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

2022-07-15 Thread David Seifert 
commit: 37c6ef284900aec1695de5b39f830b83415792ca
Author: David Seifert  gentoo  org>
AuthorDate: Fri Jul 15 08:23:58 2022 +
Commit: David Seifert  gentoo  org>
CommitDate: Fri Jul 15 08:23:58 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=37c6ef28

sci-biology/uchime: update EAPI 7 -> 8

Signed-off-by: David Seifert  gentoo.org>

 sci-biology/uchime/files/CMakeLists.patch   | 21 +
 sci-biology/uchime/files/CMakeLists.txt | 12 
 ...uchime-4.2.40.ebuild => uchime-4.2.40-r1.ebuild} | 21 +
 3 files changed, 26 insertions(+), 28 deletions(-)

diff --git a/sci-biology/uchime/files/CMakeLists.patch 
b/sci-biology/uchime/files/CMakeLists.patch
new file mode 100644
index ..c33af8c7e827
--- /dev/null
+++ b/sci-biology/uchime/files/CMakeLists.patch
@@ -0,0 +1,21 @@
+--- /dev/null
 b/CMakeLists.txt
+@@ -0,0 +1,18 @@
++cmake_minimum_required(VERSION 2.8.12)
++project(UCHIME LANGUAGES CXX)
++
++include(GNUInstallDirs)
++
++set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D_FILE_OFFSET_BITS=64 -DUCHIMES=1")
++
++# "myutils.h: error: reference to byte is ambiguous""
++# bug #786297
++set(CMAKE_CXX_STANDARD 14)
++set(CMAKE_CXX_STANDARD_REQUIRED ON)
++set(CMAKE_CXX_EXTENSIONS OFF)
++
++# Simply copy the source files from the mk script
++add_executable(uchime
++  addtargets2.cpp alignchime.cpp alignchimel.cpp 
alnparams.cpp alpha.cpp alpha2.cpp fractid.cpp getparents.cpp globalalign2.cpp 
make3way.cpp mx.cpp myutils.cpp path.cpp searchchime.cpp seqdb.cpp setnucmx.cpp 
sfasta.cpp tracebackbit.cpp uchime_main.cpp usort.cpp viterbifast.cpp 
writechhit.cpp)
++
++INSTALL(TARGETS uchime DESTINATION ${CMAKE_INSTALL_BINDIR})

diff --git a/sci-biology/uchime/files/CMakeLists.txt 
b/sci-biology/uchime/files/CMakeLists.txt
deleted file mode 100644
index a9319293e10b..
--- a/sci-biology/uchime/files/CMakeLists.txt
+++ /dev/null
@@ -1,12 +0,0 @@
-cmake_minimum_required(VERSION 2.8.12)
-project(UCHIME)
-
-include(GNUInstallDirs)
-
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D_FILE_OFFSET_BITS=64 -DUCHIMES=1")
-
-# Simply copy the source files from the mk script
-add_executable(uchime 
-   addtargets2.cpp alignchime.cpp alignchimel.cpp 
alnparams.cpp alpha.cpp alpha2.cpp fractid.cpp getparents.cpp globalalign2.cpp 
make3way.cpp mx.cpp myutils.cpp path.cpp searchchime.cpp seqdb.cpp setnucmx.cpp 
sfasta.cpp tracebackbit.cpp uchime_main.cpp usort.cpp viterbifast.cpp 
writechhit.cpp)
-
-INSTALL(TARGETS uchime DESTINATION ${CMAKE_INSTALL_BINDIR})

diff --git a/sci-biology/uchime/uchime-4.2.40.ebuild 
b/sci-biology/uchime/uchime-4.2.40-r1.ebuild
similarity index 57%
rename from sci-biology/uchime/uchime-4.2.40.ebuild
rename to sci-biology/uchime/uchime-4.2.40-r1.ebuild
index e0481aae2c70..fe35819b5eed 100644
--- a/sci-biology/uchime/uchime-4.2.40.ebuild
+++ b/sci-biology/uchime/uchime-4.2.40-r1.ebuild
@@ -1,30 +1,19 @@
 # Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
+
+inherit cmake
 
 MY_P="${PN}${PV}_src"
-inherit cmake flag-o-matic
 
 DESCRIPTION="Fast, accurate chimera detection"
 HOMEPAGE="https://www.drive5.com/usearch/manual/uchime_algo.html;
 SRC_URI="https://www.drive5.com/${PN}/${MY_P}.tar.gz;
+S="${WORKDIR}/${MY_P}"
 
 LICENSE="public-domain"
 SLOT="0"
 KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
 
