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commit: 3ea6a505ae3bfa74715b81a5ef39b726cc4abbe7 |
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Author: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org> |
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AuthorDate: Sun Oct 14 16:32:42 2018 +0000 |
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Commit: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org> |
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CommitDate: Sun Oct 14 16:34:30 2018 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3ea6a505 |
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|
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sci-biology/fasttree: Drop 2.1.7 |
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|
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Signed-off-by: Andreas Sturmlechner <asturm <AT> gentoo.org> |
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Package-Manager: Portage-2.3.51, Repoman-2.3.11 |
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|
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sci-biology/fasttree/Manifest | 3 -- |
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sci-biology/fasttree/fasttree-2.1.7.ebuild | 47 ---------------------- |
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sci-biology/fasttree/fasttree-2.1.8.ebuild | 10 ++--- |
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.../files/fasttree-2.1.7-format-security.patch | 25 ------------ |
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4 files changed, 5 insertions(+), 80 deletions(-) |
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|
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diff --git a/sci-biology/fasttree/Manifest b/sci-biology/fasttree/Manifest |
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index f59e3b0ab62..1aedce930c6 100644 |
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--- a/sci-biology/fasttree/Manifest |
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+++ b/sci-biology/fasttree/Manifest |
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@@ -1,6 +1,3 @@ |
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-DIST FastTree-2.1.7.c 383551 BLAKE2B 853881cb39355a134133b012ef311702481d7883e8398bc55bcb3d3274f8414d2579a086176c3d2abdb59ecff7bf8cb6223e89b5ea320a3292f0a9915950c6fa SHA512 e88916e6586885e095948e78e6654081f966c78fbf637cfdac01970f5337bfe5616efcd165fb5f9718af0831ff45047b165944f5da9c5931d9725ea6f49cb59e |
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DIST FastTree-2.1.8.c 385231 BLAKE2B 6f42025ef69b990e051263ccfa23f95d0cde326798c54d8f702c50127338711898c380d1dbd82ab775667eada047048ba8d68288b030af4984019a5f2c23729f SHA512 39a7d284412a602208c2a5df3d0a9a30fe3a584f7f7788d741fb1463b698692017f47bb23f70046d0873e9c8fd27c84ec23f6ca48adb0594193765ac732e6559 |
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-DIST FastTreeUPGMA-2.1.7.c 95271 BLAKE2B 1de328881f6452b9c7423c9ed381ab2eb31c4f3ee6426481a6b1089c1359627d4cbbfbea868ebeab9538f82e17f45f1bff8ec07c7370e6432bef6bae449798a8 SHA512 4d6a8e2cb28b8ee201091172a3baa59d432420839c6d2244b5fb8230ed9daa626b6bed22cb692393ca3d78b8f2d071fe18fbb4f9bdcdc47ef149c31e3f45546c |
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DIST FastTreeUPGMA-2.1.8.c 95271 BLAKE2B 1de328881f6452b9c7423c9ed381ab2eb31c4f3ee6426481a6b1089c1359627d4cbbfbea868ebeab9538f82e17f45f1bff8ec07c7370e6432bef6bae449798a8 SHA512 4d6a8e2cb28b8ee201091172a3baa59d432420839c6d2244b5fb8230ed9daa626b6bed22cb692393ca3d78b8f2d071fe18fbb4f9bdcdc47ef149c31e3f45546c |
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-DIST MOTreeComparison-2.1.7.tar.gz 13523 BLAKE2B 97638edd945412ff00e3dfcfc89ec6ea52ae8c43531d5cb680d97e9c62fcad80e861f58ec987abcd2282166dd7886101edba4875531bd9d6ac23df242e0dbd5b SHA512 24d2247650d7728942bd1d987b548cefd65a16b433a3810876613e9fd1cff223d4349ee720b3d8d10a73af220c2c9f59a24d77ad34ff009325fe9f22aa35c72b |
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DIST MOTreeComparison-2.1.8.tar.gz 13523 BLAKE2B 97638edd945412ff00e3dfcfc89ec6ea52ae8c43531d5cb680d97e9c62fcad80e861f58ec987abcd2282166dd7886101edba4875531bd9d6ac23df242e0dbd5b SHA512 24d2247650d7728942bd1d987b548cefd65a16b433a3810876613e9fd1cff223d4349ee720b3d8d10a73af220c2c9f59a24d77ad34ff009325fe9f22aa35c72b |
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|
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diff --git a/sci-biology/fasttree/fasttree-2.1.7.ebuild b/sci-biology/fasttree/fasttree-2.1.7.ebuild |
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deleted file mode 100644 |
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index aa597952269..00000000000 |
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--- a/sci-biology/fasttree/fasttree-2.1.7.ebuild |
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+++ /dev/null |
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@@ -1,47 +0,0 @@ |
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-# Copyright 1999-2015 Gentoo Foundation |
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-# Distributed under the terms of the GNU General Public License v2 |
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- |
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-EAPI=5 |
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- |
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-inherit cmake-utils |
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- |
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-DESCRIPTION="Fast inference of approximately-maximum-likelihood phylogenetic trees" |
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-HOMEPAGE="http://www.microbesonline.org/fasttree/" |
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-SRC_URI=" |
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- http://www.microbesonline.org/fasttree/FastTree-${PV}.c |
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- http://www.microbesonline.org/fasttree/FastTreeUPGMA.c -> FastTreeUPGMA-${PV}.c |
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- http://www.microbesonline.org/fasttree/MOTreeComparison.tar.gz -> MOTreeComparison-${PV}.tar.gz |
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-" |
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- |
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-LICENSE="GPL-2" |
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-SLOT="0" |
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-KEYWORDS="amd64 x86" |
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-IUSE="double-precision openmp cpu_flags_x86_sse3" |
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- |
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-REQUIRED_USE="?? ( double-precision cpu_flags_x86_sse3 )" |
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- |
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-DOCS=( README ) |
