gentoo resync : 25.11.2020

4 files changed, 52 insertions, 8 deletions

diff --git a/sci-biology/dialign-tx/Manifest b/sci-biology/dialign-tx/Manifest
index 443791cbbb26..ec6b81e67ea3 100644
--- a/sci-biology/dialign-tx/Manifest
+++ b/sci-biology/dialign-tx/Manifest
@@ -1,7 +1,8 @@
 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-fno-common.patch 556 BLAKE2B d77bf94e61f376548f66776bde79081d18798d0645ec75fd314ac1394059e3498e20f638553b484e5e077cf5c253138ff57842920ce8237b63c4e799e51951cf SHA512 03b028cf2f0bf1b8e67bbc24fbbefc652ce2bd2de89aece26b32c6e2c86b8639cdbcf24e8a6a77ad31b690b5586f262affe39111483677372b547879207eacc3
+AUX dialign-tx-1.0.2-gnu89-inline.patch 1406 BLAKE2B 6a97e3300a730a87db721572fe6f4729b9915746d68f4b911ebe0d8ee91adade8b5584da39f1fdc549d6cbb0cbb941fddb4e63f669197a8761ee680bd35d9bac SHA512 55125d6634704cc2bfa4b44f502998bfb6e051190d398c8f3d3e9d48256b3f7fb2c9e54500e8c6d01493f2f501caaf12d7f0954c1e6ab455201ac2b507f43069
 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-r2.ebuild 950 BLAKE2B 127ba32952e662b90c43dd901f4fe8aa1f6bb99d57adfc39b3bc65dfc9b52ece3809386b3fa2bf4ee649c83b5cc93306930b995ced48f586edbbb85c551a55d2 SHA512 813f6a5337e0c390ef57eedbbb80b9553f0f9bc81fbdbed58d4572e7a3d8d830b15ed54aa9033fadfa49157fcee94ec43396b9cd1c03d9889079fb2d4267cf15
+EBUILD dialign-tx-1.0.2-r2.ebuild 999 BLAKE2B 4fe11a5ee9d9fbb624911096f9a326dd0431bcf9f5e314ec9b551dbd1772284527e5f6ea4344a3698e337c4fbd75f631c72fb8c248d451902f9cb68b0d7d55fd SHA512 d8df0ccec568af8b0671101af9a7a88b7f52bcbe7095700fbc4e32c238bb464a9d213c90ab162195685361fb60f035ac7f8fbdf580633a32315005fd7378ab4d
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/dialign-tx/dialign-tx-1.0.2-r2.ebuild b/sci-biology/dialign-tx/dialign-tx-1.0.2-r2.ebuild
index 123977916f06..78681265a0b7 100644
--- a/sci-biology/dialign-tx/dialign-tx-1.0.2-r2.ebuild
+++ b/sci-biology/dialign-tx/dialign-tx-1.0.2-r2.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 inherit toolchain-funcs
 
@@ -15,12 +15,13 @@ LICENSE="LGPL-2.1"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 
-S=${WORKDIR}/${MY_P}
+S="${WORKDIR}/${MY_P}"
 PATCHES=(
 	"${FILESDIR}"/${P}-fix-build-system.patch
 	"${FILESDIR}"/${P}-implicits.patch
 	"${FILESDIR}"/${P}-modernize.patch
 	"${FILESDIR}"/${P}-gnu89-inline.patch
+	"${FILESDIR}"/${P}-fno-common.patch
 )
 
 src_configure() {
@@ -34,12 +35,12 @@ src_compile() {
 
 src_install() {
 	dobin source/dialign-tx
-	insinto /usr/$(get_libdir)/${PN}/conf
+	insinto /usr/$(get_libdir)/dialign-tx/conf
 	doins -r conf/.
 }
 
 pkg_postinst() {
 	einfo "The configuration directory is"
-	einfo "${EROOT%/}/usr/$(get_libdir)/${PN}/conf"
-	einfo "You will need to pass this to ${PN} on every run."
+	einfo "${EROOT}/usr/$(get_libdir)/dialign-tx/conf"
+	einfo "You will need to pass this to dialign-tx on every run."
 }
diff --git a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-fno-common.patch b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-fno-common.patch
new file mode 100644
index 000000000000..de3104fa0ebb
--- /dev/null
+++ b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-fno-common.patch
@@ -0,0 +1,22 @@
+--- a/source/parameters.c
++++ b/source/parameters.c
+@@ -26,6 +26,8 @@
+ 
+ extern char *optarg;
+ extern int optind, opterr, optopt;
++
++struct parameters* para;
+ /****************************
+ * PROTEIN DEFAULT VALUES!   *
+ ****************************/
+--- a/source/parameters.h
++++ b/source/parameters.h
+@@ -138,7 +138,7 @@
+     /*              global variable                 */
+     /*                                              */
+     /************************************************/
+-struct parameters* para;
++extern struct parameters* para;
+ 
+ 
+ 
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
index 21f576f07052..fc8d0284e6ab 100644
--- 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
@@ -1,5 +1,25 @@
+--- a/source/assemble.c
++++ b/source/assemble.c
+@@ -574,7 +574,7 @@
+  * returns a value <0 if there is an non-conflicting overlap
+  * returns 0 in all other non-conflicting cases
+  */
+-inline char confl_diag(struct alignment *algn, char *layer, struct diag *dg1, struct diag *dg2) {
++static inline char confl_diag(struct alignment *algn, char *layer, struct diag *dg1, struct diag *dg2) {
+   //  if(dg1->multi_dg || dg2->multi_dg) error(" confl_diag(): cannot accept multi dgs!");
+   int s1_1 = dg1->seq_p1.num;
+   int s1_2 = dg1->seq_p2.num;
 --- a/source/diag.c
 +++ b/source/diag.c
+@@ -312,7 +312,7 @@
+ /** 
+  * calculates the overlap weight for the given diag 
+  */ 
+-inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,  
++void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,  
+ 		    struct prob_dist *pdist) { 
+   int sn1 = dg->seq_p1.num; 
+   int sn2 = dg->seq_p2.num; 
 @@ -958,7 +958,7 @@
   * The pointer returned (and the ones included in the struct)  
   * has to be deallocted explicitely from memory.