fix build on SunOS

5 files changed, 131 insertions, 0 deletions

diff --git a/biology/plinkseq/patches/patch-browser_main.c b/biology/plinkseq/patches/patch-browser_main.c
new file mode 100644
index 00000000000..4b698bb5843
--- /dev/null
+++ b/biology/plinkseq/patches/patch-browser_main.c
@@ -0,0 +1,16 @@
+$NetBSD: patch-browser_main.c,v 1.1 2014/02/08 12:27:14 wiedi Exp $
+
+not needed on sunos
+--- browser/main.c.orig	2011-11-17 17:17:36.000000000 +0000
++++ browser/main.c
+@@ -21,8 +21,10 @@
+ #if defined(_WIN32)

+ #define _CRT_SECURE_NO_WARNINGS  // Disable deprecation warning in VS2005

+ #else

++#if !defined(__sun)

+ #define _XOPEN_SOURCE 600  // For PATH_MAX on linux

+ #endif

++#endif

+ 

+ #include <sys/stat.h>

+ #include <stdio.h>

diff --git a/biology/plinkseq/patches/patch-browser_mongoose.c b/biology/plinkseq/patches/patch-browser_mongoose.c
new file mode 100644
index 00000000000..2a6d30d53e6
--- /dev/null
+++ b/biology/plinkseq/patches/patch-browser_mongoose.c
@@ -0,0 +1,15 @@
+$NetBSD: patch-browser_mongoose.c,v 1.1 2014/02/08 12:27:14 wiedi Exp $
+
+not needed on sunos
+--- browser/mongoose.c.orig	2011-11-17 17:17:36.000000000 +0000
++++ browser/mongoose.c
+@@ -21,7 +21,9 @@
+ #if defined(_WIN32)

+ #define _CRT_SECURE_NO_WARNINGS // Disable deprecation warning in VS2005

+ #else

++#if !defined(__sun)

