sci-biology/abyss: respect AR override, bug #725300

Use AM_PROG_AR to default to standard AR discovery
instead of make's 'ar'.

Reported-by: Agostino Sarubbo
Closes: https://bugs.gentoo.org/725300
Package-Manager: Portage-2.3.100, Repoman-2.3.22
Signed-off-by: Sergei Trofimovich <slyfox@gentoo.org>

2 files changed, 67 insertions, 0 deletions

diff --git a/sci-biology/abyss/abyss-2.0.3-r1.ebuild b/sci-biology/abyss/abyss-2.0.3-r1.ebuild
new file mode 100644
index 000000000000..6c8571fafa60
--- /dev/null
+++ b/sci-biology/abyss/abyss-2.0.3-r1.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit autotools toolchain-funcs
+
+DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
+HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"
+SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="abyss"
+SLOT="0"
+IUSE="+mpi openmp misc-haskell"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	dev-cpp/sparsehash
+	dev-libs/boost:=
+	misc-haskell? (
+		dev-libs/gmp:0=
+		virtual/libffi:0=
+	)
+	mpi? ( sys-cluster/openmpi )"
+DEPEND="${RDEPEND}
+	misc-haskell? (
+		dev-lang/ghc
+	)"
+
+PATCHES=("${FILESDIR}"/${PN}-2.0.3-prog-AR.patch)
+
+# todo: --enable-maxk=N configure option
+# todo: fix automagic mpi toggling
+
+pkg_pretend() {
+	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+pkg_setup() {
+	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+src_prepare() {
+	default
+	sed -i -e "s/-Werror//" configure.ac || die #365195
+	sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
+	eautoreconf
+}
+
+src_configure() {
+	# disable building haskell tool Misc/samtobreak
+	# unless request by user: bug #534412
+	use misc-haskell || export ac_cv_prog_ac_ct_GHC=
+
+	econf $(use_enable openmp)
+}
diff --git a/sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch b/sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch
new file mode 100644
index 000000000000..d41c58ad261a
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch
@@ -0,0 +1,11 @@
+https://bugs.gentoo.org/725300
+--- a/configure.ac
++++ b/configure.ac
+@@ -17,6 +17,7 @@ AC_CHECK_TOOL(GHC, ghc)
+ AM_CONDITIONAL([HAVE_GHC], ["$GHC" --version])
+ AC_CHECK_PROG(PANDOC, pandoc, yes)
+ AM_CONDITIONAL([HAVE_PANDOC], [test x"$PANDOC" = x"yes"])
++AM_PROG_AR
+ 
+ # Checks for header files.
+ AC_CHECK_HEADERS([dlfcn.h fcntl.h float.h limits.h \