[pkgsrc/trunk]: pkgsrc/math/R Update to R 2.7.2

To: pkgsrc-changes-hg%NetBSD.org@localhost
Subject: [pkgsrc/trunk]: pkgsrc/math/R Update to R 2.7.2
From: markd <markd%pkgsrc.org@localhost>
Date: Thu, 14 Oct 2021 06:31:31 +0000
details:   https://anonhg.NetBSD.org/pkgsrc/rev/9edc7d94a830
branches:  trunk
changeset: 546415:9edc7d94a830
user:      markd <markd%pkgsrc.org@localhost>
date:      Sun Aug 31 12:37:27 2008 +0000

description:
Update to R 2.7.2

NEW FEATURES

    o   sprintf() returns elements of the result in UTF-8 when the
        format or any character input has a corresponding element
        declared as UTF-8.  Similarly for paste(), elements of the
        result are in UTF-8 when any input to that element is declared
        as UTF-8.

    o   axis() has new arguments 'col.ticks' and 'lwd.ticks' to allow
        the colour and line width of ticks to be set separately from
        that of the line (e.g. to set one or the other to transparent
        or zero width).

    o   legend() has a new argument 'box.col' to set the colour of the
        enclosing box.

    o   legend() gains a 'xpd' argument to make it easier to place a
        legend in the margins or outer margins.

    o   stripchart() now passes '...' to title() (as well as to
        plot.default() and axis()). (Wish of PR#12202)

    o   help.search() has new argument 'searchEngine' to go
        directly to the search form: this is needed by users of
        Firefox 3 to workaround a bug in interpreting the search
        results pages.

+ BUG FIXES

2.7.1 NEW FEATURES

    o   tools::texi2dvi() has a new argument 'texinputs' to allow the
        TeX and bibtex input paths to be specified (even on MiKTeX).

    o   dev.copy2pdf() gains an 'out.type' argument to allow it to be
        used with cairo_pdf() or quartz(type = "pdf").

    o   poly() has additional checks against user error (as in PR#11243).

    o   The Mac OS quartz() device draws contiguous lines much faster.

    o   A field containing just a sign is no longer regarded as numeric
        (it was on all platforms in 2.7.0, but not on most in earlier
        versions of R).  Similarly, '.' is now always non-numeric.

    o   CITATION files are now read in Latin-1: quite a few were
        failing if used in a multibyte locale such as UTF-8.

    o   The DESCRIPTION file of a package can specify an 'OS_type' field
        as either 'unix' or 'windows' to confine installation to that
        OS type.

    o   HoltWinters() now uses optimize() rather than optim for
        one-parameter problems which should be more reliable (PR#11469).

    o   axis() now respects the setting of par("xpd") when clipping.

    o   The 'factor' method of format() now preserves names, dims and
        dimnames in the same way as for character and numeric inputs.
        (PR#11512)

    o   read.DIF(*, transpose=TRUE) now allows to correctly read DIF files
        produced by some versions of Excel.

DEPRECATED & DEFUNCT

    o   The use of unserialize() on character strings is deprecated:
        that was a format used in R < 2.4.0.

    o   The use of embedded nuls in character strings is deprecated:
        They will no longer be allowed in R 2.8.0.


UTILITIES

    o   R CMD check checks for possible check directories in the
        sources -- in mid-2008 there were about 20 examples on CRAN.

    o   R CMD build tries harder to clean up the inst/doc directory
        from the remnants of earlier builds.

        It also removes any directories with extension .Rcheck, and
        files .DS_Store and ._* (created by tar on Mac OS X under some
        circumstances: it now sets environment variables to ask for
        such files not to be created by that tar.)


