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ESMTPS id 4VVKT41WwgzltP; Thu, 2 May 2024 03:40:24 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.17.1/8.17.1) with ESMTP id 4423eOLQ089304; Thu, 2 May 2024 03:40:24 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.17.1/8.17.1/Submit) id 4423eOnB089301; Thu, 2 May 2024 03:40:24 GMT (envelope-from git) Date: Thu, 2 May 2024 03:40:24 GMT Message-Id: <202405020340.4423eOnB089301@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Joseph Mingrone Subject: git: 2a131a985d90 - main - math/R: Update to 4.4.0 List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: dev-commits-ports-main@freebsd.org Sender: owner-dev-commits-ports-main@FreeBSD.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jrm X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 2a131a985d908ac72c3450158f195dc339236d3b Auto-Submitted: auto-generated The branch main has been updated by jrm: URL: https://cgit.FreeBSD.org/ports/commit/?id=2a131a985d908ac72c3450158f195dc339236d3b commit 2a131a985d908ac72c3450158f195dc339236d3b Author: Joseph Mingrone AuthorDate: 2024-04-25 19:37:54 +0000 Commit: Joseph Mingrone CommitDate: 2024-05-02 03:32:43 +0000 math/R: Update to 4.4.0 Changes: https://hypatia.math.ethz.ch/pipermail/r-announce/2024/000701.html Sponsored by: The FreeBSD Foundation --- math/R/Makefile | 5 +- math/R/distinfo | 6 +- .../R/files/extra-patch-src_extra_blas_Makefile.in | 21 +-- .../extra-patch-src_modules_lapack_Makefile.in | 47 ++--- math/R/files/patch-src_main_Makefile.in | 17 +- math/R/pkg-plist | 194 ++++++++++++++++++++- 6 files changed, 225 insertions(+), 65 deletions(-) diff --git a/math/R/Makefile b/math/R/Makefile index d32baa311aea..f5962fe47848 100644 --- a/math/R/Makefile +++ b/math/R/Makefile @@ -1,6 +1,5 @@ PORTNAME= R -DISTVERSION= 4.3.3 -PORTREVISION= 1 +DISTVERSION= 4.4.0 CATEGORIES= math lang MASTER_SITES= CRAN/src/base/R-${PORTVERSION:C|\..*||} @@ -14,6 +13,7 @@ ONLY_FOR_ARCHS= aarch64 amd64 armv6 armv7 i386 powerpc powerpc64 powerpc64le BUILD_DEPENDS= texi2any:print/texinfo LIB_DEPENDS= libcurl.so:ftp/curl \ + libdeflate.so:archivers/libdeflate \ libpcre2-8.so:devel/pcre2 # R packages may require GNU make or cmake to build RUN_DEPENDS= cmake:devel/cmake-core \ @@ -130,7 +130,6 @@ LLD_UNSAFE= yes .endif post-patch: - @${REINPLACE_CMD} -e "s|/usr/local|${LOCALBASE}|g" ${WRKSRC}/configure @${REINPLACE_CMD} \ -e "s|%%FULLVER%%|${DISTVERSION}|" \ -e "s|%%MAJORVER%%|${_MAJORVER}|" \ diff --git a/math/R/distinfo b/math/R/distinfo index 40dd95f18dba..521171b7c5e3 100644 --- a/math/R/distinfo +++ b/math/R/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1709307169 -SHA256 (R-4.3.3.tar.gz) = 80851231393b85bf3877ee9e39b282e750ed864c5ec60cbd68e6e139f0520330 -SIZE (R-4.3.3.tar.gz) = 35861202 +TIMESTAMP = 1714060267 +SHA256 (R-4.4.0.tar.gz) = ace4125f9b976d2c53bcc5fca30c75e30d4edc401584859cbadb080e72b5f030 +SIZE (R-4.4.0.tar.gz) = 37335563 diff --git a/math/R/files/extra-patch-src_extra_blas_Makefile.in b/math/R/files/extra-patch-src_extra_blas_Makefile.in index 07e097e92725..18a1cb6ff7ec 100644 --- a/math/R/files/extra-patch-src_extra_blas_Makefile.in +++ b/math/R/files/extra-patch-src_extra_blas_Makefile.in @@ -1,34 +1,29 @@ ---- src/extra/blas/Makefile.in.orig 2020-05-05 02:47:09 UTC +--- src/extra/blas/Makefile.in.orig 2024-05-01 15:06:18 UTC +++ src/extra/blas/Makefile.in -@@ -16,11 +16,11 @@ ALL_FFLAGS = $(ALL_FFLAGS_LO) - - SOURCES = blas00.c blas.f cmplxblas.f - --@BUILD_LTO_CHECK_FALSE@Rblas_la = libRblas$(R_DYLIB_EXT) -+@BUILD_LTO_CHECK_FALSE@Rblas_la = libRblas$(R_DYLIB_EXT).%%FULLVER%% - @BUILD_LTO_CHECK_TRUE@Rblas_la = libRblas.a +@@ -25,7 +25,7 @@ Rblas_la = libRblas$(R_DYLIB_EXT) + Rblas_la = libRblas$(R_DYLIB_EXT) ## @RBLAS_LDFLAGS@ is used on macOS ## first for internal BLAS -Rblas_la_LIBADD = @RBLAS_LDFLAGS@ $(FLIBS_IN_SO) -+Rblas_la_LIBADD = -Wl,-soname,libRblas.so.%%MAJORVER%% $(FLIBS_IN_SO) ++Rblas_la_LIBADD = @RBLAS_LDFLAGS@ -Wl,-soname,libRblas.so.%%MAJORVER%% $(FLIBS_IN_SO) ## then external one Rblas_la_LIBADD0 = @RBLAS_LDFLAGS@ -@@ -45,6 +45,8 @@ Rblas_install: $(Rblas_la) +@@ -66,6 +66,8 @@ Rblas_install: $(Rblas_la) @$(MKINSTALLDIRS) "$(DESTDIR)$(Rexeclibdir)" @$(SHELL) $(top_srcdir)/tools/copy-if-change $(Rblas_la) \ "$(DESTDIR)$(Rexeclibdir)/$(Rblas_la)" + @cd $(DESTDIR)$(Rexeclibdir) && ln -s $(Rblas_la) libRblas.so.%%MAJORVER%% -+ @cd $(DESTDIR)$(Rexeclibdir) && ln -s $(Rblas_la) libRblas.so ++ @cd $(DESTDIR)$(Rexeclibdir) && ln -s $(Rblas_la) libRblas.so.%%FULLVER%% Rblas_install-strip: $(Rblas_la) @$(MKINSTALLDIRS) "$(DESTDIR)$(Rexeclibdir)" -@@ -52,6 +54,8 @@ Rblas_install-strip: $(Rblas_la) +@@ -73,6 +75,8 @@ Rblas_install-strip: $(Rblas_la) @if test -n "$(STRIP_SHARED_LIB)"; then \ $(STRIP_SHARED_LIB) "$(DESTDIR)$(Rexeclibdir)/$(Rblas_la)" ;\ fi + @cd $(DESTDIR)$(Rexeclibdir) && ln -s $(Rblas_la) libRblas.so.%%MAJORVER%% -+ @cd $(DESTDIR)$(Rexeclibdir) && ln -s $(Rblas_la) libRblas.so ++ @cd $(DESTDIR)$(Rexeclibdir) && ln -s $(Rblas_la) libRblas.so.%%FULLVER%% mostlyclean: clean clean: diff --git a/math/R/files/extra-patch-src_modules_lapack_Makefile.in b/math/R/files/extra-patch-src_modules_lapack_Makefile.in index 3d9f84cb4fbe..e792a035ebc8 100644 --- a/math/R/files/extra-patch-src_modules_lapack_Makefile.in +++ b/math/R/files/extra-patch-src_modules_lapack_Makefile.in @@ -1,43 +1,34 @@ ---- src/modules/lapack/Makefile.in.orig 2020-05-05 03:51:08 UTC +--- src/modules/lapack/Makefile.in.orig 2024-05-02 02:59:59 UTC +++ src/modules/lapack/Makefile.in -@@ -41,7 +41,7 @@ lapack_la_OBJECTS = $(OBJECTS) - lapack_la_LDFLAGS = @LAPACK_LDFLAGS@ - lapack_la_LIBADD = $(LIBR1) @DYLIB_UNDEFINED_ALLOWED_FALSE@ $(LIBINTL) - --@BUILD_LTO_CHECK_FALSE@Rlapack_la = libRlapack$(R_DYLIB_EXT) -+@BUILD_LTO_CHECK_FALSE@Rlapack_la = libRlapack$(R_DYLIB_EXT).