[med-svn] [jellyfish] 01/02: enable build with c++11 and -Werror=deprecated-declarations compile flag

[Andreas Tille]

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tille pushed a commit to branch master
in repository jellyfish.

commit c8738f4c35ab151367cf038c7fef9fd589f84d42
Author: Andreas Tille <tille at debian.org>
Date:   Wed Dec 23 21:05:50 2015 +0100

    enable build with c++11 and -Werror=deprecated-declarations compile flag
---
 debian/changelog                                   |  8 +++++
 ...nable_c++11_error_deprecated-declarations.patch | 42 ++++++++++++++++++++++
 debian/patches/series                              |  1 +
 3 files changed, 51 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 40bd357..841744a 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+jellyfish (2.2.4-2) UNRELEASED; urgency=medium
+
+  * enable build with c++11 and -Werror=deprecated-declarations compile
+    flag (thanks for the hint to Gert Wollny)
+    Closes: #808537
+
+ -- Andreas Tille <tille at debian.org>  Wed, 23 Dec 2015 21:05:08 +0100
+
 jellyfish (2.2.4-1) unstable; urgency=medium
 
   * New upstream version
diff --git a/debian/patches/enable_c++11_error_deprecated-declarations.patch b/debian/patches/enable_c++11_error_deprecated-declarations.patch
new file mode 100644
index 0000000..b64973c
--- /dev/null
+++ b/debian/patches/enable_c++11_error_deprecated-declarations.patch
@@ -0,0 +1,42 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 23 Dec 2015 21:01:45 +0100
+Bug-Debian: https://bugs.debian.org/808537
+Description: enable build with c++11 and -Werror=deprecated-declarations compile
+ flag (thanks for the hint to Gert Wollny at
+   https://lists.debian.org/debian-mentors/2015/12/msg00360.html
+ )
+
+
+--- a/jellyfish/merge_files.cc
++++ b/jellyfish/merge_files.cc
+@@ -35,8 +35,8 @@ using jellyfish::file_header;
+ using jellyfish::RectangularBinaryMatrix;
+ using jellyfish::mer_dna;
+ using jellyfish::cpp_array;
+-typedef std::auto_ptr<binary_reader> binary_reader_ptr;
+-typedef std::auto_ptr<text_reader> text_reader_ptr;
++typedef std::unique_ptr<binary_reader> binary_reader_ptr;
++typedef std::unique_ptr<text_reader> text_reader_ptr;
+ 
+ struct file_info {
+   std::ifstream is;
+@@ -47,7 +47,7 @@ struct file_info {
+   header(is)
+   { }
+ };
+-typedef std::auto_ptr<RectangularBinaryMatrix> matrix_ptr;
++typedef std::unique_ptr<RectangularBinaryMatrix> matrix_ptr;
+ 
+ template<typename reader_type, typename writer_type>
+ void do_merge(cpp_array<file_info>& files, std::ostream& out, writer_type& writer,
+--- a/sub_commands/count_main.cc
++++ b/sub_commands/count_main.cc
+@@ -245,7 +245,7 @@ int count_main(int argc, char *argv[])
+   if(args.disk_flag)
+     ary.do_size_doubling(false);
+ 
+-  std::auto_ptr<jellyfish::dumper_t<mer_array> > dumper;
++  std::unique_ptr<jellyfish::dumper_t<mer_array> > dumper;
+   if(args.text_flag)
+     dumper.reset(new text_dumper(args.threads_arg, args.output_arg, &header));
+   else
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..7837bcd
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+enable_c++11_error_deprecated-declarations.patch

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