proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

18 files changed, 609 insertions, 0 deletions

diff --git a/sci-biology/vienna-rna/Manifest b/sci-biology/vienna-rna/Manifest
new file mode 100644
index 000000000000..d53e2f5d3ab7
--- /dev/null
+++ b/sci-biology/vienna-rna/Manifest
@@ -0,0 +1,2 @@
+DIST ViennaRNA-2.1.1.tar.gz 5327215 SHA256 bfea440dface4562d5dfb0a1c83bf226c0697bb18aacae0dc84c555282cedebe SHA512 b272afa1146543b290db605debab2badbdbf04fcdfd6130ed3b10604255476b3472b184e9af8a0bbeaa0def266f1a167c125d6cfd02aa3f7ae463697dc5226d5 WHIRLPOOL 48b6bcd96b2ff2523ba00335cac7fe141b6ed7f037a3192e6c174297266d0f967492a67afaaa6c05f8b28fdc0eb7c9b72d0d9daba286b5dd3dca4456cc058b1f
+DIST ViennaRNA-2.1.8.tar.gz 5464683 SHA256 37a0a0b7c8a167bcdab1a85d88bcb1025ad8e00a4b00a147bf36d45dc8ca7560 SHA512 84f9db1247ff7a77aa6550b6285d9bed31fa6ce179aab26eef798c65a07f5cbd89f944630dfa5d29a43401b12a439324b57ee69047a3985e3a4f1e88dffca60e WHIRLPOOL a79f30d49c9bbe047d9fe83054dc08e94535f17417ef1f412bbcdd374d1988a8f2faf679e154c1ed1d1a75799e6cc0232d30b3adf65b3fa19978322f67ace57e
diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.6.5-c-fixes.patch b/sci-biology/vienna-rna/files/vienna-rna-1.6.5-c-fixes.patch
new file mode 100644
index 000000000000..0a781667c70b
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-1.6.5-c-fixes.patch
@@ -0,0 +1,22 @@
+diff -Naur ViennaRNA-1.6.5/Cluster/statgeom.c ViennaRNA-1.6.5.new/Cluster/statgeom.c
+--- ViennaRNA-1.6.5/Cluster/statgeom.c	2001-04-05 04:36:41.000000000 -0400
++++ ViennaRNA-1.6.5.new/Cluster/statgeom.c	2007-11-24 08:55:17.000000000 -0500
+@@ -5,6 +5,7 @@
+ */
+ 
+ #include <stdio.h>
++#include <string.h>
+ #include <strings.h>
+ #include <ctype.h>
+ #include "utils.h"
+diff -Naur ViennaRNA-1.6.5/Readseq/readseq.c ViennaRNA-1.6.5.new/Readseq/readseq.c
+--- ViennaRNA-1.6.5/Readseq/readseq.c	1995-07-12 13:05:58.000000000 -0400
++++ ViennaRNA-1.6.5.new/Readseq/readseq.c	2007-11-24 08:56:16.000000000 -0500
+@@ -173,6 +173,7 @@
+ #include <stdio.h>
+ #include <string.h>
+ #include <ctype.h>
++#include <stdlib.h>
+ 
+ #include "ureadseq.h"
+ 
diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.7.2-LDFLAGS.patch b/sci-biology/vienna-rna/files/vienna-rna-1.7.2-LDFLAGS.patch
new file mode 100644
index 000000000000..37e2f8c6a880
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-1.7.2-LDFLAGS.patch
@@ -0,0 +1,24 @@
+diff -Naur ViennaRNA-1.7.2/Perl/Makefile.am ViennaRNA-1.7.2.new/Perl/Makefile.am
+--- ViennaRNA-1.7.2/Perl/Makefile.am	2007-12-19 05:33:14.000000000 -0500
++++ ViennaRNA-1.7.2.new/Perl/Makefile.am	2008-10-06 14:20:54.000000000 -0400
+@@ -4,7 +4,7 @@
+ 	     RNA.i tmaps.i
+ 
+ Makefile.perl: Makefile.PL Makefile
+-	@PerlCmd@ Makefile.PL
++	@PerlCmd@ Makefile.PL LDDLFLAGS="${LDFLAGS} -shared"
+ 
+ # the perl command repairs some errors in the SWIG CVS version
+ RNA_wrap.c: RNA.i tmaps.i
+diff -Naur ViennaRNA-1.7.2/Readseq/Makefile ViennaRNA-1.7.2.new/Readseq/Makefile
+--- ViennaRNA-1.7.2/Readseq/Makefile	2008-01-23 05:32:00.000000000 -0500
++++ ViennaRNA-1.7.2.new/Readseq/Makefile	2008-10-06 14:21:13.000000000 -0400
+@@ -40,7 +40,7 @@
+ 
+ build: $(SOURCES)
+ 	@echo "Compiling readseq..."