-S="${WORKDIR}"/${MY_P}
-
-src_prepare() {
-   cp "${FILESDIR}"/CMakeLists.txt . || die
-   cmake_src_prepare
-}
-
-src_configure() {
-   # "myutils.h: error: reference to byte is ambiguous""
-   # bug #786297
-   append-cxxflags -std=c++14
-
-   cmake_src_configure
-}
+PATCHES=( "${FILESDIR}"/CMakeLists.patch )

[gentoo-commits] repo/gentoo:master commit in: sci-biology/uchime/

2022-07-15 Thread Sam James 
commit: 77f6cb64b11c91d7fac1418731ac29bf204d6327
Author: Sam James  gentoo  org>
AuthorDate: Fri Jul 15 08:03:51 2022 +
Commit: Sam James  gentoo  org>
CommitDate: Fri Jul 15 08:04:34 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=77f6cb64

sci-biology/uchime: use append-cxxflags

Signed-off-by: Sam James  gentoo.org>

 sci-biology/uchime/uchime-4.2.40.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/uchime/uchime-4.2.40.ebuild 
b/sci-biology/uchime/uchime-4.2.40.ebuild
index 9b346f4fbc8d..e0481aae2c70 100644
--- a/sci-biology/uchime/uchime-4.2.40.ebuild
+++ b/sci-biology/uchime/uchime-4.2.40.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -24,7 +24,7 @@ src_prepare() {
 src_configure() {
# "myutils.h: error: reference to byte is ambiguous""
# bug #786297
-   append-cppflags -std=c++14
+   append-cxxflags -std=c++14
 
cmake_src_configure
 }

[gentoo-commits] repo/gentoo:master commit in: sci-biology/uchime/

2021-06-14 Thread Sam James 
commit: 9bb2017d31f4467386be5262aa036ecf5dabf97a
Author: Sam James  gentoo  org>
AuthorDate: Tue Jun 15 02:35:24 2021 +
Commit: Sam James  gentoo  org>
CommitDate: Tue Jun 15 02:35:24 2021 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9bb2017d

sci-biology/uchime: workaround failure with GCC 11

Force C++14 for now because we don't really want a large patch for
typedefs.

Closes: https://bugs.gentoo.org/786297
Signed-off-by: Sam James  gentoo.org>

 sci-biology/uchime/uchime-4.2.40.ebuild | 11 +--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/sci-biology/uchime/uchime-4.2.40.ebuild 
b/sci-biology/uchime/uchime-4.2.40.ebuild
index 75827ab3a30..9b346f4fbc8 100644
--- a/sci-biology/uchime/uchime-4.2.40.ebuild
+++ b/sci-biology/uchime/uchime-4.2.40.ebuild
@@ -4,7 +4,7 @@
 EAPI=7
 
 MY_P="${PN}${PV}_src"
-inherit cmake
+inherit cmake flag-o-matic
 
 DESCRIPTION="Fast, accurate chimera detection"
 HOMEPAGE="https://www.drive5.com/usearch/manual/uchime_algo.html;
@@ -13,7 +13,6 @@ SRC_URI="https://www.drive5.com/${PN}/${MY_P}.tar.gz;
 LICENSE="public-domain"
 SLOT="0"
 KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
-IUSE="debug"
 
 S="${WORKDIR}"/${MY_P}
 
@@ -21,3 +20,11 @@ src_prepare() {
cp "${FILESDIR}"/CMakeLists.txt . || die
cmake_src_prepare
 }
+
+src_configure() {
+   # "myutils.h: error: reference to byte is ambiguous""
+   # bug #786297
+   append-cppflags -std=c++14
+
+   cmake_src_configure
+}

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

2021-03-07 Thread Andreas Sturmlechner 
commit: 132247f2a76e16d49fa38bfc3933ca61f4db78e6
Author: Andreas Sturmlechner  gentoo  org>
AuthorDate: Sun Mar  7 16:51:50 2021 +
Commit: Andreas Sturmlechner  gentoo  org>
CommitDate: Sun Mar  7 18:53:20 2021 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=132247f2

sci-biology/uchime: EAPI-7 bump, use cmake.eclass, https, fix HOMEPAGE

Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andreas Sturmlechner  gentoo.org>

 sci-biology/uchime/files/CMakeLists.txt |  7 ---
 sci-biology/uchime/uchime-4.2.40.ebuild | 16 +++-
 2 files changed, 11 insertions(+), 12 deletions(-)

diff --git a/sci-biology/uchime/files/CMakeLists.txt 
b/sci-biology/uchime/files/CMakeLists.txt
index 54b0a3ba0d3..a9319293e10 100644
--- a/sci-biology/uchime/files/CMakeLists.txt
+++ b/sci-biology/uchime/files/CMakeLists.txt
@@ -1,11 +1,12 @@
-cmake_minimum_required(VERSION 2.6)
+cmake_minimum_required(VERSION 2.8.12)
 project(UCHIME)
 
