Re: [scipion-users] Scipion Install: CMake fails for lapack, gcc/gfortran linking problem?

[Grigory S. <sha...@gm...>]

Hello Teige,

just a wild guess: from what I can see you are using eman2 cmake instead of
the system one. Have you tried removing any eman-related stuff from your
environment and trying to recompile?

Best regards,
Grigory

--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.

MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267542 <+44%201223%20267542>
e-mail: gs...@mr...

On Fri, Sep 29, 2017 at 5:49 PM, Matthews-Palmer, Teige Rowan Seal <
t.m...@im...> wrote:

> Dear Scipion users,
>
>
> I wondered if anyone can suggest a solution to a problem I'm having
> compiling Scipion from a clone of the git on Linux Mint 17.3.
>
>
> gcc & gfortran are both version 4.8.4
>
> cmake is version 2.8.12.2
>
>
> scipion install proceeds until:
>
>
> cd software/tmp/lapack-3.5.0
> cmake -DBUILD_SHARED_LIBS:BOOL=ON -DLAPACKE:BOOL=ON
> -DCMAKE_INSTALL_PREFIX:PATH=/beebylab/software/scipion/1.1/software . >
> /beebylab/software/scipion/1.1/software/log/lapack_cmake.log 2>&1
> Error: target 'software/tmp/lapack-3.5.0/Makefile' not built
>
>
> Looking at the CMake log, it says gcc is broken and unable to compile a
> test:
>
> cat /beebylab/software/scipion/1.1/software/log/lapack_cmake.log
> -- The Fortran compiler identification is GNU 4.8.4
> -- Check for working Fortran compiler: /usr/bin/gcc
> -- Check for working Fortran compiler: /usr/bin/gcc  -- broken
> CMake Error at /beebylab/software/eman/EMAN2.2/share/cmake-3.8/Modules/
> CMakeTestFortranCompiler.cmake:44 (message):
>   The Fortran compiler "/usr/bin/gcc" is not able to compile a simple test
>   program.
>
>
> Looking at the CMake Error log to see the cause, apparently all the calls
> of gfortran procedures in the test fortran script are 'undefined' (problem
> with linking or paths but I don't understand this well, no experience of
> make or cmake).
>
> e.g. (selection of lines not in proper order, that illustrate things not
> found)
>
> gcc: error trying to exec 'f951': execvp: No such file or directory
>
> CMakeFortranCompilerId.F:(.text+0x93f): undefined reference to
> `_gfortran_st_write'
> CMakeFortranCompilerId.F:(.text+0x958): undefined reference to
> `_gfortran_transfer_character_write'
> CMakeFortranCompilerId.F:(.text+0x967): undefined reference to
> `_gfortran_st_write_done'
> testFortranCompiler.f:(.text+0x3f): undefined reference to
> `_gfortran_st_write'
> testFortranCompiler.f:(.text+0x58): undefined reference to
> `_gfortran_transfer_character_write'
> testFortranCompiler.f:(.text+0x67): undefined reference to
> `_gfortran_st_write_done'
>
>
> I'll attach the entire error log, but it's very long. Any suggestions are
> really appreciated!
>
> All the best
>
> Teige
>
>
>
>
>
>
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