Use fortran-2.eclass, bug #543204; drop old

(Portage version: 2.2.20/cvs/Linux x86_64, signed Manifest commit with key E9402A79B03529A2!)

7 files changed, 17 insertions, 304 deletions

diff --git a/sci-biology/mothur/ChangeLog b/sci-biology/mothur/ChangeLog
index 2b37c7e6e2ec..38517a441a26 100644
--- a/sci-biology/mothur/ChangeLog
+++ b/sci-biology/mothur/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-biology/mothur
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mothur/ChangeLog,v 1.12 2015/04/07 14:33:37 jlec Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mothur/ChangeLog,v 1.13 2015/07/27 18:42:15 jlec Exp $
+
+*mothur-1.27.0-r1 (27 Jul 2015)
+
+  27 Jul 2015; Justin Lecher <jlec@gentoo.org> +mothur-1.27.0-r1.ebuild,
+  -files/mothur-1.13.0-makefile.patch, -files/mothur-1.13.0-overflows.patch,
+  -files/mothur-1.13.0-overflows2.patch, -mothur-1.13.0-r1.ebuild,
+  -mothur-1.13.0-r2.ebuild, -mothur-1.27.0.ebuild:
+  Use fortran-2.eclass, bug #543204; drop old
 
   11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml:
   Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
@@ -61,4 +69,3 @@
 
