[Fink-users] issue with pangomm1.4.1 (while installing inkscape)
Hello all - I am running 10.8 on a MBP retina trying to install inkscape. During the process I am getting hung up on install of pangomm1.4.1-shlibs. Other info is: Also include the following system information: Package manager version: 0.34.4 Distribution version: selfupdate-rsync Wed Jan 9 08:32:12 2013, 10.8, x86_64 Trees: local/main stable/main unstable/main A (hopefully relevant) portion of the build log is included here: libtool: compile: g++ -DHAVE_CONFIG_H -I.. -I../.. -DG_LOG_DOMAIN=\pangomm\ -DPANGOMM_BUILD=1 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I/sw/include/glibmm-2.4 -I/sw/lib/glibmm-2.4/include -I/sw/include/sigc++-2.0 -I/sw/lib/sigc++-2.0/include -I/sw/include/cairomm-1.0 -I/sw/lib/cairomm-1.0/include -I/sw/include/cairo -I/sw/include/pango-1.0 -I/sw/lib/fontconfig2/include -DX_LOCALE -I/sw/include -Wall -Os -pipe -MT cairofontmap.lo -MD -MP -MF .deps/cairofontmap.Tpo -c cairofontmap.cc -fno-common -DPIC -o .libs/cairofontmap.o In file included from cairofontmap.cc:4: In file included from ../pangomm/cairofontmap.h:31: In file included from ../pangomm/context.h:42: In file included from /sw/include/cairomm-1.0/cairomm/context.h:24: In file included from /sw/include/cairomm-1.0/cairomm/surface.h:37: In file included from /sw/include/cairomm-1.0/cairomm/fontoptions.h:26: In file included from /sw/include/cairo/cairo-ft.h:46: /sw/include/ft2build.h:56:10: fatal error: 'freetype/config/ftheader.h' file not found #include freetype/config/ftheader.h ^ 1 error generated. make[2]: *** [cairofontmap.lo] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all] Error 2 ### execution of make failed, exit code 2 ### execution of /tmp/fink.FTIkR failed, exit code 2 It seems like a 'simple' path error since the ftheader.h file exists in /sw/include/freetype2/freetype/config/ but I can't figure out where to make the mod to get this to go forward. Any help would be much appreciated! Thanks, -geoff s. -- Geoff Smith Naval Research Laboratory 202.404.6324 geoffrey.sm...@nrl.navy.mil -- Master Java SE, Java EE, Eclipse, Spring, Hibernate, JavaScript, jQuery and much more. Keep your Java skills current with LearnJavaNow - 200+ hours of step-by-step video tutorials by Java experts. SALE $49.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122612 ___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] issue with pangomm1.4.1 (while installing inkscape)
On 1/9/2013 8:53 AM, Geoffrey Smith wrote: Hello all - I am running 10.8 on a MBP retina trying to install inkscape. During the process I am getting hung up on install of pangomm1.4.1-shlibs. Other info is: Also include the following system information: Package manager version: 0.34.4 Distribution version: selfupdate-rsync Wed Jan 9 08:32:12 2013, 10.8, x86_64 Trees: local/main stable/main unstable/main A (hopefully relevant) portion of the build log is included here: libtool: compile: g++ -DHAVE_CONFIG_H -I.. -I../.. -DG_LOG_DOMAIN=\pangomm\ -DPANGOMM_BUILD=1 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I/sw/include/glibmm-2.4 -I/sw/lib/glibmm-2.4/include -I/sw/include/sigc++-2.0 -I/sw/lib/sigc++-2.0/include -I/sw/include/cairomm-1.0 -I/sw/lib/cairomm-1.0/include -I/sw/include/cairo -I/sw/include/pango-1.0 -I/sw/lib/fontconfig2/include -DX_LOCALE -I/sw/include -Wall -Os -pipe -MT cairofontmap.lo -MD -MP -MF .deps/cairofontmap.Tpo -c cairofontmap.cc -fno-common -DPIC -o .libs/cairofontmap.o In file included from cairofontmap.cc:4: In file included from ../pangomm/cairofontmap.h:31: In file included from ../pangomm/context.h:42: In file included from /sw/include/cairomm-1.0/cairomm/context.h:24: In file included from /sw/include/cairomm-1.0/cairomm/surface.h:37: In file included from /sw/include/cairomm-1.0/cairomm/fontoptions.h:26: In file included from /sw/include/cairo/cairo-ft.h:46: /sw/include/ft2build.h:56:10: fatal error: 'freetype/config/ftheader.h' file not found #include freetype/config/ftheader.h ^ Confirming on 10.7 as well. -I%p/include/freetype2 is not being passed to compiler. Checking why... Hanspeter -- Master Java SE, Java EE, Eclipse, Spring, Hibernate, JavaScript, jQuery and much more. Keep your Java skills current with LearnJavaNow - 200+ hours of step-by-step video tutorials by Java experts. SALE $49.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122612 ___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] issue with pangomm1.4.1 (while installing inkscape)