%%FULLVER%% - @BUILD_LTO_CHECK_TRUE@Rlapack_la = libRlapack.a - Rlapack_la_OBJECTS = $(LIBOBJECTS) - ## This used to skip FLIBS, but that relied on all the functions -@@ -87,17 +87,21 @@ $(lapack_la): $(lapack_la_OBJECTS) - ## Include BLAS here, as with (static) ATLAS that pulls all the +@@ -110,12 +110,14 @@ $(Rlapack_la): $(Rlapack_la_OBJECTS) ## BLAS routines into one place. - $(Rlapack_la): $(LIBOBJECTS) -- @BUILD_LTO_CHECK_FALSE@$(DYLIB_LINK) -o $@ $(LIBOBJECTS) @RLAPACK_LDFLAGS@ @BLAS_LIBS@ $(Rlapack_la_LIBADD) -+ @BUILD_LTO_CHECK_FALSE@$(DYLIB_LINK) -o $@ $(LIBOBJECTS) -Wl,-soname,libRlapack.so.%%MAJORVER%% @BLAS_LIBS@ $(Rlapack_la_LIBADD) - @BUILD_LTO_CHECK_TRUE@$(AR) -cr $@ $(LIBOBJECTS) + ## FIXME: @BLAS_LIBS@ is probably not needed for newAccelerate. + $(Rlapack_la): $(Rlapack_la_OBJECTS) +- $(DYLIB_LINK) -o $@ $(Rlapack_la_OBJECTS) @RLAPACK_LDFLAGS@ @BLAS_LIBS@ $(Rlapack_la_LIBADD) ++ $(DYLIB_LINK) -o $@ $(Rlapack_la_OBJECTS) @RLAPACK_LDFLAGS@ -Wl,-soname,libRlapack.so.%%MAJORVER%% @BLAS_LIBS@ $(Rlapack_la_LIBADD) Rlapack_install: $(Rlapack_la) @$(MKINSTALLDIRS) "$(DESTDIR)$(Rexeclibdir)" @$(SHELL) $(top_srcdir)/tools/copy-if-change $(Rlapack_la) \ "$(Rexeclibdir)/$(Rlapack_la)" -+ @cd $(DESTDIR)$(Rexeclibdir) && ln -s $(Rlapack_la) libRlapack.so.%%MAJORVER%% -+ @cd $(DESTDIR)$(Rexeclibdir) && ln -s $(Rlapack_la) libRlapack.so ++ @cd "$(DESTDIR)$(Rexeclibdir)" && ln -sf $(Rlapack_la) libRlapack.so.%%MAJORVER%% ++ @cd "$(DESTDIR)$(Rexeclibdir)" && ln -sf $(Rlapack_la) libRlapack.so.%%FULLVER%% install: installdirs @$(SHELL) $(top_srcdir)/tools/copy-if-change $(lapack_la) "$(DESTDIR)$(Rexecmodulesdir)/$(lapack_la)" - @USE_EXTERNAL_LAPACK_FALSE@ @$(SHELL) $(top_srcdir)/tools/copy-if-change $(Rlapack_la) "$(DESTDIR)$(Rexeclibdir)/$(Rlapack_la)" -+@USE_EXTERNAL_LAPACK_FALSE@ @cd "$(DESTDIR)$(Rexeclibdir)" && ln -sf $(Rlapack_la) libRlapack.so.%%MAJORVER%% -+@USE_EXTERNAL_LAPACK_FALSE@ @cd "$(DESTDIR)$(Rexeclibdir)" && ln -sf $(Rlapack_la) libRlapack.so - installdirs: +@@ -124,11 +126,15 @@ install-strip-Rlapack: @$(MKINSTALLDIRS) "$(DESTDIR)$(Rexecmodulesdir)" install-strip-Rlapack: -@@ -110,6 +114,8 @@ install-strip: @USE_EXTERNAL_LAPACK_FALSE@ install-str + @$(SHELL) $(top_srcdir)/tools/copy-if-change $(Rlapack_la) "$(DESTDIR)$(Rexeclibdir)/$(Rlapack_la)" ++ @cd "$(DESTDIR)$(Rexeclibdir)" && ln -sf $(Rlapack_la) libRlapack.so.%%MAJORVER%% ++ @cd "$(DESTDIR)$(Rexeclibdir)" && ln -sf $(Rlapack_la) libRlapack.so.%%FULLVER%% + @if test -n "$(STRIP_SHARED_LIB)"; then \ + $(STRIP_SHARED_LIB) "$(DESTDIR)$(Rexeclibdir)/$(Rlapack_la)"; \ + fi + install-strip: @USE_EXTERNAL_LAPACK_FALSE@ install-strip-Rlapack + @$(SHELL) $(top_srcdir)/tools/copy-if-change $(lapack_la) "$(DESTDIR)$(Rexecmodulesdir)/$(lapack_la)" ++ @cd "$(DESTDIR)$(Rexeclibdir)" && ln -sf $(Rlapack_la) libRlapack.so.