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CVS commit: pkgsrc/math/R
Module Name: pkgsrc
Committed By: rumko
Date: Fri Oct 6 20:47:37 UTC 2017
Modified Files:
pkgsrc/math/R: Makefile distinfo
Added Files:
pkgsrc/math/R/patches: patch-configure.ac patch-m4_R.m4
Removed Files:
pkgsrc/math/R/patches: patch-ac
Log Message:
math/R: better fix for fbsd
Also move fixes from configure to configure.ac
m4/R.m4 fix by @joerg
Oked @joerg
To generate a diff of this commit:
cvs rdiff -u -r1.175 -r1.176 pkgsrc/math/R/Makefile
cvs rdiff -u -r1.75 -r1.76 pkgsrc/math/R/distinfo
cvs rdiff -u -r1.39 -r0 pkgsrc/math/R/patches/patch-ac
cvs rdiff -u -r0 -r1.1 pkgsrc/math/R/patches/patch-configure.ac \
pkgsrc/math/R/patches/patch-m4_R.m4
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:1.175 pkgsrc/math/R/Makefile:1.176
--- pkgsrc/math/R/Makefile:1.175 Sun Sep 10 20:36:56 2017
+++ pkgsrc/math/R/Makefile Fri Oct 6 20:47:37 2017
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.175 2017/09/10 20:36:56 rumko Exp $
+# $NetBSD: Makefile,v 1.176 2017/10/06 20:47:37 rumko Exp $
DISTNAME= R-3.3.3
PKGREVISION= 2
@@ -21,6 +21,7 @@ INSTALL_TARGET= install install-info
TEST_TARGET= check
USE_TOOLS+= gmake gzip:run makeinfo perl:run sed unzip:run xmkmf
USE_TOOLS+= pkg-config
+USE_TOOLS+= aclocal autoconf autoreconf automake
USE_LANGUAGES= c c++ fortran
USE_LIBTOOL= yes
TEXINFO_REQD= 5.1
@@ -46,10 +47,6 @@ CONFIGURE_ARGS+= --with-system-xz
CONFIGURE_ARGS+= --enable-long-double=no
.endif
-# cpow and clog are not implemented on FreeBSD
-CONFIGURE_ENV.FreeBSD+= ac_cv_have_decl_clog=no
-CONFIGURE_ENV.FreeBSD+= ac_cv_have_decl_cpow=no
-
.if ${OPSYS} != "Linux"
USE_GNU_ICONV= yes # latin1 support, iconvlist
.endif
@@ -141,6 +138,9 @@ BUILDLINK_API_DEPENDS.bzip2+= bzip2>=1.0
CONFIGURE_ARGS+= --enable-mbcs=no
.endif
+pre-configure:
+ ${RUN} cd ${WRKSRC} && autoreconf -fvi
+
# Fix library names. Relies on build system using -headerpad_max_install_names.
.if ${OPSYS} == "Darwin"
.PHONY: fix-darwin-install-name
Index: pkgsrc/math/R/distinfo
diff -u pkgsrc/math/R/distinfo:1.75 pkgsrc/math/R/distinfo:1.76
--- pkgsrc/math/R/distinfo:1.75 Sat Mar 11 09:50:34 2017
+++ pkgsrc/math/R/distinfo Fri Oct 6 20:47:37 2017
@@ -1,11 +1,12 @@
-$NetBSD: distinfo,v 1.75 2017/03/11 09:50:34 wen Exp $
+$NetBSD: distinfo,v 1.76 2017/10/06 20:47:37 rumko 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 (patch-ac) = 68c1943a352e6f8b2842331578ed746b1ac27bea
SHA1 (patch-ad) = a43b4875a2ee4677b5f762abf3f9a623fd12cbb5
+SHA1 (patch-configure.ac) = c3e77e8f7bf784a269d09c937ab1997ef701aa81
+SHA1 (patch-m4_R.m4) = 704d5514e10adf0b5217bb71b06f44a612eca6e0
SHA1 (patch-src_include_GraphicsBase.h) = eed25eaca982ca76bf75d199dd8bf48be2a99ac5
SHA1 (patch-src_library_stats_src_Makefile.in) = 4eb93292858392792c37a706399e2cef91821bbe
SHA1 (patch-src_main_character.c) = 1271cbd68ec57e28cf6a394398d21d6a18b6760b
Added files:
Index: pkgsrc/math/R/patches/patch-configure.ac
diff -u /dev/null pkgsrc/math/R/patches/patch-configure.ac:1.1
--- /dev/null Fri Oct 6 20:47:37 2017
+++ pkgsrc/math/R/patches/patch-configure.ac Fri Oct 6 20:47:37 2017
@@ -0,0 +1,114 @@
+$NetBSD: patch-configure.ac,v 1.1 2017/10/06 20:47:37 rumko 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
+@@ -33,6 +33,7 @@ m4_define([R_VERSION],
+ AC_INIT([R],[R_VERSION],[https://bugs.r-project.org],[R],[https://www.r-project.org])
+ AC_CONFIG_SRCDIR([src/include/Defn.h])
+ AC_CONFIG_AUX_DIR([tools])
++AC_CONFIG_MACRO_DIR([m4])
+
+ ### * Information on the package.
