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authorRepository mirror & CI <repomirrorci@gentoo.org>2021-08-02 10:06:21 +0000
committerRepository mirror & CI <repomirrorci@gentoo.org>2021-08-02 10:06:21 +0000
commitd6ad676c1a32c41f868d26654e89a2d8eaaed8b5 (patch)
tree9210e92b965c280e1ead9b983ddba4ff58cea8ec
parent2021-08-02 09:51:34 UTC (diff)
parentsci-biology/embassy-vienna: remove `append-cflags -std=gnu89` (diff)
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Merge updates from master
-rw-r--r--sci-biology/embassy-vienna/embassy-vienna-1.7.2.660.ebuild12
-rw-r--r--sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650-C99-inline.patch32
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 6d63add1eea0..35143accb01a 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 000000000000..1eda10172dc5
--- /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;