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[pkgsrc/trunk]: pkgsrc/math/R R: update to 3.4.2
details: https://anonhg.NetBSD.org/pkgsrc/rev/122eb828aa4a
branches: trunk
changeset: 370602:122eb828aa4a
user: markd <markd%pkgsrc.org@localhost>
date: Sat Oct 21 02:40:56 2017 +0000
description:
R: update to 3.4.2
CHANGES IN R 3.4.2:
NEW FEATURES:
* Setting the LC_ALL category in Sys.setlocale() invalidates any
cached locale-specific day/month names and the AM/PM indicator
for strptime() (as setting LC_TIME has since R 3.1.0).
* The version of LAPACK included in the sources has been updated to
3.7.1, a bug-fix release.
* The default for tools::write_PACKAGES(rds_compress=) has been
changed to "xz" to match the compression used by CRAN.
* c() and unlist() are now more efficient in constructing the
names(.) of their return value, thanks to a proposal by Suharto
Anggono. (PR#17284)
CHANGES IN R 3.4.0:
SIGNIFICANT USER-VISIBLE CHANGES:
* (Unix-alike) The default methods for download.file() and url()
now choose "libcurl" except for file:// URLs. There will be
small changes in the format and wording of messages, including in
rare cases if an issue is a warning or an error. For example,
when HTTP re-direction occurs, some messages refer to the final
URL rather than the specified one.
Those who use proxies should check that their settings are
compatible (see ?download.file: the most commonly used forms work
for both "internal" and "libcurl").
* table() has been amended to be more internally consistent and
become back compatible to R <= 2.7.2 again. Consequently,
table(1:2, exclude = NULL) no longer contains a zero count for
<NA>, but useNA = "always" continues to do so.
* summary.default() no longer rounds, but its print method does
resulting in less extraneous rounding, notably of numbers in the
ten thousands.
* factor(x, exclude = L) behaves more rationally when x or L are
character vectors. Further, exclude = <factor> now behaves as
documented for long.
* Arithmetic, logic (&, |) and comparison (aka 'relational', e.g.,
<, ==) operations with arrays now behave consistently, notably
for arrays of length zero.
Arithmetic between length-1 arrays and longer non-arrays had
silently dropped the array attributes and recycled. This now
gives a warning and will signal an error in the future, as it has
always for logic and comparison operations in these cases (e.g.,
compare matrix(1,1) + 2:3 and matrix(1,1) < 2:3).
* The JIT ('Just In Time') byte-code compiler is now enabled by
default at its level 3. This means functions will be compiled on
first or second use and top-level loops will be compiled and then
run. (Thanks to Tomas Kalibera for extensive work to make this
possible.)
For now, the compiler will not compile code containing explicit
calls to browser(): this is to support single stepping from the
browser() call.
JIT compilation can be disabled for the rest of the session using
compiler::enableJIT(0) or by setting environment variable
R_ENABLE_JIT to 0.
* xtabs() works more consistently with NAs, also in its result no
longer setting them to 0. Further, a new logical option addNA
allows to count NAs where appropriate. Additionally, for the
case sparse = TRUE, the result's dimnames are identical to the
default case's.
* Matrix products now consistently bypass BLAS when the inputs have
NaN/Inf values. Performance of the check of inputs has been
improved. Performance when BLAS is used is improved for
matrix/vector and vector/matrix multiplication (DGEMV is now used
instead of DGEMM).
One can now choose from alternative matrix product
implementations _via_ options(matprod = ). The "internal"
implementation is not optimized for speed but consistent in
precision with other summations in R (using long double
accumulators where available). "blas" calls BLAS directly for
best speed, but usually with undefined behavior for inputs with
NaN/Inf.
NEW FEATURES:
* User errors such as integrate(f, 0:1, 2) are now caught.
* Add signature argument to debug(), debugonce(), undebug() and
isdebugged() for more conveniently debugging S3 and S4 methods.
(Based on a patch by Gabe Becker.)
* Add utils::debugcall() and utils::undebugcall() for debugging the
function that would be called by evaluating the given expression.
