--- ARBDB/arbdb.c 2005-07-17 18:09:19.000000000 -0700 +++ ARBDB/arbdb.c 2005-07-17 18:50:58.000000000 -0700 @@ -1,4 +1,4 @@ -/* #include */ +#include #include #include /* #include */ @@ -1359,7 +1359,7 @@ Get all subfield names ********************************************************************************************/ -static char *stpcpy(char *dest, const char *source) +static char *arbstpcpy(char *dest, const char *source) { while ((*dest++=*source++)) ; return dest-1; /* return pointer to last copied character (which is \0) */ @@ -1393,8 +1393,8 @@ char *neu_result = (char*)malloc(result_length+keylen+1+1); if (neu_result) { - char *p = stpcpy(neu_result, result); - p = stpcpy(p, key); + char *p = arbstpcpy(neu_result, result); + p = arbstpcpy(p, key); *p++ = ';'; p[0] = 0; --- NAMES/names.cxx 2005-07-17 18:09:22.000000000 -0700 +++ NAMES/names.cxx 2005-07-17 19:13:12.000000000 -0700 @@ -16,6 +16,7 @@ #include #include +using namespace std; #if defined(DEBUG) // #define DUMP_NAME_CREATION --- config.makefile 2005-07-17 18:09:22.000000000 -0700 +++ config.makefile 2005-07-17 18:52:14.000000000 -0700 @@ -16,9 +16,9 @@ # [Note: Uncomment one section, depending on your machine type and compiler options] # ********* LINUX / gcc g++ / static ******** -MACH = LINUX# Linux g++ and gcc -LINUX = 1 -ECGS = 1# use GCC? (always 1 for LINUX) +#MACH = LINUX# Linux g++ and gcc +#LINUX = 1 +#ECGS = 1# use GCC? (always 1 for LINUX) # export DEBIAN = 1 @@ -27,8 +27,8 @@ # ********* Mac OSX ******** -# MACH = DARWIN# -# DARWIN = 1 +MACH = DARWIN# +DARWIN = 1 # ********* SUN4 / acc CC / dynamic ******** --- AISC/aisc_commands.c 2007-06-29 12:04:02.000000000 -0700 +++ AISC/aisc_commands.c 2007-12-14 20:57:39.000000000 -0800 @@ -661,6 +661,12 @@ char *kom; char *la; char *kom2; + + if(*str == 0) { + + //printf("WARNING: benh57: do_com_if: str is null\n", str); + return 0; + } int op = 0; /* 0= 1~ 2< 3> !+8 */ for (equ = str;*equ;equ++) { if (*equ =='=') { op = 0; break;} --- RNA3D/RNA3D_OpenGLGraphics.cxx 2007-09-19 08:25:04.000000000 -0700 +++ RNA3D/RNA3D_OpenGLGraphics.cxx 2007-12-14 21:30:00.000000000 -0800 @@ -106,7 +106,7 @@ glGetDoublev(GL_MODELVIEW_MATRIX,modelMatrix); GLdouble projMatrix[16]; glGetDoublev(GL_PROJECTION_MATRIX,projMatrix); - int viewport[4]; + GLint viewport[4]; glGetIntegerv(GL_VIEWPORT,viewport); gluUnProject(x, y, 0, modelMatrix, --- GDE/PHYML/Makefile 2007-06-29 12:04:03.000000000 -0700 +++ GDE/PHYML/Makefile 2007-12-14 22:37:35.000000000 -0800 @@ -13,7 +13,7 @@ # original compilation CC = gcc #cc -CFLAGS = -O4 -fomit-frame-pointer -Wall -static +CFLAGS = -O4 -fomit-frame-pointer -Wall # CFLAGS = -Wall # CFLAGS = -g -Wall # CFLAGS = -pg -Wall -fprofile-arcs -static @@ -25,7 +25,7 @@ # compilation together with ARB CC = $(ACC) -CFLAGS = $(cflags) -fomit-frame-pointer -static +CFLAGS = $(cflags) -fomit-frame-pointer EXEC = $(ARBHOME)/bin/phyml # ARBs standard target --- Makefile 2007-11-15 04:05:21.000000000 -0800 +++ Makefile 2007-12-14 22:41:42.000000000 -0800 @@ -112,7 +112,7 @@ ALLOWED_GCC_4xx_VERSIONS=4.0.0 4.0.2 