diff options
| -rw-r--r-- | sci-biology/abyss/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/abyss/abyss-2.0.3-r2.ebuild | 64 | ||||
| -rw-r--r-- | sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch | 11 |
3 files changed, 0 insertions, 76 deletions
diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest index 32cead3a3a6e..9c9041e2c936 100644 --- a/sci-biology/abyss/Manifest +++ b/sci-biology/abyss/Manifest @@ -1,2 +1 @@ -DIST abyss-2.0.3.tar.gz 1049144 BLAKE2B 1a320cac735747225723f0d636af435ffcac9efb3273323150f258c0f4c27ed81bb104cb06a726aa664118cc9d2224b745d9deebfcac055face01dae3fc9de15 SHA512 15bc833e89839be89dfa35a23ae22ad0f9a19e8efd36211010c9f59e974de7c569576db36e26d6ab302543ff427604b5efb1b7badf62489a5e82a193ef155570 DIST abyss-2.3.4.tar.gz 3511137 BLAKE2B 2b7449233055d22330f44951f9f6d5ff1a116fa3e19c09c17cd4fa517d2fc055c4f00ccb82c7e09b1b939ac6f7a1caf73cf73c33bd3c8aa9ff11879c227a2aaa SHA512 9d4e418399dd62883b53e831f51a0bd2ba228da73eda6c6459cd729c002eb0487f9613fca1c9bd0f4fbb076eed8a9b952505ee97143ab7dde537c23e4a246cd4 diff --git a/sci-biology/abyss/abyss-2.0.3-r2.ebuild b/sci-biology/abyss/abyss-2.0.3-r2.ebuild deleted file mode 100644 index b9aed09d3eec..000000000000 --- a/sci-biology/abyss/abyss-2.0.3-r2.ebuild +++ /dev/null @@ -1,64 +0,0 @@ -# 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 -> ${P}.tar.gz" - -LICENSE="abyss" -SLOT="0" -IUSE="+mpi openmp misc-haskell" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - dev-cpp/sparsehash - dev-libs/boost:= - misc-haskell? ( - dev-libs/gmp:0= - dev-libs/libffi:0= - ) - mpi? ( sys-cluster/openmpi )" -DEPEND="${RDEPEND} - misc-haskell? ( - dev-lang/ghc - )" - -PATCHES=("${FILESDIR}"/${PN}-2.0.3-prog-AR.patch) - -# GHC uses it's own native code generator. Portage's -# QA check generates false positive because it assumes -# presence of GCC-specific sections. -# -# Workaround false positiove by disabling the check completely. -# bug #677600 -QA_FLAGS_IGNORED='/usr/bin/abyss-samtobreak' - -# 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 $(use_enable openmp) -} diff --git a/sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch b/sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch deleted file mode 100644 index d41c58ad261a..000000000000 --- a/sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch +++ /dev/null @@ -1,11 +0,0 @@ -https://bugs.gentoo.org/725300 ---- a/configure.ac -+++ b/configure.ac -@@ -17,6 +17,7 @@ AC_CHECK_TOOL(GHC, ghc) - AM_CONDITIONAL([HAVE_GHC], ["$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 \ |