From 56bd759df1d0c750a065b8c845e93d5dfa6b549d Mon Sep 17 00:00:00 2001 From: "Robin H. Johnson" Date: Sat, 8 Aug 2015 13:49:04 -0700 Subject: proj/gentoo: Initial commit MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson X-Thanks: Alec Warner - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring - wrote much python to improve cvs2svn X-Thanks: Rich Freeman - validation scripts X-Thanks: Patrick Lauer - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed --- sci-biology/fasttree/Manifest | 6 +++ sci-biology/fasttree/fasttree-2.1.7.ebuild | 48 ++++++++++++++++++++++ sci-biology/fasttree/fasttree-2.1.8.ebuild | 48 ++++++++++++++++++++++ sci-biology/fasttree/files/CMakeLists.txt | 30 ++++++++++++++ .../files/fasttree-2.1.7-format-security.patch | 25 +++++++++++ .../files/fasttree-2.1.8-format-security.patch | 25 +++++++++++ sci-biology/fasttree/metadata.xml | 11 +++++ 7 files changed, 193 insertions(+) create mode 100644 sci-biology/fasttree/Manifest create mode 100644 sci-biology/fasttree/fasttree-2.1.7.ebuild create mode 100644 sci-biology/fasttree/fasttree-2.1.8.ebuild create mode 100644 sci-biology/fasttree/files/CMakeLists.txt create mode 100644 sci-biology/fasttree/files/fasttree-2.1.7-format-security.patch create mode 100644 sci-biology/fasttree/files/fasttree-2.1.8-format-security.patch create mode 100644 sci-biology/fasttree/metadata.xml (limited to 'sci-biology/fasttree') diff --git a/sci-biology/fasttree/Manifest b/sci-biology/fasttree/Manifest new file mode 100644 index 000000000000..da5370b6e7de --- /dev/null +++ b/sci-biology/fasttree/Manifest @@ -0,0 +1,6 @@ +DIST FastTree-2.1.7.c 383551 SHA256 da148297bb64711e43e38481186228496d418bb4ec0166e09df62a72248085a0 SHA512 e88916e6586885e095948e78e6654081f966c78fbf637cfdac01970f5337bfe5616efcd165fb5f9718af0831ff45047b165944f5da9c5931d9725ea6f49cb59e WHIRLPOOL c4b267d8c3d92f0e76110eed31fcbdb4c142a967c3df31ca30ef816716231e1a9867094d183173af28fc3e7cb9acba81a55d455fcb8833539b2cad0667683775 +DIST FastTree-2.1.8.c 385231 SHA256 b172d160f1b12b764d21a6937c3ce01ba42fa8743d95e083e031c6947762f837 SHA512 39a7d284412a602208c2a5df3d0a9a30fe3a584f7f7788d741fb1463b698692017f47bb23f70046d0873e9c8fd27c84ec23f6ca48adb0594193765ac732e6559 WHIRLPOOL 31331c85584c2030f56955e79250c6d6c06147007c6dd10f324c207fdebd4a1b89c87dcce52e5bab6e8d89cc69656d95a51bd808f52b8d61f6d29af40a5d4976 +DIST FastTreeUPGMA-2.1.7.c 95271 SHA256 199acc84910ca899dae9dd96d2ea133b651e76bbd855363cf620bf1b3cbd3abd SHA512 4d6a8e2cb28b8ee201091172a3baa59d432420839c6d2244b5fb8230ed9daa626b6bed22cb692393ca3d78b8f2d071fe18fbb4f9bdcdc47ef149c31e3f45546c WHIRLPOOL 538b44382137e6055452c901c76007b1c388a541c193c37f7baff26e59eb477450ce8acf7466d5debe0bc973fecc645d1f88d54f6f871670826bb151fd5b7496 +DIST FastTreeUPGMA-2.1.8.c 95271 SHA256 199acc84910ca899dae9dd96d2ea133b651e76bbd855363cf620bf1b3cbd3abd SHA512 4d6a8e2cb28b8ee201091172a3baa59d432420839c6d2244b5fb8230ed9daa626b6bed22cb692393ca3d78b8f2d071fe18fbb4f9bdcdc47ef149c31e3f45546c WHIRLPOOL 538b44382137e6055452c901c76007b1c388a541c193c37f7baff26e59eb477450ce8acf7466d5debe0bc973fecc645d1f88d54f6f871670826bb151fd5b7496 +DIST MOTreeComparison-2.1.7.tar.gz 13523 SHA256 aea482d47aca528026cdf86fc96dc59b7a9f66ea33b9e974f5c007b46335d174 SHA512 24d2247650d7728942bd1d987b548cefd65a16b433a3810876613e9fd1cff223d4349ee720b3d8d10a73af220c2c9f59a24d77ad34ff009325fe9f22aa35c72b