sci-biology/vienna-rna: remove unused patches/file

Closes: https://github.com/gentoo/gentoo/pull/3708

9 files changed, 0 insertions, 266 deletions

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
deleted file mode 100644
index 0a781667c70b..000000000000
--- a/sci-biology/vienna-rna/files/vienna-rna-1.6.5-c-fixes.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-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
deleted file mode 100644
index 37e2f8c6a880..000000000000
--- a/sci-biology/vienna-rna/files/vienna-rna-1.7.2-LDFLAGS.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-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: $(SOURCES)
diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.3-disable-gd.patch b/sci-biology/vienna-rna/files/vienna-rna-1.8.3-disable-gd.patch
deleted file mode 100644
index 2c5ac3041297..000000000000
--- a/sci-biology/vienna-rna/files/vienna-rna-1.8.3-disable-gd.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-# unfortunately, vienna-rna's build system is a little broken and sometimes detects
-# gd in RNAforested but then realizes in g2 that it can't actually build it 
-# resulting in unresolved symbols.
-
-diff -durr ViennaRNA-1.8.3.orig/RNAforester/configure.in ViennaRNA-1.8.3/RNAforester/configure.in
---- ViennaRNA-1.8.3.orig/RNAforester/configure.in	2009-09-10 13:05:40.507932827 +0000
-+++ ViennaRNA-1.8.3/RNAforester/configure.in	2009-09-10 13:06:15.171952984 +0000
-@@ -47,7 +47,7 @@
- save_CPPFLAGS=$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
deleted file mode 100644
index 025822f45c91..000000000000
--- a/sci-biology/vienna-rna/files/vienna-rna-1.8.3-gcc4.3.patch
+++ /dev/null
@@ -1,76 +0,0 @@
-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
deleted file mode 100644
index 76a5a259a862..000000000000
--- a/sci-biology/vienna-rna/files/vienna-rna-1.8.4-bindir.patch
+++ /dev/null
@@ -1,10 +0,0 @@
-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 = $(prefix)/bin
- pkgbin_PROGRAMS = b2ct popt
- 
- pscript = b2mt.pl ct2b.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl colorrna.pl coloraln.pl refold.pl
diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.4-implicits.patch b/sci-biology/vienna-rna/files/vienna-rna-1.8.4-implicits.patch
deleted file mode 100644
index c3f5b52141e8..000000000000
--- a/sci-biology/vienna-rna/files/vienna-rna-1.8.4-implicits.patch
+++ /dev/null
@@ -1,47 +0,0 @@
-Fix implicit function declarations and attempt to free non-heap obj
-
---- lib/subopt.c
-+++ lib/subopt.c
-@@ -80,12 +80,12 @@
- #include <string.h>
- #include <math.h>
- #include "fold.h"
-+#include "cofold.h"
- #include "utils.h"
- #include "energy_par.h"
- #include "fold_vars.h"
- #include "pair_mat.h"
- #include "list.h"
--#include "subopt.h"
- #include "params.h"
- 
- #define true	  1
---- Progs/RNAfold.c
-+++ Progs/RNAfold.c
-@@ -20,6 +20,7 @@
- #include "MEA.h"
- extern void  read_parameter_file(const char fname[]);
- extern plist * stackProb(double cutoff);
-+extern void init_pf_circ_fold(int length);
- 
- /*@unused@*/
- static char UNUSED rcsid[] = "$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
deleted file mode 100644
index cfadc70bc6f6..000000000000
--- a/sci-biology/vienna-rna/files/vienna-rna-1.8.4-jobserver-fix.patch
+++ /dev/null
@@ -1,18 +0,0 @@
-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
deleted file mode 100644
index fcaa5f9a53b6..000000000000
--- a/sci-biology/vienna-rna/files/vienna-rna-1.8.4-overflows.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-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
deleted file mode 100644
index 0aeaf2a116d3..000000000000
--- a/sci-biology/vienna-rna/files/vienna-rna-1.8.5-setup.py
+++ /dev/null
@@ -1,27 +0,0 @@
-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],
-      )