[MacPorts] #30342: Update ARB for Lion (OS X 10.7) and Xcode 4

MacPorts noreply at macports.org
Mon Jul 25 21:57:51 PDT 2011 

#30342: Update ARB for Lion (OS X 10.7) and Xcode 4
--------------------------------------+-------------------------------------
 Reporter:  matt.cottrell@…           |       Owner:  macports-tickets@…                   
     Type:  update                    |      Status:  new                                  
 Priority:  Normal                    |   Milestone:                                       
Component:  ports                     |     Version:  2.0.0                                
 Keywords:  lion haspatch maintainer  |        Port:  arb                                  
--------------------------------------+-------------------------------------

Comment(by matt.cottrell@…):

 Replying to [comment:6 matt.cottrell@…]:
 > The upstream developer is working on this with me.  I sent him the
 llvm-g++-4.2 error and the clang error.  If you are curious they look like
 this:
 >
 > llvm-g++-4.2 error building ARB:
 > {{{
 > -------------------- Checking bin/arb_dist
 > Target 'bin/arb_dist' not found
 > -> rebuilding bin/arb_dist (Wed Dec 31 20:59:59 1969)
 > Link bin/arb_dist
 > /Developer/usr/bin/llvm-g++-4.2   -arch x86_64   -o bin/arb_dist
 -L/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/LIBLINK
 PROBE_COM/client.a DIST/DIST.a SERVERCNTRL/SERVERCNTRL.a
 CONSENSUS_TREE/CONSENSUS_TREE.a EISPACK/EISPACK.a SL/HELIX/HELIX.a
 XML/XML.a  -lARBDB  -lstdc++ -lAW -lAWT -L/opt/local/lib -lXm -lpng -lz
 -lXt -lX11 -lXext -lXp -lXmu -lXi -lGLU -lGL
 -Wl,-dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib
 > Undefined symbols for architecture x86_64:
 >   "_llvm.eh.catch.all.value437", referenced from:
 >       anon in lto.o
 >       anon in lto.o
 >       anon in lto.o
 >       anon in lto.o
 >       anon in lto.o
 >       anon in lto.o
 >       anon in lto.o
 >       ...
 > ld: symbol(s) not found for architecture x86_64
 > collect2: ld returned 1 exit status
 > make[2]: *** [bin/arb_wetc] Error 1
 > make[2]: *** Waiting for unfinished jobs....
 > Undefined symbols for architecture x86_64:
 >   "_llvm.eh.catch.all.value950", referenced from:
 >       anon in lto.o
 >       anon in lto.o
 >       anon in lto.o
 >       anon in lto.o
 >       anon in lto.o
 >       anon in lto.o
 >       anon in lto.o
 >       ...
 > ld: symbol(s) not found for architecture x86_64
 > collect2: ld returned 1 exit status
 > make[2]: *** [bin/arb_dist] Error 1
 > make[2]: Leaving directory
 `/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779'
 > make[1]: *** [arb] Error 2
 > make[1]: Leaving directory
 `/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779'
 > make: *** [all] Error 2
 > make: Leaving directory
 `/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779'
 > shell command " cd
 "/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779"
 && /usr/bin/make -j2 -w all GCC=/Developer/usr/bin/llvm-gcc-4.2
 GPP=/Developer/usr/bin/llvm-g++-4.2 CPPreal=/Developer/usr/bin/llvm-
 cpp-4.2 " returned error 2
 > Error: Target org.macports.build returned: shell command failed (see log
 for details)
 > Warning: the following items did not execute (for arb):
 org.macports.activate org.macports.build org.macports.destroot
 org.macports.install
 > Log for arb is at:
 /opt/local/var/macports/logs/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/main.log
 > Error: Status 1 encountered during processing.
