From 3ea6a505ae3bfa74715b81a5ef39b726cc4abbe7 Mon Sep 17 00:00:00 2001 From: Andreas Sturmlechner Date: Sun, 14 Oct 2018 18:32:42 +0200 Subject: sci-biology/fasttree: Drop 2.1.7 Signed-off-by: Andreas Sturmlechner Package-Manager: Portage-2.3.51, Repoman-2.3.11 --- sci-biology/fasttree/Manifest | 3 -- sci-biology/fasttree/fasttree-2.1.7.ebuild | 47 ---------------------- sci-biology/fasttree/fasttree-2.1.8.ebuild | 10 ++--- .../files/fasttree-2.1.7-format-security.patch | 25 ------------ 4 files changed, 5 insertions(+), 80 deletions(-) delete mode 100644 sci-biology/fasttree/fasttree-2.1.7.ebuild delete mode 100644 sci-biology/fasttree/files/fasttree-2.1.7-format-security.patch (limited to 'sci-biology/fasttree') diff --git a/sci-biology/fasttree/Manifest b/sci-biology/fasttree/Manifest index f59e3b0ab62c..1aedce930c6c 100644 --- a/sci-biology/fasttree/Manifest +++ b/sci-biology/fasttree/Manifest @@ -1,6 +1,3 @@ -DIST FastTree-2.1.7.c 383551 BLAKE2B 853881cb39355a134133b012ef311702481d7883e8398bc55bcb3d3274f8414d2579a086176c3d2abdb59ecff7bf8cb6223e89b5ea320a3292f0a9915950c6fa SHA512 e88916e6586885e095948e78e6654081f966c78fbf637cfdac01970f5337bfe5616efcd165fb5f9718af0831ff45047b165944f5da9c5931d9725ea6f49cb59e DIST FastTree-2.1.8.c 385231 BLAKE2B 6f42025ef69b990e051263ccfa23f95d0cde326798c54d8f702c50127338711898c380d1dbd82ab775667eada047048ba8d68288b030af4984019a5f2c23729f SHA512 39a7d284412a602208c2a5df3d0a9a30fe3a584f7f7788d741fb1463b698692017f47bb23f70046d0873e9c8fd27c84ec23f6ca48adb0594193765ac732e6559 -DIST FastTreeUPGMA-2.1.7.c 95271 BLAKE2B 1de328881f6452b9c7423c9ed381ab2eb31c4f3ee6426481a6b1089c1359627d4cbbfbea868ebeab9538f82e17f45f1bff8ec07c7370e6432bef6bae449798a8 SHA512 4d6a8e2cb28b8ee201091172a3baa59d432420839c6d2244b5fb8230ed9daa626b6bed22cb692393ca3d78b8f2d071fe18fbb4f9bdcdc47ef149c31e3f45546c DIST FastTreeUPGMA-2.1.8.c 95271 BLAKE2B 1de328881f6452b9c7423c9ed381ab2eb31c4f3ee6426481a6b1089c1359627d4cbbfbea868ebeab9538f82e17f45f1bff8ec07c7370e6432bef6bae449798a8 SHA512 4d6a8e2cb28b8ee201091172a3baa59d432420839c6d2244b5fb8230ed9daa626b6bed22cb692393ca3d78b8f2d071fe18fbb4f9bdcdc47ef149c31e3f45546c -DIST MOTreeComparison-2.1.7.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-2.1.7.ebuild b/sci-biology/fasttree/fasttree-2.1.7.ebuild deleted file mode 100644 index aa5979522691..000000000000 --- a/sci-biology/fasttree/fasttree-2.1.7.ebuild +++ /dev/null @@ -1,47 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -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}" - $(cmake-utils_use_has cpu_flags_x86_sse3 sse3) - $(cmake-utils_use_use openmp) - $(cmake-utils_use_use double-precision double) - ) - cmake-utils_src_configure -} diff --git a/sci-biology/fasttree/fasttree-2.1.8.ebuild b/sci-biology/fasttree/fasttree-2.1.8.ebuild index 7df71ee4474d..3f9e4ad5f759 100644 --- a/sci-biology/fasttree/fasttree-2.1.8.ebuild +++ b/sci-biology/fasttree/fasttree-2.1.8.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2018 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=6 inherit cmake-utils @@ -39,9 +39,9 @@ src_prepare() { src_configure() { local mycmakeargs=( -DVERSION="${PV}" - $(cmake-utils_use_has cpu_flags_x86_sse3 sse3) - $(cmake-utils_use_use openmp) - $(cmake-utils_use_use double-precision double) + -DHAS_SSE3=$(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-2.1.7-format-security.patch b/sci-biology/fasttree/files/fasttree-2.1.7-format-security.patch deleted file mode 100644 index 31dafdad46de..000000000000 --- a/sci-biology/fasttree/files/fasttree-2.1.7-format-security.patch +++ /dev/null @@ -1,25 +0,0 @@ - FastTreeUPGMA-2.1.7.c | 4 ++-- - 1 file changed, 2 insertions(+), 2 deletions(-) - -diff --git a/FastTreeUPGMA-2.1.7.c b/FastTreeUPGMA-2.1.7.c -index af76cb1..4065f42 100644 ---- a/FastTreeUPGMA-2.1.7.c -+++ b/FastTreeUPGMA-2.1.7.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]; -- cgit v1.2.3-65-gdbad