+-	$(CC) $(CFLAGS) -o readseq readseq.c ureadseq.c
++	$(CC) $(LDFLAGS) $(CFLAGS) -o readseq readseq.c ureadseq.c
+ 
+ # if using NCBI, uncomment these lines in place of build: above
+ #build: $(SOURCES)
diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.3-disable-gd.patch b/sci-biology/vienna-rna/files/vienna-rna-1.8.3-disable-gd.patch
new file mode 100644
index 000000000000..2c5ac3041297
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-1.8.3-disable-gd.patch
@@ -0,0 +1,16 @@
+# unfortunately, vienna-rna's build system is a little broken and sometimes detects
+# gd in RNAforested but then realizes in g2 that it can't actually build it 
+# resulting in unresolved symbols.
+
+diff -durr ViennaRNA-1.8.3.orig/RNAforester/configure.in ViennaRNA-1.8.3/RNAforester/configure.in
+--- ViennaRNA-1.8.3.orig/RNAforester/configure.in	2009-09-10 13:05:40.507932827 +0000
++++ ViennaRNA-1.8.3/RNAforester/configure.in	2009-09-10 13:06:15.171952984 +0000
+@@ -47,7 +47,7 @@
+ save_CPPFLAGS=$CPPFLAGS	
+ CPPFLAGS=["-Ig2-0.70/src/ ${CPPFLAGS}"]
+ 
+-AC_CHECK_LIB(gd,main,,)
++dnl AC_CHECK_LIB(gd,main,,)
+ 		  
+ dnl Checks for header files.
+ AC_HEADER_STDC
diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.3-gcc4.3.patch b/sci-biology/vienna-rna/files/vienna-rna-1.8.3-gcc4.3.patch
new file mode 100644
index 000000000000..025822f45c91
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-1.8.3-gcc4.3.patch
@@ -0,0 +1,76 @@
+diff -durr ViennaRNA-1.8.3.orig/Cluster/AS_main.c ViennaRNA-1.8.3/Cluster/AS_main.c
+--- ViennaRNA-1.8.3.orig/Cluster/AS_main.c	2009-09-10 11:56:01.636674988 +0000
++++ ViennaRNA-1.8.3/Cluster/AS_main.c	2009-09-10 11:58:32.915952366 +0000
+@@ -1,5 +1,6 @@
+ #include <stdio.h>
+ #include <string.h>
++#include <stdlib.h>
+ #include "distance_matrix.h"
+ #include "statgeom.h"
+ #include "split.h"
+diff -durr ViennaRNA-1.8.3.orig/Cluster/statgeom.c ViennaRNA-1.8.3/Cluster/statgeom.c
+--- ViennaRNA-1.8.3.orig/Cluster/statgeom.c	2009-09-10 11:56:01.636674988 +0000
++++ ViennaRNA-1.8.3/Cluster/statgeom.c	2009-09-10 11:58:53.192452141 +0000
+@@ -7,6 +7,7 @@
+ #include <stdio.h>
+ #include <string.h>
+ #include <strings.h>
++#include <stdlib.h>
+ #include <ctype.h>
+ #include "utils.h"
+ #include "PS3D.h"
+diff -durr ViennaRNA-1.8.3.orig/Cluster/treeplot.c ViennaRNA-1.8.3/Cluster/treeplot.c
+--- ViennaRNA-1.8.3.orig/Cluster/treeplot.c	2009-09-10 11:56:01.636674988 +0000
++++ ViennaRNA-1.8.3/Cluster/treeplot.c	2009-09-10 11:59:22.457509165 +0000
+@@ -1,5 +1,6 @@
+ #include <stdio.h>
+ #include <string.h>
++#include <stdlib.h>
+ #include <math.h>
+ #include "distance_matrix.h"
+ #include "utils.h"
+diff -durr ViennaRNA-1.8.3.orig/RNAforester/src/main.cpp ViennaRNA-1.8.3/RNAforester/src/main.cpp
+--- ViennaRNA-1.8.3.orig/RNAforester/src/main.cpp	2009-09-10 11:56:01.624743558 +0000
++++ ViennaRNA-1.8.3/RNAforester/src/main.cpp	2009-09-10 12:00:37.693252890 +0000
