[gentoo-commits] repo/gentoo:master commit in: sci-biology/mira/, sci-biology/mira/files/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/mira/, sci-biology/mira/files/

[Lars Wendler]

commit:     64dd653b3b2ae8ed253ec76cacbbe45021e74543
Author:     Lars Wendler <polynomial-c <AT> gentoo <DOT> org>
AuthorDate: Fri Jan 13 16:12:59 2017 +0000
Commit:     Lars Wendler <polynomial-c <AT> gentoo <DOT> org>
CommitDate: Fri Jan 13 16:13:42 2017 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=64dd653b

sci-biology/mira: Bump to EAPI-6. Ebuild cleanup.

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/mira/files/mira-4.0.2-boost-1.50.patch | 22 ++++++++++++++++++
 sci-biology/mira/mira-4.0.2.ebuild                 | 27 ++++++++++++++--------
 2 files changed, 39 insertions(+), 10 deletions(-)

diff --git a/sci-biology/mira/files/mira-4.0.2-boost-1.50.patch b/sci-biology/mira/files/mira-4.0.2-boost-1.50.patch
new file mode 100644
index 00000000..50f83c9
--- /dev/null
+++ b/sci-biology/mira/files/mira-4.0.2-boost-1.50.patch
@@ -0,0 +1,22 @@
+ax_boost_regex.m4 |    4 ++--
+1 file changed, 2 insertions(+), 2 deletions(-)
+
+--- mira-4.0.2/m4/ax_boost_regex.m4
++++ mira-4.0.2/m4/ax_boost_regex.m4
+@@ -78,14 +78,14 @@
+                 for libextension in `ls $BOOSTLIBDIR/libboost_regex*.so* $BOOSTLIBDIR/libboost_regex*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_regex.*\)\.so.*$;\1;' -e 's;^lib\(boost_regex.*\)\.a*$;\1;'` ; do
+                      ax_lib=${libextension}
+ 				    AC_CHECK_LIB($ax_lib, exit,
+-                                 [BOOST_REGEX_LIB="-l$ax_lib"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
++                                 [BOOST_REGEX_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
+                                  [link_regex="no"])
+ 				done
+                 if test "x$link_regex" != "xyes"; then
+                 for libextension in `ls $BOOSTLIBDIR/boost_regex*.{dll,a}* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_regex.*\)\.dll.*$;\1;' -e 's;^\(boost_regex.*\)\.a*$;\1;'` ; do
+                      ax_lib=${libextension}
+ 				    AC_CHECK_LIB($ax_lib, exit,
+-                                 [BOOST_REGEX_LIB="-l$ax_lib"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
++                                 [BOOST_REGEX_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
+                                  [link_regex="no"])
+ 				done
+                 fi

diff --git a/sci-biology/mira/mira-4.0.2.ebuild b/sci-biology/mira/mira-4.0.2.ebuild
index 758e30b..5462559 100644
--- a/sci-biology/mira/mira-4.0.2.ebuild
+++ b/sci-biology/mira/mira-4.0.2.ebuild
@@ -2,7 +2,7 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=5
+EAPI=6
 
 MIRA_3RDPARTY_PV="06-07-2012"
 MY_PV="${PV/_}" # convert from mira-4.0_rc2 (Gentoo ebuild filename derived) to mira-4.0rc2 (upstream fromat)
@@ -37,12 +37,16 @@ RDEPEND="${CDEPEND}"
 #	THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf )
 DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED THANKS )
 
+PATCHES=(
+	"${FILESDIR}/${PN}-4.0.2-boost-1.50.patch"
+	"${FILESDIR}/${PN}-4.0.2-cout.patch"
+	"${FILESDIR}/${PN}-4.0.2-cmath.patch"
+)
+
 src_prepare() {
 	find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die
-	epatch \
-		"${FILESDIR}"/${PN}-3.4.0.2-boost-1.50.patch \
-		"${FILESDIR}"/${P}-cout.patch \
-		"${FILESDIR}"/${P}-cmath.patch
+
+	default
 
 	sed \
 		-e "s:-O[23]::g" \
@@ -54,13 +58,17 @@ src_prepare() {
 	# Remove C++ source files that upstream built with flex.
 	local f
 	local PREBUILT_CXX_LEXER_FILES=(
-		"$S"/src/caf/caf_flexer.cc
-		"$S"/src/io/exp_flexer.cc
-		"$S"/src/mira/parameters_flexer.cc
+		"${S}"/src/caf/caf_flexer.cc
+		"${S}"/src/io/exp_flexer.cc
+		"${S}"/src/mira/parameters_flexer.cc
 	)
 
 	for f in "${PREBUILT_CXX_LEXER_FILES[@]}"; do
-		[[ -f $f ]] && { rm "$f" || die "Failed to remove $f"; } || die "$f not found"
+		if [[ -f ${f} ]] ; then
+			rm "${f}" || die "Failed to remove ${f}"
+		else
+			die "${f} not found"
+		fi
 	done
 }
 
@@ -79,7 +87,6 @@ src_configure() {
 
 src_install() {
 	default
-	dodoc ${DOCS[@]}
 
 	dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl}
 	dodoc "${WORKDIR}"/3rdparty/{README.txt,midi_screen.fasta}