+ BUG FIXES

diffstat:

 math/R/Makefile |   7 +++--
 math/R/PLIST    |  60 ++++++++++++++++++++++++++++++++++++++++++++++++--------
 math/R/distinfo |   8 +++---
 3 files changed, 59 insertions(+), 16 deletions(-)

diffs (truncated from 345 to 300 lines):

diff -r e3b7e5e02820 -r 9edc7d94a830 math/R/Makefile
--- a/math/R/Makefile   Sun Aug 31 12:33:53 2008 +0000
+++ b/math/R/Makefile   Sun Aug 31 12:37:27 2008 +0000
@@ -1,7 +1,6 @@
-# $NetBSD: Makefile,v 1.99 2008/08/31 12:33:53 markd Exp $
+# $NetBSD: Makefile,v 1.100 2008/08/31 12:37:27 markd Exp $
 
-DISTNAME=              R-2.7.0
-PKGREVISION=           1
+DISTNAME=              R-2.7.2
 CATEGORIES=            math
 MASTER_SITES=          ${MASTER_SITE_R_CRAN:=base/R-2/}
 
@@ -49,8 +48,10 @@
 CONFIGURE_ARGS+=       --without-libmoto
 
 # Work around missing MAIN__() definition used in -lF77 by AC_CHECK_LIB.
+# and other failures due to not linking to support libs during testing
 CONFIGURE_ENV+=                ac_cv_lib_blas_dgemm=yes
 CONFIGURE_ENV+=                ac_cv_lib_blas_dgemm_=yes
+CONFIGURE_ENV+=                r_cv_complete_blas=yes
 
