[MINC-users] Minc-2 installation problems

[mohamed Ali Bahri]

Hi Claude,

I tried with your command line and it gave me the following error:

-----------------------------------------------------------------------------------------------------------
[root at localhost hdf5-1.6.6]# ./configure --disable-shared 
--prefix=/usr/local --with-build-path=/usr/local CFLAGS='${CFLAGS} 
-fpic' CPPFLAGS='${CPPFLAGS} -fpic' CXXFLAGS='${CXXFLAGS} -fpic'
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking shell variables initial values... done
checking if basename works... yes
checking if xargs works... yes
checking for cached host... none
checking for sizeof hsize_t and hssize_t... large
checking for config x86_64-unknown-linux-gnu... no
checking for config x86_64-unknown-linux-gnu... no
checking for config unknown-linux-gnu... no
checking for config unknown-linux-gnu... no
checking for config x86_64-linux-gnu... no
checking for config x86_64-linux-gnu... no
checking for config x86_64-unknown... no
checking for config linux-gnu... found
compiler 'gcc' is GNU gcc-4.3.0
checking for config ./config/site-specific/host-localhost.localdomain... no
checking for config ./config/site-specific/host-localdomain... no
checking for gcc... gcc
checking for C compiler default output file name...
configure: error: C compiler cannot create executables
See `config.log' for more details.
------------------------------------------------------------------------------------------------------
As compiler I use gcc 4.3 (gcc (GCC) 4.3.0 20080428 (Red Hat 4.3.0-8).
I also attached the config.log if this could give information about my 
problem.

Thank you very much for your help

Best regards
Mohamed





Claude LEPAGE a écrit :
> Hi,
>
>   
>> Thank you for your answer. I tried to use HDF5-1.6.6 instead of 
>> hdf5-1.8.2 but now I have errors with HDF5.
>> I use the following command lines:
>>
>> 1) FC=/usr/bin/gfortran ./configure --prefix=/usr/local/ 
>> --with-zlib=/usr/local/ --enable-fortran --enable-cxx
>> 2) make
>>     
>
> Here is how I compile HDF5-1.6.6 in 64 bits Linux:
>
> ./configure --disable-shared --prefix=/usr/local --with-build-path=/usr/local CFLAGS='${CFLAGS} -fpic' CPPFLAGS='${CPPFLAGS} -fpic' CXXFLAGS='${CXXFLAGS} -fpic'
> make 
> make install
>
> --disable-shared is optional
> no need to fuss about fortran (not needed by minc2)
>
> By the way, which compiler are you using? It looks like your C++
> compiler does not like the code. Strange...
>
> gcc --version
>
> minc2 may compile with gcc 4.2+, but not all MNI tools do (yet).
>
> Claude
>
>
>   
>> ===============================================
>>
>> g++ -O2 -I. -I../../src -I../../src -D_BSD_SOURCE -D_POSIX_SOURCE 
>> -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE 
>> -I/usr/local//include -c H5PropList.cpp -fPIC -DPIC -o .libs/H5PropList.lo
>> H5PropList.cpp: In member function 'std::string 
>> H5::PropList::getClassName() const':
>> H5PropList.cpp:428: error: 'free' was not declared in this scope
>> make[3]: *** [H5PropList.lo] Erreur 1
>> make[3]: quittant le répertoire « /usr/local/hdf5-1.6.6/c++/src »
>> make[2]: *** [lib] Erreur 1
>> make[2]: quittant le répertoire « /usr/local/hdf5-1.6.6/c++ »
>> make[1]: *** [lib] Erreur 1
>> make[1]: quittant le répertoire « /usr/local/hdf5-1.6.6 »
>> make: *** [all] Erreur 2
>> =======================================================
>>
>> Thanks a lot,
>> Mohamed
>>
>> Claude LEPAGE a écrit :
>>     
>>> Hi,
>>>
>>>   
>>>       
>>>> I have a problem with minc-2.0.17 installation (make command fails). Any 
>>>> one have an idea how I can solve that?
>>>> I use linux (Fedora 9, 64-bit).
>>>>
>>>> libtool: compile: gcc -DHAVE_CONFIG_H -I. -I./libsrc 
>>>> -I./volume_io/Include -I./volume_io/Include -I./progs/Proglib 
>>>> -I./conversion/Acr_nema -I./libsrc2 -g -O2 -MT libsrc/hdf_convenience.lo 
>>>> -MD -MP -MF libsrc/.deps/hdf_convenience.Tpo -c libsrc/hdf_convenience.c 
>>>> -o libsrc/hdf_convenience.o
>>>> libsrc/hdf_convenience.c: In function ‘hdf_id_add’:
>>>> libsrc/hdf_convenience.c:83: erreur: too few arguments to function 
>>>> ‘H5Gopen2’
>>>> libsrc/hdf_convenience.c: In function ‘hdf_var_add’:
>>>> libsrc/hdf_convenience.c:185: erreur: too few arguments to function 
>>>>     
>>>>         
>>> I haven't seen this problem, but here is an idea.
>>>
>>> Which version of HDF5 have you installed? minc2 has been tested
>>> with HDF5 up to 5-1.6.7. If you are using 5-1.8.X, I would suggest
>>> to try 5-1.6.6 (what I am currently using) or 5-1.6.7. If I recall,
>>> 5-1.8.X is not 100% compatible with previous versions.
>>>
>>> The problem may be different too, but making sure you are using
>>> a compatible version of HDF5 is the first step.
>>>
>>> Yours,
>>>
>>> Claude
>>>  
>>>   
>>> ------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> MINC-users at bic.mni.mcgill.ca
>>> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>>   
>>>       
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>>     
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>     

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