[MINC-users] minc2 build error in mincconvert

[Andrew Janke]

Hi Jim,

I have only every used zlib compression in hdf5, I am currently using
zlib 1.2.3 (as per yourself) and hdf5 1/6.5 although in my case I use
the std debian/ubuntu libraries as compared to building them myself.

I echo Vlads comment and would add that if you really do want separate
sub-dirs for each "product" then I would reccomend using something
like GNU stow to bring it all back together or you will have
horrendous link-lines and LD_LIBRARY_PATH's.

Alright, perhaps not horrendous, but decidedly "whiffy". :)

As for the specific build error you are having I would guess that
there is a compress in both zlib and szip? I have certainly not seen
this error anyhow.


a


On Nov 11, 2007 9:21 AM, EJ Nikelski <nikelski at bic.mni.mcgill.ca> wrote:
> Hi all,
>
>    I finally decided to jump onto the minc2 train, however I've run
> into a slight build problem. Here are the details:
>
> 1. I build and install some prerequisites ...
>    zlib-1.2.3, szip-2.1, hdf5-1.6.6, netcdf-3.6.2
>
>    .... all without a problem.
>
> 2.  I build minc2 with this ...
>
> ./configure
>     --prefix=/data/raid01/quarantine/Nov2007/minc2
>     --enable-minc2
>     --enable-acr-nema
>     --with-build-path=/data/raid01/quarantine/Nov2007/netcdf-3.6.2
>                      :/data/raid01/quarantine/Nov2007/hdf5-1.6.6
>                      :/data/raid01/quarantine/Nov2007/zlib-1.2.3
>
> The ./configure works OK, but the make fails (ultimately) with an
> error building mincconvert...
>
> gcc -g -O2 -o mincconvert progs/mincconvert/mincconvert.o
> -L/data/raid01/quarantine/Nov2007/netcdf-3.6.2/lib
> -L/data/raid01/quarantine/Nov2007/hdf5-1.6.6/lib
> -L/data/raid01/quarantine/Nov2007/zlib-1.2.3/lib
> ./.libs/libvolume_io2.a -L/data/raid01/quarantine/Nov2007/szip-2.1/lib
> ./.libs/libminc2.a
> /data/raid01/quarantine/Nov2007/hdf5-1.6.6/lib/libhdf5.a
> /data/raid01/quarantine/Nov2007/szip-2.1/lib/libsz.so -lz
> /data/raid01/quarantine/Nov2007/netcdf-3.6.2/lib/libnetcdf.a -lm
> -Wl,--rpath -Wl,/data/raid01/quarantine/Nov2007/szip-2.1/lib
> -Wl,--rpath -Wl,/data/raid01/quarantine/Nov2007/szip-2.1/lib
> /data/raid01/quarantine/Nov2007/zlib-1.2.3/lib/libz.a(compress.o): In
> function `compress':
> compress.c:(.text+0xe0): multiple definition of `compress'
> progs/mincconvert/mincconvert.o:(.data+0x0): first defined here
> /usr/bin/ld: Warning: size of symbol `compress' changed from 4 in
> progs/mincconvert/mincconvert.o to 178 in
> /data/raid01/quarantine/Nov2007/zlib-1.2.3/lib/libz.a(compress.o)
> /usr/bin/ld: Warning: type of symbol `compress' changed from 1 to 2 in
> /data/raid01/quarantine/Nov2007/zlib-1.2.3/lib/libz.a(compress.o)
> collect2: ld returned 1 exit status
> make[2]: *** [mincconvert] Error 1
>
> Has anyone seen this before? Could this be an inconsistency in the
> latest version of zlib?
>
> PS: I'm building minc-2.0.14 on Ubuntu Edgy.
>
>
> -Jim
>
>
>
> --
> =================================
> Jim Nikelski, Ph.D.
> Postdoctoral Research Fellow
> Bloomfield Centre for Research in Aging
> Lady Davis Institute for Medical Research
> Sir Mortimer B. Davis - Jewish General Hospital
> McGill University
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883