   04 Mar 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog:
   New package, ebuild written by me
-
diff --git a/sci-biology/mothur/files/mothur-1.13.0-makefile.patch b/sci-biology/mothur/files/mothur-1.13.0-makefile.patch
deleted file mode 100644
index 6b2f0f1bd201..000000000000
--- a/sci-biology/mothur/files/mothur-1.13.0-makefile.patch
+++ /dev/null
@@ -1,43 +0,0 @@
-Fix build with --as-needed, respect CXX, CXXFLAGS
-
-http://www.mothur.org/forum/viewtopic.php?f=4&t=590
-http://bugs.gentoo.org/show_bug.cgi?id=339753
-
---- makefile
-+++ makefile
-@@ -11,7 +11,7 @@
- 
- # Optimize to level 3:
- 
--CXXFLAGS += -O3
-+#CXXFLAGS += -O3
- 
- MOTHUR_FILES = "\"Enter_your_default_path_here\""
- 
-@@ -49,7 +49,7 @@
- 
- ifeq  ($(strip $(USEREADLINE)),yes)
-     CXXFLAGS += -DUSE_READLINE
--    LDFLAGS += \
-+    LIBS = \
-       -lreadline\
-       -lncurses
- endif
-@@ -57,7 +57,7 @@
- USEMPI ?= no
- 
- ifeq  ($(strip $(USEMPI)),yes)
--    CXX = mpic++
-+#    CXX = mpic++
-     CXXFLAGS += -DUSE_MPI
- endif
- 
-@@ -74,7 +74,7 @@
- OBJECTS=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
- 
- mothur : $(OBJECTS)
--	$(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS)
-+	$(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
- 
- install : mothur
- 	cp mothur ../Release/mothur
diff --git a/sci-biology/mothur/files/mothur-1.13.0-overflows.patch b/sci-biology/mothur/files/mothur-1.13.0-overflows.patch
deleted file mode 100644
index 0cd9d7f3a47e..000000000000
--- a/sci-biology/mothur/files/mothur-1.13.0-overflows.patch
+++ /dev/null
@@ -1,82 +0,0 @@
-Fix buffer overflows
-
-http://www.mothur.org/forum/viewtopic.php?f=4&t=591
-
---- Mothur.source/filterseqscommand.cpp
-+++ Mothur.source/filterseqscommand.cpp
-@@ -305,8 +305,8 @@
- 					
- 					//wait on chidren
- 					for(int i = 1; i < processors; i++) { 
--						char buf[4];
--						MPI_Recv(buf, 4, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status); 
-+						char buf[5];
-+						MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status); 
- 					}
- 					
- 				}else { //you are a child process
-@@ -326,11 +326,11 @@
- 					
- 					if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
- 					
--					char buf[4];
-+					char buf[5];
- 					strcpy(buf, "done"); 
- 					
- 					//tell parent you are done.
--					MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
-+					MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
- 				}
- 				
- 				MPI_File_close(&outMPI);
---- Mothur.source/distancecommand.cpp
-+++ Mothur.source/distancecommand.cpp
-@@ -271,8 +271,8 @@
- 				for(int i = 1; i < processors; i++) { 
- 					if (m->control_pressed) { MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
- 					
--					char buf[4];
--					MPI_Recv(buf, 4, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status); 
-+					char buf[5];
-+					MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status); 
- 				}
- 			}else { //you are a child process
- 				//do your part
-@@ -280,10 +280,10 @@
- 				
- 				if (m->control_pressed) { MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
- 			
--				char buf[4];
-+				char buf[5];
- 				strcpy(buf, "done"); 
- 				//tell parent you are done.
--				MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
-+				MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
- 			}
- 			
- 			MPI_File_close(&outMPI);
---- Mothur.source/chimeracheckcommand.cpp
-+++ Mothur.source/chimeracheckcommand.cpp
-@@ -269,8 +269,8 @@
- 					
- 					//wait on chidren
- 					for(int j = 1; j < processors; j++) { 
--						char buf[4];
--						MPI_Recv(buf, 4, MPI_CHAR, j, tag, MPI_COMM_WORLD, &status); 
-+						char buf[5];
-+						MPI_Recv(buf, 5, MPI_CHAR, j, tag, MPI_COMM_WORLD, &status); 
- 					}
- 				}else{ //you are a child process
- 					MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
-@@ -288,9 +288,9 @@
- 					if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   for (int j = 0; j < outputNames.size(); j++) {	remove(outputNames[j].c_str());	}  delete chimera; return 0;  }
- 					
- 					//tell parent you are done.
--					char buf[4];
-+					char buf[5];
- 					strcpy(buf, "done"); 
--					MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
