Portability to OS-X and *BSD.

TankMermaid · Jul 13, 2005 · a890c1a · a890c1a
1 parent 542745d
commit a890c1a
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Showing 11 changed files with 220 additions and 182 deletions.
diff --git a/inc/cds.h b/inc/cds.h
@@ -21,6 +21,10 @@
 #ifndef CDSH
 #define CDSH
 
+#include <stdio.h>
+#include <stdlib.h>
+#include <sys/types.h>
+
 #include <limits.h>
 #include <float.h>
 #include <inttypes.h>
@@ -108,8 +112,14 @@ typedef double float64;
    32-bit architecture
    ***********************************************************************/
 
-  #define CDS_INT64_MAX INT64_MAX
-  #define CDS_UINT64_MAX UINT64_MAX
+  /*  Newer gcc's know INT64_MAX, older ones don't.  */
+  #ifdef UINT64_MAX
+    #define CDS_INT64_MAX  INT64_MAX
+    #define CDS_UINT64_MAX UINT64_MAX
+  #else
+    #define CDS_INT64_MAX  LLONG_MAX
+    #define CDS_UINT64_MAX ULLONG_MAX
+  #endif
 
   #define F_S16     "%d"
   #define F_U16     "%u"

diff --git a/src/AS_CGB/check_breakers.c b/src/AS_CGB/check_breakers.c
@@ -23,7 +23,6 @@
 #include <string.h>
 #include <memory.h>
 #include <unistd.h>
-#include <getopt.h>
 
 #include "AS_global.h"
 #include "AS_PER_ReadStruct.h"
@@ -1386,7 +1385,7 @@ typedef CheckGlobals * CheckGlobalsp;
 void InitializeGlobals( CheckGlobalsp globals, char * program_name )
 {
   globals->program_name = program_name;
-  globals->version = "$Revision: 1.4 $";
+  globals->version = "$Revision: 1.5 $";
   globals->chims_file = NULL;
   globals->craps_file = NULL;
   globals->cgb_file = NULL;

diff --git a/src/AS_MPA/Quadrilateral.h b/src/AS_MPA/Quadrilateral.h
@@ -18,13 +18,11 @@
  * License along with this program; if not, write to the Free Software
  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
  *************************************************************************/
-/* $Id: Quadrilateral.h,v 1.4 2005-03-22 19:48:56 jason_miller Exp $ */
+/* $Id: Quadrilateral.h,v 1.5 2005-07-13 14:47:55 brianwalenz Exp $ */
 #ifndef QUADRILATERAL_H
 #define QUADRILATERAL_H
 
 #include <cmath>
-#include <values.h>
-
 #include <algorithm>
 
 #include "Point.h"

diff --git a/src/AS_MPA/Trapezoid.h b/src/AS_MPA/Trapezoid.h
@@ -18,13 +18,11 @@
  * License along with this program; if not, write to the Free Software
  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
  *************************************************************************/
-/* $Id: Trapezoid.h,v 1.4 2005-03-22 19:48:56 jason_miller Exp $ */
+/* $Id: Trapezoid.h,v 1.5 2005-07-13 14:47:55 brianwalenz Exp $ */
 #ifndef TILTEDTRAPEZOID_H
 #define TILTEDTRAPEZOID_H
 
 #include <cmath>
-#include <values.h>
-
 #include <algorithm>
 
 #include "Point.h"

diff --git a/src/AS_OVL/AS_OVL_overlap_common.h b/src/AS_OVL/AS_OVL_overlap_common.h
@@ -49,8 +49,8 @@
 *************************************************/
 
 /* RCS info
- * $Id: AS_OVL_overlap_common.h,v 1.6 2005-07-11 21:55:48 brianwalenz Exp $
- * $Revision: 1.6 $
+ * $Id: AS_OVL_overlap_common.h,v 1.7 2005-07-13 14:47:55 brianwalenz Exp $
+ * $Revision: 1.7 $
 */
 
 
@@ -68,7 +68,7 @@
 #include  <sys/stat.h>
 #include  <unistd.h>
 #include  <float.h>
-#include  "getopt.h"
+#include  "getopt.h" /*  Use AS_UTL getopt, not the system one  */
 
 /*************************************************************************/
 /* Local include files */

diff --git a/src/AS_OVL/Makefile b/src/AS_OVL/Makefile
@@ -95,24 +95,45 @@ include $(LOCAL_WORK)/src/c_make.as
 
