gentoo resync : 25.12.2017

5 files changed, 59 insertions, 21 deletions

diff --git a/sci-biology/dialign-tx/Manifest b/sci-biology/dialign-tx/Manifest
index f6accfd6b989..443791cbbb26 100644
--- a/sci-biology/dialign-tx/Manifest
+++ b/sci-biology/dialign-tx/Manifest
@@ -1,5 +1,7 @@
-AUX dialign-tx-1.0.2-implicits.patch 776 BLAKE2B e91b85b42d9e61d4895ff34f2a6d7e869cc32edc6a8e6aee0378a3083cd1d3d4e148f6b223d60a3456a5db0b07859cd63c8d624060b365d5b13a6d75fd98983d SHA512 632da19c24834f011778e1be23a8b19f64da4e52386c99838393f678e927174bd8d3d9d175716e2651fcb884673123136166c401d3e687b882e5eaf69d597a1b
+AUX dialign-tx-1.0.2-fix-build-system.patch 588 BLAKE2B 3d9757b2b66497a47bfc3412a1e014f85e0dd12c2247103c813f3406ae0b34e8ba8a68cf31481f9f184095c07e63840fa2643c04a34a3e3f2605b90b2e8bba50 SHA512 30a474f59fb18dcef572299aa6bb6a22d9d6188193a3341bd04c32d6c388358e890ea17bcb8fd31fe80cee58330be6cb004b5936bf98d204e6f5a1e40627bf4f
+AUX dialign-tx-1.0.2-gnu89-inline.patch 493 BLAKE2B d37822818faabfa55cfd0a32cf0c0f22548ff29eb7c55712b1ef8e4fe4652531cfe821236e206a7bdaec74c4cac22e5d519be41f282b717d2119d7a79e478e44 SHA512 ad63585d93a10b44b1ca810b4a1bbbd991cc5fb1e762b941931d28f50dcc6a2bb6fdedea7c5faedcf4b2452dc8b99374423752694c5aa0a481ce5e97d8f5d3dd
+AUX dialign-tx-1.0.2-implicits.patch 780 BLAKE2B b6eb50c7eaecf6439a1d27a0173661efef100a10976abf521fe50a4687d7e89e0cb094693118a84e68daae3918708ee3323073299d3d28786031a1f41c39af75 SHA512 783afc4527e0a77f0aac66bd8aa00ce3e5ddd81dd652c7459e551c609755eb3b0bd5b02566d8d1636b8840ed8567bb5652866c41ecf038ac9fe5682e1edf3e64
 AUX dialign-tx-1.0.2-modernize.patch 6149 BLAKE2B f6f3044b38d4652c2bc3aa63714beb42220ac00d0ecfe68b692b7af0f6dc1d29a8d053962d324e33bf32df2b92bd0fad40b5ec352ae837f6eaba1920f73d8d90 SHA512 cf1c1200500eb3e5f159468fe52536e8ffff60de21e09bb81e585270224ac4ce93d59fe80bd5a8212a4154ad90b23ec415be11b42792440c7fd53f75762d047a
 DIST DIALIGN-TX_1.0.2.tar.gz 1765296 BLAKE2B 3cce811a58fcf210f42c4a783e8ebb56c66436912ff04bce270058193f0d7b21114d75e2d67829c7abfbb35814e5a16f7f952611729ab211d066403a411db94a SHA512 ff43f1f2900bdd12b7a8ba382a4d6ad68e6c2e6d7ceb1a65f0e571bb891cc2dc2661fb6ce698aaabf0e20c14565b5927ae0076a7170c8611679f936851a00c43
-EBUILD dialign-tx-1.0.2-r1.ebuild 998 BLAKE2B 3f5bb90b5fb4729c351f7aea6475b849353e33dd6428b437e16b9dc1d884201d9a528c1ae551675f7a3acb48f0983a204bdac5cb1e892cdcf10a65b19d186ada SHA512 7baa791bc863006cf66828bf3a08ec87afe03f72ba181280f5e26cf826a939bcc854bb94b40551f11a818006dae3a229db15f61b09f11438dece536e150b0ad0
+EBUILD dialign-tx-1.0.2-r2.ebuild 950 BLAKE2B 127ba32952e662b90c43dd901f4fe8aa1f6bb99d57adfc39b3bc65dfc9b52ece3809386b3fa2bf4ee649c83b5cc93306930b995ced48f586edbbb85c551a55d2 SHA512 813f6a5337e0c390ef57eedbbb80b9553f0f9bc81fbdbed58d4572e7a3d8d830b15ed54aa9033fadfa49157fcee94ec43396b9cd1c03d9889079fb2d4267cf15
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild b/sci-biology/dialign-tx/dialign-tx-1.0.2-r2.ebuild
index 2f63ea80bb45..123977916f06 100644
--- a/sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild
+++ b/sci-biology/dialign-tx/dialign-tx-1.0.2-r2.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=6
 
