[97686] trunk/dports/science/tophat

[jmr at macports.org]

Revision: 97686
          http://trac.macports.org//changeset/97686
Author:   jmr at macports.org
Date:     2012-09-11 21:09:22 -0700 (Tue, 11 Sep 2012)
Log Message:
-----------
tophat: specify correct required APIs (#35063), fix incorrect C++

Modified Paths:
--------------
    trunk/dports/science/tophat/Portfile

Added Paths:
-----------
    trunk/dports/science/tophat/files/
    trunk/dports/science/tophat/files/src_GList.hh.patch

Modified: trunk/dports/science/tophat/Portfile
===================================================================
--- trunk/dports/science/tophat/Portfile	2012-09-12 02:49:07 UTC (rev 97685)
+++ trunk/dports/science/tophat/Portfile	2012-09-12 04:09:22 UTC (rev 97686)
@@ -31,3 +31,9 @@
 
 # samtools and bowtie are not universal
 universal_variant   no
+
+patchfiles          src_GList.hh.patch
+
+# defines _POSIX_SOURCE which by itself means 1003.1-1988, but uses fseeko
+# which is from 1003.1-2001, and strsep which is a BSD extension
+configure.cppflags-append -D_DARWIN_C_SOURCE

Added: trunk/dports/science/tophat/files/src_GList.hh.patch
===================================================================
--- trunk/dports/science/tophat/files/src_GList.hh.patch	                        (rev 0)
+++ trunk/dports/science/tophat/files/src_GList.hh.patch	2012-09-12 04:09:22 UTC (rev 97686)
@@ -0,0 +1,29 @@
+--- src/GList.hh.orig	2010-12-10 07:25:09.000000000 +1100
++++ src/GList.hh	2012-09-12 14:04:37.000000000 +1000
+@@ -504,7 +504,7 @@ template <class OBJ> int GArray<OBJ>::Ad
+    if (Found(*item, result))
+       if (fUnique) return -1; //cannot add a duplicate!
+    //Found sets result to the position where the item should be!
+-   idxInsert(result, *item);
++   this->idxInsert(result, *item);
+    }
+   else {
+    if (fUnique && Found(*item,result)) return -1; //set behaviour
+@@ -534,7 +534,7 @@ template <class OBJ> void GArray<OBJ>::A
+     for (int i=0;i<list.fCount;i++) Add(&list[i]);
+     }
+   else { //simply copy
+-    setCapacity(this->fCapacity+list.fCount);
++    this->setCapacity(this->fCapacity+list.fCount);
+     int s=this->fCount;
+     for (int i=0;i<list.fCount;i++)
+            this->fArray[s+i]=list.fArray[i];
+@@ -769,7 +769,7 @@ template <class OBJ> void GList<OBJ>::Ad
+     for (int i=0;i<list.Count();i++) Add(list[i]);
+     }
+   else { //simply copy
+-    setCapacity(this->fCapacity+list.fCount);
++    this->setCapacity(this->fCapacity+list.fCount);
+     memcpy( & (this->fList[this->fCount]), list.fList, list.fCount*sizeof(OBJ*));
+     this->fCount+=list.fCount;
+     }
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