 # (MP) this should take care of intermittent "don't know how to make 
 # libpthread.a" problems 
-LDFLAGS+= -lpthread
-CFLAGS+= -pthread
-CPPFLAGS+= -pthread
-#PTHREADS_LIBS=-lpthread
+
+ifeq ($(OSTYPE), Linux)
+  LDFLAGS  += -lpthread
+  CFLAGS   += -pthread
+  CPPFLAGS += -pthread
+endif
+
+ifeq ($(OSTYPE), OSF1)
+  LDFLAGS  += -lpthread
+  CFLAGS   += -pthread
+  CPPFLAGS += -pthread
+endif
+
+ifeq ($(OSTYPE), FreeBSD)
+  LDFLAGS  += -pthread
+  CFLAGS   += -pthread
+  CPPFLAGS += -pthread
+endif
+
+ifeq ($(OSTYPE), Darwin)
+  LDFLAGS  += -pthread
+  CFLAGS   += -pthread
+  CPPFLAGS += -pthread
+endif
+
 
 #ifeq ($(OSTYPE), aix)
 #  PTHREADS_LIBS=libc_r.so /usr/lib/libpthread.so
 #  PTHREADS_LIBS=libc_r.a /usr/lib/libpthread.a
-#else 
-#  ifeq ($(OSTYPE), Darwin)
-#    PTHREADS_LIBS=libc_r.so /usr/lib/libpthread.dylib
-#    PTHREADS_LIBS=libc_r.a /usr/lib/libpthread.dylib
-#  else
-#   ifeq ($(OSTYPE), OSF1)
-#    PTHREADS_LIBS=-lpthread
-    #PTHREADS_LIBS=/usr/lib/libpthread.so
-#   endif
-#  endif
+#endif
+
+#ifeq ($(OSTYPE), Darwin)
+#  PTHREADS_LIBS=libc_r.so /usr/lib/libpthread.dylib
+#  PTHREADS_LIBS=libc_r.a /usr/lib/libpthread.dylib
+#endif
+
+#ifeq ($(OSTYPE), OSF1)
+#  PTHREADS_LIBS=-lpthread
+#  PTHREADS_LIBS=/usr/lib/libpthread.so
 #endif
 
 all:    $(OBJECTS) $(LIBRARIES) $(PROGS) install

diff --git a/src/AS_UID/SYS_UIDcommon.h b/src/AS_UID/SYS_UIDcommon.h
@@ -21,11 +21,14 @@
 
 /**********************************************************************
 $Source: /work/NIGHTLY/wgs-assembler-cvs/src/AS_UID/Attic/SYS_UIDcommon.h,v $
-$Revision: 1.3 $
-$Date: 2005-03-22 19:49:28 $
+$Revision: 1.4 $
+$Date: 2005-07-13 14:47:55 $
 $Name: not supported by cvs2svn $
-$Author: jason_miller $
+$Author: brianwalenz $
 $Log: not supported by cvs2svn $
+Revision 1.3  2005/03/22 19:49:28  jason_miller
+The TIGR tip as of March 22 2005. Commit by Jason Miller at TIGR.
+
 Revision 1.4  2004/09/10 12:31:43  mschatz
 Add standard copyright notice
 
@@ -170,12 +173,13 @@ extern "C" {
 #include <string.h>
 #include <sys/types.h>
 #include <sys/socket.h>
-#include <arpa/inet.h>
 #include <netinet/in.h>
+#include <arpa/inet.h>
 #include <netdb.h>
 #include <sys/un.h>
 #include <errno.h>
 #include <unistd.h>
+#include <rpc/types.h>
 #include <rpc/xdr.h>
 #include <time.h>
 #include <sys/time.h>

diff --git a/src/AS_UID/SYS_UIDserver_main.c b/src/AS_UID/SYS_UIDserver_main.c
@@ -21,11 +21,14 @@
 
 /**********************************************************************
 $Source: /work/NIGHTLY/wgs-assembler-cvs/src/AS_UID/Attic/SYS_UIDserver_main.c,v $
-$Revision: 1.3 $
-$Date: 2005-03-22 19:49:28 $
+$Revision: 1.4 $
+$Date: 2005-07-13 14:47:56 $
 $Name: not supported by cvs2svn $
-$Author: jason_miller $
+$Author: brianwalenz $
 $Log: not supported by cvs2svn $
+Revision 1.3  2005/03/22 19:49:28  jason_miller
+The TIGR tip as of March 22 2005. Commit by Jason Miller at TIGR.
+
 Revision 1.3  2004/09/10 12:31:43  mschatz
 Add standard copyright notice
 