+@@ -19,6 +19,8 @@
+ #include <list>
+ #include <sstream>
+ #include <string>
++#include <cstring>
++#include <climits>
+ #include <map>
+ 
+ //#include <sys/timeb.h>
+diff -durr ViennaRNA-1.8.3.orig/RNAforester/src/ppforestbase.h ViennaRNA-1.8.3/RNAforester/src/ppforestbase.h
+--- ViennaRNA-1.8.3.orig/RNAforester/src/ppforestbase.h	2009-09-10 11:56:01.624743558 +0000
++++ ViennaRNA-1.8.3/RNAforester/src/ppforestbase.h	2009-09-10 12:01:41.631932654 +0000
+@@ -16,6 +16,7 @@
+ 
+ #include <algorithm>
+ #include <cassert>
++#include <cstring>
+ 
+ #include "misc.h"
+ #include "types.h"
+diff -durr ViennaRNA-1.8.3.orig/RNAforester/src/rna_algebra.h ViennaRNA-1.8.3/RNAforester/src/rna_algebra.h
+--- ViennaRNA-1.8.3.orig/RNAforester/src/rna_algebra.h	2009-09-10 11:56:01.620703294 +0000
++++ ViennaRNA-1.8.3/RNAforester/src/rna_algebra.h	2009-09-10 12:02:29.687952726 +0000
+@@ -4,6 +4,7 @@
+ #include <assert.h>
+ #include <algorithm>
+ #include <climits>
++#include <cstring>
+ 
+ #include "algebra.h"
+ #include "debug.h"
+diff -durr ViennaRNA-1.8.3.orig/Readseq/ureadseq.c ViennaRNA-1.8.3/Readseq/ureadseq.c
+--- ViennaRNA-1.8.3.orig/Readseq/ureadseq.c	2009-09-10 11:56:01.632743452 +0000
++++ ViennaRNA-1.8.3/Readseq/ureadseq.c	2009-09-10 12:03:15.343952776 +0000
+@@ -20,6 +20,7 @@
+ #include <stdio.h>
+ #include <ctype.h>
+ #include <string.h>
++#include <stdlib.h>
+ 
+ #define UREADSEQ_G
+ #include "ureadseq.h"
diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.4-bindir.patch b/sci-biology/vienna-rna/files/vienna-rna-1.8.4-bindir.patch
new file mode 100644
index 000000000000..76a5a259a862
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-1.8.4-bindir.patch
@@ -0,0 +1,10 @@
+diff --git a/Utils/Makefile.am b/Utils/Makefile.am
+index f42ebf4..d84a0f1 100644
+--- a/Utils/Makefile.am
++++ b/Utils/Makefile.am
+@@ -1,4 +1,4 @@
+-pkgbindir = $(pkgdatadir)/bin
++pkgbindir = $(prefix)/bin
+ pkgbin_PROGRAMS = b2ct popt
+ 
+ pscript = b2mt.pl ct2b.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl colorrna.pl coloraln.pl refold.pl
diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.4-implicits.patch b/sci-biology/vienna-rna/files/vienna-rna-1.8.4-implicits.patch
new file mode 100644
index 000000000000..c3f5b52141e8
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-1.8.4-implicits.patch
@@ -0,0 +1,47 @@
+Fix implicit function declarations and attempt to free non-heap obj
+
+--- lib/subopt.c
++++ lib/subopt.c
+@@ -80,12 +80,12 @@
+ #include <string.h>
+ #include <math.h>
+ #include "fold.h"
++#include "cofold.h"
+ #include "utils.h"
+ #include "energy_par.h"
+ #include "fold_vars.h"
+ #include "pair_mat.h"
+ #include "list.h"
+-#include "subopt.h"
+ #include "params.h"
+ 
+ #define true	  1
+--- Progs/RNAfold.c
++++ Progs/RNAfold.c
+@@ -20,6 +20,7 @@
+ #include "MEA.h"
+ extern void  read_parameter_file(const char fname[]);
