On 7/23/13 3:16 PM, sta...@ebi.ac.uk wrote: >> 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:$PATH >>>>> # Finished adapting your PATH environment variable for use with >>>>> MacPorts. >>>>> >>>>> >>>>> are you sure fink is trying to use gfortran? >>>>> >>>>> cheers >>>>> >>>>> ben >>>>> >>>>> >>>>> >>>>> >>>> >>>> It is _supposed_ to use Fink's gfortran as the compiler, but if you >>>> have >>>> some other incompatible Fortran compiler executable in the PATH which >>>> is >>>> getting detected and used in the configure tests, that could cause this >>>> issue. >>>> >>>> The output says to look in a config.log file, but the setup generates a >>>> bunch of them, and none were in src/pointless for me, so I didn't have >>>> a >>>> definite one for you to check. Try the following: >>>> >>>> find /sw/src/fink.build/ccp4-6.3.0-5/ccp4-6.3.0/ -name config.log | >>>> xargs grep "Fortran compiler works" -A10 >>>> >>>> --- >>>> Alexander Hansen, Ph.D. >>>> Fink User Liaison >>>> My package updates: http://finkakh.wordpress.com/ >>>> >>> >>> Thanks for sticking with me -- >>> >>> I have ccp4-6.3.0-6 instead of ccp4-6.3.0-5 -- the command does not >>> return >>> any output >>> >>> cheers >>> >> >> Ah, I'm on OS 10.8, and the version there is 6.3.0-5, and I didn't >> verify against what you already posted :-) . I'm trying a build on >> 10.6/i386 now, but it's going to be a while. >> >> The ccp4 build system is "interesting". (meaning incomprehensible to >> me). I guess I shouldn't be too surprised that the text didn't get >> logged where and how I thought it should. >> >> If you do in fact have a config.log in >> /sw/src/fink.build/ccp4-6.3.0-6/ccp4-6.3.0/src/pointless, go ahead and >> send that to me. Also, it'd be useful to see the output from >> >> fink dumpinfo -ePATH ccp4 >> -- >> Alexander Hansen, Ph.D. >> Fink User Liaison >> My package updates: http://finkakh.wordpress.com/ >> > > > great thanks again! here is the dumpinfo: > > bash-3.2$ fink dumpinfo -ePATH ccp4 > Information about 12607 packages read in 1 seconds. > PATH=/sw/var/lib/fink/path-prefix-10.6:/sw/bin:/sw/sbin:/bin:/usr/bin:/sbin:/usr/sbin:/usr/X11R6/bin > > the config.log is attached > > > cheers >
OK. It's still not using the right gfortran for some reason: configure:2785: checking for Fortran compiler version configure:2794: gfortran --version >&5 GNU Fortran (GCC) 4.6.0 Copyright (C) 2011 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 configure:2805: $? = 0 configure:2794: gfortran -v >&5 Using built-in specs. COLLECT_GCC=gfortran Target: x86_64-apple-darwin10.7.0 Configured with: ../gcc-4.6.0/configure --enable-languages=fortran Thread model: posix gcc version 4.6.0 (GCC) configure:2805: $? = 0 configure:2794: gfortran -V >&5 gfortran: error: unrecognized option '-V' gfortran: fatal error: no input files compilation terminated. configure:2805: $? = 1 configure:2794: gfortran -qversion >&5 gfortran: error: unrecognized option '-qversion' gfortran: fatal error: no input files compilation terminated. configure:2805: $? = 1 gfortran: error trying to exec 'f951': execvp: No such file or directory configure:2820: checking whether the Fortran compiler works configure:2842: gfortran -L/sw/src/fink.build/ccp4-6.3.0-6/ccp4-6.3.0/lib conftest.f >&5 configure:2846: $? = 1 configure:2884: result: no configure: failed program was: | program main | | end configure:2889: error: in `/sw/src/fink.build/ccp4-6.3.0-6/ccp4-6.3.0/src/pointless': configure:2893: error: Fortran compiler cannot create executables See `config.log' for more details. It looks like the configuration found another gfortran executable somewhere. If you have a /usr/local/bin/gfortran, I'd recommend renaming all of /usr/local, if possible, e.g. via sudo mv /usr/local /usr/local.moved while you build ccp4, and then put it back sudo mv /usr/local.moved /usr/local when you're finished. If you need stuff from /usr/local, then at least rename /usr/local/bin/gfortran. If it's not /usr/local/bin/gfortran then you can use type -a gfortran if your shell is bash or where gfortran if you're using tcsh, and then rename any gfortran which isn't in /sw. -- 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
