gentoo resync : 15.12.2019

3 files changed, 29 insertions, 19 deletions

diff --git a/sci-biology/gibbs/Manifest b/sci-biology/gibbs/Manifest
index 3a203ab08d5a..e806435c017b 100644
--- a/sci-biology/gibbs/Manifest
+++ b/sci-biology/gibbs/Manifest
@@ -1,3 +1,4 @@
+AUX gibbs-3.1-fix-CFLAGS.patch 213 BLAKE2B 9a0f7f0412569cef1cce984f5087f7b99e16163ac6c6c3e0aad27f14cd2f7ed5bfb22f21f433f1c343a9e73899dedb00ea93467adc4cc42a3dceae41aa1e3f86 SHA512 afd0fffb891eefe8799025a032a802f398ac737900e1fac86f79964bfe493ee906c3e5f42abc5e45d3de5af80887ab25ef207a885a6ddb8b6fe0d0ab1f906046
 DIST gibbs-3.1.tar.gz 563300 BLAKE2B 74b97407ccdac49d19dd2fa5fe3a5384b52a3ae871f197c1212e818fb7ce2307f2d04a91cf8a1d14c82d57b6f7266bbae849091bec9e580b8d473b595a836212 SHA512 b1ffc0d0c7debaced3c3d850eb7d2c42e13358d1e7c6ff5e6be0273446edc50bd655c52c5ae904a9054d47d7a48abd54a7684534ba7681375b657ad77fb8cb52
-EBUILD gibbs-3.1.ebuild 1080 BLAKE2B 8b300d04feca4973c43a787410f19ff6ab78f5bb18d7e073cedc88c9c4c96b476d27a487a3b5d64ded499ac1ae60a21659e4023fba7d4a62368fbf05882edc33 SHA512 d07fc647931b6d8c0634a4d089429fade0f3d3262e0369236420963ba7dd6e3450a66cc0d4fe3ecc884a67e6aba8322d3492fc7a8b7a9fa8b32813e3973bc1fb
+EBUILD gibbs-3.1.ebuild 912 BLAKE2B 29d51a769e6a477bb81da6d467a1b2befbfd2f83282184a1087de0a4a5d736a5df01f3767663141bd6282826bd4fcad5ca0ddaea916fc93e582ccd8b4a8e98b8 SHA512 975c0bd3c57a8db25324636ce8f2fd9ef9bde1de4a980ba93fbe3e7bf8362a51f06ae5b1687570d81012ef6eed6536bfde418327a045bcf54a1e1517d85d989f
 MISC metadata.xml 483 BLAKE2B e5a503d65b225af960b42424b1e2e451ed0596240e15868f04c429920a7818333819abbb21b0340cd4ec9ddbcc23cc272663bc8451fd1ab11bf6d6f17e4eae2f SHA512 3f86f0f0f673f78c65187f282c0346fccab1102a01869811afd73a6070a3efa032ff9d427a57a9e8a9922cdc055a33d6bccb771eda1196d6667b3076035fd077
diff --git a/sci-biology/gibbs/files/gibbs-3.1-fix-CFLAGS.patch b/sci-biology/gibbs/files/gibbs-3.1-fix-CFLAGS.patch
new file mode 100644
index 000000000000..6eaad637cfc8
--- /dev/null
+++ b/sci-biology/gibbs/files/gibbs-3.1-fix-CFLAGS.patch
@@ -0,0 +1,11 @@
+--- a/configure.in
++++ b/configure.in
+@@ -51,7 +51,7 @@
+ 	fi

+ 	])

+ 

+-CFLAGS="$OPTFLAGS $MPIFLAGS  -Wall -Werror $MACFLAG"

++CFLAGS="$CFLAGS $OPTFLAGS $MPIFLAGS -Wall $MACFLAG"

+ 

+ AC_PROG_CC([$COMP_LIST])

+ 

diff --git a/sci-biology/gibbs/gibbs-3.1.ebuild b/sci-biology/gibbs/gibbs-3.1.ebuild
index de8322a5068e..a06d0880ee4d 100644
--- a/sci-biology/gibbs/gibbs-3.1.ebuild
+++ b/sci-biology/gibbs/gibbs-3.1.ebuild
@@ -1,11 +1,9 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=4
+EAPI=7
 
-AUTOTOOLS_AUTORECONF=yes
-
-inherit autotools-utils multilib
+inherit autotools
 
 DESCRIPTION="Identify motifs, conserved regions, in DNA or protein sequences"
 HOMEPAGE="http://bayesweb.wadsworth.org/gibbs/gibbs.html"
@@ -13,37 +11,37 @@ SRC_URI="mirror://gentoo/gibbs-${PV}.tar.gz"
 
 LICENSE="GPL-2"
 SLOT="0"
-IUSE="mpi"
 KEYWORDS="amd64 x86"
+IUSE="mpi"
 
 DEPEND="
 	mpi? (
 		virtual/mpi
-		sys-cluster/mpe2 )"
+		sys-cluster/mpe2
+	)"
 RDEPEND="${DEPEND}"
 
+PATCHES=( "${FILESDIR}"/${PN}-3.1-fix-CFLAGS.patch )
+
 src_prepare() {
-	sed \
-		-e 's/CFLAGS="$OPTFLAGS/CFLAGS="$CFLAGS $OPTFLAGS/' \
-		-e 's/-Werror//' \
-		-i configure.in || die
-	autotools-utils_src_prepare
+	default
+	mv configure.{in,ac} || die
+	eautoreconf
 }
 
 src_configure() {
-	if use mpi; then export CC=mpicc; fi
-	local myeconfargs=( $(use_enable mpi) )
-	autotools-utils_src_configure
+	use mpi && export CC=mpicc
+	econf $(use_enable mpi)
 }
 
 src_install() {
-	autotools-utils_src_install
+	default
+
 	exeinto /usr/$(get_libdir)/${PN}
 	doexe *.pl
-	dodoc README ChangeLog
 }
 
 pkg_postinst() {
-	einfo "Supplementary Perl scripts for Gibbs have been installed into /usr/$(get_libdir)/${PN}."
+	einfo "Supplementary Perl scripts for Gibbs have been installed into ${EROOT}/usr/$(get_libdir)/${PN}."
 	einfo "These scripts require installation of sci-biology/bioperl."
 }