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/%) \