+ extern plist * stackProb(double cutoff);
++extern void init_pf_circ_fold(int length);
+ 
+ /*@unused@*/
+ static char UNUSED rcsid[] = "$Id$";
+--- Cluster/AS_main.c
++++ Cluster/AS_main.c
+@@ -1,6 +1,7 @@
+ #include <stdio.h>
+ #include <string.h>
+ #include <stdlib.h>
++#include <unistd.h>
+ #include "distance_matrix.h"
+ #include "statgeom.h"
+ #include "split.h"
+@@ -226,7 +227,7 @@
+ 	    for(j=0;j<nn[i];j++) free(ss[i][j]);
+ 	    free(ss[i]);
+          }
+-	 free(ss);
++	 // free(ss); 	//  attempt to free a non-heap object ‘ss’
+       }
+       else {
+          printf_taxa_list();
diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.4-jobserver-fix.patch b/sci-biology/vienna-rna/files/vienna-rna-1.8.4-jobserver-fix.patch
new file mode 100644
index 000000000000..cfadc70bc6f6
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-1.8.4-jobserver-fix.patch
@@ -0,0 +1,18 @@
+diff -ur ViennaRNA-1.8.4-orig/RNAforester/g2-0.70/Makefile.in ViennaRNA-1.8.4/RNAforester/g2-0.70/Makefile.in
+--- ViennaRNA-1.8.4-orig/RNAforester/g2-0.70/Makefile.in	2009-10-13 13:44:40.000000000 +0200
++++ ViennaRNA-1.8.4/RNAforester/g2-0.70/Makefile.in	2010-03-27 21:39:21.000000000 +0100
+@@ -116,12 +116,12 @@
+ 
+ 
+ clean:
+-	-(cd ./demo ; make clean)
++	-(cd ./demo ; $(MAKE) clean)
+ 	-rm -f $(OBJ)
+ 	-rm -f libg2.a config.cache config.log Makefile.bak config.status
+ 	-rm -f ./include/*.h
+ 	-$(FIND) . -name "*~" -exec rm -f {} \;
+-	-(cd ./g2_perl ; make clean)
++	-(cd ./g2_perl ; $(MAKE) clean)
+ 	-rm -f ./g2_perl/test.ps
+ 	-rm -f ./g2_perl/test.png
+ 	-rm -f ./g2_perl/test.jpg
diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.4-overflows.patch b/sci-biology/vienna-rna/files/vienna-rna-1.8.4-overflows.patch
new file mode 100644
index 000000000000..fcaa5f9a53b6
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-1.8.4-overflows.patch
@@ -0,0 +1,26 @@
+Fix buffer overflows
+
+http://bugs.gentoo.org/show_bug.cgi?id=341089
+
+--- Readseq/ureadseq.c
++++ Readseq/ureadseq.c
+@@ -1579,7 +1579,7 @@
+ 
+   short linesout = 0, seqtype = kNucleic;
+   long  i, j, l, l1, ibase;
+-  char  idword[31], endstr[10];
++  char  idword[31], endstr[15];
+   char  seqnamestore[128], *seqname = seqnamestore;
+   char  s[kMaxseqwidth], *cp;
+   char  nameform[10], numform[10], nocountsymbols[10];
+--- lib/part_func_up.c
++++ lib/part_func_up.c
+@@ -1438,7 +1438,7 @@
+ PUBLIC int plot_free_pu_out(pu_out* res, interact *pint, char *ofile, char *head) {
+   int size,s,i,len;
+   double dG_u;
+-  char nan[4], *time, startl[2], dg[10];;
++  char nan[4], *time, startl[3], dg[10];;
+   FILE *wastl;
+ 
+   wastl = fopen(ofile,"a");
diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.5-setup.py b/sci-biology/vienna-rna/files/vienna-rna-1.8.5-setup.py
new file mode 100644
index 000000000000..0aeaf2a116d3
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-1.8.5-setup.py
