[med-svn] [dnaclust] 01/04: fix building with GCC 6

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository dnaclust.

commit d7b4fbe38bea6594ca7696688271e8474a014e00
Author: Sascha Steinbiss <satta at debian.org>
Date:   Sun Jul 17 10:14:32 2016 +0000

    fix building with GCC 6
---
 debian/changelog                     |  8 ++++++++
 debian/patches/build_with_gcc6.patch | 23 +++++++++++++++++++++++
 debian/patches/series                |  1 +
 3 files changed, 32 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 6d4b110..12cb5e3 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+dnaclust (3-4) unstable; urgency=medium
+
+  * Team upload.
+  * Fix building with GCC 6.
+    Closes: #831193.
+
+ -- Sascha Steinbiss <satta at debian.org>  Sun, 17 Jul 2016 10:13:26 +0000
+
 dnaclust (3-3) unstable; urgency=medium
 
   * Fix Vcs fields
diff --git a/debian/patches/build_with_gcc6.patch b/debian/patches/build_with_gcc6.patch
new file mode 100644
index 0000000..5a42e00
--- /dev/null
+++ b/debian/patches/build_with_gcc6.patch
@@ -0,0 +1,23 @@
+Description: allow building with GCC 6
+Author: Sascha Steinbiss <satta at debian.org>
+--- a/Makefile
++++ b/Makefile
+@@ -1,6 +1,6 @@
+ #PROFILE_FLAGS = -pg -fprofile-arcs -ftest-coverage -g -O1
+ CXXFLAGS += -Wall -pedantic -std=c++98 -O2
+-CXX = g++ 
++CXX ?= g++
+ #-DCHRIS_DEBUG
+ 
+ all: dnaclust fastaselect fastasort
+--- a/dnaclust.cpp
++++ b/dnaclust.cpp
+@@ -1769,7 +1769,7 @@
+       for (sequence::Fasta::const_iterator i = inputFasta.begin(); i != inputFasta.end(); ++i)
+ 	sizes.push_back(i->sequence.length());
+       size_t median_size = *median(sizes.begin(), sizes.end());
+-      k_mer_length = static_cast<int>(floor(log(median_size) / log(NUMBER_OF_NUCLEOTIDES)));
++      k_mer_length = static_cast<int>(floor(log(median_size) / log((double) NUMBER_OF_NUCLEOTIDES)));
+     }
+ 
+     // Initializing this at the beginning is crucial.
diff --git a/debian/patches/series b/debian/patches/series
index febaaec..686d61d 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
 fix_shel_path.patch
 do_not_staically_linking.patch
 resolve_name_space_conflict_fastasort.patch
+build_with_gcc6.patch

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