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sci-biology/fasttree: Drop 2.1.8

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Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
This commit is contained in:
Andreas Sturmlechner
2021-03-07 19:53:19 +01:00
parent 78fa7b612b
commit 36c8ba7f85
3 changed files with 0 additions and 75 deletions
Download Patch File Download Diff File Expand all files Collapse all files
sci-biology/fasttree/Manifest
-3
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@@ -1,6 +1,3 @@
DIST FastTree-2.1.11.c 395543 BLAKE2B 5bea3fba66ddf077ce42c3e1791505a9fa909bb619e30e0c0370631996d932c63ca172fffc1721ac9f081a16bed3b1c99a9c7f6e4a3bb269b82545e2978904d3 SHA512 2bbb1cc078b04125a55b8c02f65c9fbfb6db894c2fbfdaac8f86cc0084f2579723cdc4f6aa63bf4338b767d0fdaffa8dd503e4126c3f5f700d4f3da9fc085ee5
DIST FastTree-2.1.8.c 385231 BLAKE2B 6f42025ef69b990e051263ccfa23f95d0cde326798c54d8f702c50127338711898c380d1dbd82ab775667eada047048ba8d68288b030af4984019a5f2c23729f SHA512 39a7d284412a602208c2a5df3d0a9a30fe3a584f7f7788d741fb1463b698692017f47bb23f70046d0873e9c8fd27c84ec23f6ca48adb0594193765ac732e6559
DIST FastTreeUPGMA-2.1.11.c 95271 BLAKE2B 1de328881f6452b9c7423c9ed381ab2eb31c4f3ee6426481a6b1089c1359627d4cbbfbea868ebeab9538f82e17f45f1bff8ec07c7370e6432bef6bae449798a8 SHA512 4d6a8e2cb28b8ee201091172a3baa59d432420839c6d2244b5fb8230ed9daa626b6bed22cb692393ca3d78b8f2d071fe18fbb4f9bdcdc47ef149c31e3f45546c
DIST FastTreeUPGMA-2.1.8.c 95271 BLAKE2B 1de328881f6452b9c7423c9ed381ab2eb31c4f3ee6426481a6b1089c1359627d4cbbfbea868ebeab9538f82e17f45f1bff8ec07c7370e6432bef6bae449798a8 SHA512 4d6a8e2cb28b8ee201091172a3baa59d432420839c6d2244b5fb8230ed9daa626b6bed22cb692393ca3d78b8f2d071fe18fbb4f9bdcdc47ef149c31e3f45546c
DIST MOTreeComparison-2.1.11.tar.gz 13523 BLAKE2B 97638edd945412ff00e3dfcfc89ec6ea52ae8c43531d5cb680d97e9c62fcad80e861f58ec987abcd2282166dd7886101edba4875531bd9d6ac23df242e0dbd5b SHA512 24d2247650d7728942bd1d987b548cefd65a16b433a3810876613e9fd1cff223d4349ee720b3d8d10a73af220c2c9f59a24d77ad34ff009325fe9f22aa35c72b
DIST MOTreeComparison-2.1.8.tar.gz 13523 BLAKE2B 97638edd945412ff00e3dfcfc89ec6ea52ae8c43531d5cb680d97e9c62fcad80e861f58ec987abcd2282166dd7886101edba4875531bd9d6ac23df242e0dbd5b SHA512 24d2247650d7728942bd1d987b548cefd65a16b433a3810876613e9fd1cff223d4349ee720b3d8d10a73af220c2c9f59a24d77ad34ff009325fe9f22aa35c72b
sci-biology/fasttree/fasttree-2.1.8.ebuild
-47
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@@ -1,47 +0,0 @@
# Copyright 1999-2018 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
inherit cmake-utils
DESCRIPTION="Fast inference of approximately-maximum-likelihood phylogenetic trees"
HOMEPAGE="http://www.microbesonline.org/fasttree/"
SRC_URI="
http://www.microbesonline.org/fasttree/FastTree-${PV}.c
http://www.microbesonline.org/fasttree/FastTreeUPGMA.c -> FastTreeUPGMA-${PV}.c
http://www.microbesonline.org/fasttree/MOTreeComparison.tar.gz -> MOTreeComparison-${PV}.tar.gz
"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="double-precision openmp cpu_flags_x86_sse3"
REQUIRED_USE="?? ( double-precision cpu_flags_x86_sse3 )"
DOCS=( README )
PATCHES=( "${FILESDIR}"/${P}-format-security.patch )
src_unpack() {
mkdir "${S}" || die
cd "${S}" || die
unpack ${A}
cp "${DISTDIR}"/{FastTreeUPGMA-${PV}.c,FastTree-${PV}.c} . || die
}
src_prepare() {
cp "${FILESDIR}"/CMakeLists.txt . || die
cmake-utils_src_prepare
}
src_configure() {
local mycmakeargs=(
-DVERSION="${PV}"
-DHAS_SSE3=$(usex cpu_flags_x86_sse3)
-DUSE_OPENMP=$(usex openmp)
-DUSE_DOUBLE=$(usex double-precision)
)
cmake-utils_src_configure
}
sci-biology/fasttree/files/fasttree-2.1.8-format-security.patch
-25
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@@ -1,25 +0,0 @@
FastTreeUPGMA-2.1.8.c | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/FastTreeUPGMA-2.1.8.c b/FastTreeUPGMA-2.1.8.c
index af76cb1..4065f42 100644
--- a/FastTreeUPGMA-2.1.8.c
+++ b/FastTreeUPGMA-2.1.8.c
@@ -535,7 +535,7 @@ int main(int argc, char **argv) {
break;
}
if(iArg < argc-1) {
- fprintf(stderr, usage);
+ fprintf(stderr, "%s", usage);
exit(1);
}
@@ -953,7 +953,7 @@ void PrintUPGMA(FILE *fp, UPGMA_t *UPGMA, char **names,
assert(first >= 0);
/* Print the name, or the subtree of duplicate names */
if (nameNext[first] == -1) {
- fprintf(fp, names[uniqueFirst[node]]);
+ fprintf(fp, "%s", names[uniqueFirst[node]]);
} else {
fprintf(fp,"(%s:0.0",names[first]);
int iName = nameNext[first];