WHIRLPOOL 7ed1009d622ce77c59cf79078a08a08dafb281e87a6ae99be7b7fba9451f2748bfd7a51036c041e3667ea8e29f7545276b799d708aabb7ea1988ea443f73f475 +DIST MOTreeComparison-2.1.8.tar.gz 13523 SHA256 aea482d47aca528026cdf86fc96dc59b7a9f66ea33b9e974f5c007b46335d174 SHA512 24d2247650d7728942bd1d987b548cefd65a16b433a3810876613e9fd1cff223d4349ee720b3d8d10a73af220c2c9f59a24d77ad34ff009325fe9f22aa35c72b WHIRLPOOL 7ed1009d622ce77c59cf79078a08a08dafb281e87a6ae99be7b7fba9451f2748bfd7a51036c041e3667ea8e29f7545276b799d708aabb7ea1988ea443f73f475 diff --git a/sci-biology/fasttree/fasttree-2.1.7.ebuild b/sci-biology/fasttree/fasttree-2.1.7.ebuild new file mode 100644 index 000000000000..522d09f60400 --- /dev/null +++ b/sci-biology/fasttree/fasttree-2.1.7.ebuild @@ -0,0 +1,48 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +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 new file mode 100644 index 000000000000..fea83a4d7696 --- /dev/null +++ b/sci-biology/fasttree/fasttree-2.1.8.ebuild @@ -0,0 +1,48 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +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) + $(cmake-utils_use_use double-precision double) + ) + cmake-utils_src_configure +} diff --git a/sci-biology/fasttree/files/CMakeLists.txt b/sci-biology/fasttree/files/CMakeLists.txt new file mode 100644 index 000000000000..e7c53afdaf36 --- /dev/null +++ b/sci-biology/fasttree/files/CMakeLists.txt @@ -0,0 +1,30 @@ +cmake_minimum_required (VERSION 2.6) +project(fasttree C) + +option(USE_OPENMP "Use OpenMP to parallelize many of the steps in computing a tree" ON) +option(USE_DOUBLE "Use double precission" OFF) +option(HAS_SSE3 "Use SSE2/SSE3 instructions to speed up some inner loops" ON) + +if(USE_OPENMP) + SET( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DOPENMP -fopenmp" ) + SET( CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -DOPENMP -fopenmp" ) +endif(USE_OPENMP) + +if(USE_DOUBLE) + SET( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DUSE_DOUBLE" ) +endif(USE_DOUBLE) + +if(NOT HAS_SSE3) + SET( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DNO_SSE" ) +endif(NOT HAS_SSE3) + + +add_executable(FastTree FastTree-${VERSION}.c) +add_executable(FastTreeUPGMA FastTreeUPGMA-${VERSION}.c) + +target_link_libraries(FastTree m) +target_link_libraries(FastTreeUPGMA m) + +install (TARGETS FastTree FastTreeUPGMA DESTINATION bin) + +install(FILES MOTree.pm CompareTree.pl CompareToBootstrap.pl DESTINATION share/fasttree) 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 new file mode 100644 index 000000000000..31dafdad46de --- /dev/null +++ b/sci-biology/fasttree/files/fasttree-2.1.7-format-security.patch @@ -0,0 +1,25 @@ + 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]; 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 new file mode 100644 index 000000000000..15f5c174ec40 --- /dev/null +++ b/sci-biology/fasttree/files/fasttree-2.1.8-format-security.patch @@ -0,0 +1,25 @@ + 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]; diff --git a/sci-biology/fasttree/metadata.xml b/sci-biology/fasttree/metadata.xml new file mode 100644 index 000000000000..5ee1f51e55df --- /dev/null +++ b/sci-biology/fasttree/metadata.xml @@ -0,0 +1,11 @@ + + + + sci-biology + + + use double precision instead of single-precision floating point + (2x memroy required) + + + -- cgit v1.2.3-65-gdbad