@@ -278,9 +281,11 @@ SYS_UIDsignalHandlerFunction(int signal)
        case SIGTTOU:
          SYS_UIDerrorMsg("UID server: received SIGTTOU signal");
          break;
+#ifdef SIGPOLL
        case SIGPOLL:
          SYS_UIDerrorMsg("UID server: received SIGPOLL signal");
          break;
+#endif
        case SIGXCPU:
          SYS_UIDerrorMsg("UID server: received SIGXCPU signal");
          break;

diff --git a/src/AS_UTL/AS_UTL_Hash.c b/src/AS_UTL/AS_UTL_Hash.c
@@ -18,7 +18,7 @@
  * License along with this program; if not, write to the Free Software
  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
  *************************************************************************/
-static char CM_ID[] = "$Id: AS_UTL_Hash.c,v 1.4 2005-03-22 19:49:28 jason_miller Exp $";
+static char CM_ID[] = "$Id: AS_UTL_Hash.c,v 1.5 2005-07-13 14:47:56 brianwalenz Exp $";
 
 #include <string.h>
 #include <math.h>
@@ -435,7 +435,7 @@ int NextHashTable_Iterator_AS(HashTable_Iterator_AS *iterator,
    table->freeList = NULL;
    assert(numItemsToHash > 0);
    {
-     int logsize = (int) ceil(log2(numItemsToHash * 2.0));
+     int logsize = (int) ceil_log2(numItemsToHash * 2.0);
      int i;
      table->numBuckets = hashsize(logsize);
      table->hashmask = hashmask(logsize);
@@ -450,7 +450,7 @@ int NextHashTable_Iterator_AS(HashTable_Iterator_AS *iterator,
      }
    }	
    {
-     int logsize = (int) ceil(log2(numItemsToHash));
+     int logsize = (int) ceil_log2(numItemsToHash);
      table->numNodesAllocated = hashsize(logsize);
 
      table->allocated = AllocateUIDHashNode_ASHeap(table->numNodesAllocated);

diff --git a/src/AS_UTL/AS_UTL_Var.c b/src/AS_UTL/AS_UTL_Var.c
@@ -18,7 +18,7 @@
  * License along with this program; if not, write to the Free Software
  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
  *************************************************************************/
-static char CM_ID[] = "$Id: AS_UTL_Var.c,v 1.7 2005-06-14 14:44:52 eliv Exp $";
+static char CM_ID[] = "$Id: AS_UTL_Var.c,v 1.8 2005-07-13 14:47:56 brianwalenz Exp $";
 /********************************************************************/
 /* Variable Length C Array Package 
  * 
@@ -30,8 +30,8 @@ static char CM_ID[] = "$Id: AS_UTL_Var.c,v 1.7 2005-06-14 14:44:52 eliv Exp $";
  * It defines a basic set of operations, and provides a set of
  * macros that expand to support typesafe manipulation of the
  * arrays.
- * Revision: $Revision: 1.7 $
- * Date:     $Date: 2005-06-14 14:44:52 $
+ * Revision: $Revision: 1.8 $
+ * Date:     $Date: 2005-07-13 14:47:56 $
  * CMM, 1999/03/29:  Ported to large arrays on the Digital systems by declaring
  * array sizes using size_t, rather than unit32.
  *
@@ -129,9 +129,9 @@ int MakeRoom_VA
     // Only allocate a power of 2 number of bytes.
     tentativeNewSize = (((size_t)1) << ceil_log2(newSize));
 
-    int halfGig = 2 << 28; // Cap malloc size at 512MB to decrease failure rate
-    if ( tentativeNewSize - newSize > halfGig )
-        tentativeNewSize = oldSize + halfGig;
+    // Cap malloc size at 512MB to decrease failure rate
+    if ( tentativeNewSize - newSize > (2 << 28) )
+        tentativeNewSize = oldSize + (2 << 28);
 
     // If we need to use the end of the block, do it
     newSize = max(newSize, tentativeNewSize);