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

Package-Manager: portage-2.2.20/cvs/Linux x86_64
Manifest-Sign-Key: 0xE9402A79B03529A2!

8 files changed, 35 insertions, 328 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/Manifest b/sci-biology/mothur/Manifest
index 33a24fe98d41..493570707e1b 100644
--- a/sci-biology/mothur/Manifest
+++ b/sci-biology/mothur/Manifest
@@ -1,36 +1,30 @@
 -----BEGIN PGP SIGNED MESSAGE-----
 Hash: SHA512
 
-AUX mothur-1.13.0-makefile.patch 867 SHA256 7eebb85b1a7ebb69e99d326f99e89a2e2103b7448a03e9f9c3158c76c263844a SHA512 0a94626bffdef81ddfa8b56951166cc0b6896b829f4a670083b5a9cf34ec46f7cb2542fcd04e7169360501b881f3ef8abc6bb85a870d08256e9a57147336eef8 WHIRLPOOL 14c7b91e9bc21d6c0fa4c45b67ac8c936ccb10dd9613b4d55728a08cbd717b695b962232f48e4e4a069dbadd2a1e1179d45f39aa0a0ca53692e6ffe055d349ad
-AUX mothur-1.13.0-overflows.patch 2685 SHA256 caa6044398ebf6342ceb5e064cb7a5576b7d493b63329fb730f60d1a4fbdb558 SHA512 ff7bf005dc27e9ef54b99e2098501b72d181149b8e8bb5be06c2766cea5c6c9c5b2c2ad94d98b8a082e7ee80564480ff53b23110ef47e5eeedb684ff8a4ca449 WHIRLPOOL 73411185f77e15e890238d13406a3a25a88bf8de60bd99efbafefe71bd1f1fe96bd6a90a876d7ac02b972bbd3e15084c77495b43f6b0b958a406da4c3f09d178
-AUX mothur-1.13.0-overflows2.patch 4494 SHA256 5e8dba3b12af4119cb433eef2cf4c21c8f6fd08995ffe2bbed7fb876c31dc777 SHA512 5de7c6e5aad2223eaf1a23c4af79760da12e00e60cb9094a2303ecdc869a0a23642981ceddf94de7332a10a6bf5d2221c2c6dfd40175fae0164e27387f5f23de WHIRLPOOL f3fea8decf5c13248d1a03db4a0dac4e7e70cb7cd59bc5332e56aa7699f57a175bac6dbe1060db924ec016427db5ccdaf8362322cfc72e9cf1eb72e8899715ce
 AUX mothur-1.27.0-makefile.patch 1196 SHA256 970d789187d58081bda269a863d965c1601ee18e09c39aa6dcaba2ef0aa89f5a SHA512 8a78ddbc926d4e116deed440fda8431ccbca3299ac182fc84850259187dc130cc43fb6f23845d055d998293fa43f94cbe35930242c5f6aa049f8275ad3e42adf WHIRLPOOL c0ae488479f430f212ff2158b74aa61ef9547b865be1db7ca3b546edf48907aa9aead69acfbc02c35b7d675209ac8f7d267a8f9a98ff167a0f73d0fc2efdd6ea
 AUX mothur-1.27.0-overflows.patch 4894 SHA256 7b1f25400aa8f78ef55bcbd7d613eb877ce2774fc2e9492b6f9c544266661b5b SHA512 aa392b2060cecc38006a7ac50aaa8e4249a020029234ac2abdc33441b12a09faabb0335144ff4d888e55a1da1838a45347981f49f6658f3546a54a30b5e2133a WHIRLPOOL 7f0f8089b938c6a30ee13e217e21a4628ca56490aba36e7b6b14657ec70f3ba043243c80088be6b3e3d145835d4c3e3e3ee68d073f6556383a06e018f0cd716f
-DIST mothur-1.13.0.zip 871838 SHA256 4fe62fcd9b8cc893aecce145ea851581d33f9c835d9dcd6405d9c80acf02ac77 SHA512 f862304120eb50edde1a3a0379d49202df52ea6725397d28490d2cadeaff67f7fd80f9c811f017855c0bde0e976a0fc2bc67ee0a62b634b741c77f1c3a1988eb WHIRLPOOL 5866487bfeb66588079d26f45cad3917fbaca65b2bf79025ca53f489f6b65cb39f316e2d31b4246fb4e05c01fd7a96f7a4d6de1cb1e83caf058d540647963e93
 DIST mothur-1.27.0.zip 7095054 SHA256 7521d0dfc849dc9ef707bf83032e471966914b9833247c49e5d30b8d9281a6c7 SHA512 81821ca95d4ce3f0d1e6aa920c4fe3fddd70f716157312ed0590c1c4ad728e6786bfe79f6badddcfb060ed5d1996cc1b5062c320a59209fef35f68e687ba3dd5 WHIRLPOOL 32e5c9c2be6e593b2dbc64be38c49b4dec3ea048cd3c972cf948136b394608a2dc168be58b7fb500a17fc6a152b7777fcd09b3f9fb3bf60c7dd92d043a4bf361