When the call is to an S4 generic or standard S3 generic,
debugcall() debugs the method that would be dispatched. A number
of internal utilities were added to support this, most notably
utils::isS3stdGeneric(). (Based on a patch by Gabe Becker.)
And many more - see the NEWS file for details.
diffstat:
math/R/Makefile | 7 ++++---
math/R/PLIST | 37 +++++++++++++++++++++++++++++++++++--
math/R/distinfo | 12 ++++++------
math/R/patches/patch-configure.ac | 22 +++++++++++-----------
4 files changed, 56 insertions(+), 22 deletions(-)
diffs (truncated from 396 to 300 lines):
diff -r b0c88ed72df2 -r 122eb828aa4a math/R/Makefile
--- a/math/R/Makefile Sat Oct 21 01:23:28 2017 +0000
+++ b/math/R/Makefile Sat Oct 21 02:40:56 2017 +0000
@@ -1,7 +1,6 @@
-# $NetBSD: Makefile,v 1.177 2017/10/18 16:14:30 adam Exp $
+# $NetBSD: Makefile,v 1.178 2017/10/21 02:40:56 markd Exp $
-DISTNAME= R-3.3.3
-PKGREVISION= 2
+DISTNAME= R-3.4.2
CATEGORIES= math
MASTER_SITES= ${MASTER_SITE_R_CRAN:=base/R-3/}
@@ -31,6 +30,7 @@
GNU_CONFIGURE= yes
CONFIGURE_ARGS+= --enable-R-shlib
CONFIGURE_ARGS+= --with-readline
+CONFIGURE_ARGS+= --with-lapack
CONFIGURE_ARGS+= --with-tcltk
CONFIGURE_ARGS+= --with-tcl-config=${BUILDLINK_PREFIX.tcl}/lib/tclConfig.sh
CONFIGURE_ARGS+= --with-tk-config=${BUILDLINK_PREFIX.tk}/lib/tkConfig.sh
@@ -174,6 +174,7 @@
.include "../../graphics/png/buildlink3.mk"
.include "../../graphics/tiff/buildlink3.mk"
.include "../../math/blas/buildlink3.mk"
+.include "../../math/lapack/buildlink3.mk"
.include "../../www/curl/buildlink3.mk"
.include "../../x11/tk/buildlink3.mk"
diff -r b0c88ed72df2 -r 122eb828aa4a math/R/PLIST
--- a/math/R/PLIST Sat Oct 21 01:23:28 2017 +0000
+++ b/math/R/PLIST Sat Oct 21 02:40:56 2017 +0000
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.27 2017/10/18 16:14:30 adam Exp $
+@comment $NetBSD: PLIST,v 1.28 2017/10/21 02:40:56 markd Exp $
bin/R
bin/Rscript
info/R-FAQ.info.gz
@@ -129,10 +129,10 @@
lib/R/include/Rversion.h
lib/R/include/S.h
lib/R/lib/libR.so
-lib/R/lib/libRlapack.so
lib/R/library/KernSmooth/DESCRIPTION
lib/R/library/KernSmooth/INDEX
lib/R/library/KernSmooth/Meta/Rd.rds
+lib/R/library/KernSmooth/Meta/features.rds
lib/R/library/KernSmooth/Meta/hsearch.rds
lib/R/library/KernSmooth/Meta/links.rds
lib/R/library/KernSmooth/Meta/nsInfo.rds
@@ -159,6 +159,7 @@
lib/R/library/MASS/INDEX
lib/R/library/MASS/Meta/Rd.rds
lib/R/library/MASS/Meta/data.rds
+lib/R/library/MASS/Meta/features.rds
lib/R/library/MASS/Meta/hsearch.rds
lib/R/library/MASS/Meta/links.rds
lib/R/library/MASS/Meta/nsInfo.rds
@@ -207,6 +208,7 @@
lib/R/library/Matrix/LICENCE
lib/R/library/Matrix/Meta/Rd.rds
lib/R/library/Matrix/Meta/data.rds
+lib/R/library/Matrix/Meta/features.rds