On 1/9/2013 9:38 AM, Hanspeter Niederstrasser wrote: On 1/9/2013 8:53 AM, Geoffrey Smith wrote: Hello all - I am running 10.8 on a MBP retina trying to install inkscape. During the process I am getting hung up on install of pangomm1.4.1-shlibs. Other info is: Also include the following system information: Package manager version: 0.34.4 Distribution version: selfupdate-rsync Wed Jan 9 08:32:12 2013, 10.8, x86_64 Trees: local/main stable/main unstable/main A (hopefully relevant) portion of the build log is included here: libtool: compile: g++ -DHAVE_CONFIG_H -I.. -I../.. -DG_LOG_DOMAIN=\pangomm\ -DPANGOMM_BUILD=1 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I/sw/include/glibmm-2.4 -I/sw/lib/glibmm-2.4/include -I/sw/include/sigc++-2.0 -I/sw/lib/sigc++-2.0/include -I/sw/include/cairomm-1.0 -I/sw/lib/cairomm-1.0/include -I/sw/include/cairo -I/sw/include/pango-1.0 -I/sw/lib/fontconfig2/include -DX_LOCALE -I/sw/include -Wall -Os -pipe -MT cairofontmap.lo -MD -MP -MF .deps/cairofontmap.Tpo -c cairofontmap.cc -fno-common -DPIC -o .libs/cairofontmap.o In file included from cairofontmap.cc:4: In file included from ../pangomm/cairofontmap.h:31: In file included from ../pangomm/context.h:42: In file included from /sw/include/cairomm-1.0/cairomm/context.h:24: In file included from /sw/include/cairomm-1.0/cairomm/surface.h:37: In file included from /sw/include/cairomm-1.0/cairomm/fontoptions.h:26: In file included from /sw/include/cairo/cairo-ft.h:46: /sw/include/ft2build.h:56:10: fatal error: 'freetype/config/ftheader.h' file not found #include freetype/config/ftheader.h ^ Confirming on 10.7 as well. -I%p/include/freetype2 is not being passed to compiler. Checking why... Apparently it's a bug in the way the new cairo (cairomm specifically) publishes compiler flags that it needs. A fix is being worked on. Hanspeter -- Master Java SE, Java EE, Eclipse, Spring, Hibernate, JavaScript, jQuery and much more. Keep your Java skills current with LearnJavaNow - 200+ hours of step-by-step video tutorials by Java experts. SALE $49.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122612 ___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] issue with pangomm1.4.1 (while installing inkscape)
On Jan 9, 2013, at 10:23 AM, Hanspeter Niederstrasser wrote: On 1/9/2013 9:38 AM, Hanspeter Niederstrasser wrote: On 1/9/2013 8:53 AM, Geoffrey Smith wrote: Hello all - I am running 10.8 on a MBP retina trying to install inkscape. During the process I am getting hung up on install of pangomm1.4.1-shlibs. Other info is: Also include the following system information: Package manager version: 0.34.4 Distribution version: selfupdate-rsync Wed Jan 9 08:32:12 2013, 10.8, x86_64 Trees: local/main stable/main unstable/main A (hopefully relevant) portion of the build log is included here: libtool: compile: g++ -DHAVE_CONFIG_H -I.. -I../.. -DG_LOG_DOMAIN=\pangomm\ -DPANGOMM_BUILD=1 -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I/sw/include/glibmm-2.4 -I/sw/lib/glibmm-2.4/include -I/sw/include/sigc++-2.0 -I/sw/lib/sigc++-2.0/include -I/sw/include/cairomm-1.0 -I/sw/lib/cairomm-1.0/include -I/sw/include/cairo -I/sw/include/pango-1.0 -I/sw/lib/fontconfig2/include -DX_LOCALE -I/sw/include -Wall -Os -pipe -MT cairofontmap.lo -MD -MP -MF .deps/cairofontmap.Tpo -c cairofontmap.cc -fno-common -DPIC -o .libs/cairofontmap.o In file included from cairofontmap.cc:4: In file included from ../pangomm/cairofontmap.h:31: In file included from ../pangomm/context.h:42: In file included from /sw/include/cairomm-1.0/cairomm/context.h:24: In file included from /sw/include/cairomm-1.0/cairomm/surface.h:37: In file included from /sw/include/cairomm-1.0/cairomm/fontoptions.h:26: In file included from /sw/include/cairo/cairo-ft.h:46: /sw/include/ft2build.h:56:10: fatal error: 'freetype/config/ftheader.h' file not found #include freetype/config/ftheader.h ^ Confirming on 10.7 as well. -I%p/include/freetype2 is not being passed to compiler. Checking why... Apparently it's a bug in the way the new cairo (cairomm specifically) publishes compiler flags that it needs. A fix is being worked on. Hanspeter Great news - thanks! -geoff -- Geoff Smith Naval Research Laboratory 202.404.6324 geoffrey.sm...@nrl.navy.mil -- Master Java SE, Java EE, Eclipse, Spring, Hibernate, JavaScript, jQuery and much more. Keep your Java skills current with LearnJavaNow - 200+ hours of step-by-step video tutorials by Java experts. SALE $49.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122612 ___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] Failed: phase compiling: svn-swig-pm588-1.7.8-1 failed
