gentoo resync : 12.03.2021

4 files changed, 27 insertions, 30 deletions

diff --git a/sci-biology/fasttree/Manifest b/sci-biology/fasttree/Manifest
index 31f22a31dfc1..ebc955155315 100644
--- a/sci-biology/fasttree/Manifest
+++ b/sci-biology/fasttree/Manifest
@@ -1,7 +1,7 @@
-AUX CMakeLists.txt 948 BLAKE2B b2a5908a2d24533f474d399b97b8941fbbe392e2b078890bc2e62dbd232912e6bbaec25fbb31592b1015c8c4234178a34ffd9bd4815935d64ea6da3dd21cd474 SHA512 9858800bfce8d256ccb834a06bad5a5230f90f025a9c9b3c9aafe7244d219d66810530f6688e02889cdb67d6a9459d8e26cd1a9fcf2e8825278b31d0e8d51ff3
-AUX fasttree-2.1.8-format-security.patch 783 BLAKE2B c400b89a17287817f82a8747082b3bf35d8097941c591923fcff073618fae0423b97fb5bc9a12a199acea0de61d451378beaf0070beb9b20274da81b936f2296 SHA512 9bbf66cddca2b6c202fdeeab4092036852cb1ebe132ebf4d96cba1bea75bb5668dd6ee97d4d020a4b7cf7111bee6d0c3004b0bd74ee4685ef98eeeb5e9a23eb3
-DIST FastTree-2.1.8.c 385231 BLAKE2B 6f42025ef69b990e051263ccfa23f95d0cde326798c54d8f702c50127338711898c380d1dbd82ab775667eada047048ba8d68288b030af4984019a5f2c23729f SHA512 39a7d284412a602208c2a5df3d0a9a30fe3a584f7f7788d741fb1463b698692017f47bb23f70046d0873e9c8fd27c84ec23f6ca48adb0594193765ac732e6559
-DIST FastTreeUPGMA-2.1.8.c 95271 BLAKE2B 1de328881f6452b9c7423c9ed381ab2eb31c4f3ee6426481a6b1089c1359627d4cbbfbea868ebeab9538f82e17f45f1bff8ec07c7370e6432bef6bae449798a8 SHA512 4d6a8e2cb28b8ee201091172a3baa59d432420839c6d2244b5fb8230ed9daa626b6bed22cb692393ca3d78b8f2d071fe18fbb4f9bdcdc47ef149c31e3f45546c
-DIST MOTreeComparison-2.1.8.tar.gz 13523 BLAKE2B 97638edd945412ff00e3dfcfc89ec6ea52ae8c43531d5cb680d97e9c62fcad80e861f58ec987abcd2282166dd7886101edba4875531bd9d6ac23df242e0dbd5b SHA512 24d2247650d7728942bd1d987b548cefd65a16b433a3810876613e9fd1cff223d4349ee720b3d8d10a73af220c2c9f59a24d77ad34ff009325fe9f22aa35c72b
-EBUILD fasttree-2.1.8.ebuild 1170 BLAKE2B afc7e5b975fea59bc720d59732dac792662717aee591f9dc532d532a43ff7a7563f401fce51d0bb9e2d31315b24fe45d098825bdbcbc5264fcfb461cba68ba03 SHA512 798b161e7c9c70e5fd0de3a8018f1e3f95c59b354517ca9539845ec1462d506ab20b4fe629b9666614969a7d05101bf01121c2df34ad9e8a86ff63e136b6f51b
+AUX CMakeLists.txt 985 BLAKE2B b812e5133464f10d25c59155bd49b933a94e6c2480996a114b91dd03e3475b755280c7b58c1195ef6faceb009d9c70220aa41a4501fa44f1c53da571845dfb7b SHA512 9f83060b59c4da4a5ad16789c285bb2c7c25b2906a0bc06614d95086753057c5cfbddcd07cc3514f11604073c8fb6c688107efdb3329e75bf8261f9304a840d3
+AUX fasttree-2.1.11-format-security.patch 788 BLAKE2B 63adc80af602d7d6582201c3184ee18d33bf744041e503d776e542e309a3c285270567b0ef7661746fb8c8bfcaf2517537276aff57e10b5989e49625404ebc50 SHA512 b46fa4f47c2b668df7c776b848583f3438a1bf792c93c57611b84ca84a9725fae2cab138fa3e6fd7080132663347ae35f027730c8845edd35d7e2ee39c900393
+DIST FastTree-2.1.11.c 395543 BLAKE2B 5bea3fba66ddf077ce42c3e1791505a9fa909bb619e30e0c0370631996d932c63ca172fffc1721ac9f081a16bed3b1c99a9c7f6e4a3bb269b82545e2978904d3 SHA512 2bbb1cc078b04125a55b8c02f65c9fbfb6db894c2fbfdaac8f86cc0084f2579723cdc4f6aa63bf4338b767d0fdaffa8dd503e4126c3f5f700d4f3da9fc085ee5
+DIST FastTreeUPGMA-2.1.11.c 95271 BLAKE2B 1de328881f6452b9c7423c9ed381ab2eb31c4f3ee6426481a6b1089c1359627d4cbbfbea868ebeab9538f82e17f45f1bff8ec07c7370e6432bef6bae449798a8 SHA512 4d6a8e2cb28b8ee201091172a3baa59d432420839c6d2244b5fb8230ed9daa626b6bed22cb692393ca3d78b8f2d071fe18fbb4f9bdcdc47ef149c31e3f45546c
+DIST MOTreeComparison-2.1.11.tar.gz 13523 BLAKE2B 97638edd945412ff00e3dfcfc89ec6ea52ae8c43531d5cb680d97e9c62fcad80e861f58ec987abcd2282166dd7886101edba4875531bd9d6ac23df242e0dbd5b SHA512 24d2247650d7728942bd1d987b548cefd65a16b433a3810876613e9fd1cff223d4349ee720b3d8d10a73af220c2c9f59a24d77ad34ff009325fe9f22aa35c72b
+EBUILD fasttree-2.1.11.ebuild 1114 BLAKE2B 72e5dd6d6165167cb7df943d31790cfc3a2742db788665efadeb00e55a71fd2ed2367088ef520875f4aab1cae81fde9614e8f7dda405598d1016cb27666438d9 SHA512 8003b7317d8d25ff703e2cb172e49bf3d8c50228d57417813f7917225ac655845c42c4edcd6b5fb15a354992590abdbb471ef10013dd56dc40e1a04e18f41518
 MISC metadata.xml 410 BLAKE2B 92ee74c67cebb5ac4db5217355e6f01f893387d7fe0da1dd5048207149e385927f05c324d8299682b42bc7ba895e1f42a0ee5d7e9442d03d33ea3511dc704ffd SHA512 6f380e2353b1a0ff33c75cd593d2cf3e12d56c99478e7a5bdb37459b10449ae88065d265820f2a9c6d61d53a295ed1a4e18b8595e23c137c9788c658080caff0
diff --git a/sci-biology/fasttree/fasttree-2.1.8.ebuild b/sci-biology/fasttree/fasttree-2.1.11.ebuild
index 3f9e4ad5f759..cb2d16791ee3 100644
--- a/sci-biology/fasttree/fasttree-2.1.8.ebuild
+++ b/sci-biology/fasttree/fasttree-2.1.11.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2018 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-inherit cmake-utils
+inherit cmake
 