lib/R/library/Matrix/Meta/hsearch.rds
lib/R/library/Matrix/Meta/links.rds
lib/R/library/Matrix/Meta/nsInfo.rds
@@ -282,6 +284,7 @@
lib/R/library/base/INDEX
lib/R/library/base/Meta/Rd.rds
lib/R/library/base/Meta/demo.rds
+lib/R/library/base/Meta/features.rds
lib/R/library/base/Meta/hsearch.rds
lib/R/library/base/Meta/links.rds
lib/R/library/base/Meta/package.rds
@@ -305,6 +308,7 @@
lib/R/library/boot/INDEX
lib/R/library/boot/Meta/Rd.rds
lib/R/library/boot/Meta/data.rds
+lib/R/library/boot/Meta/features.rds
lib/R/library/boot/Meta/hsearch.rds
lib/R/library/boot/Meta/links.rds
lib/R/library/boot/Meta/nsInfo.rds
@@ -334,6 +338,7 @@
lib/R/library/class/DESCRIPTION
lib/R/library/class/INDEX
lib/R/library/class/Meta/Rd.rds
+lib/R/library/class/Meta/features.rds
lib/R/library/class/Meta/hsearch.rds
lib/R/library/class/Meta/links.rds
lib/R/library/class/Meta/nsInfo.rds
@@ -361,6 +366,7 @@
lib/R/library/cluster/INDEX
lib/R/library/cluster/Meta/Rd.rds
lib/R/library/cluster/Meta/data.rds
+lib/R/library/cluster/Meta/features.rds
lib/R/library/cluster/Meta/hsearch.rds
lib/R/library/cluster/Meta/links.rds
lib/R/library/cluster/Meta/nsInfo.rds
@@ -392,6 +398,7 @@
lib/R/library/codetools/DESCRIPTION
lib/R/library/codetools/INDEX
lib/R/library/codetools/Meta/Rd.rds
+lib/R/library/codetools/Meta/features.rds
lib/R/library/codetools/Meta/hsearch.rds
lib/R/library/codetools/Meta/links.rds
lib/R/library/codetools/Meta/nsInfo.rds
@@ -410,6 +417,7 @@
lib/R/library/compiler/DESCRIPTION
lib/R/library/compiler/INDEX
lib/R/library/compiler/Meta/Rd.rds
+lib/R/library/compiler/Meta/features.rds
lib/R/library/compiler/Meta/hsearch.rds
lib/R/library/compiler/Meta/links.rds
lib/R/library/compiler/Meta/nsInfo.rds
@@ -429,6 +437,7 @@
lib/R/library/datasets/INDEX
lib/R/library/datasets/Meta/Rd.rds
lib/R/library/datasets/Meta/data.rds
+lib/R/library/datasets/Meta/features.rds
lib/R/library/datasets/Meta/hsearch.rds
lib/R/library/datasets/Meta/links.rds
lib/R/library/datasets/Meta/nsInfo.rds
@@ -449,6 +458,7 @@
lib/R/library/foreign/DESCRIPTION
lib/R/library/foreign/INDEX
lib/R/library/foreign/Meta/Rd.rds
+lib/R/library/foreign/Meta/features.rds
lib/R/library/foreign/Meta/hsearch.rds
lib/R/library/foreign/Meta/links.rds
lib/R/library/foreign/Meta/nsInfo.rds
@@ -459,7 +469,9 @@
lib/R/library/foreign/R/foreign.rdx
lib/R/library/foreign/files/HillRace.SYD
lib/R/library/foreign/files/Iris.syd
+lib/R/library/foreign/files/electric.sav
lib/R/library/foreign/files/sids.dbf
+lib/R/library/foreign/files/testdata.sav
lib/R/library/foreign/help/AnIndex
lib/R/library/foreign/help/aliases.rds
lib/R/library/foreign/help/foreign.rdb
@@ -480,6 +492,7 @@
lib/R/library/grDevices/INDEX
lib/R/library/grDevices/Meta/Rd.rds
