commit: 78fa7b612b071489cb9c259d639f61ab654b9c78 Author: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org> AuthorDate: Sun Mar 7 16:22:22 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=78fa7b61
sci-biology/fasttree: 2.1.11 version bump, EAPI-7, cmake.eclass Closes: https://bugs.gentoo.org/594364 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-2.1.11.ebuild | 43 ++++++++++++++++++++++ sci-biology/fasttree/files/CMakeLists.txt | 25 +++++++------ .../files/fasttree-2.1.11-format-security.patch | 25 +++++++++++++ 4 files changed, 84 insertions(+), 12 deletions(-) diff --git a/sci-biology/fasttree/Manifest b/sci-biology/fasttree/Manifest index 1aedce930c6..5874bb6347a 100644 --- a/sci-biology/fasttree/Manifest +++ b/sci-biology/fasttree/Manifest @@ -1,3 +1,6 @@ +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-2.1.11.ebuild b/sci-biology/fasttree/fasttree-2.1.11.ebuild new file mode 100644 index 00000000000..cb2d16791ee --- /dev/null +++ b/sci-biology/fasttree/fasttree-2.1.11.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit cmake + +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 + cp "${FILESDIR}"/CMakeLists.txt . || die +} + +src_configure() { + local mycmakeargs=( + -DVERSION="${PV}" + -DHAS_SSE3=$(usex cpu_flags_x86_sse3) + -DUSE_OPENMP=$(usex openmp) + -DUSE_DOUBLE=$(usex double-precision) + ) + cmake_src_configure +} diff --git a/sci-biology/fasttree/files/CMakeLists.txt b/sci-biology/fasttree/files/CMakeLists.txt index e7c53afdaf3..c52b90cc7be 100644 --- a/sci-biology/fasttree/files/CMakeLists.txt +++ b/sci-biology/fasttree/files/CMakeLists.txt @@ -1,23 +1,24 @@ -cmake_minimum_required (VERSION 2.6) +cmake_minimum_required (VERSION 2.8.12) project(fasttree C) +include(GNUInstallDirs) + option(USE_OPENMP "Use OpenMP to parallelize many of the steps in computing a tree" ON) -option(USE_DOUBLE "Use double precission" OFF) +option(USE_DOUBLE "Use double precision" OFF) option(HAS_SSE3 "Use SSE2/SSE3 instructions to speed up some inner loops" ON) if(USE_OPENMP) - SET( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DOPENMP -fopenmp" ) - SET( CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -DOPENMP -fopenmp" ) -endif(USE_OPENMP) + set( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DOPENMP -fopenmp" ) + set( CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -DOPENMP -fopenmp" ) +endif() if(USE_DOUBLE) - SET( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DUSE_DOUBLE" ) -endif(USE_DOUBLE) + set( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DUSE_DOUBLE" ) +endif() if(NOT HAS_SSE3) - SET( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DNO_SSE" ) -endif(NOT HAS_SSE3) - + set( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DNO_SSE" ) +endif() add_executable(FastTree FastTree-${VERSION}.c) add_executable(FastTreeUPGMA FastTreeUPGMA-${VERSION}.c) @@ -25,6 +26,6 @@ add_executable(FastTreeUPGMA FastTreeUPGMA-${VERSION}.c) target_link_libraries(FastTree m) target_link_libraries(FastTreeUPGMA m) -install (TARGETS FastTree FastTreeUPGMA DESTINATION bin) +install (TARGETS FastTree FastTreeUPGMA DESTINATION ${CMAKE_INSTALL_BINDIR}) -install(FILES MOTree.pm CompareTree.pl CompareToBootstrap.pl DESTINATION share/fasttree) +install(FILES MOTree.pm CompareTree.pl CompareToBootstrap.pl DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/fasttree) diff --git a/sci-biology/fasttree/files/fasttree-2.1.11-format-security.patch b/sci-biology/fasttree/files/fasttree-2.1.11-format-security.patch new file mode 100644 index 00000000000..45023e4215f --- /dev/null +++ b/sci-biology/fasttree/files/fasttree-2.1.11-format-security.patch @@ -0,0 +1,25 @@ + FastTreeUPGMA-2.1.11.c | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/FastTreeUPGMA-2.1.11.c b/FastTreeUPGMA-2.1.11.c +index af76cb1..4065f42 100644 +--- a/FastTreeUPGMA-2.1.11.c ++++ b/FastTreeUPGMA-2.1.11.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];
