[med-svn] [SCM] jellyfish branch, master, updated. upstream/1.1.2-10-g8607d56

[Andreas Tille]

The following commit has been merged in the master branch:
commit db8d6100b5480c7641d48e1a6990759fcb2be876
Author: Andreas Tille <tille at debian.org>
Date:   Sat Mar 31 08:30:31 2012 +0200

    Due to the use of hardening flags warnings about unused-but-set-variable becomes an error - start working on a patch

diff --git a/debian/changelog b/debian/changelog
index ea2bd1e..30b4afd 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -4,8 +4,11 @@ jellyfish (1.1.4-1) UNRELEASED; urgency=low
   * debian/patches/ptrdiff_t: Removed because applied upstream
   * debian/patches/cmdline: Removed because upstream code was changed
     in a way that it becomes superflous
+  * debian/patches/fix-unused-but-set-variable.patch: Due to the use
+    of hardening flags warnings about unused-but-set-variable becomes
+    an error - start working on a patch
 
- -- Andreas Tille <tille at debian.org>  Sat, 31 Mar 2012 00:25:12 +0200
+ -- Andreas Tille <tille at debian.org>  Sat, 31 Mar 2012 08:28:08 +0200
 
 jellyfish (1.1.2-1) unstable; urgency=low
 
diff --git a/debian/patches/fix-unused-but-set-variable.patch b/debian/patches/fix-unused-but-set-variable.patch
new file mode 100644
index 0000000..7786428
--- /dev/null
+++ b/debian/patches/fix-unused-but-set-variable.patch
@@ -0,0 +1,23 @@
+--- jellyfish.orig/unit_tests/test_offsets_key_value.cc
++++ jellyfish/unit_tests/test_offsets_key_value.cc
+@@ -38,7 +38,7 @@
+   uint_t                             lk_len = 4;
+   uint_t                             lv_len = kv_len - lk_len;
+   uint_t                             i      = 0;
+-  uint64_t                          *w, *pw;
++  // uint64_t                          *w, *pw;
+   
+   //   /* Still missing:
+   //    * - testing of value masks
+@@ -47,9 +47,9 @@
+   EXPECT_EQ(lv_len, this->offsets.get_lval_len());
+   
+   for(i = 0; true; i++) {
+-    w = this->offsets.get_word_offset(i, &it, &lit, NULL);
++    /* w = */ this->offsets.get_word_offset(i, &it, &lit, NULL);
+     if(i > 0) {
+-      pw = this->offsets.get_word_offset(i-1, &pit, &lpit, NULL);
++      /* pw = */ this->offsets.get_word_offset(i-1, &pit, &lpit, NULL);
+       
+       uint_t noff = pit->key.boff + kv_len;
+       if(noff > 64) {
diff --git a/debian/patches/series b/debian/patches/series
index 2a3700c..2ed35fb 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
 man
+fix-unused-but-set-variable.patch

-- 
count k-mers of DNA