[MINC-development] Debian package for ubuntu 12.04
Nicolas Rannou
nicolas.lists at gmail.com
Wed Apr 11 15:34:00 EDT 2012
Great!
I gave it a shot and it looks like in the Perl directory, the "*auto*"
directory is missing (not sure what it is, but is used by FreeSurfer as
well...):
*in the new debian pacakge:*
perl->MNI-> some files OK
some files ok
*make install from mni-perl:*
perl->auto->* missing*
->MNI-> some file OK
some files ok
Thanks,
On Wed, Apr 11, 2012 at 1:18 PM, Vladimir S. FONOV <vladimir.fonov at gmail.com
> wrote:
> Hello,
>
> I made a simple command to install files in /opt/minc/perl (also added
> PERL5LIB variable in /opt/minc/minc-toolkit-config.**sh )
>
> So, try it on http://www.bic.mni.mcgill.ca/~**
> vfonov/software/minc-toolkit-**0.3.2-20120411-Linux-x86_64.**deb<http://www.bic.mni.mcgill.ca/%7Evfonov/software/minc-toolkit-0.3.2-20120411-Linux-x86_64.deb>
>
> On 12-04-11 12:42 PM, Nicolas Rannou wrote:
>
>> That would be great! but I'm not sure on how much work it involves.
>>
>> I'm currently testing FreeSurfer against minc2 debian (provided by you)
>> + mni-perlib from github
>>
>> I'll keep you posted!
>>
>> Nicolas
>>
>> On Wed, Apr 11, 2012 at 12:31 PM, Vladimir S. FONOV
>> <vladimir.fonov at gmail.com <mailto:vladimir.fonov at gmail.**com<vladimir.fonov at gmail.com>>>
>> wrote:
>>
>> Hello,
>>
>> I can insert it into my package, but I will have to figure out how
>> to deal with it using CMake
>>
>> On 12-04-11 12:22 PM, Nicolas Rannou wrote:
>>
>> Yes that's what I meant, sorry for the confusion!
>>
>> So I guess my best bet is to build it manually and install it where
>> FreeSurfer is expecting it!
>> And maybe work a Debian packaging to make it easy for people to
>> use.
>>
>> Thanks,
>> Nicolas
>>
>> On Wed, Apr 11, 2012 at 11:54 AM, Vladimir S. FONOV
>> <v.s.fonov at ilmarin.info <mailto:v.s.fonov at ilmarin.info**>
>> <mailto:v.s.fonov at ilmarin.info
>>
>> <mailto:v.s.fonov at ilmarin.info**>__>> wrote:
>>
>> Hello Nicolas,
>>
>> I don't quite understand what Perl support means in this
>> context. Do you
>> mean mni-perllib package (
>> https://github.com/__**andrewjanke/mni-perllib<https://github.com/__andrewjanke/mni-perllib>
>>
>> <https://github.com/**andrewjanke/mni-perllib<https://github.com/andrewjanke/mni-perllib>>
>> ) ?
>>
>> On 12-04-11 11:48 AM, Nicolas Rannou wrote:
>> > Hi Vladimir,
>> >
>> > It looks like MINC is not built with Perl support in those
>> packages... :(
>> >
>> > Is it correct and if so do you plan to integrate it at some
>> point?
>> > Is there any good way I can do it or help?
>> >
>> > It is unfortunately requiered by freesurfer...!
>> >
>> > Thanks and keep up the great work!
>> > Nicolas
>> >
>> > On Mon, Apr 9, 2012 at 2:44 PM, Vladimir S. FONOV
>> > <v.s.fonov at ilmarin.info <mailto:v.s.fonov at ilmarin.info**>
>> <mailto:v.s.fonov at ilmarin.info <mailto:v.s.fonov at ilmarin.info**
>> >__>
>>
>> <mailto:v.s.fonov at ilmarin.info <mailto:v.s.fonov at ilmarin.info**>
>> <mailto:v.s.fonov at ilmarin.info
>> <mailto:v.s.fonov at ilmarin.info**>__>>> wrote:
>> >
>> > Hello,
>> >
>> >
>> > we have moved minc development to
>> > https://github.com/____**organizations/BIC-MNI<https://github.com/____organizations/BIC-MNI>
>> <https://github.com/__**organizations/BIC-MNI<https://github.com/__organizations/BIC-MNI>
>> >
>>
>> > <https://github.com/__**organizations/BIC-MNI<https://github.com/__organizations/BIC-MNI>
>> <https://github.com/**organizations/BIC-MNI<https://github.com/organizations/BIC-MNI>
>> >>
>> >
>> > I have been working on making a unified minc package, but it
>> still
>> > work in progress.
