Version BUmp; drop old

Package-Manager: portage-2.2.18/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

8 files changed, 135 insertions, 71 deletions

diff --git a/sci-biology/fasttree/ChangeLog b/sci-biology/fasttree/ChangeLog
index 5b063a229025..7d27ebf09e25 100644
--- a/sci-biology/fasttree/ChangeLog
+++ b/sci-biology/fasttree/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-biology/fasttree
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/fasttree/ChangeLog,v 1.5 2015/01/29 21:21:10 mgorny Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/fasttree/ChangeLog,v 1.6 2015/03/29 14:30:36 jlec Exp $
+
+*fasttree-2.1.8 (29 Mar 2015)
+
+  29 Mar 2015; Justin Lecher <jlec@gentoo.org> +fasttree-2.1.8.ebuild,
+  +files/fasttree-2.1.7-format-security.patch,
+  +files/fasttree-2.1.8-format-security.patch, -fasttree-2.0.1.ebuild,
+  -files/fasttree-2.0.1-asneeded.patch, fasttree-2.1.7.ebuild:
+  Version BUmp; drop old
 
   29 Jan 2015; Michał Górny <mgorny@gentoo.org> fasttree-2.1.7.ebuild:
   Switch to CPU_FLAGS_X86.
diff --git a/sci-biology/fasttree/Manifest b/sci-biology/fasttree/Manifest
index 40ba1459fdfa..0cdec5f68fb6 100644
--- a/sci-biology/fasttree/Manifest
+++ b/sci-biology/fasttree/Manifest
@@ -1,32 +1,35 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
 