-+					MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
- 				}
- 				
- 				//close files 
diff --git a/sci-biology/mothur/files/mothur-1.13.0-overflows2.patch b/sci-biology/mothur/files/mothur-1.13.0-overflows2.patch
deleted file mode 100644
index ac1103d19aa4..000000000000
--- a/sci-biology/mothur/files/mothur-1.13.0-overflows2.patch
+++ /dev/null
@@ -1,77 +0,0 @@
- clearcutcommand.cpp |   32 ++++++++++++++++----------------
- 1 files changed, 16 insertions(+), 16 deletions(-)
-
-diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp
-index 1a7ab1f..256aa4d 100644
---- a/clearcutcommand.cpp
-+++ b/clearcutcommand.cpp
-@@ -180,33 +180,33 @@ int ClearcutCommand::execute() {
- 		
- 		vector<char*> cPara;
- 		
--		char* tempClearcut = new char[8];  strcpy(tempClearcut, "clearcut");  cPara.push_back(tempClearcut);
-+		char* tempClearcut = new char[16];  strcpy(tempClearcut, "clearcut");  cPara.push_back(tempClearcut);
- 				
- 		//you gave us a distance matrix
--		if (phylipfile != "") {  char* temp = new char[10];  strcpy(temp, "--distance");  cPara.push_back(temp);	}
-+		if (phylipfile != "") {  char* temp = new char[16];  strcpy(temp, "--distance");  cPara.push_back(temp);	}
- 		
- 		//you gave us a fastafile
--		if (fastafile != "") { char* temp = new char[11];  strcpy(temp, "--alignment");  cPara.push_back(temp); 	}
-+		if (fastafile != "") { char* temp = new char[16];  strcpy(temp, "--alignment");  cPara.push_back(temp); 	}
- 		
--		if (version)			{  char* temp = new char[9];  strcpy(temp, "--version");  cPara.push_back(temp);	}
--		if (verbose)			{  char* temp = new char[9];  strcpy(temp, "--verbose");  cPara.push_back(temp);	}
--		if (quiet)				{  char* temp = new char[7];  strcpy(temp, "--quiet");  cPara.push_back(temp);	}
-+		if (version)			{  char* temp = new char[16];  strcpy(temp, "--version");  cPara.push_back(temp);	}
-+		if (verbose)			{  char* temp = new char[16];  strcpy(temp, "--verbose");  cPara.push_back(temp);	}
-+		if (quiet)				{  char* temp = new char[16];  strcpy(temp, "--quiet");  cPara.push_back(temp);	}
- 		if (seed != "*")		{  
- 			string tempSeed = "--seed=" + seed;
- 			char* temp = new char[tempSeed.length()];
- 			strcpy(temp, tempSeed.c_str());
- 			cPara.push_back(temp);
- 		}
--		if (norandom)			{  char* temp = new char[10];  strcpy(temp, "--norandom");  cPara.push_back(temp);	}
--		if (shuffle)			{  char* temp = new char[9];  strcpy(temp, "--shuffle");  cPara.push_back(temp);	}
--		if (neighbor)			{  char* temp = new char[10];  strcpy(temp, "--neighbor");  cPara.push_back(temp);	}
-+		if (norandom)			{  char* temp = new char[16];  strcpy(temp, "--norandom");  cPara.push_back(temp);	}
-+		if (shuffle)			{  char* temp = new char[16];  strcpy(temp, "--shuffle");  cPara.push_back(temp);	}
-+		if (neighbor)			{  char* temp = new char[16];  strcpy(temp, "--neighbor");  cPara.push_back(temp);	}
- 		
- 		string tempIn = "--in=" + inputFile;  
- 		char* tempI = new char[tempIn.length()];
- 		strcpy(tempI, tempIn.c_str());
- 		cPara.push_back(tempI);
- 		
--		if (stdoutWanted)		{  char* temp = new char[8];  strcpy(temp, "--stdout");  cPara.push_back(temp);	}
-+		if (stdoutWanted)		{  char* temp = new char[16];  strcpy(temp, "--stdout");  cPara.push_back(temp);	}
- 		else{  
- 			string tempOut = "--out=" + outputName;  
- 			
-@@ -215,10 +215,10 @@ int ClearcutCommand::execute() {
- 			cPara.push_back(temp);
- 		}
- 			
--		if (DNA)				{  char* temp = new char[5];  strcpy(temp, "--DNA");  cPara.push_back(temp);		}
--		if (protein)			{  char* temp = new char[9];  strcpy(temp, "--protein");  cPara.push_back(temp);	}
--		if (jukes)				{  char* temp = new char[7];  strcpy(temp, "--jukes");  cPara.push_back(temp);		}
--		if (kimura)				{ char* temp = new char[8];  strcpy(temp, "--kimura");  cPara.push_back(temp);		}
-+		if (DNA)				{  char* temp = new char[16];  strcpy(temp, "--DNA");  cPara.push_back(temp);		}
-+		if (protein)			{  char* temp = new char[16];  strcpy(temp, "--protein");  cPara.push_back(temp);	}
-+		if (jukes)				{  char* temp = new char[16];  strcpy(temp, "--jukes");  cPara.push_back(temp);		}
-+		if (kimura)				{ char* temp = new char[16];  strcpy(temp, "--kimura");  cPara.push_back(temp);		}
