
dependent ports

Approved by:    linimon (portmgr), thierry, tota, wen
Feature safe:   yes

- Move PKGNAMEPREFIX defined in each R-cran- related ports Makefile
  to Mk/bsd.cran.mk

PR:             ports/162238
Submitted by:   tota (myself)
Approved by:    wen (maintainer of Mk/bsd.cran.mk and many related ports),
                David Naylor <naylor_DOT_b_DOT_david_AT_gmail_DOT_com>
                  (maintainer of math/R-cran-RSvgDevice and math/R-cran-car),
                Dan Rue <drue_AT_therub_DOT_org>
                  (maintainer of math/R-cran-psych, timeout > 2 weeks)
Feature safe:   yes

- Update to 2.0-11

PR:             ports/161918
Submitted by:   David Naylor (maintainer)

update math/R to 2.13.2, and adjust dependent ports

update R to 2.13.1 [1], and adjust dependent ports (this
includes workarounds intended to fix the broken sparc64
build, and fixes to the static libR, which is now in a
separate slave port, math/libR)

PR:             158947 [1]
Submitted by:   wen ([1], independently)

update to 2.0-10

PR:             156858
Submitted by:   David Naylor (maintainer)

- update to 2.13.0
- switch to the bundled Rblas and Rlapack by default (this
  can be changed by setting BLAS and LAPACK) which favors
  correctness in some corner cases over a slight performance
  penalty; this will be revisited after the blas and lapack
  updates
- replace the STATIC_LIBR option with a LIBR option (on
  by default): if on, libR.a and libR.so are installed,
  and R is linked to libR.so. Otherwise, R is static, and
  no libRs are installed.
- remove the superfluous copy of libR.so in ${LOCALBASE}/lib [1]
- enable the cairo and pango elements in the X11() graphics
  device by default, controlled by new PANGOCAIRO option
- add a few small patches to dependent ports, bumping
  PORTREVISION where necessary

PR:             153309 [1]
Approved by:    thierry (rkward*), wen (rpy*, R-cran-*)

Use DISTVERSION for CRAN ports with hyphenated versions

Approved by:    wen

- Get Rid MD5 support

- Update R to 2.12.2, a bugfix release
- Bump PORTREVISION of dependent ports,
  where necessary

Approved by:    makc, miwi (mentors, implicit)

- Update R to 2.12.1
- Bump PORTREVISION of
  dependent ports

Approved by:    makc, miwi (mentors, implicit)
                pav (portmgr)
Feature safe:   yes

- Add CRAN_Include_MAINTAINER tag to Mk/bsd.cran.mk
- Rename R_MOD to USE_R_MOD to be suitable for bsd.port.mk
- Remove math/R-cran-sm/files/bsd.cran.mk to complete the moving

Approved by:    wen (via e-mail)

- Use R_MOD_AUTOPLIST instead of pkg-plist

Approved by:    wen

- Update to 1.2.16

Approved by:    maintainer(implicit)

- update to 1.4.1
Reviewed by:    exp8 run on pointyhat
Supported by:   miwi

- update to jpeg-8

- Fix build after math/R update

Submitted by:   wen@, "b. f." <bf1783@googlemail.com>

- Change maintainer's email address

PR:             ports/139655
Submitted by:   David Naylor <naylor.b.david@gmail.com> (maintainer)
Approved by:    miwi(mentor)

- bump all port that indirectly depends on libjpeg and have not yet been bumped
or updated
Requested by:   edwin

This package accompanies J. Fox, An R and S-PLUS Companion to Applied
Regression, Sage, 2002. The package contains mostly functions for applied
regression, linear models, and generalized linear models, with an emphasis on
regression diagnostics, particularly graphical diagnostic methods. There are
also some utility functions. With some exceptions, I have tried not to duplicate
capabilities in the basic distribution of R, nor in widely used packages. Where
relevant, the functions in car are consistent with na.action = na.omit or
na.exclude.

WWW:    http://cran.r-project.org/web/packages/car/index.html

PR:             ports/133708
Submitted by:   David Naylor <naylor.b.david@gmail.com>