CVS commit: pkgsrc/math/R

["Mark Davies" <markd%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   markd
Date:           Sat Oct 21 02:40:56 UTC 2017

Modified Files:
        pkgsrc/math/R: Makefile PLIST distinfo
        pkgsrc/math/R/patches: patch-configure.ac

Log Message:
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.


To generate a diff of this commit:
cvs rdiff -u -r1.177 -r1.178 pkgsrc/math/R/Makefile
cvs rdiff -u -r1.27 -r1.28 pkgsrc/math/R/PLIST
cvs rdiff -u -r1.77 -r1.78 pkgsrc/math/R/distinfo
cvs rdiff -u -r1.1 -r1.2 pkgsrc/math/R/patches/patch-configure.ac

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/math/R/Makefile
diff -u pkgsrc/math/R/Makefile:1.177 pkgsrc/math/R/Makefile:1.178
--- pkgsrc/math/R/Makefile:1.177        Wed Oct 18 16:14:30 2017
+++ pkgsrc/math/R/Makefile      Sat Oct 21 02:40:56 2017
@@ -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 @@ PTHREAD_AUTO_VARS=    yes
 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 @@ fix-darwin-install-name:
 .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"
 

Index: pkgsrc/math/R/PLIST
diff -u pkgsrc/math/R/PLIST:1.27 pkgsrc/math/R/PLIST:1.28
--- pkgsrc/math/R/PLIST:1.27    Wed Oct 18 16:14:30 2017
+++ pkgsrc/math/R/PLIST Sat Oct 21 02:40:56 2017
@@ -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/Rmath.h
 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/DESCRIPTION
 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/INDEX
 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/DESCRIPTION
 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/DESCRIPTION
 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/CITATION
 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/DESCRIPTION
 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/cluster/po/pl/LC_MESSAGES/
 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/codetools/html/R.css
 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/DESCRIPTION
 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/COPYRIGHTS
 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.rdb
 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/DESCRIPTION
 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/DESCRIPTION
 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/graphics/libs/graphics.so
 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/INDEX
 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/lattice/po/pl/LC_MESSAGES/
 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/DESCRIPTION
 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/INDEX
 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/CITATION
 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/nnet/po/pl/LC_MESSAGES/R-n
 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/DESCRIPTION
 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/CITATION
 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/spatial/ppdata/towns.dat
 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/DESCRIPTION
 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/stats/libs/stats.so
 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/DESCRIPTION
 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/splines.pdf
 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/DESCRIPTION
 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/tcltk/libs/tcltk.so
 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/translations/zh_TW/LC_MESS
 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

Index: pkgsrc/math/R/distinfo
diff -u pkgsrc/math/R/distinfo:1.77 pkgsrc/math/R/distinfo:1.78
--- pkgsrc/math/R/distinfo:1.77 Wed Oct 18 16:14:30 2017
+++ pkgsrc/math/R/distinfo      Sat Oct 21 02:40:56 2017
@@ -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 $
 
-SHA1 (R-3.3.3.tar.gz) = 9e205a817970578ecd80384f397bae35b46f13b9
-RMD160 (R-3.3.3.tar.gz) = 5f0d3aa3cf26132ac8774d2589083a12493c18ad
-SHA512 (R-3.3.3.tar.gz) = bcb0d92fc0b22c13e345a2f660e3b3cc5810f6a07c8f2e37949c81308c2b8a5edc322df0394ece563888645442b6c01a3e1e7005aa60bd9beacc718200829e75
-Size (R-3.3.3.tar.gz) = 29804326 bytes
+SHA1 (R-3.4.2.tar.gz) = fb0e555bb49121e849436ce9e7e3bc4f7893664f
+RMD160 (R-3.4.2.tar.gz) = b903e20a1cfa3819d739a823bd8c016781b8fcae
+SHA512 (R-3.4.2.tar.gz) = d432b65aad8d8ed41a8470365c4d354b83a0e1228413963420f753aead8b84596c9ca3efc58506c8797e887af9dd6fdaf833ac1ad9339ac1ffb4b5aed577803d
+Size (R-3.4.2.tar.gz) = 30255544 bytes
 SHA1 (patch-ad) = a43b4875a2ee4677b5f762abf3f9a623fd12cbb5
-SHA1 (patch-configure.ac) = c3e77e8f7bf784a269d09c937ab1997ef701aa81
+SHA1 (patch-configure.ac) = 64c7af42c2e0eadefdac6aa105e8f8c4a59e3958
 SHA1 (patch-m4_R.m4) = 704d5514e10adf0b5217bb71b06f44a612eca6e0
 SHA1 (patch-m4_cairo.m4) = a0c4ec68d7d6d3a73a2a24481d0dee8c192bf154
 SHA1 (patch-src_include_GraphicsBase.h) = eed25eaca982ca76bf75d199dd8bf48be2a99ac5

