Gentoo Archives: gentoo-commits

From: Andreas Sturmlechner <asturm@g.o>
To: gentoo-commits@l.g.o
Subject: [gentoo-commits] repo/gentoo:master commit in: sci-biology/fasttree/, sci-biology/fasttree/files/
Date: Sun, 14 Oct 2018 16:34:47
Message-Id: 1539534870.3ea6a505ae3bfa74715b81a5ef39b726cc4abbe7.asturm@gentoo
1 commit: 3ea6a505ae3bfa74715b81a5ef39b726cc4abbe7
2 Author: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
3 AuthorDate: Sun Oct 14 16:32:42 2018 +0000
4 Commit: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
5 CommitDate: Sun Oct 14 16:34:30 2018 +0000
6 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3ea6a505
7
8 sci-biology/fasttree: Drop 2.1.7
9
10 Signed-off-by: Andreas Sturmlechner <asturm <AT> gentoo.org>
11 Package-Manager: Portage-2.3.51, Repoman-2.3.11
12
13 sci-biology/fasttree/Manifest | 3 --
14 sci-biology/fasttree/fasttree-2.1.7.ebuild | 47 ----------------------
15 sci-biology/fasttree/fasttree-2.1.8.ebuild | 10 ++---
16 .../files/fasttree-2.1.7-format-security.patch | 25 ------------
17 4 files changed, 5 insertions(+), 80 deletions(-)
18
19 diff --git a/sci-biology/fasttree/Manifest b/sci-biology/fasttree/Manifest
20 index f59e3b0ab62..1aedce930c6 100644
21 --- a/sci-biology/fasttree/Manifest
22 +++ b/sci-biology/fasttree/Manifest
23 @@ -1,6 +1,3 @@
24 -DIST FastTree-2.1.7.c 383551 BLAKE2B 853881cb39355a134133b012ef311702481d7883e8398bc55bcb3d3274f8414d2579a086176c3d2abdb59ecff7bf8cb6223e89b5ea320a3292f0a9915950c6fa SHA512 e88916e6586885e095948e78e6654081f966c78fbf637cfdac01970f5337bfe5616efcd165fb5f9718af0831ff45047b165944f5da9c5931d9725ea6f49cb59e
25 DIST FastTree-2.1.8.c 385231 BLAKE2B 6f42025ef69b990e051263ccfa23f95d0cde326798c54d8f702c50127338711898c380d1dbd82ab775667eada047048ba8d68288b030af4984019a5f2c23729f SHA512 39a7d284412a602208c2a5df3d0a9a30fe3a584f7f7788d741fb1463b698692017f47bb23f70046d0873e9c8fd27c84ec23f6ca48adb0594193765ac732e6559
26 -DIST FastTreeUPGMA-2.1.7.c 95271 BLAKE2B 1de328881f6452b9c7423c9ed381ab2eb31c4f3ee6426481a6b1089c1359627d4cbbfbea868ebeab9538f82e17f45f1bff8ec07c7370e6432bef6bae449798a8 SHA512 4d6a8e2cb28b8ee201091172a3baa59d432420839c6d2244b5fb8230ed9daa626b6bed22cb692393ca3d78b8f2d071fe18fbb4f9bdcdc47ef149c31e3f45546c
27 DIST FastTreeUPGMA-2.1.8.c 95271 BLAKE2B 1de328881f6452b9c7423c9ed381ab2eb31c4f3ee6426481a6b1089c1359627d4cbbfbea868ebeab9538f82e17f45f1bff8ec07c7370e6432bef6bae449798a8 SHA512 4d6a8e2cb28b8ee201091172a3baa59d432420839c6d2244b5fb8230ed9daa626b6bed22cb692393ca3d78b8f2d071fe18fbb4f9bdcdc47ef149c31e3f45546c
28 -DIST MOTreeComparison-2.1.7.tar.gz 13523 BLAKE2B 97638edd945412ff00e3dfcfc89ec6ea52ae8c43531d5cb680d97e9c62fcad80e861f58ec987abcd2282166dd7886101edba4875531bd9d6ac23df242e0dbd5b SHA512 24d2247650d7728942bd1d987b548cefd65a16b433a3810876613e9fd1cff223d4349ee720b3d8d10a73af220c2c9f59a24d77ad34ff009325fe9f22aa35c72b
29 DIST MOTreeComparison-2.1.8.tar.gz 13523 BLAKE2B 97638edd945412ff00e3dfcfc89ec6ea52ae8c43531d5cb680d97e9c62fcad80e861f58ec987abcd2282166dd7886101edba4875531bd9d6ac23df242e0dbd5b SHA512 24d2247650d7728942bd1d987b548cefd65a16b433a3810876613e9fd1cff223d4349ee720b3d8d10a73af220c2c9f59a24d77ad34ff009325fe9f22aa35c72b
30
31 diff --git a/sci-biology/fasttree/fasttree-2.1.7.ebuild b/sci-biology/fasttree/fasttree-2.1.7.ebuild
32 deleted file mode 100644
33 index aa597952269..00000000000
34 --- a/sci-biology/fasttree/fasttree-2.1.7.ebuild
35 +++ /dev/null
36 @@ -1,47 +0,0 @@