>> >
>> > You can try
>> >
>> http://www.bic.mni.mcgill.ca/~**____vfonov/software/minc-__**
>> toolkit-__0.3.0-20120408-__**Linux-x86_64.__deb<http://www.bic.mni.mcgill.ca/%7E____vfonov/software/minc-__toolkit-__0.3.0-20120408-__Linux-x86_64.__deb>
>> <http://www.bic.mni.mcgill.ca/**%7E__vfonov/software/minc-**
>> toolkit-__0.3.0-20120408-**Linux-x86_64.__deb<http://www.bic.mni.mcgill.ca/%7E__vfonov/software/minc-toolkit-__0.3.0-20120408-Linux-x86_64.__deb>
>> >
>> <http://www.bic.mni.mcgill.ca/**__%7E__vfonov/software/minc-__**
>> toolkit-__0.3.0-20120408-__**Linux-x86_64.__deb<http://www.bic.mni.mcgill.ca/__%7E__vfonov/software/minc-__toolkit-__0.3.0-20120408-__Linux-x86_64.__deb>
>> <http://www.bic.mni.mcgill.ca/**%7E__vfonov/software/minc-**
>> toolkit-__0.3.0-20120408-**Linux-x86_64.__deb<http://www.bic.mni.mcgill.ca/%7E__vfonov/software/minc-toolkit-__0.3.0-20120408-Linux-x86_64.__deb>
>> >>
>>
>> >
>> <http://www.bic.mni.mcgill.ca/**__%7Evfonov/software/minc-__**
>> toolkit-0.3.0-20120408-Linux-_**_x86_64.deb<http://www.bic.mni.mcgill.ca/__%7Evfonov/software/minc-__toolkit-0.3.0-20120408-Linux-__x86_64.deb>
>>
>> <http://www.bic.mni.mcgill.ca/**%7Evfonov/software/minc-**
>> toolkit-0.3.0-20120408-Linux-**x86_64.deb<http://www.bic.mni.mcgill.ca/%7Evfonov/software/minc-toolkit-0.3.0-20120408-Linux-x86_64.deb>
>> >>
>> > - compiled on Ubuntu 11.10 but with most dependencies
>> built-in. All
>> > the tools will be installed in /opt/minc (this is temporary
>> place) ,
>> > source /opt/minc/minc-toolkit-config.**____sh to
>> configure
>>
>> environment.
>> >
>> >
>> >
>> > On 4/9/2012 1:15 PM, Nicolas Rannou wrote:
>> >
>> > Hi all,
>> >
>> > Do you plan to provide Debian packages for 12.04 before
>> the next
>> > release
>> > of Ubuntu 12.04? (April 26th)
>> >
>> > We are using FreeSurfer, which requires libminc2 and
>> minc
>> tools
>> > such as N3.
>> >
>> > libminc2 is already available but for instance,
>> mincbundles
>> > appears to
>> > be outdated.
>> > freesurfer relies on nu_correct for instance.
>> >
>> > root at bilbao:~# apt-get install mincbundle
>> > Reading package lists... Done
>> > Building dependency tree
>> > Reading state information... Done
>> > Some packages could not be installed. This may mean that
>> you have
>> > requested an impossible situation or if you are using
>> the
>> unstable
>> > distribution that some required packages have not yet
>> been created
>> > or been moved out of Incoming.
>> > The following information may help to resolve the
>> situation:
>> >
>> > The following packages have unmet dependencies:
>> > mincbundle : Depends: glutg3-dev but it is not
>> installable
>> > Depends: libsoqt3-dev but it is not
>> installable
>> > Depends: mincsample but it is not
>> installable
>> > Depends: mni-models-colin27-lin but it
>> is not
>> > installable
>> > Depends: mni-models-icbm152-lin but it
>> is not
>> > installable
>> > E: Unable to correct problems, you have held broken
>> packages.
>>
>
>
>
> --
> Best regards,
>
> Vladimir S. FONOV ~ vladimir <dot> fonov <at> gmail <dot> com
> ______________________________**_________________
> MINC-development mailing list
> MINC-development at bic.mni.**mcgill.ca <MINC-development at bic.mni.mcgill.ca>
> http://www.bic.mni.mcgill.ca/**mailman/listinfo/minc-**development<http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development>
>
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