Assert.cc | 2 1 + 1 - 0 !
Assert.h | 2 1 + 1 - 0 !
MultiSequence.cc | 2 1 + 1 - 0 !
ProbModel.cc | 2 1 + 1 - 0 !
4 files changed, 4 insertions(+), 4 deletions(-)

 corrects deprecated conversion from string constant to char*.
License: Use, modify, redistribute under the same terms as Proda iteslf.

Makefile | 12 6 + 6 - 0 !
1 file changed, 6 insertions(+), 6 deletions(-)

 patch for stricter use of cxxflags.
 CXXFLAGS is a "user variable" that can be overriden at compilation time. The
 Debian build system overrides CXXFLAGS, breaking ProDA's build system that
 relies on it to pass -DVERSION="\"1.00\"" to the compiler. This patch replaces
 OTHERFLAGS by CPPFLAGS. This makes sure that -DVERSION="\"1.00\"" is passed to
 the complier for proda as well as all the .o files (build by implicit rule),
 even if CXXFLAGS is overriden. More information on user variables can be found at
 http://www.gnu.org/software/libtool/manual/automake/User-Variables.html#User-Variables
 and http://www.gnu.org/prep/standards/standards.html#Command-Variables
License: Use, modify, redistribute under the same terms as Proda iteslf.

AlignedFragment.cc | 1 1 + 0 - 0 !
AlignedFragment.h | 2 2 + 0 - 0 !
Block.cc | 1 1 + 0 - 0 !
Main.cc | 1 1 + 0 - 0 !
PairAligner.cc | 2 2 + 0 - 0 !
ProbModel.cc | 1 1 + 0 - 0 !
6 files changed, 8 insertions(+)

 patch for compiling with g++-4.3.
 GCC 4.3 has a stricter requirements for the declaration of includes. Without
 this patch, ProDA would not build with g++4.3.
License: Use, modify, redistribute under the same terms as Proda iteslf.

Makefile | 6 3 + 3 - 0 !
1 file changed, 3 insertions(+), 3 deletions(-)

 honour_cxx

Main.cc | 3 2 + 1 - 0 !
1 file changed, 2 insertions(+), 1 deletion(-)

 fix_ftbfs_with_gcc6

Makefile | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 propagate hardening options