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
- 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)
- 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)
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
- 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)
- 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.
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).
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
===> 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
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.
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
and LR, and one similar bug in linearHypothesis.survreg().
* Replaced calls to require() with requireNamespace() where possible
(suggestion of Brian Ripley).
* The following functions now produce warnings rather than errors when there
are empty groups: scatterplot(), scatterplotMatrix(),scatter3d(),
densityPlot().
* Corrected name of "Blackmoor" dataset to "Blackmore".
* Added KosteckiDillon migraines dataset (contributed by Georges Monette).
* introduced linearHypothesis.rlm() for rlm models (suggestion of Matthieu
Stigler).
* Small bug fixes/improvements.
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().
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.
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)
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
- 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
- 0^0, which returned (NaN,NaN) previously, now returns (1,+0).
- Removed compatibility with K&R compilers, which was untestable due
to lack of such compilers.
- New functions
. mpc_log10
. mpc_mul_2si, mpc_div_2si
- Speed-ups
. mpc_fma
- Bug fixes
. mpc_div and mpc_norm now return a value indicating the effective
rounding direction, as the other functions.
. mpc_mul, mpc_sqr and mpc_norm now return correct results even if
there are over- or underflows during the computation.
. mpc_asin, mpc_proj, mpc_sqr: Wrong result when input variable has
infinite part and equals output variable is corrected.
. mpc_fr_sub: Wrong return value for imaginary part is corrected.
Convert to the new LIB_DEPENDS standard and remove hard-coded
.so versions from a couple of dependent ports.
Bump PORTREVISIONS of all dependent ports.
PR: 183141
Approved by: portmgr (bdrewery)
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.
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)
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 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]
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
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)
- 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-*)