Updating to svn-swig-pm588-1.7.8-1 on Package manager version: 0.34.4 Distribution version: selfupdate-rsync Sat Jan 5 15:38:09 2013, 10.5, powerpc Trees: local/main stable/main stable/crypto unstable/main unstable/crypto Xcode.app: 3.1.4 Xcode command-line tools: 3.1.4 Max. Fink build jobs: 1 failed with ... Running Makefile.PL pushd subversion/bindings/swig/perl/native ARCHFLAGS= /usr/bin/perl5.8.8 Makefile.PL PERL=/usr/bin/perl5.8.8 PREFIX=/sw INSTALLPRIVLIB=/sw/lib/perl5/5.8.8 INSTALLARCHLIB=/sw/lib/perl5/5.8.8/darwin-thread-multi-2level INSTALLSITELIB=/sw/lib/perl5/5.8.8 INSTALLSITEARCH=/sw/lib/perl5/5.8.8/darwin-thread-multi-2level INSTALLMAN1DIR=/sw/share/man/man1 INSTALLMAN3DIR=/sw/share/man/man3 INSTALLSITEMAN1DIR=/sw/share/man/man1 INSTALLSITEMAN3DIR=/sw/share/man/man3 INSTALLBIN=/sw/bin INSTALLSITEBIN=/sw/bin INSTALLSCRIPT=/sw/bin /sw/src/fink.build/svn-swig-pm588-1.7.8-1/subversion-1.7.8/subversion/bindings/swig/perl/native /sw/src/fink.build/svn-swig-pm588-1.7.8-1/subversion-1.7.8 Writing Makefile for SVN::_Core Writing MYMETA.yml and MYMETA.json Writing Makefile.client for SVN::_Client Writing MYMETA.yml and MYMETA.json Writing Makefile.delta for SVN::_Delta Writing MYMETA.yml and MYMETA.json Writing Makefile.fs for SVN::_Fs Writing MYMETA.yml and MYMETA.json Writing Makefile.ra for SVN::_Ra Writing MYMETA.yml and MYMETA.json Writing Makefile.repos for SVN::_Repos Writing MYMETA.yml and MYMETA.json Writing Makefile.wc for SVN::_Wc Writing MYMETA.yml and MYMETA.json make PERL=$PERL FULLPERL=$PERL ABSPERL=$PERL cp ../../../../../subversion/bindings/swig/perl/native/Delta.pm blib/lib/SVN/Delta.pm cp ../../../../../subversion/bindings/swig/perl/native/Ra.pm blib/lib/SVN/Ra.pm cp ../../../../../subversion/bindings/swig/perl/native/Wc.pm blib/lib/SVN/Wc.pm cp ../../../../../subversion/bindings/swig/perl/native/Base.pm blib/lib/SVN/Base.pm cp ../../../../../subversion/bindings/swig/perl/native/Core.pm blib/lib/SVN/Core.pm cp ../../../../../subversion/bindings/swig/perl/native/Repos.pm blib/lib/SVN/Repos.pm cp ../../../../../subversion/bindings/swig/perl/native/Fs.pm blib/lib/SVN/Fs.pm cp ../../../../../subversion/bindings/swig/perl/native/Client.pm blib/lib/SVN/Client.pm cc -c -I/sw/include/apache2 -I/sw/include/apache2 -I/sw/include -I../../../../../subversion/bindings/swig/perl/libsvn_swig_perl -I../../../../../subversion/include -I../../../../../subversion -I../../../../../subversion/bindings/swig -g -g -O2 -g -O2 -Werror=implicit-function-declaration -g -pipe -fno-common -DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing -Wdeclaration-after-statement -I/usr/local/include -O3 -DVERSION=\\ -DXS_VERSION=\\ -I/System/Library/Perl/5.8.8/darwin-thread-multi-2level/CORE -I/sw/include -DDARWIN -DSIGPROCMASK_SETS_THREAD_MASK -no-cpp-precomp core.c cc1: error: unrecognized command line option -Werror=implicit-function-declaration This is the same failure I have reported on 2012-10-25 for svn-swig-pm588-1.7.7-1. TIA and Happy New Year, Dominique -- Master Java SE, Java EE, Eclipse, Spring, Hibernate, JavaScript, jQuery and much more. Keep your Java skills current with LearnJavaNow - 200+ hours of step-by-step video tutorials by Java experts. SALE $49.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122612 ___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] Missing Dependency in biopython-py27
biopython-py27 seems to be missing a dependency on flex. Installing biopython-py27 (fink install biopython-py27) failed with the error below when I did a clean install of Fink after upgrading to Mountain Lion. This was fixed by installing flex (fink install flex). Best, Josh - gcc -L/sw/lib -bundle -L/sw/lib/python2.7/config -lpython2.7 -L/sw/lib -L/sw/lib -I/sw/include build/temp.macosx-10.8-x86_64-2.7/Bio/PDB/mmCIF/lex.yy.o build/temp.macosx-10.8-x86_64-2.7/Bio/PDB/mmCIF/MMCIFlexmodule.o -lfl -o build/lib.macosx-10.8-x86_64-2.7/Bio/PDB/mmCIF/MMCIFlex.so ld: library not found for -lfl clang: error: linker command failed with exit code 1 (use -v to see invocation) error: command 'gcc' failed with exit status 1 ### execution of /sw/bin/python2.7 failed, exit code 1 ### execution of /tmp/fink.oKCSM failed, exit code 1 Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-biopython-py27-1.59-1 (Reading database ... 