 # Broken test for bzlib >= 1.0.5 in R 2.7.0
 CONFIGURE_ENV+=                r_cv_have_bzlib=yes
diff -r e3b7e5e02820 -r 9edc7d94a830 math/R/PLIST
--- a/math/R/PLIST      Sun Aug 31 12:33:53 2008 +0000
+++ b/math/R/PLIST      Sun Aug 31 12:37:27 2008 +0000
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.7 2008/04/26 02:39:27 markd Exp $
+@comment $NetBSD: PLIST,v 1.8 2008/08/31 12:37:27 markd Exp $
 bin/R
 bin/Rscript
 lib/R/COPYING
@@ -235,11 +235,13 @@
 lib/R/library/MASS/R-ex/parcoord.R
 lib/R/library/MASS/R-ex/petrol.R
 lib/R/library/MASS/R-ex/plot.mca.R
+lib/R/library/MASS/R-ex/plot.profile.R
 lib/R/library/MASS/R-ex/polr.R
 lib/R/library/MASS/R-ex/predict.glmmPQL.R
 lib/R/library/MASS/R-ex/predict.lda.R
 lib/R/library/MASS/R-ex/predict.lqs.R
 lib/R/library/MASS/R-ex/predict.qda.R
+lib/R/library/MASS/R-ex/profile.glm.R
 lib/R/library/MASS/R-ex/qda.R
 lib/R/library/MASS/R-ex/rational.R
 lib/R/library/MASS/R-ex/renumerate.R
@@ -377,12 +379,14 @@
 lib/R/library/MASS/help/phones
 lib/R/library/MASS/help/plot.lda
 lib/R/library/MASS/help/plot.mca
+lib/R/library/MASS/help/plot.profile
 lib/R/library/MASS/help/polr
 lib/R/library/MASS/help/predict.glmmPQL
 lib/R/library/MASS/help/predict.lda
 lib/R/library/MASS/help/predict.lqs
 lib/R/library/MASS/help/predict.mca
 lib/R/library/MASS/help/predict.qda
+lib/R/library/MASS/help/profile.glm
 lib/R/library/MASS/help/qda
 lib/R/library/MASS/help/quine
 lib/R/library/MASS/help/rational
@@ -532,12 +536,14 @@
 lib/R/library/MASS/html/phones.html
 lib/R/library/MASS/html/plot.lda.html
 lib/R/library/MASS/html/plot.mca.html
+lib/R/library/MASS/html/plot.profile.html
 lib/R/library/MASS/html/polr.html
 lib/R/library/MASS/html/predict.glmmPQL.html
 lib/R/library/MASS/html/predict.lda.html
 lib/R/library/MASS/html/predict.lqs.html
 lib/R/library/MASS/html/predict.mca.html
 lib/R/library/MASS/html/predict.qda.html
+lib/R/library/MASS/html/profile.glm.html
 lib/R/library/MASS/html/qda.html
 lib/R/library/MASS/html/quine.html
 lib/R/library/MASS/html/rational.html
@@ -686,12 +692,14 @@
 lib/R/library/MASS/latex/phones.tex
 lib/R/library/MASS/latex/plot.lda.tex
 lib/R/library/MASS/latex/plot.mca.tex
+lib/R/library/MASS/latex/plot.profile.tex
 lib/R/library/MASS/latex/polr.tex
 lib/R/library/MASS/latex/predict.glmmPQL.tex
 lib/R/library/MASS/latex/predict.lda.tex
 lib/R/library/MASS/latex/predict.lqs.tex
 lib/R/library/MASS/latex/predict.mca.tex
 lib/R/library/MASS/latex/predict.qda.tex
+lib/R/library/MASS/latex/profile.glm.tex
 lib/R/library/MASS/latex/qda.tex
 lib/R/library/MASS/latex/quine.tex
 lib/R/library/MASS/latex/rational.tex
@@ -3376,11 +3384,13 @@
 lib/R/library/grDevices/R-ex/postscript.R
 lib/R/library/grDevices/R-ex/postscriptFonts.R
 lib/R/library/grDevices/R-ex/ps.options.R
+lib/R/library/grDevices/R-ex/quartz.R
 lib/R/library/grDevices/R-ex/quartzFonts.R
 lib/R/library/grDevices/R-ex/recordGraphics.R
 lib/R/library/grDevices/R-ex/rgb.R
 lib/R/library/grDevices/R-ex/rgb2hsv.R
 lib/R/library/grDevices/R-ex/trans3d.R
+lib/R/library/grDevices/R-ex/x11.R
 lib/R/library/grDevices/R-ex/x11Fonts.R
 lib/R/library/grDevices/R-ex/xy.coords.R
 lib/R/library/grDevices/R-ex/xyTable.R
@@ -4309,7 +4319,6 @@
 lib/R/library/grid/po/zh_CN/LC_MESSAGES/grid.mo
 lib/R/library/lattice/CONTENTS
 lib/R/library/lattice/COPYING
-lib/R/library/lattice/Changes
 lib/R/library/lattice/DESCRIPTION
 lib/R/library/lattice/INDEX
 lib/R/library/lattice/Meta/Rd.rds
@@ -4319,6 +4328,7 @@
 lib/R/library/lattice/Meta/nsInfo.rds
 lib/R/library/lattice/Meta/package.rds
