sci-biology/staden: Version Bump, move to sane portage like building

Package-Manager: portage-2.2.0_alpha142

4 files changed, 62 insertions, 123 deletions

diff --git a/sci-biology/staden/files/rpath.patch b/sci-biology/staden/files/rpath.patch
deleted file mode 100644
index 7bda2171e..000000000
--- a/sci-biology/staden/files/rpath.patch
+++ /dev/null
@@ -1,123 +0,0 @@
-diff -cr staden-2.0.0b8-src/ac_stubs/tcl.m4 staden-2.0.0b8-src.orig/ac_stubs/tcl.m4
-*** staden-2.0.0b8-src/ac_stubs/tcl.m4	Wed Feb  9 11:40:00 2011
---- staden-2.0.0b8-src.orig/ac_stubs/tcl.m4	Tue Feb 15 15:12:37 2011
-***************
-*** 2245,2250 ****
---- 2245,2252 ----
-  
-      AC_SUBST(LD_LIBRARY_PATH_VAR)
-  
-+     AC_SUBST(CC_SEARCH_FLAGS)
-+ 
-      # These must be called after we do the basic CFLAGS checks and
-      # verify any possible 64-bit or similar switches are necessary
-      TEA_TCL_EARLY_FLAGS
-diff -cr staden-2.0.0b8-src/configure staden-2.0.0b8-src.orig/configure
-*** staden-2.0.0b8-src/configure	Wed Feb  9 11:39:59 2011
---- staden-2.0.0b8-src.orig/configure	Tue Feb 15 15:12:37 2011
-***************
-*** 745,750 ****
---- 745,751 ----
-  SHLIB_LD_LIBS
-  SHLIB_CFLAGS
-  LD_LIBRARY_PATH_VAR
-+ CC_SEARCH_FLAGS
-  TCL_INCLUDES
-  TCL_TOP_DIR_NATIVE
-  TK_INCLUDES
-***************
-*** 13888,13893 ****
---- 13889,13896 ----
-  
-  
-  
-+ 
-+ 
-      # These must be called after we do the basic CFLAGS checks and
-      # verify any possible 64-bit or similar switches are necessary
-  
-***************
-*** 15886,15891 ****
---- 15889,15895 ----
-  SHLIB_LD_LIBS!$SHLIB_LD_LIBS$ac_delim
-  SHLIB_CFLAGS!$SHLIB_CFLAGS$ac_delim
-  LD_LIBRARY_PATH_VAR!$LD_LIBRARY_PATH_VAR$ac_delim
-+ CC_SEARCH_FLAGS!$CC_SEARCH_FLAGS$ac_delim
-  TCL_INCLUDES!$TCL_INCLUDES$ac_delim
-  TCL_TOP_DIR_NATIVE!$TCL_TOP_DIR_NATIVE$ac_delim
-  TK_INCLUDES!$TK_INCLUDES$ac_delim
-***************
-*** 15905,15911 ****
-  LTLIBOBJS!$LTLIBOBJS$ac_delim
-  _ACEOF
-  
-!   if test `sed -n "s/.*$ac_delim\$/X/p" conf$$subs.sed | grep -c X` = 53; then
-      break
-    elif $ac_last_try; then
-      { { echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5
---- 15909,15915 ----
-  LTLIBOBJS!$LTLIBOBJS$ac_delim
-  _ACEOF
-  
-!   if test `sed -n "s/.*$ac_delim\$/X/p" conf$$subs.sed | grep -c X` = 54; then
-      break
-    elif $ac_last_try; then
-      { { echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5
-diff -cr staden-2.0.0b8-src/staden.profile staden-2.0.0b8-src.orig/staden.profile
-*** staden-2.0.0b8-src/staden.profile	Wed Feb  9 11:40:00 2011
---- staden-2.0.0b8-src.orig/staden.profile	Tue Feb 15 15:12:37 2011
-***************
-*** 46,54 ****
-          then
-              [ x"$STADEN_PREPEND" != "x" ] \
-              && LD_LIBRARY_PATH=$STADLIB:$LD_LIBRARY_PATH \
-!             || LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$STADLIB
-          else
-!             LD_LIBRARY_PATH=$STADLIB
-          fi
-          export LD_LIBRARY_PATH
-      fi
---- 46,54 ----
-          then
-              [ x"$STADEN_PREPEND" != "x" ] \
-              && LD_LIBRARY_PATH=$STADLIB:$LD_LIBRARY_PATH \
-!             || LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$STADLIB:$STADENROOT/lib
-          else
-!             LD_LIBRARY_PATH=$STADLIB:$STADENROOT/lib
-          fi
-          export LD_LIBRARY_PATH
-      fi
-diff -cr staden-2.0.0b8-src/system.mk.in staden-2.0.0b8-src.orig/system.mk.in
-*** staden-2.0.0b8-src/system.mk.in	Wed Feb  9 11:40:00 2011
---- staden-2.0.0b8-src.orig/system.mk.in	Tue Feb 15 15:12:37 2011
-***************
-*** 61,66 ****
---- 61,67 ----
-  # How else do we get commas in a subst text or pattern?
-  comma = ,
-  
-+ LIB_RUNTIME_DIR   = ${prefix}/lib/staden
-  CC		  = @CC@
