> 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/ >
awesome, it works now!! moving the gfortran out of the way that was in /usr/bin did the trick. thanks a lot!! all the best ben ------------------------------------------------------------------------------ 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
