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* Remove # $FreeBSD$ from Makefiles.Mathieu Arnold2021-04-061-1/+0
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* - Update to 3.0.10Wen Heping2020-10-072-4/+4
| | | | Notes: svn path=/head/; revision=551626
* - Update to 3.0.9Wen Heping2020-09-262-4/+4
| | | | Notes: svn path=/head/; revision=550143
* - Update to 3.0.8Wen Heping2020-06-092-5/+4
| | | | Notes: svn path=/head/; revision=538287
* math/R: Update to version 4.0.0Joseph Mingrone2020-05-051-0/+1
| | | | | | | | | | | | | | 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 Notes: svn path=/head/; revision=534095
* - Update to 3.0.7Wen Heping2020-03-202-4/+4
| | | | Notes: svn path=/head/; revision=528766
* - Update to 3.0.6Wen Heping2020-02-222-7/+7
| | | | | | | - Take maintainership Notes: svn path=/head/; revision=526753
* Return dbn's ports to the pool after safekeeping his commit bit.Rene Ladan2020-02-031-1/+1
| | | | Notes: svn path=/head/; revision=525092
* Bump PORTREVISION for ports depending on the canonical version of GCCGerald Pfeifer2019-07-261-1/+1
| | | | | | | | | | | | | | | | | | 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 Notes: svn path=/head/; revision=507372
* Bump PORTREVISION for ports depending on the canonical version of GCCGerald Pfeifer2018-12-121-0/+1
| | | | | | | | | | | | | | | | | | 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 Notes: svn path=/head/; revision=487272
* math/R-cran-car: updated to version 3.0-2David Naylor2018-10-243-17/+14
| | | | | | | | | | | | | | | | | | | | | | | | | - 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) Notes: svn path=/head/; revision=482910
* Bump PORTREVISIONs of all users of math/mpc that we just updated toGerald Pfeifer2018-03-101-0/+1
| | | | | | | version 1.1.0 (via revision 464079). Notes: svn path=/head/; revision=464084
* math/R-cran-car: updated to version 2.1-6David Naylor2017-12-182-5/+4
| | | | | | | | | | | | - 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) Notes: svn path=/head/; revision=456600
* math/R-cran-car: updated to version 2.1-5David Naylor2017-07-092-4/+4
| | | | | | | | | - no changelog provided Generated by: portcran (0.1.5) Notes: svn path=/head/; revision=445398
* qa: add check for NO_ARCHDavid Naylor2017-06-181-2/+0
| | | | | | | | | | | | | | | | | | | | | 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 Notes: svn path=/head/; revision=443845
* math/R-cran-car: updated to version 2.1-4David Naylor2016-12-202-10/+16
| | | | | | | | | | | | | | | | | - 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) Notes: svn path=/head/; revision=428984
* Convert R-cran ports to auto-plist.David Naylor2016-11-192-30/+1
| | | | | | | These ports did not properly handle the DOCS options (in math/R). Notes: svn path=/head/; revision=426364
* math/R-cran-car: update to 2.1-3.David Naylor2016-08-152-4/+5
| | | | | | | | | | | | | | | | | | | | - 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. Notes: svn path=/head/; revision=420249
* Remove ${PORTSDIR}/ from dependencies, categories m, n, o, and p.Mathieu Arnold2016-04-011-4/+4
| | | | | | | | With hat: portmgr Sponsored by: Absolight Notes: svn path=/head/; revision=412348
* math:R-cran-car: update to 2.1-2.David Naylor2016-03-282-3/+5
| | | | | | | | | | | Changes: - Add lmtest and sandwich as test dependencies. ChangeLog: - Modified scatter3d() so that plots can be embedded in HTML. Notes: svn path=/head/; revision=412034
* math/R-cran-car: update to 2.1-1.David Naylor2016-02-133-4/+33
| | | | | | | | | | | | | | | | | | | | | | | | | | | | 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). Notes: svn path=/head/; revision=408798
* math/R-cran-car: update to 2.1-0David Naylor2015-11-283-8/+8
| | | | | | | | | | | | | | | | | | | | | | | | | | | | 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 Notes: svn path=/head/; revision=402534
* - Postpone EXPIRATION_DATE to fix math/R-cran-car andTAKATSU Tomonari2015-10-291-1/+1
| | | | | | | devel/R-cran-caret Notes: svn path=/head/; revision=400474
* Deprecate ports broken for more than 6 monthsAntoine Brodin2015-09-261-0/+2
| | | | Notes: svn path=/head/; revision=398018
* Mark BROKEN: missing dependencyAntoine Brodin2015-03-281-0/+2
| | | | | | | | | | | ===> 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 Notes: svn path=/head/; revision=382529
* math/R-cran-car: update to 2.0-25.David Naylor2015-03-222-3/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | 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. Notes: svn path=/head/; revision=381937
* Update math/R-cran-car to 2.0-22.David Naylor2014-12-052-4/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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. Notes: svn path=/head/; revision=374009
