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| author |   Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> | 2018-09-11 16:09:28 +0200 |
|---|---|---|
| committer | Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> | 2018-09-11 16:09:28 +0200 |
| commit | 5e6e183d8bca94b14d155524d8feeaaf4286e7dd (patch) | |
| tree | 06ad1aaef68fc427f282e0b62e755c94e7099730 /sci-biology/amos/amos-3.1.0-r2.ebuild | |
| parent | sci-biology/jellyfish: remove doubled econf call (diff) | |
| download | sci-5e6e183d8bca94b14d155524d8feeaaf4286e7dd.tar.gz sci-5e6e183d8bca94b14d155524d8feeaaf4286e7dd.tar.bz2 sci-5e6e183d8bca94b14d155524d8feeaaf4286e7dd.zip | |
sci-biology/amos: adjust to SLOTed jellyfish and drop qt4
Jellyfish resides in ${EPREFIX}/usr/include/jellyfish1/ now.
The package needed qt4 with qt3support enabled to compile
hawkeye utility. Let's try with qt5 core only.
Also enabling compilation of all utilities if they pass
configure checks.
Currently, jellyfish linking fails with some cxx linking error,
maybe my -lm or -lpthreads needs to be recompiled with gcc-8.2.0
too? Also, boot is somehow not picked up.
Bug: https://bugs.gentoo.org/show_bug.cgi?id=663110
Package-Manager: Portage-2.3.48, Repoman-2.3.10
Diffstat (limited to 'sci-biology/amos/amos-3.1.0-r2.ebuild')
| -rw-r--r-- | sci-biology/amos/amos-3.1.0-r2.ebuild | 20 |
1 files changed, 15 insertions, 5 deletions
diff --git a/sci-biology/amos/amos-3.1.0-r2.ebuild b/sci-biology/amos/amos-3.1.0-r2.ebuild index d4107d509..951f12c1b 100644 --- a/sci-biology/amos/amos-3.1.0-r2.ebuild +++ b/sci-biology/amos/amos-3.1.0-r2.ebuild @@ -16,13 +16,12 @@ SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" LICENSE="Artistic" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="mpi qt4" +IUSE="mpi qt5" DEPEND=" mpi? ( virtual/mpi ) dev-libs/boost - qt4? ( dev-qt/qtcore:4[qt3support] - dev-qt/qt3support:4 ) + qt5? ( dev-qt/qtcore:5 ) sci-biology/blat sci-biology/jellyfish:1" RDEPEND="${DEPEND} @@ -36,13 +35,24 @@ MAKEOPTS+=" -j1" src_prepare() { epatch \ "${FILESDIR}"/${P}-gcc-4.7.patch \ - "${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch + "${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch \ + "${FILESDIR}"/${P}-rename_to_jellyfish1.patch # $ gap-links # ERROR: Could not open file LIBGUESTFS_PATH=/usr/share/guestfs/appliance/ # $ + sh ./bootstrap || die + default + eautoreconf + # prevent GCC 6 log pollution due to hash_map deprecation in C++11 + # shutdown gcc-8.2.0 messages too + append-cxxflags -Wno-cpp -Wno-narrowing } -# --with-jellyfish location of Jellyfish headers +src_configure() { + local myconf + use X && myconf+=( --with-x ) + econf ${myconf[@]} --with-jellyfish="${EPREFIX}"/usr/include --with-Boost-dir="${EPREFIX}"/usr/include --with-qmake-qt4=qmake --enable-all +} src_install() { default |