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Mon, 2 Aug 2021 09:50:45 +0000 (UTC) From: "David Seifert" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "David Seifert" Message-ID: <1627897838.5365c04973093796a04102a22fefe61303e75d06.soap@gentoo> Subject: [gentoo-commits] repo/gentoo:master commit in: sci-biology/embassy-vienna/, sci-biology/embassy-vienna/files/ X-VCS-Repository: repo/gentoo X-VCS-Files: sci-biology/embassy-vienna/embassy-vienna-1.7.2.660.ebuild sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650-C99-inline.patch X-VCS-Directories: sci-biology/embassy-vienna/ sci-biology/embassy-vienna/files/ X-VCS-Committer: soap X-VCS-Committer-Name: David Seifert X-VCS-Revision: 5365c04973093796a04102a22fefe61303e75d06 X-VCS-Branch: master Date: Mon, 2 Aug 2021 09:50:45 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: cf1e43e2-feb3-4b92-a10e-9062d5d49326 X-Archives-Hash: 2aea54921e42d0a7d86cd6a7116f48d1 commit: 5365c04973093796a04102a22fefe61303e75d06 Author: David Seifert gentoo org> AuthorDate: Mon Aug 2 09:50:38 2021 +0000 Commit: David Seifert gentoo 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 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;