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

2024-03-22 Thread Sam James 
commit: 2186e8d7f1080d3b350e12f7c21d538c07fa14dd
Author: Sam James  gentoo  org>
AuthorDate: Fri Mar 22 08:49:27 2024 +
Commit: Sam James  gentoo  org>
CommitDate: Fri Mar 22 08:49:27 2024 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2186e8d7

sci-biology/mothur: uncomment patch...

Closes: https://bugs.gentoo.org/927495
Signed-off-by: Sam James  gentoo.org>

 sci-biology/mothur/mothur-1.48.0.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/mothur/mothur-1.48.0.ebuild 
b/sci-biology/mothur/mothur-1.48.0.ebuild
index 869b0bae718b..7d54bf273ac0 100644
--- a/sci-biology/mothur/mothur-1.48.0.ebuild
+++ b/sci-biology/mothur/mothur-1.48.0.ebuild
@@ -24,7 +24,7 @@ RDEPEND="
 DEPEND="${RDEPEND}"
 
 PATCHES=(
-   #"${FILESDIR}"/${PN}-1.48.0-build.patch
+   "${FILESDIR}"/${PN}-1.48.0-build.patch
 )
 
 src_configure() {

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

2024-03-22 Thread Sam James 
commit: 4aa71fb389486acee786f07025f7e24cfa07360a
Author: Sam James  gentoo  org>
AuthorDate: Fri Mar 22 08:11:38 2024 +
Commit: Sam James  gentoo  org>
CommitDate: Fri Mar 22 08:43:28 2024 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4aa71fb3

sci-biology/mothur: add 1.48.0

Filter LTO too, and no-SA. Not reported upstream as it has a lot of open
bugs already and seems low activity.

Closes: https://bugs.gentoo.org/862273
Signed-off-by: Sam James  gentoo.org>

 sci-biology/mothur/Manifest|  1 +
 sci-biology/mothur/files/mothur-1.48.0-build.patch | 79 ++
 sci-biology/mothur/metadata.xml|  5 ++
 sci-biology/mothur/mothur-1.48.0.ebuild| 54 +++
 4 files changed, 139 insertions(+)

diff --git a/sci-biology/mothur/Manifest b/sci-biology/mothur/Manifest
index 9d78212016cd..ada6350ceeef 100644
--- a/sci-biology/mothur/Manifest
+++ b/sci-biology/mothur/Manifest
@@ -1 +1,2 @@
 DIST mothur-1.27.0.zip 7095054 BLAKE2B 
96a6410d36f64ff50591955aa22bfddf6217c7568022c8c7f70ab70c65d57af2217477de56b6f9ceaf11237cdc5380bd354cf6564002357546539585d0f58221
 SHA512 
81821ca95d4ce3f0d1e6aa920c4fe3fddd70f716157312ed0590c1c4ad728e6786bfe79f6badddcfb060ed5d1996cc1b5062c320a59209fef35f68e687ba3dd5
+DIST mothur-1.48.0.tar.gz 1652711 BLAKE2B 
39e1d2a32a63d441267b4e0e739505bdcb3ab392c169c96d60e816dbd9fab6b92745e8a9eaae31062711f2de0130dae540bba34c6bd97e76a921711f58c11f65
 SHA512 
a43ef6a223238d40e51c15043360ba9cae86347affea2f1a4e365635fb0949981ad32001b88d4061a033b2a002e944df16923a0622a40bf061791f06143467e1