 AUX CMakeLists.txt 948 SHA256 60c21f04ea3ef04782dfc0328e317b6d04197a45af4d15c5c43f4f87a1f82c44 SHA512 9858800bfce8d256ccb834a06bad5a5230f90f025a9c9b3c9aafe7244d219d66810530f6688e02889cdb67d6a9459d8e26cd1a9fcf2e8825278b31d0e8d51ff3 WHIRLPOOL edc50a85eaec6161924f38569c33ccd35170f9ac89e17741e4a87ceb350b165fdf6e118c20bfd27a02ec1e01aa76be8665908f39c531a292d3d1b706e6c1b25a
-AUX fasttree-2.0.1-asneeded.patch 455 SHA256 f43ec50d2d4284d60b438e62a407686a5149a31e9c5e389744d894b9e55243eb SHA512 fdd5a0f475d7f00c266a35dfafe7b5131919e345e39b03f51f9ab4ef64ac7bbb5372b437354e5498a242805fb973e4357c1254148abbce64ff71c00b57610ad8 WHIRLPOOL 165ccae141b47231192c091c133a004fdeb3aadbf3539fc6abe7af2df388bedc1c9947e2c335a58aabb918f6baf921a03088d07b0e5c1335be36cfa3765fd371
+AUX fasttree-2.1.7-format-security.patch 783 SHA256 83e4b1b6de9fb5f8875a4d53ed274866bb34bbb36610b0f7bbda22ebea60fd07 SHA512 cabda061de75a1e1b34732946448ee08717f265d7fa8ea413f56eb8bad150ebde9f376a13591167a7786caf17a0d4bb1f8cb7176b74965a47f79b9608d32bcf8 WHIRLPOOL cec0331b56114bd36085c1a64b048979579984b769102358365e4c719b03b1fb6b52919f4397b97c424613811e4e1ef572f3e6fb595aa5340e25d6881bc46e97
+AUX fasttree-2.1.8-format-security.patch 783 SHA256 cd838048ce9b99adb462f75cdb56ec65274e0c96340685c736858580b38c2579 SHA512 9bbf66cddca2b6c202fdeeab4092036852cb1ebe132ebf4d96cba1bea75bb5668dd6ee97d4d020a4b7cf7111bee6d0c3004b0bd74ee4685ef98eeeb5e9a23eb3 WHIRLPOOL d20139d2ba391ed11924b70495d16fdf706171953f712214b5d0a83395cd97a0395c7dc8a6e586c3ee87579c1124c7599cc89e933ba684940909daa7eda11f2d
 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 fasttree-2.0.1.tar.bz2 149279 SHA256 968a42f126c67f471a21c6ffe621cbedb3ed406838a3d80e799487aedc137fb4 SHA512 b6c7fb9f2eb3ac859164ce459da0a258827550020973e126b984c8f4f87a7f708f46731b6c6bb148cc3fe5cf5ddc19c7c1211b78c19880644fcfb05b65b42367 WHIRLPOOL 1aa3b811afb34b4331f411005fb7e2f9972fcefc022fa3bf68d0156f13be89ec969979c8431d0cd209f6994f8241698b10ef0599c5684e3f943edb61ae59b1bc
-EBUILD fasttree-2.0.1.ebuild 783 SHA256 61f547093efad5df2ca57caa7fa35cf9c2b194c8b677fac5a008aecd3d744548 SHA512 933be57dd573f7fc0dc3f1768fc8c2366fb92a5a8c0a66c3065ee4a2b19e804b62c9ebf7f48fb9ff19a03872d8fe419f16f43325373cd081d59ca9927cd970d9 WHIRLPOOL 78c6cacbefa6525423cd2d302a4ae73df14eca0255c254e689360ff2d68e596251965b642f1fb98d1b3caed7b31323532513536be3128f436ae71b9a4bf2bec4
-EBUILD fasttree-2.1.7.ebuild 1256 SHA256 a20e4010c320b3aca1eaa1f7f5576f50eff51c0c792bc0eb5086aecf4434ab63 SHA512 833d516d269442e8fba20e8bbc4830488f0b1cadf00f01b2a8f74167f2e5127c9d624113c7bb7988ded430714e2874574ae7f80965c78ba681eccb15d493dd45 WHIRLPOOL 16adf456eb617f92d74a691fe9f7c654a432a41716a4986eedd72564761f8c001c72556429269f31dccbce5f062116638e5393f65072a7de18ceebb4295e9741
-MISC ChangeLog 983 SHA256 ef7f629a57692cda21875e30160b719c0af84ca40a4e2c46613374c7d8dabd9f SHA512 9f2807c240927d362567a18593881b536ebb3e71626461ea33dda051df99e9a754fb530e2670a7b3d86017de714b6e4e19b1bb08392d3370a2030af1b924a8c4 WHIRLPOOL 3b75ef96f0cdc16343b93afa81e9565244e79843629febb4968197932dde9cc70cebd8cbcaf1e29d7107fb0858dc09717a6ba070e49754d2ee856acf98f5f036
+DIST MOTreeComparison-2.1.8.tar.gz 13523 SHA256 aea482d47aca528026cdf86fc96dc59b7a9f66ea33b9e974f5c007b46335d174 SHA512 24d2247650d7728942bd1d987b548cefd65a16b433a3810876613e9fd1cff223d4349ee720b3d8d10a73af220c2c9f59a24d77ad34ff009325fe9f22aa35c72b WHIRLPOOL 7ed1009d622ce77c59cf79078a08a08dafb281e87a6ae99be7b7fba9451f2748bfd7a51036c041e3667ea8e29f7545276b799d708aabb7ea1988ea443f73f475
+EBUILD fasttree-2.1.7.ebuild 1308 SHA256 6f04fc0be3f01edc89f6f88e15346cf781139cbd2a3c1c809182ec8c68445f22 SHA512 0bd4859eee95c69d39fbaee92bd2550c5bfc4bc2d896afcc877e80511bff214a4069c85bfc2b0919bf6389430173460edf75349c7dc3def8a2125466e4f41b66 WHIRLPOOL fef8beffdb116954c94c80024aa2c3eaa76fb22ddb4d3382ae4161296e8837be65a5935115409ce1b72ee4b8c8a3c440d55d5f953dde95e15ded63e80b5d6d50
+EBUILD fasttree-2.1.8.ebuild 1308 SHA256 49f2a69938cccb959a4b72d12fc12bc02a8b6e2477e628583fc0467297a4ea3b SHA512 3bf356ccdd85da7d0ad41cf7883bd5d88e73dc9a41b5d73a578e38b5744b9350b696bf450d7b610bc46be8d9f994e64c5eacd60691febab2fe93c15c7a8af42a WHIRLPOOL 67ab63094f275340b8b46dd4951f45fbc9d572cfc97c536e1ce99ff2a6036e95f7e95552af675bbe82ece01b12106e53a7e815f91841488ec30097394b05c6c9
+MISC ChangeLog 1290 SHA256 05f80724b3da0f3423b2f8376bb652e8a8c57388406e5cb0cc12297180614f3a SHA512 9a7c438c763d774bd64523f7f55f9e04bdade2f141b75a60f12b03a31e6495646a9596b33ca90122a51c4f6673eacbb38e9a708d71a5b1307c261ccab0f1560d WHIRLPOOL e9a5f4fb7aceac2c9622b55ccd214ec001d7c9c483840e41ee8a89a47762bf69816b47bf98833b6d540cf71876e215bae2acdfabfa46a1657f76303c1d931393
 MISC metadata.xml 315 SHA256 3fb5d83ebb92699b2a8ef0efcd99ce41389b6561a22ca457b88745238a887dcd SHA512 4f3de85a5d5f6fac19f34a125ded80cbe4908ae8d3a385387b4742766bd6447c661d3d8df676c8642289a63ee646677c346687b9428153550f9e74e2fe961f80 WHIRLPOOL 4a28481b281c50749d53412ffd3de0c409b849678232662e9b6cb41661bcf946ac5daa0db8bb623985d46f8a6407e1afc0b573f2a39ca18c7b6d2c44278d3ac6
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+Version: GnuPG v2.0
 
