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

MacPorts noreply at macports.org
Mon Jul 25 19:17:20 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@…):

 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>

 }}}

-- 
Ticket URL: <https://trac.macports.org/ticket/30342#comment:6>
MacPorts <http://www.macports.org/>
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