128542 files and directories currently installed.) Removing fink-buildlock-biopython-py27-1.59-1 ... Failed: phase compiling: biopython-py27-1.59-1 failed . . . Also include the following system information: Package manager version: 0.34.4 Distribution version: selfupdate-rsync Thu Jan 3 18:57:20 2013, 10.8, x86_64 Trees: local/main stable/main Xcode.app: 4.5.2 Xcode command-line tools: 4.5.0.0.1.1249367152 Max. Fink build jobs: 1 - P.S. Another problem I encountered when installing biopython-py27 is the need to deal with the fact that X11/Xlib.h is not where it used to be (since XQuartz puts it in a different place than Apple X11 had it). Unfortunately I didn't think to save the error message. This URL explains the problem and gives several solutions http://stackoverflow.com/questions/11465258/xlib-h-not-found-when-building-graphviz-on-mac-os-x-10-8-mountain-lion. Creating a symlink as follows worked for me: sudo ln -s /opt/X11/include/X11 /usr/local/include/X11 -- Master Java SE, Java EE, Eclipse, Spring, Hibernate, JavaScript, jQuery and much more. Keep your Java skills current with LearnJavaNow - 200+ hours of step-by-step video tutorials by Java experts. SALE $49.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122612 ___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] the problem with installing ccp4
Hi, I use : fink selfupdate fink update-all for ccp4 : .. wall clock time: 4 minutes 9.43 seconds (249.43 seconds total) cd exe cp phaser $CCP4/bin/. cd $CCP4 # rapper manual install if [[ -x src/rapper/bin/rapper ]]; then cp src/rapper/bin/rapper $CCP4/bin/. cp src/rapper/lib/libcord.1.0.3.dylib $CCP4/lib/libcord.1.dylib cp src/rapper/lib/libgc.1.0.3.dylib $CCP4/lib/libgc.1.dylib cp src/rapper/lib/libxml2.2.dylib $CCP4/lib/libxml2.2.dylib /bin/rm -rf src/rapper/lib/*.dylib mkdir -p share/rapper cp src/rapper/LOOP/params.xml share/rapper/. cp -R src/rapper/data share/rapper/. fi * export DYLD_LIBRARY_PATH=$CLIB* * cd $CLIB/libccp4* * gfortran -m64 -fno-second-underscore -O2 -fno-second-underscore -L$CLIB -o data/fontpack data/fontpack.o -lccp4f -lccp4c* * cd data* * ./fontpack* *At line 12 of file data/fontpack.f (unit = 10, file = 'fort.10')* *Fortran runtime error: End of file* Backtrace for this error: + 0 libgfortran.3.dylib 0x0001029d1e93 _gfortrani_show_backtrace + 35 ### execution of /tmp/fink.2HF5a failed, exit code 2 ### execution of /tmp/fink.Ih6Jf failed, exit code 2 Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-ccp4-6.3.0-5 (Reading database ... 309886 files and directories currently installed.) Removing fink-buildlock-ccp4-6.3.0-5 ... Reading buildlock packages... /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/sci/gpp4-dev_1.2.0-31_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/sci/ssm-dev_0.1-31_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/sci/mmdb-dev_1.23.2-31_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/sci/clipper_2.1-31_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/sci/clipper-dev_2.1-31_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/languages/python_2.7.3-1_darwin-x86_64.deb Selecting previously deselected package gpp4-dev. (Reading database ... 309885 files and directories currently installed.) Unpacking gpp4-dev (from .../gpp4-dev_1.2.0-31_darwin-x86_64.deb) ... Selecting previously deselected package ssm-dev. Unpacking ssm-dev (from .../ssm-dev_0.1-31_darwin-x86_64.deb) ... Selecting previously deselected package mmdb-dev. Unpacking mmdb-dev (from .../mmdb-dev_1.23.2-31_darwin-x86_64.deb) ... Selecting previously deselected package clipper. Unpacking clipper (from .../clipper_2.1-31_darwin-x86_64.deb) ... Selecting previously deselected package clipper-dev. Unpacking clipper-dev (from .../clipper-dev_2.1-31_darwin-x86_64.deb) ... Selecting previously deselected package python. Unpacking python (from .../python_2.7.3-1_darwin-x86_64.deb) ... Setting up gpp4-dev (1.2.0-31) ... Clearing dependency_libs of .la files being installed Setting up ssm-dev (0.1-31) ... Clearing dependency_libs of .la files being installed Setting up mmdb-dev (1.23.2-31) ... Clearing dependency_libs of .la files being installed Setting up clipper (2.1-31) ... Setting up clipper-dev (2.1-31) ... Clearing dependency_libs of .la files being installed Setting up python (2.7.3-1) ... .. Package manager version: 0.34.4 Distribution version: selfupdate-rsync Wed Jan 9 23:24:23 2013, 10.6, x86_64 Trees: local/main stable/main stable/crypto unstable/main unstable/crypto Xcode.app: 3.2.6 Xcode command-line tools: 3.2.6 ccp4-6.3.0-5 is set to build with only one job. Thanks, Shih-Kai Chou -- Master Java SE, Java EE, Eclipse, Spring, Hibernate, JavaScript, jQuery and much more. Keep your Java skills current with LearnJavaNow - 200+ hours of step-by-step video tutorials by Java experts. SALE $49.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122612 ___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] Missing Dependency in biopython-py27
