On 7/23/13 7:26 AM, sta...@ebi.ac.uk wrote: >> On 7/23/13 5:49 AM, sta...@ebi.ac.uk wrote: >>> sorry for the omission of the subject line in the original email - >>> please >>> see below >>> >>> >>> >>> >>> >>> Hi Finkers, >>> >>> I have trouble setting up CCP4 on my Mac - I've been following the steps >>> outlined here, >>> http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Installing_CCP4_on_OS_X#Installing_from_source_code >>> >>> i.e. 'fink selfupdate', and then 'fink install ccp4' >>> >>> the installation runs for a long time (like two hours) and then >>> terminates >>> with an error connected to the configuration of pointless -- see below >>> >>> any help much appreciated! >>> >>> >>> >>> >>> [......................] >>> cd src/pointless >>> ./configure --with-clipper=$CCP4 --with-fftw=$CCP4 >>> FFTW_LIBS="-L$CCP4/lib -lrfftw -lfftw" >>> FFTW_CXXFLAGS="-I$CCP4/lib/fftw/fftw -I$CCP4/lib/fftw/rfftw >>> -I$CCP4/include -I$CCP4/lib/libccp4 -I$CCP4/lib/mmdb" >>> --with-ccp4=$CCP4 CXXFLAGS="-O2 " >>> --with-cctbx=$CCP4/lib/cctbx/cctbx_sources >>> --with-cctbx-build=$CCP4/lib/cctbx/cctbx_build CXXFLAGS="-O2 " >>> CXXFLAGS="-O2 " --prefix=$CCP4 --bindir=$CCP4/bin >>> LDFLAGS=-L$CCP4/lib CXX="g++ -arch i386" CC="gcc -arch i386" >>> checking for a BSD-compatible install... /usr/bin/install -c >>> checking whether build environment is sane... yes >>> checking for a thread-safe mkdir -p... ./install-sh -c -d >>> checking for gawk... no >>> checking for mawk... no >>> checking for nawk... no >>> checking for awk... awk >>> checking whether make sets $(MAKE)... yes >>> checking whether to enable maintainer-specific portions of Makefiles... >>> no >>> checking whether the Fortran compiler works... no >>> configure: error: in >>> `/sw/src/fink.build/ccp4-6.3.0-6/ccp4-6.3.0/src/pointless': >>> configure: error: Fortran compiler cannot create executables >>> See `config.log' for more details. >>> ### execution of /tmp/fink.tYzGA failed, exit code 77 >>> ### execution of /tmp/fink.mJbU6 failed, exit code 77 >>> Removing runtime build-lock... >>> Removing build-lock package... >>> /sw/bin/dpkg-lockwait -r fink-buildlock-ccp4-6.3.0-6 >>> (Reading database ... 15606 files and directories currently installed.) >>> Removing fink-buildlock-ccp4-6.3.0-6 ... >>> Failed: phase installing: ccp4-6.3.0-6 failed >>> >>> Before reporting any errors, please run "fink selfupdate" and try again. >>> >>> If you continue to have issues, please check to see if the FAQ on Fink's >>> website solves the problem. If not, ask on one (not both, please) of >>> these mailing lists: >>> >>> [...] >>> >>> Package manager version: 0.35.1 >>> Distribution version: selfupdate-rsync Mon Jul 22 17:37:57 2013, 10.6, >>> i386 >>> Trees: local/main stable/main stable/crypto >>> Xcode.app: 4.2 >>> Xcode command-line tools: 4.2 >>> ccp4-6.3.0-6 is set to build with only one job. >>> >>> >>> >>> >>> >> >> The two hours, at least, weren't pointless. :-) That time was spent >> successfully building dependencies. >> >> The immediate problem is the following: >> >> > checking whether the Fortran compiler works... no >> >> What do you get if you run >> >> which gfortran >> >> in a terminal window? If it isn't /sw/bin/gfortran that could well be >> the problem. >> -- >> Alexander Hansen, Ph.D. >> Fink User Liaison >> My package updates: http://finkakh.wordpress.com/ >> > > > Thanks Alexander, > > this seems to hit close to the problem: > > which gfortran gets me > /opt/local/bin/gfortran > > and > > gfortran -v > Using built-in specs. > Target: x86_64-apple-darwin10 > Configured with: ../gcc-4.4.7/configure --prefix=/opt/local > --build=x86_64-apple-darwin10 > --enable-languages=c,c++,objc,obj-c++,java,fortran > --libdir=/opt/local/lib/gcc44 --includedir=/opt/local/include/gcc44 > --infodir=/opt/local/share/info --mandir=/opt/local/share/man > --with-local-prefix=/opt/local --with-system-zlib --disable-nls > --program-suffix=-mp-4.4 > --with-gxx-include-dir=/opt/local/include/gcc44/c++/ --with-gmp=/opt/local > --with-mpfr=/opt/local --enable-stage1-checking --disable-multilib > --with-as=/opt/local/bin/as --with-ld=/opt/local/bin/ld > --with-ar=/opt/local/bin/ar --enable-fully-dynamic-string > Thread model: posix > gcc version 4.4.7 (GCC) > > > and there is no gfortran in /sw/bin/ > > I tried fink install gfortran but it did not work .. And how would i > change the default version of gfortran after installing it? > > Thanks, > ben >
Yeah, an older version of gfortran from Macports using a different architecture than what your Fink tree is set for (x86_64 vs. i386) is not going to work. I'd recommend temporarily turning off the Macports initialization in your .profile (or wherever it's set up) and starting a new terminal session to do your Fink build. Once you've started the new terminal you can restore your settings. A Fink gfortran executable should have been installed as part of the gcc47 package, though, and since that's an explicit dependency for cpp4 it should already be installed. Check whether "dpkg -L gcc47" lists /sw/bin/gfortran. If it does, try "fink reinstall gcc47". If it doesn't, then your gcc47 might have gotten misbuilt somehow, so you could try "fink rebuild gcc47". Which version would be the default is given by the order of the directory entries in your PATH environment variable. -- Alexander Hansen, Ph.D. Fink User Liaison My package updates: http://finkakh.wordpress.com/ ------------------------------------------------------------------------------ See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk _______________________________________________ Fink-beginners mailing list Fink-beginners@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.beginners Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-beginners
