From nicolas.lists at gmail.com Mon Apr 9 13:15:21 2012 From: nicolas.lists at gmail.com (Nicolas Rannou) Date: Mon, 9 Apr 2012 13:15:21 -0400 Subject: [MINC-development] Debian package for ubuntu 12.04 Message-ID: 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 libminc2 is already available but for instance, mincbundles appears to be outdated.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. Thanks, Nicolas -------------- next part -------------- An HTML attachment was scrubbed... URL: From vladimir.fonov at gmail.com Mon Apr 9 14:46:09 2012 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Mon, 09 Apr 2012 14:46:09 -0400 Subject: [MINC-development] Debian package for ubuntu 12.04 In-Reply-To: References: Message-ID: <4F832E71.9090905@gmail.com> Hello, we have moved minc development to 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 - 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.FONOV gmail com From nicolas.lists at gmail.com Mon Apr 9 15:25:52 2012 From: nicolas.lists at gmail.com (Nicolas Rannou) Date: Mon, 9 Apr 2012 15:25:52 -0400 Subject: [MINC-development] Debian package for ubuntu 12.04 In-Reply-To: <4F832E71.9090905@gmail.com> References: <4F832E71.9090905@gmail.com> Message-ID: Great I'll try it! So far the package has been installed without any dependency issue :) Thanks! Nicolas On Mon, Apr 9, 2012 at 2:46 PM, Vladimir S. FONOV wrote: > Hello, > > > we have moved minc development to 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- 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.FONOV gmail com > > ______________________________**_________________ > MINC-development mailing list > MINC-development at bic.mni.**mcgill.ca > http://www.bic.mni.mcgill.ca/**mailman/listinfo/minc-**development > -------------- next part -------------- An HTML attachment was scrubbed... URL: From vladimir.fonov at gmail.com Wed Apr 11 12:31:59 2012 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Wed, 11 Apr 2012 12:31:59 -0400 Subject: [MINC-development] Debian package for ubuntu 12.04 In-Reply-To: References: <4F832DFE.1010400@ilmarin.info> <688c89b97c1c4d8fa362e58d9de85670@CHEXHUBCASBDC1.CHBOSTON.ORG> Message-ID: <4F85B1FF.6020601@gmail.com> 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 > > 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 ) ? > > 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 > > > >> wrote: > > > > Hello, > > > > > > we have moved minc development to > > 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 > > > > > > - 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. > > > > Thanks, > > Nicolas > > > > > > _________________________________________________ > > MINC-development mailing list > > MINC-development at bic.mni.__mcgill.ca > >

> > > http://www.bic.mni.mcgill.ca/__mailman/listinfo/minc-__development > > > > > > > > > > -- > > Best regards, > > > > v.s.fonov ilmarin info > > > > > > > -- > Best regards, > Vladimir S. Fonov ~ v.s.fonov ilmarin.info > > -- Best regards, Vladimir S. FONOV ~ vladimir fonov gmail com From nicolas.lists at gmail.com Wed Apr 11 12:42:56 2012 From: nicolas.lists at gmail.com (Nicolas Rannou) Date: Wed, 11 Apr 2012 12:42:56 -0400 Subject: [MINC-development] Debian package for ubuntu 12.04 In-Reply-To: <4F85B1FF.6020601@gmail.com> References: <4F832DFE.1010400@ilmarin.info> <688c89b97c1c4d8fa362e58d9de85670@CHEXHUBCASBDC1.CHBOSTON.ORG> <4F85B1FF.6020601@gmail.com> Message-ID: 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> 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 >> > 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) ? >> >> 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 >> > >> >> >> wrote: >> > >> > Hello, >> > >> > >> > we have moved minc development to >> > 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 >> > toolkit-__0.3.0-20120408-**Linux-x86_64.__deb >> > >> >> > >> > 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. >> > >> > Thanks, >> > Nicolas >> > >> > >> > ______________________________**___________________ >> > MINC-development mailing list >> > MINC-development at bic.mni.