@@ -0,0 +1,27 @@
+from distutils.core import setup, Extension
+import os
+import sys
+ 
+old_filename = os.path.join("Perl", "RNA.py")
+new_filename = os.path.join("Perl", "__init__.py")
+if os.path.exists(old_filename):
+    os.rename(old_filename, new_filename)
+ 
+extra_link_args = []
+ 
+extension = Extension("_RNA",
+                      ["Perl/RNA_wrap.c"],
+                      libraries=['RNA'],
+                      library_dirs=['lib'],
+                      extra_link_args=extra_link_args
+                      )
+ 
+setup(name="RNA",
+      version="1.8.5",
+      description="Vienna RNA",
+      author="Ivo Hofacker, Institute for Theoretical Chemistry, University of Vienna",
+      url="http://www.tbi.univie.ac.at/RNA/",
+      package_dir = {'RNA':'Perl'},
+      packages = ['RNA'],
+      ext_modules=[extension],
+      )
diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-bindir.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-bindir.patch
new file mode 100644
index 000000000000..6d35ecea9b0f
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-bindir.patch
@@ -0,0 +1,10 @@
+diff --git a/Utils/Makefile.am b/Utils/Makefile.am
+index f42ebf4..d84a0f1 100644
+--- a/Utils/Makefile.am
++++ b/Utils/Makefile.am
+@@ -1,4 +1,4 @@
+-pkgbindir = $(pkgdatadir)/bin
++pkgbindir = $(prefix)/bin
+ pkgbin_PROGRAMS = b2ct popt
+ 
+ pscript = b2mt.pl ct2b.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl colorrna.pl coloraln.pl refold.pl switch.pl
diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch
new file mode 100644
index 000000000000..de457f318e8e
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch
@@ -0,0 +1,15 @@
+ Readseq/readseq.c | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/Readseq/readseq.c b/Readseq/readseq.c
+index 8af7b39..56a25ae 100644
+--- a/Readseq/readseq.c
++++ b/Readseq/readseq.c
+@@ -171,6 +171,7 @@ link -w -o readseq -t MPST -c 'MPS ' 
+ #include <stdio.h>
+ #include <string.h>
+ #include <ctype.h>
++#include <stdlib.h>
+ 
+ #include "ureadseq.h"
+ 
diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch
new file mode 100644
index 000000000000..ee4aef5c3308
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch
@@ -0,0 +1,30 @@
+ Readseq/Makefile | 6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/Readseq/Makefile b/Readseq/Makefile
+index f073aaa..05f2edd 100644
+--- a/Readseq/Makefile
++++ b/Readseq/Makefile
+@@ -6,11 +6,11 @@
+ #
+ 
+ # pick an ANSI C compiler (the default Sun CC is not ANSI)
+-CC=gcc  # Gnu C Compiler
++CC?=gcc  # Gnu C Compiler
+ #CC=cc  # SGI Irix
+ #CC=vcc # some DEC Ultrix
+ 
+-CFLAGS=
++CFLAGS?=
+ #CFLAGS= -DSMALLCHECKSUM  # if you prefer to use a GCG-standard 13 bit checksum
+ #    instead of a full 32 bit checksum. This may enhance compatibility w/ GCG software
+ 
+@@ -40,7 +40,7 @@ all: build test
+ 
+ build: $(SOURCES)
+ 	@echo "Compiling readseq..."