37 -# Copyright 1999-2015 Gentoo Foundation
38 -# Distributed under the terms of the GNU General Public License v2
39 -
40 -EAPI=5
41 -
42 -inherit cmake-utils
43 -
44 -DESCRIPTION="Fast inference of approximately-maximum-likelihood phylogenetic trees"
45 -HOMEPAGE="http://www.microbesonline.org/fasttree/"
46 -SRC_URI="
47 - http://www.microbesonline.org/fasttree/FastTree-${PV}.c
48 - http://www.microbesonline.org/fasttree/FastTreeUPGMA.c -> FastTreeUPGMA-${PV}.c
49 - http://www.microbesonline.org/fasttree/MOTreeComparison.tar.gz -> MOTreeComparison-${PV}.tar.gz
50 -"
51 -
52 -LICENSE="GPL-2"
53 -SLOT="0"
54 -KEYWORDS="amd64 x86"
55 -IUSE="double-precision openmp cpu_flags_x86_sse3"
56 -
57 -REQUIRED_USE="?? ( double-precision cpu_flags_x86_sse3 )"
58 -
59 -DOCS=( README )
60 -
61 -PATCHES=( "${FILESDIR}"/${P}-format-security.patch )
62 -
63 -src_unpack() {
64 - mkdir "${S}" || die
65 - cd "${S}" || die
66 - unpack ${A}
67 - cp "${DISTDIR}"/{FastTreeUPGMA-${PV}.c,FastTree-${PV}.c} . || die
68 -}
69 -
70 -src_prepare() {
71 - cp "${FILESDIR}"/CMakeLists.txt . || die
72 - cmake-utils_src_prepare
73 -}
74 -
75 -src_configure() {
76 - local mycmakeargs=(
77 - -DVERSION="${PV}"
78 - $(cmake-utils_use_has cpu_flags_x86_sse3 sse3)
79 - $(cmake-utils_use_use openmp)
80 - $(cmake-utils_use_use double-precision double)
81 - )
82 - cmake-utils_src_configure
83 -}
84
85 diff --git a/sci-biology/fasttree/fasttree-2.1.8.ebuild b/sci-biology/fasttree/fasttree-2.1.8.ebuild
86 index 7df71ee4474..3f9e4ad5f75 100644
87 --- a/sci-biology/fasttree/fasttree-2.1.8.ebuild
88 +++ b/sci-biology/fasttree/fasttree-2.1.8.ebuild
89 @@ -1,7 +1,7 @@
90 -# Copyright 1999-2015 Gentoo Foundation
91 +# Copyright 1999-2018 Gentoo Authors
92 # Distributed under the terms of the GNU General Public License v2
93
94 -EAPI=5
95 +EAPI=6
96
97 inherit cmake-utils
98
99 @@ -39,9 +39,9 @@ src_prepare() {
100 src_configure() {
101 local mycmakeargs=(
102 -DVERSION="${PV}"
103 - $(cmake-utils_use_has cpu_flags_x86_sse3 sse3)
104 - $(cmake-utils_use_use openmp)
105 - $(cmake-utils_use_use double-precision double)
106 + -DHAS_SSE3=$(usex cpu_flags_x86_sse3)
107 + -DUSE_OPENMP=$(usex openmp)
108 + -DUSE_DOUBLE=$(usex double-precision)
109 )
110 cmake-utils_src_configure
111 }
112
113 diff --git a/sci-biology/fasttree/files/fasttree-2.1.7-format-security.patch b/sci-biology/fasttree/files/fasttree-2.1.7-format-security.patch
114 deleted file mode 100644
115 index 31dafdad46d..00000000000
116 --- a/sci-biology/fasttree/files/fasttree-2.1.7-format-security.patch
117 +++ /dev/null
118 @@ -1,25 +0,0 @@
119 - FastTreeUPGMA-2.1.7.c | 4 ++--
120 - 1 file changed, 2 insertions(+), 2 deletions(-)
121 -
122 -diff --git a/FastTreeUPGMA-2.1.7.c b/FastTreeUPGMA-2.1.7.c
123 -index af76cb1..4065f42 100644
124 ---- a/FastTreeUPGMA-2.1.7.c
125 -+++ b/FastTreeUPGMA-2.1.7.c
126 -@@ -535,7 +535,7 @@ int main(int argc, char **argv) {
127 - break;
128 - }
129 - if(iArg < argc-1) {
130 -- fprintf(stderr, usage);
131 -+ fprintf(stderr, "%s", usage);
132 - exit(1);
133 - }
134 -
135 -@@ -953,7 +953,7 @@ void PrintUPGMA(FILE *fp, UPGMA_t *UPGMA, char **names,
136 - assert(first >= 0);
137 - /* Print the name, or the subtree of duplicate names */
138 - if (nameNext[first] == -1) {
139 -- fprintf(fp, names[uniqueFirst[node]]);
140 -+ fprintf(fp, "%s", names[uniqueFirst[node]]);
141 - } else {
142 - fprintf(fp,"(%s:0.0",names[first]);
143 - int iName = nameNext[first];