__mcg**ill.ca < >> http://mcgill.ca> >> > >> >> >> >> >> > http://www.bic.mni.mcgill.ca/_**_mailman/listinfo/minc-__** >> development >> > >> > >> > >> > >> > >> > -- >> > Best regards, >> > >> > v.s.fonov ilmarin info >> > >> > >> >> >> -- >> Best regards, >> Vladimir S. Fonov ~ v.s.fonov ilmarin.info > > >> >> >> > > -- > Best regards, > > Vladimir S. FONOV ~ vladimir fonov gmail com > ______________________________**_________________ > MINC-development mailing list > MINC-development at bic.mni.**mcgill.ca > http://www.bic.mni.mcgill.ca/**mailman/listinfo/minc-**development > -------------- next part -------------- An HTML attachment was scrubbed... URL: From vladimir.fonov at gmail.com Wed Apr 11 13:18:44 2012 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Wed, 11 Apr 2012 13:18:44 -0400 Subject: [MINC-development] Debian package for ubuntu 12.04 In-Reply-To: References: <4F832DFE.1010400@ilmarin.info> <688c89b97c1c4d8fa362e58d9de85670@CHEXHUBCASBDC1.CHBOSTON.ORG> <4F85B1FF.6020601@gmail.com> Message-ID: <4F85BCF4.1020801@gmail.com> 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 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 > > 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 > > __>> 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 > ) ? > > 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 > > > __> > > __>>> wrote: > > > > Hello, > > > > > > we have moved minc development to > > 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 > > > > > > > > > > - 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 fonov gmail com From nicolas.lists at gmail.com Wed Apr 11 15:34:00 2012 From: nicolas.lists at gmail.com (Nicolas Rannou) Date: Wed, 11 Apr 2012 15:34:00 -0400 Subject: [MINC-development] Debian package for ubuntu 12.04 In-Reply-To: <4F85BCF4.1020801@gmail.com> References: <4F832DFE.1010400@ilmarin.info> <688c89b97c1c4d8fa362e58d9de85670@CHEXHUBCASBDC1.CHBOSTON.ORG> <4F85B1FF.6020601@gmail.com> <4F85BCF4.1020801@gmail.com> Message-ID: 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 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 > > 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 >> >> >> 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 >> >> > >> __>> 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 >> >> > >> ) ? >> >> 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 >> > >> > >__> >> >> >> > __>>> wrote: >> > >> > Hello, >> > >> > >> > we have moved minc development to >> > 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 >> > toolkit-__0.3.0-20120408-**Linux-x86_64.__deb >> > >> > toolkit-__0.3.0-20120408-__**Linux-x86_64.__deb >> > toolkit-__0.3.0-20120408-**Linux-x86_64.__deb >> >> >> >> > >> > toolkit-0.3.0-20120408-Linux-_**_x86_64.deb >> >> > 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 fonov gmail com > ______________________________**_________________ > MINC-development mailing list > MINC-development at bic.mni.**mcgill.ca > http://www.bic.mni.mcgill.ca/**mailman/listinfo/minc-**development > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nicolas.lists at gmail.com Wed Apr 11 15:35:28 2012 From: nicolas.lists at gmail.com (Nicolas Rannou) Date: Wed, 11 Apr 2012 15:35:28 -0400 Subject: [MINC-development] Debian package for ubuntu 12.04 In-Reply-To: References: <4F832DFE.1010400@ilmarin.info> <688c89b97c1c4d8fa362e58d9de85670@CHEXHUBCASBDC1.CHBOSTON.ORG> <4F85B1FF.6020601@gmail.com> <4F85BCF4.1020801@gmail.com> Message-ID: *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 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 >> >> 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 >>> >> >>> 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 >>> >>> >> >>> __>> 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 >>> >>> > >>> ) ? >>> >>> 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 >>> > >>> >> >__> >>> >>> >>> >> __>>> wrote: >>> > >>> > Hello, >>> > >>> > >>> > we have moved minc development to >>> > 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 >>> >> toolkit-__0.3.0-20120408-**Linux-x86_64.__deb >>> > >>> >> toolkit-__0.3.0-20120408-__**Linux-x86_64.__deb >>> >> toolkit-__0.3.0-20120408-**Linux-x86_64.