commit:     2b34e4019d8a95ce7efd7db67337571a8dfd18be
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Mar  7 12:29:13 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Mar  7 12:29:13 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2b34e401

sci-biology/amos: fix include path from -I$(top_builddir) to -I$(top_builddir)

The include path is wrong when we use separate build directory.

In file included from src/Bambus/Bundler/Utilities_Bundler.cc:4:0:
src/Bambus/Bundler/Utilities_Bundler.hh:16:26: fatal error: Contig_AMOS.hh: No 
such file or directory

https://sourceforge.net/p/amos/mailman/amos-help/thread/197db37d-d83e-1371-022b-2866c5686bd9%40fold.natur.cuni.cz/#msg36246774

Package-Manager: Portage-2.3.24, Repoman-2.3.6

 sci-biology/amos/amos-9999.ebuild                        | 14 +++++++++++++-
 sci-biology/amos/files/amos-9999-fix-include-paths.patch | 13 +++++++++++++
 2 files changed, 26 insertions(+), 1 deletion(-)

diff --git a/sci-biology/amos/amos-9999.ebuild 
b/sci-biology/amos/amos-9999.ebuild
index 97ae851a3..2c911603d 100644
--- a/sci-biology/amos/amos-9999.ebuild
+++ b/sci-biology/amos/amos-9999.ebuild
@@ -3,8 +3,10 @@
 
 EAPI=5
 
+PYTHON_COMPAT=( python2_7 )
+
 PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs
+inherit perl-module eutils toolchain-funcs autotools flag-o-matic 
python-single-r1 qmake-utils
 
 AUTOTOOLS_AUTORECONF=true
 inherit autotools-utils git-r3
@@ -37,6 +39,16 @@ RDEPEND="${DEPEND}
 # ERROR:  Could not open file  LIBGUESTFS_PATH=/usr/share/guestfs/appliance/
 # $
 
+src_prepare() {
+       epatch "${FILESDIR}"/"${P}"-fix-include-paths.patch
+       default
+       eautoreconf
+
+       # prevent GCC 6 log pollution due
+       # to hash_map deprecation in C++11
+       append-cxxflags -Wno-cpp
+}
+
 src_install() {
        default
        python_replicate_script "${ED}"/usr/bin/goBambus2

diff --git a/sci-biology/amos/files/amos-9999-fix-include-paths.patch 
b/sci-biology/amos/files/amos-9999-fix-include-paths.patch
new file mode 100644
index 000000000..a6e8dc9f0
--- /dev/null
+++ b/sci-biology/amos/files/amos-9999-fix-include-paths.patch
@@ -0,0 +1,13 @@
+--- src/Bambus/Bundler/Makefile.am.old 2018-07-03 12:52:17.306095693 +0200
++++ src/Bambus/Bundler/Makefile.am     2018-07-03 12:52:19.506101530 +0200
+@@ -78,8 +78,8 @@
+ ##-- libBundler.a
+ libBundler_a_CPPFLAGS = \
+       $(BOOST_CXXFLAGS)  \
+-      -I$(top_builddir)/src/GNU \
+-      -I$(top_builddir)/src/AMOS
++      -I$(top_srcdir)/src/GNU \
++      -I$(top_srcdir)/src/AMOS
+       ## because some system headers will be built if necessary
+ libBundler_a_LIBADD = \
+       $(LIBOBJS:%=$(top_builddir)/src/GNU/%) \

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