* Update the default version of GCC in the Ports Collection from GCC 4.7.4Gerald Pfeifer2014-09-101-0/+1
| | | | | | | | | | | | | to GCC 4.8.3. Part II, Bump PORTREVISIONs. PR: 192025 Tested by: antoine (-exp runs) Approved by: portmgr (implicit) Notes: svn path=/head/; revision=367888
* Update math/R-cran-car to 2.0-21.David Naylor2014-08-232-3/+3
| | | | | | | | | | | | | | | | | | 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(). Notes: svn path=/head/; revision=365761
* Update math/R-cran-car to 2.0-20.David Naylor2014-05-032-4/+3
| | | | | | | | | | | | | | | | | | | 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. Notes: svn path=/head/; revision=352896
* Update the default version of GCC used in the Ports Collection fromGerald Pfeifer2014-03-101-1/+1
| | | | | | | | | | | | | | 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) Notes: svn path=/head/; revision=347809
* Convert Mk/bsd.cran.mk to the Uses framework.David Naylor2013-12-281-2/+1
| | | | | | | | | PR: ports/184699 Reviewed by: bapt Approved by: portmgr (bdrewery), wen (maintainer, timeout > 2 weeks) Notes: svn path=/head/; revision=337846
* Add stage support to Mk/bsd.cran.mk and all USE_R_MOD ports (aka R-cran-*).David Naylor2013-11-271-1/+0
| | | | | | | | | | | | 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 Notes: svn path=/head/; revision=335044
* Update math/R to 3.0.2 patched r64207 and math/R-cran-SuppDists to 1.1-9.1;Brendan Fabeny2013-11-131-1/+1
| | | | | | | | | adjust dependent ports Reviewed by: pfg, thierry, tota Notes: svn path=/head/; revision=333659
* Update to libmpc version 1.0.1 which brings the following fixes:Gerald Pfeifer2013-10-261-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - 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) Notes: svn path=/head/; revision=331644
* Update math/R-cran-car to 2.0.19.David Naylor2013-10-062-3/+3
| | | | | | | | | | | | | | | 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. Notes: svn path=/head/; revision=329606
* Add NO_STAGE all over the place in preparation for the staging support (cat: ↵Baptiste Daroussin2013-09-201-0/+1
| | | | | | | math) Notes: svn path=/head/; revision=327746
* Update math/R-cran-car to 2.0-18.David Naylor2013-06-172-4/+3
| | | | | | | | | | | ChangeLog: o Bug fix to boot with type="residual" o Added densityPlot() function. Approved by: eadler,bdrewery (mentors, implicit) Notes: svn path=/head/; revision=321100
* Update math/R to 3.0.1-patched, and adjust dependent ports;Brendan Fabeny2013-05-281-0/+1
| | | | | | | | | | synchronize math/rpy with upstream repository Reviewed by: wen Approved by: wen, tota Notes: svn path=/head/; revision=319316
* Update math/R-cran-car to 2.0-17.David Naylor2013-05-062-4/+3
| | | | | | | | | | | | | | | | | | 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) Notes: svn path=/head/; revision=317535
* update math/R to 2.15.3, and adjust dependent portsBrendan Fabeny2013-03-071-1/+1
| | | | Notes: svn path=/head/; revision=313562
* Update math/R-cran-car to 2.0-16.David Naylor2013-02-202-3/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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) Notes: svn path=/head/; revision=312635
* - Update to my new FreeBSD addressDavid Naylor2013-01-161-1/+1
| | | | | | | | | | - Trim header - Add myself as creator of devel/svn2git (see r272261) Approved by: eadler|bdrewery (mentor) Notes: svn path=/head/; revision=310522
* update the R base ports to 2.15.2 and adjust dependent portsBrendan Fabeny2013-01-041-0/+1
| | | | | | | Reviewed by: thierry, tota, wen Notes: svn path=/head/; revision=309935
* Update to 2.0-15.Raphael Kubo da Costa2012-10-202-3/+3
| | | | | | | | | PR: ports/172776 Submitted by: David Naylor <naylor.b.david@gmail.com> (maintainer) Feature safe: yes Notes: svn path=/head/; revision=306202
* - Update to 2.0-14 [1]Wen Heping2012-10-012-10/+5
| | | | | | | | | | - Convert to new Makefile format PR: 172136 [1] Submitted by: David Naylor <naylor.b.david@gmail.com> (maintainer) [1] Notes: svn path=/head/; revision=305102
* update math/R to 2.15.1, switch to the new options format, andBrendan Fabeny2012-06-261-1/+1
| | | | | | | adjust dependent ports Notes: svn path=/head/; revision=300051
* - update math/R-cran-psych to 1.2.1 [1]Brendan Fabeny2012-05-041-0/+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] Notes: svn path=/head/; revision=296023
* - update to 2.0-12Ruslan Makhmatkhanov2012-03-272-4/+3
| | | | | | | | | PR: 166437 Submitted by: David Naylor <naylor.b.david at gmail dot com> (maintainer) Feature safe: yes Notes: svn path=/head/; revision=293894
* update math/R to 2.14.2, and adjust dependent portsBrendan Fabeny2012-03-031-1/+1
| | | | Notes: svn path=/head/; revision=292607
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