commit: 363526d4663d10660c2c593d11a9ab3707443572 Author: Sergei Trofimovich <slyfox <AT> gentoo <DOT> org> AuthorDate: Mon May 25 10:51:11 2020 +0000 Commit: Sergei Trofimovich <slyfox <AT> gentoo <DOT> org> CommitDate: Mon May 25 10:51:11 2020 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=363526d4
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 <AT> gentoo.org> sci-biology/abyss/abyss-2.0.3-r1.ebuild | 56 +++++++++++++++++++++++ sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch | 11 +++++ 2 files changed, 67 insertions(+) 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 00000000000..6c8571fafa6 --- /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 $(use_enable openmp) +} diff --git a/sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch b/sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch new file mode 100644 index 00000000000..d41c58ad261 --- /dev/null +++ b/sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch @@ -0,0 +1,11 @@ +https://bugs.gentoo.org/725300 +--- a/configure.ac ++++ b/configure.ac +@@ -17,6 +17,7 @@ AC_CHECK_TOOL(GHC, ghc) + AM_CONDITIONAL([HAVE_GHC], ["$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 \