+
+@@ -290,7 +291,7 @@ AC_ARG_ENABLE([BLAS-shlib],
+
+ ## As from R 3.2.0 split up -L... and -lR
+ if test "${want_R_shlib}" = yes; then
+- LIBR0="-L\$(R_HOME)/lib\$(R_ARCH)"
++ LIBR0="-Wl,-R${prefix}/lib/R/lib\$(R_ARCH) -L\$(R_HOME)/lib\$(R_ARCH)"
+ LIBR1=-lR
+ else
+ LIBR0=
+@@ -689,7 +690,7 @@ case "${host_os}" in
+ ## Not so bad in later versions of Darwin,
+ ## where DYLD_FALLBACK_LIBRARY_PATH is used (see below).
+ ;;
+- *)
++ donotuse*)
+ for arg in ${LDFLAGS}; do
+ case "${arg}" in
+ -L*)
+@@ -1376,7 +1377,7 @@ rm -f libconftest${DYLIB_EXT} conftest.c
+ fpicflags="${darwin_pic}"
+ shlib_cxxldflags="${shlib_ldflags}"
+ ;;
+- freebsd*)
++ freebsd*|dragonfly*)
+ ## maybe this needs to depend on the compiler:
+ ## -export-dynamic used to work, but does not with clang.
+ ## Seems FreeBSD has used the GNU linker since at least 3.0 (Oct 1998)
+@@ -1472,6 +1473,12 @@ rm -f libconftest${DYLIB_EXT} conftest.c
+ ;;
+ netbsd*)
+ ## See the comments about FreeBSD
++ fpicflags="-fPIC"
++ case "${host_cpu}" in
++ powerpc*)
++ cpicflags="-fPIC"
++ ;;
++ esac
+ 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
+ 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.
+- shlib_ldflags="-G"
+- shlib_cxxldflags="-G"
+ if test "${GCC}" = yes; then
++ shlib_ldflags="-shared"
++ shlib_cxxldflags="-shared"
+ cpicflags="-fPIC"
+ ld=`${CC} -print-prog-name=ld`
+ ldoutput=`${ld} -v 2>&1 | grep GNU`
+ if test -n "${ldoutput}"; then
+ main_ldflags="-Wl,-export-dynamic"
+- shlib_ldflags="-shared"
+- shlib_cxxldflags="-shared"
+ else
+ ## it seems gcc c 4.6.2 needs this with Solaris linker
+ shlib_ldflags="-shared"
+ shlib_cxxldflags="-shared"
+ fi
+ else
++ shlib_ldflags="-G"
++ shlib_cxxldflags="-G"
+ 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
+ : ${CPICFLAGS="${cpicflags}"}
+ if test -z "${CPICFLAGS}"; then
+ case "${host_os}" in
+- aix*|irix*|mingw*|osf*)
++ aix*|irix*|mingw*|osf*|darwin*)
+ ;;
+ *)
+ AC_MSG_WARN([I could not determine CPICFLAGS.])
