pymol @1.5 FontTTF errors

[andrew.flaus@…]

Completely fresh installation of OSX 10.7.3, Xcode 4.3.2 fails on port install pymol

:info:destroot /usr/bin/llvm-gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -pipe -O2 -fwrapv -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_PYMOL_MODULE -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_INLINE -D_PYMOL_NUMPY -D_PYMOL_OPENGL_SHADERS -DNO_MMLIBS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_CGO_DRAWARRAYS -D_PYMOL_GL_CALLLISTS -DOPENGL_ES_2 -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/opt/local/include -I/opt/local/include/GL -I/opt/local/include/freetype2 -Imodules/cealign/src -Imodules/cealign/src/tnt -Igenerated/include -Igenerated/src -I/opt/local/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c layer1/Shaker.c -o build/temp.macosx-10.7-x86_64-2.6/layer1/Shaker.o -ffast-math -funroll-loops -O3 -fcommon
:info:destroot In file included from layer0/os_gl.h:80,
:info:destroot                  from layer1/Shaker.c:21:
:info:destroot /opt/local/include/GL/glew.h:16088: warning: function declaration isn’t a prototype
:info:destroot In file included from layer0/os_gl.h:226,
:info:destroot                  from layer1/Shaker.c:21:
:info:destroot /opt/local/include/GL/freeglut_ext.h:173: warning: function declaration isn’t a prototype
:info:destroot /usr/bin/llvm-gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -pipe -O2 -fwrapv -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_PYMOL_MODULE -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_INLINE -D_PYMOL_NUMPY -D_PYMOL_OPENGL_SHADERS -DNO_MMLIBS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_CGO_DRAWARRAYS -D_PYMOL_GL_CALLLISTS -DOPENGL_ES_2 -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/opt/local/include -I/opt/local/include/GL -I/opt/local/include/freetype2 -Imodules/cealign/src -Imodules/cealign/src/tnt -Igenerated/include -Igenerated/src -I/opt/local/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c layer1/Symmetry.c -o build/temp.macosx-10.7-x86_64-2.6/layer1/Symmetry.o -ffast-math -funroll-loops -O3 -fcommon
:info:destroot In file included from layer0/os_gl.h:80,
:info:destroot                  from layer1/CGO.h:23,
:info:destroot                  from layer0/Crystal.h:21,
:info:destroot                  from layer1/Symmetry.h:20,
:info:destroot                  from layer1/Symmetry.c:27:
:info:destroot /opt/local/include/GL/glew.h:16088: warning: function declaration isn’t a prototype
:info:destroot In file included from layer0/os_gl.h:226,
:info:destroot                  from layer1/CGO.h:23,
:info:destroot                  from layer0/Crystal.h:21,
:info:destroot                  from layer1/Symmetry.h:20,
:info:destroot                  from layer1/Symmetry.c:27:
:info:destroot /opt/local/include/GL/freeglut_ext.h:173: warning: function declaration isn’t a prototype
:info:destroot /usr/bin/llvm-gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -pipe -O2 -fwrapv -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_PYMOL_MODULE -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_INLINE -D_PYMOL_NUMPY -D_PYMOL_OPENGL_SHADERS -DNO_MMLIBS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_CGO_DRAWARRAYS -D_PYMOL_GL_CALLLISTS -DOPENGL_ES_2 -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/opt/local/include -I/opt/local/include/GL -I/opt/local/include/freetype2 -Imodules/cealign/src -Imodules/cealign/src/tnt -Igenerated/include -Igenerated/src -I/opt/local/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c layer1/Text.c -o build/temp.macosx-10.7-x86_64-2.6/layer1/Text.o -ffast-math -funroll-loops -O3 -fcommon
:info:destroot In file included from layer1/Text.c:29:
:info:destroot layer1/FontTTF.h:41859:11: error: invalid suffix "$" on integer constant
:info:destroot In file included from layer1/Text.c:29:
:info:destroot layer1/FontTTF.h:41859: error: expected ‘}’ before numeric constant
:info:destroot error: command '/usr/bin/llvm-gcc-4.2' failed with exit status 1
:info:destroot shell command " cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_pymol/pymol/work/pymol" && /opt/local/Library/Frameworks/Python.framework/Versions/2.6/bin/python2.6 setup.py --no-user-cfg install --prefix=/opt/local/Library/Frameworks/Python.framework/Versions/2.6 --root=/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_pymol/pymol/work/destroot " returned error 1
:error:destroot Target org.macports.destroot returned: shell command failed (see log for details)
:debug:destroot Backtrace: shell command failed (see log for details)
    while executing
"command_exec destroot"
    (procedure "portdestroot::destroot_main" line 2)
    invoked from within
"$procedure $targetname"
:info:destroot Warning: the following items did not execute (for pymol): org.macports.activate org.macports.destroot org.macports.install
:notice:destroot Log for pymol is at: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_pymol/pymol/main.log

[ryandesign (Ryan Carsten Schmidt)]

Please attach the main.log file.

[howarth@…]

After uninstalling and cleaning pymol here (following a port self update), pymol still builds fine.
One odd thing about the failing build is that it is using llvm-gcc-4.2 rather than clang. I don't see that with 10.7 and Xcode 4.3.2.

[andrew.flaus@…]

Mac mini Core 2 Duo 1.83, reformatted HD OSX 10.7.3, completely up-to-date Xcode 4.3.2 (4E2002, 22.03.2012) and Command Line Tools Late March (22.03.2012), downloads from ADC

Completely vanilla: Installed macports, executed port selfupdate, then port install pymol

Seems to be default to llvm-gcc-4.2?

[howarth@…]

What do you get from "xcode-select -print-path"? Is should return "/Applications/Xcode.app/Contents/Developer".
Also, it would be a good idea to move aside /usr/local and try the build again.

[andrew.flaus@…]

Yes, it returns "/Applications/Xcode.app/Contents/Developer"

/usr/local did not exist so I created it and moved inside then tried build. Same error sorry.

Should I force it to use clang, how?

[howarth@…]

I just tried a fresh installation of macports Xcode 2.0.4 and this looks like a serious bug with the new release.
Somehow it is broken the previous usage of clang by default for Xcode 4.2 and later. The fact that this release
introduces the usage of prebuilt binaries makes me wonder if this is fallout from that.

[howarth@…]

Current macports 2.0.4 looks horribly broken to me. I see absolutely not documentation or even source comments
on how to disable binary package downloads in port. This is a serious design omission if true.

[howarth@…]

Installing MacPorts 2.0.4 from sources and always passing '-s' to avoid the problematic binary releases
should work. That is...

cd MacPorts-2.0.4
./configure && make && sudo make install
sudo port -v -s selfupdate
sudo port -s upgrade outdated
sudo port -s install pymol

[andrew.flaus@…]

Tried this following through steps above but no luck, sorry. Neither the glib2 update nor pymol would build. Attaching main-120408.log

Really appreciate you looking into this. Since it's a blank installation, I hope this helps others.

[howarth@…]

Is this from a totally clean bootstrap? If not, you will at least need to rebuild the python26 package
since the Lion buildbot apparently is building against Xcode 4.2.0 such that llvm-gcc-4.2 is hardcoded in
the resulting python26.

[andrew.flaus@…]

Deleted entire macports installation, following guide section 2.5. Rebuilt everything from source (-s) as suggested. Seg faulted compiling py26-numpy ppl, py26-scipy, swig and gcc45. System resource limitations on oldish mac mini? Managed to compile each individually except gcc45, but took this as pre-compiled (i.e. no -s flag).

So success: Pymol 1.5.0.2 now running!

Hope feedback is useful. Thanks for your help.