diff --git a/sci-biology/mothur/files/mothur-1.48.0-build.patch 
b/sci-biology/mothur/files/mothur-1.48.0-build.patch
new file mode 100644
index ..da9784e20dd8
--- /dev/null
+++ b/sci-biology/mothur/files/mothur-1.48.0-build.patch
@@ -0,0 +1,79 @@
+Fix building and don't use bundled uchime.
+--- a/Makefile
 b/Makefile
+@@ -104,12 +104,19 @@ endif
+ # INCLUDE directories for mothur
+ #
+ #
+-  
VPATH=source/calculators:source/chimera:source/classifier:source/clearcut:source/commands:source/communitytype:source/datastructures:source/engines:source/metastats:source/read:source/svm:source/
++  
VPATH=source:source/calculators:source/chimera:source/classifier:source/clearcut:source/commands:source/communitytype:source/datastructures:source/engines:source/metastats:source/read:source/svm:source/
++source := source
+ skipUchime := source/uchime_src/
++skipTestMothur := source/TestMothur/
++skipSeqnoise := seqnoise.cpp
+ subdirs :=  $(sort $(dir $(filter-out  $(skipUchime), $(wildcard 
source/*/
++subdirs :=  $(filter-out  $(skipTestMothur), $(subdirs))
+ subDirIncludes = $(patsubst %, -I %, $(subdirs))
++subDirIncludes += $(patsubst %, -I %, $(source))
+ subDirLinking =  $(patsubst %, -L%, $(subdirs))
+-CXXFLAGS += -I. $(subDirIncludes)
++subDirLinking +=  $(patsubst %, -L%, $(source))
++subdirs :=  $(dir source) $(sort $(dir $(filter-out  $(skipUchime), 
$(wildcard source/*/
++CXXFLAGS += -Isource -I. $(subDirIncludes)
+ LDFLAGS += $(subDirLinking)
+ 
+ 
+@@ -118,15 +125,14 @@ endif
+ #
+ OBJECTS=$(patsubst %.cpp,%.o,$(wildcard $(addsuffix *.cpp,$(subdirs
+ OBJECTS+=$(patsubst %.c,%.o,$(wildcard $(addsuffix *.c,$(subdirs
++OBJECTS+=$(patsubst %.cpp,%.o,$(filter-out $(skipSeqnoise), $(wildcard 
source/*.cpp)))
++OBJECTS+=$(patsubst %.cpp,%.o,$(filter-out $(skipSeqnoise), $(wildcard 
source/*.c)))
+ OBJECTS+=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
+ OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))
+ 
+-mothur : $(OBJECTS) uchime
++mothur : $(OBJECTS)
+   $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
+ 
+-uchime :
+-  cd source/uchime_src && export CXX=$(CXX) && make clean && make && mv 
uchime ../../ && cd ..
+-
+ install : mothur
+ 
+ ifeq  ($(strip $(INSTALL_DIR)),"\"Enter_your_mothur_install_path_here\"")
+--- a/makefile-internal
 b/makefile-internal
+@@ -115,7 +115,6 @@ endif
+ 
+ mothur : $(OBJECTS)
+ $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
+-strip mothur
+ 
+ %.o : %.c %.h
+ $(COMPILE.c) $(OUTPUT_OPTION) $<
+--- a/source/uchime_src/makefile
 b/source/uchime_src/makefile
+@@ -1,4 +1,4 @@
+-CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1
++CXXFLAGS = -std=c++11 -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1
+ LDFLAGS = -g
+ 
+ #
+@@ -26,4 +26,4 @@ install : uchime
+ 
+ clean :
+   @rm -f $(OBJECTS)
+-  
+\ No newline at end of file
++  
+--- a/source/writer.h
 b/source/writer.h
+@@ -9,6 +9,7 @@
+ #ifndef writer_h
+ #define writer_h
+ 
++#include 
+ #include "sharedwriter.hpp"
+ 
+ /***/

diff --git a/sci-biology/mothur/metadata.xml b/sci-biology/mothur/metadata.xml
index fc926cc4aa42..15fc0072ba17 100644
--- a/sci-biology/mothur/metadata.xml

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

2022-07-30 Thread Sam James 
commit: 77c21552c350ad0843d6a5cfe17353c4d1c2a23f
Author: Sam James  gentoo  org>
AuthorDate: Sat Jul 30 08:35:11 2022 +
Commit: Sam James  gentoo  org>
CommitDate: Sat Jul 30 08:35:11 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=77c21552

sci-biology/mothur: add github upstream metadata

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

 sci-biology/mothur/metadata.xml | 11 +++
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/sci-biology/mothur/metadata.xml b/sci-biology/mothur/metadata.xml
index ccdff086e20b..fc926cc4aa42 100644
--- a/sci-biology/mothur/metadata.xml
+++ b/sci-biology/mothur/metadata.xml
@@ -1,8 +1,11 @@
 
 https://www.gentoo.org/dtd/metadata.dtd;>
 
-  
-sci-biol...@gentoo.org
-Gentoo Biology Project
-  
+   
+   sci-biol...@gentoo.org
+   Gentoo Biology Project
+   
+   
+   mothur/mothur
+