+@@ -1667,10 +1674,10 @@ case "${host_os}" in
+ DYLIB_EXT=".dylib"
+ dylib_ldflags="${darwin_dylib_ldflags}"
+ MAJR_VERSION=`echo "${PACKAGE_VERSION}" | sed -e "s/[[\.]][[1-9]]$/.0/"`
+- LIBR_LDFLAGS="-install_name libR.dylib -compatibility_version ${MAJR_VERSION} -current_version ${PACKAGE_VERSION} -headerpad_max_install_names"
+- RLAPACK_LDFLAGS="-install_name libRlapack.dylib -compatibility_version ${MAJR_VERSION} -current_version ${PACKAGE_VERSION} -headerpad_max_install_names"
++ LIBR_LDFLAGS="-install_name ${PREFIX}/lib/R/lib/libR.dylib -compatibility_version ${MAJR_VERSION} -current_version ${PACKAGE_VERSION} -headerpad_max_install_names"
++ RLAPACK_LDFLAGS="-install_name ${PREFIX}/lib/R/lib/libRlapack.dylib -compatibility_version ${MAJR_VERSION} -current_version ${PACKAGE_VERSION} -headerpad_max_install_names"
+ ## don't use version in libRblas so we can replace it with any BLAS implementation
+- RBLAS_LDFLAGS="-install_name libRblas.dylib -headerpad_max_install_names"
++ RBLAS_LDFLAGS="-install_name ${PREFIX}/lib/R/lib/libRblas.dylib -headerpad_max_install_names"
+ ;;
+ hpux*)
+ ## Needs to avoid embedding a relative path ../../../bin.
+@@ -2582,7 +2589,7 @@ case "${host_os}" in
+ r_ld_library_defaults="/usr/lib64:/lib64:/usr/lib:/lib"
+ ;;
+ solaris*)
+- r_ld_library_defaults="/usr/lib:/lib"
++ r_ld_library_defaults="/usr/lib:/lib:/usr/lib/amd64:/lib/amd64:/usr/lib/64:/lib/64"
+ ;;
+ *)
+ r_ld_library_defaults=
Index: pkgsrc/math/R/patches/patch-m4_R.m4
diff -u /dev/null pkgsrc/math/R/patches/patch-m4_R.m4:1.1
--- /dev/null Fri Oct 6 20:47:37 2017
+++ pkgsrc/math/R/patches/patch-m4_R.m4 Fri Oct 6 20:47:37 2017
@@ -0,0 +1,48 @@
+$NetBSD: patch-m4_R.m4,v 1.1 2017/10/06 20:47:37 rumko Exp $
+
+Ensure tests for clog & co. fail, not just emit warning
+
+--- m4/R.m4.orig 2017-01-05 23:15:05.000000000 +0000
++++ m4/R.m4
+@@ -226,7 +226,7 @@ if test -z "${texi2any_version_maj}" \
+ elif test ${texi2any_version_maj} -gt 5; then
+ r_cv_prog_texi2any_v5=yes
+ elif test ${texi2any_version_maj} -lt 5 \
+- || test ${texi2any_version_min} -lt 1; then
++ || test ${texi2any_version_maj} = 5 -a ${texi2any_version_min} -lt 1; then
+ r_cv_prog_texi2any_v5=no
+ else
+ r_cv_prog_texi2any_v5=yes
+@@ -1015,6 +1015,9 @@ ${F77} ${FFLAGS} -c conftestf.f 1>&AS_ME
+
+ extern void F77_SYMBOL(cftest)(int *a, int *b, double *x, double *y);
+
++int MAIN_ () { return 0; }
++int MAIN__ () { return 0; }
++
+ int main () {
+ int a[3] = {17, 237, 2000000000}, b[2], res = 0;
+ double x[3] = {3.14159265, 123.456789, 2.3e34}, z[3];
+@@ -1107,6 +1110,9 @@ typedef struct {
+
+ extern void F77_SYMBOL(cftest)(Rcomplex *x);
+
++int MAIN_ () { return 0; }
++int MAIN__ () { return 0; }
++
+ int main () {
+ Rcomplex z[3];
+
+@@ -3639,9 +3645,9 @@ R_CHECK_FUNCS([cabs carg cexp clog csqrt
+ AC_DEFUN([R_CHECK_DECL],
+ [AS_VAR_PUSHDEF([ac_Symbol], [ac_cv_have_decl_$1])dnl
+ AC_CACHE_CHECK([whether $1 exists and is declared], ac_Symbol,
+-[AC_LINK_IFELSE([AC_LANG_PROGRAM([AC_INCLUDES_DEFAULT([$4])],
+-[#ifndef $1
+- char *p = (char *) $1;
++[AC_LINK_IFELSE([AC_LANG_PROGRAM([AC_INCLUDES_DEFAULT([$4])
++#ifndef $1
++char *p = (char *) $1;
+ #endif
+ ])],
+ [AS_VAR_SET(ac_Symbol, yes)],
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