-inherit eutils multilib toolchain-funcs
+inherit toolchain-funcs
 
-MY_P=DIALIGN-TX_${PV}
+MY_P=${PN^^}_${PV}
 
 DESCRIPTION="Greedy and progressive approaches for segment-based multiple sequence alignment"
 HOMEPAGE="http://dialign-tx.gobics.de/"
@@ -13,32 +13,33 @@ SRC_URI="http://dialign-tx.gobics.de/${MY_P}.tar.gz"
 
 LICENSE="LGPL-2.1"
 SLOT="0"
-KEYWORDS="amd64 x86"
-IUSE=""
+KEYWORDS="~amd64 ~x86"
 
 S=${WORKDIR}/${MY_P}
-
-src_prepare() {
-	sed -e "s/\$(CC) -o/\$(CC) \$(LDFLAGS) -o/" \
-		-i source/Makefile || die #336533
-	epatch	"${FILESDIR}"/${P}-implicits.patch \
-		"${FILESDIR}"/${P}-modernize.patch
+PATCHES=(
+	"${FILESDIR}"/${P}-fix-build-system.patch
+	"${FILESDIR}"/${P}-implicits.patch
+	"${FILESDIR}"/${P}-modernize.patch
+	"${FILESDIR}"/${P}-gnu89-inline.patch
+)
+
+src_configure() {
+	tc-export CC
 }
 
 src_compile() {
 	emake -C source clean
-	emake -C source CC="$(tc-getCC)" \
-		CPPFLAGS=""
+	emake -C source
 }
 
 src_install() {
-	dobin "${S}"/source/dialign-tx
+	dobin source/dialign-tx
 	insinto /usr/$(get_libdir)/${PN}/conf
-	doins "${S}"/conf/*
+	doins -r conf/.
 }
 
 pkg_postinst() {
 	einfo "The configuration directory is"
-	einfo "${ROOT}usr/$(get_libdir)/${PN}/conf"
+	einfo "${EROOT%/}/usr/$(get_libdir)/${PN}/conf"
 	einfo "You will need to pass this to ${PN} on every run."
 }
diff --git a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-fix-build-system.patch b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-fix-build-system.patch
new file mode 100644
index 000000000000..cbfd458043c5
--- /dev/null
+++ b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-fix-build-system.patch
@@ -0,0 +1,24 @@
+--- a/source/Makefile
++++ b/source/Makefile
+@@ -1,4 +1,3 @@
+-CC=gcc

+ # debug

+ #CPPFLAGS=-g -O0 -Q -v -da

+ #CPPFLAGS=-g -O0 -fstack-check -Q -v -da

+@@ -8,7 +7,6 @@
+ # THIS IS FOR THE OPTIMIZED ONE

+ #CPPFLAGS=-g 

+ #CPPFLAGS=-O3 -march=i686 -funroll-loops

+-CPPFLAGS=-O3 -funroll-loops -march=i686 -mfpmath=sse -msse  -mmmx

+ #CPPFLAGS=-march=athlon-mp -g -O0 -Wall -D_USE_XOPEN -D__unix__

+ 

+ OBJ_DIR=.

+@@ -33,7 +31,7 @@
+ 

+ museq:	$(OBJ)

+ 	rm -f $(TARGET)/$@

+-	$(CC) -o $(TARGET)/$@ \

++	$(CC) $(LDFLAGS) -o $(TARGET)/$@ \

+ 	$(OBJ) \

+ 	-pipe -Wall -lm 

+ 	mv museq dialign-tx

diff --git a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-gnu89-inline.patch b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-gnu89-inline.patch
new file mode 100644
index 000000000000..21f576f07052
--- /dev/null
+++ b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-gnu89-inline.patch
@@ -0,0 +1,11 @@
+--- a/source/diag.c
++++ b/source/diag.c
+@@ -958,7 +958,7 @@
+  * The pointer returned (and the ones included in the struct)  
+  * has to be deallocted explicitely from memory. 
+  */ 
+-inline struct simple_diag_col* find_diags_dialign(struct scr_matrix *smatrix,  
++static inline struct simple_diag_col* find_diags_dialign(struct scr_matrix *smatrix,  
+ 				struct prob_dist *pdist, struct seq* seq1,  
+ 				struct seq* seq2, struct alignment *algn, 
+ 				 long double **tmp_dist, int round) { 
diff --git a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch
index a8388d03232f..d82a5bf4be33 100644
--- a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch
+++ b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch
@@ -1,5 +1,5 @@
---- source/museq.c
-+++ source/museq.c
+--- a/source/museq.c
++++ b/source/museq.c
 @@ -38,6 +38,7 @@
  //extern void calc_weight(struct diag* dg, struct scr_matrix* smatrix, 
  //		 struct prob_dist *pdist);