[gentoo-commits] repo/gentoo:master commit in: sci-biology/fasttree/, sci-biology/fasttree/files/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/fasttree/, sci-biology/fasttree/files/

[Andreas Sturmlechner]

commit:     3ea6a505ae3bfa74715b81a5ef39b726cc4abbe7
Author:     Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
AuthorDate: Sun Oct 14 16:32:42 2018 +0000
Commit:     Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
CommitDate: Sun Oct 14 16:34:30 2018 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3ea6a505

sci-biology/fasttree: Drop 2.1.7

Signed-off-by: Andreas Sturmlechner <asturm <AT> gentoo.org>
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(-)

diff --git a/sci-biology/fasttree/Manifest b/sci-biology/fasttree/Manifest
index f59e3b0ab62..1aedce930c6 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 aa597952269..00000000000
--- 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 7df71ee4474..3f9e4ad5f75 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 31dafdad46d..00000000000
--- 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];