 > To report a bug, see <http://guide.macports.org/#project.tickets>
 > }}}
 >
 > clang error building ARB:
 > {{{
 >
 --------------------------------------------------------------------------------
 Make everything in GDE
 > make[2]: Entering directory
 `/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/GDE'
 > ----------------- non-ARB code: warnings disabled
 > /usr/bin/make CLUSTAL/CLUSTAL.dummy SUPPORT/SUPPORT.dummy
 MOLPHY/MOLPHY.dummy AxML/AxML.dummy RAxML/RAxML.dummy PHYML/PHYML.dummy
 CLUSTALW/CLUSTALW.dummy PHYLIP/PHYLIP.dummy TREEPUZZLE/TREEPUZZLE.dummy
 FASTDNAML/FASTDNAML.dummy
 > make[3]: Entering directory
 `/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/GDE'
 > make[4]: Entering directory
 `/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/GDE/SUPPORT'
 > /Developer/usr/bin/clang -O4 -arch x86_64 -no-cpp-precomp -pipe
 -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL  -w -DNDEBUG
 -DARB_64  -DDARWIN    -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_SUPPORT
 -o
 /opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/bin/CAP2
 CAP2.c -I.
 -I/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/INCLUDE
 -I/opt/local/include -I/System/Library/Frameworks/OpenGL.framework/Headers
 -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers
 -lm
 > clang: warning: argument unused during compilation: '-no-cpp-precomp'
 > /Developer/usr/bin/clang -O4 -arch x86_64 -no-cpp-precomp -pipe
 -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL  -w -DNDEBUG
 -DARB_64  -DDARWIN    -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_SUPPORT
 -o
 /opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/bin/Restriction
 Restriction.c -I.
 -I/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/INCLUDE
 -I/opt/local/include -I/System/Library/Frameworks/OpenGL.framework/Headers
 -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers
 -lm
 > clang: warning: argument unused during compilation: '-no-cpp-precomp'
 > In file included from Restriction.c:5:
 > ./Flatio.c:27:9: error: non-void function 'ErrorOut' should return a
 value [-Wreturn-type]
 >         return;
 >         ^
 > ./Flatio.c:166:9: error: non-void function 'WriteData' should return a
 value [-Wreturn-type]
 >         return;
 >         ^
 > 2 errors generated.
 > make[4]: ***
 [/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/bin/Restriction]
 Error 1
 > make[4]: Leaving directory
 `/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/GDE/SUPPORT'
 > make[3]: *** [SUPPORT/SUPPORT.dummy] Error 1
 > make[3]: *** Waiting for unfinished jobs....
 > make[4]: Entering directory
 `/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/GDE/CLUSTAL'
 > /Developer/usr/bin/clang -O4 -arch x86_64 -no-cpp-precomp -pipe
 -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL  -w -DNDEBUG
 -DARB_64  -DDARWIN    -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTAL
 -c -o clustalv.o clustalv.c -I.
 -I/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/INCLUDE
 -I/opt/local/include -I/System/Library/Frameworks/OpenGL.framework/Headers
 -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers
 > clang: warning: argument unused during compilation: '-no-cpp-precomp'
 > /Developer/usr/bin/clang -O4 -arch x86_64 -no-cpp-precomp -pipe
 -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL  -w -DNDEBUG
 -DARB_64  -DDARWIN    -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTAL
 -c -o amenu.o amenu.c -I.
 -I/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/INCLUDE
 -I/opt/local/include -I/System/Library/Frameworks/OpenGL.framework/Headers
 -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers
 > clang: warning: argument unused during compilation: '-no-cpp-precomp'
 > /Developer/usr/bin/clang -O4 -arch x86_64 -no-cpp-precomp -pipe
 -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL  -w -DNDEBUG
 -DARB_64  -DDARWIN    -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTAL
 -c -o myers.o myers.c -I.
 -I/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/INCLUDE
 -I/opt/local/include -I/System/Library/Frameworks/OpenGL.framework/Headers
 -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers
 > clang: warning: argument unused during compilation: '-no-cpp-precomp'
 > /Developer/usr/bin/clang -O4 -arch x86_64 -no-cpp-precomp -pipe
 -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL  -w -DNDEBUG
 -DARB_64  -DDARWIN    -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTAL
 -c -o sequence.o sequence.c -I.
 -I/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/INCLUDE
 -I/opt/local/include -I/System/Library/Frameworks/OpenGL.framework/Headers
 -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers
 > clang: warning: argument unused during compilation: '-no-cpp-precomp'
 > /Developer/usr/bin/clang -O4 -arch x86_64 -no-cpp-precomp -pipe
 -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL  -w -DNDEBUG
 -DARB_64  -DDARWIN    -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTAL
 -c -o showpair.o showpair.c -I.
