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| author |   David Seifert <soap@gentoo.org> | 2017-09-16 12:54:51 +0200 |
|---|---|---|
| committer | David Seifert <soap@gentoo.org> | 2017-09-16 12:58:20 +0200 |
| commit | e8f6a4c4f1b147290aa62ef45d58084394ae56bd (patch) | |
| tree | b8938d20cab085929c164e9c7889dfa66a1672b4 /sci-biology | |
| parent | app-editors/sublime-text: Version bump to final 3.0 release (diff) | |
| download | gentoo-e8f6a4c4f1b147290aa62ef45d58084394ae56bd.tar.gz gentoo-e8f6a4c4f1b147290aa62ef45d58084394ae56bd.tar.bz2 gentoo-e8f6a4c4f1b147290aa62ef45d58084394ae56bd.zip | |
sci-biology/cufflinks: Fix boost TR1 header include
* Also fix missing python dependencies
Closes: https://bugs.gentoo.org/630654
Package-Manager: Portage-2.3.8, Repoman-2.3.3
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild | 35 | ||||
| -rw-r--r-- | sci-biology/cufflinks/files/cufflinks-2.2.1-boost-1.65-tr1-removal.patch | 14 |
2 files changed, 39 insertions, 10 deletions
diff --git a/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild b/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild index 3e89f70a498e..89f8484fad6a 100644 --- a/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild +++ b/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild @@ -3,37 +3,52 @@ EAPI=6 -inherit autotools flag-o-matic toolchain-funcs +PYTHON_COMPAT=( python2_7 ) + +inherit autotools flag-o-matic python-single-r1 toolchain-funcs DESCRIPTION="Transcript assembly and differential expression/regulation for RNA-Seq" HOMEPAGE="http://cufflinks.cbcb.umd.edu/" SRC_URI="http://cufflinks.cbcb.umd.edu/downloads/${P}.tar.gz" -SLOT="0" LICENSE="Artistic" -IUSE="debug" +SLOT="0" KEYWORDS="~amd64 ~x86" +IUSE="debug" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" -DEPEND="sci-biology/samtools:0.1-legacy - >=dev-libs/boost-1.59.0:= - dev-cpp/eigen:3" -RDEPEND="${DEPEND}" +RDEPEND=" + sci-biology/samtools:0.1-legacy + >=dev-libs/boost-1.62.0:= + ${PYTHON_DEPS}" +DEPEND=" + ${RDEPEND} + dev-cpp/eigen:3 + virtual/pkgconfig" PATCHES=( "${FILESDIR}"/${P}-samtools-legacy.patch "${FILESDIR}"/${P}-flags.patch "${FILESDIR}"/${P}-gcc6.patch + "${FILESDIR}"/${P}-boost-1.65-tr1-removal.patch ) src_prepare() { default + python_fix_shebang src/cuffmerge + eautoreconf - append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3) } src_configure() { - econf --disable-optim \ + # keep in sync with Boost + append-cxxflags -std=c++14 + append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3) + + econf \ + --disable-optim \ --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)/" \ --with-bam="${EPREFIX}/usr/" \ - $(use_enable debug) + $(use_enable debug) \ + PYTHON="${PYTHON}" } diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-boost-1.65-tr1-removal.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-boost-1.65-tr1-removal.patch new file mode 100644 index 000000000000..42a906e7a83a --- /dev/null +++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-boost-1.65-tr1-removal.patch @@ -0,0 +1,14 @@ +Boost 1.65 removed the TR1 headers. +Bug: https://bugs.gentoo.org/show_bug.cgi?id=630654 + +--- a/src/biascorrection.h ++++ b/src/biascorrection.h +@@ -15,7 +15,7 @@ + #include <vector> + #include <list> + #include <string> +-#include <boost/tr1/unordered_map.hpp> ++#include <boost/unordered_map.hpp> + #include <boost/thread.hpp> + #include "common.h" + |