 lib/R/library/lattice/NAMESPACE
+lib/R/library/lattice/NEWS
 lib/R/library/lattice/R-ex/Lattice.R
 lib/R/library/lattice/R-ex/axis.default.R
 lib/R/library/lattice/R-ex/banking.R
@@ -4803,6 +4813,7 @@
 lib/R/library/mgcv/NAMESPACE
 lib/R/library/mgcv/R-ex/Predict.matrix.R
 lib/R/library/mgcv/R-ex/anova.gam.R
+lib/R/library/mgcv/R-ex/cSplineDes.R
 lib/R/library/mgcv/R-ex/choose.k.R
 lib/R/library/mgcv/R-ex/exclude.too.far.R
 lib/R/library/mgcv/R-ex/extract.lme.cov.R
@@ -4810,17 +4821,19 @@
 lib/R/library/mgcv/R-ex/gam.R
 lib/R/library/mgcv/R-ex/gam.check.R
 lib/R/library/mgcv/R-ex/gam.models.R
-lib/R/library/mgcv/R-ex/gam.neg.bin.R
 lib/R/library/mgcv/R-ex/gam.selection.R
 lib/R/library/mgcv/R-ex/gam.side.R
+lib/R/library/mgcv/R-ex/gamSim.R
 lib/R/library/mgcv/R-ex/gamm.R
 lib/R/library/mgcv/R-ex/get.var.R
+lib/R/library/mgcv/R-ex/linear.functional.terms.R
 lib/R/library/mgcv/R-ex/magic.R
 lib/R/library/mgcv/R-ex/mgcv-package.R
 lib/R/library/mgcv/R-ex/mgcv.R
 lib/R/library/mgcv/R-ex/model.matrix.gam.R
 lib/R/library/mgcv/R-ex/mono.con.R
 lib/R/library/mgcv/R-ex/mroot.R
+lib/R/library/mgcv/R-ex/negbin.R
 lib/R/library/mgcv/R-ex/new.name.R
 lib/R/library/mgcv/R-ex/notExp.R
 lib/R/library/mgcv/R-ex/notExp2.R
@@ -4833,6 +4846,11 @@
 lib/R/library/mgcv/R-ex/predict.gam.R
 lib/R/library/mgcv/R-ex/s.R
 lib/R/library/mgcv/R-ex/smooth.construct.R
+lib/R/library/mgcv/R-ex/smooth.construct.ad.smooth.spec.R
+lib/R/library/mgcv/R-ex/smooth.construct.cr.smooth.spec.R
+lib/R/library/mgcv/R-ex/smooth.construct.ps.smooth.spec.R
+lib/R/library/mgcv/R-ex/smooth.construct.tp.smooth.spec.R
+lib/R/library/mgcv/R-ex/smooth.terms.R
 lib/R/library/mgcv/R-ex/step.gam.R
 lib/R/library/mgcv/R-ex/summary.gam.R
 lib/R/library/mgcv/R-ex/te.R
@@ -4846,6 +4864,7 @@
 lib/R/library/mgcv/help/AnIndex
 lib/R/library/mgcv/help/Predict.matrix
 lib/R/library/mgcv/help/anova.gam
+lib/R/library/mgcv/help/cSplineDes
 lib/R/library/mgcv/help/choose.k
 lib/R/library/mgcv/help/exclude.too.far
 lib/R/library/mgcv/help/extract.lme.cov
@@ -4859,22 +4878,23 @@
 lib/R/library/mgcv/help/gam.control
 lib/R/library/mgcv/help/gam.convergence
 lib/R/library/mgcv/help/gam.fit
-lib/R/library/mgcv/help/gam.fit2
+lib/R/library/mgcv/help/gam.fit3
 lib/R/library/mgcv/help/gam.method
 lib/R/library/mgcv/help/gam.models
-lib/R/library/mgcv/help/gam.neg.bin
 lib/R/library/mgcv/help/gam.outer
 lib/R/library/mgcv/help/gam.selection
 lib/R/library/mgcv/help/gam.setup
 lib/R/library/mgcv/help/gam.side
 lib/R/library/mgcv/help/gam2objective
 lib/R/library/mgcv/help/gamObject
+lib/R/library/mgcv/help/gamSim
 lib/R/library/mgcv/help/gamm
 lib/R/library/mgcv/help/gamm.setup
 lib/R/library/mgcv/help/get.var
 lib/R/library/mgcv/help/influence.gam
 lib/R/library/mgcv/help/initial.sp
 lib/R/library/mgcv/help/interpret.gam
+lib/R/library/mgcv/help/linear.functional.terms
 lib/R/library/mgcv/help/logLik.gam
 lib/R/library/mgcv/help/magic
 lib/R/library/mgcv/help/magic.post.proc
@@ -4884,6 +4904,7 @@
 lib/R/library/mgcv/help/model.matrix.gam
 lib/R/library/mgcv/help/mono.con
 lib/R/library/mgcv/help/mroot
+lib/R/library/mgcv/help/negbin
 lib/R/library/mgcv/help/new.name
 lib/R/library/mgcv/help/notExp
 lib/R/library/mgcv/help/notExp2
@@ -4898,6 +4919,11 @@
 lib/R/library/mgcv/help/residuals.gam
 lib/R/library/mgcv/help/s
 lib/R/library/mgcv/help/smooth.construct
+lib/R/library/mgcv/help/smooth.construct.ad.smooth.spec
+lib/R/library/mgcv/help/smooth.construct.cr.smooth.spec
+lib/R/library/mgcv/help/smooth.construct.ps.smooth.spec
+lib/R/library/mgcv/help/smooth.construct.tp.smooth.spec