 -I/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/INCLUDE
 -I/opt/local/include -I/System/Library/Frameworks/OpenGL.framework/Headers
 -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers
 > clang: warning: argument unused during compilation: '-no-cpp-precomp'
 > /Developer/usr/bin/clang -O4 -arch x86_64 -no-cpp-precomp -pipe
 -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL  -w -DNDEBUG
 -DARB_64  -DDARWIN    -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTAL
 -c -o upgma.o upgma.c -I.
 -I/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/INCLUDE
 -I/opt/local/include -I/System/Library/Frameworks/OpenGL.framework/Headers
 -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers
 > clang: warning: argument unused during compilation: '-no-cpp-precomp'
 > /Developer/usr/bin/clang -O4 -arch x86_64 -no-cpp-precomp -pipe
 -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL  -w -DNDEBUG
 -DARB_64  -DDARWIN    -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTAL
 -c -o util.o util.c -I.
 -I/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/INCLUDE
 -I/opt/local/include -I/System/Library/Frameworks/OpenGL.framework/Headers
 -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers
 > clang: warning: argument unused during compilation: '-no-cpp-precomp'
 > /Developer/usr/bin/clang -O4 -arch x86_64 -no-cpp-precomp -pipe
 -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL  -w -DNDEBUG
 -DARB_64  -DDARWIN    -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTAL
 -c -o trees.o trees.c -I.
 -I/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/INCLUDE
 -I/opt/local/include -I/System/Library/Frameworks/OpenGL.framework/Headers
 -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers
 > clang: warning: argument unused during compilation: '-no-cpp-precomp'
 > /Developer/usr/bin/clang -O4 -arch x86_64 -no-cpp-precomp -pipe
 -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL  -w -DNDEBUG
 -DARB_64  -DDARWIN    -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTAL
 -c -o gcgcheck.o gcgcheck.c -I.
 -I/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/INCLUDE
 -I/opt/local/include -I/System/Library/Frameworks/OpenGL.framework/Headers
 -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers
 > clang: warning: argument unused during compilation: '-no-cpp-precomp'
 > /Developer/usr/bin/clang -O4 -arch x86_64 -no-cpp-precomp -pipe
 -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL  -w -DNDEBUG
 -DARB_64  -DDARWIN    -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_CLUSTAL
 -o
 /opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/bin/clustalv
 clustalv.o amenu.o myers.o sequence.o showpair.o upgma.o util.o trees.o
 gcgcheck.o -lm
 > clang: warning: argument unused during compilation: '-no-cpp-precomp'
 > make[4]: Leaving directory
 `/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/GDE/CLUSTAL'
 > make[3]: Leaving directory
 `/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/GDE'
 > make[2]: *** [GDE.a] Error 2
 > make[2]: Leaving directory
 `/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/GDE'
 > make[1]: *** [GDE/GDE.dummy] Error 1
 > make[1]: *** Waiting for unfinished jobs....
 >
 --------------------------------------------------------------------------------
 Make everything in CONVERTALN
 > make[3]: Entering directory
 `/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/CONVERTALN'
 > /Developer/usr/bin/clang -O4 -arch x86_64 -no-cpp-precomp -pipe
 -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL  -W -Wall -DNDEBUG
 -DARB_64  -DDARWIN    -DFAKE_VTAB_PTR=char -DIN_ARB_CONVERTALN -Wstrict-
 prototypes -c main.c -I.
 -I/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/INCLUDE
 -I/opt/local/include -I/System/Library/Frameworks/OpenGL.framework/Headers
 -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers
 > clang: warning: argument unused during compilation: '-no-cpp-precomp'
 > /Developer/usr/bin/clang -O4 -arch x86_64 -no-cpp-precomp -pipe
 -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL  -W -Wall -DNDEBUG
 -DARB_64  -DDARWIN    -DFAKE_VTAB_PTR=char -DIN_ARB_CONVERTALN -Wstrict-
 prototypes -c fconv.c -I.
 -I/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/INCLUDE
 -I/opt/local/include -I/System/Library/Frameworks/OpenGL.framework/Headers
 -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers
 > clang: warning: argument unused during compilation: '-no-cpp-precomp'
 > /Developer/usr/bin/clang -O4 -arch x86_64 -no-cpp-precomp -pipe
 -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL  -W -Wall -DNDEBUG
 -DARB_64  -DDARWIN    -DFAKE_VTAB_PTR=char -DIN_ARB_CONVERTALN -Wstrict-
 prototypes -c mg.c -I.
