[Neurodebian-users] Developer files for Debian FSL

[Dillon Niederhut]

Hi Yaroslav,

Debian/rules the executable file? Will this configure the source FSL files
for me? Because that would be fantastic.

$ apt-cache policy libgd2-noxpm-dev libgd2-noxpm

returns

libgd2-noxpm-dev:
  Installed: (none)
  Candidate: 2.0.36~rc1~dfsg-6ubuntu2
  Version table:
     2.0.36~rc1~dfsg-6ubuntu2 0
        500 http://archive.ubuntu.com/ubuntu/ precise/main amd64 Packages
libgd2-noxpm:
  Installed: (none)
  Candidate: 2.0.36~rc1~dfsg-6ubuntu2
  Version table:
     2.0.36~rc1~dfsg-6ubuntu2 0
        500 http://archive.ubuntu.com/ubuntu/ precise/main amd64 Packages

Thanks,
Dillon


Dillon Niederhut
Doctoral Candidate
University of California, Berkeley
Department of Anthropology
232 Kroeber Hall
Berkeley, CA 94720
deniederhut.strikingly.com


On Fri, Jun 20, 2014 at 5:48 AM, Yaroslav Halchenko <debian at onerussian.com>
wrote:

>
> On Thu, 19 Jun 2014, Dillon Niederhut wrote:
> >    Thanks for the comments! Sorry for not being more precise. I
> installed FSL
> >    from the neurodebian repo, and all the normal stuff works fine. The
> good
> >    folks at FMRIB have sent me some experimental analysis tools that
> require
> >    setup and compiling. I could not get them to compile using the files
> and
> >    instructions they sent. The readme essentially says to untar the
> folder
> >    (which contains a makefile, dependencies, etc), run
> >    $ . setup.sh
> >    , then run
> >    $ make
> >    It seems that my installation is lacking "a compatible devel package",
> >    which has the default make, config, and include files that the setup
> >    scripts were expecting.
> >    I've been told that I have two options:
> >    1. Uninstall neurodebian FSL and try to build the source FSL myself
>
> probably not even needed to uninstall neurodebian FSL since it is not in
> the way unless you source /etc/fsl/fsl.sh.
>
> >    2. Download the source version of FSL, then customize those config
> files
> >    to match the neurodebian libraries and executables
>
> I guess you could indeed
>
> a. fakeroot debian/rules install # should build and install under debian/
> b. and then build your custom tool using this freshly built fsl
>
>
> >    My questions would more precisely have been stated as:
> >    1. Does neurodebian already have the FSL devel package? If so, how
> can I
> >    install it?
>
> not that I am aware of, Michael would know better
>
> >    2. If not, is there documentation on editing source FSL config files
> to
> >    work with neurodebian?
>
> all the patches are under debian/patches and all the 'build' steps are
> within debian/rules -- but that one is quite "evolved" by now
>
> >    I've attached the makefile, in case that will be of any help.
> >    Running:
> >    $ sudo apt-get build-dep fsl
> >    throws this dependency error:
> >    <The following packages have unmet dependencies:
> >     libgd2-noxpm-dev : Depends: libgd2-noxpm (=
> 2.0.36~rc1~dfsg-6ubuntu2) but
> >    it is not going to be installed
>
> what is output of
>
> apt-cache policy libgd2-noxpm-dev libgd2-noxpm
>
>
> ?
>
> --
> Yaroslav O. Halchenko, Ph.D.
> http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org
> Research Scientist,            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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