upgrade to 4.4

PR:		40612
Submitted by:	maintainer

4 files changed, 88 insertions, 2 deletions

diff --git a/biology/nab/files/config.h b/biology/nab/files/config.h
index 8166c22b49c..1d2f9ebab0a 100644
--- a/biology/nab/files/config.h
+++ b/biology/nab/files/config.h
@@ -97,8 +97,8 @@ CPP=    ucpp -l
 #
 #  Use these CFLAGS if AVS = 0
 #
-CFLAGS= 
-OCFLAGS= -O
+CFLAGS= -O -pipe
+OCFLAGS= -O -pipe
 NABFLAGS=
 #
 #  Use these CFLAGS if AVS = 1
diff --git a/biology/nab/files/patch-examples:program_7.nab b/biology/nab/files/patch-examples:program_7.nab
new file mode 100644
index 00000000000..4e6455533df
--- /dev/null
+++ b/biology/nab/files/patch-examples:program_7.nab
@@ -0,0 +1,19 @@
+*** examples/program_7.nab	Wed Mar 10 18:57:51 1999
+--- examples/program_7.nab	Sun Jun  2 13:40:36 2002
+***************
+*** 9,15 ****
+  cseq = wc_complement( "acgtacgt", "dna.amber94.rlb", "dna" );
+  
+  m = wc_helix( seq, "dna.amber94.rlb", "dna", cseq, "dna.amber94.rlb",
+!          "dna", 2.25, -4.96, 36.0, 4.38, "" );
+  
+  b = newbounds(m, "");
+  allocate xyz[ 4*m.natoms ];
+--- 9,15 ----
+  cseq = wc_complement( "acgtacgt", "dna.amber94.rlb", "dna" );
+  
+  m = wc_helix( seq, "dna.amber94.rlb", "dna", cseq, "dna.amber94.rlb",
+!          "dna", 2.25, -4.96, 36.0, 3.38, "" );
+  
+  b = newbounds(m, "");
+  allocate xyz[ 4*m.natoms ];
diff --git a/biology/nab/files/patch-src:database.c b/biology/nab/files/patch-src:database.c
new file mode 100644
index 00000000000..fc36828b3bf
--- /dev/null
+++ b/biology/nab/files/patch-src:database.c
@@ -0,0 +1,32 @@
+*** src/database.c.orig	Wed Nov 15 19:46:50 2000
+--- src/database.c	Sun Jun  2 12:57:50 2002
+***************
+*** 67,72 ****
+--- 67,79 ----
+  
+  
+  
++ #if (defined(__unix__) || defined(unix)) && !defined(USG)
++ #include <sys/param.h>
++ #endif
++ 
++ #if defined(BSD)
++ #include <math.h>
++ #endif
+  
+  
+  #include	"stdio.h"
+***************
+*** 979,985 ****
+--- 986,996 ----
+  
+      sDBRemoveLeadingSpaces( sLine );
+      sDBRemoveFirstString( sLine, sHead );
++ #if defined (linux) || defined(BSD)
++     sscanf( sHead, "%lg", dPDbl );
++ #else
+      sscanf( sHead, "%lG", dPDbl );
++ #endif
+  
+  }
+  
diff --git a/biology/nab/files/patch-tleap:database.c b/biology/nab/files/patch-tleap:database.c
new file mode 100644
index 00000000000..bdb35b202fa
--- /dev/null
+++ b/biology/nab/files/patch-tleap:database.c
@@ -0,0 +1,35 @@
+*** tleap/database.c.orig	Wed Mar 27 15:41:01 2002
+--- tleap/database.c	Sun Jun  2 12:59:14 2002
+***************
+*** 97,102 ****
+--- 97,109 ----
+  
+  
+  
++ #if (defined(__unix__) || defined(unix)) && !defined(USG)
++ #include <sys/param.h>
++ #endif
++ 
++ #if defined(BSD)
++ #include <math.h>
++ #endif
+  
+  
+  #include	"basics.h"
+***************
+*** 563,569 ****
+  
+      sRemoveLeadingSpaces( sLine );
+      sRemoveFirstString( sLine, sHead );
+! #ifdef linux
+      sscanf( sHead, "%lg", dPDbl );
+  #else
+      sscanf( sHead, "%lG", dPDbl );
+--- 570,576 ----
+  
+      sRemoveLeadingSpaces( sLine );
+      sRemoveFirstString( sLine, sHead );
+! #if defined(linux) || defined(BSD)
+      sscanf( sHead, "%lg", dPDbl );
+  #else
+      sscanf( sHead, "%lG", dPDbl );