 -I/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/INCLUDE
 -I/opt/local/include -I/System/Library/Frameworks/OpenGL.framework/Headers
 -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers
 > clang: warning: argument unused during compilation: '-no-cpp-precomp'
 > /Developer/usr/bin/clang -O4 -arch x86_64 -no-cpp-precomp -pipe
 -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL  -W -Wall -DNDEBUG
 -DARB_64  -DDARWIN    -DFAKE_VTAB_PTR=char -DIN_ARB_CONVERTALN -Wstrict-
 prototypes -c genbank.c -I.
 -I/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/INCLUDE
 -I/opt/local/include -I/System/Library/Frameworks/OpenGL.framework/Headers
 -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers
 > clang: warning: argument unused during compilation: '-no-cpp-precomp'
 > /Developer/usr/bin/clang -O4 -arch x86_64 -no-cpp-precomp -pipe
 -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL  -W -Wall -DNDEBUG
 -DARB_64  -DDARWIN    -DFAKE_VTAB_PTR=char -DIN_ARB_CONVERTALN -Wstrict-
 prototypes -c macke.c -I.
 -I/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/INCLUDE
 -I/opt/local/include -I/System/Library/Frameworks/OpenGL.framework/Headers
 -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers
 > clang: warning: argument unused during compilation: '-no-cpp-precomp'
 > /Developer/usr/bin/clang -O4 -arch x86_64 -no-cpp-precomp -pipe
 -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL  -W -Wall -DNDEBUG
 -DARB_64  -DDARWIN    -DFAKE_VTAB_PTR=char -DIN_ARB_CONVERTALN -Wstrict-
 prototypes -c phylip.c -I.
 -I/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/INCLUDE
 -I/opt/local/include -I/System/Library/Frameworks/OpenGL.framework/Headers
 -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers
 > clang: warning: argument unused during compilation: '-no-cpp-precomp'
 > /Developer/usr/bin/clang -O4 -arch x86_64 -no-cpp-precomp -pipe
 -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL  -W -Wall -DNDEBUG
 -DARB_64  -DDARWIN    -DFAKE_VTAB_PTR=char -DIN_ARB_CONVERTALN -Wstrict-
 prototypes -c paup.c -I.
 -I/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/INCLUDE
 -I/opt/local/include -I/System/Library/Frameworks/OpenGL.framework/Headers
 -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers
 > clang: warning: argument unused during compilation: '-no-cpp-precomp'
 > /Developer/usr/bin/clang -O4 -arch x86_64 -no-cpp-precomp -pipe
 -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL  -W -Wall -DNDEBUG
 -DARB_64  -DDARWIN    -DFAKE_VTAB_PTR=char -DIN_ARB_CONVERTALN -Wstrict-
 prototypes -c util.c -I.
 -I/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/INCLUDE
 -I/opt/local/include -I/System/Library/Frameworks/OpenGL.framework/Headers
 -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers
 > clang: warning: argument unused during compilation: '-no-cpp-precomp'
 > /Developer/usr/bin/clang -O4 -arch x86_64 -no-cpp-precomp -pipe
 -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL  -W -Wall -DNDEBUG
 -DARB_64  -DDARWIN    -DFAKE_VTAB_PTR=char -DIN_ARB_CONVERTALN -Wstrict-
 prototypes -c date.c -I.
 -I/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/INCLUDE
 -I/opt/local/include -I/System/Library/Frameworks/OpenGL.framework/Headers
 -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers
 > clang: warning: argument unused during compilation: '-no-cpp-precomp'
 > /Developer/usr/bin/clang -O4 -arch x86_64 -no-cpp-precomp -pipe
 -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL  -W -Wall -DNDEBUG
 -DARB_64  -DDARWIN    -DFAKE_VTAB_PTR=char -DIN_ARB_CONVERTALN -Wstrict-
 prototypes -c embl.c -I.