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

2021-04-05 Thread David Seifert 
commit: 17ca0e1b3b8cda81f6028b21303d8c64021c2947
Author: David Seifert  gentoo  org>
AuthorDate: Mon Apr  5 14:14:41 2021 +
Commit: David Seifert  gentoo  org>
CommitDate: Mon Apr  5 14:14:41 2021 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=17ca0e1b

sci-biology/mothur: Port to EAPI 7

Package-Manager: Portage-3.0.18, Repoman-3.0.3
Signed-off-by: David Seifert  gentoo.org>

 sci-biology/mothur/mothur-1.27.0-r1.ebuild | 35 +++---
 1 file changed, 17 insertions(+), 18 deletions(-)

diff --git a/sci-biology/mothur/mothur-1.27.0-r1.ebuild 
b/sci-biology/mothur/mothur-1.27.0-r1.ebuild
index 9e9bf216031..12b628475aa 100644
--- a/sci-biology/mothur/mothur-1.27.0-r1.ebuild
+++ b/sci-biology/mothur/mothur-1.27.0-r1.ebuild
@@ -1,43 +1,42 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit eutils flag-o-matic fortran-2 toolchain-funcs
+inherit flag-o-matic fortran-2 toolchain-funcs
 
 DESCRIPTION="A suite of algorithms for ecological bioinformatics"
 HOMEPAGE="https://www.mothur.org/;
 SRC_URI="https://www.mothur.org/w/images/c/cb/Mothur.${PV}.zip -> ${P}.zip"
+S="${WORKDIR}/${PN^}.source"
 
 LICENSE="GPL-3"
 SLOT="0"
-IUSE="mpi +readline"
 KEYWORDS="amd64 x86"
+IUSE="mpi +readline"
 
 RDEPEND="
sci-biology/uchime
mpi? ( virtual/mpi )"
-DEPEND="${RDEPEND}
-   app-arch/unzip"
+DEPEND="${RDEPEND}"
+BDEPEND="app-arch/unzip"
 
-S=${WORKDIR}/Mothur.source
+PATCHES=(
+   "${FILESDIR}"/${P}-makefile.patch
+   "${FILESDIR}"/${P}-overflows.patch
+)
 
-pkg_setup() {
-   fortran-2_pkg_setup
-   use mpi && export CXX=mpicxx || export CXX=$(tc-getCXX)
+src_configure() {
+   use mpi && export CXX=mpicxx || tc-export CXX
use amd64 && append-cppflags -DBIT_VERSION
 }
 
-src_prepare() {
-   epatch \
-   "${FILESDIR}"/${P}-makefile.patch \
-   "${FILESDIR}"/${P}-overflows.patch
-}
-
 src_compile() {
-   emake USEMPI=$(usex mpi) USEREADLINE=$(usex readline)
+   emake \
+   USEMPI=$(usex mpi) \
+   USEREADLINE=$(usex readline)
 }
 
 src_install() {
-   dobin ${PN}
+   dobin mothur
 }

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

2018-05-21 Thread Aaron Bauman 
commit: 1eb2ddf01f1ad34b00265cf46e5a4e6b3d82b1e7
Author: Michael Mair-Keimberger  gmail  com>
AuthorDate: Mon May 21 10:13:08 2018 +
Commit: Aaron Bauman  gentoo  org>
CommitDate: Mon May 21 17:02:31 2018 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1eb2ddf0

sci-biology/mothur: use HTTPs

 sci-biology/mothur/mothur-1.27.0-r1.ebuild | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/sci-biology/mothur/mothur-1.27.0-r1.ebuild 
b/sci-biology/mothur/mothur-1.27.0-r1.ebuild
index d12d3c9b439..9e9bf216031 100644
--- a/sci-biology/mothur/mothur-1.27.0-r1.ebuild
+++ b/sci-biology/mothur/mothur-1.27.0-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -6,8 +6,8 @@ EAPI=5
 inherit eutils flag-o-matic fortran-2 toolchain-funcs
 
 DESCRIPTION="A suite of algorithms for ecological bioinformatics"
-HOMEPAGE="http://www.mothur.org/;
-SRC_URI="http://www.mothur.org/w/images/c/cb/Mothur.${PV}.zip -> ${P}.zip"
+HOMEPAGE="https://www.mothur.org/;
+SRC_URI="https://www.mothur.org/w/images/c/cb/Mothur.${PV}.zip -> ${P}.zip"
 
 LICENSE="GPL-3"
 SLOT="0"

