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

diff --git a/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild b/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild
index 3e89f70a498eecf40344755356613f1c000ef715..89f8484fad6a63655f125ad315c0d7cd079397f9 100644 (file)
--- 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 (file)
index 0000000..42a906e
--- /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"
+