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.
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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
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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)
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)
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)
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.
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
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
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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)
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 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
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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.
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-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-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 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]
- 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 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 2.13.0
- 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-*)
- 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)
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>