+lib/R/library/mgcv/help/smooth.terms
 lib/R/library/mgcv/help/smoothCon
 lib/R/library/mgcv/help/step.gam
 lib/R/library/mgcv/help/summary.gam
@@ -4909,6 +4935,7 @@
 lib/R/library/mgcv/html/00Index.html
 lib/R/library/mgcv/html/Predict.matrix.html
 lib/R/library/mgcv/html/anova.gam.html
+lib/R/library/mgcv/html/cSplineDes.html
 lib/R/library/mgcv/html/choose.k.html
 lib/R/library/mgcv/html/exclude.too.far.html
 lib/R/library/mgcv/html/extract.lme.cov.html
@@ -4921,23 +4948,24 @@
 lib/R/library/mgcv/html/gam.control.html
 lib/R/library/mgcv/html/gam.convergence.html
 lib/R/library/mgcv/html/gam.fit.html
-lib/R/library/mgcv/html/gam.fit2.html
+lib/R/library/mgcv/html/gam.fit3.html
 lib/R/library/mgcv/html/gam.html
 lib/R/library/mgcv/html/gam.method.html
 lib/R/library/mgcv/html/gam.models.html
-lib/R/library/mgcv/html/gam.neg.bin.html
 lib/R/library/mgcv/html/gam.outer.html
 lib/R/library/mgcv/html/gam.selection.html
 lib/R/library/mgcv/html/gam.setup.html
 lib/R/library/mgcv/html/gam.side.html
 lib/R/library/mgcv/html/gam2objective.html
 lib/R/library/mgcv/html/gamObject.html
+lib/R/library/mgcv/html/gamSim.html
 lib/R/library/mgcv/html/gamm.html
 lib/R/library/mgcv/html/gamm.setup.html
 lib/R/library/mgcv/html/get.var.html
 lib/R/library/mgcv/html/influence.gam.html
 lib/R/library/mgcv/html/initial.sp.html
 lib/R/library/mgcv/html/interpret.gam.html
+lib/R/library/mgcv/html/linear.functional.terms.html
 lib/R/library/mgcv/html/logLik.gam.html
 lib/R/library/mgcv/html/magic.html
 lib/R/library/mgcv/html/magic.post.proc.html
@@ -4947,6 +4975,7 @@
 lib/R/library/mgcv/html/model.matrix.gam.html
 lib/R/library/mgcv/html/mono.con.html
 lib/R/library/mgcv/html/mroot.html
+lib/R/library/mgcv/html/negbin.html
 lib/R/library/mgcv/html/new.name.html
 lib/R/library/mgcv/html/notExp.html
 lib/R/library/mgcv/html/notExp2.html
@@ -4960,7 +4989,12 @@
 lib/R/library/mgcv/html/print.gam.html
 lib/R/library/mgcv/html/residuals.gam.html
 lib/R/library/mgcv/html/s.html
+lib/R/library/mgcv/html/smooth.construct.ad.smooth.spec.html
+lib/R/library/mgcv/html/smooth.construct.cr.smooth.spec.html
 lib/R/library/mgcv/html/smooth.construct.html
+lib/R/library/mgcv/html/smooth.construct.ps.smooth.spec.html
+lib/R/library/mgcv/html/smooth.construct.tp.smooth.spec.html
+lib/R/library/mgcv/html/smooth.terms.html
 lib/R/library/mgcv/html/smoothCon.html
 lib/R/library/mgcv/html/step.gam.html
 lib/R/library/mgcv/html/summary.gam.html
@@ -4971,6 +5005,7 @@
 lib/R/library/mgcv/html/vis.gam.html
 lib/R/library/mgcv/latex/Predict.matrix.tex
 lib/R/library/mgcv/latex/anova.gam.tex
+lib/R/library/mgcv/latex/cSplineDes.tex
 lib/R/library/mgcv/latex/choose.k.tex
 lib/R/library/mgcv/latex/exclude.too.far.tex
 lib/R/library/mgcv/latex/extract.lme.cov.tex
@@ -4983,10 +5018,9 @@
 lib/R/library/mgcv/latex/gam.control.tex
 lib/R/library/mgcv/latex/gam.convergence.tex
 lib/R/library/mgcv/latex/gam.fit.tex
-lib/R/library/mgcv/latex/gam.fit2.tex
+lib/R/library/mgcv/latex/gam.fit3.tex
 lib/R/library/mgcv/latex/gam.method.tex
 lib/R/library/mgcv/latex/gam.models.tex
-lib/R/library/mgcv/latex/gam.neg.bin.tex
 lib/R/library/mgcv/latex/gam.outer.tex
 lib/R/library/mgcv/latex/gam.selection.tex
 lib/R/library/mgcv/latex/gam.setup.tex
@@ -4994,12 +5028,14 @@
 lib/R/library/mgcv/latex/gam.tex
 lib/R/library/mgcv/latex/gam2objective.tex
 lib/R/library/mgcv/latex/gamObject.tex
+lib/R/library/mgcv/latex/gamSim.tex
 lib/R/library/mgcv/latex/gamm.setup.tex
 lib/R/library/mgcv/latex/gamm.tex
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