[med-svn] [phyml] 01/02: Some fixes to build with BEAGLE

[Andreas Tille]

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tille pushed a commit to branch master
in repository phyml.

commit 8bd9d2d07d685677cf8cc511f35fbdec8b80d135
Author: Andreas Tille <tille at debian.org>
Date:   Sat Jun 24 20:59:26 2017 +0200

    Some fixes to build with BEAGLE
---
 debian/patches/beagle.patch | 29 +++++++++++++++++++++++++++++
 debian/patches/series       |  1 +
 debian/rules                |  2 +-
 3 files changed, 31 insertions(+), 1 deletion(-)

diff --git a/debian/patches/beagle.patch b/debian/patches/beagle.patch
new file mode 100644
index 0000000..f05657a
--- /dev/null
+++ b/debian/patches/beagle.patch
@@ -0,0 +1,29 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sat, 24 Jun 2017 15:29:56 +0200
+Description: Fix some issues when linking against beagle
+
+--- a/src/utilities.c
++++ b/src/utilities.c
+@@ -6204,7 +6204,10 @@ void Swap_Partial_Lk(t_edge *a, t_edge *
+   int *buff_p_lk_loc, *buff_patt_id;
+   phydbl *buff_p_lk_tip;
+   int *buff_ui;
+-  
++
++#ifdef BEAGLE
++  int temp;
++#endif
+   
+   if(side_a == LEFT && side_b == LEFT)
+     {
+--- a/src/beagle_utils.c
++++ b/src/beagle_utils.c
+@@ -53,7 +53,7 @@ void print_beagle_flags(long inFlags) {
+     if (inFlags & BEAGLE_FLAG_SCALING_ALWAYS)     fprintf(stdout, " SCALING_ALWAYS");
+     if (inFlags & BEAGLE_FLAG_SCALING_DYNAMIC)    fprintf(stdout, " SCALING_DYNAMIC");
+     if (inFlags & BEAGLE_FLAG_SCALERS_RAW)        fprintf(stdout, " SCALERS_RAW");
+-    if (inFlags & BEAGLE_FLAG_SCALERS_log)        fprintf(stdout, " SCALERS_log");
++    if (inFlags & BEAGLE_FLAG_SCALERS_LOG)        fprintf(stdout, " SCALERS_LOG");
+     if (inFlags & BEAGLE_FLAG_VECTOR_NONE)        fprintf(stdout, " VECTOR_NONE");
+     if (inFlags & BEAGLE_FLAG_VECTOR_SSE)         fprintf(stdout, " VECTOR_SSE");
+     if (inFlags & BEAGLE_FLAG_VECTOR_AVX)         fprintf(stdout, " VECTOR_AVX");
diff --git a/debian/patches/series b/debian/patches/series
index 145a00f..bea959f 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -4,3 +4,4 @@ no-configure-ac-date.patch
 fix_declaration_of_temp.patch
 # fix_wrong_initialisation_of_array.patch
 gcc-7.patch
+beagle.patch
diff --git a/debian/rules b/debian/rules
index a5d1ebd..39e99cc 100755
--- a/debian/rules
+++ b/debian/rules
@@ -29,7 +29,7 @@ override_dh_auto_build:
 ifeq ($(BUILDARCH),$(filter $(BUILDARCH), amd64 i386 arm64 armhf))
 	$(MAKE) distclean
 	dh_auto_configure -- --enable-beagle
-	dh_auto_build -- LDFLAGS="$(LDFLAGS)"
+	dh_auto_build -- CFLAGS="$(CFLAGS) -I/usr/include/libhmsbeagle-1 -DBEAGLE" LDFLAGS="$(LDFLAGS)"
 	# move phyml binary to temporary dir inside debian/
 	mkdir -p $(CURDIR)/debian/$(PKGBEAGLE)/usr/lib/phyml/bin
 	mv src/phyml-beagle $(CURDIR)/debian/$(PKGBEAGLE)/usr/lib/phyml/bin

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