On 1/9/13 1:19 AM, Josh Granek wrote: biopython-py27 seems to be missing a dependency on flex. Installing biopython-py27 (fink install biopython-py27) failed with the error below when I did a clean install of Fink after upgrading to Mountain Lion. This was fixed by installing flex (fink install flex). Best, Josh - gcc -L/sw/lib -bundle -L/sw/lib/python2.7/config -lpython2.7 -L/sw/lib -L/sw/lib -I/sw/include build/temp.macosx-10.8-x86_64-2.7/Bio/PDB/mmCIF/lex.yy.o build/temp.macosx-10.8-x86_64-2.7/Bio/PDB/mmCIF/MMCIFlexmodule.o -lfl -o build/lib.macosx-10.8-x86_64-2.7/Bio/PDB/mmCIF/MMCIFlex.so ld: library not found for -lfl clang: error: linker command failed with exit code 1 (use -v to see invocation) error: command 'gcc' failed with exit status 1 ### execution of /sw/bin/python2.7 failed, exit code 1 ### execution of /tmp/fink.oKCSM failed, exit code 1 Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-biopython-py27-1.59-1 (Reading database ... 128542 files and directories currently installed.) Removing fink-buildlock-biopython-py27-1.59-1 ... Failed: phase compiling: biopython-py27-1.59-1 failed . . . Also include the following system information: Package manager version: 0.34.4 Distribution version: selfupdate-rsync Thu Jan 3 18:57:20 2013, 10.8, x86_64 Trees: local/main stable/main Xcode.app: 4.5.2 Xcode command-line tools: 4.5.0.0.1.1249367152 Max. Fink build jobs: 1 - P.S. Another problem I encountered when installing biopython-py27 is the need to deal with the fact that X11/Xlib.h is not where it used to be (since XQuartz puts it in a different place than Apple X11 had it). Unfortunately I didn't think to save the error message. This URL explains the problem and gives several solutions http://stackoverflow.com/questions/11465258/xlib-h-not-found-when-building-graphviz-on-mac-os-x-10-8-mountain-lion. Creating a symlink as follows worked for me: sudo ln -s /opt/X11/include/X11 /usr/local/include/X11 That symlink would be totally unacceptable in a Fink package, and we DO NOT advocate doing that. Anybody who does voids their warranty for help with build issues. Unmotivated upstreams have been relying for a while on the deprecated /usr/include/X11 - /usr/X11/include/X11 symlink, which is now gone in Xquartz, instead of looking explicitly for /usr/X11/include. And sometimes packages even let you specify the X include path but they still rely on that symlink. Depending on the package, even something as simple as adding /usr/X11/include (since that works on both 10.7 and 10.8) to the CPPFLAGS may do the job. -- Alexander Hansen, Ph.D. Fink User Liaison My package updates: http://finkakh.wordpress.com/ -- Master Java SE, Java EE, Eclipse, Spring, Hibernate, JavaScript, jQuery and much more. Keep your Java skills current with LearnJavaNow - 200+ hours of step-by-step video tutorials by Java experts. SALE $49.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122612 ___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] the problem with installing ccp4
On 1/9/13 9:41 AM, Shih-Kai Chou wrote: Hi, I use : fink selfupdate fink update-all for ccp4 : .. wall clock time: 4 minutes 9.43 seconds (249.43 seconds total) cd exe cp phaser $CCP4/bin/. cd $CCP4 # rapper manual install if [[ -x src/rapper/bin/rapper ]]; then cp src/rapper/bin/rapper $CCP4/bin/. cp src/rapper/lib/libcord.1.0.3.dylib $CCP4/lib/libcord.1.dylib cp src/rapper/lib/libgc.1.0.3.dylib $CCP4/lib/libgc.1.dylib cp src/rapper/lib/libxml2.2.dylib $CCP4/lib/libxml2.2.dylib /bin/rm -rf src/rapper/lib/*.dylib mkdir -p share/rapper cp src/rapper/LOOP/params.xml share/rapper/. cp -R src/rapper/data share/rapper/. fi * export DYLD_LIBRARY_PATH=$CLIB* * cd $CLIB/libccp4* * gfortran -m64 -fno-second-underscore -O2 -fno-second-underscore -L$CLIB -o data/fontpack data/fontpack.o -lccp4f -lccp4c* * cd data* * ./fontpack* *At line 12 of file data/fontpack.f (unit = 10, file = 'fort.10')* *Fortran runtime error: End of file* Backtrace for this error: + 0 libgfortran.3.dylib 0x0001029d1e93 _gfortrani_show_backtrace + 35 snip .. Package manager version: 0.34.4 Distribution version: selfupdate-rsync Wed Jan 9 23:24:23 2013, 10.6, x86_64 Trees: local/main stable/main stable/crypto unstable/main unstable/crypto Xcode.app: 3.2.6 Xcode command-line tools: 3.2.6 ccp4-6.3.0-5 is set to build with only one job. Thanks, Shih-Kai Chou What do you get from the following command: which gfortran -- Alexander Hansen, Ph.D. Fink User Liaison My package updates: http://finkakh.wordpress.com/ -- Master Java SE, Java EE, Eclipse, Spring, Hibernate, JavaScript, jQuery and much more. Keep your Java skills current with LearnJavaNow - 200+ hours of step-by-step video tutorials by Java experts. SALE $49.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122612 ___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] Missing Dependency in biopython-py27