- 		if (matrixout != "")	{  
- 			string tempMatrix =  "--matrixout=" + outputDir + matrixout; 
- 			char* temp = new char[tempMatrix.length()];
-@@ -233,8 +233,8 @@ int ClearcutCommand::execute() {
- 			cPara.push_back(temp);
- 		}
- 
--		if (expblen)			{ char* temp = new char[9];  strcpy(temp, "--expblen");  cPara.push_back(temp); 	}
--		if (expdist)			{ char* temp = new char[9];  strcpy(temp, "--expdist");  cPara.push_back(temp);	}
-+		if (expblen)			{ char* temp = new char[16];  strcpy(temp, "--expblen");  cPara.push_back(temp); 	}
-+		if (expdist)			{ char* temp = new char[16];  strcpy(temp, "--expdist");  cPara.push_back(temp);	}
- 		
- 		char** clearcutParameters;
- 		clearcutParameters = new char*[cPara.size()];
diff --git a/sci-biology/mothur/mothur-1.13.0-r1.ebuild b/sci-biology/mothur/mothur-1.13.0-r1.ebuild
deleted file mode 100644
index 1efa846e1e42..000000000000
--- a/sci-biology/mothur/mothur-1.13.0-r1.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mothur/mothur-1.13.0-r1.ebuild,v 1.3 2012/08/14 15:37:59 jlec Exp $
-
-EAPI="2"
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="A suite of algorithms for ecological bioinformatics"
-HOMEPAGE="http://www.mothur.org/"
-SRC_URI="mirror://gentoo/${P}.zip"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="mpi +readline"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="${RDEPEND}
-	app-arch/unzip"
-RDEPEND="mpi? ( virtual/mpi )"
-
-S=${WORKDIR}/Mothur.source
-
-pkg_setup() {
-	use mpi && CXX=mpicxx || CXX=$(tc-getCXX)
-}
-
-src_prepare() {
-	epatch "${FILESDIR}"/${P}-makefile.patch \
-		"${FILESDIR}"/${P}-overflows.patch
-}
-
-use_yn() {
-	use $1 && echo "yes" || echo "no"
-}
-
-src_compile() {
-	emake USEMPI=$(use_yn mpi) USEREADLINE=$(use_yn readline) || die
-}
-
-src_install() {
-	dobin ${PN}
-}
diff --git a/sci-biology/mothur/mothur-1.13.0-r2.ebuild b/sci-biology/mothur/mothur-1.13.0-r2.ebuild
deleted file mode 100644
index 3dad5095a7ca..000000000000
--- a/sci-biology/mothur/mothur-1.13.0-r2.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mothur/mothur-1.13.0-r2.ebuild,v 1.1 2012/08/14 15:37:59 jlec Exp $
-
-EAPI="2"
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="A suite of algorithms for ecological bioinformatics"
-HOMEPAGE="http://www.mothur.org/"
-SRC_URI="mirror://gentoo/${P}.zip"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="mpi +readline"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="${RDEPEND}
-	app-arch/unzip"
-RDEPEND="mpi? ( virtual/mpi )"
-
-S=${WORKDIR}/Mothur.source
-
-pkg_setup() {
-	use mpi && CXX=mpicxx || CXX=$(tc-getCXX)
-}
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${P}-makefile.patch \
-		"${FILESDIR}"/${P}-overflows.patch \
-		"${FILESDIR}"/${P}-overflows2.patch
-}
-
-use_yn() {
-	use $1 && echo "yes" || echo "no"
-}
-
-src_compile() {
-	emake USEMPI=$(use_yn mpi) USEREADLINE=$(use_yn readline) || die
-}
-
-src_install() {
-	dobin ${PN}
-}
diff --git a/sci-biology/mothur/mothur-1.27.0.ebuild b/sci-biology/mothur/mothur-1.27.0-r1.ebuild
index 852d09ca39ea..b6b4e4fe0be6 100644
--- a/sci-biology/mothur/mothur-1.27.0.ebuild
+++ b/sci-biology/mothur/mothur-1.27.0-r1.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mothur/mothur-1.27.0.ebuild,v 1.1 2012/08/14 15:37:59 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mothur/mothur-1.27.0-r1.ebuild,v 1.1 2015/07/27 18:42:15 jlec Exp $
 
-EAPI=4
+EAPI=5
 
-inherit eutils toolchain-funcs flag-o-matic
+inherit eutils flag-o-matic fortran-2 toolchain-funcs
 
 DESCRIPTION="A suite of algorithms for ecological bioinformatics"
 HOMEPAGE="http://www.mothur.org/"
@@ -24,9 +24,9 @@ DEPEND="${RDEPEND}
 S=${WORKDIR}/Mothur.source
 
 pkg_setup() {
+	fortran-2_pkg_setup
 	use mpi && export CXX=mpicxx || export CXX=$(tc-getCXX)
-	use amd64 && append-flags -DBIT_VERSION
-	tc-export FC
+	use amd64 && append-cppflags -DBIT_VERSION
 }
 
 src_prepare() {
@@ -35,12 +35,8 @@ src_prepare() {
 		"${FILESDIR}"/${P}-overflows.patch
 }
 
-use_yn() {
-	use $1 && echo "yes" || echo "no"
-}
-
 src_compile() {
-	emake USEMPI=$(use_yn mpi) USEREADLINE=$(use_yn readline)
+	emake USEMPI=$(usex mpi) USEREADLINE=$(usex readline)
 }
 
 src_install() {