math/R: better fix for fbsd

Also move fixes from configure to configure.ac
m4/R.m4 fix by @joerg

Oked @joerg

5 files changed, 170 insertions, 228 deletions

diff --git a/math/R/Makefile b/math/R/Makefile
index 32002455ac0..c5a5d85a1a6 100644
--- a/math/R/Makefile
+++ b/math/R/Makefile
@@ -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>=1.0.5
 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 ${OPSYS} == "Darwin"
 .PHONY: fix-darwin-install-name
diff --git a/math/R/distinfo b/math/R/distinfo
index 18837d41151..184b807d56b 100644
--- a/math/R/distinfo
+++ b/math/R/distinfo
@@ -1,11 +1,12 @@
-$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
diff --git a/math/R/patches/patch-ac b/math/R/patches/patch-ac
deleted file mode 100644
index c55f7ddcdf4..00000000000
--- a/math/R/patches/patch-ac
+++ /dev/null
@@ -1,221 +0,0 @@
-$NetBSD: patch-ac,v 1.39 2016/07/26 04:53:33 wen Exp $
-
-Do not include system paths in R_LD_LIBRARY_PATH.
-FreeBSD 10 is not FreeBSD 1.
-Fix texi2any version check.
-
---- configure.orig	2016-07-26 00:32:06.000000000 +0000
-+++ configure
-@@ -3896,7 +3896,7 @@ fi
- 
- ## 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=
-@@ -5076,7 +5076,7 @@ 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 ${texi2any_version_min} -lt 1; then
-   r_cv_prog_texi2any_v5=no
- else
-   r_cv_prog_texi2any_v5=yes
-@@ -22376,7 +22376,7 @@ case "${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*)
-@@ -24958,6 +24958,11 @@ fi
- 	  done
- 	  ;;
- 	-[lLR]*)
-+           case $ac_arg in
-+           -R*)
-+               ac_arg="${wl}$ac_arg"
-+               ;;
-+           esac
- 	    ac_exists=false
-   for ac_i in $ac_cv_f77_libs; do
-     if test x"$ac_arg" = x"$ac_i"; then
-@@ -25923,6 +25928,9 @@ cat > conftest.c <<EOF
- 
- 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];
-@@ -26018,6 +26026,9 @@ typedef struct {
- 
- extern void F77_SYMBOL(cftest)(Rcomplex *x);
- 
-+int MAIN_ () { return 0; }
-+int MAIN__ () { return 0; }
-+
- int main () {
-     Rcomplex z[3];
- 
-@@ -28175,7 +28186,7 @@ $as_echo "$as_me: WARNING: Use of flat n
-     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)
-@@ -28271,6 +28282,12 @@ $as_echo "$as_me: WARNING: Use of flat n
-     ;;
-   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"
-@@ -28313,22 +28330,22 @@ $as_echo "$as_me: WARNING: Use of flat n
-   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.
-@@ -28389,7 +28406,7 @@ fi
- : ${CPICFLAGS="${cpicflags}"}
- if test -z "${CPICFLAGS}"; then
-   case "${host_os}" in
--    aix*|irix*|mingw*|osf*)
-+    aix*|irix*|mingw*|osf*|darwin*)
-       ;;
-     *)
-       { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: I could not determine CPICFLAGS." >&5
-@@ -28489,10 +28506,10 @@ 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.
-@@ -29106,6 +29123,14 @@ _ACEOF
- ## Cygwin had rintl but not nearbyintl
- for ac_func in expm1 hypot log1p log1pl log2 log10 nearbyint nearbyintl powl rint rintl
- do
-+case $ac_func in
-+expm1|log1p|log2|log10|nearbyint|nearbyintl|rint|rintl)
-+    args="x"
-+    ;;
-+hypot|powl)
-+    args="x,x"
-+    ;;
-+esac
- as_ac_Symbol=`$as_echo "ac_cv_have_decl_$ac_func" | $as_tr_sh`
- { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $ac_func exists and is declared" >&5
- $as_echo_n "checking whether $ac_func exists and is declared... " >&6; }
-@@ -29115,24 +29140,12 @@ else
-   cat confdefs.h - <<_ACEOF >conftest.$ac_ext
- /* end confdefs.h.  */
- #include <math.h>
-+volatile long double x;
- 
--#ifdef F77_DUMMY_MAIN
--
--#  ifdef __cplusplus
--     extern "C"
--#  endif
--   int F77_DUMMY_MAIN() { return 1; }
--
--#endif
- int
- main ()
- {
--#ifndef $ac_func
--  char *p = (char *) $ac_func;
--#endif
--
--  ;
--  return 0;
-+  return $ac_func($args);;;
- }
- _ACEOF
- if ac_fn_c_try_link "$LINENO"; then :
-@@ -32092,6 +32105,14 @@ cat > conftest.c <<EOF
- # define F77_SYMBOL(x)   x
- #endif
- extern void F77_SYMBOL(test1)(int *iflag);
-+ifdef F77_DUMMY_MAIN
-+
-+#  ifdef __cplusplus
-+     extern "C"
-+#  endif
-+   int F77_DUMMY_MAIN() { return 1; }
-+
-+#endif
- 
- int main () {
-   int iflag;
-@@ -32157,6 +32178,15 @@ else
- #else
- # define F77_SYMBOL(x)   x
- #endif
-+#ifdef F77_DUMMY_MAIN
-+
-+#  ifdef __cplusplus
-+     extern "C"
-+#  endif
-+   int F77_DUMMY_MAIN() { return 1; }
-+
-+#endif
-+
- void F77_SYMBOL(xerbla)(char *srname, int *info)
- {}
- void blas_set () {
-@@ -41516,7 +41546,7 @@ case "${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=
diff --git a/math/R/patches/patch-configure.ac b/math/R/patches/patch-configure.ac
new file mode 100644
index 00000000000..86fa6ec0ebd
--- /dev/null
+++ b/math/R/patches/patch-configure.ac
@@ -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=
diff --git a/math/R/patches/patch-m4_R.m4 b/math/R/patches/patch-m4_R.m4
new file mode 100644
index 00000000000..579988965f2
--- /dev/null
+++ b/math/R/patches/patch-m4_R.m4
@@ -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)],