 DIST mothur-1.6.0.zip 465292 SHA256 75583a204d199ddcf9b845fc0adbaf240d7b1f08584fed5e6465982f68ffe121 SHA512 f775ff64991f00423108f295eca640f5c5d85a38e01b31af44ddf91f8897968e934f79899a21606dfd81fdc3e91751df277237e94d56d74f862e472e8da3386c WHIRLPOOL 31ca8decceb38ebd17f15c5f937df70b501833311cbf1aec794bb174d409a0c01e77abb399347781ad820c06411e56c566382a32818a0c57214aad2ad16cc132
-EBUILD mothur-1.13.0-r1.ebuild 892 SHA256 f7e9d30af8c801c3a5c4994a0b32532c87cbad23f837060d6fab0dea447228a1 SHA512 db53c46b2afe427e4854880d74690dc73ff1887bca139682fe7ce9d51cd8c0a938e20b31febb3cc630ce0719c5e5fd05cc2b3870aae7181ae92a632c28f6b7ed WHIRLPOOL 0c68900cc33d7ad7d4a6e1d1b109c931b1414695e5170391d0beab4a7d94261241830e3208db7f0031c53a572a905b86ab0dfef8adf6ac22879e56a132c6615f
-EBUILD mothur-1.13.0-r2.ebuild 936 SHA256 c257cf077d44c974ebfc9295cf2450f296f0b88ab3ca5532a086a6b4462c82a8 SHA512 0f701d91871de26477aa995d8e8fd186b3515461436f3917e5e30c72d2bae25172f6ad54a2a321719995edb6febbdc8da9869a3194e94b5b24b2f96483224c9d WHIRLPOOL ea9c32b5db832ebe8d7f029ccf8399f40105c62a8c275d1248c3006afe219b6d02ced4979f3a7329034ab65ca814985e984aa004c5c32cd25946b2d5614eb3f8
-EBUILD mothur-1.27.0.ebuild 1028 SHA256 55af15f8c98e5036710180fb69dbcdd18899b2d6853c8e5576d066ee25309086 SHA512 7281c59263cc316da36f25fd37a299d96167cfc5e63c5add36c2ba09ecc02b847ae5642b95344cac83846f9391abdfd4149f4d8bc3da63f056db8206482dc94b WHIRLPOOL 39634c80afdad5a87016ab5e4a1376869cef9f08035ffdd896c41e1c860a780e1bc96ee6f796811feece81b84c8bb115dbcacc0bd9406a462ff107fd58c84b8d
+EBUILD mothur-1.27.0-r1.ebuild 998 SHA256 cbacf26f73267f49baa8ce150a505e6ff460e8416b6dd2371dd73732968111d2 SHA512 6ae95d3c8cc1f6a4a2eaeef578cf4a9e38b20b7315f0a66085a3b65a9554c59bc274d45366c995bfa051aff190e448833a4fd91e7c36f7a65e14d15afad2dee9 WHIRLPOOL 10d9386fadc02c79cb29a517e1b89c38855f7b5f2fbd84d606ee772164f9c4826722cef86880bae8f4340f650738b42b3e82141bf7be2e329d7f629e6fe5681d
 EBUILD mothur-1.6.0.ebuild 723 SHA256 c7337c2cf7e5ba513ed6681f997ab50fde5b29eca205dc9bf36235d7a20642f2 SHA512 726f6794a05abcba3b2565746d7d3131352849baeb3b5817c97354b8b3e2f8fbec2459ff1e1a35933bc5eb997ebc15acb8df12d961cd551e9d1a1e227c841793 WHIRLPOOL 78d21046e8ee24a78a051802a9a59dde175855a5f3dcf869a7d1afe311880e4915acf8f3cf97b9a8643e4a9e81319cf41546ba6d091b2782bd98c8879e381c01
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+MISC ChangeLog 2607 SHA256 434ea95cd52b49386184223a293d03212b465c5acda7cdc56ae91650e5de9323 SHA512 cdbaf8d96020142a20706a3ea3585acc96f5fe89b7b589023e62dc6aa98057608915d62bed900d4a68c7c57f87912b8ea79511fa3dc2e4dc36a1285d6f197d30 WHIRLPOOL 5f46ef5308b22afc313021f273adf877bf449b0908801b8dab7248b26be719ee2e0402ecc7abe842f06294ad21d2e4bf73cba69ba62eea3580269c6f1cb8859f
 MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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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() {