-  #CDEBUG		  = -Wall -Wno-sign-compare -Wno-pointer-sign -Wno-parentheses -Wno-unused -Wno-char-subscripts -Wno-pointer-to-int-cast -Wno-int-to-pointer-cast
-  CFLAGS		  = @CFLAGS@ $(DEFINES) $(INCLUDES)
-***************
-*** 68,76 ****
-  CXXFLAGS	  = @CXXFLAGS@ $(DEFINES) $(INCLUDES)
-  CPP		  = @CPP@
-  CPPFLAGS	  = @CPPFLAGS@
-! LDFLAGS		  = -L$(L) @LDFLAGS@
-  #CLDFLAGS	  = -L$(L) -Wl,-rpath-link,$(L) $(subst -L,-Wl$(comma)-rpath-link$(comma),$(filter -L%,$(IOLIB_LIB)))
-! CLDFLAGS	  = -L$(L)
-  CXXLDFLAGS	  = $(CLDFLAGS)
-  F77		  = @F77@
-  FFLAGS		  = @FFLAGS@
---- 69,77 ----
-  CXXFLAGS	  = @CXXFLAGS@ $(DEFINES) $(INCLUDES)
-  CPP		  = @CPP@
-  CPPFLAGS	  = @CPPFLAGS@
-! LDFLAGS		  = -L$(L) @LDFLAGS@ @CC_SEARCH_FLAGS@
-  #CLDFLAGS	  = -L$(L) -Wl,-rpath-link,$(L) $(subst -L,-Wl$(comma)-rpath-link$(comma),$(filter -L%,$(IOLIB_LIB)))
-! CLDFLAGS	  = -L$(L) @CC_SEARCH_FLAGS@
-  CXXLDFLAGS	  = $(CLDFLAGS)
-  F77		  = @F77@
-  FFLAGS		  = @FFLAGS@
diff --git a/sci-biology/staden/files/staden-2.0.0_beta9-ldflags.patch b/sci-biology/staden/files/staden-2.0.0_beta9-ldflags.patch
new file mode 100644
index 000000000..735feb315
--- /dev/null
+++ b/sci-biology/staden/files/staden-2.0.0_beta9-ldflags.patch
@@ -0,0 +1,30 @@
+ abi/Makefile | 2 +-
+ alf/Makefile | 2 +-
+ 2 files changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/abi/Makefile b/abi/Makefile
+index 3c1f8fb..58b4353 100644
+--- a/abi/Makefile
++++ b/abi/Makefile
+@@ -23,7 +23,7 @@ getABISampleName: $(OBJSSN)
+ 	$(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSSN) $(LIBS) $(LIBSC)
+ 
+ getABIdate: $(OBJSD)
+-	$(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSD) $(IOUTILS_LIB) $(MISC_LIB) $(LIBSC)
++	$(CLD) $(LDFLAGS) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSD) $(IOUTILS_LIB) $(MISC_LIB) $(LIBSC)
+ 
+ getABIcomment: $(OBJSC)
+ 	$(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSC) $(LIBS) $(LIBSC)
+diff --git a/alf/Makefile b/alf/Makefile
+index 94b7480..ef41a26 100644
+--- a/alf/Makefile
++++ b/alf/Makefile
+@@ -16,7 +16,7 @@ INCLUDES_E += $(MISC_INC)
+ ALFOBJ = alfsplit.o
+ 
+ alfsplit: $(ALFOBJ)
+-	$(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(ALFOBJ) $(LIBSC)
++	$(CLD) $(LDFLAGS) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(ALFOBJ) $(LIBSC)
+ 
+ RSOBJ = $(ALFBIN)/2rs.o
+ 
diff --git a/sci-biology/staden/files/staden-2.0.0_beta9-libpng-1.5.patch b/sci-biology/staden/files/staden-2.0.0_beta9-libpng-1.5.patch
new file mode 100644
index 000000000..50694a8eb
--- /dev/null
+++ b/sci-biology/staden/files/staden-2.0.0_beta9-libpng-1.5.patch
@@ -0,0 +1,16 @@
+ tk_utils/tkTrace.c | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/tk_utils/tkTrace.c b/tk_utils/tkTrace.c
+index beeb478..42a4e11 100644
+--- a/tk_utils/tkTrace.c
++++ b/tk_utils/tkTrace.c
+@@ -2123,7 +2123,7 @@ int drawable_to_png(DNATrace *t, FILE *fp, Display *disp, Drawable d,
+ 	goto error;
+ 
+     /* PNG requires setjmp/longjmp to be used */
+-    if (setjmp(png_ptr->jmpbuf))
++    if (setjmp (png_jmpbuf (png_ptr)))
+ 	goto error;
+ 
+     /* Create the info bits */
diff --git a/sci-biology/staden/files/staden-2.0.0_beta9-zlib.patch b/sci-biology/staden/files/staden-2.0.0_beta9-zlib.patch
new file mode 100644
index 000000000..39537604e
--- /dev/null
+++ b/sci-biology/staden/files/staden-2.0.0_beta9-zlib.patch
@@ -0,0 +1,16 @@
+ gap5/zfio.c | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/gap5/zfio.c b/gap5/zfio.c
+index 35da12a..1b628e4 100644
+--- a/gap5/zfio.c
++++ b/gap5/zfio.c
+@@ -51,7 +51,7 @@ int zfpeek(zfp *zf) {
+ 	if (c != EOF)
+ 	    ungetc(c, zf->fp);
+     } else {
+-	c = gzgetc(zf->gz);
++	c = gzgetc((gzFile)zf->gz);
+ 	if (c != EOF)
+ 	    gzungetc(c, zf->gz);
+     }