[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;