Hi Yana,
I got 1.3 installed on my macbook air without any of the tweaks below
(using Xcode). Could you try that as well?
However, I have to admit I never actually tested all programs for their
functionality. In practice running on a mac is not so useful, as there are
very few mac clusters around.
HTH,
S
> 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
>
> **********************************************************************************************
>
>
> 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
>
--
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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