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

[Yaroslav Halchenko]

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