commit: 95f436ca3a6e4e65e9db762b7d0da99172593042 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sun Sep 25 12:26:00 2016 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sun Sep 25 12:26:47 2016 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=95f436ca
sci-biology/tophat: USE="threads" dep on dev-libs/boost Gentoo-bug: 594810 * Remove autoconf macros from archive, depend on sys-devel/autoconf instead for the latest versions. Package-Manager: portage-2.3.1 .../tophat-2.1.1-unbundle-seqan-samtools.patch | 60 +++++++++++++++++++--- ...phat-2.1.1-r1.ebuild => tophat-2.1.1-r2.ebuild} | 9 +++- 2 files changed, 61 insertions(+), 8 deletions(-) diff --git a/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch b/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch index c1e8bfd..9d0a269 100644 --- a/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch +++ b/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch @@ -1,9 +1,25 @@ Unbundle the included samtools and SeqAn, and use system libraries. See also: https://bugs.gentoo.org/show_bug.cgi?id=566494 ---- tophat-2.1.1/configure.ac -+++ tophat-2.1.1/configure.ac -@@ -38,16 +38,6 @@ +Remove ancient ax_boost_base.m4 and ax_boost_thread.m4, and depend +on >=sys-devel/autoconf-archive-2016.09.16 in the ebuild instead. +See also: https://bugs.gentoo.org/show_bug.cgi?id=594810 + +--- a/configure.ac ++++ b/configure.ac +@@ -28,26 +28,15 @@ + AC_PROG_INSTALL + AM_PATH_PYTHON([2.4]) + +-m4_include([ax_boost_base.m4]) +-m4_include([ax_boost_thread.m4]) + # CXXFLAGS="$CXXFLAGS $threadLib" + AX_BOOST_BASE([1.38.0]) ++AX_BOOST_SYSTEM + AX_BOOST_THREAD +-if test -z "$BOOST_THREAD_LIBS"; then ++if test -z "$BOOST_THREAD_LIB"; then + AC_MSG_ERROR([boost.thread not found. Aborting.]) fi @@ -20,7 +36,7 @@ See also: https://bugs.gentoo.org/show_bug.cgi?id=566494 # Checks for header files. AC_CHECK_HEADERS([stdlib.h string.h unistd.h]) -@@ -80,32 +70,23 @@ +@@ -80,32 +69,23 @@ # set CFLAGS and CXXFLAGS #user_CFLAGS="${CXXFLAGS}" user_CFLAGS=${CFLAGS} @@ -55,8 +71,17 @@ See also: https://bugs.gentoo.org/show_bug.cgi?id=566494 LDFLAGS="$BAM_LDFLAGS $BOOST_LDFLAGS $user_LDFLAGS" AM_INIT_AUTOMAKE([-Wall foreign tar-pax foreign]) ---- tophat-2.1.1/src/Makefile.am -+++ tophat-2.1.1/src/Makefile.am +@@ -122,7 +102,7 @@ + -- ${PACKAGE_STRING} Configuration Results -- + C++ compiler: ${CXX} ${CXXFLAGS} + Linker flags: ${LDFLAGS} +- BOOST libraries: ${BOOST_THREAD_LIBS}" ++ BOOST libraries: ${BOOST_THREAD_LIB}" + + if test x"${GCC}" = x"yes" ; then + gcc_version=`${CC} --version | head -n 1` +--- a/src/Makefile.am ++++ b/src/Makefile.am @@ -683,17 +683,12 @@ SeqAn-1.4.2/seqan/system/system_thread.h \ SeqAn-1.4.2/seqan/version.h @@ -96,6 +121,29 @@ See also: https://bugs.gentoo.org/show_bug.cgi?id=566494 noinst_HEADERS = \ reads.h \ +@@ -801,11 +793,11 @@ + prep_reads_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) + + segment_juncs_SOURCES = segment_juncs.cpp +-segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB) ++segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) + segment_juncs_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) $(BOOST_LDFLAGS) + + long_spanning_reads_SOURCES = long_spanning_reads.cpp +-long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB) ++long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) + long_spanning_reads_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) $(BOOST_LDFLAGS) + + gtf_juncs_SOURCES = gtf_juncs.cpp +@@ -817,7 +809,7 @@ + juncs_db_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) + + tophat_reports_SOURCES = tophat_reports.cpp +-tophat_reports_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB) ++tophat_reports_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) + tophat_reports_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) $(BOOST_LDFLAGS) + + fix_map_ordering_SOURCES = fix_map_ordering.cpp @@ -844,15 +836,5 @@ gtf_to_fasta_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB) gtf_to_fasta_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) diff --git a/sci-biology/tophat/tophat-2.1.1-r1.ebuild b/sci-biology/tophat/tophat-2.1.1-r2.ebuild similarity index 88% rename from sci-biology/tophat/tophat-2.1.1-r1.ebuild rename to sci-biology/tophat/tophat-2.1.1-r2.ebuild index 6c6690a..52a75a6 100644 --- a/sci-biology/tophat/tophat-2.1.1-r1.ebuild +++ b/sci-biology/tophat/tophat-2.1.1-r2.ebuild @@ -19,12 +19,13 @@ IUSE="debug" REQUIRED_USE="${PYTHON_REQUIRED_USE}" RDEPEND="${PYTHON_DEPS} - dev-libs/boost:= + dev-libs/boost:=[threads] sci-biology/samtools:0.1-legacy sci-biology/bowtie:2" DEPEND="${RDEPEND} virtual/pkgconfig - sci-biology/seqan:1.4" + sci-biology/seqan:1.4 + >=sys-devel/autoconf-archive-2016.09.16" PATCHES=( "${FILESDIR}/${P}-unbundle-seqan-samtools.patch" @@ -52,6 +53,10 @@ src_prepare() { append-cflags -Wno-unused-but-set-variable -Wno-unused-variable append-cppflags "$($(tc-getPKG_CONFIG) --cflags seqan-1.4)" + # remove ancient autoconf archive macros, wreaking havoc, + # depend on sys-devel/autoconf-archive instead, bug #594810 + rm {ax_boost_thread,ax_boost_base}.m4 || die + eautoreconf }