On 1/9/13 1:19 AM, Josh Granek wrote: biopython-py27 seems to be missing a dependency on flex. Installing biopython-py27 (fink install biopython-py27) failed with the error below when I did a clean install of Fink after upgrading to Mountain Lion. This was fixed by installing flex (fink install flex). Best, Josh - gcc -L/sw/lib -bundle -L/sw/lib/python2.7/config -lpython2.7 -L/sw/lib -L/sw/lib -I/sw/include build/temp.macosx-10.8-x86_64-2.7/Bio/PDB/mmCIF/lex.yy.o build/temp.macosx-10.8-x86_64-2.7/Bio/PDB/mmCIF/MMCIFlexmodule.o -lfl -o build/lib.macosx-10.8-x86_64-2.7/Bio/PDB/mmCIF/MMCIFlex.so ld: library not found for -lfl clang: error: linker command failed with exit code 1 (use -v to see invocation) error: command 'gcc' failed with exit status 1 ### execution of /sw/bin/python2.7 failed, exit code 1 ### execution of /tmp/fink.oKCSM failed, exit code 1 Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-biopython-py27-1.59-1 (Reading database ... 128542 files and directories currently installed.) Removing fink-buildlock-biopython-py27-1.59-1 ... Failed: phase compiling: biopython-py27-1.59-1 failed Yup. Apparently Apple used to have a /usr/lib/libfl.a, but it went away on Mountain Lion (though it's still in the 10.7 SDK). The package potentially builds differently on 10.7 whether or not Fink's flex is installed, and it needs to be coerced into using the same flex everywhere. . . . Also include the following system information: Package manager version: 0.34.4 Distribution version: selfupdate-rsync Thu Jan 3 18:57:20 2013, 10.8, x86_64 Trees: local/main stable/main Xcode.app: 4.5.2 Xcode command-line tools: 4.5.0.0.1.1249367152 Max. Fink build jobs: 1 - P.S. Another problem I encountered when installing biopython-py27 is the need to deal with the fact that X11/Xlib.h is not where it used to be (since XQuartz puts it in a different place than Apple X11 had it). Unfortunately I didn't think to save the error message. This URL explains the problem and gives several solutions http://stackoverflow.com/questions/11465258/xlib-h-not-found-when-building-graphviz-on-mac-os-x-10-8-mountain-lion. Creating a symlink as follows worked for me: sudo ln -s /opt/X11/include/X11 /usr/local/include/X11 The error must have been in some other package. I don't see this with biopython-py* on 10.8. -- Alexander Hansen, Ph.D. Fink User Liaison My package updates: http://finkakh.wordpress.com/ -- Master Java SE, Java EE, Eclipse, Spring, Hibernate, JavaScript, jQuery and much more. Keep your Java skills current with LearnJavaNow - 200+ hours of step-by-step video tutorials by Java experts. SALE $49.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122612 ___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] the problem with installing ccp4
Hi, which gfortran /sw/bin/gfortran Actually, I have installed another fortran compiler! (I think that is the newest fortran compiler called gfortran, so I do it.) But I forgot which directory is the one I installed? It looks like the new gfortran I installed replaced the fink one! Thanks, Shih-Kai Chou On Thu, Jan 10, 2013 at 7:38 AM, Alexander Hansen alexanderk.han...@gmail.com wrote: On 1/9/13 9:41 AM, Shih-Kai Chou wrote: Hi, I use : fink selfupdate fink update-all for ccp4 : .. wall clock time: 4 minutes 9.43 seconds (249.43 seconds total) cd exe cp phaser $CCP4/bin/. cd $CCP4 # rapper manual install if [[ -x src/rapper/bin/rapper ]]; then cp src/rapper/bin/rapper $CCP4/bin/. cp src/rapper/lib/libcord.1.0.3.dylib $CCP4/lib/libcord.1.dylib cp src/rapper/lib/libgc.1.0.3.dylib $CCP4/lib/libgc.1.dylib cp src/rapper/lib/libxml2.2.dylib $CCP4/lib/libxml2.2.dylib /bin/rm -rf src/rapper/lib/*.dylib mkdir -p share/rapper cp src/rapper/LOOP/params.xml share/rapper/. cp -R src/rapper/data share/rapper/. fi * export DYLD_LIBRARY_PATH=$CLIB* * cd $CLIB/libccp4* * gfortran -m64 -fno-second-underscore -O2 -fno-second-underscore -L$CLIB -o data/fontpack data/fontpack.o -lccp4f -lccp4c* * cd data* * ./fontpack* *At line 12 of file data/fontpack.f (unit = 10, file = 'fort.10')* *Fortran runtime error: End of file* Backtrace for this error: + 0 libgfortran.3.dylib 0x0001029d1e93 _gfortrani_show_backtrace + 35 snip .. Package manager version: 0.34.4 Distribution version: selfupdate-rsync Wed Jan 9 23:24:23 2013, 10.6, x86_64 Trees: local/main stable/main stable/crypto unstable/main unstable/crypto Xcode.app: 3.2.6 Xcode command-line tools: 3.2.6 ccp4-6.3.0-5 is set to build with only one job. Thanks, Shih-Kai Chou What do you get from the following command: which gfortran -- Alexander Hansen, Ph.D. Fink User Liaison My package updates: http://finkakh.wordpress.com/ -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnmore_122712___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] the problem with installing ccp4