__deb >>> >> >>> >>> > >>> >> toolkit-0.3.0-20120408-Linux-_**_x86_64.deb >>> >>> >> 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 fonov gmail com >> ______________________________**_________________ >> MINC-development mailing list >> MINC-development at bic.mni.**mcgill.ca >> http://www.bic.mni.mcgill.ca/**mailman/listinfo/minc-**development >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From vladimir.fonov at gmail.com Wed Apr 11 15:52:22 2012 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Wed, 11 Apr 2012 15:52:22 -0400 Subject: [MINC-development] Debian package for ubuntu 12.04 In-Reply-To: References: <4F832DFE.1010400@ilmarin.info> <688c89b97c1c4d8fa362e58d9de85670@CHEXHUBCASBDC1.CHBOSTON.ORG> <4F85B1FF.6020601@gmail.com> <4F85BCF4.1020801@gmail.com> Message-ID: <4F85E0F6.3020706@gmail.com> Hello, it seem to be that files which are installed in perl/MNI/ are processed by AutoSplit.pm to create auto subdirectory. Right now I don't know how to do it from CMake ... 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 > 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 > > 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 > > -- Best regards, Vladimir S. FONOV ~ vladimir fonov gmail com From vladimir.fonov at gmail.com Wed Apr 11 18:03:02 2012 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Wed, 11 Apr 2012 18:03:02 -0400 Subject: [MINC-development] Debian package for ubuntu 12.04 In-Reply-To: References: <4F832DFE.1010400@ilmarin.info> <688c89b97c1c4d8fa362e58d9de85670@CHEXHUBCASBDC1.CHBOSTON.ORG> <4F85B1FF.6020601@gmail.com> <4F85BCF4.1020801@gmail.com> Message-ID: <4F85FF96.8040107@gmail.com> 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 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 > 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 > > 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 > > > > 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 > > >> 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 > > __> > > > __>__>> 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 > > > > ) ? > > 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 > > > __> > > __>__> > > > __> > > __>__>>> wrote: > > > > Hello, > > > > > > we have moved minc development to > > 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 > > > > > >> > > > > > > >> > > - 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 fonov gmail com > _________________________________________________ > MINC-development mailing list > MINC-development at bic.mni.__mcgill.ca > > http://www.bic.mni.mcgill.ca/__mailman/listinfo/minc-__development > > > > > > > _______________________________________________ > MINC-development mailing list > MINC-development at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development -- Best regards, Vladimir S. FONOV ~ vladimir fonov gmail com From nicolas.lists at gmail.com Wed Apr 11 18:11:23 2012 From: nicolas.lists at gmail.com (Nicolas Rannou) Date: Wed, 11 Apr 2012 18:11:23 -0400 Subject: [MINC-development] Debian package for ubuntu 12.04 In-Reply-To: <4F85FF96.8040107@gmail.com> References: <4F832DFE.1010400@ilmarin.info> <688c89b97c1c4d8fa362e58d9de85670@CHEXHUBCASBDC1.CHBOSTON.ORG> <4F85B1FF.6020601@gmail.com> <4F85BCF4.1020801@gmail.com> <4F85FF96.8040107@gmail.com> Message-ID: 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 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 > > 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 > >> 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 >> >> >> 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 >> > 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 >> >> > >> > >> >>> >> 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 >> >> > __> >> > *> >> >> > __>__>> 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 >> >> > >> >> >> >> >> >> ) ? >> >> 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 >> > >> > __> >> > >> > __>__> >> >> >> > >> > __> >> > *> >> > __>__>>> wrote: >> > >> > Hello, >> > >> > >> > we have moved minc development to >> > 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 >> > **toolkit-__0.3.0-20120408-__**Linux-x86_64.__deb >> > >> > **toolkit-__0.3.0-20120408-__**Linux-x86_64.__deb >> > toolkit-__0.3.0-20120408-**Linux-x86_64.__deb >> >> >> > **____toolkit-__0.3.0-20120408-_**___Linux-x86_64.