+-	$(CC) $(LDFLAGS) $(CFLAGS) -o readseq readseq.c ureadseq.c
++	$(CC) $(LDFLAGS) $(CFLAGS) -o readseq readseq.c ureadseq.c ureadasn.c
+ 
+ # if using NCBI, uncomment these lines in place of build: above
+ #build: $(SOURCES)
diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-setup.py b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-setup.py
new file mode 100644
index 000000000000..57f6b712ba3d
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-setup.py
@@ -0,0 +1,27 @@
+from distutils.core import setup, Extension
+import os
+import sys
+ 
+old_filename = os.path.join("Perl", "RNA.py")
+new_filename = os.path.join("Perl", "__init__.py")
+if os.path.exists(old_filename):
+    os.rename(old_filename, new_filename)
+ 
+extra_link_args = []
+ 
+extension = Extension("_RNA",
+                      ["Perl/RNA_wrap.c"],
+                      libraries=['RNA'],
+                      library_dirs=['lib'],
+                      extra_link_args=extra_link_args
+                      )
+ 
+setup(name="RNA",
+      version="2.1.1",
+      description="Vienna RNA",
+      author="Ivo Hofacker, Institute for Theoretical Chemistry, University of Vienna",
+      url="http://www.tbi.univie.ac.at/RNA/",
+      package_dir = {'RNA':'Perl'},
+      packages = ['RNA'],
+      ext_modules=[extension],
+      )
diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.8-bindir.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.8-bindir.patch
new file mode 100644
index 000000000000..e54dff95b485
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-2.1.8-bindir.patch
@@ -0,0 +1,10 @@
+diff --git a/Utils/Makefile.am b/Utils/Makefile.am
+index f42ebf4..d84a0f1 100644
+--- a/Utils/Makefile.am
++++ b/Utils/Makefile.am
+@@ -1,4 +1,4 @@
+-pkgbindir = $(pkgdatadir)/bin
++pkgbindir = $(prefix)/bin
+ pkgbin_PROGRAMS = b2ct popt ct2db
+ 
+ pscript = b2mt.pl ct2b.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl colorrna.pl coloraln.pl refold.pl switch.pl
diff --git a/sci-biology/vienna-rna/metadata.xml b/sci-biology/vienna-rna/metadata.xml
new file mode 100644
index 000000000000..50f4e02d4a18
--- /dev/null
+++ b/sci-biology/vienna-rna/metadata.xml
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <longdescription>
+	The Vienna RNA Package consists of a C code library and several
+	stand-alone programs for the prediction and comparison of RNA secondary
+	structures. RNA secondary structure prediction through energy
+	minimization is the most used function in the package. We provide three
+	kinds of dynamic programming algorithms for structure prediction: the
+	minimum free energy algorithm of (Zuker and Stiegler 1981) which yields a
+	single optimal structure, the partition function algorithm of
+	(McCaskill 1990) which calculates base pair probabilities in the
+	thermodynamic ensemble, and the suboptimal folding algorithm of
+	(Wuchty et.al 1999) which generates all suboptimal structures within a
+	given energy range of the optimal energy. For secondary structure
+	comparison, the package contains several measures of distance
+	(dissimilarities) using either string alignment or tree-editing
+	(Shapiro and Zhang 1990). Finally, we provide an algorithm to design
+	sequences with a predefined structure (inverse folding).
