[med-svn] [reapr] 01/04: add patch from Ubuntu

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository reapr.

commit c2169f12d67382dc2b85aa27286d07259175a545
Author: Sascha Steinbiss <satta at debian.org>
Date:   Tue Jul 12 08:25:07 2016 +0000

    add patch from Ubuntu
---
 debian/changelog            |  7 +++++++
 debian/patches/ld_as_needed | 30 ++++++++++++++++++++++++++++++
 debian/patches/series       |  1 +
 3 files changed, 38 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 4e00481..2837ce3 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+reapr (1.0.18+dfsg-3) UNRELEASED; urgency=medium
+
+  * Rearrange linking order to fix FTBFS with ld --as-needed
+    (Thanks to Logan Rosen for the patch from Ubuntu)
+
+ -- Sascha Steinbiss <satta at debian.org>  Tue, 12 Jul 2016 08:23:42 +0000
+
 reapr (1.0.18+dfsg-2) unstable; urgency=medium
 
   * make manpage building reproducible by not using ronn anymore
diff --git a/debian/patches/ld_as_needed b/debian/patches/ld_as_needed
new file mode 100644
index 0000000..0d5a71a
--- /dev/null
+++ b/debian/patches/ld_as_needed
@@ -0,0 +1,30 @@
+Description: rearrange linking order to fix FTBFS with ld --as-needed
+ Thanks to Logan Rosen <logan at ubuntu.com> for the patch.
+Author: Sascha Steinbiss <satta at debian.org>
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -73,7 +73,7 @@
+ 	$(CC) $(CPPFLAGS) $(CFLAGS) -c bam2perfect.cpp
+ 
+ bam2fcdEstimate: bam2fcdEstimate.o $(BAM2FCDESTIMATE_OBJS)
+-	$(CC) $(CPPFLAGS) $(CFLAGS) bam2fcdEstimate.o -lbamtools $(TABIX) $(BAM2FCDESTIMATE_OBJS) -o bam2fcdEstimate $(LDFLAGS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) bam2fcdEstimate.o -lbamtools $(BAM2FCDESTIMATE_OBJS) $(TABIX) -o bam2fcdEstimate $(LDFLAGS)
+ 
+ bam2fcdEstimate.o: bam2fcdEstimate.cpp $(BAM2FCDESTIMATE_OBJS)
+ 	$(CC) $(CPPFLAGS) $(CFLAGS) -c bam2fcdEstimate.cpp
+@@ -109,13 +109,13 @@
+ 	$(CC) $(CPPFLAGS) $(CFLAGS) -c scaff2contig.cpp
+ 
+ task_gapresize: task_gapresize.o $(GAPRESIZE_OBJS)
+-	$(CC) $(CPPFLAGS) $(CFLAGS) task_gapresize.o -lbamtools $(TABIX) $(GAPRESIZE_OBJS) -o task_gapresize $(LDFLAGS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) task_gapresize.o -lbamtools $(GAPRESIZE_OBJS) $(TABIX) -o task_gapresize $(LDFLAGS)
+ 
+ task_gapresize.o: task_gapresize.cpp $(GAPRESIZE_OBJS)
+ 	$(CC) $(CPPFLAGS) $(CFLAGS) -c task_gapresize.cpp
+ 
+ task_fcdrate: task_fcdrate.o $(FCDRATE_OBJS)
+-	$(CC) $(CPPFLAGS) $(CFLAGS) task_fcdrate.o -lbamtools $(TABIX) $(FCDRATE_OBJS) -o task_fcdrate $(LDFLAGS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) task_fcdrate.o $(TABIX) $(FCDRATE_OBJS) -lbamtools -o task_fcdrate $(LDFLAGS)
+ 
+ task_fcdrate.o: task_fcdrate.cpp $(FCDRATE_OBJS)
+ 	$(CC) $(CPPFLAGS) $(CFLAGS) -c task_fcdrate.cpp
diff --git a/debian/patches/series b/debian/patches/series
index ab2bb04..0b9fd0d 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -2,3 +2,4 @@ spelling
 use_shared_libs
 hardening
 fix_sort_samtools13
+ld_as_needed

-- 
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