lib/R/library/grDevices/Meta/demo.rds
+lib/R/library/grDevices/Meta/features.rds
lib/R/library/grDevices/Meta/hsearch.rds
lib/R/library/grDevices/Meta/links.rds
lib/R/library/grDevices/Meta/nsInfo.rds
@@ -616,6 +629,7 @@
lib/R/library/graphics/INDEX
lib/R/library/graphics/Meta/Rd.rds
lib/R/library/graphics/Meta/demo.rds
+lib/R/library/graphics/Meta/features.rds
lib/R/library/graphics/Meta/hsearch.rds
lib/R/library/graphics/Meta/links.rds
lib/R/library/graphics/Meta/nsInfo.rds
@@ -648,6 +662,7 @@
lib/R/library/grid/DESCRIPTION
lib/R/library/grid/INDEX
lib/R/library/grid/Meta/Rd.rds
+lib/R/library/grid/Meta/features.rds
lib/R/library/grid/Meta/hsearch.rds
lib/R/library/grid/Meta/links.rds
lib/R/library/grid/Meta/nsInfo.rds
@@ -685,6 +700,7 @@
lib/R/library/lattice/Meta/Rd.rds
lib/R/library/lattice/Meta/data.rds
lib/R/library/lattice/Meta/demo.rds
+lib/R/library/lattice/Meta/features.rds
lib/R/library/lattice/Meta/hsearch.rds
lib/R/library/lattice/Meta/links.rds
lib/R/library/lattice/Meta/nsInfo.rds
@@ -717,6 +733,7 @@
lib/R/library/methods/DESCRIPTION
lib/R/library/methods/INDEX
lib/R/library/methods/Meta/Rd.rds
+lib/R/library/methods/Meta/features.rds
lib/R/library/methods/Meta/hsearch.rds
lib/R/library/methods/Meta/links.rds
lib/R/library/methods/Meta/nsInfo.rds
@@ -738,6 +755,7 @@
lib/R/library/mgcv/INDEX
lib/R/library/mgcv/Meta/Rd.rds
lib/R/library/mgcv/Meta/data.rds
+lib/R/library/mgcv/Meta/features.rds
lib/R/library/mgcv/Meta/hsearch.rds
lib/R/library/mgcv/Meta/links.rds
lib/R/library/mgcv/Meta/nsInfo.rds
@@ -772,6 +790,7 @@
lib/R/library/nlme/LICENCE
lib/R/library/nlme/Meta/Rd.rds
lib/R/library/nlme/Meta/data.rds
+lib/R/library/nlme/Meta/features.rds
lib/R/library/nlme/Meta/hsearch.rds
lib/R/library/nlme/Meta/links.rds
lib/R/library/nlme/Meta/nsInfo.rds
@@ -817,6 +836,7 @@
lib/R/library/nnet/DESCRIPTION
lib/R/library/nnet/INDEX
lib/R/library/nnet/Meta/Rd.rds
+lib/R/library/nnet/Meta/features.rds
lib/R/library/nnet/Meta/hsearch.rds
lib/R/library/nnet/Meta/links.rds
lib/R/library/nnet/Meta/nsInfo.rds
@@ -842,6 +862,7 @@
lib/R/library/parallel/DESCRIPTION
lib/R/library/parallel/INDEX
lib/R/library/parallel/Meta/Rd.rds
+lib/R/library/parallel/Meta/features.rds
lib/R/library/parallel/Meta/hsearch.rds
lib/R/library/parallel/Meta/links.rds
lib/R/library/parallel/Meta/nsInfo.rds
@@ -863,6 +884,7 @@
lib/R/library/rpart/INDEX
lib/R/library/rpart/Meta/Rd.rds
lib/R/library/rpart/Meta/data.rds
+lib/R/library/rpart/Meta/features.rds
lib/R/library/rpart/Meta/hsearch.rds
lib/R/library/rpart/Meta/links.rds
lib/R/library/rpart/Meta/nsInfo.rds
@@ -907,6 +929,7 @@
lib/R/library/spatial/DESCRIPTION
lib/R/library/spatial/INDEX
lib/R/library/spatial/Meta/Rd.rds