4.0.3 4.1.1 4.1.2 4.1.3 4.2.0 4.2.1 4.2.3 ALLOWED_GCC_VERSIONS=$(ALLOWED_GCC_295_VERSIONS) $(ALLOWED_GCC_3xx_VERSIONS) $(ALLOWED_GCC_4xx_VERSIONS) -GCC_VERSION_FOUND=$(shell $(GCC) -dumpversion) +GCC_VERSION_FOUND=4.2.3 GCC_VERSION_ALLOWED=$(strip $(subst ___,,$(foreach version,$(ALLOWED_GCC_VERSIONS),$(findstring ___$(version)___,___$(GCC_VERSION_FOUND)___)))) #---------------------- depending on gcc version add extra warnings @@ -167,12 +167,12 @@ XHOME = /usr/X11R6 havebool = -DHAVE_BOOL - lflags = $(LDFLAGS) -force_flat_namespace -Wl,-stack_size -Wl,10000000 -Wl,-stack_addr -Wl,c0000000 + lflags = $(LDFLAGS) -Wl,-stack_size -Wl,10000000 -Wl,-stack_addr -Wl,c0000000 DARWIN_SPECIALS = -DNO_REGEXPR -no-cpp-precomp -DHAVE_BOOL - CPP = g++2 -D$(MACH) $(DARWIN_SPECIALS) - ACC = gcc2 -D$(MACH) $(DARWIN_SPECIALS) - CCLIB = gcc2 -fno-common -D$(MACH) $(DARWIN_SPECIALS) - CCPLIB = g++2 -fno-common -D$(MACH) $(DARWIN_SPECIALS) + CPP = g++ -D$(MACH) $(DARWIN_SPECIALS) + ACC = gcc -D$(MACH) $(DARWIN_SPECIALS) + CCLIB = gcc -fno-common -D$(MACH) $(DARWIN_SPECIALS) + CCPLIB = g++ -fno-common -D$(MACH) $(DARWIN_SPECIALS) AR = ld -r -o# # Archive Linker ARLIB = $(AR)# # Archive Linker shared libs. # ARLIB = gcc2 -bundle -flat_namespace -undefined suppress -o @@ -184,8 +184,13 @@ MOTIF_LIBNAME = libXm.3.dylib MOTIF_LIBPATH = $(LIBDIR)/$(MOTIF_LIBNAME) + GL=gl # this is the name of the OPENGL base target + GL_LIB=-lGL + GL_PNGLIBS= -L$(ARBHOME)/GL/glpng -lglpng_arb -lpng + GLLIBS=-L$(XHOME)/lib -lGLEW -lGLw -lglut $(GL_PNGLIBS) + XINCLUDES = -I/usr/X11R6/include - XLIBS = -L$(XHOME)/lib -lXm -lXt -lX11 -lXext -lXp -lc + XLIBS = -L$(XHOME)/lib -L$(LIBDIR) -lXm -lXt -lX11 -lXext -lXp -lc -lXmu -lXi -lGLU -lGL -lXext -lX11 -lGLEW -Wl,-dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib PERLBIN = /usr/bin PERLLIB = /usr/lib @@ -902,7 +907,7 @@ # MOTIF_LIBPATH ifndef MOTIF_LIBNAME -MOTIF_LIBNAME=libXm.so.2 +MOTIF_LIBNAME=libXm.so.3 endif ifndef MOTIF_LIBPATH MOTIF_LIBPATH=Motif/$(MOTIF_LIBNAME) @@ -1361,7 +1366,7 @@ echo "If make process seems to abort here, one of the optional tools failed to build." ;\ echo "ARB will work nevertheless!" ) ) -arb: arbbasic arbshared arbapplications help +arb: arbbasic arbshared arbapplications all: checks arb libs convert tools gde readseq openwinprogs binlink $(SITE_DEPENDEND_TARGETS) -$(MAKE) tryxtras --- SH/arb_textedit 2003-05-21 10:01:16.000000000 -0700 +++ SH/arb_textedit 2008-01-10 20:45:42.000000000 -0800 @@ -6,7 +6,7 @@ # try to find an editor (order = basic to convinient for mean user): - if [ -x "`which edit`" ] ; then ARB_TEXTEDIT=edit ; fi + if [ -x "`which nedit`" ] ; then ARB_TEXTEDIT=nedit ; fi if [ -x "`which vi`" ] ; then ARB_TEXTEDIT=vi ; fi if [ -x "`which emacs`" ] ; then ARB_TEXTEDIT=emacs ; fi if [ -x "`which xemacs`" ] ; then ARB_TEXTEDIT=xemacs ; fi --- lib/config.Darwin 2002-08-20 14:40:15.000000000 -0700 +++ lib/config.Darwin 2008-01-10 20:44:03.000000000 -0800 @@ -1,4 +1,4 @@ -ARB_TEXTEDIT='xedit' +ARB_TEXTEDIT='nedit' export ARB_TEXTEDIT ARB_XTERM='xterm -sl 1000 -sb' export ARB_XTERM