+include(GNUInstallDirs)
+
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D_FILE_OFFSET_BITS=64 -DUCHIMES=1")
 
 # Simply copy the source files from the mk script
 add_executable(uchime 
addtargets2.cpp alignchime.cpp alignchimel.cpp 
alnparams.cpp alpha.cpp alpha2.cpp fractid.cpp getparents.cpp globalalign2.cpp 
make3way.cpp mx.cpp myutils.cpp path.cpp searchchime.cpp seqdb.cpp setnucmx.cpp 
sfasta.cpp tracebackbit.cpp uchime_main.cpp usort.cpp viterbifast.cpp 
writechhit.cpp)
 
-INSTALL(TARGETS uchime
-DESTINATION bin)
+INSTALL(TARGETS uchime DESTINATION ${CMAKE_INSTALL_BINDIR})

diff --git a/sci-biology/uchime/uchime-4.2.40.ebuild 
b/sci-biology/uchime/uchime-4.2.40.ebuild
index dd2201547ae..75827ab3a30 100644
--- a/sci-biology/uchime/uchime-4.2.40.ebuild
+++ b/sci-biology/uchime/uchime-4.2.40.ebuild
@@ -1,18 +1,17 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
-
-inherit cmake-utils
+EAPI=7
 
 MY_P="${PN}${PV}_src"
+inherit cmake
 
 DESCRIPTION="Fast, accurate chimera detection"
-HOMEPAGE="http://www.drive5.com/uchime/;
-SRC_URI="http://drive5.com/${PN}/${MY_P}.tar.gz;
+HOMEPAGE="https://www.drive5.com/usearch/manual/uchime_algo.html;
+SRC_URI="https://www.drive5.com/${PN}/${MY_P}.tar.gz;
 
-SLOT="0"
 LICENSE="public-domain"
+SLOT="0"
 KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
 IUSE="debug"
 
@@ -20,6 +19,5 @@ S="${WORKDIR}"/${MY_P}
 
 src_prepare() {
cp "${FILESDIR}"/CMakeLists.txt . || die
-
-   cmake-utils_src_prepare
+   cmake_src_prepare
 }

[gentoo-commits] repo/gentoo:master commit in: sci-biology/uchime/

2017-02-08 Thread Johannes Huber 
commit: 8ae066be32756c3fd9c4398878c71ac31f261056
Author: Johannes Huber  gentoo  org>
AuthorDate: Wed Feb  8 12:34:44 2017 +
Commit: Johannes Huber  gentoo  org>
CommitDate: Wed Feb  8 12:35:01 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8ae066be

sci-biology/uchime: EAPI 6

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/uchime/uchime-4.2.40.ebuild | 6 --
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/sci-biology/uchime/uchime-4.2.40.ebuild 
b/sci-biology/uchime/uchime-4.2.40.ebuild
index 556e29b797..06ab5a5249 100644
--- a/sci-biology/uchime/uchime-4.2.40.ebuild
+++ b/sci-biology/uchime/uchime-4.2.40.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=6
 
 inherit cmake-utils
 
@@ -21,4 +21,6 @@ S="${WORKDIR}"/${MY_P}
 
 src_prepare() {
cp "${FILESDIR}"/CMakeLists.txt . || die
+
+   cmake-utils_src_prepare
 }

[gentoo-commits] repo/gentoo:master commit in: sci-biology/uchime/

2015-09-25 Thread Agostino Sarubbo 
commit: 64aa73a6893547ccd963d564e6fcede78605c78e
Author: Agostino Sarubbo  gentoo  org>
AuthorDate: Fri Sep 25 14:23:15 2015 +
Commit: Agostino Sarubbo  gentoo  org>
CommitDate: Fri Sep 25 14:23:15 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=64aa73a6

sci-biology/uchime: x86 stable wrt bug #556066

Package-Manager: portage-2.2.20.1
RepoMan-Options: --include-arches="x86"

 sci-biology/uchime/uchime-4.2.40.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/uchime/uchime-4.2.40.ebuild 
b/sci-biology/uchime/uchime-4.2.40.ebuild
index 19b55f5..556e29b 100644
--- a/sci-biology/uchime/uchime-4.2.40.ebuild
+++ b/sci-biology/uchime/uchime-4.2.40.ebuild
@@ -14,7 +14,7 @@ SRC_URI="http://drive5.com/${PN}/${MY_P}.tar.gz;
 
 SLOT="0"
 LICENSE="public-domain"
-KEYWORDS="amd64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
 IUSE="debug"
 
 S="${WORKDIR}"/${MY_P}