[med-svn] [sga] 01/03: d/p/0007: Add patch to fix compilation with gcc-6

[Gert Wollny]

This is an automated email from the git hooks/post-receive script.

gert-guest pushed a commit to branch debian/unstable
in repository sga.

commit 5f4b91ec982914bdf9e57b2853dc2f35d290000e
Author: Gert Wollny <gw.fossdev at gmail.com>
Date:   Tue Jul 5 14:05:29 2016 +0000

    d/p/0007: Add patch to fix compilation with gcc-6
---
 debian/changelog                    |  7 +++++
 debian/patches/0007-fix-gcc-6.patch | 57 +++++++++++++++++++++++++++++++++++++
 debian/patches/series               |  1 +
 3 files changed, 65 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 5681ee7..8e72bba 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+sga (0.10.14-2) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * d/p/0007: Fix compilation with gcc-6, Closes:  #811664
+
+ -- Gert Wollny <gw.fossdev at gmail.com>  Tue, 05 Jul 2016 14:01:46 +0000
+
 sga (0.10.14-1) unstable; urgency=medium
 
   * New upstream version
diff --git a/debian/patches/0007-fix-gcc-6.patch b/debian/patches/0007-fix-gcc-6.patch
new file mode 100644
index 0000000..6cf498f
--- /dev/null
+++ b/debian/patches/0007-fix-gcc-6.patch
@@ -0,0 +1,57 @@
+Author: Matei David <matei at cs.toronto.edu>
+Date: Wed, 3 Feb 2016 23:28:04 -0500
+Bug-Debian: https://bugs.debian.org/811664
+Description: Fix compilation with gcc-6 (i.e. -std >= c++11)
+
+diff --git a/src/SGA/rmdup.cpp b/src/SGA/rmdup.cpp
+index cc7727d..5abe0a1 100644
+--- a/src/SGA/rmdup.cpp
++++ b/src/SGA/rmdup.cpp
+@@ -232,7 +232,7 @@ std::string parseDupHits(const StringVector& hitsFilenames, const std::string& o
+     while(!done)
+     {
+         // Parse a line from the current file
+-        bool valid = getline(*reader_vec[currReaderIdx], line);
++        bool valid = static_cast<bool>(getline(*reader_vec[currReaderIdx], line));
+         ++numRead;
+         // Deal with switching the active reader and the end of files
+         if(!valid || numRead == buffer_size)
+diff --git a/src/SuffixTools/STCommon.h b/src/SuffixTools/STCommon.h
+index 13e0769..38d2be5 100644
+--- a/src/SuffixTools/STCommon.h
++++ b/src/SuffixTools/STCommon.h
+@@ -96,7 +96,7 @@ struct SAElem
+         // Masks
+         static const uint8_t ID_BITS = 36; // Allows up to 68 billion IDs
+         static const uint8_t POS_BITS = 64 - ID_BITS;
+-        static const uint64_t HIGH_MASK = ~0 << POS_BITS;
++        static const uint64_t HIGH_MASK = ~0llu << POS_BITS;
+         static const uint64_t LOW_MASK = ~HIGH_MASK;
+ };
+ 
+diff --git a/src/Util/ClusterReader.cpp b/src/Util/ClusterReader.cpp
+index 5c9460b..6b626e3 100644
+--- a/src/Util/ClusterReader.cpp
++++ b/src/Util/ClusterReader.cpp
+@@ -67,7 +67,7 @@ bool ClusterReader::generate(ClusterVector& out)
+ bool ClusterReader::readCluster(ClusterRecord& record)
+ {
+     std::string line;
+-    bool good = getline(*m_pReader, line);
++    bool good = static_cast<bool>(getline(*m_pReader, line));
+     if(!good || line.empty())
+         return false;
+     std::stringstream parser(line);
+diff --git a/src/Util/StdAlnTools.cpp b/src/Util/StdAlnTools.cpp
+index b6441eb..7e72101 100644
+--- a/src/Util/StdAlnTools.cpp
++++ b/src/Util/StdAlnTools.cpp
+@@ -119,7 +119,7 @@ std::string StdAlnTools::expandCigar(const std::string& cigar)
+     char code;
+     while(parser >> length)
+     {
+-        bool success = parser >> code;
++        bool success = static_cast<bool>(parser >> code);
+         expanded.append(length, code);
+         assert(success);
+         (void)success;
diff --git a/debian/patches/series b/debian/patches/series
index 39bef58..f69845a 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -4,3 +4,4 @@
 0004-Add-help-to-sga-bam2de.pl.patch
 0005-Remove-extensions-on-scripts-we-ship.patch
 0006-remove-google-addsense.patch
+0007-fix-gcc-6.patch

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/sga.git