+ #define _XOPEN_SOURCE 600 // For flockfile() on Linux

++#endif

+ #define _LARGEFILE_SOURCE // Enable 64-bit file offsets

+ #define __STDC_FORMAT_MACROS // <inttypes.h> wants this for C++

+ #endif

diff --git a/biology/plinkseq/patches/patch-lib_annot.cpp b/biology/plinkseq/patches/patch-lib_annot.cpp
new file mode 100644
index 00000000000..1b67dd4dde4
--- /dev/null
+++ b/biology/plinkseq/patches/patch-lib_annot.cpp
@@ -0,0 +1,14 @@
+$NetBSD: patch-lib_annot.cpp,v 1.1 2014/02/08 12:27:14 wiedi Exp $
+
+rename to avoid collision on sunos
+--- lib/annot.cpp.orig	2012-03-19 20:00:45.000000000 +0000
++++ lib/annot.cpp
+@@ -34,7 +34,7 @@ std::map<seq_annot_t,std::string> popula
+   m[SPLICE3]  = "splice3";
+   m[ESPLICE3] = "esplice3";
+   m[ESPLICE5] = "esplice5"; 
+-  m[FS]       = "frameshift";
++  m[FS_]      = "frameshift";
+   m[RT]       = "readthrough";
+   return m;
+ }
diff --git a/biology/plinkseq/patches/patch-lib_annot.h b/biology/plinkseq/patches/patch-lib_annot.h
new file mode 100644
index 00000000000..aa6570c0ced
--- /dev/null
+++ b/biology/plinkseq/patches/patch-lib_annot.h
@@ -0,0 +1,14 @@
+$NetBSD: patch-lib_annot.h,v 1.1 2014/02/08 12:27:14 wiedi Exp $
+
+rename to avoid collision on sunos
+--- lib/annot.h.orig	2012-03-19 11:35:59.000000000 +0000
++++ lib/annot.h
+@@ -35,7 +35,7 @@ enum seq_annot_t { UNDEF   =  0 ,     //
+ 		   ESPLICE5 =  27 ,    // Essential 5' splice-site
+                    ESPLICE3 =  28 ,    // Essential 3' splice-site
+  		   NON      =  24 ,    // nonsense allele		   		  
+- 		   FS       =  25 ,    // frameshift 
++ 		   FS_       =  25 ,    // frameshift 
+ 		   RT       =  26 };   // readthrough
+ 
+ struct SeqInfo { 
diff --git a/biology/plinkseq/patches/patch-lib_token.cpp b/biology/plinkseq/patches/patch-lib_token.cpp
new file mode 100644
index 00000000000..61510f40f39
--- /dev/null
+++ b/biology/plinkseq/patches/patch-lib_token.cpp
@@ -0,0 +1,72 @@
+$NetBSD: patch-lib_token.cpp,v 1.1 2014/02/08 12:27:14 wiedi Exp $
+
+fix math ambiguity on sunos
+--- lib/token.cpp.orig	2012-03-17 17:06:01.000000000 +0000
++++ lib/token.cpp
+@@ -1232,7 +1232,7 @@ Token Token::operator^(const Token & rhs
+       const int sz = size();
+       if ( sz == 0 ) return Token();
+       std::vector<double> ans( sz );      
+-      if      ( rhs.is_int() )   for (int i=0; i<sz; i++) ans[i] = pow( ivec[i] , rhs.ival );
++      if      ( rhs.is_int() )   for (int i=0; i<sz; i++) ans[i] = pow( ivec[i] , (double) rhs.ival );
+       else if ( rhs.is_float() ) for (int i=0; i<sz; i++) ans[i] = pow( ivec[i] , rhs.fval );
+       return Token( ans );
+     }
+@@ -1249,7 +1249,7 @@ Token Token::operator^(const Token & rhs
+ 
+   if ( is_int() ) 
+     {
+-      if ( rhs.is_int() ) return Token( pow( ival , rhs.ival ) );
++      if ( rhs.is_int() ) return Token( pow( ival , (double) rhs.ival ) );
+       if ( rhs.is_float() ) return Token( pow( ival , rhs.fval ) );
+     }
+   if ( is_float() ) 
+@@ -2141,7 +2141,7 @@ Token TokenFunctions::fn_set( const Toke
+ 
+ Token TokenFunctions::fn_sqrt( const Token & tok ) const
+ {
+-  if ( tok.is_int() ) return Token( sqrt( tok.as_int() ) );
++  if ( tok.is_int() ) return Token( sqrt( (double) tok.as_int() ) );
+   if ( tok.is_float() ) return Token( sqrt( tok.as_float() ) );
+   if ( tok.is_int_vector() || tok.is_float_vector() ) 
+     {
+@@ -2154,7 +2154,7 @@ Token TokenFunctions::fn_sqrt( const Tok
+ 
+ Token TokenFunctions::fn_log( const Token & tok ) const
+ {
+-  if ( tok.is_int() ) return Token( log( tok.as_int() ) );
++  if ( tok.is_int() ) return Token( log( (double) tok.as_int() ) );
+   if ( tok.is_float() ) return Token( log( tok.as_float() ) );
+   if ( tok.is_int_vector() || tok.is_float_vector() ) 
+     {
+@@ -2168,7 +2168,7 @@ Token TokenFunctions::fn_log( const Toke
+ 
+ Token TokenFunctions::fn_log10( const Token & tok ) const
+ {
+-  if ( tok.is_int() ) return Token( log10( tok.as_int() ) );
++  if ( tok.is_int() ) return Token( log10( (double) tok.as_int() ) );
+   if ( tok.is_float() ) return Token( log10( tok.as_float() ) );
+   if ( tok.is_int_vector() || tok.is_float_vector() ) 
+     {
+@@ -2181,7 +2181,7 @@ Token TokenFunctions::fn_log10( const To
+ 
+ Token TokenFunctions::fn_exp( const Token & tok ) const
+ {
+-  if ( tok.is_int() ) return Token( exp( tok.as_int() ) );
++  if ( tok.is_int() ) return Token( exp( (double) tok.as_int() ) );
+   if ( tok.is_float() ) return Token( exp( tok.as_float() ) );
+   if ( tok.is_int_vector() || tok.is_float_vector() ) 
+     {
+@@ -2202,10 +2202,10 @@ Token TokenFunctions::fn_pow( const Toke
+   
+   if ( is_int_type && tok2.is_int() ) 
+     {
+-      if ( tok.is_scalar() ) return Token( (int)(pow( tok.as_int() , tok2.as_int() )) );
++      if ( tok.is_scalar() ) return Token( (int)(pow( tok.as_int() , (double) tok2.as_int() )) );
+       std::vector<int> ans = tok.as_int_vector();
+       const int ev = tok2.as_int();
+-      for (int i=0; i<ans.size(); i++) ans[i] = (int)(pow( ans[i] , ev ) );
++      for (int i=0; i<ans.size(); i++) ans[i] = (int)(pow( ans[i] , (double) ev ) );
+       return Token( ans );
+     }
+