+lib/R/library/spatial/Meta/features.rds
lib/R/library/spatial/Meta/hsearch.rds
lib/R/library/spatial/Meta/links.rds
lib/R/library/spatial/Meta/nsInfo.rds
@@ -957,6 +980,7 @@
lib/R/library/splines/DESCRIPTION
lib/R/library/splines/INDEX
lib/R/library/splines/Meta/Rd.rds
+lib/R/library/splines/Meta/features.rds
lib/R/library/splines/Meta/hsearch.rds
lib/R/library/splines/Meta/links.rds
lib/R/library/splines/Meta/nsInfo.rds
@@ -978,6 +1002,7 @@
lib/R/library/stats/INDEX
lib/R/library/stats/Meta/Rd.rds
lib/R/library/stats/Meta/demo.rds
+lib/R/library/stats/Meta/features.rds
lib/R/library/stats/Meta/hsearch.rds
lib/R/library/stats/Meta/links.rds
lib/R/library/stats/Meta/nsInfo.rds
@@ -1002,6 +1027,7 @@
lib/R/library/stats4/DESCRIPTION
lib/R/library/stats4/INDEX
lib/R/library/stats4/Meta/Rd.rds
+lib/R/library/stats4/Meta/features.rds
lib/R/library/stats4/Meta/hsearch.rds
lib/R/library/stats4/Meta/links.rds
lib/R/library/stats4/Meta/nsInfo.rds
@@ -1023,6 +1049,7 @@
lib/R/library/survival/INDEX
lib/R/library/survival/Meta/Rd.rds
lib/R/library/survival/Meta/data.rds
+lib/R/library/survival/Meta/features.rds
lib/R/library/survival/Meta/hsearch.rds
lib/R/library/survival/Meta/links.rds
lib/R/library/survival/Meta/nsInfo.rds
@@ -1053,6 +1080,9 @@
lib/R/library/survival/doc/tests.R
lib/R/library/survival/doc/tests.Rnw
lib/R/library/survival/doc/tests.pdf
+lib/R/library/survival/doc/tiedtimes.R
+lib/R/library/survival/doc/tiedtimes.Rnw
+lib/R/library/survival/doc/tiedtimes.pdf
lib/R/library/survival/doc/timedep.R
lib/R/library/survival/doc/timedep.Rnw
lib/R/library/survival/doc/timedep.pdf
@@ -1071,6 +1101,7 @@
lib/R/library/tcltk/INDEX
lib/R/library/tcltk/Meta/Rd.rds
lib/R/library/tcltk/Meta/demo.rds
+lib/R/library/tcltk/Meta/features.rds
lib/R/library/tcltk/Meta/hsearch.rds
lib/R/library/tcltk/Meta/links.rds
lib/R/library/tcltk/Meta/nsInfo.rds
@@ -1106,6 +1137,7 @@
lib/R/library/tools/DESCRIPTION
lib/R/library/tools/INDEX
lib/R/library/tools/Meta/Rd.rds
+lib/R/library/tools/Meta/features.rds
lib/R/library/tools/Meta/hsearch.rds
lib/R/library/tools/Meta/links.rds
lib/R/library/tools/Meta/nsInfo.rds
@@ -1407,6 +1439,7 @@
lib/R/library/utils/DESCRIPTION
lib/R/library/utils/INDEX
lib/R/library/utils/Meta/Rd.rds
+lib/R/library/utils/Meta/features.rds
lib/R/library/utils/Meta/hsearch.rds
lib/R/library/utils/Meta/links.rds
lib/R/library/utils/Meta/nsInfo.rds
diff -r b0c88ed72df2 -r 122eb828aa4a math/R/distinfo
--- a/math/R/distinfo Sat Oct 21 01:23:28 2017 +0000
+++ b/math/R/distinfo Sat Oct 21 02:40:56 2017 +0000
@@ -1,11 +1,11 @@
-$NetBSD: distinfo,v 1.77 2017/10/18 16:14:30 adam Exp $
+$NetBSD: distinfo,v 1.78 2017/10/21 02:40:56 markd Exp $
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