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- |
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-PATCHES=( "${FILESDIR}"/${P}-format-security.patch ) |
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- |
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-src_unpack() { |
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- mkdir "${S}" || die |
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- cd "${S}" || die |
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- unpack ${A} |
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- cp "${DISTDIR}"/{FastTreeUPGMA-${PV}.c,FastTree-${PV}.c} . || die |
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-} |
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- |
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-src_prepare() { |
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- cp "${FILESDIR}"/CMakeLists.txt . || die |
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- cmake-utils_src_prepare |
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-} |
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- |
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-src_configure() { |
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- local mycmakeargs=( |
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- -DVERSION="${PV}" |
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- $(cmake-utils_use_has cpu_flags_x86_sse3 sse3) |
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- $(cmake-utils_use_use openmp) |
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- $(cmake-utils_use_use double-precision double) |
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- ) |
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- cmake-utils_src_configure |
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-} |
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|
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diff --git a/sci-biology/fasttree/fasttree-2.1.8.ebuild b/sci-biology/fasttree/fasttree-2.1.8.ebuild |
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index 7df71ee4474..3f9e4ad5f75 100644 |
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--- a/sci-biology/fasttree/fasttree-2.1.8.ebuild |
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+++ b/sci-biology/fasttree/fasttree-2.1.8.ebuild |
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@@ -1,7 +1,7 @@ |
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-# Copyright 1999-2015 Gentoo Foundation |
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+# Copyright 1999-2018 Gentoo Authors |
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# Distributed under the terms of the GNU General Public License v2 |
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|
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-EAPI=5 |
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+EAPI=6 |
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|
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inherit cmake-utils |
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|
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@@ -39,9 +39,9 @@ src_prepare() { |
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src_configure() { |
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local mycmakeargs=( |
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-DVERSION="${PV}" |
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- $(cmake-utils_use_has cpu_flags_x86_sse3 sse3) |
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- $(cmake-utils_use_use openmp) |
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- $(cmake-utils_use_use double-precision double) |
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+ -DHAS_SSE3=$(usex cpu_flags_x86_sse3) |
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+ -DUSE_OPENMP=$(usex openmp) |
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+ -DUSE_DOUBLE=$(usex double-precision) |
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) |
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cmake-utils_src_configure |
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} |
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|
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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 |
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deleted file mode 100644 |
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index 31dafdad46d..00000000000 |
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--- a/sci-biology/fasttree/files/fasttree-2.1.7-format-security.patch |
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+++ /dev/null |
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@@ -1,25 +0,0 @@ |
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- FastTreeUPGMA-2.1.7.c | 4 ++-- |
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- 1 file changed, 2 insertions(+), 2 deletions(-) |
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- |
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-diff --git a/FastTreeUPGMA-2.1.7.c b/FastTreeUPGMA-2.1.7.c |
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-index af76cb1..4065f42 100644 |
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---- a/FastTreeUPGMA-2.1.7.c |
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-+++ b/FastTreeUPGMA-2.1.7.c |
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-@@ -535,7 +535,7 @@ int main(int argc, char **argv) { |
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- break; |
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- } |
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- if(iArg < argc-1) { |
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-- fprintf(stderr, usage); |
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-+ fprintf(stderr, "%s", usage); |
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- exit(1); |
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- } |
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- |
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-@@ -953,7 +953,7 @@ void PrintUPGMA(FILE *fp, UPGMA_t *UPGMA, char **names, |
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- assert(first >= 0); |
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- /* Print the name, or the subtree of duplicate names */ |
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- if (nameNext[first] == -1) { |
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-- fprintf(fp, names[uniqueFirst[node]]); |
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-+ fprintf(fp, "%s", names[uniqueFirst[node]]); |
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- } else { |
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- fprintf(fp,"(%s:0.0",names[first]); |
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- int iName = nameNext[first]; |