fabian.fabians-imac { ..amber14 }-> gcc -v
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 5.1 (clang-503.0.40) (based on LLVM 3.4svn)
Target: x86_64-apple-darwin13.1.0
Thread model: posix
On May 14, 2014, at 2:47 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Wed, 2014-05-14 at 11:48 +0300, Fabian Glaser wrote:
>> Hi all,
>>
>> I am trying for a while to install AmberTools14 on my OSX 10.9.2, and I solved several issues, but still am not able to install it :-(
>>
>> Here is the last trial, can somebody please help me????
>>
>>
>> ==========================================================
>>
>>
>> fabian.fabians-imac { ..amber14 }-> ./configure -macAccelerate gnu
>> Checking for updates...
>> Checking for available patches online. This may take a few seconds...
>>
>> Available AmberTools 14 patches:
>>
>> No patches available
>> Searching for python2... Found python2.7: /opt/local/bin/python2.7
>>
>> Obtaining the gnu suite version:
>> gcc -v
>> The version is version
>> ./configure2: line 786: [: version: integer expression expected
>> ./configure2: line 805: [: version: integer expression expected
>> ./configure2: line 806: [: version: integer expression expected
>
> This isn't good. What is the output of "gcc -v" in your terminal?
>
>>
>> Testing the gcc compiler:
>> gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
>> ld: warning: directory not found for option '-L/Developer/SDKs/MacOSX10.5.sdk/usr/lib'
>> OK
>>
>> Testing the g++ compiler:
>> g++ -o testp testp.cpp
>> ld: warning: directory not found for option '-L/Developer/SDKs/MacOSX10.5.sdk/usr/lib'
>> OK
>>
>> Testing the gfortran compiler:
>> gfortran -O0 -o testp testp.f
>> OK
>>
>> Testing mixed C/Fortran compilation:
>> gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o testp.c
>> gfortran -O0 -c -o testp.f.o testp.f
>> gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c.o testp.f.o -lgfortran -w -framework Accelerate
>> Undefined symbols for architecture x86_64:
>> "__gfortran_transfer_character_write", referenced from:
>> _hello_ in testp.f.o
>> ld: symbol(s) not found for architecture x86_64
>> clang: error: linker command failed with exit code 1 (use -v to see invocation)
>> ./configure2: line 1762: ./testp: No such file or directory
>> Error: Unable to compile mixed C/Fortran code.
>> Please check your compiler settings and configure flags.
>> Configure failed due to the errors above!
>
> Your compilers appear broken. Please follow the instructions here to
> get your compilers set up properly: http://jswails.wikidot.com/mac-os-x
>
> I think the instructions for Mac OS X 10.9 should be compatible with
> 10.8.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________
Fabian Glaser, PhD
Head of the Structural Bioinformatics section
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary
Center for Life Sciences and Engineering
Technion - Israel Institute of Technology
Haifa 32000, ISRAEL
fglaser.technion.ac.il
Tel: +972 4 8293701
Fax: +972 4 8225153
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Received on Wed May 14 2014 - 07:00:02 PDT