 -I/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/INCLUDE
 -I/opt/local/include -I/System/Library/Frameworks/OpenGL.framework/Headers
 -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers
 > clang: warning: argument unused during compilation: '-no-cpp-precomp'
 > /Developer/usr/bin/clang -O4 -arch x86_64 -no-cpp-precomp -pipe
 -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL  -W -Wall -DNDEBUG
 -DARB_64  -DDARWIN    -DFAKE_VTAB_PTR=char -DIN_ARB_CONVERTALN -Wstrict-
 prototypes -c gcg.c -I.
 -I/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/INCLUDE
 -I/opt/local/include -I/System/Library/Frameworks/OpenGL.framework/Headers
 -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers
 > clang: warning: argument unused during compilation: '-no-cpp-precomp'
 > /Developer/usr/bin/clang -O4 -arch x86_64 -no-cpp-precomp -pipe
 -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL  -W -Wall -DNDEBUG
 -DARB_64  -DDARWIN    -DFAKE_VTAB_PTR=char -DIN_ARB_CONVERTALN -Wstrict-
 prototypes -c printable.c -I.
 -I/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/INCLUDE
 -I/opt/local/include -I/System/Library/Frameworks/OpenGL.framework/Headers
 -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers
 > clang: warning: argument unused during compilation: '-no-cpp-precomp'
 > /Developer/usr/bin/clang -O4 -arch x86_64 -no-cpp-precomp -pipe
 -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL  -W -Wall -DNDEBUG
 -DARB_64  -DDARWIN    -DFAKE_VTAB_PTR=char -DIN_ARB_CONVERTALN -Wstrict-
 prototypes -c alma.c -I.
 -I/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/INCLUDE
 -I/opt/local/include -I/System/Library/Frameworks/OpenGL.framework/Headers
 -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers
 > clang: warning: argument unused during compilation: '-no-cpp-precomp'
 > /Developer/usr/bin/clang -O4 -arch x86_64 -no-cpp-precomp -pipe
 -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL  -W -Wall -DNDEBUG
 -DARB_64  -DDARWIN    -DFAKE_VTAB_PTR=char -DIN_ARB_CONVERTALN -Wstrict-
 prototypes -c routines.c -I.
 -I/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/INCLUDE
 -I/opt/local/include -I/System/Library/Frameworks/OpenGL.framework/Headers
 -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers
 > clang: warning: argument unused during compilation: '-no-cpp-precomp'
 > /Developer/usr/bin/clang -O4 -arch x86_64 -no-cpp-precomp -pipe
 -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL  -W -Wall -DNDEBUG
 -DARB_64  -DDARWIN    -DFAKE_VTAB_PTR=char -DIN_ARB_CONVERTALN -Wstrict-
 prototypes -c convert.c -I.
 -I/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/INCLUDE
 -I/opt/local/include -I/System/Library/Frameworks/OpenGL.framework/Headers
 -I/usr/include/krb5 -I/System/Library/Frameworks/GLUT.framework/Headers
 > clang: warning: argument unused during compilation: '-no-cpp-precomp'
 > /Developer/usr/bin/clang++   -arch x86_64   -o
 /opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/bin/arb_convert_aln
 main.o fconv.o mg.o genbank.o macke.o phylip.o paup.o util.o date.o embl.o
 gcg.o printable.o alma.o routines.o convert.o
 ../SL/FILE_BUFFER/FILE_BUFFER.a
 -L/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/LIBLINK
 -lARBDB
 > make[3]: Leaving directory
 `/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779/CONVERTALN'
 > make[2]: Leaving directory
 `/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779'
 > make[1]: Leaving directory
 `/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779'
 > make: *** [all] Error 2
 > make: Leaving directory
 `/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779'
 > shell command " cd
 "/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/arbsrc_6779"
 && /usr/bin/make -j2 -w all GCC=/Developer/usr/bin/clang
 GPP=/Developer/usr/bin/clang++ CPPreal= " returned error 2
 > Error: Target org.macports.build returned: shell command failed (see log
 for details)
 > Warning: the following items did not execute (for arb):
 org.macports.activate org.macports.build org.macports.destroot
 org.macports.install
 > Log for arb is at:
 /opt/local/var/macports/logs/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/main.log
 > Error: Status 1 encountered during processing.
 > To report a bug, see <http://guide.macports.org/#project.tickets>
 >
 > }}}

 ARB now builds on OS X 10.7 Lion using clang with the attached patches.

-- 
Ticket URL: <https://trac.macports.org/ticket/30342#comment:7>
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