+</longdescription>
+</pkgmetadata>
diff --git a/sci-biology/vienna-rna/vienna-rna-2.1.1.ebuild b/sci-biology/vienna-rna/vienna-rna-2.1.1.ebuild
new file mode 100644
index 000000000000..df5c8eb50f90
--- /dev/null
+++ b/sci-biology/vienna-rna/vienna-rna-2.1.1.ebuild
@@ -0,0 +1,113 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+DISTUTILS_OPTIONAL=true
+AUTOTOOLS_AUTORECONF=true
+AUTOTOOLS_IN_SOURCE_BUILD=1
+
+inherit autotools-utils distutils-r1 multilib perl-module toolchain-funcs
+
+DESCRIPTION="RNA secondary structure prediction and comparison"
+HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA/"
+SRC_URI="http://www.tbi.univie.ac.at/~ronny/RNA/ViennaRNA-${PV}.tar.gz"
+
+SLOT="0"
+LICENSE="vienna-rna"
+KEYWORDS="amd64 ppc x86"
+IUSE="doc openmp python static-libs"
+
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
+
+DEPEND="
+	dev-lang/perl
+	media-libs/gd
+	doc? ( dev-texlive/texlive-latex )
+	python? (
+		${PYTHON_DEPS}
+		dev-lang/swig )"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/ViennaRNA-${PV}"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-bindir.patch
+	"${FILESDIR}"/${P}-prll.patch
+	"${FILESDIR}"/${P}-impl-decl.patch
+)
+
+src_prepare() {
+	sed -i 's/ getline/ v_getline/' Readseq/ureadseq.c || die
+	sed -i 's/@PerlCmd@ Makefile.PL/& INSTALLDIRS=vendor/' Perl/Makefile.am || die
+
+	autotools-utils_src_prepare
+
+	if use python; then
+		cp "${FILESDIR}"/${P}-setup.py "${S}"/setup.py || die
+		PATCHES=()
+		distutils-r1_src_prepare
+	fi
+}
+
+src_configure() {
+	local myeconfargs=(
+		--with-cluster
+		$(use_enable openmp) )
+
+	use doc || \
+		myeconfargs+=(
+			--without-doc-pdf
+			--without-doc-html
+			--without-doc
+			)
+	autotools-utils_src_configure
+	sed \
+		-e "s:LIBDIR = /usr/lib:LIBDIR = ${D}/usr/$(get_libdir):" \
+		-e "s:INCDIR = /usr/include:INCDIR = ${D}/usr/include:" \
+		-i RNAforester/g2-0.70/Makefile || die
+	sed \
+		-e "s:CC=gcc:CC=$(tc-getCC):" \
+		-e "s:^CFLAGS=:CFLAGS=${CFLAGS}:" \
+		-i Readseq/Makefile || die
+	use python && distutils-r1_src_configure
+}
+
+src_compile() {
+	autotools-utils_src_compile
+	autotools-utils_src_compile -C Readseq build CC=$(tc-getCC)
+
+	# TODO: Add (optional?) support for the NCBI toolkit.
