[MacPorts] #33928: pymol @1.5 FontTTF errors
#33928: pymol @1.5 FontTTF errors ---------------------------------------+------------------------------------ Reporter: andrew.flaus@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.0.4 Keywords: | Port: pymol ---------------------------------------+------------------------------------ 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 }}} -- Ticket URL: <https://trac.macports.org/ticket/33928> MacPorts <http://www.macports.org/> Ports system for Mac OS
#33928: pymol @1.5 FontTTF errors ---------------------------------------+------------------------------------ Reporter: andrew.flaus@… | Owner: howarth@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.0.4 Keywords: | Port: pymol ---------------------------------------+------------------------------------ Changes (by ryandesign@…): * owner: macports-tickets@… => howarth@… -- Ticket URL: <https://trac.macports.org/ticket/33928#comment:1> MacPorts <http://www.macports.org/> Ports system for Mac OS
#33928: pymol @1.5 FontTTF errors ---------------------------------------+------------------------------------ Reporter: andrew.flaus@… | Owner: howarth@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.0.4 Keywords: | Port: pymol ---------------------------------------+------------------------------------ Comment(by ryandesign@…): Please attach the main.log file. -- Ticket URL: <https://trac.macports.org/ticket/33928#comment:2> MacPorts <http://www.macports.org/> Ports system for Mac OS
#33928: pymol @1.5 FontTTF errors ---------------------------------------+------------------------------------ Reporter: andrew.flaus@… | Owner: howarth@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.0.4 Keywords: | Port: pymol ---------------------------------------+------------------------------------ Comment(by howarth@…): After uninstalling and cleaning pymol here (following a port self update), pymol still builds fine. [[BR]] 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. -- Ticket URL: <https://trac.macports.org/ticket/33928#comment:3> MacPorts <http://www.macports.org/> Ports system for Mac OS
#33928: pymol @1.5 FontTTF errors ---------------------------------------+------------------------------------ Reporter: andrew.flaus@… | Owner: howarth@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.0.4 Keywords: | Port: pymol ---------------------------------------+------------------------------------ Comment(by 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? -- Ticket URL: <https://trac.macports.org/ticket/33928#comment:4> MacPorts <http://www.macports.org/> Ports system for Mac OS
#33928: pymol @1.5 FontTTF errors ---------------------------------------+------------------------------------ Reporter: andrew.flaus@… | Owner: howarth@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.0.4 Keywords: | Port: pymol ---------------------------------------+------------------------------------ Comment(by howarth@…): What do you get from "xcode-select -print-path"? Is should return "/Applications/Xcode.app/Contents/Developer".[[BR]] Also, it would be a good idea to move aside /usr/local and try the build again. -- Ticket URL: <https://trac.macports.org/ticket/33928#comment:5> MacPorts <http://www.macports.org/> Ports system for Mac OS
#33928: pymol @1.5 FontTTF errors ---------------------------------------+------------------------------------ Reporter: andrew.flaus@… | Owner: howarth@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.0.4 Keywords: | Port: pymol ---------------------------------------+------------------------------------ Comment(by 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? -- Ticket URL: <https://trac.macports.org/ticket/33928#comment:6> MacPorts <http://www.macports.org/> Ports system for Mac OS
#33928: pymol @1.5 FontTTF errors ---------------------------------------+------------------------------------ Reporter: andrew.flaus@… | Owner: howarth@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.0.4 Keywords: | Port: pymol ---------------------------------------+------------------------------------ Comment(by howarth@…): I just tried a fresh installation of macports Xcode 2.0.4 and this looks like a serious bug with the new release.[[BR]] Somehow it is broken the previous usage of clang by default for Xcode 4.2 and later. The fact that this release[[BR]] introduces the usage of prebuilt binaries makes me wonder if this is fallout from that. -- Ticket URL: <https://trac.macports.org/ticket/33928#comment:7> MacPorts <http://www.macports.org/> Ports system for Mac OS
#33928: pymol @1.5 FontTTF errors ---------------------------------------+------------------------------------ Reporter: andrew.flaus@… | Owner: howarth@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.0.4 Keywords: | Port: pymol ---------------------------------------+------------------------------------ Comment(by howarth@…): Current macports 2.0.4 looks horribly broken to me. I see absolutely not documentation or even source comments [[BR]] on how to disable binary package downloads in port. This is a serious design omission if true. -- Ticket URL: <https://trac.macports.org/ticket/33928#comment:8> MacPorts <http://www.macports.org/> Ports system for Mac OS
#33928: pymol @1.5 FontTTF errors ---------------------------------------+------------------------------------ Reporter: andrew.flaus@… | Owner: howarth@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.0.4 Keywords: | Port: pymol ---------------------------------------+------------------------------------ Comment(by howarth@…): Installing MacPorts 2.0.4 from sources and always passing '-s' to avoid the problematic binary releases[[BR]] should work. That is...[[BR]] [[BR]] cd MacPorts-2.0.4[[BR]] ./configure && make && sudo make install[[BR]] sudo port -v -s selfupdate[[BR]] sudo port -s upgrade outdated[[BR]] sudo port -s install pymol[[BR]] -- Ticket URL: <https://trac.macports.org/ticket/33928#comment:9> MacPorts <http://www.macports.org/> Ports system for Mac OS
#33928: pymol @1.5 FontTTF errors ---------------------------------------+------------------------------------ Reporter: andrew.flaus@… | Owner: howarth@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.0.4 Keywords: | Port: pymol ---------------------------------------+------------------------------------ Comment(by 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. -- Ticket URL: <https://trac.macports.org/ticket/33928#comment:10> MacPorts <http://www.macports.org/> Ports system for Mac OS
#33928: pymol @1.5 FontTTF errors ---------------------------------------+------------------------------------ Reporter: andrew.flaus@… | Owner: howarth@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.0.4 Keywords: | Port: pymol ---------------------------------------+------------------------------------ Comment(by howarth@…): Is this from a totally clean bootstrap? If not, you will at least need to rebuild the python26 package[[BR]] since the Lion buildbot apparently is building against Xcode 4.2.0 such that llvm-gcc-4.2 is hardcoded in[[BR]] the resulting python26. -- Ticket URL: <https://trac.macports.org/ticket/33928#comment:11> MacPorts <http://www.macports.org/> Ports system for Mac OS
#33928: pymol @1.5 FontTTF errors ---------------------------------------+------------------------------------ Reporter: andrew.flaus@… | Owner: howarth@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.0.4 Keywords: | Port: pymol ---------------------------------------+------------------------------------ Comment(by 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. -- Ticket URL: <https://trac.macports.org/ticket/33928#comment:12> MacPorts <http://www.macports.org/> Ports system for Mac OS
#33928: pymol @1.5 FontTTF errors ----------------------------------------+----------------------------------- Reporter: andrew.flaus@… | Owner: howarth@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.0.4 Resolution: worksforme | Keywords: Port: pymol | ----------------------------------------+----------------------------------- Changes (by macsforever2000@…): * status: new => closed * resolution: => worksforme -- Ticket URL: <https://trac.macports.org/ticket/33928#comment:13> MacPorts <http://www.macports.org/> Ports system for Mac OS
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