Normally fink's gfortran shouldn't get overwritten (unless you switch versions within Fink), but let's verify that with the following command: /sw/bin/gfortran --version Also, let's verify the PATH which is being used in your build: fink dumpinfo -ePATH ccp4 On 1/9/13 7:18 PM, Shih-Kai Chou wrote: Hi, which gfortran /sw/bin/gfortran Actually, I have installed another fortran compiler! (I think that is the newest fortran compiler called gfortran, so I do it.) But I forgot which directory is the one I installed? It looks like the new gfortran I installed replaced the fink one! Thanks, Shih-Kai Chou On Thu, Jan 10, 2013 at 7:38 AM, Alexander Hansen alexanderk.han...@gmail.com mailto:alexanderk.han...@gmail.com wrote: On 1/9/13 9:41 AM, Shih-Kai Chou wrote: Hi, I use : fink selfupdate fink update-all for ccp4 : .. wall clock time: 4 minutes 9.43 seconds (249.43 seconds total) cd exe cp phaser $CCP4/bin/. cd $CCP4 # rapper manual install if [[ -x src/rapper/bin/rapper ]]; then cp src/rapper/bin/rapper $CCP4/bin/. cp src/rapper/lib/libcord.1.0.3.dylib $CCP4/lib/libcord.1.dylib cp src/rapper/lib/libgc.1.0.3.dylib $CCP4/lib/libgc.1.dylib cp src/rapper/lib/libxml2.2.dylib $CCP4/lib/libxml2.2.dylib /bin/rm -rf src/rapper/lib/*.dylib mkdir -p share/rapper cp src/rapper/LOOP/params.xml share/rapper/. cp -R src/rapper/data share/rapper/. fi * export DYLD_LIBRARY_PATH=$CLIB* * cd $CLIB/libccp4* * gfortran -m64 -fno-second-underscore -O2 -fno-second-underscore -L$CLIB -o data/fontpack data/fontpack.o -lccp4f -lccp4c* * cd data* * ./fontpack* *At line 12 of file data/fontpack.f (unit = 10, file = 'fort.10')* *Fortran runtime error: End of file* Backtrace for this error: + 0 libgfortran.3.dylib 0x0001029d1e93 _gfortrani_show_backtrace + 35 snip .. Package manager version: 0.34.4 Distribution version: selfupdate-rsync Wed Jan 9 23:24:23 2013, 10.6, x86_64 Trees: local/main stable/main stable/crypto unstable/main unstable/crypto Xcode.app: 3.2.6 Xcode command-line tools: 3.2.6 ccp4-6.3.0-5 is set to build with only one job. Thanks, Shih-Kai Chou What do you get from the following command: which gfortran -- Alexander Hansen, Ph.D. Fink User Liaison My package updates: http://finkakh.wordpress.com/ -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnmore_122712 ___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] the problem with installing ccp4
Hi, Thank you. /sw/bin/gfortran --version GNU Fortran (GCC) 4.7.2 Copyright (C) 2012 Free Software Foundation, Inc. GNU Fortran comes with NO WARRANTY, to the extent permitted by law. You may redistribute copies of GNU Fortran under the terms of the GNU General Public License. For more information about these matters, see the file named COPYING fink dumpinfo -ePATH ccp4 PATH=/sw/var/lib/fink/path-prefix-clang:/sw/bin:/sw/sbin:/bin:/usr/bin:/sbin:/usr/sbin:/usr/X11R6/bin:/sw/share/xtal/ccp4-6.2.0/etc:/sw/share/xtal/ccp4-6.2.0/bin:/sw/share/xtal/ccp4-6.2.0/ccp4i/bin:/sw/share/xtal/ccp4-6.2.0/share/dbccp4i/bin:/sw/share/xtal/ccp4-6.2.0/share/XIAROOT/xia2/Applications:/sw/share/tinker/bin Thanks, Shih-Kai Chou On Thu, Jan 10, 2013 at 10:34 AM, Alexander Hansen alexanderk.han...@gmail.com wrote: Normally fink's gfortran shouldn't get overwritten (unless you switch versions within Fink), but let's verify that with the following command: /sw/bin/gfortran --version Also, let's verify the PATH which is being used in your build: fink dumpinfo -ePATH ccp4 On 1/9/13 7:18 PM, Shih-Kai Chou wrote: Hi, which gfortran /sw/bin/gfortran Actually, I have installed another fortran compiler! (I think that is the newest fortran compiler called gfortran, so I do it.) But I forgot which directory is the one I installed? It looks like the new gfortran I installed replaced the fink one! Thanks, Shih-Kai Chou On Thu, Jan 10, 2013 at 7:38 AM, Alexander Hansen alexanderk.han...@gmail.com mailto:alexanderk.han...