4 files changed, 62 insertions, 2 deletions

diff --git a/biology/avida/Makefile b/biology/avida/Makefile
index 4a70bf606bf0..825a3dc3b317 100644
--- a/biology/avida/Makefile
+++ b/biology/avida/Makefile
@@ -48,8 +48,6 @@ pre-configure:
 		${WRKSRC}/Makefile.in
 .endif
 
-BROKEN=		Broken pkg-plist
-
 .if !defined(WITHOUT_QT)
 post-install:
 	${INSTALL_PROGRAM} ${WRKSRC}/work/qt-viewer ${PREFIX}/bin
diff --git a/biology/avida/files/patch-configure b/biology/avida/files/patch-configure
new file mode 100644
index 000000000000..789380563b84
--- /dev/null
+++ b/biology/avida/files/patch-configure
@@ -0,0 +1,20 @@
+--- configure.orig	Thu Oct 16 19:31:57 2003
++++ configure	Sun May  9 09:54:12 2004
+@@ -3488,7 +3488,7 @@
+   enableval="$enable_debug"
+   CPPFLAGS="-g -Wall -pedantic -DDEBUG"; qmake_debug="debug"
+ else
+-  CPPFLAGS="-O3 -ffast-math"; qmake_debug="release"
++  CPPFLAGS+="-ffast-math"; qmake_debug="release"
+ fi;
+ 
+ # Check whether --enable-gnu-debug or --disable-gnu-debug was given.
+@@ -3545,7 +3545,7 @@
+   CPPFLAGS="${CPPFLAGS} -pedantic"
+ fi;
+ 
+-htmldir='${datadir}/doc_html'
++htmldir='${prefix}/share/doc/avida'
+ HTMLDIR=${htmldir}
+ 
+ # Check whether --enable-primitive or --disable-primitive was given.
diff --git a/biology/avida/files/patch-source::main::config.cc b/biology/avida/files/patch-source::main::config.cc
new file mode 100644
index 000000000000..ef4cea87bd04
--- /dev/null
+++ b/biology/avida/files/patch-source::main::config.cc
@@ -0,0 +1,23 @@
+--- ./source/main/config.cc.orig	Thu Oct 16 18:15:17 2003
++++ ./source/main/config.cc	Mon May 10 20:39:45 2004
+@@ -132,15 +132,15 @@
+   
+   file_group->Add(default_dir, DEFAULT_DIR, "DEFAULT_DIR",
+ 		  "Directory in which config files are found");
+-  file_group->Add(inst_filename, "inst_set.default", "INST_SET",
++  file_group->Add(inst_filename, "../work/inst_set.default", "INST_SET",
+ 		  "File containing instruction set");
+-  file_group->Add(event_filename, "events.cfg", "EVENT_FILE",
++  file_group->Add(event_filename, "../work/events.cfg", "EVENT_FILE",
+ 		  "File containing list of events during run");
+-  file_group->Add(analyze_filename, "analyze.cfg", "ANALYZE_FILE",
++  file_group->Add(analyze_filename, "../work/analyze.cfg", "ANALYZE_FILE",
+ 		  "File used for analysis mode");
+-  file_group->Add(env_filename, "environment.cfg", "ENVIRONMENT_FILE",
++  file_group->Add(env_filename, "../work/environment.cfg", "ENVIRONMENT_FILE",
+ 		  "File that describes the environment");
+-  file_group->Add(start_creature, "organism.default", "START_CREATURE",
++  file_group->Add(start_creature, "../work/organism.default", "START_CREATURE",
+ 		  "Organism to seed the soup");
+ 
+   // Reproduction group.
diff --git a/biology/avida/files/patch-source::support::genesis b/biology/avida/files/patch-source::support::genesis
new file mode 100644
index 000000000000..ccc0ce6681f2
--- /dev/null
+++ b/biology/avida/files/patch-source::support::genesis
@@ -0,0 +1,19 @@
+--- source/support/genesis.orig	Thu Oct 16 02:45:16 2003
++++ source/support/genesis	Sun May  9 23:40:24 2004
+@@ -22,11 +22,11 @@
+ 
+ ### Configuration Files ###
+ DEFAULT_DIR ../work/              # Directory in which config files are found
+-INST_SET inst_set.default         # File containing instruction set
+-EVENT_FILE events.cfg             # File containing list of events during run
+-ANALYZE_FILE analyze.cfg          # File used for analysis mode
+-ENVIRONMENT_FILE environment.cfg  # File that describes the environment
+-START_CREATURE organism.default   # Organism to seed the soup
++INST_SET ../work/inst_set.default         # File containing instruction set
++EVENT_FILE ../work/events.cfg             # File containing list of events during run
++ANALYZE_FILE ../work/analyze.cfg          # File used for analysis mode
++ENVIRONMENT_FILE ../work/environment.cfg  # File that describes the environment
++START_CREATURE ../work/organism.default   # Organism to seed the soup
+ 
+ ### Reproduction ###
+ BIRTH_METHOD 4    # 0 = Replace random organism in neighborhood