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diff --git a/sci-biology/fasttree/fasttree-2.0.1.ebuild b/sci-biology/fasttree/fasttree-2.0.1.ebuild
deleted file mode 100644
index 7a2691703290..000000000000
--- a/sci-biology/fasttree/fasttree-2.0.1.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/fasttree/fasttree-2.0.1.ebuild,v 1.2 2010/06/20 18:20:40 xarthisius Exp $
-
-EAPI="2"
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Fast inference of approximately-maximum-likelihood phylogenetic trees"
-HOMEPAGE="http://www.microbesonline.org/fasttree/"
-#SRC_URI="http://www.microbesonline.org/fasttree/FastTree.c"
-SRC_URI="mirror://gentoo/${P}.tar.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-pkg_setup() {
-	tc-export CC
-}
-
-src_prepare() {
-	epatch "${FILESDIR}"/${P}-asneeded.patch
-}
-
-src_install() {
-	dobin FastTree FastTreeUPGMA || die
-	insinto /usr/share/${PN}
-	doins *.pl *.pm || die
-	dodoc README* || die
-}
diff --git a/sci-biology/fasttree/fasttree-2.1.7.ebuild b/sci-biology/fasttree/fasttree-2.1.7.ebuild
index 69375a55c1a1..0abdd3ed4b24 100644
--- a/sci-biology/fasttree/fasttree-2.1.7.ebuild
+++ b/sci-biology/fasttree/fasttree-2.1.7.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/fasttree/fasttree-2.1.7.ebuild,v 1.2 2015/01/29 21:21:10 mgorny Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/fasttree/fasttree-2.1.7.ebuild,v 1.3 2015/03/29 14:30:36 jlec Exp $
 
 EAPI=5
 
@@ -23,6 +23,8 @@ REQUIRED_USE="?? ( double-precision cpu_flags_x86_sse3 )"
 
 DOCS=( README )
 
+PATCHES=( "${FILESDIR}"/${P}-format-security.patch )
+
 src_unpack() {
 	mkdir "${S}" || die
 	cd "${S}" || die
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..940344629c51
--- /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
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/fasttree/fasttree-2.1.8.ebuild,v 1.1 2015/03/29 14:30:36 jlec Exp $
+
+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/fasttree-2.0.1-asneeded.patch b/sci-biology/fasttree/files/fasttree-2.0.1-asneeded.patch
deleted file mode 100644
index faef13e735aa..000000000000
--- a/sci-biology/fasttree/files/fasttree-2.0.1-asneeded.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Respect FLAGS and fix as-needed issues
-
-https://bugs.gentoo.org/show_bug.cgi?id=295199
-
---- Makefile
-+++ Makefile
-@@ -1,6 +1,5 @@
--CFLAGS := ${CFLAGS} -Wall -O3 -finline-functions -funroll-loops 
- LIBS := -lm
- 
- all:
--	${CC} ${CFLAGS} ${LIBS} -o FastTree FastTree.c
--	${CC} ${CFLAGS} ${LIBS} -o FastTreeUPGMA FastTreeUPGMA.c
-+	${CC} ${CFLAGS} ${LDFLAGS} -o FastTree FastTree.c ${LIBS}
-+	${CC} ${CFLAGS} ${LDFLAGS} -o FastTreeUPGMA FastTreeUPGMA.c ${LIBS}
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];