Index: pkgsrc/math/R/patches/patch-configure.ac
diff -u pkgsrc/math/R/patches/patch-configure.ac:1.1 pkgsrc/math/R/patches/patch-configure.ac:1.2
--- pkgsrc/math/R/patches/patch-configure.ac:1.1        Fri Oct  6 20:47:37 2017
+++ pkgsrc/math/R/patches/patch-configure.ac    Sat Oct 21 02:40:56 2017
@@ -1,9 +1,9 @@
-$NetBSD: patch-configure.ac,v 1.1 2017/10/06 20:47:37 rumko Exp $
+$NetBSD: patch-configure.ac,v 1.2 2017/10/21 02:40:56 markd Exp $
 
 Do not include system paths in R_LD_LIBRARY_PATH.
 NetBSD, FreeBSD, DragonFly, Darwin and Solaris fixes
 
---- configure.ac.orig  2016-10-04 09:15:04.000000000 +0000
+--- configure.ac.orig  2017-08-04 22:15:02.000000000 +0000
 +++ configure.ac
 @@ -33,6 +33,7 @@ m4_define([R_VERSION],
  AC_INIT([R],[R_VERSION],[https://bugs.r-project.org],[R],[https://www.r-project.org])
@@ -22,7 +22,7 @@ NetBSD, FreeBSD, DragonFly, Darwin and S
    LIBR1=-lR
  else
    LIBR0=
-@@ -689,7 +690,7 @@ case "${host_os}" in
+@@ -702,7 +703,7 @@ case "${host_os}" in
      ## Not so bad in later versions of Darwin, 
      ## where DYLD_FALLBACK_LIBRARY_PATH is used (see below).
      ;;
@@ -31,7 +31,7 @@ NetBSD, FreeBSD, DragonFly, Darwin and S
      for arg in ${LDFLAGS}; do
        case "${arg}" in
          -L*)
-@@ -1376,7 +1377,7 @@ rm -f libconftest${DYLIB_EXT} conftest.c
+@@ -1339,7 +1340,7 @@ rm -f libconftest${DYLIB_EXT} conftest.c
      fpicflags="${darwin_pic}"
      shlib_cxxldflags="${shlib_ldflags}"
      ;;
@@ -40,7 +40,7 @@ NetBSD, FreeBSD, DragonFly, Darwin and S
      ## maybe this needs to depend on the compiler:
      ## -export-dynamic used to work, but does not with clang.
      ## Seems FreeBSD has used the GNU linker since at least 3.0 (Oct 1998)
-@@ -1472,6 +1473,12 @@ rm -f libconftest${DYLIB_EXT} conftest.c
+@@ -1428,6 +1429,12 @@ rm -f libconftest${DYLIB_EXT} conftest.c
      ;;
    netbsd*)
      ## See the comments about FreeBSD
@@ -53,7 +53,7 @@ NetBSD, FreeBSD, DragonFly, Darwin and S
      if ${CPP} - -dM < /dev/null | grep __ELF__ >/dev/null ; then
        main_ldflags="-Wl,--export-dynamic"
        shlib_ldflags="-shared"
-@@ -1514,22 +1521,22 @@ rm -f libconftest${DYLIB_EXT} conftest.c
+@@ -1464,22 +1471,22 @@ rm -f libconftest${DYLIB_EXT} conftest.c
    solaris*)
  ## SPARC has only an 8k global object table, 1024 entries on 64-bit,
  ## so need PIC not pic.  They are the same on other Solaris platforms.
@@ -80,16 +80,16 @@ NetBSD, FreeBSD, DragonFly, Darwin and S
        cpicflags="-KPIC"
        if test "`basename ${CXX}`" = "CC" ; then
          ## Forte version 7 needs -lCstd: Forte 6 does not.    
-@@ -1584,7 +1591,7 @@ R_SH_VAR_ADD(MAIN_LDFLAGS, [${main_ldfla
+@@ -1534,7 +1541,7 @@ R_SH_VAR_ADD(MAIN_LDFLAGS, [${main_ldfla
  : ${CPICFLAGS="${cpicflags}"}
  if test -z "${CPICFLAGS}"; then
    case "${host_os}" in
--    aix*|irix*|mingw*|osf*)
-+    aix*|irix*|mingw*|osf*|darwin*)
+-    aix*|mingw*)
++    aix*|mingw*|darwin*)
        ;;
      *)
        AC_MSG_WARN([I could not determine CPICFLAGS.])
-@@ -1667,10 +1674,10 @@ case "${host_os}" in
+@@ -1616,10 +1623,10 @@ case "${host_os}" in
      DYLIB_EXT=".dylib"
      dylib_ldflags="${darwin_dylib_ldflags}"
      MAJR_VERSION=`echo "${PACKAGE_VERSION}" | sed  -e "s/[[\.]][[1-9]]$/.0/"` 
@@ -103,7 +103,7 @@ NetBSD, FreeBSD, DragonFly, Darwin and S
      ;;
    hpux*)
      ## Needs to avoid embedding a relative path ../../../bin.
-@@ -2582,7 +2589,7 @@ case "${host_os}" in
+@@ -2558,7 +2565,7 @@ case "${host_os}" in
      r_ld_library_defaults="/usr/lib64:/lib64:/usr/lib:/lib"
      ;;
    solaris*)