Hello,
Following this last year thread (below):
I installed relion1.3 on my mac, and did all the steps suggested below to fix possible problems. There are no errors when installing, just a few warnings. Yet, when I am running relion1.3 tutorial, even just for generating a star file, I got this error:
relion_manualpick(62063,0x7fff7d7a5180) malloc: *** error for object 0x110461820: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
Any idea how to fix this?
Thanks,
Yana
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Hello.
So I seem to have resolved the trouble I was having. The problem, besides the ones that Sjors mentioned, and as far as I could tell, lay in the gcc compiler I was using. After switching the Makefiles to use clang instead of gcc, everything seemed to work. For those of you who do not have a fresh install of Mountain Lion, but have upgraded from an older OS, you may still have gcc set as your default, even though Xcode has stopped shipping recent versions of gcc after their switch to GPL3.
Summary:
- "Just uncomment the "#define MAC_OSX" statement on line 3895." you'll find this in the file: src/ml_optimiser.cpp
- "replace line 122 in external/fltk-1.3.0/src/filename_list.cxx by: int n = scandir(dirloc, list, 0, (int(*)(const dirent **, const dirent **))sort);
- after running configure for each component, alter the Makefile or makeinclude so that it uses CC=clang and CXX=clang++ You can use the INSTALL.sh script to guide you.
hope it helps.
mike
On Jul 9, 2013, at 3:55 PM, Sjors Scheres <[log in to unmask]> wrote:
> Hi again,
>
> Had a bit closer look into the fltk issue on new Macs. Apparently, this is
> a known bug in the fltk-version which ships with relion
> (http://article.gmane.org/gmane.comp.lib.fltk.bugs/10755/match=filename_list+cxx+122).
> The solution appears to be to replace line 122 in
> external/fltk-1.3.0/src/filename_cxx.cpp
> by
> int n = scandir(dirloc, list, 0, (int(*)(const dirent **, const dirent
> **))sort);
>
> Then everyhting compiles just fine (on my mountain lion at least). For
> relion-1.3 (next year or so) I will include a more modern version of fltk.
>
> Best,
> Sjors
>
>> Hello,
>>
>> I have so far been unable to install relion1.2 on my mac system. FFTW
>> compilation fails with messages like:
>>
>> configure: WARNING: unknown Fortran name-mangling scheme
>> /usr/bin/ranlib: file: .libs/libfftw3.a(debug.o) has no symbols
>>
>> FLTK fails with errors such as:
>>
>> configure: WARNING: sys/select.h: accepted by the compiler, rejected by
>> the preprocessor!
>> g++: error: language objective-c++ not recognized
>>
>> I have set the system variable MAC_OSX=true as suggested on the wiki, but
>> can't seem to get any farther in the process. Does anyone have relion
>> working on macos? If so, could you let me know what you did to make it
>> work? I have tried gcc 4.2 and gcc 4.7.1, using both gfortran and g77
>> (3.4)
>>
>> I would appreciate any help you could lend.
>> mike
>>
>
>
> --
> Sjors Scheres
> MRC Laboratory of Molecular Biology
> Francis Crick Avenue, Cambridge Biomedical Campus
> Cambridge CB2 0QH, U.K.
> tel: +44 (0)1223 267061
> http://www2.mrc-lmb.cam.ac.uk/groups/scheres
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