diff options
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/Manifest.gz | bin | 22146 -> 22143 bytes | |||
| -rw-r--r-- | sci-biology/embassy-vienna/Manifest | 3 | ||||
| -rw-r--r-- | sci-biology/embassy-vienna/embassy-vienna-1.7.2.660.ebuild | 12 | ||||
| -rw-r--r-- | sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650-C99-inline.patch | 32 |
4 files changed, 39 insertions, 8 deletions
diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz Binary files differindex c2d8ff11cb80..512237955165 100644 --- a/sci-biology/Manifest.gz +++ b/sci-biology/Manifest.gz diff --git a/sci-biology/embassy-vienna/Manifest b/sci-biology/embassy-vienna/Manifest index dcf9c44204c2..d3e38a4ed499 100644 --- a/sci-biology/embassy-vienna/Manifest +++ b/sci-biology/embassy-vienna/Manifest @@ -1,4 +1,5 @@ +AUX embassy-vienna-1.7.2.650-C99-inline.patch 1457 BLAKE2B 0911b395427e1564d89557a1312e54fb414d0413aa368a8d93fe71dd821af828127c387ba561135e2ba4e16a9e1f9cdeac18e9b0c750844fc8eea3ea65c7e6b9 SHA512 c9a2e8004a7a0ae4e7078ccc223f0b2c16386c56a6458596c32de0afbdd6498cc9a01514a70f137ad0d12cffbc0a237762ae5440cce604f86428fe319983efeb AUX embassy-vienna-1.7.2.650_fix-build-system.patch 3349 BLAKE2B c6d12bee84b5bc5bb987929a1d606c28cab1d5bb318fdf294f01569d90ae4736c818ddf3d5d2fd506fe3d012c35d320c74c0b3185540e19a03b0e7dbcac9e0d6 SHA512 4da6e09711974bf10259558f78208d207f3e07b0156488acfce788d83f05a6872246d6acf3c318195285e1d84b3788aec65d82f989c682b56129c4dfb6df8eae DIST embassy-vienna-1.7.2.660.tar.gz 873165 BLAKE2B 46e976e52ad65490237563af09e483c212a6170c8c79fac8a2f2609040ee6a4cf60c04b00159c4c33d8c2a10f6e457e412287409fc0ea5724c5687dbd65ff06c SHA512 1484ca419ebcb7776d8f92dd633d4fda1a752a73ccb5189b58f7417a5611e015e9b42cbb37b51f4d5c7a27df0d5cab2cdf1e95ebd70a8359ffc8fa1633d28103 -EBUILD embassy-vienna-1.7.2.660.ebuild 433 BLAKE2B 2feaec37d75ccd9bb4798f56ed58a06944e06488d4ce8bb2ba924dda2cbce5abf54e6ef1e15cca61620db06b51132143cc001e0ef84f5eeeb4f3e7b95bc23bfc SHA512 0481fac0f109b153119e6e12907cea9083a52b3a85e1c26985b14e45cf9a68e36b188bc16c10f528eb19df73fad511afc13742eaa8cd653e5fdd6559497c7184 +EBUILD embassy-vienna-1.7.2.660.ebuild 397 BLAKE2B 9f190749fed69294abeec16e993515ade0b94d5c99b00a47775ac702cedb1c01d789dc9b34e54dd64ae0e3b692e7d36a267b6e3a801de64b4dd77479ed2fd1e0 SHA512 b27a9747ec96c704ad6eebf9a122dc97f9d2995f97a44195641573fabd0cd69c6ca9e5dca58a77cc525e8175230a8e86898bcc328089fc04f3cb97cc5516e8c7 MISC metadata.xml 347 BLAKE2B 2368d452e759747738601ae0e5e5e7181167badeaa28ed89aa8e07b55ebc9d2f1dbcd351cd5569a4548c307cfaa23b26756d88778c078685848db72dd9b094e7 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e 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; |