 DESCRIPTION="Fast inference of approximately-maximum-likelihood phylogenetic trees"
 HOMEPAGE="http://www.microbesonline.org/fasttree/"
@@ -29,11 +29,7 @@ src_unpack() {
 	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() {
@@ -43,5 +39,5 @@ src_configure() {
 		-DUSE_OPENMP=$(usex openmp)
 		-DUSE_DOUBLE=$(usex double-precision)
 	)
-	cmake-utils_src_configure
+	cmake_src_configure
 }
diff --git a/sci-biology/fasttree/files/CMakeLists.txt b/sci-biology/fasttree/files/CMakeLists.txt
index e7c53afdaf36..c52b90cc7be2 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-2.1.8-format-security.patch b/sci-biology/fasttree/files/fasttree-2.1.11-format-security.patch
index 15f5c174ec40..45023e4215f6 100644
--- a/sci-biology/fasttree/files/fasttree-2.1.8-format-security.patch
+++ b/sci-biology/fasttree/files/fasttree-2.1.11-format-security.patch
@@ -1,10 +1,10 @@
- FastTreeUPGMA-2.1.8.c | 4 ++--
+ FastTreeUPGMA-2.1.11.c | 4 ++--
  1 file changed, 2 insertions(+), 2 deletions(-)
 
-diff --git a/FastTreeUPGMA-2.1.8.c b/FastTreeUPGMA-2.1.8.c
+diff --git a/FastTreeUPGMA-2.1.11.c b/FastTreeUPGMA-2.1.11.c
 index af76cb1..4065f42 100644
---- a/FastTreeUPGMA-2.1.8.c
-+++ b/FastTreeUPGMA-2.1.8.c
+--- a/FastTreeUPGMA-2.1.11.c
++++ b/FastTreeUPGMA-2.1.11.c
 @@ -535,7 +535,7 @@ int main(int argc, char **argv) {
        break;
    }