%%MAJORVER%% ++ @cd "$(DESTDIR)$(Rexeclibdir)" && ln -sf $(Rlapack_la) libRlapack.so.%%FULLVER%% @if test -n "$(STRIP_SHARED_LIB)"; then \ $(STRIP_SHARED_LIB) "$(DESTDIR)$(Rexecmodulesdir)/$(lapack_la)"; \ fi -+ @cd $(DESTDIR)$(Rexeclibdir) && ln -s $(Rlapack_la) libRlapack.so.%%MAJORVER%% -+ @cd $(DESTDIR)$(Rexeclibdir) && ln -s $(Rlapack_la) libRlapack.so - uninstall: - @rm -f "$(Rexecmodulesdir)/$(lapack_la)" - diff --git a/math/R/files/patch-src_main_Makefile.in b/math/R/files/patch-src_main_Makefile.in index ddc961a8ac69..92740d31f0e0 100644 --- a/math/R/files/patch-src_main_Makefile.in +++ b/math/R/files/patch-src_main_Makefile.in @@ -1,27 +1,20 @@ ---- src/main/Makefile.in.orig 2020-05-05 02:47:09 UTC +--- src/main/Makefile.in.orig 2024-05-01 21:07:24 UTC +++ src/main/Makefile.in -@@ -105,13 +105,13 @@ R_bin_OBJECTS = Rmain.o @WANT_R_SHLIB_FALSE@$(OBJECTS) - @WANT_R_SHLIB_TRUE@R_bin_LDADD = -lR @BLAS_SHLIB_TRUE@-lRblas - @BUILD_LTO_FALSE@R_bin_DEPENDENCIES =@WANT_R_SHLIB_FALSE@ libR.a @USE_EXPORTFILES_TRUE@ $(top_builddir)/etc/R.exp - --libR_la = libR$(R_DYLIB_EXT) -+libR_la = libR$(R_DYLIB_EXT).%%FULLVER%% - libR_la_OBJECTS = $(OBJECTS) - libR_la_LIBADD = $(MAIN_OBJS) $(EXTRA_STATIC_LIBS) $(EXTRA_LIBS) @WANT_R_SHLIB_TRUE@ @USE_EXPORTFILES_TRUE@ -Wl,-bE:$(top_builddir)/etc/R.exp +@@ -115,7 +115,7 @@ libR_la_DEPENDENCIES = $(STATIC_LIBS) $(R_TZONE) @WANT libR_la_DEPENDENCIES = $(STATIC_LIBS) $(R_TZONE) @WANT_R_SHLIB_TRUE@ @USE_EXPORTFILES_TRUE@ $(top_builddir)/etc/R.exp ## The next is needed for macOS only at present -LIBR_LDFLAGS = @LIBR_LDFLAGS@ -+LIBR_LDFLAGS = -Wl,-soname,libR.so.4 ++LIBR_LDFLAGS = @LIBR_LDFLAGS@ -Wl,-soname,libR.so.%%MAJORVER%% all: R -@@ -201,6 +201,8 @@ install-bin: installdirs +@@ -203,6 +203,8 @@ install-lib: installdirs install-lib: installdirs @$(MKINSTALLDIRS) "$(DESTDIR)$(Rexeclibdir)" @$(SHELL) $(top_srcdir)/tools/copy-if-change $(libR_la) "$(DESTDIR)$(Rexeclibdir)/$(libR_la)" + @cd "$(DESTDIR)$(Rexeclibdir)" && ln -s $(libR_la) libR.so.%%MAJORVER%% -+ @cd "$(DESTDIR)$(Rexeclibdir)" && ln -s $(libR_la) libR.so ++ @cd "$(DESTDIR)$(Rexeclibdir)" && ln -s $(libR_la) libR.so.%%FULLVER%% install-static: installdirs @$(MKINSTALLDIRS) "$(DESTDIR)$(Rexeclibdir)" @$(SHELL) $(top_srcdir)/tools/copy-if-change libR.a "$(DESTDIR)$(Rexeclibdir)/libR.a" diff --git a/math/R/pkg-plist b/math/R/pkg-plist index ec44182d1be8..6bd91016464f 100644 --- a/math/R/pkg-plist +++ b/math/R/pkg-plist @@ -189,15 +189,49 @@ lib/R/library/Matrix/doc/Intro2Matrix.pdf lib/R/library/Matrix/doc/Introduction.R lib/R/library/Matrix/doc/Introduction.Rnw lib/R/library/Matrix/doc/Introduction.pdf -lib/R/library/Matrix/doc/SuiteSparse/AMD.txt -lib/R/library/Matrix/doc/SuiteSparse/CHOLMOD.txt -lib/R/library/Matrix/doc/SuiteSparse/COLAMD.txt -lib/R/library/Matrix/doc/SuiteSparse/SPQR.txt -lib/R/library/Matrix/doc/SuiteSparse/SuiteSparse_config.txt +lib/R/library/Matrix/doc/SuiteSparse/AMD/Doc/ChangeLog +lib/R/library/Matrix/doc/SuiteSparse/AMD/Doc/License.txt +lib/R/library/Matrix/doc/SuiteSparse/AMD/README.txt +lib/R/library/Matrix/doc/SuiteSparse/CAMD/Doc/ChangeLog +lib/R/library/Matrix/doc/SuiteSparse/CAMD/Doc/License.txt +lib/R/library/Matrix/doc/SuiteSparse/CAMD/README.txt +lib/R/library/Matrix/doc/SuiteSparse/CCOLAMD/Doc/ChangeLog +lib/R/library/Matrix/doc/SuiteSparse/CCOLAMD/Doc/License.txt +lib/R/library/Matrix/doc/SuiteSparse/CCOLAMD/README.txt +lib/R/library/Matrix/doc/SuiteSparse/CHOLMOD/Doc/ChangeLog +lib/R/library/Matrix/doc/SuiteSparse/CHOLMOD/Doc/License.txt +lib/R/library/Matrix/doc/SuiteSparse/CHOLMOD/README.txt +lib/R/library/Matrix/doc/SuiteSparse/CHOLMOD/SuiteSparse_metis/Changelog +lib/R/library/Matrix/doc/SuiteSparse/CHOLMOD/SuiteSparse_metis/LICENSE.txt +lib/R/library/Matrix/doc/SuiteSparse/CHOLMOD/SuiteSparse_metis/README.txt +lib/R/library/Matrix/doc/SuiteSparse/COLAMD/Doc/ChangeLog +lib/R/library/Matrix/doc/SuiteSparse/COLAMD/Doc/License.txt +lib/R/library/Matrix/doc/SuiteSparse/COLAMD/README.txt +lib/R/library/Matrix/doc/SuiteSparse/CXSparse/Doc/ChangeLog +lib/R/library/Matrix/doc/SuiteSparse/CXSparse/Doc/License.txt +lib/R/library/Matrix/doc/SuiteSparse/CXSparse/README.txt +lib/R/library/Matrix/doc/SuiteSparse/ChangeLog +lib/R/library/Matrix/doc/SuiteSparse/LICENSE.txt +lib/R/library/Matrix/doc/SuiteSparse/README.md +lib/R/library/Matrix/doc/SuiteSparse/SuiteSparse_config/README.txt lib/R/library/Matrix/doc/index.html lib/R/library/Matrix/doc/sparseModels.R lib/R/library/Matrix/doc/sparseModels.Rnw lib/R/library/Matrix/doc/sparseModels.pdf +lib/R/library/Matrix/scripts/AMD.patch +lib/R/library/Matrix/scripts/CAMD.patch +lib/R/library/Matrix/scripts/CCOLAMD.patch +lib/R/library/Matrix/scripts/CHOLMOD.patch +lib/R/library/Matrix/scripts/COLAMD.patch +lib/R/library/Matrix/scripts/CXSparse.patch +lib/R/library/Matrix/scripts/SuiteSparse_config.patch +lib/R/library/Matrix/scripts/api.patch +lib/R/library/Matrix/scripts/disclaimer.txt +lib/R/library/Matrix/scripts/rules.mk +lib/R/library/Matrix/scripts/rules.sh +lib/R/library/Matrix/scripts/sources.mk +lib/R/library/Matrix/scripts/ssget.sh +lib/R/library/Matrix/scripts/wall.patch lib/R/library/Matrix/external/CAex_slots.rda lib/R/library/Matrix/external/KNex_slots.rda lib/R/library/Matrix/external/USCounties_slots.rda @@ -497,8 +531,24 @@ lib/R/library/grDevices/afm/Helvetica-Bold.afm.gz lib/R/library/grDevices/afm/Helvetica-BoldOblique.afm.gz lib/R/library/grDevices/afm/Helvetica-Oblique.afm.gz lib/R/library/grDevices/afm/Helvetica.afm.gz +lib/R/library/grDevices/afm/LICENSE.LPPL lib/R/library/grDevices/afm/MustRead.html +lib/R/library/grDevices/afm/NimbusMonoPS-Bold.afm.gz +lib/R/library/grDevices/afm/NimbusMonoPS-BoldItalic.afm.gz +lib/R/library/grDevices/afm/NimbusMonoPS-Italic.afm.gz 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