[MINC-development] Debian package for ubuntu 12.04
Nicolas Rannou
nicolas.lists at gmail.com
Wed Apr 11 15:35:28 EDT 2012
*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>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> 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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