+	if use python; then
+		pushd Perl > /dev/null
+			mv RNA_wrap.c{,-perl} || die
+			swig -python RNA.i || die
+		popd > /dev/null
+		distutils-r1_src_compile
+		mv Perl/RNA_wrap.c{-perl,} || die
+	fi
+}
+
+src_test() {
+	autotools-utils_src_compile -C Perl check
+	autotools-utils_src_compile -C Readseq test
+}
+
+src_install() {
+	autotools-utils_src_install
+
+	if ! use static-libs; then
+		rm -f "${ED}"/usr/$(get_libdir)/*.a || die
+	fi
+
+	newbin Readseq/readseq readseq-vienna
+	dodoc Readseq/Readseq.help
+	newdoc Readseq/Readme README.readseq
+	newdoc Readseq/Formats Formats.readseq
+
+	# remove perlocal.pod to avoid file collisions (see #240358)
+	perl_delete_localpod || die "Failed to remove perlocal.pod"
+	use python && distutils-r1_src_install
+}
diff --git a/sci-biology/vienna-rna/vienna-rna-2.1.8.ebuild b/sci-biology/vienna-rna/vienna-rna-2.1.8.ebuild
new file mode 100644
index 000000000000..8b862403e25f
--- /dev/null
+++ b/sci-biology/vienna-rna/vienna-rna-2.1.8.ebuild
@@ -0,0 +1,114 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+DISTUTILS_OPTIONAL=true
+AUTOTOOLS_AUTORECONF=true
+AUTOTOOLS_IN_SOURCE_BUILD=1
+
+inherit autotools-utils distutils-r1 multilib perl-module toolchain-funcs
+
+DESCRIPTION="RNA secondary structure prediction and comparison"
+HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA/"
+SRC_URI="http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-${PV}.tar.gz"
+
+SLOT="0"
+LICENSE="vienna-rna"
+KEYWORDS="~amd64 ~ppc ~x86"
+IUSE="doc openmp python static-libs"
+
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
+
+DEPEND="
+	dev-lang/perl
+	media-libs/gd
+	doc? ( dev-texlive/texlive-latex )
+	python? (
+		${PYTHON_DEPS}
+		dev-lang/swig )"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/ViennaRNA-${PV}"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-bindir.patch
+	"${FILESDIR}"/${PN}-2.1.1-prll.patch
+	"${FILESDIR}"/${PN}-2.1.1-impl-decl.patch
+)
+
+src_prepare() {
+	sed -i 's/ getline/ v_getline/' Readseq/ureadseq.c || die
+	sed -i 's/@PerlCmd@ Makefile.PL/& INSTALLDIRS=vendor/' interfaces/Perl/Makefile.am || die
+
+	autotools-utils_src_prepare
+
+	if use python; then
+		cd interfaces/Python || die
+		local PATCHES=()
+		distutils-r1_src_prepare
+	fi
+}
+
+src_configure() {
+	local myeconfargs=(
+		--with-cluster
+		$(use_enable openmp)
+	)
+
+	use doc || \
+		myeconfargs+=(
+			--without-doc-pdf
+			--without-doc-html
+			--without-doc
+			)
+	autotools-utils_src_configure
+	sed \
+		-e "s:CC=gcc:CC=$(tc-getCC):" \
+		-e "s:^CFLAGS=:CFLAGS=${CFLAGS}:" \
+		-i Readseq/Makefile || die
+	if use python; then
+		cd interfaces/Python || die
+		distutils-r1_src_configure
+	fi
+}
+
+src_compile() {
+	autotools-utils_src_compile
+	autotools-utils_src_compile -C Readseq build CC=$(tc-getCC)
+
+	# TODO: Add (optional?) support for the NCBI toolkit.
+	if use python; then
+		cd interfaces/Python || die
+		emake RNA_wrap.c
+		distutils-r1_src_compile
+	fi
+}
+
+src_test() {
+	autotools-utils_src_compile -C interfaces/Perl check
+	use python && autotools-utils_src_compile -C interfaces/Python check
+	autotools-utils_src_compile -C Readseq test
+}
+
+src_install() {
+	autotools-utils_src_install
+
+	if ! use static-libs; then
+		rm -f "${ED}"/usr/$(get_libdir)/*.a || die
+	fi
+
+	newbin Readseq/readseq readseq-vienna
+	dodoc Readseq/Readseq.help
+	newdoc Readseq/Readme README.readseq
+	newdoc Readseq/Formats Formats.readseq
+
+	# remove perlocal.pod to avoid file collisions (see #240358)
+	perl_delete_localpod || die "Failed to remove perlocal.pod"
+	if use python; then
+		cd interfaces/Python || die
+		distutils-r1_src_install
+	fi
+}