[Neurodebian-users] afni library errors on 64-bit ubuntu 12.04 (undefined symbol: AFNI_dataset_slice)

[Stephen Towler]

Hi Yaroslav,

Thanks for the quick response. I will let you know how the testing goes as
soon as the update hits.

best,
Stephen


--
voice and txt: 352-358-1110


On Mon, Sep 2, 2013 at 8:30 PM, Yaroslav Halchenko <debian at onerussian.com>wrote:

> Hi Stephen,
>
> A friend of ours already emailed us a similar report and we nearly called
> him a
> lier since "it works for us" (on Debian systems) and he did not provide
> details
> about his system.  Your report had all relevant information to reproduce
> this
> issue specific to some elderly Ubuntus -- thanks!
>
> Meanwhile you could try to mitigate this by prepending calls to those
> commands
> with
>
> LD_PRELOAD=/usr/lib/afni/lib/libafni_warp.so
>
> which should provide that symbol and which librickr.so should have been
> linked against.   We will provide fixed build tomorrow or day after the
> latest.
>
> Cheers,
>
> On Mon, 02 Sep 2013, Stephen Towler wrote:
>
> >    Hello neurodebian uesrs,
> >    Anyone else having problems with most recent afni binaries on 64-bit
> >    platforms? 3dcalc and 3dinfo (and maybe others) are producing error
> >    "symbol lookup error: /usr/lib/afni/lib/librickr.so: undefined symbol:
> >    AFNI_dataset_slice"
> >    Details:�
> >    ----------- active afni version and variables: -----------
> >    Version AFNI_2011_12_21_1014
> >    [[Precompiled binary =Debian-i686-1-gnu: Aug 31 2013]]
> >    The command 'afni' will launch: /usr/bin/afni
> >    The command '3dinfo' will launch: /usr/lib/afni/bin/3dinfo
> >    AFNI environmental variables, if any exist:
> >    AFNI_PLUGINPATH=/usr/lib/afni/plugins
> >    AFNI_TTATLAS_DATASET=/usr/share/afni/atlases
> >    AFNI_IMSAVE_WARNINGS=NO
> >    AFNI_MODELPATH=/usr/lib/afni/models
> >    ----------------------------------------------------------
> >    # at least two commands give the same error:
> >    stowler-local at larry:~$ 3dcalc
> >    3dcalc: symbol lookup error: /usr/lib/afni/lib/librickr.so: undefined
> >    symbol: AFNI_dataset_slice
> >    stowler-local at larry:~$ 3dinfo
> >    3dinfo: symbol lookup error: /usr/lib/afni/lib/librickr.so: undefined
> >    symbol: AFNI_dataset_slice
> >    # doesn't look like there's version confusion, as there's only one
> >    librickr.so:
> >    stowler-local at larry:~$ find /usr/lib/afni | grep librickr
> >    /usr/lib/afni/lib/librickr.so
> >    # host and library info to help the maintainers troubleshoot:
> >    stowler-local at larry:~$ uname -a
> >    Linux [1]larry.birc.emory.edu 3.2.0-52-generic-pae #78-Ubuntu SMP
> Fri Jul
> >    26 16:43:19 UTC 2013 i686 i686 i386 GNU/Linux
> >    stowler-local at larry:~$ file /usr/lib/afni/lib/librickr.so
> >    /usr/lib/afni/lib/librickr.so: ELF 32-bit LSB shared object, Intel
> 80386,
> >    version 1 (SYSV), dynamically linked,
> >    BuildID[sha1]=0xf3dbd827219f30b6bf68849be2e22890b20df8fe, stripped
> >    stowler-local at larry:~$ cat
> >    /etc/apt/sources.list.d/neurodebian.sources.list�
> >    deb [2]http://masi.vuse.vanderbilt.edu/neurodebian data main contrib
> >    non-free
> >    #deb-src [3]http://masi.vuse.vanderbilt.edu/neurodebian data main
> contrib
> >    non-free
> >    deb [4]http://masi.vuse.vanderbilt.edu/neurodebian precise main
> contrib
> >    non-free
> >    #deb-src [5]http://masi.vuse.vanderbilt.edu/neurodebian precise main
> >    contrib non-free
> >    Thanks,
> >    Stephen
> --
> Yaroslav O. Halchenko, Ph.D.
> http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org
> Senior Research Associate,     Psychological and Brain Sciences Dept.
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
> WWW:   http://www.linkedin.com/in/yarik
>
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