@gmail.com wrote: On 1/9/13 9:41 AM, Shih-Kai Chou wrote: Hi, I use : fink selfupdate fink update-all for ccp4 : .. wall clock time: 4 minutes 9.43 seconds (249.43 seconds total) cd exe cp phaser $CCP4/bin/. cd $CCP4 # rapper manual install if [[ -x src/rapper/bin/rapper ]]; then cp src/rapper/bin/rapper $CCP4/bin/. cp src/rapper/lib/libcord.1.0.3.dylib $CCP4/lib/libcord.1.dylib cp src/rapper/lib/libgc.1.0.3.dylib $CCP4/lib/libgc.1.dylib cp src/rapper/lib/libxml2.2.dylib $CCP4/lib/libxml2.2.dylib /bin/rm -rf src/rapper/lib/*.dylib mkdir -p share/rapper cp src/rapper/LOOP/params.xml share/rapper/. cp -R src/rapper/data share/rapper/. fi * export DYLD_LIBRARY_PATH=$CLIB* * cd $CLIB/libccp4* * gfortran -m64 -fno-second-underscore -O2 -fno-second-underscore -L$CLIB -o data/fontpack data/fontpack.o -lccp4f -lccp4c* * cd data* * ./fontpack* *At line 12 of file data/fontpack.f (unit = 10, file = 'fort.10')* *Fortran runtime error: End of file* Backtrace for this error: + 0 libgfortran.3.dylib 0x0001029d1e93 _gfortrani_show_backtrace + 35 snip .. Package manager version: 0.34.4 Distribution version: selfupdate-rsync Wed Jan 9 23:24:23 2013, 10.6, x86_64 Trees: local/main stable/main stable/crypto unstable/main unstable/crypto Xcode.app: 3.2.6 Xcode command-line tools: 3.2.6 ccp4-6.3.0-5 is set to build with only one job. Thanks, Shih-Kai Chou What do you get from the following command: which gfortran -- Alexander Hansen, Ph.D. Fink User Liaison My package updates: http://finkakh.wordpress.com/ -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnmore_122712___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] the problem with installing ccp4
Those look normal. I will check whether I can replicate your failure on a 10.6 setup with the same Xcode. On 1/9/13 7:40 PM, Shih-Kai Chou wrote: Hi, Thank you. /sw/bin/gfortran --version GNU Fortran (GCC) 4.7.2 Copyright (C) 2012 Free Software Foundation, Inc. GNU Fortran comes with NO WARRANTY, to the extent permitted by law. You may redistribute copies of GNU Fortran under the terms of the GNU General Public License. For more information about these matters, see the file named COPYING fink dumpinfo -ePATH ccp4 PATH=/sw/var/lib/fink/path-prefix-clang:/sw/bin:/sw/sbin:/bin:/usr/bin:/sbin:/usr/sbin:/usr/X11R6/bin:/sw/share/xtal/ccp4-6.2.0/etc:/sw/share/xtal/ccp4-6.2.0/bin:/sw/share/xtal/ccp4-6.2.0/ccp4i/bin:/sw/share/xtal/ccp4-6.2.0/share/dbccp4i/bin:/sw/share/xtal/ccp4-6.2.0/share/XIAROOT/xia2/Applications:/sw/share/tinker/bin Thanks, Shih-Kai Chou On Thu, Jan 10, 2013 at 10:34 AM, Alexander Hansen alexanderk.han...@gmail.com mailto:alexanderk.han...@gmail.com wrote: Normally fink's gfortran shouldn't get overwritten (unless you switch versions within Fink), but let's verify that with the following command: /sw/bin/gfortran --version Also, let's verify the PATH which is being used in your build: fink dumpinfo -ePATH ccp4 On 1/9/13 7:18 PM, Shih-Kai Chou wrote: Hi, which gfortran /sw/bin/gfortran Actually, I have installed another fortran compiler! (I think that is the newest fortran compiler called gfortran, so I do it.) But I forgot which directory is the one I installed? It looks like the new gfortran I installed replaced the fink one! Thanks, Shih-Kai Chou On Thu, Jan 10, 2013 at 7:38 AM, Alexander Hansen alexanderk.han...@gmail.com mailto:alexanderk.han...@gmail.com mailto:alexanderk.han...@gmail.com mailto:alexanderk.han...@gmail.com wrote: On 1/9/13 9:41 AM, Shih-Kai Chou wrote: Hi, I use : fink selfupdate fink update-all for ccp4 : .. wall clock time: 4 minutes 9.43 seconds (249.43 seconds total) cd exe cp phaser $CCP4/bin/. cd $CCP4 # rapper manual install if [[ -x src/rapper/bin/rapper ]]; then cp src/rapper/bin/rapper $CCP4/bin/. cp src/rapper/lib/libcord.1.0.3.dylib $CCP4/lib/libcord.1.dylib cp src/rapper/lib/libgc.1.0.3.dylib $CCP4/lib/libgc.1.dylib cp src/rapper/lib/libxml2.2.dylib $CCP4/lib/libxml2.2.dylib /bin/rm -rf src/rapper/lib/*.dylib mkdir -p share/rapper cp src/rapper/LOOP/params.xml share/rapper/. cp -R src/rapper/data share/rapper/. fi * export DYLD_LIBRARY_PATH=$CLIB* * cd $CLIB/libccp4* * gfortran -m64 -fno-second-underscore -O2 -fno-second-underscore -L$CLIB -o data/fontpack data/fontpack.o -lccp4f -lccp4c* * cd data* * ./fontpack* *At line 12 of file data/fontpack.f (unit = 10, file = 'fort.10')* *Fortran runtime error: End of file* Backtrace for this error: + 0 libgfortran.3.dylib 0x0001029d1e93 _gfortrani_show_backtrace + 35 snip .. Package manager version: 0.34.4 Distribution version: selfupdate-rsync Wed Jan 9 23:24:23 2013, 10.6, x86_64 Trees: local/main stable/main stable/crypto unstable/main unstable/crypto Xcode.app: 3.2.6 Xcode command-line tools: 3.2.6 ccp4-6.3.0-5 is set to build with only one job. Thanks, Shih-Kai Chou What do you get from the following command: which gfortran -- Alexander Hansen, Ph.D. Fink User Liaison My package updates: http://finkakh.wordpress.com/ -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
