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

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

[David Seifert]

commit:     5365c04973093796a04102a22fefe61303e75d06
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Mon Aug  2 09:50:38 2021 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Mon Aug  2 09:50:38 2021 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5365c049

sci-biology/embassy-vienna: remove `append-cflags -std=gnu89`

Signed-off-by: David Seifert <soap <AT> gentoo.org>

 .../embassy-vienna/embassy-vienna-1.7.2.660.ebuild | 12 ++++----
 .../embassy-vienna-1.7.2.650-C99-inline.patch      | 32 ++++++++++++++++++++++
 2 files changed, 37 insertions(+), 7 deletions(-)

diff --git a/sci-biology/embassy-vienna/embassy-vienna-1.7.2.660.ebuild b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.660.ebuild
index 6d63add1eea..35143accb01 100644
--- a/sci-biology/embassy-vienna/embassy-vienna-1.7.2.660.ebuild
+++ b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.660.ebuild
@@ -7,14 +7,12 @@ EBO_DESCRIPTION="Vienna RNA package - RNA folding"
 
 EBO_EAUTORECONF=1
 
-inherit emboss-r2 flag-o-matic
+inherit emboss-r2
 
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 
 S="${WORKDIR}/VIENNA-1.7.2.650"
-PATCHES=( "${FILESDIR}"/${PN}-1.7.2.650_fix-build-system.patch )
-
-src_configure() {
-	append-cflags -std=gnu89
-	emboss-r2_src_configure
-}
+PATCHES=(
+	"${FILESDIR}"/${PN}-1.7.2.650_fix-build-system.patch
+	"${FILESDIR}"/${PN}-1.7.2.650-C99-inline.patch
+)

diff --git a/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650-C99-inline.patch b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650-C99-inline.patch
new file mode 100644
index 00000000000..1eda10172dc
--- /dev/null
+++ b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650-C99-inline.patch
@@ -0,0 +1,32 @@
+--- a/src/fold.c
++++ b/src/fold.c
+@@ -65,9 +65,9 @@
+ PRIVATE int fill_arrays(const char *sequence);
+ /*@unused@*/
+ INLINE PRIVATE  int oldLoopEnergy(int i, int j, int p, int q, int type, int type_2);
+-INLINE int  LoopEnergy(int n1, int n2, int type, int type_2,
++int  LoopEnergy(int n1, int n2, int type, int type_2,
+ 			 int si1, int sj1, int sp1, int sq1);
+-INLINE int  HairpinE(int size, int type, int si1, int sj1, const char *string);
++int  HairpinE(int size, int type, int si1, int sj1, const char *string);
+ int loop_energy(short * ptable, short *s, short *s1, int i);
+ char *backtrack_fold_from_pair(char *sequence, int i, int j);
+ void export_circfold_arrays(int *Fc_p, int *FcH_p, int *FcI_p, int *FcM_p, int **fM2_p,
+@@ -831,7 +831,7 @@
+ }
+ /*---------------------------------------------------------------------------*/
+ 
+-INLINE int HairpinE(int size, int type, int si1, int sj1, const char *string) {
++int HairpinE(int size, int type, int si1, int sj1, const char *string) {
+   int energy;
+   energy = (size <= 30) ? P->hairpin[size] :
+     P->hairpin[30]+(int)(P->lxc*log((size)/30.));
+@@ -901,7 +901,7 @@
+ 
+ /*--------------------------------------------------------------------------*/
+ 
+-INLINE int LoopEnergy(int n1, int n2, int type, int type_2,
++int LoopEnergy(int n1, int n2, int type, int type_2,
+ 		      int si1, int sj1, int sp1, int sq1) {
+   /* compute energy of degree 2 loop (stack bulge or interior) */
+   int nl, ns, energy;

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

[David Seifert]

commit:     b535a6feef62d51277c88bb392c69d5f5ad52c96
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Feb 13 23:28:46 2022 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Feb 13 23:28:46 2022 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b535a6fe

sci-biology/embassy-vienna: update EAPI 7 -> 8

Signed-off-by: David Seifert <soap <AT> gentoo.org>

 ...-1.7.2.660.ebuild => embassy-vienna-1.7.2.660-r1.ebuild} | 13 ++++++++-----
 .../files/embassy-vienna-1.7.2.650_fix-build-system.patch   |  4 ++--
 2 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/sci-biology/embassy-vienna/embassy-vienna-1.7.2.660.ebuild b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.660-r1.ebuild
similarity index 73%
rename from sci-biology/embassy-vienna/embassy-vienna-1.7.2.660.ebuild
rename to sci-biology/embassy-vienna/embassy-vienna-1.7.2.660-r1.ebuild
index 35143accb01a..241194af375e 100644
--- a/sci-biology/embassy-vienna/embassy-vienna-1.7.2.660.ebuild
+++ b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.660-r1.ebuild
@@ -1,13 +1,11 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
 EBO_DESCRIPTION="Vienna RNA package - RNA folding"
 
-EBO_EAUTORECONF=1
-
-inherit emboss-r2
+inherit autotools emboss-r3
 
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 
@@ -16,3 +14,8 @@ PATCHES=(
 	"${FILESDIR}"/${PN}-1.7.2.650_fix-build-system.patch
 	"${FILESDIR}"/${PN}-1.7.2.650-C99-inline.patch
 )
+
+src_prepare() {
+	default
+	eautoreconf
+}

diff --git a/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch
index 8bd816b0e672..ea96e9d47fa9 100644
--- a/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch
+++ b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch
@@ -1,5 +1,5 @@
---- a/configure.ac
-+++ b/configure.ac
+--- a/configure.in
++++ b/configure.in
 @@ -649,33 +649,6 @@