commit: 36c8ba7f8501ebe4fd3988a5d65db5ccf1deea98 Author: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org> AuthorDate: Sun Mar 7 16:23:00 2021 +0000 Commit: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org> CommitDate: Sun Mar 7 18:53:19 2021 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=36c8ba7f
sci-biology/fasttree: Drop 2.1.8 Package-Manager: Portage-3.0.16, Repoman-3.0.2 Signed-off-by: Andreas Sturmlechner <asturm <AT> gentoo.org> sci-biology/fasttree/Manifest | 3 -- sci-biology/fasttree/fasttree-2.1.8.ebuild | 47 ---------------------- .../files/fasttree-2.1.8-format-security.patch | 25 ------------ 3 files changed, 75 deletions(-) diff --git a/sci-biology/fasttree/Manifest b/sci-biology/fasttree/Manifest index 5874bb6347a..cf6d3bc2033 100644 --- a/sci-biology/fasttree/Manifest +++ b/sci-biology/fasttree/Manifest @@ -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 diff --git a/sci-biology/fasttree/fasttree-2.1.8.ebuild b/sci-biology/fasttree/fasttree-2.1.8.ebuild deleted file mode 100644 index 3f9e4ad5f75..00000000000 --- a/sci-biology/fasttree/fasttree-2.1.8.ebuild +++ /dev/null @@ -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 -} diff --git a/sci-biology/fasttree/files/fasttree-2.1.8-format-security.patch b/sci-biology/fasttree/files/fasttree-2.1.8-format-security.patch deleted file mode 100644 index 15f5c174ec4..00000000000 --- a/sci-biology/fasttree/files/fasttree-2.1.8-format-security.patch +++ /dev/null @@ -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];
