On 7/23/13 2:32 PM, sta...@ebi.ac.uk wrote: >> On 7/23/13 11:10 AM, sta...@ebi.ac.uk wrote: >>>> 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/ >>>> >>> >>> >>> >>> Hi, >>> >>> I re-installed gcc47 to get a sane gfortran version and deactivated >>> MacPorts in .bash_profile (see below), and fired up a new shell - it >>> still >>> crashes at the same spot, >>> >>> 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.xTX95 failed, exit code 77 >>> ### execution of /tmp/fink.iVJwP 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: >>> >>> The Fink Users List <fink-us...@lists.sourceforge.net> >>> The Fink Beginners List <fink-beginners@lists.sourceforge.net>, >>> >>> with a carbon copy to the maintainer: >>> >>> W. G. Scott <wgsc...@users.sourceforge.net> >>> >>> Note that this is preferable to emailing just the maintainer directly, >>> since most fink package maintainers do not have access to all possible >>> hardware and software configurations. >>> >>> Please try to include the complete error message in your report. This >>> generally consists of a compiler line starting with e.g. "gcc" or "g++" >>> followed by the actual error output from the compiler. >>> >>> Also include the following system information: >>> Package manager version: 0.35.1 >>> Distribution version: selfupdate-rsync Tue Jul 23 17:22:38 2013, 10.6, >>> i386 >>> Trees: local/main stable/main stable/crypto unstable/main >>> unstable/crypto >>> Xcode.app: 4.2 >>> Xcode command-line tools: 4.2 >>> ccp4-6.3.0-6 is set to build with only one job. >>> >>> >>> >>> >>> that's my gfortran version now: >>> >>> >>> bash-3.2$ which gfortran >>> /sw/bin/gfortran >>> >>> bash-3.2$ /sw/bin/gfortran -v >>> Using built-in specs. >>> COLLECT_GCC=/sw/bin/gfortran >>> COLLECT_LTO_WRAPPER=/sw/lib/gcc4.7/libexec/gcc/i386-apple-darwin10.8.0/4.7.3/lto-wrapper >>> Target: i386-apple-darwin10.8.0 >>> Configured with: ../gcc-4.7.3/configure --prefix=/sw >>> --prefix=/sw/lib/gcc4.7 --mandir=/sw/share/man >>> --infodir=/sw/lib/gcc4.7/info >>> --enable-languages=c,c++,fortran,lto,objc,obj-c++,java --with-gmp=/sw >>> --with-libiconv-prefix=/sw --with-ppl=/sw --with-cloog=/sw >>> --with-mpc=/sw >>> --with-system-zlib --x-includes=/usr/X11R6/include >>> --x-libraries=/usr/X11R6/lib --program-suffix=-fsf-4.7 >>> --enable-cloog-backend=isl >>> Thread model: posix >>> gcc version 4.7.3 (GCC) >>> >>> >>> and here's my ~/.bash_profile: >>> >>> >>> bash-3.2$ cat .bash_profile >>> >>> # Setting PATH for MacPython 2.6 >>> # The orginal version is saved in .bash_profile.pysave >>> PATH="/Library/Frameworks/Python.framework/Versions/2.6/bin:${PATH}" >>> export PATH >>> >>> test -r /sw/bin/init.sh && . /sw/bin/init.sh >>> >>> ## >>> # Your previous /Users/stauch/.bash_profile file was backed up as >>> /Users/stauch/.bash_profile.macports-saved_2012-06-04_at_15:56:13 >>> ## >>> >>> # MacPorts Installer addition on 2012-06-04_at_15:56:13: adding an >>> appropriate PATH variable for use with MacPorts. >>> #export PATH=/opt/local/bin:/opt/local/sbin:$PATH >>> # Finished adapting your PATH environment variable for use with >>> MacPorts. >>> >>> >>> ## >>> # Your previous /Users/stauch/.bash_profile file was backed up as >>> /Users/stauch/.bash_profile.macports-saved_2013-03-18_at_14:09:16 >>> ## >>> >>> # MacPorts Installer addition on 2013-03-18_at_14:09:16: adding an >>> appropriate PATH variable for use with MacPorts. >>> #export PATH=/opt/local/bin:/opt/local/sbin:$PATH >>> # Finished adapting your PATH environment variable for use with >>> MacPorts. >>> >>> >>> are you sure fink is trying to use gfortran? >>> >>> cheers >>> >>> ben >>> >>> >>> >>> >> >> It is _supposed_ to use Fink's gfortran as the compiler, but if you have >> some other incompatible Fortran compiler executable in the PATH which is >> getting detected and used in the configure tests, that could cause this >> issue. >> >> The output says to look in a config.log file, but the setup generates a >> bunch of them, and none were in src/pointless for me, so I didn't have a >> definite one for you to check. Try the following: >> >> find /sw/src/fink.build/ccp4-6.3.0-5/ccp4-6.3.0/ -name config.log | >> xargs grep "Fortran compiler works" -A10 >> >> --- >> Alexander Hansen, Ph.D. >> Fink User Liaison >> My package updates: http://finkakh.wordpress.com/ >> > > Thanks for sticking with me -- > > I have ccp4-6.3.0-6 instead of ccp4-6.3.0-5 -- the command does not return > any output > > cheers >
Ah, I'm on OS 10.8, and the version there is 6.3.0-5, and I didn't verify against what you already posted :-) . I'm trying a build on 10.6/i386 now, but it's going to be a while. The ccp4 build system is "interesting". (meaning incomprehensible to me). I guess I shouldn't be too surprised that the text didn't get logged where and how I thought it should. If you do in fact have a config.log in /sw/src/fink.build/ccp4-6.3.0-6/ccp4-6.3.0/src/pointless, go ahead and send that to me. Also, it'd be useful to see the output from fink dumpinfo -ePATH ccp4 -- 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
