[MINC-development] Debian package for ubuntu 12.04
Nicolas Rannou
nicolas.lists at gmail.com
Wed Apr 11 18:11:23 EDT 2012
Cool I'll try it tomorrow as soon as I arrive in my office!
Thanks
Nicolas
On Wed, Apr 11, 2012 at 6:03 PM, Vladimir S. FONOV <vladimir.fonov at gmail.com
> wrote:
> Hello,
>
> ok, I figured out how to generate these files, I included the changes in
>
> 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 03:35 PM, Nicolas Rannou wrote:
>
>> *in the new debian pacakge:*
>> perl->MNI: ok
>>
>> -> auto : *missing*
>> some files ok
>>
>> *make install from mni-perl:*
>> perl->MNI: ok
>> ->auto:*ok*
>>
>> some files ok
>>
>> On Wed, Apr 11, 2012 at 3:34 PM, Nicolas Rannou <nicolas.lists at gmail.com
>> <mailto:nicolas.lists at gmail.**com <nicolas.lists at gmail.com>>> wrote:
>>
>> 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 <mailto:vladimir.fonov at gmail.**com<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/%7E__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<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>
>> >
>> <mailto: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**>__>
>> <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 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>
>> >
>>
>>
>> <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**>__>__>
>>
>>
>> <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
>> <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>
>> >>
>>
>> > <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/**____%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/%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>
>> >
>>
>>
>> <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.__mcg**ill.ca <http://mcgill.ca>
>> <mailto: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>
>> <http://www.bic.mni.mcgill.ca/**mailman/listinfo/minc-**
>> development<http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development>
>> >
>>
>>
>>
>>
>>
>> ______________________________**_________________
>> 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>
>>
>
>
> --
> 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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