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

2015-09-25 Thread Justin Lecher 
commit: 06eacdf47da231ea1e9beebcad176a8fda063afe
Author: Justin Lecher  gentoo  org>
AuthorDate: Fri Sep 25 18:40:53 2015 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Fri Sep 25 18:40:53 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=06eacdf4

sci-biology/mothur: Drop old

Package-Manager: portage-2.2.21
Signed-off-by: Justin Lecher  gentoo.org>

 sci-biology/mothur/Manifest|  1 -
 sci-biology/mothur/mothur-1.6.0.ebuild | 33 -
 2 files changed, 34 deletions(-)

diff --git a/sci-biology/mothur/Manifest b/sci-biology/mothur/Manifest
index e0cf36a..1ed7618 100644
--- a/sci-biology/mothur/Manifest
+++ b/sci-biology/mothur/Manifest
@@ -1,2 +1 @@
 DIST mothur-1.27.0.zip 7095054 SHA256 
7521d0dfc849dc9ef707bf83032e471966914b9833247c49e5d30b8d9281a6c7 SHA512 
81821ca95d4ce3f0d1e6aa920c4fe3fddd70f716157312ed0590c1c4ad728e6786bfe79f6badddcfb060ed5d1996cc1b5062c320a59209fef35f68e687ba3dd5
 WHIRLPOOL 
32e5c9c2be6e593b2dbc64be38c49b4dec3ea048cd3c972cf948136b394608a2dc168be58b7fb500a17fc6a152bfcd09b3f9fb3bf60c7dd92d043a4bf361
-DIST mothur-1.6.0.zip 465292 SHA256 
75583a204d199ddcf9b845fc0adbaf240d7b1f08584fed5e6465982f68ffe121 SHA512 
f775ff64991f00423108f295eca640f5c5d85a38e01b31af44ddf91f8897968e934f79899a21606dfd81fdc3e91751df277237e94d56d74f862e472e8da3386c
 WHIRLPOOL 
31ca8decceb38ebd17f15c5f937df70b501833311cbf1aec794bb174d409a0c01e77abb399347781ad820c06411e56c566382a32818a0c57214aad2ad16cc132

diff --git a/sci-biology/mothur/mothur-1.6.0.ebuild 
b/sci-biology/mothur/mothur-1.6.0.ebuild
deleted file mode 100644
index 034f6fa..000
--- a/sci-biology/mothur/mothur-1.6.0.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit toolchain-funcs
-
-DESCRIPTION="A suite of algorithms for ecological bioinformatics"
-HOMEPAGE="http://www.mothur.org/;
-SRC_URI="mirror://gentoo/${P}.zip"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE=""
-KEYWORDS="amd64 x86"
-
-DEPEND="app-arch/unzip"
-RDEPEND=""
-
-S="${WORKDIR}/mothur-v.${PV}"
-
-src_prepare() {
-   sed \
-   -e 's/CC_OPTIONS =.*$/CC_OPTIONS = ${CXXFLAGS} /' \
-   -e 's|CC = g++|CC = '$(tc-getCXX)'|' \
-   -e '/^LNK_OPTIONS/s:$:${LDFLAGS}:g' \
-   -i makefile || die
-}
-
-src_install() {
-   dobin ${PN}
-}

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

2015-09-25 Thread Agostino Sarubbo 
commit: 9f365a9d5634350da97913fd8a45374b24b3127d
Author: Agostino Sarubbo  gentoo  org>
AuthorDate: Fri Sep 25 14:23:11 2015 +
Commit: Agostino Sarubbo  gentoo  org>
CommitDate: Fri Sep 25 14:23:11 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9f365a9d

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

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

 sci-biology/mothur/mothur-1.27.0-r1.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/mothur/mothur-1.27.0-r1.ebuild 
b/sci-biology/mothur/mothur-1.27.0-r1.ebuild
index 3de23de..dcdf23f 100644
--- a/sci-biology/mothur/mothur-1.27.0-r1.ebuild
+++ b/sci-biology/mothur/mothur-1.27.0-r1.ebuild
@@ -13,7 +13,7 @@ SRC_URI="http://www.mothur.org/w/images/c/cb/Mothur.${PV}.zip 
-> ${P}.zip"
 LICENSE="GPL-3"
 SLOT="0"
 IUSE="mpi +readline"
-KEYWORDS="amd64 ~x86"
+KEYWORDS="amd64 x86"
 
 RDEPEND="
sci-biology/uchime