__deb >> > **toolkit-__0.3.0-20120408-__**Linux-x86_64.__deb >> > >> > **toolkit-__0.3.0-20120408-__**Linux-x86_64.__deb >> > toolkit-__0.3.0-20120408-**Linux-x86_64.__deb >> >>> >> >> > >> > **__toolkit-0.3.0-20120408-**Linux-____x86_64.deb >> > toolkit-0.3.0-20120408-Linux-_**_x86_64.deb >> > >> >> >> > toolkit-0.3.0-20120408-Linux-_**_x86_64.deb >> > 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 fonov gmail com >> ______________________________**___________________ >> MINC-development mailing list >> MINC-development at bic.mni.__mcg**ill.ca >> >> > >> http://www.bic.mni.mcgill.ca/_**_mailman/listinfo/minc-__** >> development >> > development >> > >> >> >> >> >> >> ______________________________**_________________ >> MINC-development mailing list >> MINC-development at bic.mni.**mcgill.ca >> http://www.bic.mni.mcgill.ca/**mailman/listinfo/minc-**development >> > > > -- > Best regards, > > Vladimir S. FONOV ~ vladimir fonov gmail com > ______________________________**_________________ > MINC-development mailing list > MINC-development at bic.mni.**mcgill.ca > http://www.bic.mni.mcgill.ca/**mailman/listinfo/minc-**development > -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.janke at gmail.com Wed Apr 11 20:09:31 2012 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 12 Apr 2012 10:09:31 +1000 Subject: [MINC-development] Debian package for ubuntu 12.04 In-Reply-To: References: <4F832DFE.1010400@ilmarin.info> <688c89b97c1c4d8fa362e58d9de85670@CHEXHUBCASBDC1.CHBOSTON.ORG> <4F85B1FF.6020601@gmail.com> <4F85BCF4.1020801@gmail.com> Message-ID: You may be better off to just include this as a sub-package. http://packages.bic.mni.mcgill.ca/ubuntu-maverick/libmni-perllib-perl_0.08-1_all.deb Perl packages on debian have to be packaged using dh-make-perl which takes care of all the various deb magic. This package hasn't changed in a long time and should be safe to use on either debian or ubuntu. a On 12 April 2012 05:34, Nicolas Rannou 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 > 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 >> >> 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 >>> > 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 >>> ? ? ? ? >>> ? ? ? ?>> >>> ? ? ? ?__>> 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 >>> >>> ? ? ? ? ) ? >>> >>> ? ? ? ? ? ?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 >>> ? ? ? ? > >>> ? ? ? ?__> >>> >>> ? ? ? ? >>> ? ? ? ?>> ? ? ? ?__>>> wrote: >>> ? ? ? ? > >>> ? ? ? ? > ? ? Hello, >>> ? ? ? ? > >>> ? ? ? ? > >>> ? ? ? ? > ? ? we have moved minc development to >>> ? ? ? ? > 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 >>> >>> ? >>> >>> ?>> >>> ?> >>> >>> ? ? ? ? > >>> >>> ?>> >>> >>> ?> >>> ? ? ? ? > ? ? - 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 fonov gmail com >> _______________________________________________ >> MINC-development mailing list >> MINC-development at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development > > > > _______________________________________________ > MINC-development mailing list > MINC-development at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development > From vladimir.fonov at gmail.com Fri Apr 13 09:07:58 2012 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Fri, 13 Apr 2012 09:07:58 -0400 Subject: [MINC-development] Debian package for ubuntu 12.04 In-Reply-To: References: <4F832DFE.1010400@ilmarin.info> <688c89b97c1c4d8fa362e58d9de85670@CHEXHUBCASBDC1.CHBOSTON.ORG> <4F85B1FF.6020601@gmail.com> <4F85BCF4.1020801@gmail.com> <4F85FF96.8040107@gmail.com> Message-ID: <4F88252E.3010302@gmail.com> Hello Everybody, it turns out that N3 is not working properly in the package mentioned below - I am still investigating. On 4/11/2012 6:11 PM, Nicolas Rannou wrote: > 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 > > 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 > > > > 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 > > >> 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 > > >> 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 > > > > > > > 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 > > > > ____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 > > __> > > __>__> > > __> > >