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commit: 363526d4663d10660c2c593d11a9ab3707443572 |
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Author: Sergei Trofimovich <slyfox <AT> gentoo <DOT> org> |
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AuthorDate: Mon May 25 10:51:11 2020 +0000 |
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Commit: Sergei Trofimovich <slyfox <AT> gentoo <DOT> org> |
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CommitDate: Mon May 25 10:51:11 2020 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=363526d4 |
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|
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sci-biology/abyss: respect AR override, bug #725300 |
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|
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Use AM_PROG_AR to default to standard AR discovery |
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instead of make's 'ar'. |
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|
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Reported-by: Agostino Sarubbo |
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Closes: https://bugs.gentoo.org/725300 |
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Package-Manager: Portage-2.3.100, Repoman-2.3.22 |
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Signed-off-by: Sergei Trofimovich <slyfox <AT> gentoo.org> |
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|
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sci-biology/abyss/abyss-2.0.3-r1.ebuild | 56 +++++++++++++++++++++++ |
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sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch | 11 +++++ |
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2 files changed, 67 insertions(+) |
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|
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diff --git a/sci-biology/abyss/abyss-2.0.3-r1.ebuild b/sci-biology/abyss/abyss-2.0.3-r1.ebuild |
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new file mode 100644 |
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index 00000000000..6c8571fafa6 |
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--- /dev/null |
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+++ b/sci-biology/abyss/abyss-2.0.3-r1.ebuild |
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@@ -0,0 +1,56 @@ |
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+# Copyright 1999-2020 Gentoo Authors |
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+# Distributed under the terms of the GNU General Public License v2 |
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+ |
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+EAPI=6 |
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+ |
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+inherit autotools toolchain-funcs |
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+ |
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+DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler" |
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+HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/" |
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+SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz" |
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+ |
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+LICENSE="abyss" |
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+SLOT="0" |
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+IUSE="+mpi openmp misc-haskell" |
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+KEYWORDS="~amd64 ~x86" |
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+ |
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+RDEPEND=" |
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+ dev-cpp/sparsehash |
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+ dev-libs/boost:= |
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+ misc-haskell? ( |
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+ dev-libs/gmp:0= |
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+ virtual/libffi:0= |
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+ ) |
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+ mpi? ( sys-cluster/openmpi )" |
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+DEPEND="${RDEPEND} |
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+ misc-haskell? ( |
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+ dev-lang/ghc |
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+ )" |
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+ |
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+PATCHES=("${FILESDIR}"/${PN}-2.0.3-prog-AR.patch) |
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+ |
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+# todo: --enable-maxk=N configure option |
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+# todo: fix automagic mpi toggling |
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+ |
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+pkg_pretend() { |
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+ [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp |
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+} |
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+ |
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+pkg_setup() { |
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+ [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp |
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+} |
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+ |
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+src_prepare() { |
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+ default |
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+ sed -i -e "s/-Werror//" configure.ac || die #365195 |
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+ sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die |
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+ eautoreconf |
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+} |
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+ |
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+src_configure() { |
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+ # disable building haskell tool Misc/samtobreak |
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+ # unless request by user: bug #534412 |
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+ use misc-haskell || export ac_cv_prog_ac_ct_GHC= |
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+ |
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+ econf $(use_enable openmp) |
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+} |
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|
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diff --git a/sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch b/sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch |
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new file mode 100644 |
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index 00000000000..d41c58ad261 |
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--- /dev/null |
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+++ b/sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch |
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@@ -0,0 +1,11 @@ |
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+https://bugs.gentoo.org/725300 |
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+--- a/configure.ac |
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++++ b/configure.ac |
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+@@ -17,6 +17,7 @@ AC_CHECK_TOOL(GHC, ghc) |
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+ AM_CONDITIONAL([HAVE_GHC], ["$GHC" --version]) |
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+ AC_CHECK_PROG(PANDOC, pandoc, yes) |
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+ AM_CONDITIONAL([HAVE_PANDOC], [test x"$PANDOC" = x"yes"]) |
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++AM_PROG_AR |
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+ |
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+ # Checks for header files. |
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+ AC_CHECK_HEADERS([dlfcn.h fcntl.h float.h limits.h \ |