Received: by mail.netbsd.org (Postfix, from userid 605) id 0FEEF84DC0; Sat, 21 Oct 2017 02:40:59 +0000 (UTC) Received: from localhost (localhost [127.0.0.1]) by mail.netbsd.org (Postfix) with ESMTP id 8FEB784DB1 for ; Sat, 21 Oct 2017 02:40:58 +0000 (UTC) X-Virus-Scanned: amavisd-new at netbsd.org Received: from mail.netbsd.org ([127.0.0.1]) by localhost (mail.netbsd.org [127.0.0.1]) (amavisd-new, port 10025) with ESMTP id VRqAMknOqpAi for ; Sat, 21 Oct 2017 02:40:57 +0000 (UTC) Received: from cvs.NetBSD.org (ivanova.NetBSD.org [IPv6:2001:470:a085:999:28c:faff:fe03:5984]) by mail.netbsd.org (Postfix) with ESMTP id 18A0D84D58 for ; Sat, 21 Oct 2017 02:40:57 +0000 (UTC) Received: by cvs.NetBSD.org (Postfix, from userid 500) id 13548FBC7; Sat, 21 Oct 2017 02:40:57 +0000 (UTC) Content-Transfer-Encoding: 7bit Content-Type: multipart/mixed; boundary="_----------=_1508553657273450" MIME-Version: 1.0 Date: Sat, 21 Oct 2017 02:40:57 +0000 From: "Mark Davies" Subject: CVS commit: pkgsrc/math/R To: pkgsrc-changes@NetBSD.org Reply-To: markd@netbsd.org X-Mailer: log_accum Message-Id: <20171021024057.13548FBC7@cvs.NetBSD.org> Sender: pkgsrc-changes-owner@NetBSD.org List-Id: pkgsrc-changes.NetBSD.org Precedence: bulk List-Unsubscribe: This is a multi-part message in MIME format. --_----------=_1508553657273450 Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" 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 , 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 = 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. --_----------=_1508553657273450 Content-Disposition: inline Content-Length: 16292 Content-Transfer-Encoding: binary Content-Type: text/x-diff; charset=us-ascii 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*) --_----------=_1508553657273450--